Volume 40 Issue 8
Aug.  2021
Turn off MathJax
Article Contents
Wenlin Wu, Hongyun Li, Tiantian Ma, Xiaobo Zhang. Characterization of DNA polymerase δ from deep-sea hydrothermal vent shrimp Rimicaris exoculata[J]. Acta Oceanologica Sinica, 2021, 40(8): 168-175. doi: 10.1007/s13131-021-1823-1
Citation: Wenlin Wu, Hongyun Li, Tiantian Ma, Xiaobo Zhang. Characterization of DNA polymerase δ from deep-sea hydrothermal vent shrimp Rimicaris exoculata[J]. Acta Oceanologica Sinica, 2021, 40(8): 168-175. doi: 10.1007/s13131-021-1823-1

Characterization of DNA polymerase δ from deep-sea hydrothermal vent shrimp Rimicaris exoculata

doi: 10.1007/s13131-021-1823-1
Funds:  The National Basic Research Program of China under contract No. 2015CB755903; the National Natural Science Foundation of China under contract Nos U1605214 and 31470133; the Foundation of Quanzhou Normal University under contract No. 2016YYKJ16.
More Information
  • Corresponding author: These authors contributed equally to this work.; zxb0812@zju.edu.cn
  • Received Date: 2020-03-04
  • Accepted Date: 2020-09-24
  • Available Online: 2021-06-25
  • Publish Date: 2021-08-31
  • DNA polymerase δ (Polδ) plays a crucial and versatile role in DNA replication and DNA repair processes. Vent shrimp Rimicaris exoculata is the primary megafaunal community living in hydrothermal vents. In this study, the Polδ from shrimp Rimicaris exoculata was cloned, expressed and characterized. The results showed that the Polδ catalytic subunit (POLD1), 852 amino acids in length, shared high homology with crayfish Procambarus clarkii and shrimp Oratosquilla oratoria. The recombinant POLD1 expressed in Escherichia coli showed that the enzyme was active in a range of 20°C to 40°C with an optimum temperature at 25°C and in a wide range of pH with an optimum at pH 6.0. The activities of POLD1 were significantly enhanced in the presence of Triton-X 100, Tween 20 and Mn2+. The Km (dNTP) value of POLD1 was 4.7 μmol/L. The present study would be helpful to reveal the characterization of Polδ of deep-sea vent animals.
  • †These authors contributed equally to this work.
  • loading
  • [1]
    Baranovskiy A G, Babayeva N D, Liston V G, et al. 2008. X-ray structure of the complex of regulatory subunits of human DNA polymerase delta. Cell Cycle, 7(19): 3026–3036. doi: 10.4161/cc.7.19.6720
    [2]
    Biertümpfel C, Zhao Ye, Kondo S, et al. 2010. Structure and mechanism of human DNA polymerase η. Nature, 465(7301): 1044–1048. doi: 10.1038/nature09196
    [3]
    Burgers P M J, Kunkel T A. 2017. Eukaryotic DNA replication fork. Annual Review of Biochemistry, 86: 417–438. doi: 10.1146/annurev-biochem-061516-044709
    [4]
    Desbruyères D, Biscoito M, Caprais J C, et al. 2001. Variations in deep-sea hydrothermal vent communities on the Mid-Atlantic Ridge near the Azores plateau. Deep-Sea Research Part I: Oceanographic Research Papers, 48(5): 1325–1346. doi: 10.1016/S0967-0637(00)00083-2
    [5]
    Fortune J M, Pavlov Y I, Welch C M, et al. 2005. Saccharomyces cerevisiae DNA polymerase δ: high fidelity for base substitutions but lower fidelity for single-and multi-base deletions. Journal of Biologial Chemistry, 280(33): 29980–29987. doi: 10.1074/jbc.M505236200
    [6]
    Haki G D, Rakshit S K. 2003. Developments in industrially important thermostable enzymes: a review. Bioresource Technology, 89(1): 17–34. doi: 10.1016/S0960-8524(03)00033-6
    [7]
