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细菌DNA损伤反应蛋白UmuD二聚体交换界面的鉴定

Identification of the Dimer Exchange Interface of the Bacterial DNA Damage Response Protein UmuD.

作者信息

Murison David A, Timson Rebecca C, Koleva Bilyana N, Ordazzo Michael, Beuning Penny J

机构信息

Department of Chemistry and Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States.

出版信息

Biochemistry. 2017 Sep 12;56(36):4773-4785. doi: 10.1021/acs.biochem.7b00560. Epub 2017 Aug 29.


DOI:10.1021/acs.biochem.7b00560
PMID:28806503
Abstract

The Escherichia coli SOS response, an induced DNA damage response pathway, confers survival on bacterial cells by providing accurate repair mechanisms as well as the potentially mutagenic pathway translesion synthesis (TLS). The umuD gene products are upregulated after DNA damage and play roles in both nonmutagenic and mutagenic aspects of the SOS response. Full-length UmuD is expressed as a homodimer of 139-amino-acid subunits, which eventually cleaves its N-terminal 24 amino acids to form UmuD'. The cleavage product UmuD' and UmuC form the Y-family polymerase DNA Pol V (UmuD'C) capable of performing TLS. UmuD and UmuD' exist as homodimers, but their subunits can readily exchange to form UmuDD' heterodimers preferentially. Heterodimer formation is an essential step in the degradation pathway of UmuD'. The recognition sequence for ClpXP protease is located within the first 24 amino acids of full-length UmuD, and the partner of full-length UmuD, whether UmuD or UmuD', is degraded by ClpXP. To better understand the mechanism by which UmuD subunits exchange, we measured the kinetics of exchange of a number of fluorescently labeled single-cysteine UmuD variants as detected by Förster resonance energy transfer. Labeling sites near the dimer interface correlate with increased rates of exchange, indicating that weakening the dimer interface facilitates exchange, whereas labeling sites on the exterior decrease the rate of exchange. In most but not all cases, homodimer and heterodimer exchange exhibit similar rates, indicating that somewhat different molecular surfaces mediate homodimer exchange and heterodimer formation.

摘要

大肠杆菌的SOS反应是一种诱导性DNA损伤反应途径,它通过提供精确的修复机制以及潜在的诱变途径——跨损伤合成(TLS),使细菌细胞得以存活。umuD基因产物在DNA损伤后上调,并在SOS反应的非诱变和诱变方面发挥作用。全长UmuD以由139个氨基酸亚基组成的同二聚体形式表达,最终会切割其N端的24个氨基酸以形成UmuD'。切割产物UmuD'和UmuC形成能够进行跨损伤合成的Y家族聚合酶DNA聚合酶V(UmuD'C)。UmuD和UmuD'以同二聚体形式存在,但其亚基可以很容易地交换,优先形成UmuDD'异二聚体。异二聚体的形成是UmuD'降解途径中的一个关键步骤。ClpXP蛋白酶的识别序列位于全长UmuD的前24个氨基酸内,全长UmuD的伙伴,无论是UmuD还是UmuD',都会被ClpXP降解。为了更好地理解UmuD亚基交换的机制,我们通过Förster共振能量转移测量了一些荧光标记的单半胱氨酸UmuD变体的交换动力学。二聚体界面附近的标记位点与交换速率增加相关,这表明削弱二聚体界面有利于交换,而外部的标记位点则降低了交换速率。在大多数但并非所有情况下,同二聚体和异二聚体交换表现出相似的速率,这表明介导同二聚体交换和异二聚体形成的分子表面略有不同。

相似文献

[1]
Identification of the Dimer Exchange Interface of the Bacterial DNA Damage Response Protein UmuD.

Biochemistry. 2017-9-12

[2]
Dimer exchange and cleavage specificity of the DNA damage response protein UmuD.

Biochim Biophys Acta. 2013-2

[3]
Conformational dynamics of the Escherichia coli DNA polymerase manager proteins UmuD and UmuD'.

J Mol Biol. 2010-3-4

[4]
Regulation of SOS mutagenesis by proteolysis.

Proc Natl Acad Sci U S A. 1996-9-17

[5]
Structural insights into the regulation of SOS mutagenesis.

Acta Biochim Pol. 1998

[6]
Distinct peptide signals in the UmuD and UmuD' subunits of UmuD/D' mediate tethering and substrate processing by the ClpXP protease.

Proc Natl Acad Sci U S A. 2003-11-11

[7]
Escherichia coli DNA polymerase V subunit exchange: a post-SOS mechanism to curtail error-prone DNA synthesis.

J Biol Chem. 2003-12-26

[8]
Specific in vivo protein-protein interactions between Escherichia coli SOS mutagenesis proteins.

J Bacteriol. 1996-5

[9]
The Escherichia coli SOS mutagenesis proteins UmuD and UmuD' interact physically with the replicative DNA polymerase.

Proc Natl Acad Sci U S A. 1999-10-26

[10]
Subunit-specific degradation of the UmuD/D' heterodimer by the ClpXP protease: the role of trans recognition in UmuD' stability.

EMBO J. 2000-10-2

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[1]
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Molecules. 2019-5-7

[2]
Insight Into the Diversity and Possible Role of Plasmids in the Adaptation of Psychrotolerant and Metalotolerant spp. to Extreme Antarctic Environments.

Front Microbiol. 2018-12-18

[3]
The SOS system: A complex and tightly regulated response to DNA damage.

Environ Mol Mutagen. 2019-5

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