CA2364997A1 - Encryption of traits using split gene sequences - Google Patents

Abstract

Methods of unencrypting trait encrypted gene sequences to provide unencrypted RNAs or polypeptides. The invention also relates to methods of encrypting traits including splitting genes between two parental organisms or between a host organism and a vector. The gene sequences are unencrypted when the two parental organisms are mated or when the vector infects the host organism by trans-splicing either the split RNAs or split polypeptides upon expression of the split gene sequences. The invention also includes methods of providing multiple levels of trait encryption and reliable methods of producing hybrid organisms. Additional methods include those related to unencrypting engineered genetic elements to provide polypeptide functions and those directed at recombining non-overlapping gene sequences. The invention also includes integrated systems and various compositions related to the disclosed methods.

Description

ENCRYPTION OF TRAITS USING SPLIT GENE SEQUENCES
S
CROSS-REFERENCES TO RELATED APPLICATIONS
This application is related to USSN 60/122,943 "RECOMBINATION OF
INSERTION MODIFIED NUCLEIC ACIDS" by Patten et al., filed March 5, 1999. This application is also related to USSN 60/142,299 "RECOMBINATION OF INSERTION
MODIFIED NUCLEIC ACIDS" by Patten et al., filed July 02, 1999. This application is also related to USSN 60/164,617 "RECOMBINATION OF INSERTION MODIFIED
NUCLEIC ACIDS" by Patten et al., filed November 10, 1999. This case is also related to Patten et al. "ENCRYPTION OF TRAITS USING SPLIT GENE SEQUENCES AND
ENGINEERED GENETIC ELEMENTS" USSN 60/164,618, Filed November 10, 1999.
This case is also related to co-filed application "RECOMBINATION OF INSERTION
MODIFIED NUCLEIC ACIDS" by Patten et al (USSN~ attorney docket number 02-305-2US and co-filed application application "RECOMBINATION OF INSERTION
MODIFIED NUCLEIC ACIDS" by Patten et al (USSN~ attorney docket number 02-305-2PC. The disclosures of each of these related applications are incorporated by reference. The present application claims priority to and the benefit of each of these related applications, pursuant to 35. U.S.C. 119(e) and 120, as appropriate.
FIELD OF THE INVENTION
The present invention provides methods of encrypting traits, including, e.g., splitting genes between two parental organisms or between a host organism and a vector.
The invention also relates to methods of unencrypting trait encrypted gene sequences to provide unencrypted RNAs or polypeptides. Gene sequences are unencrypted when the two parental organisms are mated, or when the vector infects the host organism by trans-splicing either the split RNAs or split polypeptides upon expression of the split gene sequences. The invention also includes methods of providing multiple levels of trait encryption and reliable methods of producing hybrid organisms. Additional methods include those directed at unencrypting engineered genetic elements to provide unencrypted polypeptide functions and those related to recombining non-overlapping gene sequences.
Furthermore, the present invention includes integrated systems and various compositions related to the methods disclosed herein.
BACKGROUND OF THE INVENTION
Intermolecular splicing is termed trans-splicing. The mechanism of splicing two independently transcribed pre-mRNAs was discovered in trypanosomes.
Murphy, W.J. et al. (1986) Cell 47, 517-525 and Sutton, R. and Boothroyd, J.C.
(1986) Cell 47, 527-535. Thereafter, trans-splicing was also described in other organisms, e.g., C.
elegans (Krause, M. and Hirsch, D. (1987) Cell 49, 753-761, Huang, X.Y. and Hirsch, D.
(1989) Proc. Nat. Acad. Sci. USA 86, 8640-8644, and Hannon, G.J. et al. (1990) Cell 61, 1247-1255), Schistosoma mansoni (Rajkovic, A., et al. (1990) Proc. Nat. Acad.
Sci. USA
87, 8879-8883 and Davis, R.E. et al. (1995) J. Biol. Chem. 270, 21813-21819), and plant mitochondria (Malek, O. et al. (1997) Proc. Nat. Acad. Sci. USA 94, 553-558).
Targeted traps-splicing has been demonstrated in HeLa nuclear extracts, in cultured H1299 human lung cancer cells, and in H1299 tumor bearing athymic mice. Puttaraju, M. et al. (1999) Nat. Biotech. 17, 246-252. Suggested practical applications of targeted traps-splicing are, e.g., as a means for gene therapy. Id.
Various ribozymes capable of precisely traps-splicing, either in vitro or in vivo, exon sequences into target RNA sequences have been described in, e.g., Haseloff et al., U.S. Pat. No. 5,882,907 "CELL ABLATION USING TRAMS-SPLICING
RIBOZYMES," Haseloff et al., U.S. Pat. No. 5,874,414 "TRAMS-SPLICING
RIBOZYMES," Haseloff et al., U.S. Pat. No. 5,866,384 "CELL ABLATION USING
TRAMS-SPLICING RIBOZYMES," Haseloff et al., U.S. Pat. No. 5,863,774 "CELL
ABLATION USING TRAMS-SPLICING RIBOZYMES," Haseloff et al., U.S. Pat. No.
5,849,548 "CELL ABLATION USING TRAMS-SPLICING RIBOZYMES," and Haseloff et al., U.S. Pat. No. 5,641,673 "CELL ABLATION USING TRAMS-SPLICING
RIBOZYMES." Methods of ablating cells in vivo involving targeted traps-splicing to provide toxic products that generate sterile plants have also been described in, e.g., Haseloff et al., U.S. Pat. No. 5,866,384, supra. The techniques referenced above generally involve traps-splicing RNA sequences into native target RNAs.

Genetically male-sterile plants can be desirable for the production of hybrid seeds, because they avoid the need for expensive and laborious removal of, e.g., anthers from flowers to prevent self fertilization. Transgenic methods of regenerating functionally male-sterile plants have included the development of pollen cells that are ablated specifically by the expression of fungal or bacterial ribonuclease transgenes fused to a pollen-specific promoter from the particular plant. Mariani, C. et al. (1992) Nature 357, 384-387. See also, Haseloff et al., U.S. Pat. No. 5,866,384, supra.
In addition to traps-splicing RNAs, protein traps-splicing is also known.
For example, certain modified proteins have been described which include "controllable intervening protein sequences" inserted into or adj acent to target proteins.
Comb, et al.
U.S. Pat. No. 5,834,247 "MODIFIED PROTEINS COMPRISING CONTROLLABLE
INTERVENING PROTEIN SEQUENCES OR THEIR ELEMENTS METHODS OF
PRODUCING SAME AND METHODS FOR PURIFICATION OF A TARGET
PROTEIN COMPRISED BY A MODIFIED PROTEIN." The inserted intervening sequences are capable of cleaving the modified protein in traps under controllable conditions, e.g., increased temperature, exposure to light, treatment with chemical reagents, etc. Furthermore, these intervening protein sequences can also be inserted into a target protein sequence so as to render the target inactive. Id. See also, Comb, et al. U.S.
Pat. No. 5,496,714 "MODIFICATION OF PROTEIN BY USE OF A CONTROLLABLE
INTERVENING PROTEIN SEQUENCE" and Belfort, U.S. Pat. No. 5,795,731 "INTEINS
AS ANTIMICROBIAL TARGETS: GENETIC SCREENS FOR 1NTE1N FUNCTION."
Spontaneous (native) traps-splicing of both inteins and RNAs is also known.
More generally, relevant features of inteins and intein splicing, as well as certain forms of chemical ligation of polypeptides, are described in the abundant literature on the topics, including the references noted above and, e.g.: Clarke (1994) "A proposed mechanism for the self splicing of proteins" Proc. Natl. Acad. Sci. USA
91:11084-11088;
Clyman (1995) "Some Microbes have splicing proteins" ASM News 61:344-347;
Colston and Davis (1994) "The ins and outs of protein splicing elements" Molecular Microbiolo~y 12, 359-363; Cooper et al. (1993) "Protein splicing of the yeast TFP1 intervening protein sequence: a model for self excision" EMBO J. 12:2575-2583; Cooper and Stevens (1993) "Protein splicing: Excision of intervening sequences at the protein level"
BioEssays 15, 667-673; Cooper and Stevens (1995) "Protein splicing: Self splicing of genetically mobile elements at the protein level" TIES 20, 351-357; Cook et al. (1995) "Photochemically initiated protein splicing" Ang_ew. Chem. Int. Ed. En~el 34, 1620-1630;
Dalgaard, J.
(1994) "Mobile introns and inteins: friend or foe?" Trends Genet 10, 306-7;
Davis et al.
S (1992) "Protein Splicing in the Maturation of M. Tuberculosis RecA Protein:
A
Mechanism for Tolerating a Novel Class of Intervening Sequence" Cell 71:201-210; Davis et al. (1991) "Novel Structure of the recA Locus of Mycobacterium tuberculosis Implies Processing of the Gene Product" J. Bacteriol. 173:5653-5662; Davis et al.
(1994) "Evidence of selection for protein introns in the RecAs of pathogenic Mycobacteria"
EMBO J. 13, 699-703; Davis et al. (1995) "Protein splicing--the lengths some proteins will go to" Antonie Van Leeuwenhoek 67:131-137; Doolittle, (1993) "The comings and goings of homing endonucleases and mobile introns" Proc. Natl. Acad. Sci. USA.
90:5379-5381;
Doolittle and Stoltzfus (1993) "Genes-in-pieces revisited" Nature 361:403;
Hirata and Anraku (1992) "Mutations at the Putative Junction Sites of the Yeast VMA1 Protein, the Catalytic Subunit of the Vacuolar Membrane H+-ATPase, Inhibit its Processing by Protein Splicing" Biochem. Biophys. Res. Comm. 188:40-47; Hirata et al. (1990) "Molecular Structure of a Gene, VMAl, Encoding the Catalytic Subunit of H+-Translocating Adenosine Triphosphatase from Vacuolar Membranes of Saccharomyces cereviaiae"
J.
Biol. Chem. 265, 6726-6733; Hodges et al. (1992) "Protein splicing removes intervening sequences in an archaea DNA polymerase" Nucleic Acids Res. 20:6153-6157; Kane et al.
(1990) "Protein Splicing Converts the Yeast TFPl Gene Product to the 69-kD
Subunit of the Vacuolar H+-Adenosine Triphosphatase" Science 250:651-657; Koonin (1995) "A
protein splice junction motif in hedgehog family proteins" Trends Biochem.
Sci. 20:41-142; Kumar et al. (1996) "Functional characterization of the precursor and spliced forms of recA protein of Mycobacterium tuberculosis" Biochemistry 35:1793-1802, and Kawasaki, M., et al., Biochemical and Biophysical Research Communications, vol. 222, "Folding-dependent in vitro protein splicing of the Saccharomyces cerevisiae VMA1 protozyme", pp. 827-832, 1996. Gimble and Thorner (1992) Nature 35?:301-306; Gimble and Thorner (1993) J. Biol. Chem., 268:21844-21853; Pietrovski (1996) "A new intein in cyanobacteria and its significance for the spread of inteins" Trends in Genetics 12:287-288;
Shao et al.
(1996) "Proteins splicing: Evidence for an N-O acyl rearrangement as the initial step in the splicing process" Biochemistry, 35:3810-3815; Shub and Goodrich-Blair (1992) Cell, 71:183-186; WO 98/49274; WO 98/49275; WO 98/40394; WO 99/11655; WO 96/34878;
WO 98/28434; Kent et al. U.S. Pat. No. 5,910,437; Dawson et al. 5,891,993; and Jocbs et al., U.S. Pat. No. 5,981,182. Additional details on protein splicing generally can be found at the Intein Databases web site (www.neb.com/neb/inteins/intein intro.html);
and in, e.g., Nucleic Acids Research 26(7):1741-1758.
Methods of encrypting gene sequences and engineered genetic elements, and additional recombination methods would be desirable. The present invention provides new methods to encrypt traits including trans-splicing at the RNA and/or protein levels and new methods of recombining non-overlapping gene sequences, as well as a variety of additional features which will become apparent upon review of the following description.
SUMMARY OF THE INVENTION
The present invention provides methods of unencrypting trait encrypted gene sequences, e.g., cDNAs, to provide unencrypted RNAs or polypeptides, e.g., full-1 S length proteins. The methods include providing a first plurality of split gene sequences in which each split gene sequence includes a subsequence of a genetic element and transcribing the first plurality of split gene sequences to provide a plurality of RNA
segments that can include traps-splicing introns. The steps of this aspect of the invention can occur either in vitro or in vivo. Two or more of the plurality of RNA
segments can be traps-spliced together to provide an unencrypted RNA. The unencrypted RNA can optionally be selected for a desired trait or property, or translated to provide a second unencrypted polypeptide. The second unencrypted polypeptide can also optionally be selected for a desired trait or property.
Alternately, the plurality of RNA segments can be translated to provide a plurality of polypeptide segments that can include traps-splicing inteins and two or more of that plurality can be traps-spliced together to provide a first unencrypted polypeptide.
The first unencrypted polypeptide can optionally be selected for at least one desired trait or property.
The first plurality of split gene sequences can optionally be provided by mating a first parental organism that includes a second plurality of split gene sequences with a second parental organism that includes a third plurality of split gene sequences to produce a progeny organism. The progeny organism includes one or more of both the second and the third plurality of split gene sequences. Thereafter, one or more of the second and the third plurality of split gene sequences can be transcribed to provide a plurality of RNA segments. Additionally, the progeny organism can optionally be selected for a desired trait or property, and in so doing, unencrypted RNAs are selected. The unencrypted RNAs can optionally be translated to provide an unencrypted polypeptide.
The unencrypted polypeptides can optionally be selected for a desired trait or property.
The first and second parental organisms of the first aspect of the present invention can be, e.g., animals, plants, fungi, or bacteria. In certain preferred embodiments they are plants, yeast or other fungi.
A first parental organism can include a first plurality of enhancer-linked split gene sequences. Each enhancer-linked split gene sequence includes a subsequence of a genetic element with a first enhancer sequence linked thereto. The first parental organism also includes one or more first traps-acting transcription factor sequences that are unlinked to the first plurality of enhancer-linked split gene sequences. This third aspect also includes a second parental organism that includes a second plurality of enhancer-linked split gene sequences in which each enhancer-linked split gene sequence includes a subsequence of the genetic element with a second enhancer sequence linked thereto. The second parental organism also includes one or more second traps-acting transcription factor sequences that are unlinked to the second plurality of enhancer-linked split gene sequences.
The two parental organisms can be mated to produce a progeny organism that includes the first and the second plurality of enhancer-linked split gene sequences and the first and the second traps-acting transcription factor sequences. The first and the second plurality of enhancer-linked split gene sequences can be transcribed to provide a plurality of RNA segments in which the first plurality of enhancer-linked split gene sequences are regulated by a second traps-acting transcription factor and the second plurality of enhancer-linked split gene sequences are regulated by a first traps-acting transcription factor. The progeny organism can optionally be selected for a desired trait or property. Unencrypted RNAs can optionally be translated to provide unencrypted polypeptides that, in turn, can be selected for a desired trait or property.
Furthermore, the first and second parental organisms can be, e.g., animals, plants, fungi, or bacteria.
However, in certain preferred embodiments they are plants, yeast or other fungi.
A first parental organism can include a second plurality of split gene sequences in which each split gene sequence includes a subsequence of a toxic genetic element and a second parental organism can include a third plurality of split gene sequences in which each split gene sequence also includes a subsequence of the toxic genetic element. The first and second parental organisms of this aspect of the invention can be mated and the second and third plurality of split gene sequences can be expressed in a progeny organism to produce a second and third plurality of polypeptide sequences.
Thereafter, one or more of the second and third plurality of polypeptide sequences can be trans-spliced together to provide a toxic polypeptide. The toxic polypeptide, in turn, renders the progeny organism incapable of reproducing when it is male.
However, the progeny organism can reproduce when it is female and when it does, the progeny organism produces hybrid progeny organisms in which the toxic genetic element is not expressed.
A toxic polypeptide can render the progeny organism incapable of reproducing when it is female. However, this progeny organism is capable of reproducing when it is male and when it does, the progeny organism produces hybrid progeny organisms in which the toxic genetic element is not expressed.
In another embodiment of the present invention, a first plurality of split gene sequences is provided by infecting a host organism that includes a second plurality of split gene sequences with a vector, e.g., a virus, that includes a third plurality of split gene sequences to produce an infected organism. The infected organism includes the second and third plurality of split gene sequences. The second and third plurality of split gene sequences can be transcribed to provide a plurality of RNA segments.
Additionally, an unencrypted RNA can optionally be selected for a desired trait or property, or a second unencrypted RNA can be translated to provide a second unencrypted polypeptide.
The first or second unencrypted polypeptides can optionally be selected for a desired trait or property.
The present invention also provides methods of unencrypting engineered genetic elements to provide unencrypted polypeptide functions that can occur in vitro or in vivo. This method includes providing a first engineered genetic element, e.g., a cDNA, which corresponds to an encoded first polypeptide, e.g., an engineered biotin ligase that is functional. It also includes providing a second engineered genetic element that corresponds to an encoded second polypeptide, e.g., an engineered biotin dependent glyphosate resistance polypeptide, that is nonfunctional in the absence of a modification performed by the first polypeptide. Thereafter, the first and second engineered genetic elements can be mixed and expressed to produce the encoded first and second polypeptides. The encoded first polypeptide then modifies the encoded second polypeptide to provide a functional encoded second polypeptide.
In an embodiment of the methods of unencrypting engineered genetic elements, the providing and mixing steps include mating a first parental organism that includes the first engineered genetic element and a second parental organism that includes the second engineered genetic element to produce a progeny organism that includes both engineered genetic elements. Thereafter, the genetic elements in the progeny organism can be expressed to produce the encoded first and second polypeptides. The first and second parental organisms of this first aspect of the invention can be, e.g., animals, plants, fungi, or bacteria. In certain preferred embodiments they are plants, yeast or other fungi.
The providing and mixing steps, of the methods of unencrypting engineered genetic elements, optionally include infecting a host organism that includes the first engineered genetic element with a vector that includes the second engineered genetic element to produce an infected organism. Alternatively, the vector can include the first engineered genetic element and the host organism can include the second engineered genetic element. In either case, the infected organism ultimately includes both the first and the second engineered genetic elements. Thereafter, both engineered genetic elements can be expressed in the progeny organism to produce the encoded first and second polypeptides.
The present invention also provides a composition that includes libraries of two or more populations, e.g., homologous genetic elements, of split gene sequences.
These libraries collectively include a plurality of split gene sequence member types in which combinations or subcombinations of those member types collectively correspond to one or more complete genetic elements.

