Bacterial cellular engineering by genome editing and gene silencing

International Journal of Molecular Sciences

Volumn 15, Issue 2, 2014, Pages 2773-2793

  Nakashima, Nobutaka ^a,b   Miyazaki, Kentaro ^a,c  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^b NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^c UNIVERSITY OF TOKYO   (Japan)

Author keywords

Allelic exchange; Antisense RNA; Gene knock in; Gene knockdown; Gene knockout; Gene silencing; Genome editing; Mobile group II intron; RNA guided nucleases

Indexed keywords

ACETATE KINASE; BETA GALACTOSIDASE; COMPLEMENTARY RNA; DOXYCYCLINE; ELONGATION FACTOR G; PEPTIDE NUCLEIC ACID; PYRUVATE DEHYDROGENASE; ZINC FINGER NUCLEASE; ANTISENSE OLIGONUCLEOTIDE; SMALL INTERFERING RNA;

BACILLUS SUBTILIS; BACTERIAL CELL; BASE PAIRING; CELL ENGINEERING; CYTOTOXICITY; DNA CLEAVAGE; DNA REPLICATION; DNA SEQUENCE; GENE DELETION; GENE DOSAGE; GENE EXPRESSION; GENE INACTIVATION; GENE SILENCING; GENE TARGETING; GENOME EDITING; MOLECULAR BIOLOGY; NONHUMAN; POLYMERASE CHAIN REACTION; REVIEW; BACTERIA; BACTERIAL GENOME; GENETIC ENGINEERING; GENETICS; METABOLISM;

BACTERIA; GENE KNOCK-IN TECHNIQUES; GENE KNOCKOUT TECHNIQUES; GENE SILENCING; GENETIC ENGINEERING; GENOME, BACTERIAL; OLIGONUCLEOTIDES, ANTISENSE; RNA, SMALL INTERFERING;

EID: 84894079582     PISSN: 16616596     EISSN: 14220067     Source Type: Journal    
DOI: 10.3390/ijms15022773     Document Type: Review

References (120)

1. Curtis, T.P.; Sloan, W.T.; Scannell, J.W. Estimating prokaryotic diversity and its limits. Proc. Natl. Acad. Sci. USA 2002, 99, 10494-10499.
2. Ward, B.B. How many species of prokaryotes are there? Proc. Natl. Acad. Sci. USA 2002, 99, 10234-10236.
3. Hardy, S.; Legagneux, V.; Audic, Y.; Paillard, L. Reverse genetics in eukaryotes. Biol. Cell 2010, 102, 561-580.
4. Collins, J.J.; Endy, D.; Hutchison, C.A.; Roberts, R.J. Editorial-synthetic biology. Nucleic Acids Res. 2010, 38, 2513.
5. Reyrat, J.M.; Pelicic, V.; Gicquel, B.; Rappuoli, R. Counterselectable markers: Untapped tools for bacterial genetics and pathogenesis. Infect. Immun. 1998, 66, 4011-4017.
6. Hamilton, C.M.; Aldea, M.; Washburn, B.K.; Babitzke, P.; Kushner, S.R. New method for generating deletions and gene replacements in Escherichia coli. J. Bacteriol. 1989, 171, 4617-4622.
7. Emmerson, J.R.; Gally, D.L.; Roe, A.J. Generation of gene deletions and gene replacements in Escherichia coli O157: H7 using a temperature sensitive allelic exchange system. Biol. Proced. Online 2006, 8, 153-162.
8. Blomfield, I.C.; Vaughn, V.; Rest, R.F.; Eisenstein, B.I. Allelic exchange in Escherichia coli using the Bacillus subtilis sacB gene and a temperature-sensitive pSC101 replicon. Mol. Microbiol. 1991, 5, 1447-1457.
9. Link, A.J.; Phillips, D.; Church, G.M. Methods for generating precise deletions and insertions in the genome of wild-type Escherichia coli: Application to open reading frame characterization. J. Bacteriol. 1997, 179, 6228-6237.
