Phosphorothioate DNA as an antioxidant in bacteria

Nucleic Acids Research

Volumn 40, Issue 18, 2012, Pages 9115-9124

  Xie, Xinqiang ^a   Liang, Jingdan ^a   Pu, Tianning ^a   Xu, Fei ^a   Yao, Fen ^a   Yang, Yan ^a   Zhao, Yi Lei ^a   You, Delin ^a   Zhou, Xiufen ^a   Deng, Zixin ^a   Wang, Zhijun ^a  

^a Shanghai Jiao Tong University   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIOXIDANT; BACTERIAL DNA; GENOMIC DNA; HYDROGEN PEROXIDE; PHOSPHOROTHIOIC ACID; SULFUR;

ARTICLE; BACTERIAL GENE; BACTERIAL GROWTH; CHEMICAL BINDING; CONTROLLED STUDY; DNA CLEAVAGE; DNA DEGRADATION; DNA MODIFICATION; DOUBLE STRANDED DNA BREAK; DPTB GENE; GENE CLUSTER; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HOST PATHOGEN INTERACTION; HYDROLYSIS; IN VITRO STUDY; IN VIVO STUDY; MASS SPECTROMETRY; MICROBIAL ACTIVITY; MUTANT; NONHUMAN; OXIDATION REDUCTION REACTION; PRIORITY JOURNAL; SALMONELLA ENTERICA; STRUCTURE ANALYSIS; WILD TYPE;

ANTIOXIDANTS; DNA BREAKS, DOUBLE-STRANDED; DNA CLEAVAGE; DNA, BACTERIAL; HYDROGEN PEROXIDE; OXIDANTS; OXIDATION-REDUCTION; PERACETIC ACID; PHOSPHOROTHIOATE OLIGONUCLEOTIDES; REDUCING AGENTS; SALMONELLA ENTERICA; SULFUR; THIONUCLEOTIDES;

EID: 84867559698     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks650     Document Type: Article

References (43)

