1
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Lee W, Iwasaki H, Tsubouchi H, Li HW. Hop2-Mnd1 and Swi5-Sfr1 stimulate Dmc1 filament assembly using distinct mechanisms. Nucleic Acids Res 2023; 51:8550-8562. [PMID: 37395447 PMCID: PMC10484676 DOI: 10.1093/nar/gkad561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 06/12/2023] [Accepted: 06/20/2023] [Indexed: 07/04/2023] Open
Abstract
In meiosis, Dmc1 recombinase and the general recombinase Rad51 are responsible for pairing homologous chromosomes and exchanging strands. Fission yeast (Schizosaccharomyces pombe) Swi5-Sfr1 and Hop2-Mnd1 stimulate Dmc1-driven recombination, but the stimulation mechanism is unclear. Using single-molecule fluorescence resonance energy transfer (smFRET) and tethered particle motion (TPM) experiments, we showed that Hop2-Mnd1 and Swi5-Sfr1 individually enhance Dmc1 filament assembly on single-stranded DNA (ssDNA) and adding both proteins together allows further stimulation. FRET analysis showed that Hop2-Mnd1 enhances the binding rate of Dmc1 while Swi5-Sfr1 specifically reduces the dissociation rate during the nucleation, about 2-fold. In the presence of Hop2-Mnd1, the nucleation time of Dmc1 filaments shortens, and doubling the ss/double-stranded DNA (ss/dsDNA) junctions of DNA substrates reduces the nucleation times in half. Order of addition experiments confirmed that Hop2-Mnd1 binds on DNA to recruit and stimulate Dmc1 nucleation at the ss/dsDNA junction. Our studies directly support the molecular basis of how Hop2-Mnd1 and Swi5-Sfr1 act on different steps during the Dmc1 filament assembly. DNA binding of these accessory proteins and nucleation preferences of recombinases thus dictate how their regulation can take place.
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Affiliation(s)
- Wei Lee
- Department of Chemistry, National Taiwan University, Taiwan
| | - Hiroshi Iwasaki
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Japan
| | - Hideo Tsubouchi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Japan
| | - Hung-Wen Li
- Department of Chemistry, National Taiwan University, Taiwan
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2
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M S, N RP, Rajendrasozhan S. Bacterial redox response factors in the management of environmental oxidative stress. World J Microbiol Biotechnol 2022; 39:11. [PMID: 36369499 DOI: 10.1007/s11274-022-03456-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 11/02/2022] [Indexed: 11/13/2022]
Abstract
Bacteria evolved to survive in the available environmental chemosphere via several cellular mechanisms. A rich pool of antioxidants and stress regulators plays a significant role in the survival of bacteria in unfavorable environmental conditions. Most of the microbes exhibit resistant phenomena in toxic environment niches. Naturally, bacteria possess efficient thioredoxin reductase, glutaredoxin, and peroxiredoxin redox systems to handle environmental oxidative stress. Further, an array of transcriptional regulators senses the oxidative stress conditions. Transcription regulators, such as OxyR, SoxRS, PerR, UspA, SsrB, MarA, OhrR, SarZ, etc., sense and transduce bacterial oxidative stress responses. The redox-sensitive transcription regulators continuously recycle the utilized antioxidant enzymes during oxidative stress. These regulators promote the expression of antioxidant enzymes such as superoxide dismutase, catalase, and peroxides that overcome oxidative insults. Therefore, the transcriptional regulations maintain steady-state activities of antioxidant enzymes representing the resistance against host cell/environmental oxidative insults. Further, the redox system provides reducing equivalents to synthesize biomolecules, thereby contributing to cellular repair mechanisms. The inactive transcriptional regulators in the undisturbed cells are activated by oxidative stress. The oxidized transcriptional regulators modulate the expression of antioxidant and cellular repair enzymes to survive in extreme environmental conditions. Therefore, targeting these antioxidant systems and response regulators could alter cellular redox homeostasis. This review presents the mechanisms of different redox systems that favor bacterial survival in extreme environmental oxidative stress conditions.
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Affiliation(s)
- Sudharsan M
- Department of Biochemistry and Biotechnology, Annamalai University, Annamalainagar, Chidambaram, Tamil Nadu, 608 002, India
| | - Rajendra Prasad N
- Department of Biochemistry and Biotechnology, Annamalai University, Annamalainagar, Chidambaram, Tamil Nadu, 608 002, India.