    Hays H, Berdis A J. 2002. Manganese substantially alters the dynamics of translesion DNA synthesis. Biochemistry, 41(15): 4771–4778. doi: 10.1021/bi0120648
    [8]
    Hübscher U, Maga G, Spadari S. 2002. Eukaryotic DNA polymerases. Annual Review of Biochemistry, 71: 133–163. doi: 10.1146/annurev.biochem.71.090501.150041
    [9]
    Hutnak M, Fisher A T, Harris R, et al. 2008. Large heat and fluid fluxes driven through mid-plate outcrops on ocean crust. Nature Geoscience, 1: 611–614. doi: 10.1038/ngeo264
    [10]
    Jin Y H, Obert R, Burgers P M J, et al. 2001. The 3′→5′ exonuclease of DNA polymerase δ can substitute for the 5′ flap endonuclease Rad27/Fen1 in processing Okazaki fragments and preventing genome instability. Proceedings of the National Academy of Sciences of the United States of America, 98(9): 5122–5127. doi: 10.1073/pnas.091095198
    [11]
    Johnson R E, Prakash L, Prakash S. 2012. Pol31 and Pol32 subunits of yeast DNA polymerase δ are also essential subunits of DNA polymerase ζ. Proceedings of the National Academy of Sciences of the United States of America, 109(31): 12455–12460. doi: 10.1073/pnas.1206052109
    [12]
    Komaï T, Segonzac M. 2008. Taxonomic review of the hydrothermal vent shrimp genera Rimicaris Williams & Rona and Chorocaris Martin & Hessler (Crustacea: Decapoda: Caridea: Alvinocarididae). Journal of Shellfish Research, 27(1): 21–41. doi: 10.2983/0730-8000(2008)27[21:TROTHV]2.0.CO;2
    [13]
    Konn C, Charlou J L, Holm N G, et al. 2015. The production of methane, hydrogen, and organic compounds in ultramafic-hosted hydrothermal vents of the Mid-Atlantic Ridge. Astrobiology, 15(5): 381–399. doi: 10.1089/ast.2014.1198
    [14]
    Kumar S, Stecher G, Tamura K. 2016. MEGA7: Molecular evolutionary genetics analysis version 7. 0 for bigger datasets. Molecular Biology and Evolution, 33(7): 1870–1874. doi: 10.1093/molbev/msw054
    [15]
    Kunkel T A, Burgers P M J. 2017. Arranging eukaryotic nuclear DNA polymerases for replication: Specific interactions with accessory proteins arrange Pols α, δ, and ϵ in the replisome for leading-strand and lagging-strand DNA replication. Bioessays, 39(8): 1700070. doi: 10.1002/bies.201700070
    [16]
    Le Bloa S, Durand L, Cueff-Gauchard V, et al. 2017. Highlighting of quorum sensing lux genes and their expression in the hydrothermal vent shrimp Rimicaris exoculata ectosymbiontic community. Possible use as biogeographic markers. PLoS ONE, 12(3): e0174338
    [17]
    Maga G, Villani G, Tillement V, et al. 2001. Okazaki fragment processing: modulation of the strand displacement activity of DNA polymerase δ by the concerted action of replication protein A, proliferating cell nuclear antigen, and flap endonuclease-1. Proceedings of the National Academy of Sciences of the United States of America, 98(25): 14298–14303. doi: 10.1073/pnas.251193198
    [18]
    Marchler-Bauer A, Derbyshire M K, Gonzales N R, et al. 2015. CDD: NCBI’s conserved domain database. Nucleic Acids Research, 43: D222–D226. doi: 10.1093/nar/gku1221
    [19]
    Marchler-Bauer A, Lu Shennan, Anderson J B, et al. 2011. CDD: a conserved domain database for the functional annotation of proteins. Nucleic Acids Research, 39: D225–D229. doi: 10.1093/nar/gkq1189
    [20]
    Prindle M J, Loeb L A. 2012. DNA polymerase delta in DNA replication and genome maintenance. Environmental and Molecular Mutagenesis, 53(9): 666–682. doi: 10.1002/em.21745
