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Zhu S, Zheng T, Kong L, Li J, Cao B, DeMott MS, Sun Y, Chen Y, Deng Z, Dedon PC, You D. Development of Methods Derived from Iodine-Induced Specific Cleavage for Identification and Quantitation of DNA Phosphorothioate Modifications. Biomolecules 2020; 10:biom10111491. [PMID: 33126637 PMCID: PMC7692671 DOI: 10.3390/biom10111491] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 01/06/2023] Open
Abstract
DNA phosphorothioate (PT) modification is a novel modification that occurs on the DNA backbone, which refers to a non-bridging phosphate oxygen replaced by sulfur. This exclusive DNA modification widely distributes in bacteria but has not been found in eukaryotes to date. PT modification renders DNA nuclease tolerance and serves as a constitute element of bacterial restriction-modification (R-M) defensive system and more biological functions are awaiting exploration. Identification and quantification of the bacterial PT modifications are thus critical to better understanding their biological functions. This work describes three detailed methods derived from iodine-induced specific cleavage-an iodine-induced cleavage assay (ICA), a deep sequencing of iodine-induced cleavage at PT site (ICDS) and an iodine-induced cleavage PT sequencing (PT-IC-Seq)-for the investigation of PT modifications. Using these approaches, we have identified the presence of PT modifications and quantized the frequency of PT modifications in bacteria. These characterizations contributed to the high-resolution genomic mapping of PT modifications, in which the distribution of PT modification sites on the genome was marked accurately and the frequency of the specific modified sites was reliably obtained. Here, we provide time-saving and less labor-consuming methods for both of qualitative and quantitative analysis of genomic PT modifications. The application of these methodologies will offer great potential for better understanding the biology of the PT modifications and open the door to future further systematical study.
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Affiliation(s)
- Sucheng Zhu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China; (S.Z.); (T.Z.); (L.K.); (J.L.); (Y.S.); (Y.C.); (Z.D.)
| | - Tao Zheng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China; (S.Z.); (T.Z.); (L.K.); (J.L.); (Y.S.); (Y.C.); (Z.D.)
| | - Lingxin Kong
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China; (S.Z.); (T.Z.); (L.K.); (J.L.); (Y.S.); (Y.C.); (Z.D.)
| | - Jinli Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China; (S.Z.); (T.Z.); (L.K.); (J.L.); (Y.S.); (Y.C.); (Z.D.)
| | - Bo Cao
- College of Life Sciences, Qufu Normal University, Qufu 273165, Shandong, China;
| | - Michael S. DeMott
- Department of Biological Engineering and Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (M.S.D.); (P.C.D.)
| | - Yihua Sun
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China; (S.Z.); (T.Z.); (L.K.); (J.L.); (Y.S.); (Y.C.); (Z.D.)
| | - Ying Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China; (S.Z.); (T.Z.); (L.K.); (J.L.); (Y.S.); (Y.C.); (Z.D.)
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China; (S.Z.); (T.Z.); (L.K.); (J.L.); (Y.S.); (Y.C.); (Z.D.)
| | - Peter C. Dedon
- Department of Biological Engineering and Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (M.S.D.); (P.C.D.)
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore 138602, Singapore
| | - Delin You
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China; (S.Z.); (T.Z.); (L.K.); (J.L.); (Y.S.); (Y.C.); (Z.D.)
- Correspondence: ; Tel.: +86-21-62933765
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DNA Phosphorothioate Modifications Are Widely Distributed in the Human Microbiome. Biomolecules 2020; 10:biom10081175. [PMID: 32806589 PMCID: PMC7464106 DOI: 10.3390/biom10081175] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/07/2020] [Accepted: 08/10/2020] [Indexed: 01/17/2023] Open
Abstract
The DNA phosphorothioate (PT) modification existing in many prokaryotes, including bacterial pathogens and commensals, confers multiple characteristics, including restricting gene transfer, influencing the global transcriptional response, and reducing fitness during exposure to chemical mediators of inflammation. While PT-containing bacteria have been investigated in a variety of environments, they have not been studied in the human microbiome. Here, we investigated the distribution of PT-harboring strains and verified their existence in the human microbiome. We found over 2000 PT gene-containing strains distributed in different body sites, especially in the gastrointestinal tract. PT-modifying genes are preferentially distributed within several genera, including Pseudomonas, Clostridioides, and Escherichia, with phylogenic diversities. We also assessed the PT modification patterns and found six new PT-linked dinucleotides (CpsG, CpsT, ApsG, TpsG, GpsC, ApsT) in human fecal DNA. To further investigate the PT in the human gut microbiome, we analyzed the abundance of PT-modifying genes and quantified the PT-linked dinucleotides in the fecal DNA. These results confirmed that human microbiome is a rich reservoir for PT-containing microbes and contains a wide variety of PT modification patterns.