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3
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Fan HF, Su S. The regulation mechanism of the C-terminus of RecA proteins during DNA strand-exchange process. Biophys J 2021; 120:3166-3179. [PMID: 34197804 DOI: 10.1016/j.bpj.2021.06.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 04/21/2021] [Accepted: 06/03/2021] [Indexed: 12/14/2022] Open
Abstract
The C-terminus of Escherichia coli RecA protein can affect the DNA binding affinity, interact with accessory proteins, and regulate the RecA activity. A substantial upward shift in the pH-reaction profile of RecA-mediated DNA strand-exchange reactions was observed for C-terminal-truncated E. coli ΔC17 RecA, Deinococcus radiodurans RecA, and Deinococcus ficus RecA. Here, the process of RecA-mediated strand exchange from the beginning to the end was investigated with florescence resonance energy transfer and tethered particle motion experiments to determine the detailed regulation mechanism. RecA proteins with a shorter C-terminus possess more stable nuclei, higher DNA binding affinities, and lower protonation requirements for the formation of nucleoprotein filaments. Moreover, more stable synaptic complexes in the homologous sequence searching process were also observed for RecA proteins with a shorter C-terminus. Our results suggest that the C-terminus of RecA proteins regulates not only the formation of RecA nucleoprotein filaments but also the entrance of secondary DNA into RecA nucleoprotein filaments.
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Affiliation(s)
- Hsiu-Fang Fan
- Institute of Medical Science and Technology, Kaohsiung, Taiwan; Department of Chemistry, Kaohsiung, Taiwan; Aerosol Science Research Center, National Sun Yat-sen University, Kaohsiung, Taiwan.
| | - Shu Su
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
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4
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Lin YY, Li MH, Chang YC, Fu PY, Ohniwa RL, Li HW, Lin JJ. Dynamic DNA Shortening by Telomere-Binding Protein Cdc13. J Am Chem Soc 2021; 143:5815-5825. [PMID: 33831300 DOI: 10.1021/jacs.1c00820] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Telomeres are essential for chromosome maintenance. Cdc13 is a single-stranded telomeric DNA binding protein that caps telomeres and regulates telomerase function in yeast. Although specific binding of Cdc13 to telomeric DNA is critical for telomere protection, the detail mechanism how Cdc13-DNA complex protects telomere is unclear. Using two single-molecule methods, tethered particle motion and atomic force microscopy, we demonstrate that specific binding of Cdc13 on single-stranded telomeric DNA shortens duplex DNA into distinct states differed by ∼70-80 base pairs. DNA shortening by Cdc13 is dynamic and independent of duplex DNA sequences or length. Significantly, we found that Pif1 helicase is incapable of removing Cdc13 from the shortened DNA-Cdc13 complex, suggesting that Cdc13 forms structurally stable complex by shortening of the bound DNA. Together our data identified shortening of DNA by Cdc13 and provided an indication for efficient protection of telomere ends by the shortened DNA-Cdc13 complex.
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Affiliation(s)
- Yi-Yun Lin
- Institute of Biochemistry and Molecular Biology, National Taiwan University, Taipei City 10617, Taiwan
| | - Min-Hsuan Li
- Institute of Biochemistry and Molecular Biology, National Taiwan University, Taipei City 10617, Taiwan
| | - Yen-Chan Chang
- Department of Chemistry, National Taiwan University, Taipei City 10617, Taiwan
| | - Peng-Yu Fu
- Institute of Biochemistry and Molecular Biology, National Taiwan University, Taipei City 10617, Taiwan
| | - Ryosuke L Ohniwa
- Faculty of Medicine, University of Tsukuba, Ibaraki 305-8577, Japan.,Center for Biotechnology, National Taiwan University, Taipei City 10617, Taiwan
| | - Hung-Wen Li
- Department of Chemistry, National Taiwan University, Taipei City 10617, Taiwan
| | - Jing-Jer Lin
- Institute of Biochemistry and Molecular Biology, National Taiwan University, Taipei City 10617, Taiwan.,Institute of Biopharmaceutical Sciences, National Yang-Ming University, Taipei City 112, Taiwan
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5
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Single-Molecule Insights into ATP-Dependent Conformational Dynamics of Nucleoprotein Filaments of Deinococcus radiodurans RecA. Int J Mol Sci 2020; 21:ijms21197389. [PMID: 33036395 PMCID: PMC7583915 DOI: 10.3390/ijms21197389] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/01/2020] [Accepted: 10/04/2020] [Indexed: 11/17/2022] Open
Abstract
Deinococcus radiodurans (Dr) has one of the most robust DNA repair systems, which is capable of withstanding extreme doses of ionizing radiation and other sources of DNA damage. DrRecA, a central enzyme of recombinational DNA repair, is essential for extreme radioresistance. In the presence of ATP, DrRecA forms nucleoprotein filaments on DNA, similar to other bacterial RecA and eukaryotic DNA strand exchange proteins. However, DrRecA catalyzes DNA strand exchange in a unique reverse pathway. Here, we study the dynamics of DrRecA filaments formed on individual molecules of duplex and single-stranded DNA, and we follow conformational transitions triggered by ATP hydrolysis. Our results reveal that ATP hydrolysis promotes rapid DrRecA dissociation from duplex DNA, whereas on single-stranded DNA, DrRecA filaments interconvert between stretched and compressed conformations, which is a behavior shared by E. coli RecA and human Rad51. This indicates a high conservation of conformational switching in nucleoprotein filaments and suggests that additional factors might contribute to an inverse pathway of DrRecA strand exchange.