1. Liang,J.D., Wang,Z.J., He,X.Y., Li,J.L., Zhou,X.F. and Deng,Z.X. (2007) DNA modification by sulfur: Analysis of the sequence recognition specificity surrounding the modification sites. Nucleic Acids Res., 35, 2944-2954.
2. Wang,L., Chen,S., Xu,T., Taghizadeh,K., Wishnok,J.S., Zhou,X., You,D., Deng,Z. and Dedon,P.C. (2007) Phosphorothioation of DNA in bacteria by dnd genes. Nat. Chem. Biol., 3, 709-710. (Pubitemid 47609115)
3. Xu,T.G., Liang,J.D., Chen,S., Wang,L.R., He,X.Y., You,D.L., Wang,Z.J., Li,A.Y., Xu,Z.L., Zhou,X.F. et al. (2009) DNA phosphorothioation in Streptomyces lividans: Mutational analysis of the dnd locus. BMC Microbiol., 9, 41.
4. Zhou,X.F., Deng,Z.X., Firmin,J.L., Hopwood,D.A. and Kieser,T. (1988) Site-specific degradation of Streptomyces lividans DNA during electrophoresis in buffers contaminated with ferrous iron. Nucleic Acids Res., 16, 4341-4352.
5. Zhou,X., He,X., Liang,J., Li,A., Xu,T., Kieser,T., Helmann,J.D. and Deng,Z. (2005) A novel DNA modification by sulphur. Mol. Microbiol., 57, 1428-1438. (Pubitemid 41176533)
6. Wang,L., Chen,S., Vergin,K.L., Giovannoni,S.J., Chan,S.W., DeMott,M.S., Taghizadeh,K., Cordero,O.X., Cutler,M., Timberlake,S. et al. (2011) DNA phosphorothioation is widespread and quantized in bacterial genomes. Proc. Natl Acad. Sci. USA, 108, 2963-2968.
7. He,X., Ou,H.Y., Yu,Q., Zhou,X., Wu,J., Liang,J., Zhang,W., Rajakumar,K. and Deng,Z. (2007) Analysis of a genomic island housing genes for DNA S-modification system in Streptomyces lividans 66 and its counterparts in other distantly related bacteria. Mol. Microbiol., 65, 1034-1048. (Pubitemid 47221081)
8. Ou,H.Y., He,X., Shao,Y., Tai,C., Rajakumar,K. and Deng,Z. (2009) dndDB: A database focused on phosphorothioation of the DNA backbone. PLoS One, 4,-e5132.
9. Liu,G.A., Ou,H.Y., Wang,T., Li,L., Tan,H.R., Zhou,X.F., Rajakumar,K., Deng,Z.X. and He,X.Y. (2010) Cleavage of phosphorothioated DNA and methylated DNA by the type IV restriction endonuclease ScoMcrA. PLos Genet., 6.,-e1001253.
10. Xu,T.G., Yao,F., Zhou,X.F., Deng,Z.X. and You,D.L. (2010) A novel host-specific restriction system associated with DNA backbone S-modification in Salmonella. Nucleic Acids Res., 38, 7133-7141.
11. Ray,T., Weaden,J. and Dyson,P. (1992) Tris-dependent site-specific cleavage of Streptomyces lividans DNA. FEMS Microbiol. Lett., 96, 247-252.
12. Ray,T., Mills,A. and Dyson,P. (1995) Tris-dependent oxidative DNA strand scission during electrophoresis. Electrophoresis, 16, 888-894.
13. Sambrook,J. (2001) Molecular Cloning: A Laboratory Manual. 3rd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
14. O'Reilly,L.C. (2011) A method for overcoming DNA degradation during PFGE for Serratia marcescens. J. Microbiol. Methods, 85, 173-174.
15. Miled-Bennour,R.,-ells,T.C., Pagotto,F.J., Farber,J.M., Kerouanton,A., Meheut,T., Colin,P., Joosten,H., Leclercq,A. and Besse,N.G. (2010) Genotypic and phenotypic characterisation of a collection of Cronobacter (Enterobacter sakazakii) isolates. Int. J. Food Microbiol., 139, 116-125.
16. Ribeiro,R.L., Machry,L., Brazil,J.M., Ramos,T.M., Avelar,K.E. and Pereira,M.M. (2009) Technical improvement to prevent DNA degradation of Leptospira spp. in pulsed field gel electrophoresis. Lett. Appl. Microbiol., 49, 289-291.
17. Bosilevac,J.M., Guerini,M.N., Kalchayanand,N. and Koohmaraie,M. (2009) Prevalence and characterization of salmonellae in commercial ground beef in the United States. Appl. Environ. Microbiol., 75, 1892-1900.
18. Banerjee,S.K. and Farber,J.M. (2009) Susceptibility of Vibrio parahaemolyticus to tris-dependent DNA degradation during pulsed-field gel electrophoresis. J. Clin. Microbiol., 47, 870-871.
19. Leclair,D., Pacyotto,F., Farber,J.M., Cadieux,B. and Austin,J.W. (2006) Comparison of DNA fingerprinting methods for use in investigation of type E botulism outbreaks in the Canadian arctic. J. Clin. Microbiol., 44, 1635-1644. (Pubitemid 43726249)
20. Ciofu,O., Riis,B., Pressler,T., Poulsen,H.E. and Hoiby,N. (2005) Occurrence of hypermutable Pseudomonas aeruginosa in cystic fibrosis patients is associated with the oxidative stress caused by chronic lung inflammation. Antimicrobial Agents Chemother., 49, 2276-2282. (Pubitemid 40734454)
21. Zhang,Y.S., Yakrus,M.A., Graviss,E.A., Williams-Bouyer,N., Turenne,C., Kabani,A. and Wallace,R.J. (2004) Pulsed-field gel electrophoresis study of Mycobacterium abscessus isolates previously affected by DNA degradation. J. Clin. Microbiol., 42, 5582-5587. (Pubitemid 39664340)
