A series of template plasmids for Escherichia coli genome engineering

Journal of Microbiological Methods

Volumn 125, Issue , 2016, Pages 49-57

  Deb, Shalini S ^a   Reshamwala, Shamlan M S ^a   Lali, Arvind M ^a  

^a INSTITUTE OF CHEMICAL TECHNOLOGY   (India)

Author keywords

E. coli; Gene integration; Genome engineering; Promoter replacement; Template plasmids

Indexed keywords

BETA GALACTOSIDASE; FATTY ACID; PHOTOPROTEIN; RED FLUORESCENT PROTEIN;

ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; BACTERIAL STRAIN; DNA INTEGRATION; DNA SEQUENCE; DNA TEMPLATE; ESCHERICHIA COLI; EXPRESSION VECTOR; EXTRACELLULAR MATRIX; GENE CONSTRUCT; GENE EXPRESSION; GENE INSERTION; GENE OVEREXPRESSION; GENE SEQUENCE; GENETIC ENGINEERING; GENETIC MANIPULATION; GENOTYPE; MCHERRY GENE; NONHUMAN; PLASMID; PRIORITY JOURNAL; PROMOTER REGION; RNA EDITING; TRANSPOSON; CHROMOSOME; GENE TARGETING; GENE VECTOR; GENETICS; MOLECULAR CLONING; PROCEDURES;

CHROMOSOMES; CLONING, MOLECULAR; ESCHERICHIA COLI; GENE TARGETING; GENETIC ENGINEERING; GENETIC VECTORS; GENOME, BACTERIAL; LUMINESCENT PROTEINS; PLASMIDS; PROMOTER REGIONS, GENETIC;

EID: 84962909268     PISSN: 01677012     EISSN: 18728359     Source Type: Journal    
DOI: 10.1016/j.mimet.2016.04.006     Document Type: Article

References (54)

