Phenotypic screen of chimeric proteins

Abstract

In one aspect, a library of nucleic acids that encode different artificial, chimeric proteins is screened to identify a chimeric protein that alters a phenotypic trait of a cell or organism. The chimeric protein can be identified without a priori knowledge of a particular target gene or pathway. Some chimeric proteins include multiple zinc finger domains and can induce, for example, thermotolerance, solvent-tolerance, altered cellular growth, insulin production, differentiation, and drug resistance.

What is claimed is:  
     
         1 . A modified cell comprising a heterologous nucleic acid encoding an artificial transcription factor that confers stress resistance to the modified cell relative to a reference cell that is substantially identical to the modified cell and that lacks the heterologous nucleic acid and the artificial transcription factor.  
     
     
         2 . The modified cell of  claim 1 , wherein the artificial transcription factor comprises two zinc finger domains.  
     
     
         3 . The modified cell of  claim 1 , wherein the cell is bacterial cell.  
     
     
         4 . The modified cell of  claim 1 , wherein the cell is a eukaryotic cell.  
     
     
         5 . The modified cell of  claim 2 , wherein the stress resistance includes one or more the following traits: heat resistance, solvent resistance, heavy metal resistance, osmolarity resistance, resistance to extreme pH, chemical resistance, cold resistance, and resistance to a genotoxic agent, resistance to radioactivity.  
     
     
         6 . The modified cell of  claim 1 , wherein the cell expresses the artificial transcription factor and resists stress to a greater extent than a substantially identical culture cell that lacks the artificial transcription factor  
     
     
         7 . A method of producing a cellular product, the method comprising: 
 providing the modified cell of  claim 1;     maintaining the modified cell under conditions in which the artificial transcription factor is produced; and    recovering a product produced by the cultured cell, wherein the product is other than the artificial transcription factor.    
     
     
         8 . The method of  claim 7 , wherein the modified cell includes a nucleic acid encoding a heterologous protein, other than the artificial transcription factor, and the product is the heterologous protein.  
     
     
         9 . The method of  claim 7 , wherein the product is a metabolite or an endogenous protein.  
     
     
         10 . The method of  claim 8 , wherein the modified cell further includes a second nucleic acid encoding a heterologous protein, and the heterologous protein participates in production of the metabolite.  
     
     
         11 . The method of  claim 7 , wherein the modified cell is maintained at a temperature between 20° C. and 40° C.  
     
     
         12 . The method of  claim 7 , wherein the modified cell is maintained under conditions which would inhibit the growth of a substantially identical cell that lacks the artificial transcription factor.  
     
     
         13 . The method of  claim 7 , wherein the artificial transcription factor comprises a zinc finger domain.  
     
     
         14 . The method of  claim 13 , wherein the zinc finger domain comprises DNA contacting residues that correspond to the DNA contacting residues of a zinc finger domain listed in Table 15.  
     
     
         15 . The method of  claim 14 , wherein the artificial transcription factor comprises an array of at least three zinc finger domains, wherein the DNA contacting residues of three of the zinc finger domains of the array correspond respectively to DNA contacting residues of any three consecutive zinc finger domains listed in a horizontal row of Table 15.  
     
     
         16 . The method of  claim 7 , wherein the stress resistance includes one or more the following traits: heat resistance, solvent resistance, heavy metal resistance, osmolarity resistance, resistance to extreme pH, chemical resistance, cold resistance, and resistance to radioactivity.  
     
     
         17 . A target protein-expressing cell that contains (a) a coding nucleic acid that encodes a target protein and (b) a heterologous nucleic acid that comprises a sequence encoding an artificial protein chimera that (1) increases the amount of the protein produced by the cell relative to an otherwise-identical cell that does not include the heterologous nucleic acid, and (2) binds to DNA, but (3) does not bind to a transcriptional regulatory region that directly regulates transcription of the coding nucleic acid encoding the target protein.  
     
     
         18 . The target-protein expressing cell of  claim 17 , wherein the artificial protein chimera comprises two zinc finger domains and binds to DNA.  
     
     
         19 . The target protein-expressing cell of  claim 17 , wherein the target protein-expressing cell is a eukaryotic cell, and the artificial protein chimera competes with PB08, K_F02, or K_D10 for binding to a genomic DNA site.  
     
