Regulation of DNA phosphorothioate modification in Salmonella enterica by DndB

Scientific Reports

Volumn 5, Issue , 2015, Pages

  He, Wei ^a   Huang, Teng ^a,b   Tang, You ^a   Liu, Yanhua ^c   Wu, Xiaolin ^a   Chen, Si ^a   Chan, Wan ^d   Wang, Yajie ^a,b   Liu, Xiaoyun ^c   Chen, Shi ^a   Wang, Lianrong ^a  

^a WUHAN UNIVERSITY   (China)

^b HUBEI UNIVERSITY OF MEDICINE   (China)

^c PEKING UNIVERSITY   (China)

^d HONG KONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Hong Kong)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; BACTERIAL PROTEIN; PROTEIN BINDING; PROTEOME;

BACTERIAL GENE; BINDING SITE; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; INVERTED REPEAT; METABOLISM; MUTATION; NUCLEOTIDE MOTIF; NUCLEOTIDE SEQUENCE; OPERON; PROTEOMICS; SALMONELLA ENTERICA;

BACTERIAL PROTEINS; BASE SEQUENCE; BINDING SITES; DNA, BACTERIAL; GENE EXPRESSION REGULATION, BACTERIAL; GENES, BACTERIAL; INVERTED REPEAT SEQUENCES; MUTATION; NUCLEOTIDE MOTIFS; OPERON; PROTEIN BINDING; PROTEOME; PROTEOMICS; SALMONELLA ENTERICA; TRANSCRIPTION, GENETIC;

EID: 84937802514     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep12368     Document Type: Article

References (36)

