Roles for Mycobacterial DinB2 in Frameshift and Substitution Mutagenesis

Overview

Journal Elife

Specialty Biology

Date 2023 May 4

PMID 37141254

Authors

Pierre Dupuy

Shreya Ghosh

Allison Fay

Oyindamola Adefisayo

Richa Gupta

Stewart Shuman

Michael S Glickman

Affiliations

Soon will be listed here.

Abstract

Translesion synthesis by translesion polymerases is a conserved mechanism of DNA damage tolerance. In bacteria, DinB enzymes are the widely distributed promutagenic translesion polymerases. The role of DinBs in mycobacterial mutagenesis was unclear until recent studies revealed a role for mycobacterial DinB1 in substitution and frameshift mutagenesis, overlapping with that of translesion polymerase DnaE2. encodes two additional DinBs (DinB2 and DinB3) and encodes DinB2, but the roles of these polymerases in mycobacterial damage tolerance and mutagenesis is unknown. The biochemical properties of DinB2, including facile utilization of ribonucleotides and 8-oxo-guanine, suggest that DinB2 could be a promutagenic polymerase. Here, we examine the effects of DinB2 and DinB3 overexpression in mycobacterial cells. We demonstrate that DinB2 can drive diverse substitution mutations conferring antibiotic resistance. DinB2 induces frameshift mutations in homopolymeric sequences, both in vitro and in vivo. DinB2 switches from less to more mutagenic in the presence of manganese in vitro. This study indicates that DinB2 may contribute to mycobacterial mutagenesis and antibiotic resistance acquisition in combination with DinB1 and DnaE2.

Citing Articles

Frequently arising ESX-1-associated phase variants influence fitness in the presence of host and antibiotic pressures.

Luna M, Oluoch P, Miao J, Culviner P, Papavinasasundaram K, Jaecklein E mBio. 2025; 16(3):e0376224.

PMID: 39873486 PMC: 11898584. DOI: 10.1128/mbio.03762-24.

A nucleoid-associated protein is involved in the emergence of antibiotic resistance by promoting the frequent exchange of the replicative DNA polymerase in .

Ng W, Rego E mSphere. 2024; 9(5):e0012224.

PMID: 38591887 PMC: 11237743. DOI: 10.1128/msphere.00122-24.

A nucleoid-associated protein is involved in the emergence of antibiotic resistance by promoting the frequent exchange of the replicative DNA polymerase in .

Ng W, Rego E bioRxiv. 2024; .

PMID: 38260554 PMC: 10802252. DOI: 10.1101/2023.06.12.544663.

Investigating the composition and recruitment of the mycobacterial ImuA'-ImuB-DnaE2 mutasome.

Gessner S, Martin Z, Reiche M, Santos J, Dinkele R, Ramudzuli A Elife. 2023; 12.

PMID: 37530405 PMC: 10421592. DOI: 10.7554/eLife.75628.

References

Kana B, Abrahams G, Sung N, Warner D, Gordhan B, Machowski E . Role of the DinB homologs Rv1537 and Rv3056 in Mycobacterium tuberculosis. J Bacteriol. 2010; 192(8):2220-7. PMC: 2849458. DOI: 10.1128/JB.01135-09. View

Dupuy P, Howlader M, Glickman M . A multilayered repair system protects the mycobacterial chromosome from endogenous and antibiotic-induced oxidative damage. Proc Natl Acad Sci U S A. 2020; 117(32):19517-19527. PMC: 7431094. DOI: 10.1073/pnas.2006792117. View

Ordonez H, Shuman S . Mycobacterium smegmatis DinB2 misincorporates deoxyribonucleotides and ribonucleotides during templated synthesis and lesion bypass. Nucleic Acids Res. 2014; 42(20):12722-34. PMC: 4227753. DOI: 10.1093/nar/gku1027. View

Yang M, Gao C, Cui T, An J, He Z . A TetR-like regulator broadly affects the expressions of diverse genes in Mycobacterium smegmatis. Nucleic Acids Res. 2011; 40(3):1009-20. PMC: 3273814. DOI: 10.1093/nar/gkr830. View

Dupuy P, Ghosh S, Adefisayo O, Buglino J, Shuman S, Glickman M . Distinctive roles of translesion polymerases DinB1 and DnaE2 in diversification of the mycobacterial genome through substitution and frameshift mutagenesis. Nat Commun. 2022; 13(1):4493. PMC: 9346131. DOI: 10.1038/s41467-022-32022-8. View