     
         20 . The target protein-expressing cell of  claim 17 , wherein the artificial protein chimera alters the rate of cell cycle progression by the cell.  
     
     
         21 . The target protein-expressing cell of  claim 17 , wherein the coding nucleic acid is an endogenous nucleic acid.  
     
     
         22 . An artificial transcription factor that (1) increases the amount of a target protein produced by a eukaryotic test cell relative to an otherwise-identical cell that does not include the artificial transcription factor, and (2) does not bind to a transcriptional regulatory region that directly regulates transcription of a DNA encoding the target protein in the test cell.  
     
     
         23 . An artificial transcription factor comprising a plurality of zinc finger domains, wherein the artificial transcription factor alters the rate of cell cycle progression in a eukaryotic cell and at least two zinc finger domains are heterologous to each other.  
     
     
         24 . A method of producing a protein, the method comprising: 
 providing the target-protein expressing cell of  claim 17 , and    maintaining the target-protein expressing cell under conditions in which the artificial protein chimera increases the amount of the target protein produced by the target-protein expressing cell relative to an otherwise identical cell that does not include the heterologous nucleic acid.    
     
     
         25 . The method of  claim 24 , wherein the protein is a secreted protein.  
     
     
         26 . A transfected cell that contains an endogenous gene encoding a secreted protein and a heterologous nucleic acid that comprises a sequence encoding an artificial transcription factor that increases the amount of the secreted protein produced by the cell relative to an otherwise identical cell that does not include the heterologous nucleic acid.  
     
     
         27 . The transfected cell of  claim 26 , wherein the transfected cell is a eukaryotic cell, and the secreted protein is insulin.  
     
     
         28 . The transfected cell of  claim 26 , wherein the artificial transcription factor specifically binds to an endogenous DNA site that is also specifically bound by 08_D04_p65.  
     
     
         29 . The transfected cell of  claim 26 , wherein the artificial transcription factor specifically binds to an endogenous DNA site and the artificial transcription factor can compete with 08_D04_p65 for binding to the endogenous DNA site.  
     
     
         30 . The transfected cell of  claim 26 , wherein the artificial transcription factor comprises an amino acid sequence as follows: 
 CX (2-5) CXXXBXRXSHJXRHX (3-5) HX (1-6) BXCX (2-5) CXXXBXRXDHJXTHX (3-5) H (SEQ ID NO:45); or    CX (2-5) CXXXBXRXDHJXTHX (3-5) HX (1-6) BXCX (2-5) CXXXBXVXSSJXRHX (3-5) H (SEQ ID NO:46)    where B is phenylalanine or tyrosine; J is a hydrophobic amino acid, and X is any amino acid.    
     
     
         31 . A method of producing insulin, the method comprising: 
 providing the transfected cell of  claim 27 , and    maintaining the transfected cell under conditions in which the artificial transcription factor increases the amount of insulin transcript produced by the transfected cell relative to an otherwise identical cell that does not include the heterologous nucleic acid.    
     
     
         32 . An artificial transcription factor comprising at least two zinc finger domain, wherein the artificial transcription factor induces expression of an endogenous insulin gene in a mammalian cell that does not express an endogenous insulin gene in the absence of the artificial transcription factor.  
     
     
         33 . An artificial transcription factor that alters sensitivity of a reference cell to a toxic agent relative to an otherwise identical cell that does not contain the nucleic acid.  
     
     
         34 . A transfected cell that contains and expresses a nucleic acid encoding an artificial transcription factor that alters sensitivity of the cell to a toxic agent relative to an identical cell that does not contain the nucleic acid.  
     
     
         35 . The transfected cell of  claim 34 , wherein the toxic agent is a drug.  
     
     
         36 . The transfected cell of  claim 34 , wherein the sensitivity is increased.  
     
     
         37 . The transfected cell of  claim 34 , wherein the sensitivity is decreased.  
     
     
         38 . The transfected cell of  claim 34 , wherein the cell is a fungal cell.  
     
     
         39 . The transfected cell of  claim 38 , wherein the toxic agent is ketoconazole.  
     
     
         40 . The transfected cell of  claim 34 , wherein the artificial transcription factor comprises three zinc finger domains.  
     