1. Ajikumar P.K., Xiao W.-H., Tyo K.E.J., Wang Y., Simeon F., Leonard E., Mucha O., Phon T.H., Pfeifer B., Stephanopoulos G. Isoprenoid pathway optimization for Taxol precursor overproduction in Escherichia coli. Science 2010, 330:70-74.
2. Albermann C., Trachtmann N., Sprenger G.A. A simple and reliable method to conduct and monitor expression cassette integration into the Escherichia coli chromosome. Biotechnol. J. 2010, 5:32-38.
3. Block D.H., Hussein R., Liang L.W., Lim H.N. Regulatory consequences of gene translocation in bacteria. Nucleic Acids Res. 2012, 40:8979-8992.
4. Bryant J.A., Sellars L.E., Busby S.J., Lee D.J. Chromosome position effects on gene expression in Escherichia coli K-12. Nucleic Acids Res. 2014, 42:11383-11392.
5. Cherepanov P.P., Wackernagel W. Gene disruption in Escherichia coli: TcR and KmR cassettes with the option of Flp-catalyzed excision of the antibiotic-resistance determinant. Gene 1995, 158:9-14.
6. Datsenko K.A., Wanner B.L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl. Acad. Sci. U. S. A. 2000, 97:6640-6645.
7. De Mey M., Maertens J., Boogmans S., Soetaert W.K., Vandamme E.J., Cunin R., Foulquié-Moreno M.R. Promoter knock-in: a novel rational method for the fine tuning of genes. BMC Biotechnol. 2010, 10:26.
8. Doublet B., Douard G., Targant H., Meunier D., Madec J.Y., Cloeckaert A. Antibiotic marker modifications of λ Red and FLP helper plasmids, pKD46 and pCP20, for inactivation of chromosomal genes using PCR products in multidrug-resistant strains. J. Microbiol. Methods 2008, 75:359-361.
9. Dunlop M.J., Dossani Z.Y., Szmidt H.L., Chu H.C., Lee T.S., Keasling J.D., Hadi M.Z., Mukhopadhyay A. Engineering microbial biofuel tolerance and export using efflux pumps. Mol. Syst. Biol. 2011, 7:487.
10. Guyer M.S., Reed R.R., Steitz J.A., Low K.B. Identification of a sex-factor-affinity site in E. coli as gamma delta. Cold Spring Harb. Symp. Quant. Biol. 1981, 45:135-140.
11. Haldimann A., Wanner B.L. Conditional-replication, integration, excision, and retrieval plasmid-host systems for gene structure-function studies of bacteria. J. Bacteriol. 2001, 183:6384-6393.
12. Hanahan D. Studies on transformation of Escherichia coli with plasmids. J. Mol. Biol. 1983, 166:557-580.
13. Handke P., Lynch S.A., Gill R.T. Application and engineering of fatty acid biosynthesis in Escherichia coli for advanced fuels and chemicals. Metab. Eng. 2011, 13:28-37.
14. Hollands K., Busby S.J., Lloyd G.S. New targets for the cyclic AMP receptor protein in the Escherichia coli K-12 genome. FEMS Microbiol. Lett. 2007, 274:89-94.
15. Jiang W., Bikard D., Cox D., Zhang F., Marraffini L.A. RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat. Biotechnol. 2013, 31:233-239.
16. Jiang Y., Chen B., Duan C., Sun B., Yang J., Yang S. Multigene editing in the Escherichia coli genome via the CRISPR-Cas9 system. Appl. Environ. Microbiol. 2015, 81:2506-2514.
17. Jing F., Cantu D.C., Tvaruzkova J., Chipman J.P., Nikolau B.J., Yandeau-Nelson M.D., Reilly P.J. Phylogenetic and experimental characterization of an acyl-ACP thioesterase family reveals significant diversity in enzymatic specificity and activity. BMC Biochem. 2011, 12:44.
18. Juhas M., Ajioka J.W. Flagellar region 3b supports strong expression of integrated DNA and the highest chromosomal integration efficiency of the Escherichia coli flagellar regions. Microb. Biotechnol. 2015, 8:726-738.
19. Juhas M., Evans L.D., Frost J., Davenport P.W., Yarkoni O., Fraser G.M., Ajioka J.W. Escherichia coli flagellar genes as target sites for integration and expression of genetic circuits. PLoS One 2014, 9.
20. Koma D., Yamanaka H., Moriyoshi K., Ohmoto T., Sakai K. A convenient method for multiple insertions of desired genes into target loci on the Escherichia coli chromosome. Appl. Microbiol. Biotechnol. 2012, 93:815-829.
21. Kuhlman T.E., Cox E.C. Site-specific chromosomal integration of large synthetic constructs. Nucleic Acids Res. 2010, 38.
22. Kuhlman T.E., Cox E.C. A place for everything: chromosomal integration of large constructs. Bioeng. Bugs 2010, 1:296-299.
23. Lamberg A., Nieminen S., Qiao M., Savilahti H. Efficient insertion mutagenesis strategy for bacterial genomes involving electroporation of in vitro-assembled DNA transposition complexes of bacteriophage Mu. Appl. Environ. Microbiol. 2002, 68:705-712.
24. Lee D.J., Bingle L.E.H., Heurlier K., Pallen M.J., Penn C.W., Busby S.J.W., Hobman J.L. Gene doctoring: a method for recombineering in laboratory and pathogenic Escherichia coli strains. BMC Microbiol. 2009, 9:252.
25. Lemuth K., Steuer K., Albermann C. Engineering of a plasmid-free Escherichia coli strain for improved in vivo biosynthesis of astaxanthin. Microb. Cell Factories 2011, 10:29.
26. Lennen R.M., Pfleger B.F. Engineering Escherichia coli to synthesize free fatty acids. Trends Biotechnol. 2012, 30:659-667.
27. Li Y., Lin Z., Huang C., Zhang Y., Wang Z., Tang Y., Chen T., Zhao X. Metabolic engineering of Escherichia coli using CRISPR-Cas9 meditated genome editing. Metab. Eng. 2015, 31:13-21.