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6
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Fan HF, Su S, Kuo YA, Chen CJ. Influence of the C-Terminal Tail of RecA Proteins from Alkaline pH-Resistant Bacterium Deinococcus Ficus. ACS OMEGA 2020; 5:19868-19876. [PMID: 32803083 PMCID: PMC7424711 DOI: 10.1021/acsomega.0c02865] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 07/14/2020] [Indexed: 06/11/2023]
Abstract
Deinococcus ficus CC-FR2-10T, resistant to ultraviolet, ionizing radiation, and chemicals which may cause DNA damage, was identified in Taiwan. The expression level of D. ficus RecA, which has 92% sequence identity with Deinococcus radiodurans (Dr.) RecA, will be upregulated upon UV radiation. Multiple sequence alignment of RecA proteins from bacteria belonging to Escherichia coli and the Deinococcus genus reveals that the C-terminal tail of D. ficus RecA is shorter and contains less acidic residues than E. coli RecA. D. ficus RecA exhibits a higher ATPase activity toward single-stranded (ss) DNA and efficiently promotes DNA strand exchange that a filament is first formed on ssDNA, followed by uptake of the double-stranded (ds) substrate. Moreover, D. ficus RecA exhibits a pH-reaction profile for DNA strand exchange similar to E. coli ΔC17 RecA. Later, a chimera D. ficus C17 E. coli RecA with more acidic residues in the C-terminal tail was constructed and purified. Increased negativity in the C-terminal tail makes the pH reaction profile for Chimera D. ficus C17 E. coli RecA DNA strand exchange exhibit a reaction optimum similar to E. coli RecA. To sum up, D. ficus RecA exhibits reaction properties in substrate-dependent ATPase activity and DNA strand exchange similar to E. coli RecA. Our data indicate that the negativity in the C-terminal tail plays an important role in the regulation of pH-dependent DNA strand exchange activity.
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Affiliation(s)
- Hsiu-Fang Fan
- Institute
of Medical Science and Technology, National
Sun Yat-sen University, Kaohsiung 80424, Taiwan
- Department
of Chemistry, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
- Aerosol
Science Research Center, National Sun Yat-sen
University, Kaohsiung 80424, Taiwan
| | - Shu Su
- Department
of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 11221, Taiwan
| | - Ying-An Kuo
- Department
of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 11221, Taiwan
| | - Cyuan-Ji Chen
- Department
of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 11221, Taiwan
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7
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Rad51 facilitates filament assembly of meiosis-specific Dmc1 recombinase. Proc Natl Acad Sci U S A 2020; 117:11257-11264. [PMID: 32404423 DOI: 10.1073/pnas.1920368117] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Dmc1 recombinases are essential to homologous recombination in meiosis. Here, we studied the kinetics of the nucleoprotein filament assembly of Saccharomyces cerevisiae Dmc1 using single-molecule tethered particle motion experiments and in vitro biochemical assay. ScDmc1 nucleoprotein filaments are less stable than the ScRad51 ones because of the kinetically much reduced nucleation step. The lower nucleation rate of ScDmc1 results from its lower single-stranded DNA (ssDNA) affinity, compared to that of ScRad51. Surprisingly, ScDmc1 nucleates mostly on the DNA structure containing the single-stranded and duplex DNA junction with the allowed extension in the 5'-to-3' polarity, while ScRad51 nucleation depends strongly on ssDNA lengths. This nucleation preference is also conserved for mammalian RAD51 and DMC1. In addition, ScDmc1 nucleation can be stimulated by short ScRad51 patches, but not by EcRecA ones. Pull-down experiments also confirm the physical interactions of ScDmc1 with ScRad51 in solution, but not with EcRecA. Our results are consistent with a model that Dmc1 nucleation can be facilitated by a structural component (such as DNA junction and protein-protein interaction) and DNA polarity. They provide direct evidence of how Rad51 is required for meiotic recombination and highlight a regulation strategy in Dmc1 nucleoprotein filament assembly.
