دورية أكاديمية
أعرض في EDS

Metagenome mining and functional analysis reveal oxidized guanine DNA repair at the Lost City Hydrothermal Field.

التفاصيل البيبلوغرافية
العنوان: Metagenome mining and functional analysis reveal oxidized guanine DNA repair at the Lost City Hydrothermal Field.
المؤلفون: Utzman PH; School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America., Mays VP; School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America., Miller BC; School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America., Fairbanks MC; School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America., Brazelton WJ; School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America., Horvath MP; School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America.
المصدر: PloS one [PLoS One] 2024 May 08; Vol. 19 (5), pp. e0284642. Date of Electronic Publication: 2024 May 08 (Print Publication: 2024).
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS One Subsets: MEDLINE
أسماء مطبوعة: Original Publication: San Francisco, CA : Public Library of Science
مواضيع طبية MeSH: DNA Repair* , Oxidation-Reduction* , Metagenome* , Guanine*/metabolism, Hydrothermal Vents/microbiology
مستخلص: The GO DNA repair system protects against GC → TA mutations by finding and removing oxidized guanine. The system is mechanistically well understood but its origins are unknown. We searched metagenomes and abundantly found the genes encoding GO DNA repair at the Lost City Hydrothermal Field (LCHF). We recombinantly expressed the final enzyme in the system to show MutY homologs function to suppress mutations. Microbes at the LCHF thrive without sunlight, fueled by the products of geochemical transformations of seafloor rocks, under conditions believed to resemble a young Earth. High levels of the reductant H2 and low levels of O2 in this environment raise the question, why are resident microbes equipped to repair damage caused by oxidative stress? MutY genes could be assigned to metagenome-assembled genomes (MAGs), and thereby associate GO DNA repair with metabolic pathways that generate reactive oxygen, nitrogen and sulfur species. Our results indicate that cell-based life was under evolutionary pressure to cope with oxidized guanine well before O2 levels rose following the great oxidation event.
Competing Interests: The authors have declared that no competing interests exist.
(Copyright: © 2024 Utzman et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
References: Nat Methods. 2022 Jun;19(6):679-682. (PMID: 35637307)
J Bacteriol. 1988 Nov;170(11):5405-7. (PMID: 3053667)
Proc Natl Acad Sci U S A. 2015 Nov 3;112(44):E5990-9. (PMID: 26460006)
Nature. 2001 Jul 12;412(6843):145-9. (PMID: 11449263)
Protein Sci. 2023 Nov;32(11):e4792. (PMID: 37774136)
Nucleic Acids Res. 2023 Feb 22;51(3):1034-1049. (PMID: 36631987)
Proc Natl Acad Sci U S A. 1998 Jun 23;95(13):7406-11. (PMID: 9636162)
Am Nat. 2011 Dec;178(6):E162-73. (PMID: 22089878)
Proc Natl Acad Sci U S A. 2021 Oct 5;118(40):. (PMID: 34593633)
Comput Biol Chem. 2009 Dec;33(6):445-50. (PMID: 19896904)
J Mol Microbiol Biotechnol. 2017;27(6):356-362. (PMID: 29339632)
J Comput Chem. 2004 Jul 15;25(9):1157-74. (PMID: 15116359)
J Food Prot. 1996 Nov;59(11):1233-1241. (PMID: 31195444)
Proc Natl Acad Sci U S A. 2018 Feb 6;115(6):1274-1279. (PMID: 29358381)
DNA Repair (Amst). 2003 May 13;2(5):593-608. (PMID: 12713816)
Methods Enzymol. 2018;599:69-99. (PMID: 29746250)
J Chem Inf Model. 2021 Aug 23;61(8):3891-3898. (PMID: 34278794)
Mol Syst Biol. 2011 Oct 11;7:539. (PMID: 21988835)
Nucleic Acids Res. 2002 Mar 15;30(6):1354-63. (PMID: 11884633)
Nat Biotechnol. 2017 Nov;35(11):1026-1028. (PMID: 29035372)
Biochemistry. 1998 Oct 20;37(42):14756-64. (PMID: 9778350)
Expert Opin Drug Discov. 2018 Jan;13(1):23-37. (PMID: 29139324)
Proc Natl Acad Sci U S A. 2009 Nov 3;106(44):18497-502. (PMID: 19841264)
Antioxidants (Basel). 2022 Dec 17;11(12):. (PMID: 36552695)
ACS Chem Biol. 2020 Jan 17;15(1):93-102. (PMID: 31829624)
Physiol Biochem Zool. 2010 Mar-Apr;83(2):356-65. (PMID: 19327040)
Nucleic Acids Res. 2023 Jan 6;51(D1):D587-D592. (PMID: 36300620)
J Comput Chem. 2009 Dec;30(16):2785-91. (PMID: 19399780)