1. Wang, L. et al. Phosphorothioation of DNA in bacteria by dnd genes. Nat Chem Biol 3, 709-10 (2007).
2. He, X. et al. 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, 1034-48 (2007).
3. Zhou, X. et al. A novel DNA modification by sulphur. Mol Microbiol 57, 1428-38 (2005).
4. An, X. et al. A novel target of IscS in Escherichia coli: participating in DNA phosphorothioation. PLoS One 7, e51265 (2012).
5. Wang, L., Chen, S. & Deng, Z. Phosphorothioation: An unusual post-replicative modification on the DNA backbone. in DNA Replication - Current Advances (ed. Seligmann, H.) (Intech, Rijeka, Croatia, 2011).
6. Gan, R. et al. DNA phosphorothioate modifications influence the global transcriptional response and protect DNA from doublestranded breaks. Sci Rep 4, 6642 (2014).
7. Xu, T., Yao, F., Zhou, X., Deng, Z. & You, D. A novel host-specific restriction system associated with DNA backbone S-modification in Salmonella. Nucleic Acids Res 38, 7133-41 (2010).
8. Murphy, J., Mahony, J., Ainsworth, S., Nauta, A. & van Sinderen, D. Bacteriophage orphan DNA methyltransferases: insights from their bacterial origin, function, and occurrence. Appl Environ Microbiol 79, 7547-55 (2013).
9. Xie, X. et al. Phosphorothioate DNA as an antioxidant in bacteria. Nucleic Acids Res 40, 9115-24 (2012).
10. You, D., Wang, L., Yao, F., Zhou, X. & Deng, Z. A novel DNA modification by sulfur: DndA is a NifS-like cysteine desulfurase capable of assembling DndC as an iron-sulfur cluster protein in Streptomyces lividans. Biochemistry 46, 6126-33 (2007).
11. Yao, F., Xu, T., Zhou, X., Deng, Z. & You, D. Functional analysis of spfD gene involved in DNA phosphorothioation in Pseudomonas fluorescens Pf0-1. FEBS Lett 583, 729-33 (2009).
12. Hu, W. et al. Structural insights into DndE from Escherichia coli B7A involved in DNA phosphorothioation modification. Cell Res 22, 1203-6 (2012).
13. Lai, C. et al. In vivo mutational characterization of DndE involved in DNA phosphorothioate modification. PLoS One 9, e107981 (2014).
14. Cao, B. et al. Pathological phenotypes and in vivo DNA cleavage by unrestrained activity of a phosphorothioate-based restriction system in Salmonella. Mol Microbiol 93, 776-85 (2014).
15. Wang, L. et al. DNA phosphorothioation is widespread and quantized in bacterial genomes. Proc Natl Acad Sci USA 108, 2963-8 (2011).
16. Cao, B. et al. Genomic mapping of phosphorothioates reveals partial modification of short consensus sequences. Nat Commun 5, 3951 (2014).
17. Ray, T., Mills, A. & Dyson, P. Tris-dependent oxidative DNA strand scission during electrophoresis. Electrophoresis 16, 888-94 (1995).
18. Liang, J. et al. DNA modification by sulfur: analysis of the sequence recognition specificity surrounding the modification sites. Nucleic Acids Res 35, 2944-54 (2007).
19. Sun, F. et al. Protein cysteine phosphorylation of SarA/MgrA family transcriptional regulators mediates bacterial virulence and antibiotic resistance. Proc Natl Acad Sci USA 109, 15461-6 (2012).
20. Kullik, I., Toledano, M.B., Tartaglia, L.A. & Storz, G. Mutational analysis of the redox-sensitive transcriptional regulator OxyR: regions important for oxidation and transcriptional activation. J Bacteriol 177, 1275-84 (1995).
21. Kobayashi, I. Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution. Nucleic Acids Res 29, 3742-56 (2001).
22. Bandaru, B., Gopal, J. & Bhagwat, A.S. Overproduction of DNA cytosine methyltransferases causes methylation and C -> T mutations at non-canonical sites. J Biol Chem 271, 7851-9 (1996).
23. Shen, J.C., Rideout, W.M., 3rd & Jones, P.A. High frequency mutagenesis by a DNA methyltransferase. Cell 71, 1073-80 (1992).
24. Zechiedrich, E.L. & Cozzarelli, N.R. Roles of topoisomerase IV and DNA gyrase in DNA unlinking during replication in Escherichia coli. Genes Dev 9, 2859-69 (1995).
25. Li, G.M. Mechanisms and functions of DNA mismatch repair. Cell Res 18, 85-98 (2008).
26. Truglio, J.J., Croteau, D.L., Van Houten, B. & Kisker, C. Prokaryotic nucleotide excision repair: the UvrABC system. Chem Rev 106, 233-52 (2006).
27. Branum, M.E., Reardon, J.T. & Sancar, A. DNA repair excision nuclease attacks undamaged DNA. A potential source of spontaneous mutations. J Biol Chem 276, 25421-6 (2001).
28. Xu, T. et al. DNA phosphorothioation in Streptomyces lividans: mutational analysis of the dnd locus. BMC Microbiol 9, 41 (2009).
29. Bradford, M.M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72, 248-54 (1976).
30. Miller, J. in Experiments in Molecular Genetics (Cold Spring Harbor Laboratory, Cod Spring Harbor, NY, 1972).
31. Zhang, X. & Bremer, H. Control of the Escherichia coli rrnB P1 promoter strength by ppGpp. J Biol Chem 270, 11181-9 (1995).
32. Wang, Y., Cen, X.F., Zhao, G.P. & Wang, J. Characterization of a new GlnR binding box in the promoter of amtB in Streptomyces coelicolor inferred a PhoP/GlnR competitive binding mechanism for transcriptional regulation of amtB. J Bacteriol 194, 5237-44 (2012).
33. Hu, M., Liu, Y., Yu, K. & Liu, X. Decreasing the amount of trypsin in in-gel digestion leads to diminished chemical noise and improved protein identifications. J Proteomics 109, 16-25 (2014).
34. Alting-Mees, M.A. & Short, J.M. pBluescript II: gene mapping vectors. Nucleic Acids Res 17, 9494 (1989).
35. Zhou, J. et al. The crystal structure of human IRE1 luminal domain reveals a conserved dimerization interface required for activation of the unfolded protein response. Proc Natl Acad Sci USA 103, 14343-8 (2006).
36. Chao, H. & Zhou, N.Y. Involvement of the global regulator GlxR in 3-hydroxybenzoate and gentisate utilization by Corynebacterium glutamicum. Appl Environ Microbiol 80, 4215-25 (2014).