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Mechanism Underlying the Bypass of Apurinic/Pyrimidinic Site Analogs by Sulfolobus acidocaldarius DNA Polymerase IV
International Journal of Molecular Sciences ( IF 4.9 ) Pub Date : 2022-03-01 , DOI: 10.3390/ijms23052729
Qin-Ying Huang 1 , Dong Song 1 , Wei-Wei Wang 1, 2 , Li Peng 1 , Hai-Feng Chen 1 , Xiang Xiao 1, 3 , Xi-Peng Liu 1, 3
Affiliation  

The spontaneous depurination of genomic DNA occurs frequently and generates apurinic/pyrimidinic (AP) site damage that is mutagenic or lethal to cells. Error-prone DNA polymerases are specifically responsible for the translesion synthesis (TLS) of specific DNA damage, such as AP site damage, generally with relatively low fidelity. The Y-family DNA polymerases are the main error-prone DNA polymerases, and they employ three mechanisms to perform TLS, including template-skipping, dNTP-stabilized misalignment, and misincorporation-misalignment. The bypass mechanism of the dinB homolog (Dbh), an archaeal Y-family DNA polymerase from Sulfolobus acidocaldarius, is unclear and needs to be confirmed. In this study, we show that the Dbh primarily uses template skipping accompanied by dNTP-stabilized misalignment to bypass AP site analogs, and the incorporation of the first nucleotide across the AP site is the most difficult. Furthermore, based on the reported crystal structures, we confirmed that three conserved residues (Y249, R333, and I295) in the little finger (LF) domain and residue K78 in the palm subdomain of the catalytic core domain are very important for TLS. These results deepen our understanding of how archaeal Y-family DNA polymerases deal with intracellular AP site damage and provide a biochemical basis for elucidating the intracellular function of these polymerases.

中文翻译:

Sulfolobus acidocaldarius DNA 聚合酶 IV 绕过无嘌呤/嘧啶位点类似物的机制

基因组 DNA 的自发脱嘌呤经常发生并产生对细胞具有致突变性或致死性的脱嘌呤/嘧啶 (AP) 位点损伤。容易出错的 DNA 聚合酶专门负责特定 DNA 损伤的跨损伤合成 (TLS),例如 AP 位点损伤,通常保真度相对较低。Y 家族 DNA 聚合酶是主要的容易出错的 DNA 聚合酶,它们采用三种机制来执行 TLS,包括模板跳跃、dNTP 稳定错位和错配错位。dinB 同源物 (Dbh) 是一种来自酸热硫化叶菌的古细菌 Y 家族 DNA 聚合酶,其旁路机制尚不清楚,需要确认。在这项研究中,我们表明 Dbh 主要使用模板跳过以及 dNTP 稳定的错位来绕过 AP 位点类似物,并且第一个核苷酸穿过 AP 位点的掺入是最困难的。此外,根据报道的晶体结构,我们证实小指(LF)结构域中的三个保守残基(Y249、R333 和 I295)和催化核心结构域的手掌子结构域中的残基 K78 对 TLS 非常重要。这些结果加深了我们对古菌 Y 家族 DNA 聚合酶如何处理细胞内 AP 位点损伤的理解,并为阐明这些聚合酶的细胞内功能提供了生化基础。小指 (LF) 域中的 I295) 和催化核心域的手掌子域中的残基 K78 对 TLS 非常重要。这些结果加深了我们对古菌 Y 家族 DNA 聚合酶如何处理细胞内 AP 位点损伤的理解,并为阐明这些聚合酶的细胞内功能提供了生化基础。小指 (LF) 域中的 I295) 和催化核心域的手掌子域中的残基 K78 对 TLS 非常重要。这些结果加深了我们对古菌 Y 家族 DNA 聚合酶如何处理细胞内 AP 位点损伤的理解,并为阐明这些聚合酶的细胞内功能提供了生化基础。
更新日期:2022-03-01
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