The invention additionally provides a composition that includes libraries of two or more populations of enhancer-linked split gene sequences. These libraries collectively include a plurality of enhancer-linked split gene sequence member types, each regulated by a different traps-acting transcription factor in which combinations or subcombinations of the plurality of enhancer-linked split gene sequence member types collectively correspond to one or more complete genetic elements. This composition can include a traps-acting transcription factor corresponding to one of the two or more populations of enhancer-linked split gene sequences that can regulate the enhancer-linked split gene sequences of another population. This composition can also include a first traps-acting transcription factor that corresponds to a first population of enhancer-linked split gene sequences that regulates the enhancer-linked split gene sequences of a second population, and a second traps-acting transcription factor that corresponds to the second population of enhancer-linked split gene sequences that regulates the enhancer-linked split gene sequences of the first population.
The present invention also relates to a method of recombining non-overlapping gene sequences that can occur in vitro or in vivo. The methods include providing a plurality of non-overlapping gene sequences in which each non-overlapping gene sequence corresponds to a different subsequence of a genetic element. The methods also include providing a plurality of gap nucleic acid sequences in which each gap nucleic acid sequence overlaps two or more of the non-overlapping gene sequences. The non-overlapping gene sequences can be recombined with the gap nucleic acid sequences to provide recombined non-overlapping gene sequences. The recombined non-overlapping gene sequences can optionally be selected for a desired trait or property and then recombined again. This process of selecting and recombining the recombined non-overlapping gene sequences can be repeated until a desired recombined genetic element is obtained. Furthermore; the plurality of non-overlapping gene sequences can be derived, e.g., from a cry3Bb gene and the plurality of gap nucleic acid sequences can be derived, e.g., from a cryl Ba, a cryl Ca, and a crylla gene.
The present invention is also directed at compositions that include libraries of gap nucleic acids. The libraries of gap nucleic acids include a plurality of gap nucleic acid member types in which each gap nucleic acid member type includes subsequence identity or complementarity with at least two split gene sequence member types.
The invention additionally provides an integrated system that includes a computer or computer readable medium that includes a data set corresponding to a set of character strings. Those character strings can correspond to split gene sequences, enhancer-linked split gene sequences, traps-acting transcription factor sequences, engineered genetic elements, non-overlapping gene sequences and gap nucleic acids. The system can further include a sequence search and comparison instruction set for searching for specified nucleic acid sequences. The integrated system can also optionally include an automatic sequencer and/or synthesizer coupled to an output of the computer or computer readable medium, which can accept instructions from the computer or computer readable medium that direct the sequencing and/or synthesis of selected sequences.
The integrated system can optionally include robotic control elements for incubating, denaturing, hybridizing, and elongating a set of recombined non-overlapping gene sequences and gap nucleic acids. The system can also include a detector for detecting a nucleic acid produced by elongation of the set of recombined non-overlapping gene sequences and gap nucleic acids, or an encoded product thereof.
Definitions Unless otherwise indicated, the following definitions supplement those in the art.
A "set" as used herein refers to a collection of at least two molecule types.
Two nucleic acid sequences "correspond" when they have the same sequence, or when one nucleic acid sequence is a subsequence of the other, or when one sequence is derived, by natural or artificial manipulation from the other.
An "unencrypted RNA" is an RNA generated by traps-splicing at least two RNA segments together. An "unencrypted polypeptide" is a polypeptide generated by traps-splicing at least two polypeptide segments together. The term "polypeptide"
includes inteins, exteins, polypeptides, proteins, polyproteins, and the like.
Traits are encrypted using "split gene sequences." Split gene sequences are subsequences of a genetic element. The subsequences can be distributed, e.g., between two parental organisms, but collectively they correspond to the entire genetic element. A

"subsequence" of a genetic element is any polynucleotide sequence that is identical or substantially identical to a portion of that genetic element. A "genetic element" includes a segment of DNA involved in producing a polypeptide chain and/or RNA chain. It can include regions preceding (e.g., leader) and following (e.g., trailer) the coding region in addition to intervening sequences (e.g., introns) between individual coding segments (e.g., exons). Genetic elements can include individual exons, introns, promoters, enhancers, genes, gene clusters, gene families, operons, and the like. An "engineered genetic element" is a designed or otherwise artificially constructed genetic element.
An "enhancer-linked split gene sequence" is a subsequence of a genetic element that is linked to an enhancer. An "enhancer" is a cis-acting regulatory nucleotide sequence involved in the transcriptional activation of certain genetic elements. Activation of an enhancer can elevate the rate of transcription. Studies have shown that enhancers can operate when located either 5' or 3' to the transcriptional start site or promoter. They have also been shown to function at distances greater than three kilobases from the start site.
Enhancers generally operate as binding sites for transcriptional activating proteins and are tissue specific. They can be incorporated into various expression vectors to optimize the expression of a chosen DNA sequence.
A "traps-acting transcription factor" is a regulatory protein that controls transcription by binding to a specific enhancer, e.g., an enhancer that is linked to an enhancer-linked split gene sequence. The DNA sequence that encodes the transcription factor is not linked to the enhancer sequence upon which that transcription factor acts.
The term "traps-splicing" includes the joining of at least two distinct RNA
molecules or of at least two distinct polypeptide molecules to produce at least one trait encrypted RNA or at least one trait encrypted polypeptide, respectively.
A "full-length protein" is a protein with substantially the same sequence domains as a corresponding protein encoded by a natural gene. Such a protein can have altered sequences relative to the corresponding naturally encoded gene, e.g., due to recombination and selection, but unless specified to the contrary, is typically at least about 95% the length of a corresponding naturally encoded protein. The protein can include additional sequences such as purification tags not found in the corresponding naturally encoded protein.

A "toxic genetic element" includes a segment of DNA that encodes a polypeptide, that upon expression, produces sterility in certain organisms, e.g., male sterility in plants. A "toxic polypeptide" is a polypeptide encoded by a toxic genetic element.
The term "non-overlapping gene sequences" refers to polynucleotide sequences that can be homologous to subsequences of a genetic element, but which do not share sequence identity or complementarity amongst themselves. A "gap nucleic acid" is a nucleic acid sequence that includes regions that are identical or complementary to at least two non-overlapping gene sequences.
BRIEF DESCRIPTION OF THE DRAWING
Figure 1 is a schematic of the use of split genes in encoding traits in Fl but not parentals and only in 1/4t" of F2.
Figure 2 is a schematic of a strategy for encrypting engineered traits in F 1 using multiple levels of encryption to provide mature gene products.
Figure 3 is a schematic illustrating the use of split herbicide resistance genes.
Figure 4 schematically shows a strategy for using split gene sequences for the production of hybrids.
Figure 5 schematically shows a traps-spliced protein product of E. coli DnaE gene.
Figure 6 provides intein sequence information from various organisms.
Figure 7 illustrates a strategy for the recombination of non-overlapping gene sequences in which no parental genes are rescued.
Figure 8 shows data involving the recombination of cry3Bb non-overlapping gene sequences with cryl Ba, 1 Ca, and IIa gene sequences.
DETAILED DISCUSSION OF THE INVENTION
In certain situations it is desirable to provide genes in formats where the final protein to be selected for activity is expressed as an active protein in vitro or in vivo only under controlled conditions. For example, this approach can be useful in cases where a mature protein is toxic to the cell (e.g., RNAses, DNAses, toxins such as ricin, proteases, apoptopsis inducing factors, etc.) and it is therefore advantageous to express the protein in an inactive form, e.g., from split gene sequences, such that it can be conditionally activated. This strategy allows one to direct the expression of otherwise toxic proteins, among many others, and to manipulate genes in ways that have advantages with respect to intellectual property considerations.
The present invention relates to methods of unencrypting trait encrypted gene sequences to provide unencrypted RNAs or polypeptides. The methods of encrypting traits include splitting gene sequences that are subsequently unencrypted by traps-splicing either split RNAs or split polypeptides upon expression of those split gene sequences. The invention also includes methods of providing multiple levels of trait encryption and reliable methods of producing hybrid organisms. Additional methods include those directed at unencrypting engineered genetic elements to provide polypeptide functions and those related to recombining non-overlapping gene sequences. Furthermore, the present invention includes integrated systems and various compositions related to the methods disclosed herein.
In overview, the present invention entails various embodiments of the methods of providing unencryped RNAs or polypeptides including splitting gene sequences between two parental organisms. Upon mating the two parental organisms, the split gene sequences are expressed and the resulting expression products can then be trans-spliced together at either the RNA or polypeptide levels to provide, e.g., mature mRNAs, or full-length proteins. Trait encrypted RNAs or polypeptides can similarly be provided by splitting gene sequences between a host organism and a vector. Any genetic element can be so encrypted, including certain toxic genetic elements which can provide, e.g., plant breeders with assorted commercial advantages when creating hybrid plants.
Multiple levels of encryption can be achieved through the use of enhancer-linked split gene sequences.
The methods of unencrypting genetic elements to provide polypeptide function can involve splitting functionally related genetic elements between two parental organisms or between a host organism and a vector. Functional protein products of the genetic elements are created, e.g., upon mating or infection. Furthermore, the invention provides methods of recombining non-overlapping gene sequences that would not otherwise recombine. This method includes using gap nucleic acid sequences that overlap, e.g., share regions of complementarity with two or more of the non-overlapping gene sequences.
The following provides details regarding various aspects of the methods of providing unencrypted RNAs or polypeptides, including sequence selection, synthesis and S encryption. It also provides details pertaining to the methods of evolving engineered proteins and recombining non-overlapping nucleic acid sequences, to applicable integrated systems, and to various nucleic acid compositions.
UNENCRYPTING TRAIT ENCRYPTED GENE SEQUENCES TO PROVIDE
UNENCRYPTED RNAS OR POLYPEPTIDES
The methods of the present invention include those related to unencrypting gene sequences, e.g., DNA or cDNAs, to provide unencrypted RNAs or polypeptides. The methods include providing split gene sequences in which each split gene sequence includes, e.g., a subsequence of a gene, and transcribing those split gene sequences to provide a population of RNA segments. This process can optionally occur in vitro or in vivo. At least two of those RNA segments can be trans-spliced together (discussed further, infra) to provide an unencrypted RNA. The unencrypted RNA can optionally be selected for a desired trait or property, or translated to provide an unencrypted polypeptide, e.g., a full-length protein, which can also optionally be selected for a desired trait or property.
Alternatively, the population of RNA segments can be translated to provide a population of polypeptide segments and two or more of those polypeptides can be trans-spliced together (discussed further, infra) to provide an unencrypted polypeptide that can optionally be selected for a desired trait or property.
In one embodiment of these methods, two parental organisms, each of which includes a plurality of split gene sequences (introduction of split gene sequences is described, infra) can be mated to produce a progeny organism that includes split gene sequences from both parents. Thereafter, those split gene sequences can be transcribed to provide a population of RNA segments, which as above can optionally be trans-spliced together to provide unencrypted RNAs or the RNA segments can optionally be translated to provide a population of polypeptides which can then be trans-spliced together to provide unencrypted polypeptides.

Figure 1 illustrates the commercial advantages of splitting, e.g., the Bacillus thuringiensis (Bt) toxin gene between two plant parentals. Neither parent would express the complete Bt toxin gene, because amino-terminal portion of gene 100 is present in only one of the parents, while carboxyl-terminal portion of gene 102 is only present in the other parent. A cross between these two parents produces F1 seeds in which both portions of the gene are present. The F1 seeds can then be sold to consumers. As further depicted in Figure 1, the F1 plants express mature traps-spliced Bt toxin that can afford protection from insect attack without the need for spraying. However, F2 seeds would be of little use to consumers as only 25 percent of those seeds would contain both portions of the split Bt toxin gene. This logic is applicable to any gene of interest.
Selection of Parental Or anisms As described below, essentially any plant can be transduced with the nucleic acid sequences taught herein. Some suitable plants for use with respect to the methods of the present invention, include those selected from the genera:
Fragaria, Lotus, 1 S Medicago, Onobrychis, Trifolium, Trigonella, Vigna, Citrus, Linum, Geranium, Manihot, Daucus, Arabidopsis, Brassica, Raphanus, Sinapis, Atropa, Capsicum, Datura, Hyoscyamus, Lycopersicon, Nicotiana, Solanum, Petunia, Digitalis, Majorana, Cichorium, Helianthus, Lactuca, Bromus, Asparagus, Antirrhinum, Heterocallis, Nemesia, Pelargonium, Panicum, Pennisetum, Ranunculus, Senecio, Salpiglossis, Cucumis, Browaalia, Lolium, Malus, Apium, Gossypium, Vicia, Lathyrus, Lupinus, Pachyrhizus, Wisteria, and Stizolobium.
Important commercial crops include both monocots and dicots. Monocots include plants in the grass family plants (Gramineae), such as plants in the sub-families Fetucoideae and Poacoideae, which together include several hundred genera including plants in the genera Agrostis, Phleum, Dactylis, Sorghum, Setaria, Zea (e.g., corn), Oryza (e.g., rice), Triticum (e.g., wheat), Secale (e.g., rye), Avena (e.g., oats), Hordeum (e.g., barley), Saccharum, Poa, Festuca, Stenotaphrum, Cynodon, Coix, Olyreae, Phareae, Glycine, Pisum, Cicer, Phaseolus, Lens, Arachis, and many others. Additional commercially important crop plants are, e.g., from the families Compositae (the largest family of vascular plants, including at least 1,000 genera, including important commercial crops such as sunflower), and Leguminosae or "pea family," which includes several hundred genera, including many commercially valuable crops such as pea, beans, lentil, peanut, yam bean, cowpeas, velvet beans, soybean, clover, alfalfa, lupine, vetch, sweet clover, wisteria, and sweetpea. Other common crops applicable to the methods of the invention, include rapeseed and canola.
S In addition to plants, microbes, fungi, and animals can be transduced with the target nucleic acid sequences of the invention. Various methods have been developed, especially for use in animal cells, to facilitate this process, including the use of polycations such as DEAE-dextran (McCutchan, J.H. and Pagano, J.S. (1968) J. Natl. Cancer Inst. 41, 351-357 and Kawai, S. and Nishizawa, M. (1984) Mol. Cell. Biol. 4, 1172-1174), calcium phosphate coprecipitation (Graham, F.L. and Van der Eb, A.J. (1973) Virology 52, 456-467), electroporation (Neuman, E. et al. (1982) EMBO J. 7, 841-845), lipofection (Felgner, P.L. et al. (1987) Proc. Natl. Acad. Sci. USA 84, 7413-7417), retrovirus vectors (Cepko, C.L. et al. (1984) Cell 37, 1053-1062), and microinjection (Capecchi, M.R.
(1980) Cell 22, 479-488.
1 S In addition to the references noted throughout, one of skill can find guidance as to animal cell culture in Freshney, Culture of Animal Cells, a Manual of Basic Technique, 3rd Ed., Wiley-Liss, New York (1994) and the references cited therein provides a general guide to the culture of cells. See also, Kuchler, et al. (1977) Biochemical Methods in Cell Culture and Virology, Kuchler, R.J., Dowden, Hutchinson and Ross, Inc., and Inaba, et al. (1992) J. Exp. Med., 176:1693-1702. Additional information on cell culture is found in Current Protocols in Molecular Biology, F.M. Ausubel et al., eds., Current Protocols, a joint venture between Greene Publishing Associates, Inc.
and John Wiley & Sons, Inc., (supplemented through 1999) (Ausubel), Sambrook et al., Molecular Cloning - A Laboratory Manual (2nd Ed.), Vol. 1-3, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 1989 (Sambrook), and Berger and Kimmel, Guide to Molecular Cloning Techniques, Methods in Enzymology volume 152 Academic Press, Inc., San Diego, CA (Berger). Cell culture media are described in Atlas and Parks (eds) The Handbook of Microbiological Media (1993) CRC Press, Boca Raton, FL. Generally, one of skill is fully able to transduce cells from animals, plants, fungi, bacteria and other cells using available techniques. Moreover, one of skill can transduce whole organisms with the nucleic acids of the present invention using available techniques.

