Skip to main content
NCBI home page
Protein & Cell logoLink to Protein & Cell
. 2010 Feb 7;1(1):14–21. doi: 10.1007/s13238-010-0009-y

Twenty years hunting for sulfur in DNA

Shi Chen 1,✉, Lianrong Wang 1, Zixin Deng 1,✉
PMCID: PMC4875114  PMID: 21203994

Abstract

Here we tell a 20-year long story. It began with an easily overlooked DNA degradation (Dnd) phenomenon during electrophoresis and eventually led to the discovery of an unprecedented DNA sulfur modification governed by five dnd genes. This unusual DNA modification, called phosphorothioation, is the first physiological modification identified on the DNA backbone, in which the nonbridging oxygen is replaced by sulfur in a sequence selective and stereo-specific manner. Homologous dnd gene clusters have been identified in diverse and distantly related bacteria and thus have drawn immediate attention of the entire microbial scientific community. Here, we summarize the progress in chemical, genetic, enzymatic, bioinformatical and analytical aspects of this novel postreplicative DNA modification. We also discuss perspectives on the physiological functions of the DNA phosphorothioate modification in bacteria and their implications.

Keywords: DNA sulfur modification, DNA phosphorothioate modification, DNA degradation

Contributor Information

Shi Chen, Email: shichen1976@gmail.com.

Zixin Deng, Email: zxdeng@sjtu.edu.cn.