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8
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Lin YH, Chu CC, Fan HF, Wang PY, Cox MM, Li HW. A 5'-to-3' strand exchange polarity is intrinsic to RecA nucleoprotein filaments in the absence of ATP hydrolysis. Nucleic Acids Res 2019; 47:5126-5140. [PMID: 30916331 PMCID: PMC6547424 DOI: 10.1093/nar/gkz189] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 03/08/2019] [Accepted: 03/11/2019] [Indexed: 01/13/2023] Open
Abstract
RecA is essential to recombinational DNA repair in which RecA filaments mediate the homologous DNA pairing and strand exchange. Both RecA filament assembly and the subsequent DNA strand exchange are directional. Here, we demonstrate that the polarity of DNA strand exchange is embedded within RecA filaments even in the absence of ATP hydrolysis, at least over short DNA segments. Using single-molecule tethered particle motion, we show that successful strand exchange in the presence of ATP proceeds with a 5′-to-3′ polarity, as demonstrated previously. RecA filaments prepared with ATPγS also exhibit a 5′-to-3′ progress of strand exchange, suggesting that the polarity is not determined by RecA disassembly and/or ATP hydrolysis. RecAΔC17 mutants, lacking a C-terminal autoregulatory flap, also promote strand exchange in a 5′-to-3′ polarity in ATPγS, a polarity that is largely lost with this RecA variant when ATP is hydrolyzed. We propose that there is an inherent strand exchange polarity mediated by the structure of the RecA filament groove, associated by conformation changes propagated in a polar manner as DNA is progressively exchanged. ATP hydrolysis is coupled to polar strand exchange over longer distances, and its contribution to the polarity requires an intact RecA C-terminus.
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Affiliation(s)
- Yu-Hsuan Lin
- Department of Chemistry, National Taiwan University, 10617, Taiwan
| | - Chia-Chieh Chu
- Department of Chemistry, National Taiwan University, 10617, Taiwan
| | - Hsiu-Fang Fan
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, 11221 Taiwan
| | - Pang-Yen Wang
- Department of Chemistry, National Taiwan University, 10617, Taiwan
| | - Michael M Cox
- Department of Biochemistry, University of Wisconsin, Madison, 53706, USA
| | - Hung-Wen Li
- Department of Chemistry, National Taiwan University, 10617, Taiwan
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9
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Wang W, Ma Y, He J, Qi H, Xiao F, He S. Gene regulation for the extreme resistance to ionizing radiation of Deinococcus radiodurans. Gene 2019; 715:144008. [DOI: 10.1016/j.gene.2019.144008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 07/24/2019] [Accepted: 07/24/2019] [Indexed: 01/05/2023]
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10
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Zhao XC, Fu H, Song L, Yang YJ, Zhou EC, Liu GX, Chen XF, Li Z, Wu WQ, Zhang XH. S-DNA and RecA/RAD51-Mediated Strand Exchange in Vitro. Biochemistry 2019; 58:2009-2016. [PMID: 30900876 DOI: 10.1021/acs.biochem.8b01125] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
S-DNA (stretched DNA) is an elongated base-paired DNA conformation under high tension. Because the RecA/Rad51 family DNA recombinases form helical filaments on DNA and mediate the formation of the DNA triplex (D-loop), in which the DNA is stretched, and because the extension of these nucleoprotein filaments is similar to the extension of S-DNA, S-DNA has long been hypothesized as a possible state of DNA that participants in RecA/Rad51-mediated DNA strand exchange in homologous recombination. Such a hypothesis, however, is still lacking direct experimental studies. In this work, we have studied the polymerization and strand exchange on S-DNA mediated by Escherichia coli RecA, human Rad51, and Saccharomyces cerevisiae Rad51 by single-molecule magnetic tweezers. We report that RecA/Rad51 polymerizes faster on S-DNA than on B-DNA with the same buffer conditions. Furthermore, the RecA/Rad51-mediated DNA triplex forms faster from S-DNA than from B-DNA together with the homologous single-stranded DNA. These results provide evidence that S-DNA can interact with RecA and Rad51 and shed light on the possible functions of S-DNA.