Vector-Mediated Trait Encryption The concept of splitting genes to encrypt traits disclosed, supra, can be generalized to include the delivery of split gene sequence using a vector, e.g., a viral vector. This strategy can be particularly useful, e.g., when it proves difficult to provide engineered organisms with sufficiently tight regulation to prevent a highly toxic protein from being expressed.
In one embodiment of the present invention, a host organism (e.g., one of the types of parental organisms discussed, supra) that includes a plurality of split gene sequences is infected with a vector, such as a virus, that also includes a plurality of split gene sequences to produce an infected organism that includes both host and vector split gene sequences. As with the other embodiments of these methods, the split gene sequences can be transcribed to provide a population of RNA segments which, in turn, can be traps-spliced together and then translated, or translated directly and traps-spliced as polypeptide segments to provide desired unencrypted proteins.
In certain preferred embodiments of these vector-mediated methods, the vectors are plant viruses. Plant viruses designed to have new and desirable transformation and expression properties are also preferred embodiments. Viruses are typically useful as vectors for expressing exogenous DNA sequences, e.g., split gene sequences, in a transient manner in plant hosts. In contrast to Agrobacterium-mediated transformation, discussed infra, which results in the stable integration of DNA sequences in the plant genome, viral vectors are generally replicated and expressed without the need for chromosomal integration. Plant virus vectors offer a number of advantages, including as follows:
(1) DNA copies of viral genomes can be readily manipulated in E.coli, and transcribed in vitro, to produce infectious RNA copies;
(2) Naked DNA, RNA, or viral particles can be easily introduced into mechanically wounded leaves of intact plants;
(3) High copy numbers of viral genomes per cell results in high expression levels of introduced genes;
(4) Common laboratory plant species as well as monocot and dicot crop species are readily infected by various virus strains;

(5) Infection of whole plants permits repeated tissue sampling of single library clones;
(6) Recovery and purification of recombinant viral particles is simple and rapid;
and, (7) As replication occurs without chromosomal insertion, expression is not subject to positional effects.
Over 650 plant viruses have been identified, and are amenable in the vector-mediated methods of the invention. Plant.viruses are known which infect every major food-crop, as well as most species of horticultural interest. The host range varies between viruses, with some viruses infecting a broad host range (e.g., alfalfa mosaic virus infects more than 400 species in 50 plant families) while others have a narrow host range, sometimes limited to a single species (e.g., barley yellow mosaic virus). Host range is among the many traits for which it is possible to select appropriate vectors according to the methods provided by the present invention.
Approximately 75% of the known plant viruses have genomes which are single-stranded (ss) messenger sense (+) RNA polynucleotides. Major taxonomic classifications of ss-RNA(+) plant viruses include the bromovirus, capillovirus, carlavirus, carmovirus, closterovirus, comovirus, cucumovirus, fabavirus, furovirus, hordeivirus, ilarvirus, luteovirus; potexvirus, potyvirus, tobamovirus, tobravirus, tombusvirus, and many others. Other plant viruses exist which have single-stranded antisense (-) RNA (e.g., rhabdoviridae), double-stranded (ds) RNA (e.g., cryptovirus, reoviridae), or ss or ds DNA
genomes (e.g., geminivirus and caulimovirus, respectively).
Preferred embodiments of the invention include engineered vectors that are both RNA and DNA viruses. Examples of such embodiments include viruses selected from among: an alfamovirus, a bromovirus, a capillovirus, a carlavirus, a carmovirus, a caulimovirus, a closterovirus, a comovirus, a cryptovirus, a cucumovirus, a dianthovirus, a fabavirus, a fijivirus, a furovirus, a geminivirus, a hordeivirus, a ilarvirus, a luteovirus, a machlovirus, a maize chlorotic dwarf virus, a marafivirus, a necrovirus, a nepovirus, a parsnip yellow fleck virus, a pea enation mosaic virus, a potexvirus, a potyvirus, a reovirus, a rhabdovirus, a sobemovirus, a tenuivirus, a tobamovirus, a tobravirus, a tomato spotted wilt virus, a tombusvirus, and a tymovirus.

Plant viruses can be engineered as vectors to accomplish a variety of functions. Examples of both DNA and RNA viruses have been used as vectors for gene replacement, gene insertion, epitope presentation and complementation, (see, e.g., Scholthof, et al. (1996) "Plant Virus Gene Vectors for Transient Expression of Foreign Proteins in Plants," Annu. Rev. Phytopathol. 34:299-323.) Methods for the transformation of plants and plant cells using sequences derived from plant viruses include direct transformation techniques relating to DNA
molecules, see e.g., Jones, ed. (1995) Plant Gene Transfer and Expression Protocols, Humana Press, Totowa, NJ, for a recent compilation. In addition viral sequences can be cloned adjacent T-DNA border sequences and introduced via Agrobacterium-mediated transformation, or Agroinfection. Viral particles comprising the plant virus vectors of the invention can also be introduced by mechanical inoculation using techniques well known in the art (see e.g., Cunningham and Porter, eds. (1997) Methods in Biotechnology, Vol.3.
Recombinant Proteins from Plants: Production and Isolation of Clinically Useful Compounds, for detailed protocols). Briefly, for experimental purposes, young plant leaves are dusted with silicon carbide (carborundum), then inoculated with a solution of viral transcript, or encapsidated virus and gently rubbed. Large scale adaptations for infecting crop plants are also well known in the art, and typically involve mechanical maceration of leaves using a mower or other mechanical implement, followed by localized spraying of viral suspensions, or spraying leaves with a buffered virus/carborundum suspension at high pressure. Any of these techniques, mentioned above, can be adapted to the vector-mediated trait encryption methods of the present invention.
Enhancer-Linked Split Gene Sequences and Trans-Acting Factors In another embodiment of these methods, a first parental organism can include a plurality of first enhancer-linked split gene sequences, each of which includes a subsequence of a genetic element, e.g., a herbicide resistance gene, with a first enhancer sequence linked thereto. As depicted in Figure 2, this first parental organism also includes first traps-acting transcription factor sequences (TAF 1) that are unlinked to the plurality of first enhancer-linked split gene sequences. See also, Figure 3. This embodiment also includes a second parental organism that includes a second plurality of enhancer-linked split gene sequences in which, similarly, each enhancer-linked split gene sequence includes a subsequence of the genetic element with a second enhancer sequence linked thereto.
(FIG. 2). The second parental organism also includes second trans-acting transcription factor sequences (TAF 2) that are unlinked to the second plurality of enhancer-linked split gene sequences.
In this embodiment, the two parental organisms can be mated to produce a progeny organism that includes the first and the second plurality of enhancer-linked split gene sequences and the first and the second trans-acting transcription factor sequences.
(FIG. 2). The first and the second plurality of enhancer-linked split gene sequences can be transcribed to provide a plurality of RNA segments in which the first plurality of enhancer-linked split gene sequences are regulated by TAF 2 and the second plurality of enhancer-linked split gene sequences are regulated by TAF 1. The plurality of RNA
segments can optionally be traps-spliced directly and then translated or translated directly and then traps-spliced together as polypeptides to provide trait encrypted polypeptides.
As shown in Figure 3, Fl seeds produced using this embodiment of the present invention could be sold to consumers as the complete herbicide resistance gene product would be expressed in plants produced therefrom. However, F2 seeds would not be useful, because only 1/l6th of those seeds would have all four components, i.e., the 5'-and 3'-portions of the split herbicide resistance gene in addition to both TAF
l and 2.
Enhancers are sequences involved in stimulating transcription initiation.
They can be located at substantial distances from the startpoints of coding sequences, either on the 5' or the 3' side of them, and in either orientation. They can include various modular components that resemble those of the promoter, but those components are generally organized in a closely packed sequence. Enhancer sequences are targets for tissue-specific or temporal regulation and can increase the activity of any promoter located in their vicinity.
Transcription factors, like the traps-acting transcription factors of the present invention, are proteins that are needed for the initiation of transcription. They are distinct from RNA polymerases. They can act by recognizing and binding to cis-acting sites, i.e., the enhancers linked to split gene sequences. Transcription factors can also recognize other factors or RNA polymerases, or can be incorporated into an initiation complex only in the presence of several other proteins. There are many references that can be consulted regarding various aspects of enhancers, transcription factors, and their interaction, e.g., Banjeri, J. et al. (1981) "Expression of (3-globin gene is enhanced by remote SV40," Cell 27, 299-308; Zenke, M. et al. (1986) "Multiple Motifs are Involved in SV40 Enhancer Function," EMBO J. 5, 387-397; Mueler-Storm, H.P. et al. (1989) "An enhancer stimulates transcription in traps when attached to the promoter via a protein bridge," Cell 58, 767-777; Kustu, A.K. and Weiss, D.S. (1991) "Prokayotic Transcriptional Enhancers and Enhancer-Binding Proteins," Trends Biochem. Sci. 16:397-402;
Kadonaga, J. et al. (1987) "Isolation of cDNA Encoding Transcription Factor Spl and functional analysis of the DNA Binding Domain," Cell 51. 1079-1090; Ma, J. and Ptashne, M. (1987) "A new class of Yeast Transcriptional Activators," Cell 79, 93-105; and Muller, M.M. et al. (1988) "Enhancer Sequences and the Regulation of Gene Transcription," Eur.
J.
Biochem. 176, 485-495.
Toxic Genetic Elements It is not uncommon for hybrid offspring to outperform their parents by various measures, including yield, adaptability to environmental changes, disease resistance, pest resistance, solids content, sugar content, water content, and the like. As such, there is considerable commercial importance in generating hybrids with desirable traits. The improved properties observed in hybrids relative to parents are collectively referred to as "hybrid vigor" or "heterosis." Hybridization between parents of dissimilar genetic stock has been used in animal husbandry and especially for improving major plant crops, such as corn, sugarbeet and sunflower.
It has proven difficult, however, to commercialize genetically engineered variants of many plants due to the fact that hybrids cannot be bred reliably.
In the case of corn, for example, hybrids have been created by the laborious task of removing the tassels from one parent and pollinating with another. In general, one attempt to address the problems related to hybrids has been to engineer plants that conditionally express toxins, specifically in pollen, that render plants sterile with respect to self pollination. However, this approach has raised the concern of regulators, e.g., due to the risk of sterility genes spreading to wild plants. Furthermore, this technique requires engineering an expression system that is tightly regulated to prevent expression of the toxic genes in the soma of these plants. As discussed throughout this disclosure, the methods of encrytping traits provided by the present invention resolve many of these issues.
For example, the present invention provides a solution to the problems associated with the production of hybrids by encoding engineered genes, e.g., Bt toxin genes (FIG. 1), in split gene sequences. In doing so, the desired protein product is then expressed upon breeding plants that encode, e.g., each half of the split gene sequence. A
full-length protein is made by either traps-splicing mRNA fragments corresponding to the split gene sequences followed by translation, or as depicted in Figure 1, translating the mRNA fragments directly and then traps-splicing at the polypeptide level. This solution provides plants breeders with potential commercial benefits, as consumers would not be able to easily propagate seed that breeds true, i.e., that are homozygous for the trait under consideration (see e.g., FIG. 4), but without the costs otherwise associated with the creation of plants engineered for male sterility.
As depicted in Figure 4, in another embodiment of the present invention, two parental organisms, each including split gene sequences in which each split gene sequence includes a subsequence of a toxic genetic element are mated and the split gene sequences can be expressed in the progeny organism to provide a toxic polypeptide after traps-splicing at the RNA or the polypeptide levels as described above. The toxic polypeptide, in turn, renders the progeny organism incapable of reproducing when it is male, i.e., the progeny organism acquires a "hybrid vigor." (FIG. 4). However, the progeny organism can reproduce when it is female and when it does, the progeny organism produces hybrid progeny organisms in which the toxic genetic element is not expressed. In a related embodiment of this method, a toxic polypeptide renders the progeny organism incapable of reproducing when it is female. However, this progeny organism is capable of reproducing when it is male and when it does, the progeny organism produces hybrid progeny organisms in which the toxic genetic element is not expressed.
As further depicted in Figure 4, F 1 plants would not express the toxic gene product and as such, there would be no loss of yield. However, F2 may not be useful, because the "hybrid vigor" of F1 is lost.

