High-throughput cloning and expression library creation for functional proteomics

Proteomics

Volumn 13, Issue 9, 2013, Pages 1381-1399

  Festa, Fernanda ^a   Steel, Jason ^a   Bian, Xiaofang ^a   Labaer, Joshua ^a  

^a ARIZONA STATE UNIVERSITY   (United States)

Author keywords

Gene libraries; High throughput functional studies; ORF libraries gene transfer; Protein expression; Recombination and restriction enzyme based cloning; Technology

Indexed keywords

DNA;

ANALYTIC METHOD; ARTICLE; CLONING; EXPRESSION LIBRARY CREATION; FUNCTIONAL PROTEOMICS; GENE EXPRESSION SYSTEM; GENE SYNTHESIS; HIGH THROUGHPUT SEQUENCING; MOLECULAR CLONING; NONHUMAN; OPEN READING FRAME; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FUNCTION; RECOMBINATION BASED CLONING; RESTRICTION ENZYME BASED CLONING; SCALE UP;

BACTERIOPHAGE LAMBDA; CELL-FREE SYSTEM; CLONING, MOLECULAR; DNA RESTRICTION ENZYMES; ENZYMES; GENE EXPRESSION; GENE LIBRARY; HUMANS; OPEN READING FRAMES; PROMOTER REGIONS, GENETIC; PROTEOMICS; RECOMBINATION, GENETIC; VIBRIO CHOLERAE;

EID: 84876458624     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201200456     Document Type: Article

References (99)

