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不同细菌生长条件下大肠杆菌复制蛋白的相互作用网络。

Interaction networks of Escherichia coli replication proteins under different bacterial growth conditions.

机构信息

Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdansk, Gdansk, 80-308, Poland.

Univ Lyon, Université Claude Bernard Lyon 1, INSA-Lyon, Lyon, CNRS, UMR5240 MAP, F-69622, France.

出版信息

Sci Data. 2023 Nov 10;10(1):788. doi: 10.1038/s41597-023-02710-1.

DOI:10.1038/s41597-023-02710-1
PMID:37949936
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10638427/
Abstract

In this work we analyzed protein-protein interactions (PPIs) formed by E. coli replication proteins under three disparate bacterial growth conditions. The chosen conditions corresponded to fast exponential growth, slow exponential growth and growth cessation at the stationary phase. We performed affinity purification coupled with mass spectrometry (AP-MS) of chromosomally expressed proteins (DnaA, DnaB, Hda, SeqA, DiaA, DnaG, HolD, NrdB), tagged with sequential peptide affinity (SPA) tag. Composition of protein complexes was characterized using MaxQuant software. To filter out unspecific interactions, we employed double negative control system and we proposed qualitative and quantitative data analysis strategies that can facilitate hits identification in other AP-MS datasets. Our motivation to undertake this task was still insufficient understanding of molecular mechanisms coupling DNA replication to cellular growth. Previous works suggested that such control mechanisms could involve physical interactions of replication factors with metabolic or cell envelope proteins. However, the dynamic replication protein interaction network (PIN) obtained in this study can be used to characterize links between DNA replication and various cellular processes in other contexts.

摘要

在这项工作中，我们分析了三种不同细菌生长条件下大肠杆菌复制蛋白形成的蛋白质-蛋白质相互作用（PPIs）。选择的条件分别对应于快速指数生长、缓慢指数生长和生长停滞在静止期。我们对染色体表达的蛋白质（DnaA、DnaB、Hda、SeqA、DiaA、DnaG、HolD、NrdB）进行了亲和纯化结合质谱（AP-MS），这些蛋白质都带有顺序肽亲和（SPA）标签。使用 MaxQuant 软件对蛋白质复合物的组成进行了表征。为了过滤非特异性相互作用，我们采用了双阴性对照系统，并提出了定性和定量数据分析策略，这有助于在其他 AP-MS 数据集识别命中。我们开展这项任务的动机仍然是对将 DNA 复制与细胞生长相偶联的分子机制的理解不足。以前的工作表明，这种控制机制可能涉及复制因子与代谢或细胞包膜蛋白的物理相互作用。然而，本研究获得的动态复制蛋白相互作用网络（PIN）可用于在其他背景下描述 DNA 复制与各种细胞过程之间的联系。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b053/10638427/c3a1fc55098f/41597_2023_2710_Fig11_HTML.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b053/10638427/4f04ef0348f8/41597_2023_2710_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b053/10638427/bc50674d6cdd/41597_2023_2710_Fig8_HTML.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b053/10638427/3ca9f5ac23ed/41597_2023_2710_Fig10_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b053/10638427/c3a1fc55098f/41597_2023_2710_Fig11_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b053/10638427/cbdf041d066e/41597_2023_2710_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b053/10638427/df50c8078eba/41597_2023_2710_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b053/10638427/331b11853e18/41597_2023_2710_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b053/10638427/60a89b7d4dda/41597_2023_2710_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b053/10638427/847f63cbd368/41597_2023_2710_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b053/10638427/92e5e0ed452d/41597_2023_2710_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b053/10638427/4f04ef0348f8/41597_2023_2710_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b053/10638427/bc50674d6cdd/41597_2023_2710_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b053/10638427/2ca2fbf6dab6/41597_2023_2710_Fig9_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b053/10638427/3ca9f5ac23ed/41597_2023_2710_Fig10_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b053/10638427/c3a1fc55098f/41597_2023_2710_Fig11_HTML.jpg

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