10. Wu, S.S.; Kaiser, D. Markerless deletions of pil genes in Myxococcus xanthus generated by counterselection with the Bacillus subtilis sacB gene. J. Bacteriol. 1996, 178, 5817-5821.
11. Okibe, N.; Suzuki, N.; Inui, M.; Yukawa, H. Efficient markerless gene replacement in Corynebacterium glutamicum using a new temperature-sensitive plasmid. J. Microbiol. Methods 2011, 85, 155-163.
12. Van der Geize, R.; Hessels, G.I.; van Gerwen, R.; Vrijbloed, J.W.; van der Meijden, P.; Dijkhuizen, L. Targeted disruption of the kstD gene encoding a 3-ketosteroid Δ1-dehydrogenase isoenzyme of Rhodococcus erythropolis strain SQ1. Appl. Environ. Microbiol. 2000, 66, 2029-2036.
13. Graf, N.; Altenbuchner, J. Development of a method for markerless gene deletion in Pseudomonas putida. Appl. Environ. Microbiol. 2011, 77, 5549-5552.
14. Datsenko, K.A.; Wanner, B.L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl. Acad. Sci. USA 2000, 97, 6640-6645.
15. Solano, C.; Garcia, B.; Valle, J.; Berasain, C.; Ghigo, J.M.; Gamazo, C.; Lasa, I. Genetic analysis of Salmonella enteritidis biofilm formation: Critical role of cellulose. Mol. Microbiol. 2002, 43, 793-808.
16. Van Kessel, J.C.; Hatfull, G.F. Recombineering in Mycobacterium tuberculosis. Nat. Methods 2007, 4, 147-152.
17. Gust, B.; Chandra, G.; Jakimowicz, D.; Tian, Y.Q.; Bruton, C.J.; Chater, K.F. λ red-mediated genetic manipulation of antibiotic-producing Streptomyces. Adv. Appl. Microbiol. 2004, 54, 107-128.
18. Wang, Y.; Weng, J.; Waseem, R.; Yin, X.H.; Zhang, R.F.; Shen, Q.R. Bacillus subtilis genome editing using ssDNA with short homology regions. Nucleic Acids Res. 2012, 40, e91.
19. Blank, K.; Hensel, M.; Gerlach, R.G. Rapid and highly efficient method for scarless mutagenesis within the Salmonella enterica chromosome. PLoS One 2011, 6, e15763.
20. Geng, S.Z.; Jiao, X.A.; Pan, Z.M.; Chen, X.J.; Zhang, X.M.; Chen, X. An improved method to knock out the asd gene of Salmonella enterica serovar Pullorum. J. Biomed. Biotechnol. 2009, 2009, 646380.
21. Murphy, K.C.; Campellone, K.G.; Poteete, A.R. PCR-mediated gene replacement in Escherichia coli. Gene 2000, 246, 321-330.
22. Sun, W.; Wang, S.; Curtiss, R, III. Highly efficient method for introducing successive multiple scarless gene deletions and markerless gene insertions into the Yersinia pestis chromosome. Appl. Environ. Microbiol. 2008, 74, 4241-4245.
23. Ried, J.L.; Collmer, A. An nptI-sacB-sacR cartridge for constructing directed, unmarked mutations in gram-negative bacteria by marker exchange-eviction mutagenesis. Gene 1987, 57, 239-246.
24. Nakashima, N.; Tamura, T. A new carbon catabolite repression mutation of Escherichia coli, mlc, and its use for producing isobutanol. J. Biosci. Bioeng. 2012, 114, 38-44.
25. Costantino, N.; Court, D.L. Enhanced levels of λ Red mediated recombinants in mismatch repair mutants. Proc. Natl. Acad. Sci. USA 2003, 100, 15748-15753.
26. Wang, H.H.; Xu, G.; Vonner, A.J.; Church, G. Modified bases enable high-efficiency oligonucleotide-mediated allelic replacement via mismatch repair evasion. Nucleic Acids Res. 2011, 39, 7336-7347.