1. Webber, H. J., New horticultural and agricultural terms. Science 1903, XVIII, 501-503.
2. Jackson, D. A., Symons, R. H., Berg, P., Biochemical method for inserting new genetic information into DNA of Simian Virus 40: circular SV40 DNA molecules containing lambda phage genes and the galactose operon of Escherichia coli. Proc. Natl. Acad. Sci. USA 1972, 69, 2904-2909.
3. Cohen, S. N., Chang, A. C., Boyer, H. W., Helling, R. B., Construction of biologically functional bacterial plasmids in vitro. Proc. Natl. Acad. Sci. USA 1973, 70, 3240-3244.
4. Avery, O. T., Macleod, C. M., McCarty, M., Studies on the chemical nature of the substance inducing transformation of pneumococcal types: induction of transformation by a desoxyribonucleic acid fraction isolated from Pneumococcus Type Iii. J. Exp. Med. 1944, 79, 137-158.
5. Weiss, B., Richardson, C. C., Enzymatic breakage and joining of deoxyribonucleic acid, I. Repair of single-strand breaks in DNA by an enzyme system from Escherichia coli infected with T4 bacteriophage. Proc. Natl. Acad. Sci. USA 1967, 57, 1021-1028.
6. Mizutani, S., Boettiger, D., Temin, H. M., A DNA-depenent DNA polymerase and a DNA endonuclease in virions of Rous sarcoma virus. Nature 1970, 228, 424-427.
7. Smith, H. O., Wilcox, K. W., A restriction enzyme from Hemophilus influenzae. I. Purification and general properties. J. Mol. Biol. 1970, 51, 379-391.
8. Danna, K., Nathans, D., Specific cleavage of simian virus 40 DNA by restriction endonuclease of Hemophilus influenzae. Proc. Natl. Acad. Sci. USA 1971, 68, 2913-2917.
9. Sanger, F., Coulson, A. R., A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J. Mol. Biol. 1975, 94, 441-448.
10. Sanger, F., Nicklen, S., Coulson, A. R., DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA 1977, 74, 5463-5467.
11. Maxam, A. M., Gilbert, W., A new method for sequencing DNA. Proc. Natl. Acad. Sci. USA 1977, 74, 560-564.
12. Sanger, F., Air, G. M., Barrell, B. G., Brown, N. L. et al., Nucleotide sequence of bacteriophage phi X174 DNA. Nature 1977, 265, 687-695.
13. Sanger, F., Coulson, A. R., Friedmann, T., Air, G. M. et al., The nucleotide sequence of bacteriophage phiX174. J. Mol. Biol. 1978, 125, 225-246.
14. Fleischmann, R. D., Adams, M. D., White, O., Clayton, R. A. et al., Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 1995, 269, 496-512.
15. Goffeau, A., Barrell, B. G., Bussey, H., Davis, R. W. et al., Life with 6000 genes. Science 1996, 274, 546, 563-547.
16. Coulson, A., The Caenorhabditis elegans genome project. C. elegans genome consortium. Biochem. Soc. Trans. 1996, 24, 289-291.
17. Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C. et al., Initial sequencing and analysis of the human genome. Nature 2001, 409, 860-921.
18. Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W. et al., The sequence of the human genome. Science 2001, 291, 1304-1351.
19. Hudson, J. R., Jr., Dawson, E. P., Rushing, K. L., Jackson, C. H. et al., The complete set of predicted genes from Saccharomyces cerevisiae in a readily usable form. Genome Res. 1997, 7, 1169-1173.
20. Ma, H., Kunes, S., Schatz, P. J., Botstein, D., Plasmid construction by homologous recombination in yeast. Gene 1987, 58, 201-216.
21. Oldenburg, K. R., Vo, K. T., Michaelis, S., Paddon, C., Recombination-mediated PCR-directed plasmid construction in vivo in yeast. Nucleic Acids Res. 1997, 25, 451-452.
22. Martzen, M. R., McCraith, S. M., Spinelli, S. L., Torres, F. M. et al., A biochemical genomics approach for identifying genes by the activity of their products. Science 1999, 286, 1153-1155.
23. Zhu, H., Bilgin, M., Bangham, R., Hall, D. et al., Global analysis of protein activities using proteome chips. Science 2001, 293, 2101-2105.
24. Uetz, P., Giot, L., Cagney, G., Mansfield, T. A. et al., A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 2000, 403, 623-627.
25. Ito, T., Chiba, T., Ozawa, R., Yoshida, M. et al., A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. USA 2001, 98, 4569-4574.
26. Ptacek, J., Devgan, G., Michaud, G., Zhu, H. et al., Global analysis of protein phosphorylation in yeast. Nature 2005, 438, 679-684.