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Pu T, Mei Z, Zhang W, Liang WJ, Zhou X, Liang J, Deng Z, Wang Z. An in vitro DNA phosphorothioate modification reaction. Mol Microbiol 2019; 113:452-463. [PMID: 31749226 DOI: 10.1111/mmi.14430] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 11/10/2019] [Accepted: 11/17/2019] [Indexed: 12/25/2022]
Abstract
Phosphorothioation (PT) involves the replacement of a nonbridging phosphate oxygen on the DNA backbone with sulfur. In bacteria, the procedure is both sequence- and stereo-specific. We reconstituted the PT reaction using purified DndCDE from Salmonella enterica and IscS from Escherichia coli. We determined that the in vitro process of PT was oxygen sensitive. Only one strand on a double-stranded (ds) DNA substrate was modified in the reaction. The modification was dominant between G and A in the GAAC/GTTC conserved sequence. The modification between G and T required the presence of PT between G and A on the opposite strand. Cysteine, S-adenosyl methionine (SAM) and the formation of an iron-sulfur cluster in DndCDE (DndCDE-FeS) were essential for the process. Results from SAM cleavage reactions support the supposition that PT is a radical SAM reaction. Adenosine triphosphate (ATP) promoted the reaction but was not essential. The data and conclusions presented suggest that the PT reaction in bacteria involves three steps. The first step is the binding of DndCDE-FeS to DNA and searching for the modification sequence, possibly with the help of ATP. Cysteine locks DndCDE-FeS to the modification site with an appropriate protein conformation. SAM triggers the radical SAM reaction to complete the oxygen-sulfur swapping.
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Affiliation(s)
- Tianning Pu
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Zhiling Mei
- Shanghai Thinkgene Biotech CO., LTD, Shanghai, People's Republic of China
| | - Wei Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Wei-Jun Liang
- Department of Life and Environmental Sciences, Faculty of Science and Technology, Bournemouth University, Poole, UK
| | - Xiufen Zhou
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Jingdan Liang
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Zhijun Wang
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
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Chen Y, Zheng T, Li J, Cui J, Deng Z, You D, Yang L. Novel Iodine-induced Cleavage Real-time PCR Assay for Accurate Quantification of Phosphorothioate Modified Sites in Bacterial DNA. Sci Rep 2019; 9:7485. [PMID: 31097783 PMCID: PMC6522622 DOI: 10.1038/s41598-019-44011-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 04/17/2019] [Indexed: 12/16/2022] Open
Abstract
DNA Phosphorothioate (PT), replacing a non-bridging phosphate oxygen atom with a sulfur atom, is one kind of common DNA modification in bacteria. Whole genome scale description of the location and frequency of PT modification is the key to understand its biological function. Herein we developed a novel method, named with iodine-induced cleavage quantitative real-time PCR (IC-qPCR), to evaluate the frequency of PT modification at a given site in bacterial DNA. The efficiency, dynamic range, sensitivity, reproducibility and accuracy of IC-qPCR were well tested and verified employing an E. coli B7A strain as example. The amplification efficiency of IC-qPCR assay ranged from 91% to 99% with a high correlation coefficient ≥0.99. The limit of quantification was determined as low as 10 copies per reaction for the 607710 and 1818096 sites, and 5 copies for the 302695 and 4120753 sites. Based on the developed IC-qPCR method, the modification frequency of four PTs in E. coli B7A was determined with high accuracy, and the results showed that the PT modification was partial and that the modification frequency varied among investigated PT sites. All these results showed that IC-qPCR was suitable for evaluating the PT modification, which would be helpful to further understand the biological function of PT modification.