27. Wang, H.H.; Isaacs, F.J.; Carr, P.A.; Sun, Z.Z.; Xu, G.; Forest, C.R.; Church, G.M. Programming cells by multiplex genome engineering and accelerated evolution. Nature 2009, 460, 894-898.
28. Isaacs, F.J.; Carr, P.A.; Wang, H.H.; Lajoie, M.J.; Sterling, B.; Kraal, L.; Tolonen, A.C.; Gianoulis, T.A.; Goodman, D.B.; Reppas, N.B.; et al. Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science 2011, 333, 348-353.
29. Van Kessel, J.C.; Hatfull, G.F. Efficient point mutagenesis in mycobacteria using single-stranded DNA recombineering: Characterization of antimycobacterial drug targets. Mol. Microbiol. 2008, 67, 1094-1107.
30. Swingle, B.; Bao, Z.; Markel, E.; Chambers, A.; Cartinhour, S. Recombineering using RecTE from Pseudomonas syringae. Appl. Environ. Microbiol. 2010, 76, 4960-4968.
31. Van Pijkeren, J.P.; Britton, R.A. High efficiency recombineering in lactic acid bacteria. Nucleic Acids Res. 2012, 40, e76.
32. Nakashima, N.; Tamura, T. Gene silencing in Escherichia coli using antisense RNAs expressed from doxycycline-inducible vectors. Lett. Appl. Microbiol. 2013, 56, 436-442.
33. Stolworthy, T.S.; Krabbenhoft, E.; Black, M.E. A novel Escherichia coli strain allows functional analysis of guanylate kinase drug resistance and sensitivity. Anal. Biochem. 2003, 322, 40-47.
34. Yamada, J.; Yamasaki, S.; Hirakawa, H.; Hayashi-Nishino, M.; Yamaguchi, A.; Nishino, K. Impact of the RNA chaperone Hfq on multidrug resistance in Escherichia coli. J. Antimicrob. Chemother. 2010, 65, 853-858.
35. Tyo, K.E.; Ajikumar, P.K. Stephanopoulos, G. Stabilized gene duplication enables long-term selection-free heterologous pathway expression. Nat. Biotechnol. 2009, 27, 760-765.
36. Karberg, M.; Guo, H.T.; Zhong, J.; Coon, R.; Perutka, J.; Lambowitz, A.M. Group II introns as controllable gene targeting vectors for genetic manipulation of bacteria. Nat. Biotechnol. 2001, 19, 1162-1167.
37. Simon, D.M.; Clarke, N.A.C.; McNeil, B.A.; Johnson, I.; Pantuso, D.; Dai, L.X.; Chai, D.G.; Zimmerly, S. Group II introns in eubacteria and archaea: ORF-less introns and new varieties. RNA 2008, 14, 1704-1713.
38. Martínez-Abarca, F.; Toro, N. Group II introns in the bacterial world. Mol. Microbiol. 2000, 38, 917-926.
39. Michel, F.; Ferat, J.L. Structure and activities of group-II introns. Annu. Rev. Biochem. 1995, 64, 435-461.
40. Quiroga, C.; Kronstad, L.; Ritlop, C.; Filion, A.; Cousineau, B. Contribution of base-pairing interactions between group II intron fragments during trans-splicing in vivo. RNA 2011, 17, 2212-2221.
41. Plante, I.; Cousineau, B. Restriction for gene insertion within the Lactococcus lactis Ll. LtrB group II intron. RNA 2006, 12, 1980-1992.
42. Guo, H.T.; Zimmerly, S.; Perlman, P.S.; Lambowitz, A.M. Group II intron endonucleases use both RNA and protein subunits for recognition of specific sequences in double-stranded DNA. EMBO J. 1997, 16, 6835-6848.
43. Perutka, J.; Wang, W.J.; Goerlitz, D.; Lambowitz, A.M. Use of computer-designed group II introns to disrupt Escherichia coli DExH/D-box protein and DNA helicase genes. J. Mol. Biol. 2004, 336, 421-439.