28. McKenzie G.J., Craig N.L. Fast, easy and efficient: site-specific insertion of transgenes into enterobacterial chromosomes using Tn7 without need for selection of the insertion event. BMC Microbiol. 2006, 6:39.
29. Meynial-Salles I., Cervin M.A., Soucaille P. New tool for metabolic pathway engineering in Escherichia coli: one-step method to modulate expression of chromosomal genes. Appl. Environ. Microbiol. 2005, 71:2140-2144.
30. Munjal N., Mattam A.J., Pramanik D., Srivastava P.S., Yazdani S.S. Modulation of endogenous pathways enhances bioethanol yield and productivity in Escherichia coli. Microb. Cell Factories 2012, 11:145.
31. Murphy K.C. Use of bacteriophage λ recombination functions to promote gene replacement in Escherichia coli. J. Bacteriol. 1998, 180:2063-2071.
32. Murphy K.C., Campellone K.G. Lambda Red-mediated recombinogenic engineering of enterohemorrhagic and enteropathogenic E. coli. BMC Mol. Biol. 2003, 4:11.
33. Murphy K.C., Campellone K.G., Poteete A.R. PCR-mediated gene replacement in Escherichia coli. Gene 2000, 246:321-330.
34. Norrander J., Kempe T., Messing J. Construction of improved M13 vectors using oligodeoxynucleotide-directed mutagenesis. Gene 1983, 26:101-106.
35. Reshamwala S.M.S., Noronha S.B. Co-production of two recombinant proteins in Escherichia coli using the promoter region of the divergently expressed curli genes. J. Biotechnol. 2013, 164:121-122.
36. Royce L.A., Yoon J.M., Chen Y., Rickenbach E., Shanks J.V., Jarboe L.R. Evolution for exogenous octanoic acid tolerance improves carboxylic acid production and membrane integrity. Metab. Eng. 2015, 29:180-188.
37. Sabido A., Martínez L.M., de Anda R., Martínez A., Bolívar F., Gosset G. A novel plasmid vector designed for chromosomal gene integration and expression: use for developing a genetically stable Escherichia coli melanin production strain. Plasmid 2013, 69:16-23.
38. Sabri S., Steen J.A., Bongers M., Nielsen L.K., Vickers C.E. Knock-in/Knock-out (KIKO) vectors for rapid integration of large DNA sequences, including whole metabolic pathways, onto the Escherichia coli chromosome at well-characterised loci. Microb. Cell Factories 2013, 12:60.
39. Sousa C., de Lorenzo V., Cebolla A. Modulation of gene expression through chromosomal positioning in Escherichia coli. Microbiology 1997, 143:2071-2078.
40. Steen E.J., Kang Y., Bokinsky G., Hu Z., Schirmer A., McClure A., Del Cardayre S.B., Keasling J.D. Microbial production of fatty-acid-derived fuels and chemicals from plant biomass. Nature 2010, 463:559-562.
41. St-Pierre F., Cui L., Priest D.G., Endy D., Dodd I.B., Shearwin K.E. One-step cloning and chromosomal integration of DNA. ACS Synth. Biol. 2013, 2:537-541.
42. Stringer A.M., Singh N., Yermakova A., Petrone B.L., Amarasinghe J.J., Reyes-Diaz L., Mantis N.J., Wade J.T. FRUIT, a scar-free system for targeted chromosomal mutagenesis, epitope tagging, and promoter replacement in Escherichia coli and Salmonella enterica. PLoS One 2012, 7.
43. Studier F.W., Moffatt B.A. Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. J. Mol. Biol. 1986, 189:113-130.
44. Tas H., Nguyen C.T., Patel R., Kim N.H., Kuhlman T.E. An integrated system for precise genome modification in Escherichia coli. PLoS One 2015, 10.
45. Tee T.W., Chowdhury A., Maranas C.D., Shanks J.V. Systems metabolic engineering design: fatty acid production as an emerging case study. Biotechnol. Bioeng. 2014, 111:849-857.
46. Tischer B.K., von Einem J., Kaufer B., Osterrieder N. Two-step red-mediated recombination for versatile high-efficiency markerless DNA manipulation in Escherichia coli. Biotechniques 2006, 40:191-197.
47. Uzzau S., Figueroa-Bossi N., Rubino S., Bossi L. Epitope tagging of chromosomal genes in Salmonella. Proc. Natl. Acad. Sci. U. S. A. 2001, 98:15264-15269.
48. Wei X.X., Shi Z.Y., Li Z.J., Cai L., Wu Q., Chen G.Q. A mini-Mu transposon-based method for multiple DNA fragment integration into bacterial genomes. Appl. Microbiol. Biotechnol. 2010, 87:1533-1541.
49. Wolfe A.J. The acetate switch. Microbiol. Mol. Biol. Rev. 2005, 69:12-50.
50. Yamamoto S., Izumiya H., Morita M., Arakawa E., Watanabe H. Application of λ Red recombination system to Vibrio cholerae genetics: simple methods for inactivation and modification of chromosomal genes. Gene 2009, 438:57-64.
51. Yang J., Sun B., Huang H., Jiang Y., Diao L., Chen B., Xu C., Wang X., Liu J., Jiang W., Yang S. High-efficiency scarless genetic modification in Escherichia coli by using lambda red recombination and I-SceI cleavage. Appl. Environ. Microbiol. 2014, 80:3826-3834.
52. Yu D., Ellis H.M., Lee E.C., Jenkins N.A., Copeland N.G., Court D.L. An efficient recombination system for chromosome engineering in Escherichia coli. Proc. Natl. Acad. Sci. U. S. A. 2000, 97:5978-5983.
53. Yu B.J., Kang K.H., Lee J.H., Sung B.H., Kim M.S., Kim S.C. Rapid and efficient construction of markerless deletions in the Escherichia coli genome. Nucleic Acids Res. 2008, 36.
54. Yuan L.Z., Rouvière P.E., LaRossa R.A., Suh W. Chromosomal promoter replacement of the isoprenoid pathway for enhancing carotenoid production in E. coli. Metab. Eng. 2006, 8:79-90.