Traps-Splicing RNAs and Polype tides Traps-splicing includes splicing two independently transcribed pre-mRNAs together. The mechanism of traps-splicing proceeds through two phosphoryl transfer reactions similar to that of cis-splicing. Moore, J.M. et al. In The RNA World (eds Gesteland, R.F. & Atkins, J.F.) 303-357 (Cold Spring Harbor Laboratory Press, New York, 1993). The first yields the formation of a 2'-5' phospodiester bond producing a Y-shaped branched intermediate, equivalent to the lariat intermediate in cis-splicing.
Id. The second reaction, exon ligation, also proceeds as in cis-splicing. Additionally, sequences at the 3' splice site and some of the small nuclear ribonucleoprotein particles (snRNPs) that catalyze the traps-splicing reaction closely resemble their counterparts involved in cis-splicing.
Murphy, W.J. et al. (1986) "Identification of a Novel Branch Structure as an Intermediate in Trypanosome mRNA Processing: Evidence for Traps-Splicing," Cell 47, 517-525 and Curotto de Lafaille, M.A. (1992) "Gene Expression in Leishmania: Analysis of Essential 5' DNA Sequences," Proc. Natl. Acad. Sci. USA 89, 2703-2707. As applicable to the present invention, traps-splicing of RNAs can also involve a process in which an intron of one pre-mRNA interacts with an intron of a second pre-mRNA, enhancing the recombination of splice sites between two conventional pre-mRNAs. Puttaraju, M. et al.
(1999) "Spliceosome-Mediated RNA Traps-Splicing as a Tool for Gene Therapy,"
Nat.
Biotechnol. 17, 246-252. This type of traps-splicing was demonstrated, e.g., in c-myb pre-mRNA (Vellard, M. et al. (1992) " A Potential Splicing Factor is Encoded by Opposite Strand of the Traps-Spliced c-myb Exon," Proc. Natl. Acad. Sci. USA 89, 2511-2515) and with respect to SV40 transcripts in cultured cells (Eul, J. et al. (1995) "Experimental Evidence for RNA Traps-Splicing in Mammalian Cells," EMBO J. 14, 3226-3235).
Relatively efficient traps-splicing in vitro has been shown between RNAs capable of base pairing to each other. Konarsha, M.M. et al. (1985) "Traps-Splicing of mRNA
Precursors In Vitro," Cell 42, 165-171 and Pasman, Z. and Garcia-Blanco, M.A. (1996) "The 5' and 3' Splice Sites Come Together Via A Three-Dimensional Diffusion Mechanism,"
Nucleic Acids Res. 24, 1638-1645. For purposes of the present invention, the use of spliceosome-mediated targeted traps-splicing reactions to generate traps-spliced chimeric mRNA and functional chimeric proteins therefrom has been confirmed both in vitro and in vivo.
Puttaraju, M. et al. (1999) Nat. Biotechnol. 17, 246-252, supra. As such, this mechanism can be used in the various embodiments of the present invention to provide trait encrypted RNAs.
In addition to traps-splicing of RNAs, traps-splicing of inteins is also used in the present invention. In one preferred embodiment, proteins of interest are encoded in split genes which are expressed to produce polypeptide fragments. These fragments are subsequently recombined to form the protein of interest. Examples of traps-intein splicing systems are available, such as the DnaE gene, encoded by dnaE-n and dnaE-c in the Synchocystis sp. PCC6803 genome. This is illustrated in Figure 5, where DnaE-related sequences are denoted as exteins Ext-n and Ext-c, while intein-related sequences are indicated as Int-n and Int-c. Furthermore, the functional domains of the traps-spliced protein product are also shown. Figure 6 provides DnaB and DnaE intein sequence information from various organisms, including Porphyra purpurea, Rhodothermus marinus, and Mycobacterium tuberuclosis.
UNENCRYPTING ENGINEERED GENETIC ELEMENTS TO PROVIDE
POLYPEPTIDE FUNCTION
Trait encryption can also be accomplished utilizing post-translational modifications. For example, there are proteins that ligate biotin onto surface lysines in a site-specific manner. One can take advantage of this and other equivalent mechanisms (e.g., glycosylation, proteolysis, farnesylation, cholesterol esterification, acetylation, methylation, phosphorylation, dephosphorylation, and the like) for purposes of encryption by evolving a variant of a protein that requires biotinylation (or any other modification) for activity. Methods of evolving proteins, including non-overlapping gene sequence mediated-recombination, among many others, are discussed further, infra. A
biotin ligase can be evolved that activates another protein by specifically ligating biotin onto the other protein in vivo. This provides an additional encryption system where, for instance, transgenic wheat plants require both the biotin ligase and an engineered glyphosate resistance gene to be present in the same plant in order to get functional protein. One commercial advantage of these methods is that the producer of the seed with the engineered trait then controls the ability to produce a seed that breeds true.
The methods of unencrypting engineered genetic elements to provide encrypted polypeptide functions of the present invention can occur in vitro or in vivo. The methods include providing a first engineered genetic element that corresponds to an encoded first polypeptide, e.g., an engineered biotin ligase that is functional. It also includes providing a second engineered genetic element that corresponds to an encoded second polypeptide, e.g., an engineered biotin dependent glyphosate resistance polypeptide, that is nonfunctional in the absence of the post-translational modification, i.e., biotinylation performed by the first polypeptide. Thereafter, the first and second engineered genetic elements can be mixed and expressed to produce the encoded first and second polypeptides. The encoded first polypeptide then modifies the encoded second polypeptide to provide a functional encoded second polypeptide.
Embodiments of these methods that can be performed in vivo include mating a first parental organism that includes the first engineered genetic element and a second parental organism that includes the second engineered genetic element to produce a progeny organism that includes both engineered genetic elements. Thereafter, the genetic elements in the progeny organism can be expressed to produce the encoded first and second polypeptides. The first and second parental organisms of this embodiment can be, e.g., animals, plants, fungi, or bacteria. The selection of suitable parental organisms is discussed further, supra. However, in certain preferred embodiments they are plants or yeast.
Another embodiment of these methods of unencrypting engineered genetic elements that can be performed in vivo includes infecting a host organism that includes a first engineered genetic element with a vector that includes a second engineered genetic element to produce an infected organism. Following infection, the infected organism includes both the first and the second engineered genetic elements.
Thereafter, both engineered genetic elements can similarly be expressed in the progeny organism to produce the encoded first polypeptide which modifies the second polypeptide to render it functional.
SELECTION OF TRAIT ENCRYPTED RNAS AND POLYPEPTIDES AND
ENGINEERED GENETIC ELEMENTS
The precise selection technique used in the methods disclosed herein is not a critical aspect of the invention. In general, one of skill can practice appropriate screening or selection methods, by reference to the activity to be selected for.
Furthermore, methods of transducing cells, including plant and animal cells, with nucleic acids are generally available, as are methods of expressing proteins encoded by those nucleic acids. These and other methods are described and related references are given, infra.
NON-OVERLAPPING GENE SEQUENCE RECOMBINATION
When several homologous genes are recombined or shuffled together, it is possible that the original genes are reassembled and rescued. To avoid simply recovering the original genes, discontinued genes, i.e., non-overlapping gene sequences can be used.
Since the gene sequences to be recombined are non-overlapping, they are not rescued unless the non-overlapping sequences are connected with the other genes by recombination. This concept is illustrated in Figure 7, where two cloned non-overlapping cry3Bb gene sequences are shuffled with a population of gap nucleic acids, which are represented by the black sequences in the figure. As shown, no complete parental cry3Bb genes are recovered from the shuffling step. (FIG. 7).
The methods of recombining non-overlapping gene sequences of the present invention can occur in vitro or in vivo. The methods include providing a plurality of non-overlapping gene sequences in which each non-overlapping gene sequence corresponds to a different subsequence of a genetic element, e.g., a gene. The methods further include providing a plurality of gap nucleic acid sequences in which each gap nucleic acid sequence overlaps two or more of the non-overlapping gene sequences. The non-overlapping gene sequences can be recombined with the gap nucleic acid sequences to provide recombined non-overlapping gene sequences. As described further below, the recombined non-overlapping gene sequences can optionally be selected for a desired trait or property and then recombined again. This process of selecting and recombining the recombined non-overlapping gene sequences can be repeated until a desired recombined genetic element is obtained.
Two non-overlapping gene sequences derived from a cry3Bb gene were recombined and a plurality of gap nucleic acid sequences derived from a cryl Ba, a cryl Ca, and a crylla gene using these methods. The results of this recombination are depicted in Figure 8. The shuffled DNA was recovered with primers specific to the start and end of the cry3Bb gene. Recovered DNA was cloned and 16 colonies were picked for PCR
analysis using seven primers (represented by A4 to A10) at various locations within cry3Bb and one at the end of the gene. The boxes, representing approximately nucleotides prior to an annealing site, are darkened to indicate where primers annealed and produced the right-sized PCR fragment. (FIG. 8).
Recombination Strate ies The polynucleotides of the present invention, e.g., the engineered genetic elements discussed, supra, are optionally used as substrates for a variety of recombination and recursive recombination (e.g., DNA shuffling) reactions. In general, the nucleic acids provided by the methods herein can be shuffled to produce encoded protein products with desired properties. A variety of such reactions are known, including those developed by the inventors and their co-workers.
The following publications describe a variety of recursive recombination procedures and/or methods which can be incorporated into such procedures:
Stemmer, et al. (1999) "Molecular breeding of viruses for targeting and other clinical properties"
Tumor Targeting 4:1-4; Ness et al. (1999) "DNA Shuffling of subgenomic sequences of subtilisin" Nature Biotechnology 17:893-896; Chang et al. (1999) "Evolution of a cytokine using DNA family shuffling" Nature Biotechnology 17:793-797; Minshull and Stemmer (1999) "Protein evolution by molecular breeding" Current Opinion in Chemical Biology 3:284-290; Christians et al. (1999) "Directed evolution of thymidine kinase for AZT
phosphorylation using DNA family shuffling" Nature Biotechnology 17:259-264;
Crameri et al. (1998) "DNA shuffling of a family of genes from diverse species accelerates directed evolution" Nature 391:288-291; Crameri et al. (1997) "Molecular evolution of an arsenate detoxification pathway by DNA shuffling," Nature Biotechnology 15:436-438;
Zhang et al. (1997) "Directed evolution of an effective fucosidase from a galactosidase by DNA
shuffling and screening" Proc. Natl. Acad. Sci. USA 94:4504-4509; Patten et al. (1997) "Applications of DNA Shuffling to Pharmaceuticals and Vaccines" Current Opinion in Biotechnology 8:724-733; Crameri et al. (1996) "Construction and evolution of antibody-phage libraries by DNA shuffling" Nature Medicine 2:100-103; Crameri et al.
(1996) "Improved green fluorescent protein by molecular evolution using DNA
shuffling" Nature Biotechnology 14:315-319; Gates et al. (1996) "Affinity selective isolation of ligands from peptide libraries through display on a lac repressor 'headpiece dimer"' Journal of Molecular Biology 255:373-386; Stemmer (1996) "Sexual PCR and Assembly PCR"
In:

The Encyclopedia of Molecular Biology. VCH Publishers, New York. pp.447-457;
Crameri and Stemmer (1995) "Combinatorial multiple cassette mutagenesis creates all the permutations of mutant and wildtype cassettes" BioTechniques 18:194-195;
Stemmer et al.
(1995) "Single-step assembly of a gene and entire plasmid form large numbers of oligodeoxyribonucleotides" Gene, 164:49-53; Stemmer (1995) "The Evolution of Molecular Computation" Science 270: 1 S 10; Stemmer (1995) "Searching Sequence Space"
BiolTechnology 13:549-553; Stemmer (1994) "Rapid evolution of a protein in vitro by DNA shuffling" Nature 370:389-391; and.Stemmer (1994) "DNA shuffling by random fragmentation and reassembly: In vitro recombination for molecular evolution."
Proc.
Natl. Acad. Sci. USA 91:10747-10751.
Additional details regarding DNA shuffling methods are found in U.S.
Patents by the inventors and their co-workers, including: United States Patent 5,605,793 to Stemmer (February 25, 1997), "METHODS FOR IN VITRO RECOMBINATION;"
United States Patent 5,811,238 to Stemmer et al. (September 22, 1998) "METHODS
FOR
GENERATING POLYNUCLEOTIDES HAVING DESIRED CHARACTERISTICS BY
ITERATIVE SELECTION AND RECOMBINATION;" United States Patent 5,830,721 to Stemmer et al. (November 3, 1998), "DNA MUTAGENESIS BY RANDOM
FRAGMENTATION AND REASSEMBLY;" United States Patent 5,834,252 to Stemmer et al. (November 10, 1998) "END-COMPLEMENTARY POLYMERASE REACTION,"
and United States Patent 5,837,458 to Minshull et al. (November 17, 1998), "METHODS
AND COMPOSITIONS FOR CELLULAR AND METABOLIC ENGINEERING."
In addition, details and formats for DNA shuffling are found in a variety of PCT and foreign patent application publications, including: Stemmer and Crameri, "DNA
MUTAGENESIS BY RANDOM FRAGMENTATION AND REASEMBLY" WO
95/22625; Stemmer and Lipschutz, "END COMPLEMENTARY POLYMERASE CHAIN
REACTION" WO 96/33207; Stemmer and Crameri, "METHODS FOR GENERATING
POLYNUCLEOTIDES HAVING DESIRED CHARACTERISTICS BY ITERATIVE
SELECTION AND RECOMBINATION" WO 97/0078; Minshul and Stemmer, "METHODS AND COMPOSITIONS FOR CELLULAR AND METABOLIC
ENGINEERING" WO 97/35966; Punnonen et al., "TARGETING OF GENETIC
VACCINE VECTORS" WO 99/41402; Punnonen et al., "ANTIGEN LIBRARY

Il~f~~IUNIZATION" WO 99/41383; Punnonen et al., "GENETIC VACCINE VECTOR
ENGINEERING" WO 99/41369; Punnonen et al., "OPTIMIZATION OF
IIVIMUNOMODULATORY PROPERTIES OF GENETIC VACCINES" WO 9941368;
Stemmer and Crameri, "DNA MUTAGENESIS BY RANDOM FRAGMENTATION
AND REASSEMBLY" EP 0934999; Stemmer, "EVOLVING CELLULAR DNA
UPTAKE BY RECURSIVE SEQUENCE RECOMBINATION" EP 0932670; Stemmer et al., "MODIFICATION OF VIRUS TROPISM AND HOST RANGE BY VIRAL
GENOME SHUFFLING" WO 9923107; Apt et al., "HUMAN PAPILLOMAVIRUS
VECTORS" WO 9921979; Del Cardayre et al., "EVOLUTION OF WHOLE CELLS
AND ORGANISMS BY RECURSIVE SEQUENCE RECOMBINATION" WO 9831837;
Patten and Stemmer, "METHODS AND COMPOSITIONS FOR POLYPEPTIDE
ENGINEERING" WO 9827230; and Stemmer et al., "METHODS FOR OPTIMIZATION
OF GENE THERAPY BY RECURSIVE SEQUENCE SHUFFLING AND SELECTION"
W09813487.
Certain U.S. Applications provide additional details regarding DNA
shuffling and related techniques, including "SHUFFLING OF CODON ALTERED
GENES" by Patten et al. filed September 29, 1998, (USSN 60/102,362), January 29, 1999 (USSN 60/117,729), and September 28, 1999, (USSN 09/407,800); "EVOLUTION OF
WHOLE CELLS AND ORGANISMS BY RECURSIVE SEQUENCE
RECOMBINATION" by del Cardayre et al. filed July 15, 1998 (USSN 09/166,188), and July 15, 1999 (USSN 09/354,922); "OLIGONUCLEOTIDE MEDIATED NUCLEIC
ACID RECOMBINATION" by Crameri et al., filed February 5, 1999 (USSN
60/118,813) and filed June 24, 1999 (USSN 60/141,049) and filed September 28, 1999 (USSN
09/408,392); and "USE OF CODON-VARIED OLIGONUCLEOTIDE SYNTHESIS FOR
SYNTHETIC SHUFFLING" by Welch et al., filed September 28, 1999 (USSN
09/408,393); and "METHODS FOR MAKING CHARACTER STRINGS, POLYNUCLEOTIDES & POLYPEPTIDES HAVING DESIRED CHARACTERISTICS"
by Selifonov and Stemmer, filed February 5, 1999 (USSN 60/118,854).
As review of the foregoing publications, patents, published applications and U.S. patent applications reveals, shuffling (or "recursive recombination") of nucleic acids to provide new nucleic acids with desired properties can be carned out by a number of established methods. Any of these methods can be adapted to the present invention to evolve, e.g., the engineered genetic elements like the engineered biotin ligase and engineered biotin dependent glyphosate resistance polypeptide, discussed herein to produce new engineered genetic elements with improved properties. In addition, any trait encrypted nucleic acid/protein can be shuffled to improve splicing or activity.
In brief, at least 5 different general classes of recombination methods are applicable to the present invention. First, nucleic acids can be recombined in vitro by any of a variety of techniques discussed in the references above, including e.g., DNAse digestion of nucleic acids to be recombined followed by ligation and/or PCR
reassembly of the nucleic acids. Second, nucleic acids can be recursively recombined in vivo, e.g., by allowing recombination to occur between nucleic acids in cells. Third, whole cell genome recombination methods can be used in which whole genomes of cells are recombined, optionally including spiking of the genomic recombination mixtures with desired library components such as engineered genetic element sequences, or non-overlapping gene sequences and gap nucleic acids. Fourth, synthetic recombination methods can be used, in which oligonucleotides corresponding to different non-overlapping gene sequences and gap nucleic acids are synthesized and reassembled in PCR or ligation reactions which include oligonucleotides which correspond to more than one parental nucleic acid, thereby generating new recombined nucleic acids. Oligonucleotides can be made by standard nucleotide addition methods, or can be made by tri-nucleotide synthetic approaches. Fifth, in silico methods of recombination can be effected in which genetic algorithms are used in a computer to recombine sequence strings which correspond, e.g., to engineered genetic elements. The resulting recombined sequence strings are optionally converted into nucleic acids by synthesis of nucleic acids that correspond to the recombined sequences, e.g., in concert with oligonucleotide synthesis/gene reassembly techniques. Any of the preceding general recombination formats can be practiced in a reiterative fashion to generate a more diverse set of recombinant nucleic acids.
DNA shuffling and related techniques provide a robust, widely applicable, means of generating diversity useful for the engineering of trait encrypted nucleic acids and proteins. In addition to the basic formats described above, it is sometimes desirable to combine recombination methodologies with other techniques for generating additional diversity. In conjunction with (or separately from) recombination-based methods, a variety of other diversity generation methods can be practiced and the results (i.e., diverse populations of nucleic acids) screened for. Additional diversity can be introduced into insertion modified nucleic acids by methods which result in the alteration of individual nucleotides or groups of contiguous or non-contiguous nucleotides, e.g., mutagenesis methods. Mutagenesis methods include, for example, recombination (PCT/US98/05223;
Publ. No. W098/42727); oligonucleotide-directed mutagenesis (for review see, Smith, Ann. Rev.Genet. 19: 423-462 (1985)); Botstein and Shortle, Science 229: 1193-(1985); Carter, Biochem. J. 237: 1-7 (1986); Kunkel, "The efficiency of oligonucleotide directed mutagenesis" in Nucleic acids & Molecular Biolo~y, Eckstein and Lilley, eds., Springer Verlag, Berlin (1987)). Included among these methods are oligonucleotide-directed mutagenesis (Zoller and Smith, Nucl. Acids Res. 10: 6487-6500 (1982), Methods in Enzymol. 100: 468-500 (1983), and Methods in Enzvmol. 154: 329-350 (1987)) phosphothioate-modified DNA mutagenesis (Taylor et al., Nucl. Acids Res. 13:

(1985); Taylor et al., Nucl. Acids Res. 13: 8765-8787 (1985); Nakamaye and Eckstein, Nucl. Acids Res. 14: 9679-9698 (1986); Sayers et al., Nucl. Acids Res. 16:791-802 (1988);
Sayers et al., Nucl. Acids Res. 16: 803-814 (1988)), mutagenesis using uracil-containing templates (Kunkel, Proc. Nat'l. Acad. Sci. USA 82: 488-492 (1985) and Kunkel et al., Methods in Enz~mol. 154:367-382)); mutagenesis using gapped duplex DNA (Kramer et al., Nucl. Acids Res. 12: 9441-9456 (1984); Kramer and Fritz, Methods in Enzymol.
154:350-367 (1987); Kramer et al., Nucl. Acids Res. 16: 7207 (1988)); and Fritz et al., Nucl. Acids Res. 16: 6987-6999 (1988)). Additional suitable methods include point mismatch repair (Kramer et al., Cell 38: 879-887 (1984)), mutagenesis using repair-deficient host strains (Carter et al., Nucl. Acids Res. 13: 4431-4443 (1985);
Carter, Methods in Enzymol. 154: 382-403 (1987)), deletion mutagenesis (Eghtedarzadeh and Henikoff, Nucl. Acids Res. 14: 5115 (1986)), restriction-selection and restriction-purification (Wells et al., Phil. Trans. R. Soc. Lond. A 317: 415-423 (1986)), mutagenesis by total gene synthesis (Nambiar et al., Science 223: 1299-1301 (1984);
Sakamar and Khorana, Nucl. Acids Res. 14: 6361-6372 (1988); Wells et al., Gene 34:315-323 (1985);
and Grundstrom et al., Nucl. Acids Res. 13: 3305-3316 (1985). Kits for mutagenesis are commercially available (e.g., Bio-Rad, Amersham International, Anglian Biotechnology).