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Affiliation(s)
- Xiao-Cong Zhao
- College of Life Sciences, The Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis , Wuhan University , Wuhan 430072 , China
| | - Hang Fu
- College of Life Sciences, The Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis , Wuhan University , Wuhan 430072 , China
| | - Lun Song
- College of Life Sciences, The Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis , Wuhan University , Wuhan 430072 , China
| | - Ya-Jun Yang
- College of Life Sciences, The Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis , Wuhan University , Wuhan 430072 , China
| | - Er-Chi Zhou
- College of Life Sciences, The Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis , Wuhan University , Wuhan 430072 , China
| | - Guang-Xue Liu
- College of Life Sciences, The Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis , Wuhan University , Wuhan 430072 , China
| | - Xue-Feng Chen
- College of Life Sciences, The Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis , Wuhan University , Wuhan 430072 , China
| | - Zhuo Li
- Third Institute of Oceanography , State Oceanic Administration , Xiamen 361005 , China
| | - Wen-Qiang Wu
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology , Henan University , Kaifeng 475001 , China
| | - Xing-Hua Zhang
- College of Life Sciences, The Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis , Wuhan University , Wuhan 430072 , China
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11
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Sharma DK, Siddiqui MQ, Gadewal N, Choudhary RK, Varma AK, Misra HS, Rajpurohit YS. Phosphorylation of deinococcal RecA affects its structural and functional dynamics implicated for its roles in radioresistance of Deinococcus radiodurans. J Biomol Struct Dyn 2019; 38:114-123. [PMID: 30688163 DOI: 10.1080/07391102.2019.1568916] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Deinococcus RecA (DrRecA) protein is a key repair enzyme and contributes to efficient DNA repair of Deinococcus radiodurans. Phosphorylation of DrRecA at Y77 (tyrosine 77) and T318 (threonine 318) residues modifies the structural and conformational switching that impart the efficiency and activity of DrRecA. Dynamics comparisons of DrRecA with its phosphorylated analogues support the idea that phosphorylation of Y77 and T318 sites could change the dynamics and conformation plasticity of DrRecA. Furthermore, docking studies showed that phosphorylation increases the binding preference of DrRecA towards dATP versus ATP and for double-strand DNA versus single-strand DNA. This work supporting the idea that phosphorylation can modulate the crucial functions of this protein and having good concordance with the experimental data. AbbreviationsDrRecADeinococcus RecADSBDNA double-strand breakshDNAheteroduplex DNASTYPKserine/threonine/tyrosine protein kinaseT318threonine 318Y77tyrosine 77Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Nikhil Gadewal
- Advance Centre for Treatment Research and Education in Cancer, Kharghar, Maharashtra, India
| | - Rajan Kumar Choudhary
- Advance Centre for Treatment Research and Education in Cancer, Kharghar, Maharashtra, India
| | - Ashok Kumar Varma
- Advance Centre for Treatment Research and Education in Cancer, Kharghar, Maharashtra, India
| | - Hari Sharan Misra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India.,Department of Atomic Energy, Homi Bhabha National Institute, Mumbai, Maharashtra, India
| | - Yogendra Singh Rajpurohit
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India.,Department of Atomic Energy, Homi Bhabha National Institute, Mumbai, Maharashtra, India
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12
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Lim S, Jung JH, Blanchard L, de Groot A. Conservation and diversity of radiation and oxidative stress resistance mechanisms in Deinococcus species. FEMS Microbiol Rev 2019; 43:19-52. [PMID: 30339218 PMCID: PMC6300522 DOI: 10.1093/femsre/fuy037] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 10/17/2018] [Indexed: 12/17/2022] Open
Abstract
Deinococcus bacteria are famous for their extreme resistance to ionising radiation and other DNA damage- and oxidative stress-generating agents. More than a hundred genes have been reported to contribute to resistance to radiation, desiccation and/or oxidative stress in Deinococcus radiodurans. These encode proteins involved in DNA repair, oxidative stress defence, regulation and proteins of yet unknown function or with an extracytoplasmic location. Here, we analysed the conservation of radiation resistance-associated proteins in other radiation-resistant Deinococcus species. Strikingly, homologues of dozens of these proteins are absent in one or more Deinococcus species. For example, only a few Deinococcus-specific proteins and radiation resistance-associated regulatory proteins are present in each Deinococcus, notably the metallopeptidase/repressor pair IrrE/DdrO that controls the radiation/desiccation response regulon. Inversely, some Deinococcus species possess proteins that D. radiodurans lacks, including DNA repair proteins consisting of novel domain combinations, translesion polymerases, additional metalloregulators, redox-sensitive regulator SoxR and manganese-containing catalase. Moreover, the comparisons improved the characterisation of several proteins regarding important conserved residues, cellular location and possible protein–protein interactions. This comprehensive analysis indicates not only conservation but also large diversity in the molecular mechanisms involved in radiation resistance even within the Deinococcus genus.
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Affiliation(s)
- Sangyong Lim
- Biotechnology Research Division, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea
| | - Jong-Hyun Jung
- Biotechnology Research Division, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea
| | | | - Arjan de Groot
- Aix Marseille Univ, CEA, CNRS, BIAM, Saint Paul-Lez-Durance, France
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13
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Anaganti N, Padwal MK, Dani P, Basu B. Pleiotropic effects of a cold shock protein homolog PprM on the proteome of Deinococcus radiodurans. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1867:98-106. [PMID: 30389625 DOI: 10.1016/j.bbapap.2018.10.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 10/26/2018] [Accepted: 10/29/2018] [Indexed: 12/15/2022]
Abstract
An extremophile D. radiodurans encodes a non-cold shock inducible cold shock protein homolog DR_0907 (also known as PprM). The DR_0907 ORF was deleted by knockout mutagenesis and the resultant deletion mutant (ΔpprM D. radiodurans) displayed growth defect as well as gamma-radiation sensitivity (D10 values = ΔpprM D. radiodurans: 12.1 kGy versus wild type (WT) D. radiodurans: 14 kGy). 2D gel based comparative proteomics revealed a comparable induction of DNA repair proteins in ΔpprM D. radiodurans and WT D. radiodurans recovering from 5 kGy gamma irradiation (60Co gamma source, dose rate: 2 kGy/h), suggesting that pprM does not cause radiation sensitivity through modulation of DdrO-regulated DNA repair genes. However, deletion of pprM did result in repression of several proteins that belonged to vital housekeeping pathways such as metabolism and protein homeostasis that might contribute to slow growth phenotype. These deficiencies intrinsic to ΔpprM D. radiodurans might also contribute to its radiation sensitivity.
