The bacterial stress response polymerase DinB tolerates sugar modifications and preferentially incorporates arabinosyl nucleotides

IF 3.1 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY
Christina M. Hurley, Jeffrey M. Kubiak, Michael B. Cory, Jared B. Parker, Christian E. Loo, Laura C. Wang and Rahul M. Kohli
{"title":"The bacterial stress response polymerase DinB tolerates sugar modifications and preferentially incorporates arabinosyl nucleotides","authors":"Christina M. Hurley, Jeffrey M. Kubiak, Michael B. Cory, Jared B. Parker, Christian E. Loo, Laura C. Wang and Rahul M. Kohli","doi":"10.1039/D5CB00100E","DOIUrl":null,"url":null,"abstract":"<p >The bacterial DNA damage (SOS) response promotes DNA repair, DNA damage tolerance, and survival in the setting of genotoxic stress, including stress induced by antibiotics. In <em>E. coli</em>, translesion DNA synthesis can be fulfilled by Y-family DNA polymerases, including DNA polymerase IV (DinB). DinB features a more open active site and lacks proofreading ability, promoting error-prone replication. While DinB is known to tolerate damaged nucleobases like 8-oxo-guanine (8-oxoG), its ability to accommodate sugar-modified nucleotides has been underexplored, a question of importance given that such analogs are commonly used to inhibit viral and other polymerases. To explore DinB's selectivity, we screened a variety of sugar-modified noncanonical nucleotide triphosphates (nNTPs) and determined that DinB is intolerant of most 3′-modifications but can incorporate a subset of 2′-modifications. In particular, arabinosyl nucleotide triphosphates (araNTPs) showed efficient incorporation and limited extension. Furthermore, araNTPs can effectively compete with natural nucleotide triphosphates leading to stalled replication by DinB. We show that this tolerance extends to combined nucleobase and sugar modifications, with preferred misincorporation of 2′-fluoroarabinosyl-8-oxo-GTP opposite A more than C. Overall, our work highlights the potential for exploiting substrate promiscuity to target DinB and, thereby, slow bacterial adaptation to antibiotics.</p>","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 10","pages":" 1650-1656"},"PeriodicalIF":3.1000,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12415624/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"RSC Chemical Biology","FirstCategoryId":"1085","ListUrlMain":"https://pubs.rsc.org/en/content/articlelanding/2025/cb/d5cb00100e","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
引用次数: 0

Abstract

The bacterial DNA damage (SOS) response promotes DNA repair, DNA damage tolerance, and survival in the setting of genotoxic stress, including stress induced by antibiotics. In E. coli, translesion DNA synthesis can be fulfilled by Y-family DNA polymerases, including DNA polymerase IV (DinB). DinB features a more open active site and lacks proofreading ability, promoting error-prone replication. While DinB is known to tolerate damaged nucleobases like 8-oxo-guanine (8-oxoG), its ability to accommodate sugar-modified nucleotides has been underexplored, a question of importance given that such analogs are commonly used to inhibit viral and other polymerases. To explore DinB's selectivity, we screened a variety of sugar-modified noncanonical nucleotide triphosphates (nNTPs) and determined that DinB is intolerant of most 3′-modifications but can incorporate a subset of 2′-modifications. In particular, arabinosyl nucleotide triphosphates (araNTPs) showed efficient incorporation and limited extension. Furthermore, araNTPs can effectively compete with natural nucleotide triphosphates leading to stalled replication by DinB. We show that this tolerance extends to combined nucleobase and sugar modifications, with preferred misincorporation of 2′-fluoroarabinosyl-8-oxo-GTP opposite A more than C. Overall, our work highlights the potential for exploiting substrate promiscuity to target DinB and, thereby, slow bacterial adaptation to antibiotics.

Abstract Image

细菌应激反应聚合酶DinB耐受糖修饰并优先结合阿拉伯糖基核苷酸。
细菌DNA损伤(SOS)反应促进DNA修复,DNA损伤耐受性,以及在基因毒性应激环境下的生存,包括抗生素诱导的应激。在大肠杆菌中,翻译DNA合成可以通过y家族DNA聚合酶完成,包括DNA聚合酶IV (DinB)。DinB具有更开放的活性位点,缺乏校对能力,容易导致复制错误。虽然已知DinB可以耐受受损的核碱基,如8-氧鸟嘌呤(8-oxoG),但其适应糖修饰核苷酸的能力尚未得到充分探索,这是一个重要的问题,因为此类类似物通常用于抑制病毒和其他聚合酶。为了探索DinB的选择性,我们筛选了多种糖修饰的非典型三磷酸核苷酸(nNTPs),并确定DinB不耐受大多数3'-修饰,但可以结合2'-修饰的子集。特别是,阿拉伯糖基核苷酸三磷酸(araNTPs)表现出有效的结合和有限的延伸。此外,araNTPs可以有效地与天然核苷酸三磷酸竞争,导致DinB的复制停滞。我们发现这种耐受性扩展到核碱基和糖的组合修饰,与A相反的2'-氟阿拉伯糖基-8-氧基- gtp的错误结合比c更受欢迎。总之,我们的工作强调了利用底物乱交靶向DinB的潜力,从而减缓细菌对抗生素的适应。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 求助全文
来源期刊
CiteScore
6.10
自引率
0.00%
发文量
128
审稿时长
10 weeks
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:604180095
Book学术官方微信