Research progress and prospects of phosphorothioate modification-A review
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    Abstract:

    DNA phosphorothioate modification was the first reported physiological modification in the DNA backbone. Five putative proteins encoded by the five-member dndABCDE gene cluster replaced the non-bridging oxygen in the sugar-phosphate backbone with a sulfur. Phosphorothioate modification occurrs in sequence-selective and Rp stereo-specific manner in diverse bacterial stains. In recent years, researchers have made systemic achievements in this area. To have a comprehensive understanding of this unusual modification, we reviewed the discovery and research progress in DNA phosphorothioate modification and also discussed opportunities and challenges in the future.

    Reference
    [1] Hershey AD,Chase M.Independent functions of protein and nucleic acid in growth of bacteriophage.Journal of General Physiology,1952,36(1):39-56.
    [2] Watson JD,Crick FHC.Molecular structure of nucleic acids:a structure for deoxyribose nucleic acid.Nature,1953,171(4356):737-738.
    [3] Gold M,Hurwitz J,Anders M.The enzymatic methylation of RNA and DNA.I.Biochemical and Biophysical Research Communications,1963,11(2):107-114.
    [4] Donahue JP,Peek RM.Restriction and modification systems//Mobley HLT,Mendz GL,Hazell SL.Helicobacter pylori:physiology and genetics.Washington,DC:The American Society for Microbiology Press,2001.
    [5] Robertson KD.DNA methylation and human disease.Nature Reviews Genetics,2005,6(8):597-610.
    [6] Zhou XF,He XY,Liang JD,Li AY,Xu TG,Kieser T,Helmann JD,Deng ZX.A novel DNA modification by sulphur.Molecular Microbiology,2005,57(5):1428-1438.
    [7] Eckstein F,Gish G.Phosphorothioates in molecular biology.Trends in Biochemical Sciences,1989,14(3):97-100.
    [8] Kieser T.Factors affecting the isolation of CCC DNA from Streptomyces lividans and Escherichia coli.Plasmid,1984,12(1):19-36.
    [9] Zhou XF,Deng ZX,Firmin JL,Hopwood DA,Kieser T.Site-specific degradation of Streptomyces lividans DNA during electrophoresis in buffers contaminated with ferrous iron.Nucleic Acids Research,1988,16(10):4341-4352.
    [10] Kieser HM,Kieser T,Hopwood DA.A combined genetic and physical map of the Streptomyces coelicolor A3(2) chromosome.Journal of Bacteriology,1992,174(17):5496-5507.
    [11] Evans M,Kaczmarek FS,Stutzman-Engwall K,Dyson PC.Characterization of a Streptomyces-lividans-type site-specific DNA modification system in the avermectin-producer Streptomyces avermitilis permits investigation of two novel giant linear plasmids,pSA1 and pSA2.Microbiology,1994,140(6):1367-1371.
    [12] 张劭翀.除虫链霉菌DNA降解基因簇add的定位和异源表达.武汉:华中农业大学硕士学位论文,1999.
    [13] Ray T,Mills A,Dyson P.Tris-dependent oxidative DNA strand scission during electrophoresis.Electrophoresis,1995,16(1):888-894.
    [14] Evans M,Dyson PC.Pulsed-field gel electrophoresis of Streptomyces lividans DNA.Trends in Genetics,1993,9(3):72.
    [15] Ray T,Weaden J,Dyson PC.Tris-dependent site-specific cleavage of Streptomyces lividans DNA.FEMS Microbiology Letters,1992,75(2/3):247-252.
    [16] Warren RAJ.Modified bases in bacteriophage DNAs.Annual Review of Microbiology,1980,34(1):137-158.
    [17] McClelland M,Nelson M,Raschke E.Effect of site-specific modification on restriction endonucleases and DNA modification methyltransferases.Nucleic Acids Research,1994,22(17):3640-3659.
    [18] Dyson P,Evans M.Novel post-replicative DNA modification in Streptomyces:analysis of the preferred modification site of plasmid pIJ101.Nucleic Acids Research,1998,26(5):1248-1253.
    [19] Zhou XF,Deng ZX,Hopwood DA,Kieser T.Streptomyces lividans 66 contains a gene for phage resistance which is similar to the phage λea59 endonuclease gene.Molecular Microbiology,1994,12(5):789-997.
    [20] Zhou XF,Deng ZX,Hopwood DA,Kieser T.Characterization of phi HAU3,a broad-host-range temperate streptomyces phage,and development of phasmids.Journal of Bacteriology,1994,176(7):2096-2099.