References

  1. Boybek A., Ray T.D., Evans M.C., Dyson P.J. 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. 1998;26:3364–3371. doi: 10.1093/nar/26.14.3364. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Brody R.S., Frey P.A. Unambiguous determination of the stereochemistry of nucleotidyl transfer catalyzed by DNA polymerase I from Escherichia coli. Biochemistry. 1981;20:1245–1252. doi: 10.1021/bi00508a030. [DOI] [PubMed] [Google Scholar]
  3. Burgers P.M., Eckstein F. Diastereomers of 5′-Oadenosyl 3′-O-uridyl phosphorothioate: chemical synthesis and enzymatic properties. Biochemistry. 1979;18:592–596. doi: 10.1021/bi00571a007. [DOI] [PubMed] [Google Scholar]
  4. Connelly J.C., Kirkham L.A., Leach D.R. The SbcCD nuclease of Escherichia coli is a structural maintenance of chromosomes (SMC) family protein that cleaves hairpin DNA. Proc Natl Acad Sci U S A. 1998;95:7969–7974. doi: 10.1073/pnas.95.14.7969. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Dyson P., Evans M. Novel post-replicative DNA modification in Streptomyces: analysis of the preferred modification site of plasmid pIJ101. Nucleic Acids Res. 1998;26:1248–1253. doi: 10.1093/nar/26.5.1248. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Eckstein F. Nucleoside phosphorothioates. Annu Rev Biochem. 1985;54:367–402. doi: 10.1146/annurev.bi.54.070185.002055. [DOI] [PubMed] [Google Scholar]
  7. Eckstein F. Interaction of DNA containing phosphorothioate groups with restriction enzymes. Ann N Y Acad Sci. 1986;471:217–225. doi: 10.1111/j.1749-6632.1986.tb48037.x. [DOI] [PubMed] [Google Scholar]
  8. Evans M., Kaczmarek F.S., Stutzman-Engwall K., Dyson P. Characterization of a Streptomyces-lividans-type sitespecific DNA modification system in the avermectin-producer Streptomyces avermitilis permits investigation of two novel giant linear plasmids, pSA1 and pSA2. Microbiology. 1994;140:1367–1371. doi: 10.1099/00221287-140-6-1367. [DOI] [PubMed] [Google Scholar]
  9. Gish G., Eckstein F. DNA and RNA sequence determination based on phosphorothioate chemistry. Science. 1988;240:1520–1522. doi: 10.1126/science.2453926. [DOI] [PubMed] [Google Scholar]
  10. Gupta A.P., Benkovic P.A., Benkovic S.J. The effect of the 3′,5′ thiophosphoryl linkage on the exonuclease activities of T4 polymerase and the Klenow fragment. Nucleic Acids Res. 1984;12:5897–5911. doi: 10.1093/nar/12.14.5897. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. He X., Ou H.Y., Yu Q., Zhou X., Wu J., Liang J., Zhang W., Rajakumar K., Deng Z. 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. 2007;65:1034–1048. doi: 10.1111/j.1365-2958.2007.05846.x. [DOI] [PubMed] [Google Scholar]
  12. Kambampati R., Lauhon C.T. Evidence for the transfer of sulfane sulfur from IscS to ThiI during the in vitro biosynthesis of 4-thiouridine in Escherichia coli tRNA. J Biol Chem. 2000;275:10727–10730. doi: 10.1074/jbc.275.15.10727. [DOI] [PubMed] [Google Scholar]
  13. Kurreck J. Antisense technologies. Improvement through novel chemical modifications. Eur J Biochem. 2003;270:1628–1644. doi: 10.1046/j.1432-1033.2003.03555.x. [DOI] [PubMed] [Google Scholar]
  14. Labeit S., Lehrach H., Goody R.S. DNA sequencing using alpha-thiodeoxynucleotides. Methods Enzymol. 1987;155:166–177. doi: 10.1016/0076-6879(87)55015-7. [DOI] [PubMed] [Google Scholar]
  15. Lauhon C.T., Kambampati R. The iscS gene in Escherichia coli is required for the biosynthesis of 4-thiouridine, thiamin, and NAD. J Biol Chem. 2000;275:20096–20103. doi: 10.1074/jbc.M002680200. [DOI] [PubMed] [Google Scholar]
  16. Liang J., Wang Z., He X., Li J., Zhou X., Deng Z. DNA modification by sulfur: analysis of the sequence recognition specificity surrounding the modification sites. Nucleic Acids Res. 2007;35:2944–2954. doi: 10.1093/nar/gkm176. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Matsukura M., Shinozuka K., Zon G., Mitsuya H., Reitz M., Cohen J.S., Broder S. Phosphorothioate analogs of oligodeoxynucleotides: inhibitors of replication and cytopathic effects of human immunodeficiency virus. Proc Natl Acad Sci U S A. 1987;84:7706–7710. doi: 10.1073/pnas.84.21.7706. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. McClelland M., Nelson M., Raschke E. Effect of sitespecific modification on restriction endonucleases and DNA modification methyltransferases. Nucleic Acids Res. 1994;22:3640–3659. doi: 10.1093/nar/22.17.3640. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Mueller E.G., Buck C.J., Palenchar P.M., Barnhart L.E., Paulson J.L. Identification of a gene involved in the generation of 4-thiouridine in tRNA. Nucleic Acids Res. 1998;26:2606–2610. doi: 10.1093/nar/26.11.2606. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Mueller E.G., Palenchar P.M., Buck C.J. The role of the cysteine residues of ThiI in the generation of 4-thiouridine in tRNA. J Biol Chem. 2001;276:33588–33595. doi: 10.1074/jbc.M104067200. [DOI] [PubMed] [Google Scholar]
