Literature DB >> 21285367

DNA phosphorothioation is widespread and quantized in bacterial genomes.

Lianrong Wang1, Shi Chen, Kevin L Vergin, Stephen J Giovannoni, Simon W Chan, Michael S DeMott, Koli Taghizadeh, Otto X Cordero, Michael Cutler, Sonia Timberlake, Eric J Alm, Martin F Polz, Jarone Pinhassi, Zixin Deng, Peter C Dedon.   

Abstract

Phosphorothioate (PT) modification of DNA, with sulfur replacing a nonbridging phosphate oxygen, was recently discovered as a product of the dnd genes found in bacteria and archaea. Given our limited understanding of the biological function of PT modifications, including sequence context, genomic frequencies, and relationships to the diversity of dnd gene clusters, we undertook a quantitative study of PT modifications in prokaryotic genomes using a liquid chromatography-coupled tandem quadrupole mass spectrometry approach. The results revealed a diversity of unique PT sequence contexts and three discrete genomic frequencies in a wide range of bacteria. Metagenomic analyses of PT modifications revealed unique ecological distributions, and a phylogenetic comparison of dnd genes and PT sequence contexts strongly supports the horizontal transfer of dnd genes. These results are consistent with the involvement of PT modifications in a type of restriction-modification system with wide distribution in prokaryotes.

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Year:  2011        PMID： 21285367      PMCID： PMC3041111          DOI： 10.1073/pnas.1017261108

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN： 0027-8424            Impact factor:   11.205


  35 in total

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Authors:  Robert C Edgar
Journal:  Nucleic Acids Res       Date:  2004-03-19       Impact factor: 16.971

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Authors:  S J Giovannoni; E F DeLong; T M Schmidt; N R Pace
Journal:  Appl Environ Microbiol       Date:  1990-08       Impact factor: 4.792

4.  Inhibition of the restriction endonuclease BanII using modified DNA substrates. Determination of phosphate residues critical for the formation of an active enzyme-DNA complex.

Authors:  D B Olsen; G Kotzorek; J R Sayers; F Eckstein
Journal:  J Biol Chem       Date:  1990-08-25       Impact factor: 5.157

5.  Novel post-replicative DNA modification in Streptomyces: analysis of the preferred modification site of plasmid pIJ101.

Authors:  P Dyson; M Evans
Journal:  Nucleic Acids Res       Date:  1998-03-01       Impact factor: 16.971

6.  Investigation of the inhibitory role of phosphorothioate internucleotidic linkages on the catalytic activity of the restriction endonuclease EcoRV.

Authors:  D B Olsen; G Kotzorek; F Eckstein
Journal:  Biochemistry       Date:  1990-10-16       Impact factor: 3.162

7.  Immunity to enterotoxigenic Escherichia coli.

Authors:  M M Levine; D R Nalin; D L Hoover; E J Bergquist; R B Hornick; C R Young
Journal:  Infect Immun       Date:  1979-03       Impact factor: 3.441

8.  A novel host-specific restriction system associated with DNA backbone S-modification in Salmonella.

Authors:  Tiegang Xu; Fen Yao; Xiufen Zhou; Zixin Deng; Delin You
Journal:  Nucleic Acids Res       Date:  2010-07-12       Impact factor: 16.971

9.  Site-specific degradation of Streptomyces lividans DNA during electrophoresis in buffers contaminated with ferrous iron.

Authors:  X Zhou; Z Deng; J L Firmin; D A Hopwood; T Kieser
Journal:  Nucleic Acids Res       Date:  1988-05-25       Impact factor: 16.971

Review 10.  Phosphorothioates in molecular biology.

Authors:  F Eckstein; G Gish
Journal:  Trends Biochem Sci       Date:  1989-03       Impact factor: 13.807
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  65 in total

1.  Purification, crystallization and preliminary X-ray analysis of the DndE protein from Salmonella enterica serovar Cerro 87, which is involved in DNA phosphorothioation.

Authors:  Fukun Chen; Kui Lin; Zhenyi Zhang; Leyi Chen; Xiaoshan Shi; Chunyang Cao; Zhijun Wang; Jingdan Liang; Zixin Deng; Geng Wu
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2011-10-27

2.  Structural insights into DndE from Escherichia coli B7A involved in DNA phosphorothioation modification.

Authors:  Wei Hu; Chengkun Wang; Jingdan Liang; Tianlong Zhang; Zhongpei Hu; Zhijun Wang; Wenxian Lan; Fang Li; Houming Wu; Jianping Ding; Geng Wu; Zixin Deng; Chunyang Cao
Journal:  Cell Res       Date:  2012-04-24       Impact factor: 25.617

3.  Comparison of large-insert, small-insert and pyrosequencing libraries for metagenomic analysis.

Authors:  Thomas Danhorn; Curtis R Young; Edward F DeLong
Journal:  ISME J       Date:  2012-04-26       Impact factor: 10.302

4.  Convergence of DNA methylation and phosphorothioation epigenetics in bacterial genomes.

Authors:  Chao Chen; Lianrong Wang; Si Chen; Xiaolin Wu; Meijia Gu; Xi Chen; Susu Jiang; Yunfu Wang; Zixin Deng; Peter C Dedon; Shi Chen
Journal:  Proc Natl Acad Sci U S A       Date:  2017-04-11       Impact factor: 11.205

Review 5.  Entering the era of bacterial epigenomics with single molecule real time DNA sequencing.

Authors:  Brigid M Davis; Michael C Chao; Matthew K Waldor
Journal:  Curr Opin Microbiol       Date:  2013-02-19       Impact factor: 7.934

6.  BREX is a novel phage resistance system widespread in microbial genomes.

Authors:  Tamara Goldfarb; Hila Sberro; Eyal Weinstock; Ofir Cohen; Shany Doron; Yoav Charpak-Amikam; Shaked Afik; Gal Ofir; Rotem Sorek
Journal:  EMBO J       Date:  2014-12-01       Impact factor: 11.598

7.  Crystallization and preliminary X-ray analysis of the type IV restriction endonuclease ScoMcrA from Streptomyces coelicolor, which cleaves both Dcm-methylated DNA and phosphorothioated DNA.

Authors:  Guang Liu; Zhenyi Zhang; Gong Zhao; Zixin Deng; Geng Wu; Xinyi He
Journal:  Acta Crystallogr F Struct Biol Commun       Date:  2015-01-01       Impact factor: 1.056

8.  Abundant SAR11 viruses in the ocean.

Authors:  Yanlin Zhao; Ben Temperton; J Cameron Thrash; Michael S Schwalbach; Kevin L Vergin; Zachary C Landry; Mark Ellisman; Tom Deerinck; Matthew B Sullivan; Stephen J Giovannoni
Journal:  Nature       Date:  2013-02-13       Impact factor: 49.962

9.  Phosphorothioated DNA Is Shielded from Oxidative Damage.

Authors:  Tianning Pu; Jingdan Liang; Zhiling Mei; Yan Yang; Jialiang Wang; Wei Zhang; Wei-Jun Liang; Xiufen Zhou; Zixin Deng; Zhijun Wang
Journal:  Appl Environ Microbiol       Date:  2019-04-04       Impact factor: 4.792

10.  Stereospecific Effects of Oxygen-to-Sulfur Substitution in DNA Phosphate on Ion Pair Dynamics and Protein-DNA Affinity.

Authors:  Dan Nguyen; Levani Zandarashvili; Mark A White; Junji Iwahara
Journal:  Chembiochem       Date:  2016-07-13       Impact factor: 3.164
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