    [21] Zhou XF,He XY,Li YA,Lei F,Kieser T,Deng ZX.Streptomyces coelicolor A3(2) lacks a genomic island present in the chromosome of Streptomyces lividans 66.Applied and Environmental Microbiology,2004,70(12):7110-7118.
    [22] 李爱英.变铅青链霉菌DNA异常修饰系统的分子生物学研究.武汉:华中农业大学博士学位论文,2000.
    [23] Liang JD,Wang ZJ,He XY,Li JL,Zhou XF,Deng ZX.DNA modification by sulfur:analysis of the sequence recognition specificity surrounding the modification sites.Nucleic Acids Research,2007,35(9):2944-2954.
    [24] Wang LR,Chen S,Xu TG,Taghizadeh K,Wishnok JS,Zhou XF,You DL,Deng ZX,Dedon PC.Phosphorothioation of DNA in bacteria by dnd genes.Nature Chemical Biology,2007,3(11):709-710.
    [25] 王连荣.dnd基因簇对细菌DNA骨架的磷硫酰化硫修饰.上海:上海交通大学博士学位论文,2007.
    [26] Pang B,Zhou X,Yu H,Dong M,Taghizadeh K,Wishnok JS,Tannenbaum SR,Dedon PC.Lipid peroxidation dominates the chemistry of DNA adduct formation in a mouse model of inflammation.Carcinogenesis,2007,28(8):1807-1813.
    [27] He XY,Ou HY,Yu Q,Zhou XF,Wu J,Liang JD,Zhang W,Rajakumar K,Deng ZX.Analysis of a genomic island housing genes for DNA S-modification system in Streptomyces lividans 66 and its counterparts in other distantly related bacteria.Molecular Microbiology,2007,65(4):1034-1048.
    [28] Ou HY,He XY,Shao YC,Tai C,Rajakumar K,Deng ZX.dndDB:a database focused on phosphorothioation of the DNA backbone.PLoS One,2009,4(4):e5132.
    [29] Schmidt H,Hensel M.Pathogenicity islands in bacterial pathogenesis.Clinical Microbiology Reviews,2004,17(1):14-56.
    [30] Murase T,Nagato M,Shirota K,Katoh H,Otsuki K.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.Veterinary Microbiology,2004,99(2):139-143.
    [31] Liesegang A,Tschäpe H.Modified pulsed-field gel electrophoresis method for DNA degradation-sensitive Salmonella enterica and Escherichia coli strains.International Journal of Medical Microbiology,2002,291(8):645-648.
    [32] Koort JMK,Lukinmaa S,Rantala M,Unkila E,Siitonen A.Technical improvement to prevent DNA degradation of enteric pathogens in pulsed-field gel electrophoresis.Journal of Clinical Microbiology,2002,40(9):3497-3498.
    [33] Lauhon CT,Kambampati R.The iscS gene in Escherichia coli is required for the biosynthesis of 4-thiouridine,thiamin,and NAD.The Journal of Biological Chemistry,2000,275(26):20096-20103.
    [34] Silbert S,Boyken L,Hollis RJ,Pfaller MA.Improving typeability of multiple bacterial species using pulsed-field gel electrophoresis and thiourea.Diagnostic Microbiology and Infectious Disease,2003,47(4):619-621.
    [35] 徐铁钢.细菌DNA磷硫酰化修饰与限制.上海:上海交通大学博士学位论文,2008.
    [36] Wang LR,Chen S,Vergin KL,Giovannoni SJ,Chan SW,DeMott MS,Taghizadeh K,Cordero OX,Cutler M,Timberlake S,Alm EJ,Polz MF,Pinhassi J,Deng hioate oligodeoxynucleotides.Chemistry&Biology,1996,3(5):319-323. bacterial genomes.Proceedings of the National Academy of Sciences of the United States of America,2011,108(7):2963-2968.
    [37] Zheng LM,White RH,Cach VL,Jack RF,Dean DR.Cysteine desulfurase activity indicates a role for NIFS in metallocluster biosynthesis.Proceedings of the National Academy of Sciences of the United States of America,1993,90(7):2754-2758.
    [38] You DL,Wang LR,Yao F,Zhou XF,Deng ZX.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(20):6126-6133.
    [39] Chen FK,Zhang ZY,Lin K,Qian TL,Zhang Y,You DL,He XY,Wang ZJ,Liang JD,Deng ZX,Wu G.Crystal structure of the cysteine desulfurase DndA from Streptomyces lividans which is involved in DNA phosphorothioation.PLoS One,2012,7(5):e36635.