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Affiliation(s)
- Narasimha Anaganti
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Mahesh Kumar Padwal
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Pratiksha Dani
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Bhakti Basu
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India.
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14
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Swi5-Sfr1 stimulates Rad51 recombinase filament assembly by modulating Rad51 dissociation. Proc Natl Acad Sci U S A 2018; 115:E10059-E10068. [PMID: 30297419 DOI: 10.1073/pnas.1812753115] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Eukaryotic Rad51 protein is essential for homologous-recombination repair of DNA double-strand breaks. Rad51 recombinases first assemble onto single-stranded DNA to form a nucleoprotein filament, required for function in homology pairing and strand exchange. This filament assembly is the first regulation step in homologous recombination. Rad51 nucleation is kinetically slow, and several accessory factors have been identified to regulate this step. Swi5-Sfr1 (S5S1) stimulates Rad51-mediated homologous recombination by stabilizing Rad51 nucleoprotein filaments, but the mechanism of stabilization is unclear. We used single-molecule tethered particle motion experiments to show that mouse S5S1 (mS5S1) efficiently stimulates mouse RAD51 (mRAD51) nucleus formation and inhibits mRAD51 dissociation from filaments. We also used single-molecule fluorescence resonance energy transfer experiments to show that mS5S1 promotes stable nucleus formation by specifically preventing mRAD51 dissociation. This leads to a reduction of nucleation size from three mRAD51 to two mRAD51 molecules in the presence of mS5S1. Compared with mRAD51, fission yeast Rad51 (SpRad51) exhibits fast nucleation but quickly dissociates from the filament. SpS5S1 specifically reduces SpRad51 disassembly to maintain a stable filament. These results clearly demonstrate the conserved function of S5S1 by primarily stabilizing Rad51 on DNA, allowing both the formation of the stable nucleus and the maintenance of filament length.
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15
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Lu CH, Chang TT, Cho CC, Lin HC, Li HW. Stable Nuclei of Nucleoprotein Filament and High ssDNA Binding Affinity Contribute to Enhanced RecA E38K Recombinase Activity. Sci Rep 2017; 7:14964. [PMID: 29097773 PMCID: PMC5668366 DOI: 10.1038/s41598-017-15088-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 10/20/2017] [Indexed: 11/10/2022] Open
Abstract
RecA plays central roles in the homologous recombination to repair double-stranded DNA break damage in E. coli. A previously identified recA strain surviving high doses of UV radiation includes a dominant RecA E38K mutation. Using single-molecule experiments, we showed that the RecA E38K variant protein assembles nucleoprotein filaments more rapidly than the wild-type RecA. We also used a single-molecule fluorescence resonance energy transfer (smFRET) experiment to compare the nucleation cluster dynamics of wild-type RecA and RecA E38K mutants on various short ssDNA substrates. At shorter ssDNA, nucleation clusters of RecA E38K form dynamically, while only few were seen in wild-type RecA. RecA E38K also forms stable nuclei by specifically lowering the dissociation rate constant, kd. These observations provide evidence that greater nuclei stability and higher ssDNA binding affinity contribute to the observed enhanced recombination activity of the RecA E38K mutant. Given that assembly of RecA nucleoprotein filaments is the first committed step in recombinational repair processes, enhancement at this step gives rise to a more efficient recombinase.
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Affiliation(s)
- Chih-Hao Lu
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Ting-Tzu Chang
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Chia-Chuan Cho
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Hui-Cin Lin
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Hung-Wen Li
- Department of Chemistry, National Taiwan University, Taipei, Taiwan.