22. Murase,T., Nagato,M., Shirota,K., Katoh,H. and Otsuki,K. (2004) Pulsed-field gel electrophoresis-based subtyping of DNA degradation-sensitive Salmonella enterica subsp enterica serovar Livingstone and serovar Cerro isolates obtained from a chicken layer farm. Vet. Microbiol., 99, 139-143. (Pubitemid 38281246)
23. Silbert,S., Boyken,L., Hollis,R.J. and Pfaller,M.A. (2003) Improving typeability of multiple bacterial species using pulsed-field gel electrophoresis and thiourea. Diagn. Micr. Infec. Dis., 47, 619-621. (Pubitemid 38058290)
24. Hata,M., Suzuki,M., Matsumoto,M., Takahashi,M., Yamazaki,M., Hiramatsu,R., Matsui,H., Sakae,K., Suzuki,Y. and Miyazaki,Y. (2003) A new clonal line of Salmonella Saintpaul having emerged and prevailed since 1999 in Aichi, Japan. Jpn J. Infect. Dis., 56, 77-79. (Pubitemid 36926785)
25. Liesegang,A. and Tschape,H. (2002) Modified pulsed-field gel electrophoresis method for DNA degradation-sensitive Salmonella enterica and Escherichia coli strains. IJMM, 291, 645-648. (Pubitemid 34294499)
26. Koort,J.M.K., Lukinmaa,S., Rantala,M., Unkila,E. and Siitonen,A. (2002) Technical improvement to prevent DNA degradation of enteric pathogens in pulsed-field gel electrophoresis. J. Clin. Microbiol., 40, 3497-3498. (Pubitemid 34977477)
27. Klaassen,C.H.W., de Valk-Van Haren,H.A. and Horrevorts,A.M. (2002) Pulsed-field gel electrophoresis can yield DNA fingerprints of degradation-susceptible Clostridium difficile strains -Reply. J. Clin. Microbiol., 40, 3547-3547.
28. Inglis,T.J.J., O'Reilly,L., Foster,N., Clair,A. and Sampson,J. (2002) Comparison of rapid, automated ribotyping and DNA macrorestriction analysis of Burkholderia pseudomallei. J. Clin. Microbiol., 40, 3198-3203. (Pubitemid 34977428)
29. Fawley,W.N. and Wilcox,M.H. (2002) Pulsed-field gel electrophoresis can yield DNA fingerprints of degradation-susceptible Clostridium difficile strains. J. Clin. Microbiol., 40, 3546-3547. (Pubitemid 34977494)
30. Romling,U. and Tummler,B. (2000) Achieving 100% typeability of Pseudomonas aeruginosa by pulsed-field gel electrophoresis. J. Clin. Microbiol., 38, 464-465. (Pubitemid 30043347)
31. Corkill,J.E., Graham,R., Hart,C.A. and Stubbs,S. (2000) Pulsed-field gel electrophoresis of degradation-sensitive DNAs from Clostridium difficile PCR ribotype 1 strains. J. Clin. Microbiol., 38, 2791-2792. (Pubitemid 30485177)
32. Boybek,A., Ray,T.D.,-evans,M.C. and Dyson,P.J. (1998) Novel site-specific DNA modification in Streptomyces: Analysis of preferred intragenic modification sites present in a 5.7 kb amplified DNA sequence. Nucleic Acids Res., 26, 3364-3371. (Pubitemid 28321400)
33. Mongkolsuk,S. and Helmann,J.D. (2002) Regulation of inducible peroxide stress responses. Mol. Microbiol., 45, 9-15. (Pubitemid 35025929)
34. Antelmann,H. and Helmann,J.D. (2011) Thiol-based redox switches and gene regulation. Antioxid. Redox. Sign., 14, 1049-1063.
35. Faulkner,M.J. and Helmann,J.D. (2011) Peroxide stress elicits adaptive changes in bacterial metal ion homeostasis. Antioxid. Redox. Sign., 15, 175-189.
36. Newton,G.L., Rawat,M., La Clair,J.J., Jothivasan,V.K., Budiarto,T., Hamilton,C.J., Claiborne,A., Helmann,J.D. and Fahey,R.C. (2009) Bacillithiol is an antioxidant thiol produced in Bacilli. Nat. Chem. Biol., 5, 625-627.
37. Holmgren,A., Ohlsson,I. and Grankvist,M.L. (1978) Thiroedoxin from Escherichia coli. Radioimmunological and enzymatic determinations in wild type cells and mutants defective in phage T7 DNA replication. J. Biol. Chem., 253, 430-436. (Pubitemid 8267668)
38. Allocati,N., Federici,L., Masulli,M. and Di Ilio,C. (2009) Glutathione transferases in bacteria. FEBS J., 276, 58-75.
39. Allocati,N., Federici,L., Masulli,M. and Di Ilio,C. (2012) Distribution of glutathione transferases in Gram-positive bacteria and Archaea. Biochimie, 94, 588-596.
40. Masip,L., Veeravalli,K. and Georgiou,G. (2006) The many faces of glutathione in bacteria. Antioxid. Redox. Sig., 8, 753-762. (Pubitemid 44036494)
41. Nordberg,J. and Arner,E.S. (2001) Reactive oxygen species, antioxidants, and the mammalian thioredoxin system. Free Rad. Biol. Med., 31, 1287-1312. (Pubitemid 33145299)
42. Park,S., You,X. and Imlay,J.A. (2005) Substantial DNA damage from submicromolar intracellular hydrogen peroxide detected in Hpx-mutants of Escherichia coli. Proc. Natl Acad. Sci. USA, 102, 9317-9322. (Pubitemid 40923561)
43. Imlay,J.A. and Linn,S. (1988) DNA damage and oxygen radical toxicity. Science, 240, 1302-1309.