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Zhai F, Hao L, Chen X, Jiang T, Guo Q, Xie L, Ma Y, Du X, Zheng Z, Chen K, Fan J. Single-molecule tracking of PprI in D. radiodurans without interference of autoblinking. Front Microbiol 2023; 14:1256711. [PMID: 38029090 PMCID: PMC10652783 DOI: 10.3389/fmicb.2023.1256711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/10/2023] [Indexed: 12/01/2023] Open
Abstract
Autoblinking is a widespread phenomenon and exhibits high level of intensity in some bacteria. In Deinococcus radiodurans (D. radiodurans), strong autoblinking was found to be indistinguishable from PAmCherry and greatly prevented single-molecule tracking of proteins of interest. Here we employed the bright photoswitchable fluorescent protein mMaple3 to label PprI, one essential DNA repair factor, and characterized systematically the fluorescence intensity and bleaching kinetics of both autoblinking and PprI-mMaple3 molecules within cells grown under three different conditions. Under minimal media, we can largely separate autoblinking from mMaple3 molecules and perform reliably single-molecule tracking of PprI in D. radiodurans, by means of applying signal-to-noise ratio and constraining the minimal length for linking the trajectories. We observed three states of PprI molecules, which bear different subcellular localizations and distinct functionalities. Our strategy provides a useful means to study the dynamics and distributions of proteins of interest in bacterial cells with high level of autoblinking.
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Affiliation(s)
- Fanfan Zhai
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- NHC Key Laboratory of Nuclear Technology Medical Transformation (Mianyang Central Hospital), Mianyang, Sichuan, China
| | - Li Hao
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Xiaomin Chen
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Ting Jiang
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Qianhong Guo
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Liping Xie
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Ying Ma
- NHC Key Laboratory of Nuclear Technology Medical Transformation (Mianyang Central Hospital), Mianyang, Sichuan, China
| | - Xiaobo Du
- NHC Key Laboratory of Nuclear Technology Medical Transformation (Mianyang Central Hospital), Mianyang, Sichuan, China
| | - Zhiqin Zheng
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
- NHC Key Laboratory of Nuclear Technology Medical Transformation (Mianyang Central Hospital), Mianyang, Sichuan, China
- School of Biological Engineering and Wuliangye Liquor, Sichuan University of Science and Engineering, Yibin, Sichuan, China
| | - Kun Chen
- School of Optoelectronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- Yangtze Delta Region Institute (Huzhou), University of Electronic Science and Technology of China, Huzhou, Zhejiang, China
| | - Jun Fan
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- Yangtze Delta Region Institute (Huzhou), University of Electronic Science and Technology of China, Huzhou, Zhejiang, China
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Alekseev A, Pobegalov G, Morozova N, Vedyaykin A, Cherevatenko G, Yakimov A, Baitin D, Khodorkovskii M. A new insight into RecA filament regulation by RecX from the analysis of conformation-specific interactions. eLife 2022; 11:78409. [PMID: 35730924 PMCID: PMC9252578 DOI: 10.7554/elife.78409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 06/21/2022] [Indexed: 11/13/2022] Open
Abstract
RecA protein mediates homologous recombination repair in bacteria through assembly of long helical filaments on ssDNA in an ATP-dependent manner. RecX, an important negative regulator of RecA, is known to inhibit RecA activity by stimulating the disassembly of RecA nucleoprotein filaments. Here we use a single-molecule approach to address the regulation of (Escherichia coli) RecA-ssDNA filaments by RecX (E. coli) within the framework of distinct conformational states of RecA-ssDNA filament. Our findings revealed that RecX effectively binds the inactive conformation of RecA-ssDNA filaments and slows down the transition to the active state. Results of this work provide new mechanistic insights into the RecX-RecA interactions and highlight the importance of conformational transitions of RecA filaments as an additional level of regulation of its biological activity.
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Affiliation(s)
- Aleksandr Alekseev
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russian Federation
| | - Georgii Pobegalov
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russian Federation
| | - Natalia Morozova
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russian Federation
| | - Alexey Vedyaykin
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russian Federation
| | - Galina Cherevatenko
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russian Federation
| | - Alexander Yakimov
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russian Federation
| | - Dmitry Baitin
- Kurchatov Institute, St. Petersburg, Russian Federation
| | - Mikhail Khodorkovskii
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russian Federation
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Single-molecule characterization of compressed RecA nucleoprotein filaments. Biochem Biophys Res Commun 2022; 614:29-33. [PMID: 35567941 DOI: 10.1016/j.bbrc.2022.04.130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 04/27/2022] [Indexed: 11/21/2022]
Abstract
RecA is a central enzyme of homologous recombination in bacteria, which plays a major role in DNA repair, natural transformation and SOS-response activation. RecA forms nucleoprotein filaments on single-stranded DNA with a highly conserved architecture that is also shared by eukaryotic recombinases. One of the key features of these filaments is the ability to switch between stretched and compressed conformations in response to ATP binding and hydrolysis. However, the functional role of such conformational changes is not fully understood. Structural data revealed that in the absence of ATP RecA binds DNA with the stoichiometry of 5 nucleotides per one monomer, while in the presence of ATP the binding stoichiometry is 3:1. Such differences suggest incompatibility of the active and inactive conformations, yet dynamic single-molecule studies demonstrated that ATP and apo conformations can be directly interconvertible. In the present work we use a single-molecule approach to address the features of inactive RecA nucleoprotein filaments formed de novo in the absence of nucleotide cofactors. We show that compressed RecA-DNA filaments can exist with both 5:1 and 3:1 binding stoichiometry which is determined by conditions of the filament assembly. However, only a 3:1 stoichiometry allows direct interconvertibility with the active ATP-bound conformation.
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