44. Belhocine, K.; Mak, A.B.; Cousineau, B. Trans-splicing of the Ll. LtrB group II intron in Lactococcus lactis. Nucleic Acids Res. 2007, 35, 2257-2268.
45. Jones, J.P., III; Kierlin, M.N.; Coon, R.G.; Perutka, J.; Lambowitz, A.M.; Sullenger, B.A. Retargeting mobile group II introns to repair mutant genes. Mol. Ther. 2005, 11, 687-694.
46. Heap, J.T.; Kuehne, S.A.; Ehsaan, M.; Cartman, S.T.; Cooksley, C.M.; Scott, J.C.; Minton, N.P. The ClosTron: Mutagenesis in Clostridium refined and streamlined. J. Microbiol. Methods 2010, 80, 49-55.
47. Yao, J.; Lambowitz, A.A. Gene targeting in gram-negative bacteria by use of a mobile group II intron ("targetron") expressed from a broad-host-range vector. Appl. Environ. Microbiol. 2007, 73, 2735-2743.
48. Frazier, C.L.; San Filippo, J.; Lambowitz, A.M.; Mills, D.A. Genetic manipulation of Lactococcus lactis by using targeted group II introns: Generation of stable insertions without selection. Appl. Environ. Microbiol. 2003, 69, 1121-1128.
49. Mohr, G.; Hong, W.; Zhang, J.; Cui, G.Z.; Yang, Y.; Cui, Q.; Liu, Y.J.; Lambowitz, A.M. A targetron system for gene targeting in thermophiles and its application in Clostridium thermocellum. PLoS One 2013, 8, e69032.
50. Chen, Y.; McClane, B.A.; Fisher, D.J.; Rood, J.I.; Gupta, P. Construction of an alpha toxin gene knockout mutant of Clostridium perfringens type A by use of a mobile group II intron. Appl. Environ. Microbiol. 2005, 71, 7542-7547.
51. Yao, J.; Zhong, J.; Fang, Y.; Geisinger, E.; Novick, R.P.; Lambowitz, A.M. Use of targetrons to disrupt essential and nonessential genes in Staphylococcus aureus reveals temperature sensitivity of Ll. LtrB group II intron splicing. RNA 2006, 12, 1271-1281.
52. Corvaglia, A.R.; François, P.; Hernandez, D.; Perron, K.; Linder, P.; Schrenzel, J. A type III-like restriction endonuclease functions as a major barrier to horizontal gene transfer in clinical Staphylococcus aureus strains. Proc. Natl. Acad. Sci. USA 2010, 107, 11954-11958.
53. King, N.P.; Beatson, S.A.; Totsika, M.; Ulett, G.C.; Alm, R.A.; Manning, P.A.; Schembri, M.A. UafB is a serine-rich repeat adhesin of Staphylococcus saprophyticus that mediates binding to fibronectin, fibrinogen and human uroepithelial cells. Microbiology 2011, 157, 1161-1175.
54. Upadhyay, A.; Srivastava, S. Phenazine-1-carboxylic acid is a more important contributor to biocontrol Fusarium oxysporum than pyrrolnitrin in Pseudomonas fluorescens strain Psd. Microbiol. Res. 2011, 166, 323-335.
55. Malhotra, M.; Srivastava, S. An ipdC gene knock-out of Azospirillum brasilense strain SM and its implications on indole-3-acetic acid biosynthesis and plant growth promotion. Antonie Van Leeuwen. 2008, 93, 425-433.
56. Rodriguez, S.A.; Yu, J.J.; Davis, G.; Arulanandam, B.P.; Klose, K.E. Targeted inactivation of Francisella tularensis genes by group II introns. Appl. Environ. Microbiol. 2008, 74, 2619-2626.
57. Alonzo, F.; Port, G.C.; Cao, M.; Freitag, N.E. The posttranslocation chaperone PrsA2 contributes to multiple facets of Listeria monocytogenes pathogenesis. Infect. Immun. 2009, 77, 2612-2623.