Other relevant references which describe methods of diversify nucleic acids include Schellenberger U.S. Patent No. 5,756,316; U.S. Patent No. 5,965,408;
Ostermeier et al. (1999) "A combinatorial approach to hybrid enzymes independent of DNA
homology" Nature Biotech 17:1205; U.S. Patent No. 5,783,431; U.S. Patent No.5,824,485;
U.S. Patent 5,958,672; Jirholt et al. (1998) "Exploiting sequence space:
shuffling in vivo formed complementarity determining regions into a master framework" Gene 215:
471;
U.S. Patent No. 5,939,250; WO 99/10539; WO 98/58085 and WO 99/10539.
Any of these diversity generating methods can be combined, in any combination selected by the user, to produce nucleic acid diversity, which may be screened for using any available screening method.
Non-Overlapping_Gene Sequence Shuffling Targets Virtually any nucleic acid can be recombined by the methods described in this disclosure. No attempt is made to identify the hundreds of thousands of known nucleic acids. However, certain preferred target sequences for non-overlapping gene sequence mediated-recombination include inhibitors of transcription or toxins of crop pests (e.g., insects, fungi, weed plants, etc.), recombinases (e.g., Cre-lox, VDJ, etc.), integrases (e.g., ~, integrase), and the like. As discussed further below, common sequence repositories for known proteins include GenBank~, Entrez~, EMBL, DDBJ, GSDB, NDB
and the NCBI. Other repositories can easily be identified by searching the Internet.
Post-Recombination Screening Techniques The precise screening technique that is used in the recombination methods disclosed herein is not a critical aspect of the invention. In general, one of skill can practice appropriate screening or selection methods, by reference to the activity to be selected for.
In any case, one or more recombination cycles) is/are usually followed by at least one cycle of screening or selection for molecules having a desired property or characteristic. If a recombination cycle is performed in vitro, the products of recombination, i.e., recombinant segments, are sometimes introduced into cells before the screening step. Recombinant segments can also be linked to an appropriate vector or other regulatory sequences before screening. Alternatively, products of recombination generated in vitro are sometimes packaged in viruses (e.g., bacteriophage) before screening. If recombination is performed in vivo, recombination products can sometimes be screened in the cells in which recombination occurred. In other applications, recombinant segments are extracted from the cells, and optionally packaged as viruses, before screening.
The nature of screening or selection depends on what property or characteristic is to be acquired or the property or characteristic for which improvement is sought, and many examples are discussed below. It is not usually necessary to understand the molecular basis by which particular products of recombination (recombinant segments) have acquired new or improved properties or characteristics relative to the starting substrates. For example, a gene can have many component sequences, each having a different intended role (e.g., coding sequence, regulatory sequences, targeting sequences, stability-confernng sequences, subunit sequences and sequences affecting integration).
Each of these component sequences can be varied and recombined simultaneously.
Screening/selection can then be performed, for example, for recombinant segments that have increased ability to confer activity upon a cell without the need to attribute such improvement to any of the individual component sequences of the vector.
Depending on the particular screening protocol used for a desired property, initial rounds) of screening can sometimes be performed using bacterial cells due to high transfection efficiencies and ease of culture. However, bacterial expression is often not practical or desired, and yeast, fungal or other eukaryotic systems are also used for library expression and screening. Similarly, other types of screening which are not amenable to screening in bacterial or simple eukaryotic library cells, are performed in cells selected for use in an environment close to that of their intended use. Final rounds of screening can be performed in the precise cell type of intended use.
If further improvement in a property is desired, at least one and usually a collection of recombinant segments surviving a first round of screening/selection are subject to a further round of recombination. These recombinant segments can be recombined with each other or with exogenous segments representing the original substrates or further variants thereof. Again, recombination can proceed in vitro or in vivo.
If the previous screening step identifies desired recombinant segments as components of cells, the components can be subjected to further recombination in vivo, or can be subjected to further recombination in vitro, or can be isolated before performing a round of in vitro recombination. Conversely, if the previous screening step identifies desired recombinant segments in naked form or as components of viruses, these segments can be introduced into cells to perform a round of in vivo recombination. The second round of recombination, irrespective how performed, generates further recombinant segments which encompass additional diversity than is present in recombinant segments resulting from previous rounds.
The second round of recombination can be followed by a further round of screening/selection according to the principles discussed above for the first round. The stringency of screening/selection can be increased between rounds. Also, the nature of the screen and the property being screened for can vary between rounds if improvement in more than one property is desired or if acquiring more than one new property is desired.
Additional rounds of recombination and screening can then be performed until the recombinant segments have sufficiently evolved to acquire the desired new or improved property or function.
TARGET GENE SEQUENCE PREPARATION
An initial inquiry applicable to the methods of the present invention includes determining the sequence of nucleotides in target sequences, e.g., in genes to be split between two parental organisms or between a host organism and a vector, in engineered genetic elements, or in non-overlapping gene sequences. Thereafter, polynucleotides such as gap nucleic acid sequences can be designed based upon this sequence information. Target sequences can be prepared using various methods or combinations thereof, including certain DNA synthetic techniques (e.g., mononucleotide-and/or trinucleotide-based synthesis, reverse-transcription, etc.), DNA
amplification, restriction enzyme digestion, etc.
Split gene sequences can be designed to ensure that trans-splicing will be accurately targeted. See Puttaraju, M. et al. (1999) Nat. Biotech. 17, 246-252. For example, a gene encoding a desired product, e.g., a growth hormone, Bt toxin, etc. can be split, e.g., between two coding subsequences. A first coding subsequence can include a target binding domain that is complementary to a downstream intron (e.g., (3hCG6 intron 1) of the second coding subsequence. The first coding subsequence can also include a spacer region, a branch point sequence (e.g., a UACUAAC yeast consensus branch point sequence), a polypyrimidine tract, and an AG dinucleotide at the 3' splice site immediately upstream of the coding region of the first subsequence. A similar construct has been utilized to achieve very precise traps-splicing. Id. Promoter and transcriptional terminator sequences that control the expression of the coding regions can also be included. For example, if the coding sequences are to be expressed constitutively throughout a plant, the 35S RNA promoter from the cauliflower mosaic virus can be used. Cell-specific specific promoters are also available and known to those of skill. Similarly, sequences can be shuffled and selected for desired splicing.
Taxget coding sequences to be split according to the methods of the present invention can be derived from any type of organism. Plant-related target sequences, however, include those that confer herbicide-resistance to permit lower treatment with herbicides like glyphosate, and various suphonylurea, phosphinothricin, and bromoxynil compounds. Other target sequences include those that provide plants with insect resistance (e.g., 8-endotoxin from Bacillus thuringiensis), viral resistance, male sterility, and the like.
Gene Sequence Information, Selection, and Design Searchable sequence information available from various nucleic acid databases can be utilized during the nucleic acid sequence selection and/or design processes. Genbank~, Entrez~, EMBL, DDBJ, GSDB, NDB, and the NCBI are examples of public database/search services that can be accessed. These databases are generally available via the Internet or on a contract basis from a variety of companies specializing in genomic information generation andlor storage. These and other helpful resources are readily available and known to those of skill.
The sequence of a polynucleotide to be used in any of the methods of the present invention can also be readily determined using techniques well-known to those of skill, including Maxam-Gilbert, Sanger Dideoxy, and Sequencing by Hybridization methods. For general descriptions of these processes consult, e.g., Stryer, L., Biochemistry (4th Ed.) W.H. Freeman and Company, New York, 1995 (Stryer) and Lewin, B.
Genes VI
Oxford University Press, Oxford, 1997 (Lewin). See also, Maxam, A.M. and Gilbert, W.
(1977) "A New Method for Sequencing DNA," Proc. Natl. Acad. Sci. 74:560-564, Sanger, F. et al. (1977) "DNA Sequencing with Chain-Terminating Inhibitors," Proc.
Natl. Acad.
Sci. 74:5463-5467, Hunkapiller, T. et al. (1991) "Large-Scale and Automated DNA

Sequence Determination," Science 254:59-67, and Pease, A.C. et al. (1994) "Light-Generated Oligonucleotide Arrays for Rapid DNA Sequence Analysis," Proc. Natl.
Acad.
Sci. 91:5022-5026.
In certain aspects, the present invention also optionally includes aligning S target nucleic acid sequences and/or searching those sequences for specific subsequences.
For example, an obj ect of methods of recombining non-overlapping gene sequences herein is to avoid reassembling original gene sequences. The alignment and comparison of fragments of a gene sequence to be recombined, in this manner, can be utilized to ensure that no regions of overlap, i.e., homology or complementarity exist among the fragments to be recombined. Sequence comparison and alignment can also be of use in the process of designing gap nucleic acids which are sequences that include regions that are homologous or substantially homologous with at least two non-overlapping gene sequences.
Additionally, as discussed further below, split genes can be created, e.g., upon digestion by certain restriction endonucleases that generate blunt ends. As such, the process of designing split genes can involve searching a particular gene sequence to be split for specific restriction sites.
In the processes of sequence comparison and homology determination, one sequence, e.g., one fragment or subsequence of a gene sequence to be recombined, can be used as a reference against which other test nucleic acid sequences are compared. This comparison can be accomplished with the aid of a sequence comparison instruction set, i.e., algorithm, or by visual inspection. When an algorithm is employed, test and reference sequences are input into a computer, subsequence coordinates are designated, as necessary, and sequence algorithm program parameters are specified. The algorithm then calculates the percent sequence identity for the test nucleic acid sequences) relative to the reference sequence, based on the specified program parameters. Integrated systems that are relevant to the invention are discussed further, infra.
For purposes of the present invention, suitable sequence comparisons can be executed, e.g., by the local homology algorithm of Smith & Waterman, Adv.
Appl. Math.
2:482 (1981), by the homology alignment algorithm of Needleman & Wunsch, J.
Mol.
Biol. 48:443 (1970), by the search for similarity method of Pearson & Lipman, Proc. Nat'l.
Acad. Sci. USA 85:2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, WI), or by visual inspection. See generally, Current Protocols in Molecular Biology, F.M. Ausubel et al., eds., Current Protocols, a joint venture between Greene Publishing Associates, Inc. and John Wiley &
Sons, Inc., (supplemented through 1999), supra).
One example search algorithm that is suitable for determining percent sequence identity and sequence similarity is the Basic Local Alignment Search Tool (BLAST) algorithm, which is described in Altschul et al., J. Mol. Biol.
215:403-410 (1990). Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (http://www.ncbi.nhn.nih.gov~.
Target Sequence Acguisition After sequence information has been obtained as described above, that information can be used to design and synthesize target nucleic acid sequences corresponding to, e.g., split gene sequences, enhancer-linked split gene sequences, trans-acting transcription factor sequences, engineered genetic elements, non-overlapping gene sequences, and gap nucleic acids. These sequences can be synthesized utilizing various solid-phase strategies involving mononucleotide- and/or trinucleotide-based phosphoramidite coupling chemistry. In these approaches, nucleic acid sequences are synthesized by the sequential addition of activated monomers and/or trimers to an elongating polynucleotide chain. See e.g., Caruthers, M.H. et al. (1992) Meth.
Enzymol.
211:3-20.
In the formats involving trimers, trinucleotide phosphoramidites representing codons for all 20 amino acids are used to introduce entire codons into the growing oligonucleotide sequences being synthesized. The details on synthesis of trinucleotide phoshoramidites, their subsequent use in oligonucleotide synthesis, and related issues are described in, e.g., Virnekas, B., et al. (1994) Nucleic Acids Res., 22, 5600-5607, Kayushin, A. L. et al. (1996) Nucleic Acids Res., 24, 3748-3755, Huse, U.S.
Pat. No. 5,264,563 "PROCESS FOR SYNTHESIZING OLIGONUCLEOTIDES WITH
RANDOM CODONS," Lyttle et al., U.S. Pat. No. 5,717,085 "PROCESS FOR
PREPARING CODON AMIDITES," Shortle et al., U.S. Pat. No. 5,869,644 "SYNTHESIS
OF DIVERSE AND USEFUL COLLECTIONS OF OLIGONUCLEOTIDES," Greyson, U.S. Pat. No. 5,789,577 "METHOD FOR THE CONTROLLED SYNTHESIS OF
POLYNUCLEOTIDE MIXTURES WHICH ENCODE DESIRED MIXTURES OF
PEPTIDES," and Huse, WO 92/06176 "SURFACE EXPRESSION LIBRARIES OF
RANDOMIZED PEPTIDES."
The chemistry involved in these synthetic methods is known by those of skill. In general, they utilize phosphoramidite solid-phase chemical synthesis in which the 3' ends of nucleic acid substrate sequences are covalently attached to a solid support, e.g., controlled pore glass. The 5' protecting groups can be, e.g., a triphenylmethyl group, such as, dimethoxyltrityl (DMT) or monomethyoxytrityl, a carbonyl-containing group, such as, 9-fluorenylmethyloxycarbonyl (FMOC) or levulinoyl, an acid-clearable group, such as, pixyl, a fluoride-cleavable alkylsilyl group, such as, tert-butyl dimethylsilyl (T-BDMSi), triisopropyl silyl, or trimethylsilyl. The 3' protecting groups can be, e.g., /3-cyanoethyl groups.
These formats can optionally be performed in an integrated automated synthesizer system that automatically performs the synthetic steps. See also, Integrated Systems, infra. This aspect includes inputting character string information into a computer, the output of which then directs the automated synthesizer to perform the steps necessary to synthesize the desired nucleic acid sequences. Automated synthesizers are available from many commercial suppliers including PE Biosystems and Beckman Instruments, Inc.
To further ensure that target gene sequences, e.g., non-overlapping or split gene sequences are ultimately obtained, certain techniques can be utilized following DNA
synthesis. For example, gel purification is one method that can be used to purify synthesized oligonucleotides. High-performance liquid chromatography can be similarly employed. Furthermore, translational coupling can be used to assess gene functionality, e.g., to test whether full-length sequences such as engineered genetic elements are generated. In this process, the translation of a reporter protein, e.g., green fluorescent protein or (3-galactosidase is coupled to that of the target gene product.
This enables one to distinguish, e.g., full-length engineered genetic elements from those that contain deletions or frame shifts. The subsequent selection of desired traits or properties of target gene sequences is discussed further, supra.