     
         41 . The transfected cell of  claim 39 , wherein the artificial transcription factor binds to an endogenous DNA site and the artificial transcription factor can compete with a zinc finger protein listed in Table 5 for binding to the endogenous DNA site.  
     
     
         42 . A method of altering the drug resistance of a fungal cell, the method comprising: 
 altering the expression or activity of a protein that is at least 70% identical to AQY1, YJR147W, YLL052C, YLL053C, or YPL091W in the cell.    
     
     
         43 . A method of identifying an artificial chimeric protein that alters the sensitivity of a cell to a toxic agent, the method comprising: 
 providing a nucleic acid library that comprises a plurality of nucleic acids, each nucleic acid of the plurality encoding an artificial chimeric protein that comprises an array of at least three zinc finger domains of which at least two adjacent zinc finger domains do not occur adjacent to each other in a naturally occurring protein;    introducing members of the library into cells to yield modified cells;    cultivating the modified cells in the presence of a toxic agent; and    identifying, from the modified cells, a test cell whose sensitivity to the toxic agent is altered relative to an untransformed but otherwise identical cell.    
     
     
         44 . The method of  claim 43 , wherein the test cell is a fungal cell, and the toxic agent is an anti-fungal agent.  
     
     
         45 . The method of  claim 43 , wherein the test cell is a cancer cell, and the toxic agent is an anti-mitotic agent.  
     
     
         46 . The method of  claim 43 , wherein the chimeric protein encoded by each nucleic acid of the plurality comprises a transcriptional regulatory domain.  
     
     
         47 . The method of  claim 46  further comprising constructing a nucleic acid that encodes a second chimeric protein that comprises the array of zinc finger domains of the artificial chimeric protein, but does not include the transcriptional regulatory domain of the artificial chimeric protein.  
     
     
         48 . The method of  claim 47  further comprising constructing a nucleic acid that encodes a second chimeric protein that comprises (i) the array of zinc finger domains of the artificial chimeric protein, and (ii) a transcriptional regulatory domain, other than the transcriptional regulatory domain of the artificial chimeric protein.  
     
     
         49 . A nucleic acid comprising a sequence encoding an artificial transcription factor comprising three zinc finger domains, wherein expression of the artificial transcription factor in a vertebrate cell induces a neuronal phenotype in at least one vertebrate cell.  
     
     
         50 . The nucleic acid of  claim 49 , wherein at least one of the zinc finger domains has the sequence: 
 Cys-X 2-5 -Cys-X 3 -X a -X-Gln-X b -X-Ser-Asn-His-X 3-5 -His (SEQ ID NO:250)    Cys-X 2-5 -Cys-X 3 -X a -X-Gln-X b -X-Ser-Asn-His-X 3-5 -His (SEQ ID NO:251); or    Cys-X 2-5 -Cys-X 3 -X a -X-Cys-X b -X-Ser-Asn-His-X 3-5 -His (SEQ ID NO:252), wherein X a  is phenylalanine or tyrosine; and X b  is a hydrophobic amino acid.    
     
     
         51 . The nucleic acid of  claim 50 , wherein the artificial transcription factor comprises the sequence: Cys-X 2-5 -Cys-X 3 -X a -X-Gln-X b -X-Ser-Asn-His-X 3-5 -His-X 1-6 -Cys-X 2-5 -Cys-X 3 -X a -X-Gln-X b -X-Ser-Asn-His-X 3-5 -His-X 1-6 -Cys-X 2-5 -Cys-X3-X a -X-Cys-X b -X-Ser-Asn-His-X 3-5 -His (SEQ ID NO:253), wherein X a  is phenylalanine or tyrosine; and X b  is a hydrophobic amino acid.  
     
     
         52 . A method of inducing neurite formation in a vertebrate cell, the method comprising: 
 providing a vertebrate cell that contains the nucleic acid of  claim 49;  and    maintaining the vertebrate cell under conditions in which the artificial transcription factor is produced and neurite formation is induced.    
     
     
         53 . The method of  claim 52 , wherein the vertebrate cell is a mammalian cell.  
     
     
         54 . The method of  claim 52 , wherein the mammalian cell is a human cell.  
     