58. Zarschler, K.; Janesch, B.; Zayni, S.; Schäffer, C.; Messner, P. Construction of a gene knockout system for application in Paenibacillus alvei CCM 2051T, exemplified by the S-layer glycan biosynthesis initiation enzyme WsfP. Appl. Environ. Microbiol. 2009, 75, 3077-3085.
59. Steen, J.A.; Steen, J.A.; Harrison, P.; Seemann, T.; Wilkie, I.; Harper, M.; Adler, B.; Boyce, J.D. Fis is essential for capsule production in Pasteurella multocida and regulates expression of other important virulence factors. PLoS Pathog. 2010, 6, e1000750.
60. Park, J.M.; Jang, Y.S.; Kim, T.Y.; Lee, S.Y. Development of a gene knockout system for Ralstonia eutropha H16 based on the broad-host-range vector expressing a mobile group II intron. FEMS Microbiol. Rev. 2010, 309, 193-200.
61. Palonen, E.; Lindström, M.; Karttunen, R.; Somervuo, P.; Korkeala, H. Expression of signal transduction system encoding genes of Yersinia pseudotuberculosis IP32953 at 28 and 3 C. PLoS One 2011, 6, e25063.
62. Palonen, E.; Lindström, M.; Somervuo, P.; Johansson, P.; Björkroth, J.; Korkeala, H. Requirement for RNA helicase CsdA for growth of Yersinia pseudotuberculosis IP32953 at low temperatures. Appl. Environ. Microbiol. 2012, 78, 1298-1301.
63. Maltz, M.A.; Weiss, B.L.; O'Neill, M.; Wu, Y.; Aksoy, S. OmpA-mediated biofilm formation is essential for the commensal bacterium Sodalis glossinidius to colonize the tsetse fly gut. Appl. Environ. Microbiol. 2012, 78, 7760-7768.
64. Akhtar, P.; Khan, S.A. Two independent replicons can support replication of the anthrax toxin-encoding plasmid pXO1 of Bacillus anthracis. Plasmid 2012, 67, 111-117.
65. Zhong, J.; Karberg, M.; Lambowitz, A.M. Targeted and random bacterial gene disruption using a group II intron (targetron) vector containing a retrotransposition-activated selectable marker. Nucleic Acids Res. 2003, 31, 1656-1664.
66. Enyeart, P.J.; Chirieleison, S.M.; Dao, M.N.; Perutka, J.; Quandt, E.M.; Yao, J.; Whitt, J.T.; Keatinge-Clay, A.T.; Lambowitz, A.M.; Ellington, A.D. Generalized bacterial genome editing using mobile group II introns and Cre-lox. Mol. Syst. Biol. 2013, 9, 685.
67. Jinek, M.; Chylinski, K.; Fonfara, I.; Hauer, M.; Doudna, J.A.; Charpentier, E. A Programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 2012, 337, 816-821.
68. Gasiunas, G.; Barrangou, R.; Horvath, P.; Siksnys, V. Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc. Natl. Acad. Sci. USA 2012, 109, E2579-E2586.
69. Hruscha, A.; Krawitz, P.; Rechenberg, A.; Heinrich, V.; Hecht, J.; Haass, C.; Schmid, B. Efficient CRISPR/Cas9 genome editing with low off-target effects in zebrafish. Development 2013, 140, 4982-4987.
70. Chen, K.; Gao, C. Targeted genome modification technologies and their applications in crop improvements. Plant Cell Rep. 2013, doi:10.1007/s00299-013-1539-6.
71. Malina, A.; Mills, J.R.; Cencic, R.; Yan, Y.; Fraser, J.; Schippers, L.M.; Paquet, M.; Dostie, J.; Pelletier, J. Repurposing CRISPR/Cas9 for in situ functional assays. Genes Dev. 2013, 27, 2602-2614.
