A Mimicking-of-DNA-Methylation-Patterns Pipeline for Overcoming the Restriction Barrier of Bacteria

PLoS Genetics

Volumn 8, Issue 9, 2012, Pages

  Zhang, Guoqiang ^a   Wang, Wenzhao ^a   Deng, Aihua ^a   Sun, Zhaopeng ^a   Zhang, Yun ^a   Liang, Yong ^a   Che, Yongsheng ^b   Wen, Tingyi ^a  

^a INSTITUTE OF MICROBIOLOGY   (China)

^b BEIJING INSTITUTE OF PHARMACOLOGY AND TOXICOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; DNA METHYLTRANSFERASE; GREEN FLUORESCENT PROTEIN; URACIL PHOSPHORIBOSYLTRANSFERASE;

AMINO ACID SEQUENCE; ARTICLE; BACILLUS AMYLOLIQUEFACIENS; BACILLUS CEREUS; BACTERIAL STRAIN; BACTERIUM TRANSFORMATION; DNA METHYLATION; DNA MODIFICATION; DOT HYBRIDIZATION; ENZYME ASSAY; ENZYME SPECIFICITY; ESCHERICHIA COLI; FUNCTIONAL GENOMICS; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MOLECULAR CLONING; NITROBACTER; NITROBACTER HAMBURGENSIS; NONHUMAN; OPERON; PLASMID; PROTEIN ASSEMBLY; PROTEIN EXPRESSION; SACCHAROMYCES CEREVISIAE; SOUTHERN BLOTTING; STRAIN DIFFERENCE;

BACILLUS; BACTERIA; DNA METHYLATION; DNA RESTRICTION ENZYMES; DNA RESTRICTION-MODIFICATION ENZYMES; DNA-CYTOSINE METHYLASES; ESCHERICHIA COLI; NITROBACTER; SACCHAROMYCES CEREVISIAE; TRANSFORMATION, GENETIC;

BACILLUS AMYLOLIQUEFACIENS; BACILLUS CEREUS; BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; NEGIBACTERIA; NITROBACTER HAMBURGENSIS; POSIBACTERIA; SACCHAROMYCES CEREVISIAE;

EID: 84866950194     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1002987     Document Type: Article

References (51)