     
         55 . The method of  claim 52 , wherein the vertebrate cell is a stem cell prior to production of the artificial transcription factor.  
     
     
         56 . A nucleic acid comprising a sequence encoding an artificial transcription factor comprising three zinc finger domains, wherein expression of the artificial transcription factor in a vertebrate cell induces osteogenesis in at least one vertebrate cell.  
     
     
         57 . The nucleic acid of  claim 56 , wherein at least one of the zinc finger domains has the sequence: 
 Cys-X 2-5 -Cys-X 3 -X a -X-Arg-X b -X-Asp-Lys-His-X 3-5 -His (SEQ ID NO:254);    Cys-X 2-5 -Cys-X 3 -X a -X-Gln-X b -X-Thr-His-His-X 3-5 -His (SEQ ID NO:255);    Cys-X 2-5 -Cys-X 3 -X a -X-Val-X b -X-Ser-Thr-His-X 3-5 -His (SEQ ID NO:256) or;    Cys-X 2-5 -Cys-X 3 -X a -X-Arg-X b -X-Asp-Lys-His-X 3-5 -His (SEQ ID NO:257), wherein X a  is phenylalanine or tyrosine; and X b  is a hydrophobic amino acid.    
     
     
         58 . The nucleic acid of  claim 57 , wherein the artificial transcription factor comprises the amino acid sequence: 
 Cys-X 2-5 -Cys-X 3 -X a -X-Arg-X b -X-Asp-Lys-His-X 3-5 -His-X 1-6 -Cys-X 2-5 -Cys-X 3 -X a -X-Gln-X b -X-Thr-His-His-X 3-5 -His-X 1-6 -Cys-X 2-5 -Cys-X 3 -X a -X-Val-X b -X-Ser-Thr-His-X 3-5 -His-X 1-6 -Cys-X 2-5 -Cys-X 3 -X a -X-Arg-X b -X-Asp-Lys-His-X 3-5 -His (SEQ ID NO:258), wherein X a  is phenylalanine or tyrosine; and X b  is a hydrophobic amino acid..    
     
     
         59 . A method of inducing osteogenesis in a vertebrate cell, the method comprising: 
 providing a vertebrate cell that contains the nucleic acid of  claim 56;  and    maintaining the vertebrate cell under conditions in which the artificial transcription factor is produced and osteogenesis is induced.    
     
     
         60 . A method of altering the differentiative capacity of a stem cell, the method comprising: 
 providing a stem cell and a nucleic acid that comprises a sequence encoding an artificial transcription factor comprising a plurality of zinc finger domains, wherein the artificial transcription factor alters the differentiative capacity of the stem cell;    introducing the nucleic acid into the stem cell; and    maintaining the stem cell under conditions in which the artificial transcription factor is produced, thereby altering the differentiative capacity of the stem cell.    
     
     
         61 . The method of  claim 60 , wherein the artificial transcription factor induces differentiation of the stem cell.  
     
     
         62 . The method of  claim 60 , wherein the artificial transcription factor enhances self-renewal potential of the stem cell.  
     
     
         63 . The method of  claim 60 , wherein the stem cell is an embryonic stem cell.  
     
     
         64 . The method of  claim 60 , wherein the stem cell is a vertebrate stem cell or a plant stem cell.  
     
     
         65 . The method of  claim 62 , wherein the stem cell is a hematopoietic stem cell, a neuronal progenitor cell or muscular progenitor cell.  
     
     
         66 . A method of identifying an artificial transcription factor, the method comprising: 
 providing a nucleic acid library that comprises a plurality of nucleic acids, each encoding a different artificial transcription factor, each artificial transcription comprising an array of at least two zinc finger domains and a regulatory domain that activates or represses transcription;    providing cells that have a given trait;    introducing members of the nucleic acid library into the cells;    identifying a member of the library that alters the given trait; and    preparing a coding nucleic acid that comprises a sequence encoding a DNA binding polypeptide that comprises an array of zinc finger domains identical to that of the identified member, but does not include a regulatory domain identical to the regulatory domain of the identified member.    
     
     
         67 . The method of  claim 66 , wherein the DNA binding polypeptide lacks a regulatory domain.  
     