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Affiliation(s)
- Yi Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Tao Zheng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Jinli Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Jinjie Cui
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences/State Key Laboratory of Cotton Biology, Anyang, Henan, 455000, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Delin You
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China.
| | - Litao Yang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China.
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences/State Key Laboratory of Cotton Biology, Anyang, Henan, 455000, China.
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Li J, Chen Y, Zheng T, Kong L, Zhu S, Sun Y, Deng Z, Yang L, You D. Quantitative mapping of DNA phosphorothioatome reveals phosphorothioate heterogeneity of low modification frequency. PLoS Genet 2019; 15:e1008026. [PMID: 30933976 PMCID: PMC6459556 DOI: 10.1371/journal.pgen.1008026] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 04/11/2019] [Accepted: 02/17/2019] [Indexed: 12/31/2022] Open
Abstract
Phosphorothioate (PT) modifications of the DNA backbone, widespread in prokaryotes, are first identified in bacterial enteropathogens Escherichia coli B7A more than a decade ago. However, methods for high resolution mapping of PT modification level are still lacking. Here, we developed the PT-IC-seq technique, based on iodine-induced selective cleavage at PT sites and high-throughput next generation sequencing, as a mean to quantitatively characterizing the genomic landscape of PT modifications. Using PT-IC-seq we foud that most PT sites are partially modified at a lower PT frequency (< 5%) in E. coli B7A and Salmonella enterica serovar Cerro 87, and both show a heterogeneity pattern of PT modification similar to those of the typical methylation modification. Combining the iodine-induced cleavage and absolute quantification by droplet digital PCR, we developed the PT-IC-ddPCR technique to further measure the PT modification level. Consistent with the PT-IC-seq measurements, PT-IC-ddPCR analysis confirmed the lower PT frequency in E. coli B7A. Our study has demonstrated the heterogeneity of PT modification in the bacterial population and we also established general tools for rigorous mapping and characterization of PT modification events at whole genome level. We describe to our knowledge the first genome-wide quantitative characterization of PT landscape and provides appropriate strategies for further functional studies of PT modification.
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Affiliation(s)
- Jinli Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yi Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Tao Zheng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Lingxin Kong
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Sucheng Zhu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yihua Sun
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Litao Yang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- * E-mail: (LY); (DY)
| | - Delin You
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- * E-mail: (LY); (DY)
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Structural basis for the recognition of sulfur in phosphorothioated DNA. Nat Commun 2018; 9:4689. [PMID: 30409991 PMCID: PMC6224610 DOI: 10.1038/s41467-018-07093-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 10/12/2018] [Indexed: 12/23/2022] Open
Abstract
There have been very few reports on protein domains that specifically recognize sulfur. Here we present the crystal structure of the sulfur-binding domain (SBD) from the DNA phosphorothioation (PT)-dependent restriction endonuclease ScoMcrA. SBD contains a hydrophobic surface cavity that is formed by the aromatic ring of Y164, the pyrolidine ring of P165, and the non-polar side chains of four other residues that serve as lid, base, and wall of the cavity. The SBD and PT-DNA undergo conformational changes upon binding. The S187RGRR191 loop inserts into the DNA major groove to make contacts with the bases of the GPSGCC core sequence. Mutating key residues of SBD impairs PT-DNA association. More than 1000 sequenced microbial species from fourteen phyla contain SBD homologs. We show that three of these homologs bind PT-DNA in vitro and restrict PT-DNA gene transfer in vivo. These results show that SBD-like PT-DNA readers exist widely in prokaryotes.
