Twenty years hunting for sulfur in DNA

Protein and Cell

Volumn 1, Issue 1, 2010, Pages 14-21

  Chen, Shi ^a,b   Wang, Lianrong ^a,c   Deng, Zixin ^a  

^a SHANGHAI JIAO TONG UNIVERSITY   (China)

^b HARVARD MEDICAL SCHOOL   (United States)

^c USA   (United States)

Author keywords

DNA degradation; DNA phosphorothioate modification; DNA sulfur modification

Indexed keywords

PHOSPHOROTHIOIC ACID; SULFUR;

DNA DEGRADATION; DNA DETERMINATION; DNA MODIFICATION; DNA REPLICATION; DNA SEQUENCE; ELECTROPHORESIS; GENE CLUSTER; GENE FUNCTION; GENE IDENTIFICATION; GENETIC DISTANCE; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; REVIEW;

EID: 79953128019     PISSN: 1674800X     EISSN: 16748018     Source Type: Journal    
DOI: 10.1007/s13238-010-0009-y     Document Type: Review

References (38)

1. 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.
2. Brody, R. S., and Frey, P. A. (1981). Unambiguous determination of the stereochemistry of nucleotidyl transfer catalyzed by DNA polymerase I from Escherichia coli. Biochemistry 20, 1245-1252.
3. Burgers, P. M., and Eckstein, F. (1979). Diastereomers of 5′-Oadenosyl 3′-O-uridyl phosphorothioate: chemical synthesis and enzymatic properties. Biochemistry 18, 592-596.
4. Connelly, J. C., Kirkham, L. A., and Leach, D. R. (1998). 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 95, 7969-7974.
5. Dyson, P., and Evans, M. (1998). Novel post-replicative DNA modification in Streptomyces: analysis of the preferred modification site of plasmid pIJ101. Nucleic Acids Res 26, 1248-1253.
6. Eckstein, F. (1985). Nucleoside phosphorothioates. Annu Rev Biochem 54, 367-402.
7. Eckstein, F. (1986). Interaction of DNA containing phosphorothioate groups with restriction enzymes. Ann N Y Acad Sci 471, 217-225.
8. Evans, M., Kaczmarek, F. S., Stutzman-Engwall, K., and Dyson, P. (1994). 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 140, 1367-1371.
9. Gish, G., and Eckstein, F. (1988). DNA and RNA sequence determination based on phosphorothioate chemistry. Science 240, 1520-1522.
10. Gupta, A. P., Benkovic, P. A., and Benkovic, S. J. (1984). The effect of the 3′, 5′ thiophosphoryl linkage on the exonuclease activities of T4 polymerase and the Klenow fragment. Nucleic Acids Res 12, 5897-5911.
11. 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.
12. Kambampati, R., and Lauhon, C. T. (2000). 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 275, 10727-10730.
13. Kurreck, J. (2003). Antisense technologies. Improvement through novel chemical modifications. Eur J Biochem 270, 1628-1644.
14. Labeit, S., Lehrach, H., and Goody, R. S. (1987). DNA sequencing using alpha-thiodeoxynucleotides. Methods Enzymol 155, 166-177.
15. Lauhon, C. T., and Kambampati, R. (2000). The iscS gene in Escherichia coli is required for the biosynthesis of 4-thiouridine, thiamin, and NAD. J Biol Chem 275, 20096-20103.
16. Liang, J., Wang, Z., He, X., Li, J., Zhou, X., and Deng, Z. (2007). DNA modification by sulfur: analysis of the sequence recognition specificity surrounding the modification sites. Nucleic Acids Res 35, 2944-2954.
17. Matsukura, M., Shinozuka, K., Zon, G., Mitsuya, H., Reitz, M., Cohen, J. S., and Broder, S. (1987). Phosphorothioate analogs of oligodeoxynucleotides: inhibitors of replication and cytopathic effects of human immunodeficiency virus. Proc Natl Acad Sci U S A 84, 7706-7710.