  21. Nakamura Y., Kaneko T., Sato S., Ikeuchi M., Katoh H., Sasamoto S., Watanabe A., Iriguchi M., Kawashima K., Kimura T., et al. Complete genome structure of the thermophilic cyanobacterium Thermosynechococcus elongates BP-1. DNA Res. 2002;9:123–130. doi: 10.1093/dnares/9.4.123. [DOI] [PubMed] [Google Scholar]
  22. Olsen D.B., Eckstein F. High-efficiency oligonucleotidedirected plasmid mutagenesis. Proc Natl Acad Sci U S A. 1990;87:1451–1455. doi: 10.1073/pnas.87.4.1451. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Olsen D.B., Kotzorek G., Eckstein F. Investigation of the inhibitory role of phosphorothioate internucleotidic linkages on the catalytic activity of the restriction endonuclease EcoRV. Biochemistry. 1990;29:9546–9551. doi: 10.1021/bi00493a008. [DOI] [PubMed] [Google Scholar]
  24. Potter B.V., Romaniuk P.J., Eckstein F. Stereochemical course of DNA hydrolysis by nuclease S1. J Biol Chem. 1983;258:1758–1760. [PubMed] [Google Scholar]
  25. Ray T., Mills A., Dyson P. Tris-dependent oxidative DNA strand scission during electrophoresis. Electrophoresis. 1995;16:888–894. doi: 10.1002/elps.11501601149. [DOI] [PubMed] [Google Scholar]
  26. Ray T., Weaden J., Dyson P. Tris-dependent sitespecific cleavage of Streptomyces lividans DNA. FEMS Microbiol Lett. 1992;75:247–252. doi: 10.1111/j.1574-6968.1992.tb05425.x. [DOI] [PubMed] [Google Scholar]
  27. Stein C.A. Exploiting the potential of antisense: beyond phosphorothioate oligodeoxynucleotides. Chem Biol. 1996;3:319–323. doi: 10.1016/S1074-5521(96)90113-1. [DOI] [PubMed] [Google Scholar]
  28. Verma S., Eckstein F. Modified oligonucleotides: synthesis and strategy for users. Annu Rev Biochem. 1998;67:99–134. doi: 10.1146/annurev.biochem.67.1.99. [DOI] [PubMed] [Google Scholar]
  29. Wang L., Chen S., Xu T., Taghizadeh K., Wishnok J.S., Zhou X., You D., Deng Z., Dedon P.C. Phosphorothioation of DNA in bacteria by dnd genes. Nat Chem Biol. 2007;3:709–710. doi: 10.1038/nchembio.2007.39. [DOI] [PubMed] [Google Scholar]
  30. Xu T., Liang J., Chen S., Wang L., He X., You D., Wang Z., Li A., Xu Z., Zhou X., et al. DNA phosphorothioation in Streptomyces lividans: mutational analysis of the dnd locus. BMC Microbiol. 2009;9:41. doi: 10.1186/1471-2180-9-41. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. 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. 2009;583:729–733. doi: 10.1016/j.febslet.2009.01.029. [DOI] [PubMed] [Google Scholar]
  32. 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. 2007;46:6126–6133. doi: 10.1021/bi602615k. [DOI] [PubMed] [Google Scholar]
  33. Zhang Y., Yakrus M.A., Graviss E.A., Williams-Bouyer N., Turenne C., Kabani A., Wallace R.J., Jr. Pulsed-field gel electrophoresis study of Mycobacterium abscessus isolates previously affected by DNA degradation. J Clin Microbiol. 2004;42:5582–5587. doi: 10.1128/JCM.42.12.5582-5587.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Zhou X., Deng Z., Firmin J.L., Hopwood D.A., Kieser T. Site-specific degradation of Streptomyces lividans DNA during electrophoresis in buffers contaminated with ferrous iron. Nucleic Acids Res. 1988;16:4341–4352. doi: 10.1093/nar/16.10.4341. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Zhou X., Deng Z., Hopwood D.A., Kieser T. Characterization of phi HAU3, a broad-host-range temperate streptomyces phage, and development of phasmids. J Bacteriol. 1994;176:2096–2099. doi: 10.1128/jb.176.7.2096-2099.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Zhou X., Deng Z., Hopwood D.A., Kieser T. Streptomyces lividans 66 contains a gene for phage resistance which is similar to the phage lambda ea59 endonuclease gene. Mol Microbiol. 1994;12:789–797. doi: 10.1111/j.1365-2958.1994.tb01065.x. [DOI] [PubMed] [Google Scholar]
  37. Zhou X., He X., Li A., Lei F., Kieser T., Deng Z. Streptomyces coelicolor A3(2) lacks a genomic island present in the chromosome of Streptomyces lividans 66. Appl Environ Microbiol. 2004;70:7110–7118. doi: 10.1128/AEM.70.12.7110-7118.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Zhou X., He X., Liang J., Li A., Xu T., Kieser T., Helmann J.D., Deng Z. A novel DNA modification by sulphur. Mol Microbiol. 2005;57:1428–1438. doi: 10.1111/j.1365-2958.2005.04764.x. [DOI] [PubMed] [Google Scholar]

Articles from Protein & Cell are provided here courtesy of Oxford University Press

RESOURCES