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Yang J, Stolee JA, Jiang H, Xiao L, Kiesman WF, Antia FD, Fillon YA, Ng A, Shi X. Solid-Phase Synthesis of Phosphorothioate Oligonucleotides Using Sulfurization Byproducts for in Situ Capping. J Org Chem 2018; 83:11577-11585. [PMID: 30179468 DOI: 10.1021/acs.joc.8b01553] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Oligonucleotides containing phosphorothioate (PS) linkages have recently demonstrated significant clinical utility. PS oligonucleotides are manufactured via a solid-phase chain elongation process in which a four-reaction cycle consisting of detritylation, coupling, sulfurization, and failure sequence capping with Ac2O is repeated. In the capping step, uncoupled sequences are acetylated at the 5'-OH to stop the chain growth and control the levels of deletion, or ( n-1), impurities. Herein, we report that the byproducts of commonly used sulfurization reagents react with the 5'-OH and cap the failure sequences. The standard Ac2O capping step can therefore be eliminated, and this 3-reaction cycle process affords a higher yield and higher or comparable overall purity compared to the conventional 4-reaction synthesis. This improvement results in reducing the number of reactions from ∼80 to ∼60 for the synthesis of a typical length 20-mer oligonucleotide. For every kilogram of an oligonucleotide intermediate synthesized, > 500 L of reagents and organic solvents is saved, and the E-factor is decreased to <1500 from ∼2000.
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Affiliation(s)
- Jimin Yang
- Antisense Oligonucleotide Development and Manufacturing; Analytical Development , Biogen , 115 Broadway , Cambridge , Massachusetts 02142 , United States
| | - Jessica A Stolee
- Antisense Oligonucleotide Development and Manufacturing; Analytical Development , Biogen , 115 Broadway , Cambridge , Massachusetts 02142 , United States
| | - Hong Jiang
- Antisense Oligonucleotide Development and Manufacturing; Analytical Development , Biogen , 115 Broadway , Cambridge , Massachusetts 02142 , United States
| | - Li Xiao
- Antisense Oligonucleotide Development and Manufacturing; Analytical Development , Biogen , 115 Broadway , Cambridge , Massachusetts 02142 , United States
| | - William F Kiesman
- Antisense Oligonucleotide Development and Manufacturing; Analytical Development , Biogen , 115 Broadway , Cambridge , Massachusetts 02142 , United States
| | - Firoz D Antia
- Antisense Oligonucleotide Development and Manufacturing; Analytical Development , Biogen , 115 Broadway , Cambridge , Massachusetts 02142 , United States
| | - Yannick A Fillon
- Antisense Oligonucleotide Development and Manufacturing; Analytical Development , Biogen , 115 Broadway , Cambridge , Massachusetts 02142 , United States
| | - Austen Ng
- Antisense Oligonucleotide Development and Manufacturing; Analytical Development , Biogen , 115 Broadway , Cambridge , Massachusetts 02142 , United States
| | - Xianglin Shi
- Antisense Oligonucleotide Development and Manufacturing; Analytical Development , Biogen , 115 Broadway , Cambridge , Massachusetts 02142 , United States
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Ahlgren NA, Chen Y, Needham DM, Parada AE, Sachdeva R, Trinh V, Chen T, Fuhrman JA. Genome and epigenome of a novel marine Thaumarchaeota strain suggest viral infection, phosphorothioation DNA modification and multiple restriction systems. Environ Microbiol 2017; 19:2434-2452. [PMID: 28418097 DOI: 10.1111/1462-2920.13768] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 04/08/2017] [Accepted: 04/11/2017] [Indexed: 11/29/2022]
Abstract
Marine Thaumarchaeota are abundant ammonia-oxidizers but have few representative laboratory-cultured strains. We report the cultivation of Candidatus Nitrosomarinus catalina SPOT01, a novel strain that is less warm-temperature tolerant than other cultivated Thaumarchaeota. Using metagenomic recruitment, strain SPOT01 comprises a major portion of Thaumarchaeota (4-54%) in temperate Pacific waters. Its complete 1.36 Mbp genome possesses several distinguishing features: putative phosphorothioation (PT) DNA modification genes; a region containing probable viral genes; and putative urea utilization genes. The PT modification genes and an adjacent putative restriction enzyme (RE) operon likely form a restriction modification (RM) system for defence from foreign DNA. PacBio sequencing showed >98% methylation at two motifs, and inferred PT guanine modification of 19% of possible TGCA sites. Metagenomic recruitment also reveals the putative virus region and PT modification and RE genes are present in 18-26%, 9-14% and <1.5% of natural populations at 150 m with ≥85% identity to strain SPOT01. The presence of multiple probable RM systems in a highly streamlined genome suggests a surprising importance for defence from foreign DNA for dilute populations that infrequently encounter viruses or other cells. This new strain provides new insights into the ecology, including viral interactions, of this important group of marine microbes.