    [21]
    Ravaux J, Cottin D, Chertemps T, et al. 2009. Hydrothermal vent shrimps display low expression of the heat-inducible hsp70 gene in nature. Marine Ecology Progress Series, 396: 153–156. doi: 10.3354/meps08293
    [22]
    Ravaux J, Léger N, Hamel G, et al. 2019. Assessing a species thermal tolerance through a multiparameter approach: the case study of the deep-sea hydrothermal vent shrimp Rimicaris exoculata. Cell Stress and Chaperones, 24: 647–659. doi: 10.1007/s12192-019-01003-0
    [23]
    Rayner E, van Gool I C, Palles C, et al. 2016. A panoply of errors: polymerase proofreading domain mutations in cancer. Nature Review Cancer, 16: 71–81. doi: 10.1038/nrc.2015.12
    [24]
    Seal G, Shearman C W, Loeb L A. 1979. On the fidelity of DNA replication: studies with human placenta DNA polymerases. Journal of Biological Chemistry, 254(12): 5229–5237. doi: 10.1016/S0021-9258(18)50583-4
    [25]
    Swan M K, Johnson R E, Prakash L, et al. 2009. Structural basis of high-fidelity DNA synthesis by yeast DNA polymerase δ. Nature Structural & Moecularl Biology, 16: 979–986
    [26]
    Tveit H, Kristensen T. 2001. Fluorescence-based DNA polymerase assay. Analytical Biochemistry, 289(1): 96–98. doi: 10.1006/abio.2000.4903
    [27]
    Vaisman A, Ling Hong, Woodgate R, et al. 2005. Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis. EMBO Journal, 24: 2957–2967. doi: 10.1038/sj.emboj.7600786
    [28]
    Vashishtha A K, Wang Jimin, Konigsberg W H. 2016. Different divalent cations alter the kinetics and fidelity of DNA polymerases. Journal of Biological Chemistry, 291(40): 20869–20875. doi: 10.1074/jbc.R116.742494
    [29]
    Vasuvat J, Montree A, Moonsom S, et al. 2016. Biochemical and functional characterization of Plasmodium falciparum DNA polymerase δ. Malaria Journal, 15: 116. doi: 10.1186/s12936-016-1166-0
    [30]
    Weedon M N, Ellard S, Prindle M J, et al. 2013. An in-frame deletion at the polymerase active site of POLD1 causes a multisystem disorder with lipodystrophy. Nature Genetics, 45: 947–950. doi: 10.1038/ng.2670
    [31]
    Williams A B, Rona P A. 1986. Two new caridean shrimps (bresiliidae) from a hydrothermal field on the Mid-Atlantic Ridge. Journal of Crustacean Biology, 6(3): 446–462. doi: 10.1163/193724086X00299
    [32]
    Zhang Jian, Sun Qinglei, Luan Zhendong, et al. 2017. Comparative transcriptome analysis of Rimicaris sp. reveals novel molecular features associated with survival in deep-sea hydrothermal vent. Scientific Reports, 7: 2000
    [33]
    Zheng Ping, Wang Minxiao, Li Chaolun, et al. 2017. Insights into deep-sea adaptations and host-symbiont interactions: a comparative transcriptome study on Bathymodiolus mussels and their coastal relatives. Molecular Ecology, 26(19): 5133–5148. doi: 10.1111/mec.14160
    [34]
    Zhou Li, Cao Lei, Wang Xiaocheng, et al. 2020. Metal adaptation strategies of deep-sea Bathymodiolus mussels from a cold seep and three hydrothermal vents in the West Pacific. Science of the Total Environment, 707: 136046. doi: 10.1016/j.scitotenv.2019.136046
  • 加载中

Catalog

    通讯作者: 陈斌, bchen63@163.com
    • 1. 

      沈阳化工大学材料科学与工程学院 沈阳 110142

    1. 本站搜索
    2. 百度学术搜索
    3. 万方数据库搜索
    4. CNKI搜索

    Figures(6)

    Article Metrics

    Article views (730) PDF downloads(10) Cited by()
    Proportional views
    Related

    /

    DownLoad:  Full-Size Img  PowerPoint
    Return
    Return