     
         68 . The method of  claim 66 , wherein the DNA binding polypeptide comprises a regulatory domain that is at least 80% identical to the regulatory domain of the identified member.  
     
     
         69 . The method of  claim 67 , wherein the DNA binding polypeptide comprises a regulatory domain of opposite functionality relative to the regulatory domain of the identified member.  
     
     
         70 . The method of  claim 66 , further comprising introducing the coding nucleic acid into a test cell and assessing the given trait of the test cell.  
     
     
         71 . The method of  claim 66 , wherein the identifying step comprises identifying a cell having a property selected from the group consisting of: resistance to a given environmental condition; differentiation; dedifferentiation; proliferation; apoptosis; serum-independence; pathogen resistance; and pathogen sensitivity.  
     
     
         72 . A nucleic acid library comprising a first plurality of nucleic acids and a second plurality of nucleic acids, wherein 
 (a) each nucleic acid of the first plurality encodes an artificial protein chimera comprising at least two zinc finger domains and a first functional domain that activates transcription; and    (b) each nucleic acid of the second plurality encodes an artificial protein chimera comprising at least two zinc finger domains, and does not include the first functional domain.    
     
     
         73 . The nucleic acid library of  claim 72 , wherein the artificial protein chimera encoded by each nucleic acid of the second plurality comprises a second functional domain, different from the first functional domain.  
     
     
         74 . The nucleic acid library of  claim 73 , wherein the first functional domain is an activation domain and the second functional domain is a repression domain.  
     
     
         75 . The nucleic acid library of  claim 73 , wherein the first functional domain is an activation domain and the second functional domain is an activation domain, with different efficacy from the first activation domain.  
     
     
         76 . The nucleic acid library of  claim 72 , wherein the first functional domain is a histone deacetylase domain.  
     
     
         77 . A method of identifying a protein chimera, the method comprising: 
 providing the nucleic acid library of  claim 72;     introducing members of the nucleic acid library into cells that have a given trait; and    identifying a member of the library that alters the given trait.    
     
     
         78 . A method of identifying a plurality of protein chimeras, the method comprising: 
 providing a population of cells, each of which comprises a first nucleic acid encoding a first artificial protein chimera, wherein expression of the first artificial protein chimera alters a given trait of the cells;    introducing members of a nucleic acid library into the cells to produce a population of test cells, the nucleic acid library comprising a plurality of nucleic acids, each encoding a different artificial protein chimera that comprises two zinc finger domains; and    screening the test cells to identify a test cell in which the given trait is further altered, wherein each test cell expresses the first nucleic acid and a second nucleic acid that is a member of the nucleic acid library.    
     
     
         79 . A method of preparing a modified cell, the method comprising 
 providing a nucleic acid library that comprises a plurality of nucleic acids, each encoding a different artificial protein chimera, each protein chimera comprising at least two zinc finger domains;    identifying a first and a second member of the library, each of which alters a given trait of a cell; and    preparing a test cell that expresses a first and second protein chimera encoded by the first and second identified library members, respectively.    
     
     
         80 . The method of  claim 79 , wherein the identifying step comprises introducing members of the nucleic acid library into cells to provide transformed cells, and identifying a first engineered cell and a second engineered cell in which the given trait is altered.  
     
     
         81 . The method of  claim 79  further comprising evaluating the given trait in the test cell.  
     
     
         82 . The method of  claim 79 , wherein the preparing step comprises introducing into the test cell a first coding sequence encoding the first protein chimera and a second coding sequence encoding the second protein chimera into the cell.  
     
     
         83 . The method of  claim 82 , wherein the first and second gene are components of the same nucleic acid molecule.  
     
     
         84 . The method of  claim 79 , wherein the preparing comprises fusing a first cell that comprises a first coding sequence encoding the first protein chimera to a second cell that comprises a second coding sequence encoding the second protein chimera.  
     