In lieu of synthesizing the desired sequences; essentially any nucleic acid can optionally be custom ordered from any of a variety of commercial sources, such as The Midland Certified Reagent Company (mcrc@oligos.com), The Great American Gene Company (www.genco.com), ExpressGen, Inc. (www.expressgen.com), Operon Technologies, Inc. (www.operon.com), and many others.
Target nucleic acid sequences, e.g., split or non-overlapping gene sequences can be derived from expression products, e.g., mRNAs expressed from genes within a cell of a plant or other organism. A number o.f techniques are available for detecting RNAs.
For example, northern blot hybridization is widely used for RNA detection, and is generally taught in a variety of standard texts on molecular biology, including Ausubel, Sambrook, and Bergen supra. Furthermore, one of skill will appreciate that essentially any RNA can be converted into a double stranded DNA using a reverse transcriptase enzyme and a polymerise. See, Ausubel, Sambrook and Bergen Messenger RNAs can be detected by converting, e.g., mRNAs into cDNAs, which are subsequently detected in, e.g., a standard "Southern blot" format.
Examples of techniques sufficient to direct persons of skill through in vitro amplification methods, useful e.g., for amplifying synthesized split gene sequences, non-overlapping gene sequences, gap nucleic acids, or for reassembling genes comprising non-overlapping gene sequences, include the polymerise chain reaction (PCR), the ligase chain reaction (LCR), Q~3-replicase amplification, and other RNA polymerise mediated techniques (e.g., NASBA). These techniques are found in Ausubel, Sambrook, and Bergen as well as in Mullis et al., (1987) U.S. Patent No. 4,683,202; PCR
Protocols A
Guide to Methods and Applications (Innis et al. eds) Academic Press Inc. San Diego, CA
(1990) (Innis); Arnheim & Levinson (October 1, 1990) C&EN 36-47; The Journal Of NIH
Research (1991) 3, 81-94; Kwoh et al. (1989) Proc. Natl. Acid. Sci. USA 86, 1173;
Guatelli et al. (1990) Proc. Natl. Acid. Sci. USA 87, 1874; Lomell et al.
(1989) J. Clin.
Chem 35, 1826; Landegren et al. (1988) Science 241, 1077-1080; Van Brunt (1990) Biotechnology 8, 291-294; Wu and Wallace, (1989) Gene 4, 560; Barringer et al.
(1990) Gene 89, 117, and Sooknanan and Malek (1995) Biotechnology 13: 563-564.
Improved methods of cloning in vitro amplified nucleic acids are described in Wallace et al., U.S.
Pat. No. 5,426,039. Improved methods of amplifying large nucleic acids, e.g., engineered genetic elements, by PCR are summarized in Cheng et al. (1994) Nature 369: 684-685 and the references therein, in which PCR amplicons of up to 40kb are generated.
In one preferred method, assembled sequences are checked for incorporation of non-overlapping gene sequences. This can be done by cloning and sequencing the nucleic acids, and/or by restriction digestion, e.g., as essentially taught in Ausubel, Sambrook, and Berger, supra. In addition, sequences can be PCR
amplified and sequenced directly. Thus, in addition to, e.g., Ausubel, Sambrook, Bergen and Innis, additional PCR sequencing methodologies are also particularly useful. For example, direct sequencing of PCR generated amplicons by selectively incorporating boronated nuclease resistant nucleotides into the amplicons during PCR and digestion of the amplicons with a nuclease to produce sized template fragments has been performed (Porter et al.
(1997) Nucleic Acids Res. 25(8):1611-1617).
Aside from directly synthesizing, e.g., split gene sequences and non-overlapping gene sequences, as described above, certain restriction endonucleases can also be used to generate these sequences. For example, populations of specific genes of interest can be obtained, e.g., from an mRNA population which has been reverse-transcribed and amplified as mentioned, supra. Uniform sets of split gene and non-overlapping gene sequences can be created from these cDNA populations upon digestion, e.g., with blunt cutting restriction endonucleases (e.g., Alu I (AG~.CT), Dra I (TTT~.AAA), Eco RV
(GAT~~ATC), Hae III (GG~~CC), Hind II (GT(T,C)~.(A,G)AC), Hpa I (GTT~~AAC), Mlu NI (TGG~~CCA), Nru I (TCG.~CGA), Pvu II (CAG.~CTG), Rsa I (GT~~AC), Sca I
(AGT~.ACT), Sma I (CCC.~GGG), Ssp I (AATJ.ATT), Stu I (AGG~~CCT), Swa I
(ATTT~.AAAT), and the like). Furthermore, the sequence information derived, e.g., as described supra, can be referenced to determine the number of fragments to be generated upon the digestion of a particular gene sequence. Various algorithms, also mentioned supra, can be helpful in searching for and determining the frequency of occurrence of restriction sites in a gene sequence, which information is useful in the design of both split gene and non-overlapping gene sequences.

INTRODUCTION OF NUCLEIC ACID SEQUENCES INTO THE CELLS OF
ORGANISMS OF INTEREST
In certain embodiments of the present invention, nucleic acid sequences are introduced into the cells of particular organisms of interest, including plants and animals.
For example, split gene sequences, e.g., split herbicide resistance genes (FIG. 2), split toxic gene sequences (FIGS. 1 and 3), and the like can be introduced into the genomes of two parental organisms, e.g., corn, wheat, or other commercially important crops, e.g., for the ultimate production of hybrid progeny, for the creation of libraries of split genes, and the like. Similarly, enhancer-linked split gene sequences, trans-acting factors, engineered genetic elements, and recombined non-overlapping gene sequences can also be introduced into various organisms.
As applied to the present invention, upon identification of particular nucleic acids which encode, e.g., products of desirable quantitative traits (see, Edwards, et al.
(1987) Genetics 115:113) or other genes or loci of interest, it is desirable to clone nucleic acids which are genetically linked to DNAs encoding these products for transduction into cells (e.g., coding sequences for the desired expression products, or genetically linked coding or non-coding sequences), especially to make, e.g., transgenic plants.
The cloned sequences are also useful as molecular tags for selected plant strains, e.g., to identify parentage, and are further useful for encoding expression products, including nucleic acids and polypeptides.
A DNA linked to a locus encoding an expression product, e.g., a split gene sequence, an engineered genetic element, etc., is introduced into plant cells, either in culture or in organs of a plant, e.g., leaves, stems, fruit, seed, etc. The expression of natural or synthetic nucleic acids encoded by nucleic acids linked to expression product or target coding nucleic acids can be achieved by operably linking a cloned nucleic acid of interest, such as an expression product or a genetically linked nucleic acid, to a promoter, incorporating the construct into an expression vector and introducing the vector into a suitable host cell. Alternatively, an endogenous promoter linked to the nucleic acids can be used.
Clonin~of Expression Product Seguences into Bacterial Hosts There are several well-known methods of introducing target nucleic acids into bacterial cells, any of which may be used in the present invention. These include:

fusion of the recipient cells with bacterial protoplasts containing the DNA, electroporation, projectile bombardment, and infection with viral vectors (discussed further, below), etc.
Bacterial cells can be used to amplify the number of plasmids containing DNA
constructs of this invention. The bacteria are grown to log phase and the plasmids within the bacteria can be isolated by a variety of methods known in the art (see, for instance, Sambrook). In addition, a plethora of kits are commercially available for the purification of plasmids from bacteria. For their proper use, follow the manufacturer's instructions (see, for example, EasyPrepTM, FlexiPrepTM, both from Pharmacia Biotech; StrataCleanTM, from Stratagene;
and, QIAexpress Expression SystemTM from Qiagen). The isolated and purified plasmids are then further manipulated to produce other plasmids, used to transfect plant cells or incorporated into Agrobacterium tumefaciens related vectors to infect plants.
Typical vectors contain transcription and translation terminators, transcription and translation initiation sequences, and promoters useful for regulation of the expression of the particular target nucleic acid. The vectors optionally comprise generic expression cassettes containing at least one independent terminator sequence, sequences permitting replication of the cassette in eukaryotes, or prokaryotes, or both, (e.g., shuttle vectors) and selection markers for both prokaryotic and eukaryotic systems. Vectors are suitable for replication and integration in prokaryotes, eukaryotes, or preferably both. See, Giliman &
Smith, Gene 8:81 (1979); Roberts, et al., Nature, 328:731 (1987); Schneider, B., et al., Protein Expr. Purif. 6435:10 (1995); Ausubel, Sambrook, Berger (all supra). A
catalogue of Bacteria and Bacteriophages useful for cloning is provided, e.g., by the ATCC, e.g., The ATCC Catalogue of Bacteria and Bacteriophage (1992) Gherna et al. (eds) published by the ATCC. Additional basic procedures for sequencing, cloning and other aspects of molecular biology and underlying theoretical considerations are also found in Watson et al.
(1992) Recombinant DNA Second Edition Scientific American Books, NY.
Transfectin~ and Manipulating Plant Cells Methods of transducing plant cells with nucleic acids are generally available and known by those of skill. In addition to Ausubel, Sambrook, and Berger, supra, useful general references for plant cell cloning, culture and regeneration include Payne include Payne et al. (1992) Plant Cell and Tissue Culture in Liquid Systems John Wiley & Sons, Inc. New York, NY (Payne); and Gamborg and Phillips (eds) (1995) Plant Cell, Tissue and Organ Culture; Fundamental Methods Springer Lab Manual, Springer-Verlag (Berlin Heidelberg New York) (Gamborg). A variety of Cell culture media are described in Atlas and Parks (eds) The Handbook of Microbiological Media (1993) CRC
Press, Boca Raton, FL (Atlas). Additional information for plant cell culture is found in available commercial literature such as the Life Science Research Cell Culture Catalogue (1999) from Sigma-Aldrich, Inc (St Louis, MO) (Sigma-LSRCCC) and, e.g., the Plant Culture Catalogue and supplement (1999) also from Sigma-Aldrich, Inc (St Louis, MO) (Sigma-PCCS).
The various nucleic acid constructs of the invention, e.g., split gene sequences, engineered genetic elements, recombined non-overlapping gene sequences, etc., can be introduced into plant cells, either in culture or in the organs of a plant by a variety of conventional techniques. For example, the DNA construct can be introduced directly into the genomic DNA of the plant cell using techniques such as electroporation and microinjection of plant cell protoplasts, or the DNA constructs can be introduced directly to plant cells using ballistic methods, such as DNA particle bombardment.
Alternatively, the DNA constructs are combined with suitable T-DNA flanking regions and introduced into a conventional A. tumefaciens host vector. The virulence functions of the A.
tumefaciens host direct the insertion of the construct and adjacent marker into the plant cell DNA when the cell is infected by the bacteria.
Microinjection techniques are known in the art and well described in the scientific and patent literature. The introduction of DNA constructs using polyethylene glycol precipitation is described in Paszkowski, et al. (1984) EMBO J. 3:2717.
Electroporation techniques are described in Fromm, et al. (1985) Proc. Nat'l.
Acad. Sci.
USA 82:5824. Ballistic transformation techniques are described in Klein, et al. (1987) Nature 327:70-73.
A. tumefaciens-mediated transformation techniques, including disarming and use of binary vectors, are also well described in the scientific literature. See, for example Horsch, et al. (1984) Science 233:496-498, and Fraley, et al. (1983) Proc. Nat'l.
Acad. Sci. USA 80:4803. Agrobacterium-mediated transformation is a preferred method of transformation of dicots.

To use isolated sequences corresponding to or linked to target nucleic acid sequences in the above techniques, recombinant DNA vectors suitable for transformation of plant cells are prepared. A DNA sequence coding for the desired mRNA, polypeptide, or non-expressed sequence is transduced into the plant. Where the sequence is expressed, the sequence is optionally combined with transcriptional and translational initiation regulatory sequences that will direct the transcription of the sequence from the gene in the intended tissues of the transformed plant.
Promoters, in nucleic acids linked to loci identified by detecting expression products, are identified, e.g., by analyzing the 5' sequences upstream of a coding sequence in linkage disequilibrium with the loci. Optionally, such promoters will be associated with a desirable quantitative trait. Sequences characteristic of promoter sequences can be used to identify the promoter. Sequences controlling eukaryotic gene expression have been extensively studied. For instance, promoter sequence elements include the TATA
box consensus sequence (TATAAT), which are usually 20 to 30 base pairs upstream of a transcription start site. In most instances the TATA box aids in accurate transcription initiation. In plants, further upstream from the TATA box, at positions -80 to -100, there is typically a promoter element with a series of adenines surrounding the trinucleotide G (or T) N G. See, e.g., J. Messing, et al., in Genetic Engineering in Plants, pp.

(Kosage, Meredith and Hollaender, eds. (1983)). A number of methods are known to those of skill in the art for identifying and characterizing promoter regions in plant genomic DNA. See, e.g., Jordano, et al. (1989) Plant Cell 1:855-866; Bustos, et al.
(1989) Plant Cell 1:839-854; Green, et al. (1988) EMBO J. 7:4035-4044; Meier, et al. (1991) Plant Cell 3:309-316; and Zhang, et al. (1996) Plant Physiology 110:1069-1079.
In construction of recombinant expression cassettes of the invention, a plant promoter fragment is optionally employed which directs expression of a target nucleic acid, e.g., split gene sequences, engineered genetic elements, etc., in any or all tissues of a regenerated plant. Examples of constitutive promoters include the cauliflower mosaic virus (CaMV) 355 transcription initiation region, the 1'- or 2'- promoter derived from T-DNA of A. tumafaciens, and other transcription initiation regions from various plant genes known to those of skill. Alternatively, the plant promoter may direct expression of the polynucleotide of the invention in a specific tissue (tissue-specific promoters) or may be otherwise under more precise environmental control (inducible promoters).
Examples of tissue-specific promoters under developmental control include promoters that initiate transcription only in certain tissues, such as fruit, seeds, or flowers.
Any of a number of promoters which direct transcription in plant cells can be suitable. The promoter can be either constitutive or inducible. In addition to the promoters noted above, promoters of bacterial origin that operate in plants include the octopine synthase promoter, the nopaline synthase promoter and other promoters derived from native Ti plasmids. See, Herrara-Estrella et al. (1983) Nature, 303:209-213. As mentioned above, viral promoters include the 35S and 19S RNA promoters of cauliflower mosaic virus. See, Odell et al. (1985) Nature, 313:810-812. Other plant promoters include the ribulose-1,3-bisphosphate carboxylase small subunit promoter and the phaseolin promoter. The promoter sequence from the E8 gene and other genes may also be used.
The isolation and sequence of the E8 promoter is described in detail in Deikman and Fischer (1988) EMBO J. 7:3315-3327.
If polypeptide expression is desired, e.g., when a toxic polypeptide is sought, a polyadenylation region at the 3'-end of the coding region is typically included.
The polyadenylation region can be derived from the natural gene, from a variety of other plant genes, or from T-DNA.
The vector comprising the sequences (e.g., promoters or coding regions) from genes encoding target nucleic acids of the invention can comprise a nucleic acid subsequence which confers a selectable phenotype on plant cells. The vector comprising the sequence optionally comprises a marker gene that confers a selectable phenotype on plant cells. For example, the marker may encode biocide tolerance, particularly antibiotic tolerance, such as tolerance to kanamycin, 6418, bleomycin, hygromycin, or herbicide tolerance, such as tolerance to chlorosluforon, or phosphinothricin (the active ingredient in the herbicides bialaphos and Basta). For example, crop selectivity to specific herbicides can be conferred by engineering genetic elements into crops which encode appropriate herbicide metabolizing enzymes from other organisms, such as microbes. See, Padgette et al. (1996) "New Weed Control Opportunities: Development of Soybeans with a Round UP
ReadyTM Gene" In: Herbicide-Resistant Crops (Duke, ed.), pp 53-84, CRC Lewis Publishers, Boca Raton (Padgette); and Vasil (1996) "Phosphinothricin-Resistant Crops"

