Engineering of the DNA replication and repair machinery to develop binary mutators for rapid genome evolution of Corynebacterium glutamicum.

Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE

Publication: 1992- : Oxford : Oxford University Press
Original Publication: London, Information Retrieval ltd.

DNA Polymerase III*/genetics ; Corynebacterium glutamicum*/genetics ; Corynebacterium glutamicum*/metabolism; DNA Replication/genetics ; Mutation ; Mutation Rate ; Metabolic Engineering

Corynebacterium glutamicum is an important industrial workhorse for production of amino acids and chemicals. Although recently developed genome editing technologies have advanced the rational genetic engineering of C. glutamicum, continuous genome evolution based on genetic mutators is still unavailable. To address this issue, the DNA replication and repair machinery of C. glutamicum was targeted in this study. DnaQ, the homolog of ϵ subunit of DNA polymerase III responsible for proofreading in Escherichia coli, was proven irrelevant to DNA replication fidelity in C. glutamicum. However, the histidinol phosphatase (PHP) domain of DnaE1, the α subunit of DNA polymerase III, was characterized as the key proofreading element and certain variants with PHP mutations allowed elevated spontaneous mutagenesis. Repression of the NucS-mediated post-replicative mismatch repair pathway or overexpression of newly screened NucS variants also impaired the DNA replication fidelity. Simultaneous interference with the DNA replication and repair machinery generated a binary genetic mutator capable of increasing the mutation rate by up to 2352-fold. The mutators facilitated rapid evolutionary engineering of C. glutamicum to acquire stress tolerance and protein overproduction phenotypes. This study provides efficient tools for evolutionary engineering of C. glutamicum and could inspire the development of mutagenesis strategy for other microbial hosts.
(© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Trends Biotechnol. 2021 Apr;39(4):331-335. (PMID: 33008644)
Biotechnol Biofuels. 2015 Jun 26;8:93. (PMID: 26136829)
Nat Genet. 2015 Jun;47(6):677-81. (PMID: 25894501)
Appl Environ Microbiol. 2017 Sep 29;83(20):. (PMID: 28802267)
Nat Commun. 2017 Jan 27;8:14246. (PMID: 28128207)
Annu Rev Chem Biomol Eng. 2013;4:259-88. (PMID: 23540289)
Metab Eng. 2016 Nov;38:344-357. (PMID: 27553884)
Sci Rep. 2016 Jan 11;6:19044. (PMID: 26750307)
Nat Commun. 2017 Oct 11;8(1):855. (PMID: 29021523)
Appl Environ Microbiol. 2013 Nov;79(22):6974-83. (PMID: 24014532)
Nat Commun. 2021 Jan 29;12(1):678. (PMID: 33514753)
Structure. 2016 Nov 1;24(11):1960-1971. (PMID: 27773688)
Trends Microbiol. 2012 Feb;20(2):94-101. (PMID: 22264657)
J Biotechnol. 2003 Sep 4;104(1-3):287-99. (PMID: 12948646)
Commun Biol. 2020 May 7;3(1):217. (PMID: 32382107)
BMC Mol Biol. 2007 Nov 15;8:104. (PMID: 18005413)
Trends Microbiol. 2019 Jun;27(6):524-537. (PMID: 30819548)
Microb Cell Fact. 2019 Jun 11;18(1):106. (PMID: 31186003)
Nat Rev Mol Cell Biol. 2002 May;3(5):364-76. (PMID: 11988770)
J Biotechnol. 2013 Jan 20;163(2):225-32. (PMID: 22982516)
Nucleic Acids Res. 2021 Aug 20;49(14):8396-8405. (PMID: 34197612)
ACS Synth Biol. 2020 Aug 21;9(8):2023-2038. (PMID: 32649183)
EMBO J. 2009 Aug 19;28(16):2479-89. (PMID: 19609302)
Nucleic Acids Res. 2016 Feb 29;44(4):1669-80. (PMID: 26609135)
Sci Adv. 2022 Sep 2;8(35):eabq2157. (PMID: 36044571)
Trends Biotechnol. 2021 Mar;39(3):286-297. (PMID: 32912649)
Nucleic Acids Res. 2018 Jul 6;46(12):6152-6165. (PMID: 29878158)
Science. 1996 Nov 15;274(5290):1208-11. (PMID: 8895473)
Nucleic Acids Res. 2022 Apr 22;50(7):e38. (PMID: 34928386)
Trends Biotechnol. 2020 Jun;38(6):650-666. (PMID: 31932066)
Sci Adv. 2021 Jul 16;7(29):. (PMID: 34272238)
Front Microbiol. 2021 Apr 07;12:654058. (PMID: 33897668)
Metab Eng. 2023 Jan;75:192-204. (PMID: 36572334)
Sci Adv. 2020 Feb 12;6(7):eaay4453. (PMID: 32095527)
Nat Methods. 2013 Apr;10(4):354-60. (PMID: 23474465)
Protein Cell. 2013 Nov;4(11):854-62. (PMID: 24214875)
J Bacteriol. 2008 Dec;190(24):8033-44. (PMID: 18849435)
PLoS One. 2009;4(5):e5553. (PMID: 19436741)
Antimicrob Agents Chemother. 2008 Apr;52(4):1209-14. (PMID: 18250188)
Trends Biotechnol. 2009 Dec;27(12):664-72. (PMID: 19793618)
Chem Rev. 2006 Feb;106(2):302-23. (PMID: 16464007)
BMC Microbiol. 2015 Oct 16;15:216. (PMID: 26474849)
Microb Biotechnol. 2013 Mar;6(2):103-17. (PMID: 23305350)
Appl Environ Microbiol. 2015 Apr;81(7):2284-98. (PMID: 25595768)
Trends Biotechnol. 2022 Aug;40(8):918-931. (PMID: 35120750)
Curr Opin Struct Biol. 2018 Dec;53:159-168. (PMID: 30292863)
Biotechnol Biofuels. 2013 Sep 27;6(1):137. (PMID: 24070173)
Cells. 2021 May 25;10(6):. (PMID: 34070467)
Microbiology (Reading). 2017 Dec;163(12):1740-1758. (PMID: 29171825)
Essays Biochem. 2021 Jul 26;65(2):197-212. (PMID: 34096577)
Biotechnol J. 2017 Oct;12(10):. (PMID: 28857502)
Gene. 1994 Jul 22;145(1):69-73. (PMID: 8045426)
Mol Cell. 2016 Jun 2;62(5):745-55. (PMID: 27259205)
J Bacteriol. 2007 Apr;189(8):2955-66. (PMID: 17293426)
Nat Commun. 2022 Feb 16;13(1):891. (PMID: 35173152)
Chromosoma. 2015 Dec;124(4):443-62. (PMID: 25862369)
Biotechnol Lett. 2015 Dec;37(12):2445-52. (PMID: 26354854)
Res Microbiol. 2009 Nov;160(9):618-28. (PMID: 19732826)
Science. 1997 Sep 19;277(5333):1833-4. (PMID: 9324769)
Nucleic Acids Res. 2018 Jul 6;46(12):6206-6217. (PMID: 29846672)

EC 2.7.7.7 (DNA Polymerase III)

Date Created: 20230714 Date Completed: 20230911 Latest Revision: 20231004

20231215

PMC10484736

10.1093/nar/gkad602

37449409