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在生理条件下,单链DNA结合(SSB)蛋白的球状区域和无序区域之间经过微调的相互作用对于动态凝聚是必需的。

Fine-tuned interactions between globular and disordered regions of single-stranded DNA binding (SSB) protein are required for dynamic condensation under physiological conditions.

作者信息

Kovács Zoltán J, Ecsédi Péter, Harami Gábor M, Pálinkás János, Botros Mina, Mahmudova Lamiya, Katran Viktoria, Érfalvy Dávid, Cervenak Miklós, Smeller László, Kovács Mihály

机构信息

ELTE-MTA "Momentum" Motor Enzymology Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary.

HUN-REN-ELTE Motor Pharmacology Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary.

出版信息

Protein Sci. 2025 Apr;34(4):e70109. doi: 10.1002/pro.70109.

DOI:10.1002/pro.70109
PMID:40143738
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11947617/
Abstract

Increasing evidence points to the importance of liquid-liquid phase separation (LLPS)-driven protein condensation in both eukaryotic and bacterial cell physiology. The formation of condensates may involve interactions between both structured (globular) domains and intrinsically disordered protein regions and requires multivalency that is often brought about by oligomerization. Here we dissect such contributions by assessing engineered variants of bacterial (Escherichia coli) single-stranded DNA binding (SSB) protein whose condensation has recently been implicated in bacterial genome metabolism. A truncated SSB variant (SSBdC, lacking the conserved C-terminal peptide (CTP)) was used to assess the importance of interactions between SSB's globular oligonucleotide/oligosaccharide binding (OB) domain and the CTP. We show that OB-CTP interactions are essential for dynamic condensation in physiological (crowded, glutamate-rich) environments. Via assessment of a protein variant (SSB) from the known thermosensitive ssb-1 mutant, we also show that the perturbation of OB-OB contacts significantly impairs the stability of SSB tetramers and results in thermally induced protein aggregation, underscoring the importance of multivalence brought about by stereospecific contacts. Our data point to adaptive fine-tuning of SSB interactions to physiological condensation and demonstrate that SSB represents a versatile system for selective engineering of condensation-driving interactions between globular and disordered regions.

摘要

越来越多的证据表明,液-液相分离(LLPS)驱动的蛋白质凝聚在真核细胞和细菌细胞生理学中都具有重要意义。凝聚物的形成可能涉及结构化(球状)结构域和内在无序蛋白质区域之间的相互作用,并且需要由寡聚化产生的多价性。在这里,我们通过评估细菌(大肠杆菌)单链DNA结合(SSB)蛋白的工程变体来剖析这些贡献,其凝聚最近被认为与细菌基因组代谢有关。一种截短的SSB变体(SSBdC,缺乏保守的C末端肽(CTP))被用于评估SSB的球状寡核苷酸/寡糖结合(OB)结构域与CTP之间相互作用的重要性。我们表明,OB-CTP相互作用对于生理(拥挤、富含谷氨酸)环境中的动态凝聚至关重要。通过评估来自已知热敏性ssb-1突变体的蛋白质变体(SSB),我们还表明,OB-OB接触的扰动会显著损害SSB四聚体的稳定性,并导致热诱导的蛋白质聚集,强调了立体特异性接触带来的多价性的重要性。我们的数据表明,SSB相互作用对生理凝聚具有适应性微调,并证明SSB代表了一个用于选择性工程化球状和无序区域之间凝聚驱动相互作用的通用系统。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ec13/11947617/20eb2c9fda2f/PRO-34-e70109-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ec13/11947617/5edd638764f0/PRO-34-e70109-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ec13/11947617/fb1c263ca9ae/PRO-34-e70109-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ec13/11947617/d3136acc7026/PRO-34-e70109-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ec13/11947617/cae1f2e293ed/PRO-34-e70109-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ec13/11947617/af0b4f2c0ba6/PRO-34-e70109-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ec13/11947617/406801fb6634/PRO-34-e70109-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ec13/11947617/d19e534983f5/PRO-34-e70109-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ec13/11947617/20eb2c9fda2f/PRO-34-e70109-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ec13/11947617/5edd638764f0/PRO-34-e70109-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ec13/11947617/fb1c263ca9ae/PRO-34-e70109-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ec13/11947617/d3136acc7026/PRO-34-e70109-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ec13/11947617/cae1f2e293ed/PRO-34-e70109-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ec13/11947617/af0b4f2c0ba6/PRO-34-e70109-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ec13/11947617/406801fb6634/PRO-34-e70109-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ec13/11947617/d19e534983f5/PRO-34-e70109-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ec13/11947617/20eb2c9fda2f/PRO-34-e70109-g004.jpg

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Single-molecule biophysics experiments : Toward a physical model of a replisome.单分子生物物理实验:迈向复制体的物理模型
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How Glutamate Promotes Liquid-liquid Phase Separation and DNA Binding Cooperativity of E. coli SSB Protein.
谷氨酸如何促进大肠杆菌单链结合蛋白的液-液相分离及DNA结合协同性。
J Mol Biol. 2022 May 15;434(9):167562. doi: 10.1016/j.jmb.2022.167562. Epub 2022 Mar 26.
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The mechanism of action of the SSB interactome reveals it is the first OB-fold family of genome guardians in prokaryotes.SSB 相互作用组的作用机制揭示了它是原核生物中第一个 OB 折叠家族的基因组守护者。
Protein Sci. 2021 Sep;30(9):1757-1775. doi: 10.1002/pro.4140. Epub 2021 Jun 14.
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The emergence of phase separation as an organizing principle in bacteria.相分离作为细菌中的一种组织原则的出现。
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