1. Bottone EJ, (2010) Bacillus cereus, a volatile human pathogen. Clin Microbiol Rev 23: 382-398.
2. Salter SJ, (2011) You cannot B. cereus. Nat Rev Micro 9: 83.
3. Huo Y-X, Cho KM, Rivera JGL, Monte E, Shen CR, et al. (2011) Conversion of proteins into biofuels by engineering nitrogen flux. Nat Biotech 29: 346-351.
4. Nawy T, (2012) Non-model organisms. Nat Meth 9: 37.
5. Roberts RJ, Vincze T, Posfai J, Macelis D, (2010) REBASE-a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res 38: D234-D236.
6. Roberts RJ, Belfort M, Bestor T, Bhagwat AS, Bickle TA, et al. (2003) A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Nucleic Acids Res 31: 1805-1812.
7. Labrie SJ, Samson JE, Moineau S, (2010) Bacteriophage resistance mechanisms. Nat Rev Micro 8: 317-327.
8. Starkenburg SR, Arp DJ, Bottomley PJ, (2008) d-Lactate metabolism and the obligate requirement for CO2 during growth on nitrite by the facultative lithoautotroph Nitrobacter hamburgensis. Microbiology 154: 2473-2481.
9. Arp DJ, Bottomley PJ, (2006) Nitrifiers: more than 100 years from isolation to genome sequences. Microbe 1: 229-234.
10. Starkenburg SR, Larimer FW, Stein LY, Klotz MG, Chain PSG, et al. (2008) Complete genome sequence of Nitrobacter hamburgensis X14 and comparative genomic analysis of species within the genus Nitrobacter. Appl Environ Microbiol 74: 2852-2863.
11. Rasko DA, Ravel J, Økstad OA, Helgason E, Cer RZ, et al. (2004) The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1. Nucleic Acids Res 32: 977-988.
12. Arnaud M, Chastanet A, Débarbouillé M, (2004) New vector for efficient allelic replacement in naturally nontransformable, low-GC-content, Gram-positive bacteria. Appl Environ Microbiol 70: 6887-6891.
13. Lindbäck T, Kolstø A-B, (1997) A Bacillus cereus member of the SNF2 family. Microbiology 143: 171-174.
14. Lindbäck T, Økstad OA, Rishovd A-L, Kolstø A-B, (1999) Insertional inactivation of hblC encoding the L2 component of Bacillus cereus ATCC 14579 haemolysin BL strongly reduces enterotoxigenic activity, but not the haemolytic activity against human erythrocytes. Microbiology 145: 3139-3146.
15. Xu S-y, Nugent RL, Kasamkattil J, Fomenkov A, Gupta Y, et al. (2011) Characterization of Type II and III restriction-modification systems from Bacillus cereus strains ATCC 10987 and ATCC 14579. J Bacteriol 194: 49-60.
16. Zhang G, Deng A, Xu Q, Liang Y, Chen N, et al. (2011) Complete genome sequence of Bacillus amyloliquefaciens TA208, a strain for industrial production of guanosine and ribavirin. J Bacteriol 193: 3142-3143.
17. Zhang G, Bao P, Zhang Y, Deng A, Chen N, et al. (2011) Enhancing electro-transformation competency of recalcitrant Bacillus amyloliquefaciens by combining cell-wall weakening and cell-membrane fluidity disturbing. Anal Biochem 409: 130-137.
18. Kong H, Lin LF, Porter N, Stickel S, Byrd D, et al. (2000) Functional analysis of putative restriction-modification system genes in the Helicobacter pylori J99 genome. Nucleic Acids Res 28: 3216-3223.
19. Zhou H, Wang Y, Yu Y, Bai T, Chen L, et al. (2012) A non-restricting and non-methylating Escherichia coli strain for DNA cloning and high-throughput conjugation to Streptomyces coelicolor. Curr Microbiol 64: 185-190.
20. Marinus MG, (2010) DNA methylation and mutator genes in Escherichia coli K-12. Mutat Res 705: 71-76.
21. Le T, Kim K-P, Fan G, Faull KF, (2011) A sensitive mass spectrometry method for simultaneous quantification of DNA methylation and hydroxymethylation levels in biological samples. Anal Biochem 412: 203-209.
22. Boye E, Løbner-Olesen A, (1990) The role of dam methyltransferase in the control of DNA replication in E. coli. Cell 62: 981-989.
23. Hegna IK, Bratland H, Kolst A-B, (2001) BceS1, a new addition to the type III restriction and modification family. FEMS Microbiol Lett 202: 189-193.
24. Turgeon N, Laflamme C, Ho J, Duchaine C, (2006) Elaboration of an electroporation protocol for Bacillus cereus ATCC 14579. J Microbiol Methods 67: 543-548.
25. Fazzini MM, Schuch R, Fischetti VA, (2010) A novel spore protein, ExsM, regulates formation of the exosporium in Bacillus cereus and Bacillus anthracis and affects spore size and shape. J Bacteriol 192: 4012-4021.
26. Fabret C, Dusko Ehrlich S, Noirot P, (2002) A new mutation delivery system for genome-scale approaches in Bacillus subtilis. Mol Microbiol 46: 25-36.