Castaneda-Garcia A, Prieto A, Rodriguez-Beltran J, Alonso N, Cantillon D, Costas C . A non-canonical mismatch repair pathway in prokaryotes. Nat Commun. 2017; 8:14246. PMC: 5290159. DOI: 10.1038/ncomms14246. View

Schroeder J, Randall J, Hirst W, ODonnell M, Simmons L . Mutagenic cost of ribonucleotides in bacterial DNA. Proc Natl Acad Sci U S A. 2017; 114(44):11733-11738. PMC: 5676920. DOI: 10.1073/pnas.1710995114. View

Timinskas K, Venclovas C . New insights into the structures and interactions of bacterial Y-family DNA polymerases. Nucleic Acids Res. 2019; 47(9):4393-4405. PMC: 6511836. DOI: 10.1093/nar/gkz198. View

Cole S, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D . Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature. 1998; 393(6685):537-44. DOI: 10.1038/31159. View

10.

Johnson M, Kottur J, Nair D . A polar filter in DNA polymerases prevents ribonucleotide incorporation. Nucleic Acids Res. 2019; 47(20):10693-10705. PMC: 6846668. DOI: 10.1093/nar/gkz792. View

11.

Vargas Jr R, Luna M, Freschi L, Marin M, Froom R, Murphy K . Phase variation as a major mechanism of adaptation in complex. Proc Natl Acad Sci U S A. 2023; 120(28):e2301394120. PMC: 10334774. DOI: 10.1073/pnas.2301394120. View

12.

Snapper S, Melton R, Mustafa S, Kieser T, Jacobs Jr W . Isolation and characterization of efficient plasmid transformation mutants of Mycobacterium smegmatis. Mol Microbiol. 1990; 4(11):1911-9. DOI: 10.1111/j.1365-2958.1990.tb02040.x. View

13.

Ordonez H, Uson M, Shuman S . Characterization of three mycobacterial DinB (DNA polymerase IV) paralogs highlights DinB2 as naturally adept at ribonucleotide incorporation. Nucleic Acids Res. 2014; 42(17):11056-70. PMC: 4176160. DOI: 10.1093/nar/gku752. View

14.

Barman A, Patra M, Das Gupta S . The respiratory lipoquinone, menaquinone, functions as an inducer of genes regulated by the repressor MSMEG_2295. Microbiology (Reading). 2022; 168(5). DOI: 10.1099/mic.0.001192. View

15.

Gupta A, Alland D . Reversible gene silencing through frameshift indels and frameshift scars provide adaptive plasticity for Mycobacterium tuberculosis. Nat Commun. 2021; 12(1):4702. PMC: 8339072. DOI: 10.1038/s41467-021-25055-y. View

16.

Safi H, Gopal P, Lingaraju S, Ma S, Levine C, Dartois V . Phase variation in produces transiently heritable drug tolerance. Proc Natl Acad Sci U S A. 2019; 116(39):19665-19674. PMC: 6765255. DOI: 10.1073/pnas.1907631116. View

17.

Tran H, Keen J, Kricker M, Resnick M, Gordenin D . Hypermutability of homonucleotide runs in mismatch repair and DNA polymerase proofreading yeast mutants. Mol Cell Biol. 1997; 17(5):2859-65. PMC: 232138. DOI: 10.1128/MCB.17.5.2859. View

18.

van Loon B, Markkanen E, Hubscher U . Oxygen as a friend and enemy: How to combat the mutational potential of 8-oxo-guanine. DNA Repair (Amst). 2010; 9(6):604-16. DOI: 10.1016/j.dnarep.2010.03.004. View

19.

Bellerose M, Baek S, Huang C, Moss C, Koh E, Proulx M . Common Variants in the Glycerol Kinase Gene Reduce Tuberculosis Drug Efficacy. mBio. 2019; 10(4). PMC: 6667613. DOI: 10.1128/mBio.00663-19. View

20.

Joseph A, Badrinarayanan A . Visualizing mutagenic repair: novel insights into bacterial translesion synthesis. FEMS Microbiol Rev. 2020; 44(5):572-582. PMC: 7476773. DOI: 10.1093/femsre/fuaa023. View