     
         85 . A method of preparing a library encoding protein chimeras, the method comprising: 
 providing a nucleic acid library that comprises a plurality of nucleic acids, each encoding a different artificial protein chimera that comprises at least two zinc finger domains;    introducing members of the nucleic acid library into cells that have a given trait;    identifying a member of the library which alters the given trait; and    preparing a second library that comprises a plurality of nucleic acids, each encoding 
 (1) a variant that differs from the artificial protein chimera corresponding to the identified member by between one and six amino acid substitutions, insertions, or deletions,  
 (2) a protein chimera that comprises the zinc finger domains of the artificial protein chimera corresponding to the identified member and an additional zinc finger domain, wherein the additional zinc finger domain varies among the members of the second library,  
 (3) a variant of the artificial protein chimera corresponding to the identified member, wherein the variant has a subset of the zinc finger domain positions replaced with other zinc finger domains and at least one invariant zinc finger domain that is identical to the zinc finger domain at a corresponding position in the artificial protein chimera corresponding to the identified member, or  
 (4) a variant of the artificial protein chimera corresponding to the identified member, wherein, among the members of the second library, one or more zinc finger domain positions are varied such that the particular domain in the artificial protein chimera corresponding to the identified member at that position occurs at a frequency greater than other zinc finger domains at that position.  
   
     
     
         86 . A method of identifying a target of artificial transcription factors, the method comprising: 
 providing a nucleic acid library that comprises a plurality of nucleic acids, each encoding a different artificial transcription factor, each transcription factor comprising at least two zinc finger domains;    introducing members of the library into replicates of a test cell to provide a plurality of transformed cells;    maintaining the transformed cells under conditions in which the artificial transcription factor is expressed;    identifying a plurality of phenotypically altered cells from the plurality of transformed cells, wherein each phenotypically altered cell has an altered phenotype relative to the test cell;    profiling transcripts or protein abundance in each phenotypically altered cell of the plurality to provide a profile for each phenotypically altered cell; and    comparing the profiles to each other to identify one or more transcripts or proteins whose abundance is similarly altered in at least two phenotypically altered cells of the plurality relative to the test cell.    
     
     
         87 . A method of evaluating a cell, the method comprising: 
 providing a modified cell that contains a heterologous nucleic acid comprising a sequence encoding an artificial transcription factor comprising at least two zinc finger domains, wherein expression of the artificial transcription factor alters a phenotypic trait of the cell relative to a reference cell that does not express the artificial transcription factor;    identifying a target gene whose expression is altered in modified cell relative to the reference cell; and    evaluating the phenotypic trait of a test cell wherein the test cell contains the heterologous nucleic acid and expresses the artificial transcription factor, and the activity of the target gene is altered in the test cell.    
     
     
         88 . The method of  claim 87 , wherein the activity of the target gene is altered by a genetic mutation.  
     
     
         89 . The method of  claim 87 , wherein the activity of the target gene is altered by treatment with a double-stranded RNA or an antisense oligonucleotide or a ribozyme.  
     
     
         90 . The method of  claim 87 , wherein the activity of the target gene is altered by overexpression of the target gene.  
     
     
         91 . A method of evaluating an artificial transcription factor, the method comprising: 
 providing a modified cell that contains a heterologous nucleic acid comprising a sequence encoding an artificial transcription factor comprising at least two zinc finger domains, wherein expression of the artificial transcription factor alters a phenotypic trait of the cell relative to a reference cell that does not express the artificial transcription factor; and    introducing library nucleic acids into replicates of the modified cell; and    identifying a library nucleic acid which attenuates the alteration of the phenotypic trait by the artificial transcription factor.    
     
     
         92 . The method of  claim 91 , wherein the library nucleic acids comprise cDNA library nucleic acids.  
     
     
         93 . The method of  claim 91 , wherein the library nucleic acids comprises nucleic acids encoding different artificial protein chimeras.  
     
     
         94 . The method of  claim 93 , wherein the different artificial protein chimeras include different zinc finger domains.  
     
     
         95 . A method of identifying a protein chimera, the method comprising: 
 providing a nucleic acid library that comprises a plurality of nucleic acids, each encoding a different artificial protein chimera that comprises at least two zinc finger domains, wherein at least one zinc finger domain is from a naturally-occurring protein;    introducing members of the nucleic acid library into cells that have a given trait; and    identifying a cell in which a member of the library alters the given trait.    
     