72. Beumer, K.J.; Carroll, D. Targeted genome engineering techniques in Drosophila. Methods 2014, doi:10.1016/j.ymeth.2013.12.002.
73. Wang, T.; Wei, J.J.; Sabatini, D.M.; Lander, E.S. Genetic screens in human cells using the CRISPR-Cas9 system. Science 2014, 343, 80-84.
74. 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.
75. Wood, A.J.; Lo, T.W.; Zeitler, B.; Pickle, C.S.; Ralston, E.J.; Lee, A.H.; Amora, R.; Miller, J.C.; Leung, E.; Meng, X.D.; et al. Targeted genome editing across species using ZFNs and TALENs. Science 2011, 333, 307-307.
76. Urnov, F.D.; Rebar, E.J.; Holmes, M.C.; Zhang, H.S.; Gregory, P.D. Genome editing with engineered zinc finger nucleases. Nat. Rev. Genet. 2010, 11, 636-646.
77. Gupta, A.; Christensen, R.G.; Rayla, A.L.; Lakshmanan, A.; Stormo, G.D.; Wolfe, S.A. An optimized two-finger archive for ZFN-mediated gene targeting. Nat. Methods 2012, 9, 588-590.
78. Cermak, T.; Doyle, E.L.; Christian, M.; Wang, L.; Zhang, Y.; Schmidt, C.; Baller, J.A.; Somia, N.V.; Bogdanove, A.J.; Voytas, D.F. Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Res. 2011, 39, e82.
79. Curtin, S.J.; Voytas, D.F.; Stupar, R.M. Genome engineering of crops with designer nucleases. Plant Genome 2012, 5, 42-50.
80. Mussolino, C.; Cathomen, T. TALE nucleases: Tailored genome engineering made easy. Curr. Opin. Biotechnol. 2012, 23, 644-650.
81. Christian, M.L.; Demorest, Z.L.; Starker, C.G.; Osborn, M.J.; Nyquist, M.D.; Zhang, Y.; Carlson, D.F.; Bradley, P.; Bogdanove, A.J.; Voytas, D.F. Targeting G with TAL effectors: A comparison of activities of TALENs constructed with NN and NK repeat variable di-Residues. PLoS One 2012, 7, e45383.
82. Li, T.; Huang, S.; Zhao, X.F.; Wright, D.A.; Carpenter, S.; Spalding, M.H.; Weeks, D.P.; Yang, B. Modularly assembled designer TAL effector nucleases for targeted gene knockout and gene replacement in eukaryotes. Nucleic Acids Res. 2011, 39, 6315-6325.
83. Good, L.; Nielsen, P.E. Antisense inhibition of gene expression in bacteria by PNA targeted to mRNA. Nat. Biotechnol. 1998, 16, 355-358.
84. Good, L.; Awasthi, S.K.; Dryselius, R.; Larsson, O.; Nielsen, P.E. Bactericidal antisense effects of peptide-PNA conjugates. Nat. Biotechnol. 2001, 19, 360-364.
85. Lundin, K.E.; Good, L.; Strömberg, R.; Gräslund, A.; Smith, C.I.E. Biological activity and biotechnological aspects of peptide nucleic acid. Adv. Genet. 2006, 56, 1-51.
86. Hansen, M.E.; Bentin, T.; Nielsen, P.E. High-affinity triplex targeting of double stranded DNA using chemically modified peptide nucleic acid oligomers. Nucleic Acids Res. 2009, 37, 4498-4507.
87. McNeer, N.A.; Chin, J.Y.; Schleifman, E.B.; Fields, R.J.; Glazer, P.M.; Saltzman, W.M. Nanoparticles deliver triplex-forming PNAs for site-specific genomic recombination in CD34+ human hematopoietic progenitors. Mol. Ther. 2011, 19, 172-180.
88. Schleifman, E.B.; Bindra, R.; Leif, J.; del Campo, J.; Rogers, F.A.; Uchil, P.; Kutsch, O.; Shultz, L.D.; Kumar, P.; Greiner, D.L.; et al. Targeted disruption of the CCR5 gene inhuman hematopoietic stem cells stimulated by peptide nucleic acids. Chem. Biol. 2011, 18, 1189-1198.