27. Kung, L. A., Tao, S. C., Qian, J., Smith, M. G. et al., Global analysis of the glycoproteome in Saccharomyces cerevisiae reveals new roles for protein glycosylation in eukaryotes. Mol. Syst. Biol. 2009, 5, 308.
28. Marsischky, G., LaBaer, J., Many paths to many clones: a comparative look at high-throughput cloning methods. Genome Res. 2004, 14, 2020-2028.
29. Colwill, K., Wells, C. D., Elder, K., Goudreault, M. et al., Modification of the Creator recombination system for proteomics applications-improved expression by addition of splice sites. BMC Biotechnol. 2006, 6, 13.
30. Nagase, T., Koga, H., Ohara, O., Kazusa mammalian cDNA resources: towards functional characterization of KIAA gene products. Brief Funct. Genomic Proteomic 2006, 5, 4-7.
31. Stemmer, W. P., Crameri, A., Ha, K. D., Brennan, T. M. et al., Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides. Gene 1995, 164, 49-53.
32. Young, L., Dong, Q., Two-step total gene synthesis method. Nucleic Acids Res. 2004, 32, e59.
33. Qian, W., Yang, J. R., Pearson, N. M., Maclean, C. et al., Balanced codon usage optimizes eukaryotic translational efficiency. PLoS Genet. 2012, 8, e1002603.
34. Qin, J. Y., Zhang, L., Clift, K. L., Hulur, I. et al., Systematic comparison of constitutive promoters and the doxycycline-inducible promoter. PloS One 2010, 5, e10611.
35. Baneyx, F., Recombinant protein expression in Escherichia coli. Curr. Opin. Biotechnol. 1999, 10, 411-421.
36. Swiech, K., Picanco-Castro, V., Covas, D. T., Human cells: new platform for recombinant therapeutic protein production. Protein Expr. Purif. 2012, 84, 147-153.
37. Baneyx, F., Mujacic, M., Recombinant protein folding and misfolding in Escherichia coli. Nat. Biotechnol. 2004, 22, 1399-1408.
38. Festa, F., Rollins, S. M., Vattem, K., Hathaway, M. et al., Robust microarray production of freshly expressed proteins in a human milieu. Proteomics Clin. Appl. 2012. doi: 10.1002/prca.201200063.
39. Carlson, E. D., Gan, R., Hodgman, C. E., Jewett, M. C., Cell-free protein synthesis: applications come of age. Biotechnol. Adv. 2012, 30, 1185-1194.
40. Ramachandran, N., Raphael, J. V., Hainsworth, E., Demirkan, G. et al., Next-generation high-density self-assembling functional protein arrays. Nat. Methods 2008, 5, 535-538.
41. Goshima, N., Kawamura, Y., Fukumoto, A., Miura, A. et al., Human protein factory for converting the transcriptome into an in vitro-expressed proteome. Nat. Methods 2008, 5, 1011-1017.
42. Busso, D., Kim, R., Kim, S. H., Expression of soluble recombinant proteins in a cell-free system using a 96-well format. J. Biochem. Biophys. Methods 2003, 55, 233-240.
43. Cline, J., Braman, J. C., Hogrefe, H. H., PCR fidelity of pfu DNA polymerase and other thermostable DNA polymerases. Nucleic Acids Res. 1996, 24, 3546-3551.
44. Taycher, E., Rolfs, A., Hu, Y., Zuo, D. et al., A novel approach to sequence validating protein expression clones with automated decision making. BMC Bioinform. 2007, 8, 198.
45. Blommel, P. G., Martin, P. A., Wrobel, R. L., Steffen, E. et al., High efficiency single step production of expression plasmids from cDNA clones using the Flexi Vector cloning system. Protein Expr. Purif. 2006, 47, 562-570.
46. Nagase, T., Yamakawa, H., Tadokoro, S., Nakajima, D. et al., Exploration of human ORFeome: high-throughput preparation of ORF clones and efficient characterization of their protein products. DNA Res. 2008, 15, 137-149.
47. Yamakawa, H., High-throughput construction of ORF clones for production of the recombinant proteins. Methods Mol. Biol. 2009, 577, 25-39.
48. Skalamera, D., Ranall, M. V., Wilson, B. M., Leo, P. et al., A high-throughput platform for lentiviral overexpression screening of the human ORFeome. PloS One 2011, 6, e20057.
49. Brizuela, L., Richardson, A., Marsischky, G., Labaer, J., The FLEXGene repository: exploiting the fruits of the genome projects by creating a needed resource to face the challenges of the post-genomic era. Arch. Med. Res. 2002, 33, 318-324.