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16
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RecA-SSB Interaction Modulates RecA Nucleoprotein Filament Formation on SSB-Wrapped DNA. Sci Rep 2017; 7:11876. [PMID: 28928411 PMCID: PMC5605508 DOI: 10.1038/s41598-017-12213-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 09/05/2017] [Indexed: 01/14/2023] Open
Abstract
E. coli RecA recombinase catalyzes the homology pairing and strand exchange reactions in homologous recombinational repair. RecA must compete with single-stranded DNA binding proteins (SSB) for single-stranded DNA (ssDNA) substrates to form RecA nucleoprotein filaments, as the first step of this repair process. It has been suggested that RecA filaments assemble mainly by binding and extending onto the free ssDNA region not covered by SSB, or are assisted by mediators. Using the tethered particle motion (TPM) technique, we monitored individual RecA filament assembly on SSB-wrapped ssDNA in real-time. Nucleation times of the RecA E38K nucleoprotein filament assembly showed no apparent dependence among DNA substrates with various ssDNA gap lengths (from 60 to 100 nucleotides) wrapped by one SSB in the (SSB)65 binding mode. Our data have shown an unexpected RecA filament assembly mechanism in which a RecA-SSB-ssDNA interaction exists. Four additional pieces of evidence support our claim: the nucleation times of the RecA assembly varied (1) when DNA substrates contained different numbers of bound SSB tetramers; (2) when the SSB wrapping mode conversion is induced; (3) when SSB C-terminus truncation mutants are used; and (4) when an excess of C-terminal peptide of SSB is present. Thus, a RecA-SSB interaction should be included in discussing RecA regulatory mechanism.
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17
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Bakhlanova IV, Baitin DM. Deinococcus radiodurans RecX and Escherichia coli RecX proteins are capable to replace each other in vivo and in vitro. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416030030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Pobegalov G, Cherevatenko G, Alekseev A, Sabantsev A, Kovaleva O, Vedyaykin A, Morozova N, Baitin D, Khodorkovskii M. Deinococcus radiodurans RecA nucleoprotein filaments characterized at the single-molecule level with optical tweezers. Biochem Biophys Res Commun 2015; 466:426-30. [DOI: 10.1016/j.bbrc.2015.09.042] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 09/08/2015] [Indexed: 01/08/2023]
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19
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Recent progress in understanding the molecular mechanisms of radioresistance in Deinococcus bacteria. Extremophiles 2015; 19:707-19. [DOI: 10.1007/s00792-015-0759-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 05/17/2015] [Indexed: 12/17/2022]
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20
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Warfel JD, LiCata VJ. Enhanced DNA binding affinity of RecA protein from Deinococcus radiodurans. DNA Repair (Amst) 2015; 31:91-6. [PMID: 26021744 DOI: 10.1016/j.dnarep.2015.05.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 05/03/2015] [Accepted: 05/04/2015] [Indexed: 11/19/2022]
Abstract
Deinococcus radiodurans (Dr) has a significantly more robust DNA repair response than Escherichia coli (Ec), which helps it survive extremely high doses of ionizing radiation and prolonged periods of desiccation. DrRecA protein plays an essential part in this DNA repair capability. In this study we directly compare the binding of DrRecA and EcRecA to the same set of short, defined single (ss) and double stranded (ds) DNA oligomers. In the absence of cofactors (ATPγS or ADP), DrRecA binds to dsDNA oligomers more than 20 fold tighter than EcRecA, and binds ssDNA up to 9 fold tighter. Binding to dsDNA oligomers in the absence of cofactor presumably predominantly monitors DNA end binding, and thus suggests a significantly higher affinity of DrRecA for ds breaks. Upon addition of ATPγS, this species-specific affinity difference is nearly abolished, as ATPγS significantly decreases the affinity of DrRecA for DNA. Other findings include that: (1) both proteins exhibit a dependence of binding affinity on the length of the ssDNA oligomer, but not the dsDNA oligomer; (2) the salt dependence of binding is modest for both species of RecA, and (3) in the absence of DNA, DrRecA produces significantly shorter and/or fewer free-filaments in solution than does EcRecA. The results suggest intrinsic biothermodynamic properties of DrRecA contribute directly to the more robust DNA repair capabilities of D. radiodurans.
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Affiliation(s)
- Jaycob D Warfel
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Vince J LiCata
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
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21
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Wang Y, Xu Q, Lu H, Lin L, Wang L, Xu H, Cui X, Zhang H, Li T, Hua Y. Protease activity of PprI facilitates DNA damage response: Mn2+-dependence and substrate sequence-specificity of the proteolytic reaction. PLoS One 2015; 10:e0122071. [PMID: 25811789 PMCID: PMC4374696 DOI: 10.1371/journal.pone.0122071] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 02/10/2015] [Indexed: 01/21/2023] Open
Abstract
The extremophilic bacterium Deinococcus radiodurans exhibits an extraordinary resistance to ionizing radiation. Previous studies established that a protein named PprI, which exists only in the Deinococcus-Thermus family, acts as a general switch to orchestrate the expression of a number of DNA damage response (DDR) proteins involved in cellular radio-resistance. Here we show that the regulatory mechanism of PprI depends on its Mn(2+)-dependent protease activity toward DdrO, a transcription factor that suppresses DDR genes’ expression. Recognition sequence-specificity around the PprI cleavage site is essential for DNA damage repair in vivo. PprI and DdrO mediate a novel DNA damage response pathway differing from the classic LexA-mediated SOS response system found in radiation-sensitive bacterium Escherichia coli. This PprI-mediated pathway in D. radiodurans is indispensable for its extreme radio-resistance and therefore its elucidation significantly advances our understanding of the DNA damage repair mechanism in this amazing organism.