    [40] An XH,Xiong W,Yang Y,Li FH,Zhou XF,Wang ZJ,Deng ZX,Liang JD.A novel target of IscS in Escherichia coli:participating in DNA phosphorothioation.PLoS One,2012,7(12):e51265.
    [41] He W,Huang T,Tang Y,Liu YH,Wu XL,Chen S,Chan W,Wang YJ,Liu XY,Chen S,Wang LR.Regulation of DNA phosphorothioate modification in Salmonella enterica by DndB.Scientific Reports,2015,5:12368.
    [42] Yao F,Xu TG,Zhou XF,Deng ZX,You DL.Functional analysis of spfD gene involved in DNA phosphorothioation in Pseudomonas fluorescens Pf0-1.FEBS Letters,2009,583(4):729-733.
    [43] Nakamura Y,Kaneko T,Sato S,Ikeuchi M,Katoh H,Sasamoto S,Watanabe A,Iriguchi M,Kawashima K,Kimura T,Kishida Y,Kiyokawa C,Kohara M,Matsumoto M,Matsuno A,Nakazaki N,Shimpo S,Sugimoto M,Takeuchi C,Yamada M,Tabata S.Complete genome structure of the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1.DNA Research,2002,9(4):123-130.
    [44] Hu W,Wang CK,Liang JD,Zhang TL,Hu ZP,Wang ZJ,Lan WX,Li F,Wu HM,Ding JP,Wu G,Deng ZX,Cao CY.Structural insights into DndE from Escherichia coli B7A involved in DNA phosphorothioation modification.Cell Research,2012,22(7):1203-1206.
    [45] 谢新强.磷硫酰化DNA在细菌中作为抗氧化剂的机制研究.上海:上海交通大学博士学位论文,2012.
    [46] Xie XQ,Liang JD,Pu TN,Xu F,Yao F,Yang Y,Zhao YL,You DL,Zhou XF,Deng ZX,Wang ZJ.Phosphorothioate DNA as an antioxidant in bacteria.Nucleic Acids Research,2012,40(18):9115-9124.
    [47] Cao B,Chen C,DeMott MS,Cheng QX,Clark TA,Xiong XL,Zheng XQ,Butty V,Levine SS,Yuan G,Boitano M,Luong K,Song Y,Zhou XF,Deng ZX,Turner SW,Korlach J,You DL,Wang LR,Chen S,Dedon PC.Genomic mapping of phosphorothioates reveals partial modification of short consensus sequences.Nature Communications,2014,5:3951.
    [48] Arber W,Linn S.DNA modification and restriction.Annual Review of Biochemistry,1969,38:467-500.
    [49] Arber W,Wauters-Willems D.Host specificity of DNA produced by Escherichia coli.XⅡ.The two restriction and modification systems of strain 15T.Molecular and General Genetics,1970,108(3):203-217.
    [50] Xu TG,Yao F,Zhou XF,Deng ZX,You DL.A novel host-specific restriction system associated with DNA backbone S-modification in Salmonella.Nucleic Acids Research,2010,38(20):7133-7141.
    [51] Cao B,Cheng QX,Gu C,Yao F,DeMott MS,Zheng XQ,Deng ZX,Dedon PC,You DL.Pathological phenotypes and in vivo DNA cleavage by unrestrained activity of a phosphorothioate-based restriction system in Salmonella.Molecular Microbiology,2014,93(4):776-785.
    [52] Gan R,Wu XL,He W,Liu ZH,Wu SJ,Chen C,Chen S,Xiang QR,Deng ZX,Liang DQ,Chen S,Wang LR.DNA phosphorothioate modifications influence the global transcriptional response and protect DNA from double-stranded breaks.Scientific Reports,2014,4:6642.
    [53] Stein CA,Cheng YC.Antisense oligonucleotides as therapeutic agents-is the bullet really magical.Science,1993,261(5124):1004-1012.
    [54] Putney SD,Benkovic SJ,Schimmel PR.A DNA fragment with an alpha-phosphorothioate nucleotide at one end is asymmetrically blocked from digestion by exonuclease Ⅲ and can be replicated in vivo.Proceedings of the National Academy of Sciences of the United States of America,1981,78(12):7350-7354.
    [55] Stein CA.Exploiting the potential of antisense:beyond phosphorot
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Yali Gao, Zixin Deng, Shi Chen. Research progress and prospects of phosphorothioate modification-A review. [J]. Acta Microbiologica Sinica, 2016, 56(12): 1831-1839

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  • Received:April 02,2016
  • Revised:May 17,2016
  • Online: November 29,2016
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