50. Rolfs, A., Montor, W. R., Yoon, S. S., Hu, Y. et al., Production and sequence validation of a complete full length ORF collection for the pathogenic bacterium Vibrio cholerae. Proc. Natl. Acad. Sci. USA 2008, 105, 4364-4369.
51. Yamada, K., Lim, J., Dale, J. M., Chen, H. et al., Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 2003, 302, 842-846.
52. Walhout, A. J., Temple, G. F., Brasch, M. A., Hartley, J. L. et al., GATEWAY recombinational cloning: application to the cloning of large numbers of open reading frames or ORFeomes. Methods Enzymol. 2000, 328, 575-592.
53. Sternberg, N., Hamilton, D., Bacteriophage P1 site-specific recombination. I. Recombination between loxP sites. J. Mol. Biol. 1981, 150, 467-486.
54. Abremski, K., Hoess, R., Bacteriophage P1 site-specific recombination. Purification and properties of the Cre recombinase protein. J. Biol. Chem. 1984, 259, 1509-1514.
55. Hoess, R. H., Abremski, K., Interaction of the bacteriophage P1 recombinase Cre with the recombining site loxP. Proc. Natl. Acad. Sci. USA 1984, 81, 1026-1029.
56. Clontech Laboratories, Inc. Clontech Creator DNA cloning & expression system. Clontechniques 2000, XI, 7-11.
57. Clontech In-Fusion® HD Cloning Kit. User Manual 2012.
58. MCLAB Choo-Choo PCR Cloning® Kit. User Manual 2012.
59. Cold Fusion Cloning Kit. User Manual 2009.
60. Lederberg, E. M., Lysogenicity in Escherichia coli strain K-12. Microb Genet Bull 1950, 1, 5-8.
61. Invitrogen Corporation. Gateway® Technology-a universal technology to clone DNA sequences for functional analysis and expression in multiple systems. User Manual 2010.
62. Yang, X., Boehm, J. S., Salehi-Ashtiani, K., Hao, T. et al., A public genome-scale lentiviral expression library of human ORFs. Nat. Methods 2011, 8, 659-661.
63. Rolfs, A., Hu, Y., Ebert, L., Hoffmann, D. et al., A biomedically enriched collection of 7000 human ORF clones. PloS One 2008, 3, e1528.
64. Witt, A. E., Hines, L. M., Collins, N. L., Hu, Y. et al., Functional proteomics approach to investigate the biological activities of cDNAs implicated in breast cancer. J. Proteome Res. 2006, 5, 599-610.
65. Lamesch, P., Li, N., Milstein, S., Fan, C. et al., hORFeome v3.1: a resource of human open reading frames representing over 10, 000 human genes. Genomics 2007, 89, 307-315.
66. Rual, J. F., Hirozane-Kishikawa, T., Hao, T., Bertin, N. et al., Human ORFeome version 1.1: a platform for reverse proteomics. Genome Res. 2004, 14, 2128-2135.
67. Rajagopala, S. V., Yamamoto, N., Zweifel, A. E., Nakamichi, T. et al., The Escherichia coli K-12 ORFeome: a resource for comparative molecular microbiology. BMC Genomics 2010, 11, 470.
68. Pellet, J., Tafforeau, L., Lucas-Hourani, M., Navratil, V. et al., ViralORFeome: an integrated database to generate a versatile collection of viral ORFs. Nucleic Acids Res. 2010, 38, D371-D378.
69. Murthy, T., Rolfs, A., Hu, Y., Shi, Z. et al., A full-genomic sequence-verified protein-coding gene collection for Francisella tularensis. PloS One 2007, 2, e577.
70. Gong, W., Shen, Y. P., Ma, L. G., Pan, Y. et al., Genome-wide ORFeome cloning and analysis of Arabidopsis transcription factor genes. Plant Physiol. 2004, 135, 773-782.
71. Reboul, J., Vaglio, P., Tzellas, N., Thierry-Mieg, N. et al., Open-reading-frame sequence tags (OSTs) support the existence of at least 17, 300 genes in C. elegans. Nat. Genet. 2001, 27, 332-336.
72. Reboul, J., Vaglio, P., Rual, J. F., Lamesch, P. et al., C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression. Nat. Genet. 2003, 34, 35-41.
73. Aguiar, J. C., LaBaer, J., Blair, P. L., Shamailova, V. Y. et al., High-throughput generation of P. falciparum functional molecules by recombinational cloning. Genome Res. 2004, 14, 2076-2082.
74. Sleight, S. C., Bartley, B. A., Lieviant, J. A., Sauro, H. M., In-Fusion BioBrick assembly and re-engineering. Nucleic Acids Res. 2010, 38, 2624-2636.
75. Gibson, D. G., Young, L., Chuang, R. Y., Venter, J. C. et al., Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 2009, 6, 343-345.
76. Gibson, D. G., Enzymatic assembly of overlapping DNA fragments. Methods Enzymol. 2011, 498, 349-361.