In: Herbicide-Resistant Crops (Duke, ed.), pp 85-91, CRC Lewis Publishers, Boca Raton) (Vasil). Transgenic plants have been engineered to express a variety of herbicide tolerance/metabolizing genes, from a variety of organisms. For example, acetohydroxy acid synthase, which has been found to make plants which express this enzyme resistant to multiple types of herbicides, has been cloned into a variety of plants (see, e.g., Hattori, J., et al. (1995) Mol. Gen. Genet. 246(4):419). Other genes that confer tolerance to herbicides include: a gene encoding a chimeric protein of rat cytochrome P4507A1 and yeast NADPH-cytochrome P450 oxidoreductase (Shiota, et al. (1994) Plant Physiol.
106(1)17, genes for glutathione reductase and superoxide dismutase (Aono, et al. (1995) Plant Cell Physiol. 36(8):1687, and genes for various phosphotransferases (Datta, et al.
(1992) Plant Mol. Biol. 20(4):619. Similarly, crop selectivity can be conferred by altering the gene coding for an herbicide target site so that the altered protein is no longer inhibited by the herbicide (Padgette). Several such crops have been engineered with specific microbial enzymes for confer selectivity to specific herbicides (Vasil).
Further, target nucleic acids which can be cloned and introduced into plants to modify or complement expression of a gene, including a silenced gene, a dominant gene, and additive gene or the like, can be any of a variety of constructs, depending on the particular application. Thus, a nucleic acid encoding a cDNA expressed from an identified gene can be expressed in a plant under the control of a heterologous promoter.
Similarly, a nucleic acid encoding a traps-acting transcription factor that regulates an enhancer-linked split gene sequence identified by the methods herein, or that encodes any other moiety affecting transcription, can be cloned and transduced into a plant. Methods of identifying such factors are replete throughout the literature. For a basic introduction to genetic regulation, see, Lewin (1997) Genes VI Oxford University Press Inc., NY
(Lewin), and the references cited therein.
Stable plants producing one or more split gene sequences) can be produced, with the unencrypted sequence being produced only upon transduction with a vector which encodes one or more additional split gene sequences.
Rye eneration of Trans~enic Plants Transformed plant cells which are derived by any of the above transformation techniques can be cultured to regenerate a whole plant which possesses the transformed genotype and thus the desired phenotype. Such regeneration techniques rely on the manipulation of certain phytohormones in a tissue culture growth medium, typically relying on a biocide and/or herbicide marker which has been introduced together with the desired nucleotide sequences. Plant regeneration from cultured protoplasts is described in Evans, et al., Protoplasts Isolation and Culture, Handbook of Plant Cell Culture, pp. 124-176, Macmillian Publishing Company, New York, (1983); and Binding, Regeneration of Plants, Plant Protoplasts, pp. 21-73, CRC Press, Boca Raton, (1985).
Regeneration can also be obtained from plant callus, explants, somatic embryos (Dandekar, et al., J. Tissue Cult. Meth. 12:145 (1989); McGranahan, et al., Plant Cell Rep. 8:512 (1990)), organs, or parts thereof. Such regeneration techniques are described generally in Klee, et al. (1987) Ann. Rev. Plant Phys. 38:467-486.
One of skill will recognize that after the expression cassette is stably incorporated in transgenic plants and confirmed to be operable, it can be introduced into other plants by sexual crossing. Any of a number of standard breeding techniques can be used, depending upon the species to be crossed.
COMPOSITIONS
The present invention provides various compositions including libraries of split gene sequence populations. These libraries collectively include a plurality of split gene sequence member types in which combinations or subcombinations of those member types collectively correspond to complete genetic elements, e.g., genes.
The invention additionally relates to a composition that includes libraries of enhancer-linked split gene sequence populations. These libraries collectively include a plurality of enhancer-linked split gene sequence member types, each regulated by a different trans-acting transcription factor in which combinations or subcombinations of the plurality of enhancer-linked split gene sequence member types collectively correspond to complete genetic elements. This composition can optionally include a trans-acting transcription factor corresponding to one of the two or more populations of enhancer-linked split gene sequences that can regulate the enhancer-linked split gene sequences of another population. This composition can also optionally include a first traps-acting transcription factor that corresponds to a first population of enhancer-linked split gene sequences that regulates the enhancer-linked split gene sequences of a second population, and a second traps-acting transcription factor that corresponds to the second population of enhancer-linked split gene sequences that regulates the enhancer-linked split gene sequences of the first population.
The invention also provides compositions that include libraries of gap nucleic acids. The libraries of gap nucleic acids include a plurality of gap nucleic acid member types in which each gap nucleic acid member type includes subsequence identity or complementarity with at least two split gene sequence member types.
The various composition members, i.e., the split gene sequences, the enhancer-linked split gene sequences, the traps-acting transcription factor sequences, the non-overlapping gene sequences, and the gap nucleic acids, can be cloned. As mentioned above, assorted cloning techniques are well-known. See e.g., Ausubel, Sambrook, and Bergen supra. A wide variety of cloning kits and associated products are commercially available from, e.g., Pharmacia Biotech, Stratagene, Sigma-Aldrich Co., Novagen, Inc., Fermentas, and 5 Prime ~ 3 Prime, Inc.
SYSTEM INTEGRATION
As noted, supra, an initial inquiry that can be apply to the methods of the present invention includes determining the sequence of nucleotides in target sequences, e.g., genes to be split. Additionally, gap nucleic acid sequences can be designed based upon non-overlapping gene sequence information. As such, automated sequencing and sequence selection involving the alignment and search of nucleic acid sequences can be performed with the assistance of a computer and sequence alignment and comparison software in an integrated system. Target DNA sequences can then optionally be synthesized as an additional component of the integrated systems provided by the present invention. Other important integrated system components, however, can also provide for high-throughput screening assays, in addition to the coupling of such assays to oligonucleotide selection and recombination, e.g., recombined non-overlapping gene sequences.
In the high-throughput assays of the invention, it is possible to screen up to several thousand different recombination products in a single day. For example, each well of a microtiter plate can be used to run a separate assay, or, if concentration or incubation time effects are to be observed, every 5-10 wells can test a single product.
Thus, a single standard microtiter plate can assay about 100 (e.g., 96) reactions. If 1536 well plates are used, then a single plate can easily assay from about 100 to approximately 1500 different reactions. It is possible to assay several different plates per day; assay screens for up to about 6,000-20,000 different assays (i.e., involving different nucleic acids, encoded proteins, concentrations, etc.) are possible using the integrated systems of the invention.
More recently, microfluidic approaches to reagent manipulation have been developed, e.g., by Caliper Technologies (Mountain View, CA).
A number of well-known robotic systems have also been developed for solution phase chemistries useful in assay systems that are applicable to the present invention. These systems include automated workstations like the automated synthesis apparatus developed by Takeda Chemical Industries, LTD. (Osaka, Japan) and many robotic systems utilizing robotic arms (Zymate II, Zymark Corporation, Hopkinton, Mass.;
Orca, Beckman, Fullerton, CA) which mimic the manual synthetic operations performed by a scientist. Any of the above devices are suitable for use with the present invention, e.g., for high-throughput screening of molecules assembled from the various nucleic acid sequence sets described herein. The nature and implementation of modifications to these devices (if any) so that they can operate as discussed herein with reference to the integrated system will be apparent to persons skilled in the relevant art.
High-throughput screening systems are commercially available (see, e.g., Zymark Corp., Hopkinton, MA; Air Technical Industries, Mentor, OH; Beckman Instruments, Inc. Fullerton, CA; Precision Systems, Inc., Natick, MA, etc.).
These systems typically automate entire procedures including all sample and reagent pipetting, liquid dispensing, timed incubations, and final readings of the microplate in detectors) appropriate for the assay. These configurable systems provide high throughput and rapid start up as well as a high degree of flexibility and customization. The manufacturers of such systems provide detailed protocols the various high-throughput. Thus, for example, Zymark Corp. provides technical bulletins describing screening systems for detecting the modulation of gene transcription, ligand binding, and the like.
Integrated systems for assay analysis in the present invention optionally include a digital computer with high-throughput liquid control software, image analysis software, data interpretation software, a robotic liquid control armature for transferring, e.g., split gene sequence solutions, engineered genetic element solutions, non-overlapping gene sequence compositions, and gap nucleic acid compositions from a source to a destination operably linked to the digital computer, an input device (e.g., a computer keyboard) for entering data to the digital computer to control high-throughput liquid S transfer by the robotic liquid control armature.
These assay systems can also include integrated systems incorporating nucleic acid selection elements, such as a computer, database with nucleic acid sequences of interest, sequence alignment software, and oligonucleotide selection software. Suitable alignment algorithms, e.g., BLAST and others are discussed, supra. However, sequence alignment can optionally be achieved manually. Once sequences to be synthesized, e.g., gap nucleic acids or split gene sequences, are selected, they can be converted into lines of character string information in data sets in a computer corresponding to the desired nucleic acids to be obtained.
The system also includes a user interface allowing a user to selectively view one or more sequence database programs for aligning and manipulating sequences. In addition, standard text manipulation software such as word processing software (e.g., Microsoft WordT"" or Corel WordperfectT"") and database software (e.g., spreadsheet software such as Microsoft ExcelT"", Corel Quattro ProT"", or database programs such as Microsoft AccessT"" or ParadoxT"") can be used in conjunction with a user interface (e.g., a GUI in a standard operating system such as a Windows, Macintosh or Linux system) to manipulate strings of characters. As noted, specialized alignment software such as BLAST
can also be included.
Additional software can be included, such as, components for ordering the selected nucleic acid sequences, and/or directing synthesis of such sequences by an operably linked automated synthesizer. In this case, the character string information in the output of an integrated computer directs the robotic arm of the automated synthesizer to perform the steps necessary to synthesize the desired polynucleotide sequences.
Although the integrated system elements of the invention optionally include any of the above components to facilitate, e.g., high-throughput recombination and selection. It will be appreciated that these high-throughput recombination elements can be in systems separate from those for performing selection assays, or as discussed, the two can be integrated.
Modifications can be made to the method and materials as hereinbefore described without departing from the spirit or scope of the invention as claimed, and the invention can be put to a number of different uses, including:
The use of an integrated system to select, e.g., non-overlapping gene sequences and gap nucleic acids, and to test recombined non-overlapping sequences for activity, including in an iterative process. .
An assay, kit or system utilizing a use of any one of the selection strategies, materials, components, methods or substrates hereinbefore described. Kits will optionally additionally comprise instructions for performing methods or assays, packaging materials, one or more containers which contain assay, device or system components, or the like.
In an additional aspect, the present invention provides kits embodying the methods and apparatus herein. Kits of the invention optionally comprise one or more of the following: (1) a non-overlapping gene sequence recombination component as described herein; (2) instructions for practicing the methods described herein, and/or for operating the nucleic acid sequencing, synthesis, or recombined nucleic acid selection procedures herein; (3) one or more assay component(s); (4) a container for holding nucleic acids or enzymes, other nucleic acids, transgenic plants, animals, cells, or the like and, (5) packaging materials.
In a further aspect, the present invention provides for the use of any component or kit herein, for the practice of any method or assay herein, and/or for the use of any apparatus or kit to practice any assay or method herein.
While the foregoing invention has been described in some detail for purposes of clarity and understanding, it will be clear to one skilled in the art from a reading of this disclosure that various changes in form and detail can be made without departing from the true scope of the invention. For example, all the techniques and apparatus described above may be used in various combinations. All publications and patent documents cited in this application are incorporated by reference in their entirety for all purposes to the same extent as if each individual publication or patent document were individually so denoted.

Claims (123)

WHAT IS CLAIMED IS:

1. A method of unencrypting trait encrypted gene sequences to provide at least one unencrypted RNA or polypeptide, the method comprising:
providing a first plurality of split gene sequences, wherein each split gene sequence comprises a subsequence of a genetic element;
transcribing the first plurality of split gene sequences to provide a plurality of RNA
segments; and, trans-splicing at least two of the plurality of RNA segments together to provide at least one unencrypted RNA; or, alternately, translating the plurality of RNA segments to provide a plurality of polypeptide segments and trans-splicing at least two of the plurality of polypeptide segments together to provide at least one first unencrypted polypeptide.

2. The method of claim 1, wherein the plurality of RNA segments comprises trans-splicing introns.

3. The method of claim 1, wherein the plurality of polypeptide segments comprises trans-splicing inteins.

4. The method of claim 1, the method further comprising selecting the at least one unencrypted RNA for at least one desired trait or property.

5. The method of claim 1, wherein the at least one first unencrypted polypeptide is a full-length protein.

6. The method of claim 1, the method further comprising translating the at least one unencrypted RNA to provide at least one second unencrypted polypeptide.

7. The method of claim 6, wherein the at least one second unencrypted polypeptide is a full-length protein.

8. The method of claim 6, the method further comprising selecting the at least one second unencrypted polypeptide for at least one desired trait or property.

9. The method of claim 1, the method further comprising selecting the at least one first unencrypted polypeptide for at least one desired trait or property.

10. The method of claim 1, wherein at least one step occurs in vitro.

11. The method of claim 1, wherein at least one step occurs in vivo.

12. The method of claim 1, wherein at least one of the split gene sequences is a cDNA.

13. The method of claim 1, wherein the first plurality of split gene sequences is provided by mating at least one first parental organism comprising a second plurality of split gene sequences with at least one second parental organism comprising a third plurality of split gene sequences to produce at least one progeny organism comprising at least one of the second plurality of split gene sequences and at least one of the third plurality of split gene sequences, thereby providing the first plurality of split gene sequences.

14. The method of claim 13, wherein the transcribing step comprises transcribing at least one of the second plurality of split gene sequences and at least one of the third plurality of split gene sequences to provide the plurality of RNA
segments.

15. The method of claim 14, the method further comprising selecting the at least one progeny organism for a desired trait or property, thereby selecting the at least one unencrypted RNA.

16. The method of claim 14, the method further comprising translating the at least one unencrypted RNA to provide at least one second unencrypted polypeptide.

17. The method of claim 16, wherein the at least one second unencrypted polypeptide is a full-length protein.

18. The method of claim 16, the method further comprising selecting the at least one second unencrypted polypeptide for at least one desired trait or property.

19. The method of claim 13, the method further comprising selecting the at least one first unencrypted polypeptide for at least one desired trait or property.

20. The method of claim 13, wherein at least one of the split gene sequences is a cDNA.

21. The at least one first parental organism made by the method of claim 13.

22. The at least one second parental organism made by the method of claim 13.

23. The at least one progeny organism made by the method of claim 13.

24. The method of claim 13, wherein the at least one first parental organism and the at least one second parental organism are selected from:
animals, plants, fungi, and bacteria.

25. The method of claim 13, wherein the at least one first parental organism and the at least one second parental organism are plants selected from the genera:
Fragaria, Lotus, Medicago, Onobrychis, Trifolium, Trigonella, Vigna, Citrus, Linum, Geranium, Manihot, Daucus, Arabidopsis, Brassica, Raphanus, Sinapis, Atropa, Capsicum, Datura, Hyoscyamus, Lycopersicon, Nicotiana, Solanum, Petunia, Digitalis, Majorana, Cichorium, Helianthus, Lactuca, Bromus, Asparagus, Antirrhinum, Heterocallis, Nemesia, Pelargonium, Panicum, Pennisetum, Ranunculus, Senecio, Salpiglossis, Cucumis, Browaalia, Lolium, Malus, Apium, Gossypium, Vicia, Lathyrus, Lupinus, Pachyrhizus, Wisteria, and Stizolobium.

26. The method of claim 13, wherein the at least one first parental organism and the at least one second parental organism are crop plants selected from the genera: Agrostis, Phleum, Dactylis, Sorghum, Setaria, Zea, Oryza, Triticum, Secale, Avena, Hordeum, Saccharum, Poa, Festuca, Stenotaphrum, Cynodon, Coix, Olyreae, Phareae, Glycine, Pisum, Cicer, Phaseolus, Lens, and Arachis.

27. The method of claim 13, wherein the at least one first parental organism and the at least one second parental organism are plants selected from: corn, rice, cotton, soybean, sorghum, wheat, oats, barley, millet, sunflower, rapeseed, canola, peas, beans, lentils, peanuts, yam beans, cowpeas, velvet beans, clover, alfalfa, lupine, vetch, lotus, sweet clover, wisteria, and sweetpea.

28. The method of claim 13, wherein the at least one first parental organism and the at least one second parental organism are yeast.

29. The method of claim 13, wherein the at least one first parental organism comprises a first plurality of enhancer-linked split gene sequences, wherein each enhancer-linked split gene sequence comprises a subsequence of the genetic element with a first enhancer sequence linked thereto, the first parental organism also comprising at least one first trans-acting transcription factor sequence which is unlinked to the first plurality of enhancer-linked split gene sequences, and wherein the at least one second parental organism comprises a second plurality of enhancer-linked split gene sequences, wherein each enhancer-linked split gene sequence comprises a subsequence of the genetic element with a second enhancer sequence linked thereto, the second parental organism also comprising at least one second trans-acting transcription factor sequence which is unlinked to the second plurality of enhancer-linked split gene sequences.

30. The method of claim 29, wherein the at least one progeny organism comprises at least one of the first plurality of enhancer-linked split gene sequences, the at least one first trans-acting transcription factor sequence, at least one of the second plurality of enhancer-linked split gene sequences, and the at least one second trans-acting transcription factor sequence, wherein at least one of the first plurality of enhancer-linked split gene sequences and at least one of the second plurality of enhancer-linked split gene sequences are transcribed to provide the plurality of RNA segments, wherein at least one of the first plurality of enhancer-linked split gene sequences is regulated by the second trans-acting transcription factor and at least one of the second plurality of enhancer-linked split gene sequences is regulated by the first trans-acting transcription factor.