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Affiliation(s)
- Nathan A Ahlgren
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Yangyang Chen
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China.,Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - David M Needham
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Alma E Parada
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Rohan Sachdeva
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Vickie Trinh
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Ting Chen
- Bioinformatics Division, TNLIST, Department of Computer Science and Technology, Tsinghua University, Beijing, China
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
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9
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Mechanistic Investigation on ROS Resistance of Phosphorothioated DNA. Sci Rep 2017; 7:42823. [PMID: 28216673 PMCID: PMC5316992 DOI: 10.1038/srep42823] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 01/16/2017] [Indexed: 11/23/2022] Open
Abstract
Phosphorothioated DNA (PT-DNA) exhibits a mild anti-oxidant property both in vivo and in vitro. It was found that 8-OHdG and ROS levels were significantly lower in dnd+ (i.e. S+) E. coli., compared to a dnd− (i.e. S−) strain. Furthermore, different from traditional antioxidants, phosphorothioate compound presents an unexpectedly high capacity to quench hydroxyl radical. Oxidative product analysis by liquid chromatography-mass spectrometry and quantum mechanistic computation supported its unique anti-oxidant characteristic of the hydroxyl selectivity: phosphorothioate donates an electron to either hydroxyl radical or guanine radical derived from hydroxyl radical, leading to a PS• radical; a complex of PS• radical and OH− (i.e. the reductive product of hydroxyl radical) releases a highly reductive HS• radical, which scavenges more equivalents of oxidants in the way to high-covalent sulphur compounds such as sulphur, sulphite and sulphate. The PS-PO conversion (PS and PO denote phosphorus-sulphur and phosphorus-oxygen compounds, respectively) made a switch of extremely oxidative OH• to highly reductive HS• species, endowing PT-DNA with the observed high capacity in hydroxyl-radical neutralization. This plausible mechanism provides partial rationale as to why bacteria develop the resource-demanding PT modification on guanine-neighboring phosphates in genome.
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Zheng T, Jiang P, Cao B, Cheng Q, Kong L, Zheng X, Hu Q, You D. DndEi Exhibits Helicase Activity Essential for DNA Phosphorothioate Modification and ATPase Activity Strongly Stimulated by DNA Substrate with a GAAC/GTTC Motif. J Biol Chem 2015; 291:1492-500. [PMID: 26631733 DOI: 10.1074/jbc.m115.694018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Indexed: 11/06/2022] Open
Abstract
Phosphorothioate (PT) modification of DNA, in which the non-bridging oxygen of the backbone phosphate group is replaced by sulfur, is governed by the DndA-E proteins in prokaryotes. To better understand the biochemical mechanism of PT modification, functional analysis of the recently found PT-modifying enzyme DndEi, which has an additional domain compared with canonical DndE, from Riemerella anatipestifer is performed in this study. The additional domain is identified as a DNA helicase, and functional deletion of this domain in vivo leads to PT modification deficiency, indicating an essential role of helicase activity in PT modification. Subsequent analysis reveals that the additional domain has an ATPase activity. Intriguingly, the ATPase activity is strongly stimulated by DNA substrate containing a GAAC/GTTC motif (i.e. the motif at which PT modifications occur in R. anatipestifer) when the additional domain and the other domain (homologous to canonical DndE) are co-expressed as a full-length DndEi. These results reveal that PT modification is a biochemical process with DNA strand separation and intense ATP hydrolysis.
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Affiliation(s)
- Tao Zheng
- From the State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030
| | - Pan Jiang
- the Shanghai Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Shanghai 200240, and
| | - Bo Cao
- From the State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030
| | - Qiuxiang Cheng
- From the State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030
| | - Lingxin Kong
- From the State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030
| | - Xiaoqing Zheng
- From the State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030
| | - Qinghai Hu
- the Shanghai Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Shanghai 200240, and
| | - Delin You
- From the State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, the Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
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