77. Aslanidis, C., de Jong, P. J., Ligation-independent cloning of PCR products (LIC-PCR). Nucleic Acids Res. 1990, 18, 6069-6074.
78. Aslanidis, C., de Jong, P. J., Schmitz, G., Minimal length requirement of the single-stranded tails for ligation-independent cloning (LIC) of PCR products. PCR Methods Appl. 1994, 4, 172-177.
79. Eschenfeldt, W. H., Lucy, S., Millard, C. S., Joachimiak, A. et al., A family of LIC vectors for high-throughput cloning and purification of proteins. Methods Mol. Biol. 2009, 498, 105-115.
80. Li, M. Z., Elledge, S. J., SLIC: a method for sequence- and ligation-independent cloning. Methods Mol. Biol. 2012, 852, 51-59.
81. Klock, H. E., Koesema, E. J., Knuth, M. W., Lesley, S. A., Combining the polymerase incomplete primer extension method for cloning and mutagenesis with microscreening to accelerate structural genomics efforts. Proteins 2008, 71, 982-994.
82. Tillett, D., Neilan, B. A., Enzyme-free cloning: a rapid method to clone PCR products independent of vector restriction enzyme sites. Nucleic Acids Res. 1999, 27, e26, i-iii.
83. de Jong, R. N., Daniels, M. A., Kaptein, R., Folkers, G. E., Enzyme free cloning for high throughput gene cloning and expression. J. Struct. Funct. Genomics 2006, 7, 109-118.
84. Dortay, H., Akula, U. M., Westphal, C., Sittig, M. et al., High-throughput protein expression using a combination of ligation-independent cloning (LIC) and infrared fluorescent protein (IFP) detection. PloS One 2011, 6, e18900.
85. Luna-Vargas, M. P., Christodoulou, E., Alfieri, A., van Dijk, W. J. et al., Enabling high-throughput ligation-independent cloning and protein expression for the family of ubiquitin specific proteases. J. Struct. Biol. 2011, 175, 113-119.
86. Schmid-Burgk, J. L., Schmidt, T., Kaiser, V., Honing, K. et al., A ligation-independent cloning technique for high-throughput assembly of transcription activator-like effector genes. Nat. Biotechnol. 2012, 1, 76-81.
87. Engler, C., Kandzia, R., Marillonnet, S., A one pot, one step, precision cloning method with high throughput capability. PloS One 2008, 3, e3647.
88. Engler, C., Gruetzner, R., Kandzia, R., Marillonnet, S., Golden gate shuffling: a one-pot DNA shuffling method based on type IIs restriction enzymes. PloS One 2009, 4, e5553.
89. Weber, E., Engler, C., Gruetzner, R., Werner, S. et al., A modular cloning system for standardized assembly of multigene constructs. PloS One 2011, 6, e16765.
90. Sarrion-Perdigones, A., Falconi, E. E., Zandalinas, S. I., Juarez, P. et al., GoldenBraid: an iterative cloning system for standardized assembly of reusable genetic modules. PloS One 2011, 6, e21622.
91. Geertsma, E. R., Dutzler, R., A versatile and efficient high-throughput cloning tool for structural biology. Biochemistry 2011, 50, 3272-3278.
92. Kotera, I., Nagai, T., A high-throughput and single-tube recombination of crude PCR products using a DNA polymerase inhibitor and type IIS restriction enzyme. J. Biotechnol. 2008, 137, 1-7.
93. Liu, Q., Li, M. Z., Leibham, D., Cortez, D. et al., The univector plasmid-fusion system, a method for rapid construction of recombinant DNA without restriction enzymes. Curr. Biol. 1998, 8, 1300-1309.
94. McKevitt, M., Patel, K., Smajs, D., Marsh, M. et al., Systematic cloning of Treponema pallidum open reading frames for protein expression and antigen discovery. Genome Res. 2003, 13, 1665-1674.
95. Peyret, N., Seneviratne, P. A., Allawi, H. T., SantaLucia, J., Jr., Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A.A, C.C, G.G, and T.T mismatches. Biochemistry 1999, 38, 3468-3477.
96. Breslauer, K. J., Frank, R., Blocker, H., Marky, L. A., Predicting DNA duplex stability from the base sequence. Proc. Natl. Acad. Sci. USA 1986, 83, 3746-3750.
97. Schoenfeld, T., Harper, T., Slater, M., RecA cleavage and protection for genomic mapping and subcloning. Promega Notes Mag. 1995, 50, 9-13.
98. Szybalski, W., RecA-mediated Achilles' heel cleavage. Curr. Opin. Biotechnol. 1997, 8, 75-81.
99. Yoshimura, H. Y., Yoshino, T., Hirose, T., Nakamura, Y. et al., Biological characteristics of palindromic DNA (ii). J. Gen. Appl. Microbiol. 1986, 32, 396-404.