     
         96 . A method of identifying a protein chimera, the method comprising: 
 providing a nucleic acid library that comprises a plurality of nucleic acids, each encoding a different artificial protein chimera that comprises at least two zinc finger domains, wherein at least one zinc finger domain of at least one member of the plurality comprises an amino acid sequence listed in Table 1;    introducing members of the nucleic acid library into cells that have a given trait; and    identifying a cell in which a member of the library alters the given trait.    
     
     
         97 . A method of identifying a protein chimera, the method comprising: 
 providing a library of cells, the library comprising a plurality of cells, wherein each cell includes a nucleic acid encoding a polypeptide comprising a first and a second zinc finger domain, wherein (1) the first and second zinc finger domains of the polypeptide encoded by each nucleic acid of the plurality are each identical to zinc finger domains from naturally occurring proteins and either (i) do not occur in the same naturally occurring protein or (ii) occur in the same naturally occurring protein in a different configuration than in the polypeptide, (2) the first zinc finger domain varies among nucleic acids of the plurality, and (3) the second zinc finger domain varies among nucleic acids of the plurality;    identifying a library cell whose phenotype differs from a reference cell; and    recovering the nucleic acid from the identified library cell.    
     
     
         98 . An isolated nucleic acid encoding an artificial transcription factor that improves solubility of a heterologous, over-expressed protein in a cell that produces the artificial transcription factor.  
     
     
         99 . The nucleic acid of  claim 98 , wherein the artificial transcription factor comprises a plurality of zinc finger domains.  
     
     
         100 . The nucleic acid of  claim 98 , wherein the cell is bacterial cell.  
     
     
         101 . The nucleic acid of  claim 100 , wherein the protein is a mammalian protein.  
     
     
         102 . The nucleic acid of  claim 100 , wherein the protein comprises the AKT protein.  
     
     
         103 . The nucleic acid of  claim 99 , wherein the plurality of zinc finger domains comprise domains: QSTR-DSAR-RDHT-WSNR or VSTR-DGNV-QSNR-QSNK.  
     
     
         104 . A modified cell comprising the heterologous nucleic acid of  claim 98 .  
     
     
         105 . A method of producing a heterologous target protein, the method comprising: 
 providing the modified cell of  claim 104 , wherein the modified cell comprises a second nucleic acid that comprises a sequence encoding a heterologous target protein; and    maintaining the modified cell under conditions wherein the artificial transcription factor and the heterologous target protein are produced.    
     
     
         106 . The method of  claim 105 , wherein the modified cell is in a subject.  
     
     
         107 . A method of producing a cellular product, the method comprising: 
 providing a modified cell of  claim 1;     maintaining the modified cell under conditions in which the artificial transcription factor is produced; and    recovering a product produced by the cultured cell, wherein the product is other than the artificial transcription factor.    
     
     
         108 . A method of transferring an altered trait from a first cell to a second cell, the method comprising: 
 providing a nucleic acid library that comprises a plurality of nucleic acids, each encoding a different artificial protein chimera that comprises at least two zinc finger domains;    introducing members of the nucleic acid library into first cells that have a given trait to provide transformed cells;    identifying an altered cell from the transformed cells in which a member of the library alters the given trait;    recovering a nucleic acid library member from the identified, altered cell;    introducing the nucleic acid library member into second cells, wherein the second cells differ from the first cells by a phenotypic trait other than the given trait; and    evaluating a second cell that includes the nucleic acid library member and expresses the artificial protein chimera that the nucleic acid library member encodes.    
     
     
         109 . An isolated polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 260, 262, and 264.  
     
     
         110 . An isolated nucleic acid comprising a nucleic acid sequence that encodes the polypeptide of  claim 109 .  
     
     
         111 . A nucleic acid comprising a sequence encoding an artificial transcription factor comprised of three zinc finger domains, wherein (a) expression of the artificial transcription factor alters a property of at least one eukaryotic cell, the property being selected from the group consisting of viral replication, virus production, and viral infectivity; (b) expression of the artificial transcription factor alters an ability of a eukaryotic cell to regulate a stem cell that is co-cultured with the eukaryotic cell or that is cultured in media conditioned by the eukaryotic cell; (c) expression of the artificial transcription factor alters an ability of a mammalian culture cell to glycosylate a secreted protein; or (d) expression of the artificial transcription factor alters the ability of a cell to take up exogenous nucleic acid.