27. Carsiotis M, Khanna S (1989) Genetic engineering of enhanced microbial nitrification. Cincinnati, OH: US Environmental Protection Agency, Risk Reduction Engineering Laboratory.
28. Sayavedra-Soto LA, Stein LY, (2011) Genetic transformation of ammonia-oxidizing bacteria. Methods Enzymol 486: 389-402.
29. Clark TA, Murray IA, Morgan RD, Kislyuk AO, Spittle KE, et al. (2012) Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing. Nucleic Acids Res 40: e29.
30. Drozdz M, Piekarowicz A, Bujnicki JM, Radlinska M, (2012) Novel non-specific DNA adenine methyltransferases. Nucleic Acids Res 40: 2119-2130.
31. Szomolányi É, Kiss A, Venetianer P, (1980) Cloning the modification methylase gene of Bacillus sphaericus R in Escherichia coli. Gene 10: 219-225.
32. Donahue JP, Israel DA, Peek RM, Blaser MJ, Miller GG, (2000) Overcoming the restriction barrier to plasmid transformation of Helicobacter pylori. Mol Microbiol 37: 1066-1074.
33. Groot MN, Nieboer F, Abee T, (2008) Enhanced transformation efficiency of recalcitrant Bacillus cereus and Bacillus weihenstephanensis isolates upon in vitro methylation of plasmid DNA. Appl Environ Microbiol 74: 7817-7820.
34. Van der Rest ME, Lange C, Molenaar D, (1999) A heat shock following electroporation induces highly efficient transformation of Corynebacterium glutamicum with xenogeneic plasmid DNA. Appl Microbiol Biotechnol 52: 541-545.
35. Dong H, Zhang Y, Dai Z, Li Y, (2010) Engineering Clostridium strain to accept unmethylated DNA. PLoS ONE 5: e9038 doi:10.1371/journal.pone.0009038.
36. Veiga H, Pinho MG, (2009) Inactivation of the SauI Type I restriction-modification system is not sufficient to generate Staphylococcus aureus strains capable of efficiently accepting foreign DNA. Appl Environ Microbiol 75: 3034-3038.
37. Marrero R, Welkos SL, (1995) The transformation frequency of plasmids into Bacillus anthracis is affected by adenine methylation. Gene 152: 75-78.
38. Sitaraman R, Leppla SH, (2012) Methylation-dependent DNA restriction in Bacillus anthracis. Gene 494: 44-50.
39. Okibe N, Suzuki N, Inui M, Yukawa H, (2011) Efficient markerless gene replacement in Corynebacterium glutamicum using a new temperature-sensitive plasmid. J Microbiol Methods 85: 155-163.
40. O'Connell Motherway M, O'Driscoll J, Fitzgerald GF, Van Sinderen D, (2009) Overcoming the restriction barrier to plasmid transformation and targeted mutagenesis in Bifidobacterium breve UCC2003. Microbial Biotechnology 2: 321-332.
41. Rego ROM, Bestor A, Rosa PA, (2011) Defining the plasmid-borne restriction-modification systems of the lyme disease spirochete Borrelia burgdorferi. J Bacteriol 193: 1161-1171.
42. Raleigh EA, Murray NE, Revel H, Blumenthal RM, Westaway D, et al. (1988) McrA and McrB restriction phenotypes of some E. coli strains and implications for gene cloning. Nucleic Acids Res 16: 1563-1575.
43. Waite-Rees PA, Keating CJ, Moran LS, Slatko BE, Hornstra LJ, et al. (1991) Characterization and expression of the Escherichia coli Mrr restriction system. J Bacteriol 173: 5207-5219.
44. Morgan RD, Dwinell EA, Bhatia TK, Lang EM, Luyten YA, (2009) The MmeI family: type II restriction-modification enzymes that employ single-strand modification for host protection. Nucleic Acids Res 37: 5208-5221.
45. Marinus MG, Casadesus J, (2009) Roles of DNA adenine methylation in host-pathogen interactions: mismatch repair, transcriptional regulation, and more. FEMS Microbiol Rev 33: 488-503.
46. Walkinshaw MD, Taylor P, Sturrock SS, Atanasiu C, Berge T, et al. (2002) Structure of Ocr from bacteriophage T7, a protein that mimics B-form DNA. Mol Cell 9: 187-194.
47. Patrick S, Houston S, Thacker Z, Blakely GW, (2009) Mutational analysis of genes implicated in LPS and capsular polysaccharide biosynthesis in the opportunistic pathogen Bacteroides fragilis. Microbiology 155: 1039-1049.
48. Xu T, Yao F, Zhou X, Deng Z, You D, (2010) A novel host-specific restriction system associated with DNA backbone S-modification in Salmonella. Nucleic Acids Res 38: 7133-7141.
49. Shao Z, Zhao H, (2009) DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways. Nucleic Acids Res 37: e16.
50. Daniel Gietz R, Woods RA, (2002) Transformation of yeast by lithium acetate/single-stranded carrier DNA/polyethylene glycol method. Methods Enzymol 350: 87-96.
51. Robzyk K, Kassir Y, (1992) A simple and highly efficient procedure for rescuing autonomous plasmids from yeast. Nucleic Acids Res 20: 3790.