89. Osiak, A.; Radecke, F.; Guhl, E.; Radecke, S.; Dannemann, N.; Lütge, F.; Glage, S.; Rudolph, C.; Cantz, T.; Schwarz, K.; et al. Selection-independent generation of gene knockout mouse embryonic stem cells using zinc-finger nucleases. PLoS One 2011, 6, e28911.
90. Vos, M.; Didelot, X. A comparison of homologous recombination rates in bacteria and archaea. ISME J. 2009, 3, 199-208.
91. Cradick, T.J.; Ambrosini, G.; Iseli, C.; Bucher, P.; McCaffrey, A.P. ZFN-site searches genomes for zinc finger nuclease target sites and off-target sites. BMC Bioinf. 2011, 12, 152.
92. Sawitzke, J.A.; Thomason, L.C.; Costantino, N.; Bubunenko, M.; Datta, S.; Court, D.L. Recombineering: In vivo genetic engineering in E. coli, S. enterica, and beyond. Methods Enzymol. 2007, 421, 171-199.
93. Nakashima, N.; Goh, S.; Good, L.; Tamura, T. Multiple-gene silencing using antisense RNAs in Escherichia coli. Methods Mol. Biol. 2012, 815, 307-319.
94. Nakashima, N.; Tamura, T. Conditional gene silencing of multiple genes with antisense RNAs and generation of a mutator strain of Escherichia coli. Nucleic Acids Res. 2009, 37, e103.
95. Nakashima, N.; Tamura, T.; Good, L. Paired termini stabilize antisense RNAs and enhance conditional gene silencing in Escherichia coli. Nucleic Acids Res. 2006, 34, e138.
96. Brantl, S. Antisense-RNA regulation and RNA interference. Biochim. Biophys. Acta 2002, 1575, 15-25.
97. Sharma, V.; Yamamura, A.; Yokobayashi, Y. Engineering artificial small RNAs for conditional gene silencing in Escherichia coli. ACS Synth. Biol. 2012, 1, 6-13.
98. Stefan, A.; Schwarz, F.; Bressanin, D.; Hochkoeppler, A. Shine-Dalgarno sequence enhances the efficiency of lacZ repression by artificial anti-lac antisense RNAs in Escherichia coli. J. Biosci. Bioeng. 2010, 110, 523-528.
99. Goh, S.; Boberek, J.M.; Nakashima, N.; Stach, J.; Good, L. Concurrent growth rate and transcript analyses reveal essential gene stringency in Escherichia coli. PLoS One 2009, 4, e6061.
100. Pestka, S.; Daugherty, B.L.; Jung, V.; Hotta, K.; Pestka, R.K. Anti-mRNA; specific inhibition of translation of single mRNA molecules. Proc. Natl. Acad. Sci. USA 1984, 81, 7525-7528.
101. Srivastava, R.; Cha, H.J.; Peterson, M.S.; Bentley, W.E. Antisense downregulation of σ32 as a transient metabolic controller in Escherichia coli: Effects on yield of active organophosphorus hydrolase. Appl. Environ. Microbiol. 2000, 66, 4366-4371.
102. Krylov, A.A.; Airich, L.G.; Kiseleva, E.M.; Minaeva, N.I.; Biryukova, I.V.; Mashko, S.V. Conditional silencing of the Escherichia coli pykF gene results from artificial convergent transcription protected from rho-dependent termination. J. Mol. Microbiol. Biotechnol. 2010, 18, 1-13.
103. Chen, H.; Ferbeyre, G.; Cedergren, R. Efficient hammerhead ribozyme and antisense RNA targeting in a slow ribosome Escherichia coli mutant. Nat. Biotechnol. 1997, 15, 432-435.
104. Kim, J.Y.H.; Cha, H.J. Down-regulation of acetate pathway through antisense strategy in Escherichia coli: Improved foreign protein production. Biotechnol. Bioeng. 2003, 83, 841-853.