18. McClelland, M., Nelson, M., and Raschke, E. (1994). Effect of sitespecific modification on restriction endonucleases and DNA modification methyltransferases. Nucleic Acids Res 22, 3640-3659.
19. Mueller, E. G., Buck, C. J., Palenchar, P. M., Barnhart, L. E., and Paulson, J. L. (1998). Identification of a gene involved in the generation of 4-thiouridine in tRNA. Nucleic Acids Res 26, 2606-2610.
20. Mueller, E. G., Palenchar, P. M., and Buck, C. J. (2001). The role of the cysteine residues of ThiI in the generation of 4-thiouridine in tRNA. J Biol Chem 276, 33588-33595.
21. Nakamura, Y., Kaneko, T., Sato, S., Ikeuchi, M., Katoh, H., Sasamoto, S., Watanabe, A., Iriguchi, M., Kawashima, K., Kimura, T., et al. (2002). Complete genome structure of the thermophilic cyanobacterium Thermosynechococcus elongates BP-1. DNA Res 9, 123-130.
22. Olsen, D. B., and Eckstein, F. (1990). High-efficiency oligonucleotidedirected plasmid mutagenesis. Proc Natl Acad Sci U S A 87, 1451-1455.
23. Olsen, D. B., Kotzorek, G., and Eckstein, F. (1990). Investigation of the inhibitory role of phosphorothioate internucleotidic linkages on the catalytic activity of the restriction endonuclease EcoRV. Biochemistry 29, 9546-9551.
24. Potter, B. V., Romaniuk, P. J., and Eckstein, F. (1983). Stereochemical course of DNA hydrolysis by nuclease S1. J Biol Chem 258, 1758-1760.
25. Ray, T., Mills, A., and Dyson, P. (1995). Tris-dependent oxidative DNA strand scission during electrophoresis. Electrophoresis 16, 888-894.
26. Ray, T., Weaden, J., and Dyson, P. (1992). Tris-dependent sitespecific cleavage of Streptomyces lividans DNA. FEMS Microbiol Lett 75, 247-252.
27. Stein, C. A. (1996). Exploiting the potential of antisense: beyond phosphorothioate oligodeoxynucleotides. Chem Biol 3, 319-323.
28. Verma, S., and Eckstein, F. (1998). Modified oligonucleotides: synthesis and strategy for users. Annu Rev Biochem 67, 99-134.
29. 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.
30. Xu, T., Liang, J., Chen, S., Wang, L., He, X., You, D., Wang, Z., Li, A., Xu, Z., Zhou, X., et al. (2009). DNA phosphorothioation in Streptomyces lividans: mutational analysis of the dnd locus. BMC Microbiol 9, 41.
31. Yao, F., Xu, T., Zhou, X., Deng, Z., and You, D. (2009). Functional analysis of spfD gene involved in DNA phosphorothioation in Pseudomonas fluorescens Pf0-1. FEBS Lett 583, 729-733.
32. You, D., Wang, L., Yao, F., Zhou, X., and Deng, Z. (2007). 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, 6126-6133.
33. Zhang, Y., Yakrus, M. A., Graviss, E. A., Williams-Bouyer, N., Turenne, C., Kabani, A., and Wallace, R. J., Jr. (2004). Pulsed-field gel electrophoresis study of Mycobacterium abscessus isolates previously affected by DNA degradation. J Clin Microbiol 42, 5582-5587.
34. Zhou, X., Deng, Z., 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.
35. Zhou, X., Deng, Z., Hopwood, D. A., and Kieser, T. (1994a). Characterization of phi HAU3, a broad-host-range temperate streptomyces phage, and development of phasmids. J Bacteriol 176, 2096-2099.
36. Zhou, X., Deng, Z., Hopwood, D. A., and Kieser, T. (1994b). Streptomyces lividans 66 contains a gene for phage resistance which is similar to the phage lambda ea59 endonuclease gene. Mol Microbiol 12, 789-797.
37. Zhou, X., He, X., Li, A., Lei, F., Kieser, T., and Deng, Z. (2004). Streptomyces coelicolor A3(2) lacks a genomic island present in the chromosome of Streptomyces lividans 66. Appl Environ Microbiol 70, 7110-7118.
38. 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.