Appl Environ Microbiol. 2022 Sep 13;88(17):e0092922. (PMID: 35950875)
Science. 2005 Mar 4;307(5714):1428-34. (PMID: 15746419)
Gigascience. 2020 Nov 19;9(11):. (PMID: 33215210)
Science. 2008 Feb 1;319(5863):604-7. (PMID: 18239121)
Front Genet. 2012 Feb 28;3:3. (PMID: 22403581)
Appl Environ Microbiol. 2006 Sep;72(9):6257-70. (PMID: 16957253)
Nature. 2004 Feb 12;427(6975):652-6. (PMID: 14961129)
J Bacteriol. 1999 Jul;181(14):4223-36. (PMID: 10400579)
Nat Protoc. 2016 May;11(5):905-19. (PMID: 27077332)
J Biol Chem. 2015 Jul 10;290(28):17096-105. (PMID: 25995449)
Proc Natl Acad Sci U S A. 2001 Jul 3;98(14):8030-5. (PMID: 11416172)
Nucleic Acids Res. 2012 Nov;40(21):11126-38. (PMID: 22965127)
J Bacteriol. 1976 May;126(2):646-53. (PMID: 177402)
ACS Chem Biol. 2017 Sep 15;12(9):2335-2344. (PMID: 28723094)
Annu Rev Genet. 1986;20:201-30. (PMID: 3545059)
Geobiology. 2010 Dec;8(5):355-71. (PMID: 20572872)
Philos Trans A Math Phys Eng Sci. 2020 Feb 21;378(2165):20180429. (PMID: 31902336)
Nature. 2021 Aug;596(7873):583-589. (PMID: 34265844)
Nucleic Acids Res. 2003 Jul 1;31(13):3784-8. (PMID: 12824418)
DNA Repair (Amst). 2021 Dec;108:103231. (PMID: 34649144)
PLoS Comput Biol. 2005 Oct;1(5):e55. (PMID: 16261196)
Mol Biol Evol. 2003 Oct;20(10):1603-11. (PMID: 12832627)
Astrobiology. 2017 Nov;17(11):1138-1160. (PMID: 28910143)
Nucleic Acids Res. 2021 Jul 2;49(W1):W293-W296. (PMID: 33885785)
Biochemistry. 1999 May 18;38(20):6374-9. (PMID: 10350454)
Genome Integr. 2010 Sep 01;1(1):12. (PMID: 20809962)
J Comput Chem. 2010 Jan 30;31(2):455-61. (PMID: 19499576)
FEBS J. 2016 Feb;283(3):521-40. (PMID: 26613369)
BMC Evol Biol. 2011 Oct 03;11:285. (PMID: 21966992)
PLoS Comput Biol. 2017 Jul 26;13(7):e1005659. (PMID: 28746339)
Nat Genet. 2002 Feb;30(2):227-32. (PMID: 11818965)
Genome Res. 2004 Jun;14(6):1188-90. (PMID: 15173120)
Biochem J. 2006 Jan 1;393(Pt 1):381-7. (PMID: 16201966)
FEMS Microbiol Rev. 1997 Aug;21(1):43-54. (PMID: 9299701)
Nat Rev Microbiol. 2021 Dec;19(12):774-785. (PMID: 34183820)
Eur J Biochem. 1991 Dec 18;202(3):715-28. (PMID: 1765088)
J Chem Inf Model. 2020 Apr 27;60(4):2189-2198. (PMID: 32227880)
Nucleic Acids Res. 1990 Oct 25;18(20):6097-100. (PMID: 2172928)
Bioinformatics. 2023 Jun 1;39(6):. (PMID: 37252824)
J Mol Biol. 2016 Feb 22;428(4):726-731. (PMID: 26585406)
EMBO J. 1987 Oct;6(10):3177-83. (PMID: 3319582)
Proteins. 2006 Nov 15;65(3):712-25. (PMID: 16981200)
J Bacteriol. 2003 Nov;185(22):6624-32. (PMID: 14594836)
Nucleic Acids Res. 2016 Jan 29;44(2):801-10. (PMID: 26673696)
Hum Mutat. 2015 Jul;36(7):704-11. (PMID: 25820570)
Nature. 1992 Jan 16;355(6357):273-5. (PMID: 1309939)
Biochemistry. 2005 Jun 28;44(25):9238-45. (PMID: 15966748)
Astrobiology. 2012 Aug;12(8):775-84. (PMID: 22970865)
Proc Natl Acad Sci U S A. 2008 Nov 18;105(46):17878-83. (PMID: 19001264)
Prog Mol Biol Transl Sci. 2012;110:71-91. (PMID: 22749143)
Proc Natl Acad Sci U S A. 1988 Apr;85(8):2709-13. (PMID: 3128795)
J Am Chem Soc. 2020 Aug 5;142(31):13283-13287. (PMID: 32664726)
Protein Sci. 2005 Jun;14(6):1673-8. (PMID: 15883188)
J Biol Chem. 1999 Apr 9;274(15):10119-28. (PMID: 10187794)
J Am Chem Soc. 2023 Jun 21;145(24):13114-13125. (PMID: 37285289)
J Biol Chem. 2002 Jun 21;277(25):22605-15. (PMID: 11960995)
Genes Environ. 2017 Aug 1;39:21. (PMID: 28781714)
Proc Natl Acad Sci U S A. 1989 Jul;86(14):5345-9. (PMID: 2501784)
Nucleic Acids Res. 2000 Jan 1;28(1):27-30. (PMID: 10592173)
Nucleic Acids Res. 1996 Nov 15;24(22):4572-6. (PMID: 8948651)
Proc Natl Acad Sci U S A. 1992 Aug 1;89(15):7022-5. (PMID: 1495996)
Bioinformatics. 2019 Nov 15;:. (PMID: 31730192)
Nat Rev Microbiol. 2013 Jul;11(7):443-54. (PMID: 23712352)
Biochemistry. 1992 Nov 17;31(45):10964-8. (PMID: 1445834)
Structure. 1997 Dec 15;5(12):1543-50. (PMID: 9438868)
Nucleic Acids Res. 2008 Apr;36(7):2295-300. (PMID: 18287115)
J Biol Chem. 2003 Jun 6;278(23):20708-15. (PMID: 12670952)
المشرفين على المادة: 5Z93L87A1R (Guanine)
تواريخ الأحداث: Date Created: 20240508 Date Completed: 20240508 Latest Revision: 20240510
رمز التحديث: 20240510
مُعرف محوري في PubMed: PMC11078426
DOI: 10.1371/journal.pone.0284642
PMID: 38718041
قاعدة البيانات: MEDLINE
الوصف
تدمد:1932-6203
DOI:10.1371/journal.pone.0284642