105. Boberek, J.M.; Stach, J.; Good, L. Genetic evidence for inhibition of bacterial division protein FtsZ by berberine. PLoS One 2010, 5, e13745.
106. Meng, J.; Kanzaki, G.; Meas, D.; Lam, C.K.; Crummer, H.; Tain, J.; Xu, H.H. A genome-wide inducible phenotypic screen identifies antisense RNA constructs silencing Escherichia coli essential genes. FEMS Microbiol. Lett. 2012, 329, 45-53.
107. Setoyama, D.; Ito, R.; Takagi, Y.; Sekiguchi, M. Molecular actions of Escherichia coli MutT for control of spontaneous mutagenesis. Mutat. Res. 2011, 707, 9-14.
108. Ji, Y.D.; Zhang, B.; van Horn, S.F.; Warren, P.; Woodnutt, G.; Burnham, M.K.R.; Rosenberg, M. Identification of critical staphylococcal genes using conditional phenotypes generated by antisense RNA. Science 2001, 293, 2266-2269.
109. Desai, R.P.; Papoutsakis, E.T. Antisense RNA strategies for metabolic engineering of Clostridium acetobutylicum. Appl. Environ. Microbiol. 1999, 65, 936-945.
110. Biedendieck, R.; Malten, M.; Barg, H.; Bunk, B.; Martens, J.H.; Deery, E.; Leech, H.; Warren, M.J.; Jahn, D. Metabolic engineering of cobalamin (vitamin B12) production in Bacillus megaterium. Microb. Biotechnol. 2010, 3, 24-37.
111. Uguru, G.C.; Mondhe, M.; Goh, S.; Hesketh, A.; Bibb, M.J. Synthetic RNA silencing of actinorhodin biosynthesis in Streptomyces coelicolor A3(2). PLoS One 2013, 8, e67509.
112. Bouazzaoui, K.; LaPointe, G. Use of antisense RNA to modulate glycosyltransferase gene expression and exopolysaccharide molecular mass in Lactobacillus rhamnosus. J. Microbiol. Methods 2006, 65, 216-225.
113. Kaur, P.; Agarwal, S.; Datta, S. Delineating bacteriostatic and bactericidal targets in Mycobacteria using IPTG inducible antisense expression. PLoS One 2009, 4, e5923.
114. Parish, T.; Stoker, N.G. Development and use of a conditional antisense mutagenesis system in Mycobacteria. FEMS Microbiol. Lett. 1997, 154, 151-157.
115. Thomason, M.K.; Storz, G. Bacterial antisense RNAs: How many are there, and what are they doing? Annu. Rev. Genet. 2010, 44, 167-188.
116. Nakashima, N.; Ohno, S.; Yoshikawa, K.; Shimizu, H.; Tamura, T. A vector library for silencing central carbon metabolism genes with antisense RNAs in Escherichia coli. Appl. Environ. Microbiol. 2014, 80, 564-573.
117. Na, D.; Yoo, S.M.; Chung, H.; Park, H.; Park, J.H.; Lee, S.Y. Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs. Nat. Biotechnol. 2013, 31, 170-174.
118. Stach, J.E.M.; Good, L. Synthetic RNA silencing in bacteria-antimicrobial discovery and resistance breaking. Front. Microbiol. 2011, 2, 185.
119. Bistué, A.; Martín, F.A.; Vozza, N.; Ha, H.; Joaquín, J.C.; Zorreguieta, A.; Tolmasky, M.E. Inhibition of aac(6')-Ib-mediated amikacin resistance by nuclease-resistant external guide sequences in bacteria. Proc. Natl. Acad. Sci. USA 2009, 106, 13230-13235.
120. Rasmussen, L.C.V.; Sperling-Petersen, H.U.; Mortensen, K.K. Hitting bacteria at the heart of the central dogma: Sequence-specific inhibition. Microb. Cell Fact. 2007, 6, 24.