31. The method of claim 30, the method further comprising selecting the at least one progeny organism for a desired trait or property, thereby selecting the at least one unencrypted RNA.

32. The method of claim 30, the method further comprising translating the at least one unencrypted RNA to provide at least one second unencrypted polypeptide.

33. The method of claim 32, wherein the at least one second unencrypted polypeptide is a full-length protein.

34. The method of claim 32, the method further comprising selecting the at least one second unencrypted polypeptide for at least one desired trait or property.

35. The method of claim 30, the method further comprising selecting the at least one first unencrypted polypeptide for at least one desired trait or property.

36. The method of claim 30, wherein at least one of the first plurality of enhancer-linked split gene sequences and at least one of the second plurality of enhancer-linked split gene sequences are cDNAs.

37. The method of claim 30, wherein the at least one first trans-acting transcription factor sequence and the at least one second trans-acting transcription factor sequence are cDNAs.

38. The at least one first parental organism made by the method of claim 30.

39. The at least one second parental organism made by the method of claim 30.

40. The at least one progeny organism made by the method of claim 30.

41. The method of claim 30, wherein the at least one first parental organism and the at least one second parental organism are selected from:
animals, plants, fungi, and bacteria.

42. The method of claim 41, wherein the at least one first parental organism and the at least one second parental organism are plants selected from the genera:
Fragaria, Lotus, Medicago, Onobrychis, Trifolium, Trigonella, Vigna, Citrus, Linum, Geranium, Manihot, Daucus, Arabidopsis, Brassica, Raphanus, Sinapis, Atropa, Capsicum, Datura, Hyoscyamus, Lycopersicon, Nicotiana, Solanum, Petunia, Digitalis, Majorana, Cichorium, Helianthus, Lactuca, Bromus, Asparagus, Antirrhinum, Heterocallis, Nemesia, Pelargonium, Panicum, Pennisetum, Ranunculus, Senecio, Salpiglossis, Cucumis, Browaalia, Lolium, Malus, Apium, Gossypium, Vicia, Lathyrus, Lupinus, Pachyrhizus, Wisteria, and Stizolobium.

43. The method of claim 41, wherein the at least one first parental organism and the at least one second parental organism are crop plants selected from the genera: Agrostis, Phleum, Dactylis, Sorghum, Setaria, Zea, Oryza, Triticum, Secale, Avena, Hordeum, Saccharum, Poa, Festuca, Stenotaphrum, Cynodon, Coix, Olyreae, Phareae, Glycine, Pisum, Cicer, Phaseolus, Lens, and Arachis.

44. The method of claim 41, wherein the at least one first parental organism and the at least one second parental organism are plants selected from: corn, rice, cotton, soybean, sorghum, wheat, oats, barley, millet, sunflower, rapeseed, canola, peas, beans, lentils, peanuts, yam beans, cowpeas, velvet beans, clover, alfalfa, lupine, vetch, lotus, sweet clover, wisteria, and sweetpea.

45. The method of claim 41, wherein the fungi are yeast.

46. The method of claim 13, wherein the at least one first parental organism comprises a second plurality of split gene sequences, wherein each split gene sequence comprises a subsequence of a toxic genetic element and the at least one second parental organism comprises a third plurality of split gene sequences, wherein each split gene sequence comprises a subsequence of the toxic genetic element.

47. The method of claim 46, wherein at least one of the second plurality of split gene sequences and at least one of the third plurality of split gene sequences are expressed in the at least one progeny organism to produce at least one of a second plurality of polypeptide sequences and at least one of a third plurality of polypeptide sequences, wherein at least one of the second plurality of polypeptide sequences and at least one of the third plurality of polypeptide sequences are spliced together to provide at least one toxic polypeptide, wherein the at least one toxic polypeptide renders the at least one progeny organism incapable of reproducing when the at least one progeny organism is male.

48. The method of claim 47, wherein the at least one progeny organism is capable of reproducing when the at least one progeny organism is female.

49. The method of claim 48, wherein the at least one progeny organism reproduces as a female to produce a hybrid progeny organism, wherein the toxic genetic element is not expressed in the hybrid progeny organism.

50. The method of claim 46, wherein at least one of the second plurality of split gene sequences and at least one of the third plurality of split gene sequences are expressed in the at least one progeny organism to produce at least one of a second plurality of polypeptide sequences and at least one of a third plurality of polypeptide sequences, wherein at least one of the second plurality of polypeptide sequences and at least one of the third plurality of polypeptide sequences are trans-spliced together to provide at least one toxic polypeptide, wherein the at least one toxic polypeptide renders the at least one progeny organism incapable of reproducing when the at least one progeny organism is female.

51. The method of claim 47, wherein the at least one progeny organism is capable of reproducing when the at least one progeny organism is male.

52. The method of claim 48, wherein the at least one progeny organism reproduces as a male to produce a hybrid progeny organism, wherein the toxic genetic element is not expressed in the hybrid progeny organism.

53. The method of claim 46, wherein at least one of the fourth plurality of split gene sequences and at least one of the fifth plurality of the split gene sequences are cDNAs.

54. The method of claim 1, wherein the first plurality of split gene sequences is provided by infecting at least one host organism comprising a second plurality of split gene sequences with at least one vector comprising a third plurality of split gene sequences to produce at least one infected organism comprising at least one of the second plurality of split gene sequences and at least one of the third plurality of split gene sequences.

55. The method of claim 54, wherein the transcribing step comprises transcribing at least one of the second plurality of split gene sequences and at least one of the third plurality of split gene sequences to provide the plurality of RNA
segments.

56. The method of claim 55, the method further comprising selecting the at least one unencrypted RNA.

57. The method of claim 55, the method further comprising translating the at least one unencrypted RNA to provide at least one second unencrypted polypeptide.

58. The method of claim 57, wherein the at least one second unencrypted polypeptide is a full-length protein.

59. The method of claim 57, the method further comprising selecting the at least one second unencrypted polypeptide for at least one desired trait or property.

60. The method of claim 54, the method further comprising selecting the at least one first unencrypted polypeptide for at least one desired trait or property.

61. The method of claim 54, wherein at least one of the split gene sequences is a cDNA.

62. The method of claim 54, wherein the at least one vector comprises a virus.

63. The at least one host organism is made by the method of claim 54.

64. The at least one vector is made by the method of claim 54.

65. The at least one infected organism is made by the method of claim 54.

66. A method of unencrypting engineered genetic elements to provide at least one unencrypted polypeptide function, the method comprising:
providing at least one first engineered genetic element corresponding to an encoded first polypeptide, wherein the first polypeptide is functional;
providing at least one second engineered genetic element corresponding to an encoded second polypeptide, wherein the second polypeptide is nonfunctional in the absence of a modification performed by the first polypeptide;
mixing the at least one first engineered genetic element and the at least one second engineered genetic element;
expressing the at least one first and the at least one second engineered genetic elements to produce the at least one encoded first polypeptide and the at least one encoded second polypeptide; and, modifying the at least one encoded second polypeptide with the at least one encoded first polypeptide to provide at least one functional encoded second polypeptide, thereby providing the at least one unencrypted polypeptide function.

67. The method of claim 66, wherein the modification of the second polypeptide performed by the first polypeptide is selected from the group consisting of glycosylation, proteolysis, farnesylation, cholesterol esterification, acetylation, methylation, phosphorylation and dephosphorylation.

68. The method of claim 66, wherein at least one step occurs in vitro.

69. The method of claim 66, wherein at least one step occurs in vivo.

70. The method of claim 66, wherein the at least one first engineered genetic element and the at least one second engineered genetic element are cDNAs.

71. The at least one first engineered genetic element made by the method of claim 66.

72. The at least one second engineered genetic element made by the method of claim 66.

73. The at least one encoded first polypeptide made by the method of claim 66.

74. The at least one encoded second polypeptide made by the method of claim 66.

75. The method of claim 66, wherein the at least one first engineered genetic element encodes an engineered biotin ligase and the at least one second engineered genetic element encodes an engineered biotin dependent glyphosate resistance polypeptide.

76. The method of claim 66, wherein the providing and mixing steps comprise mating at least one first parental organism comprising the at least one first engineered genetic element and at least one second parental organism comprising the at least one second engineered genetic element to produce at least one progeny organism comprising the at least one first engineered genetic element and the at least one second engineered genetic element.

77. The method of claim 76, wherein the expressing step comprises expressing the at least one first engineered genetic element and the at least one second engineered genetic element in the at least one progeny organism to produce the at least one encoded first polypeptide and the at least one encoded second polypeptide.

78. The method of claim 77, wherein the at least one first engineered genetic element and the at least one second engineered genetic element are cDNAs.

79. The at least one first engineered genetic element made by the method of claim 77.

80. The at least one second engineered genetic element made by the method of claim 77.

81. The at least one encoded first polypeptide made by the method of claim 77.

82. The at least one encoded second polypeptide made by the method of claim 77.

83. The at least one first parental organism made by the method of claim 77.

84. The at least one second parental organism made by the method of claim 77.

85. The at least one progeny organism made by the method of claim 77.

86. The method of claim 77, wherein the at least one first parental organism and the at least one second parental organism are selected from:
animals, plants, fungi, and bacteria.

87. The method of claim 86, wherein the at least one first parental organism and the at least one second parental organism are plants are selected from the genera: Fragaria, Lotus, Medicago, Onobrychis, Trifolium, Trigonella, Vigna, Citrus, Linum, Geranium, Manihot, Daucus, Arabidopsis, Brassica, Raphanus, Sinapis, Atropa, Capsicum, Datura, Hyoscyamus, Lycopersicon, Nicotiana, Solanum, Petunia, Digitalis, Majorana, Cichorium, Helianthus, Lactuca, Bromus, Asparagus, Antirrhinum, Heterocallis, Nemesia, Pelargonium, Panicum, Pennisetum, Ranunculus, Senecio, Salpiglossis, Cucumis, Browaalia, Lolium, Malus, Apium, Gossypium, Vicia, Lathyrus, Lupinus, Pachyrhizus, Wisteria, and Stizolobium.

88. The method of claim 86, wherein the at least one first parental organism and the at least one second parental organism are crop plants selected from the genera: Agrostis, Phleum, Dactylis, Sorghum, Setaria, Zea, Oryza, Triticum, Secale, Avena, Hordeum, Saccharum, Poa, Festuca, Stenotaphrum, Cynodon, Coix, Olyreae, Phareae, Glycine, Pisum, Cicer, Phaseolus, Lens, and Arachis.

89. The method of claim 86, wherein the at least one first parental organism and the at least one second parental organism are plants are selected from: corn, rice, cotton, soybean, sorghum, wheat, oats, barley, millet, sunflower, rapeseed, canola, peas, beans, lentils, peanuts, yam beans, cowpeas, velvet beans, clover, alfalfa, lupine, vetch, lotus, sweet clover, wisteria, and sweetpea.

90. The method of claim 86, wherein the at least one first parental organism and the at least one second parental organism are yeast.

91. The method of claim 66, wherein the providing and mixing steps comprise infecting at least one host organism comprising the at least one first engineered genetic element with at least one vector comprising the at least one second engineered genetic element to produce at least one infected organism comprising the at least one first engineered genetic element and the at least one second engineered genetic element.

92. The method of claim 91, wherein the expressing step comprises expressing the at least one first engineered genetic element and the at least one second engineered genetic element in the at least one progeny organism to produce the at least one encoded first polypeptide and the at least one encoded second polypeptide.

93. The method of claim 92, wherein the at least one vector comprises the at least one first engineered genetic element and the at least one host organism comprises the at least one second engineered genetic element.

94. The method of claim 92, wherein the at least one first engineered genetic element and the at least one second engineered genetic element are cDNAs.

95. The at least one first engineered genetic element made by the method of claim 92.

96. The at least one second engineered genetic element made by the method of claim 93.

97. The at least one encoded first polypeptide made by the method of claim 92.

98. The at least one encoded second polypeptide made by the method of claim 92.

99. The at least one host organism made by the method of claim 91.

100. The at least one vector made by the method of claim 91.

101. The at least one vector made by the method of claim 93.

102. The at least one host organism made by the method of claim 93.

103. The at least one infected organism made by the method of claim 91.

104. The method of claim 91, wherein the vector comprises a virus.

105. The method of claim 93, wherein the vector comprises a virus.

106. A composition comprising one or more libraries of at least two populations of split gene sequences, the libraries collectively comprising a plurality of split gene sequence member types, wherein combinations or subcombinations of the plurality of split gene sequence member types collectively correspond to at least one complete genetic element.

107. The composition of claim 106, wherein the at least two populations comprise homologous genetic elements.

108. A composition comprising one or more libraries of at least two populations of enhancer-linked split gene sequences, the libraries collectively comprising a plurality of enhancer-linked split gene sequence member types, each regulated by a different traps-acting transcription factor wherein combinations or subcombinations of the plurality of enhancer-linked split gene sequence member types collectively correspond to at least one complete genetic element.

109. The composition of 108, wherein a trans-acting transcription factor corresponding to one of the at least two populations of enhancer-linked split gene sequences regulates the enhancer-linked split gene sequences of another population.

110. The composition of 108, wherein a first trans-acting transcription factor corresponding to a first population of enhancer-linked split gene sequences regulates the enhancer-linked split gene sequences of a second population, and a second trans-acting transcription factor corresponding to the second population of enhancer-linked split gene sequences regulates the enhancer-linked split gene sequences of the first population.

111. A method of recombining non-overlapping gene sequences, the method comprising:
providing a plurality of non-overlapping gene sequences, wherein each non-overlapping gene sequence corresponds to a different subsequence of a genetic element;
providing a plurality of gap nucleic acid sequences, wherein each gap nucleic acid sequence overlaps two or more of the non-overlapping gene sequences; and, recombining the plurality of non-overlapping gene sequences with the plurality of gap nucleic acid sequences to provide recombined non-overlapping gene sequences.

112. The method of claim 111, the method further comprising:
selecting the recombined non-overlapping gene sequences for at least one desired trait or property;
recombining the recombined non-overlapping sequences; and, repeating the selecting and second recombining steps until a desired recombined genetic element is obtained.

113. The method of claim 111, wherein the plurality of non-overlapping gene sequences is derived from a cry3Bb gene.

114. The method of claim 111, wherein the plurality of gap nucleic acid sequences is derived from a cry1B.alpha., a cry1C.alpha., and a cry1I.alpha.
gene.

115. The method of claim 111, wherein at least one step occurs in vitro.

116. The method of claim 111, wherein at least one step occurs in vivo.

117. A composition comprising one or more libraries of gap nucleic acids, the libraries comprising a plurality of gap nucleic acid member types, wherein each gap nucleic acid member type comprises subsequence identity or complementarity with at least two split gene sequence member types.

118. An integrated system comprising a computer or computer readable medium comprising a data set corresponding to a set of character strings corresponding to a set selected from the group consisting of split gene sequences, enhancer-linked split gene sequences, trans-acting transcription factor sequences, engineered genetic elements, non-overlapping gene sequences and gap nucleic acids.

119. The integrated system of claim 118, wherein the system further comprises a sequence search and comparison instruction set for searching for specified nucleic acid sequences.

120. The integrated system of claim 118, wherein the system further comprises an automatic sequencer coupled to an output of the computer or computer readable medium, which automatic sequencer accepts instructions from the computer or computer readable medium, which instructions direct sequencing of sequences selected from a group consisting of split gene sequences, enhancer-linked split gene sequences, trans-acting transcription factor sequences, engineered genetic elements, non-overlapping gene sequences and gap nucleic acids.

121. The integrated system of claim 118, wherein the system further comprises an automatic synthesizer coupled to an output of the computer or computer readable medium, which automatic synthesizer accepts instructions from the computer or computer readable medium, which instructions direct synthesis of the set selected from the group consisting of split gene sequences, enhancer-linked split gene sequences, trans-acting transcription factor sequences, engineered genetic elements, non-overlapping gene sequences and gap nucleic acids.

122. The integrated system of claim 121, further comprising one or more robotic control elements for incubating, denaturing, hybridizing, and elongating a set of recombined non-overlapping gene sequences and gap nucleic acids.

123. The integrated system of claim 122, further comprising a detector for detecting a nucleic acid produced by elongation of the set of recombined non-overlapping gene sequences and gap nucleic acids, or an encoded product thereof.