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Affiliation(s)
- Yunguang Wang
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Qiang Xu
- Zhejiang Key Laboratory of Radiation Oncology, Zhejiang Cancer Research Institute, Zhejiang Cancer Hospital, Hangzhou, China
| | - Huiming Lu
- National Institute on Aging, Biomedical Research Center, National Institutes of Health, Baltimore, United States of America
| | - Lin Lin
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Liangyan Wang
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Hong Xu
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Xianyan Cui
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Hui Zhang
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Tingting Li
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Yuejin Hua
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
- * E-mail:
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22
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Piechura JR, Tseng TL, Hsu HF, Byrne RT, Windgassen TA, Chitteni-Pattu S, Battista JR, Li HW, Cox MM. Biochemical characterization of RecA variants that contribute to extreme resistance to ionizing radiation. DNA Repair (Amst) 2014; 26:30-43. [PMID: 25559557 DOI: 10.1016/j.dnarep.2014.12.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 11/26/2014] [Accepted: 12/01/2014] [Indexed: 02/01/2023]
Abstract
Among strains of Escherichia coli that have evolved to survive extreme exposure to ionizing radiation, mutations in the recA gene are prominent and contribute substantially to the acquired phenotype. Changes at amino acid residue 276, D276A and D276N, occur repeatedly and in separate evolved populations. RecA D276A and RecA D276N exhibit unique adaptations to an environment that can require the repair of hundreds of double strand breaks. These two RecA protein variants (a) exhibit a faster rate of filament nucleation on DNA, as well as a slower extension under at least some conditions, leading potentially to a distribution of the protein among a higher number of shorter filaments, (b) promote DNA strand exchange more efficiently in the context of a shorter filament, and (c) are markedly less inhibited by ADP. These adaptations potentially allow RecA protein to address larger numbers of double strand DNA breaks in an environment where ADP concentrations are higher due to a compromised cellular metabolism.
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Affiliation(s)
- Joseph R Piechura
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, United States
| | - Tzu-Ling Tseng
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Hsin-Fang Hsu
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Rose T Byrne
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, United States
| | - Tricia A Windgassen
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Sindhu Chitteni-Pattu
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, United States
| | - John R Battista
- Department of Biological Sciences, Louisiana State University and A & M College, Baton Rouge, LA 70803, United States
| | - Hung-Wen Li
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, United States.
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23
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Lu YW, Huang T, Tsai CT, Chang YY, Li HW, Hsu CH, Fan HF. Using Single-Molecule Approaches To Study Archaeal DNA-Binding Protein Alba1. Biochemistry 2013; 52:7714-22. [DOI: 10.1021/bi4010478] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yen-Wen Lu
- Department
of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, 112 Taiwan
| | - Tao Huang
- Department
of Chemistry, National Taiwan University, 106 Taiwan
| | - Cheng-Ting Tsai
- Department
of Chemistry, National Taiwan University, 106 Taiwan
| | - Yu-Yung Chang
- Department
of Agricultural Chemistry, National Taiwan University, 106 Taiwan
| | - Hung-Wen Li
- Department
of Chemistry, National Taiwan University, 106 Taiwan
| | - Chun-Hua Hsu
- Department
of Agricultural Chemistry, National Taiwan University, 106 Taiwan
- Center
for Systems Biology, National Taiwan University, 106 Taiwan
| | - Hsiu-Fang Fan
- Department
of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, 112 Taiwan
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24
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Fu H, Le S, Muniyappa K, Yan J. Dynamics and Regulation of RecA Polymerization and De-Polymerization on Double-Stranded DNA. PLoS One 2013; 8:e66712. [PMID: 23825559 PMCID: PMC3688958 DOI: 10.1371/journal.pone.0066712] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2013] [Accepted: 05/09/2013] [Indexed: 11/19/2022] Open
Abstract
The RecA filament formed on double-stranded (ds) DNA is proposed to be a functional state analogous to that generated during the process of DNA strand exchange. RecA polymerization and de-polymerization on dsDNA is governed by multiple physiological factors. However, a comprehensive understanding of how these factors regulate the processes of polymerization and de-polymerization of RecA filament on dsDNA is still evolving. Here, we investigate the effects of temperature, pH, tensile force, and DNA ends (in particular ssDNA overhang) on the polymerization and de-polymerization dynamics of the E. coli RecA filament at a single-molecule level. Our results identified the optimal conditions that permitted spontaneous RecA nucleation and polymerization, as well as conditions that could maintain the stability of a preformed RecA filament. Further examination at a nano-meter spatial resolution, by stretching short DNA constructs, revealed a striking dynamic RecA polymerization and de-polymerization induced saw-tooth pattern in DNA extension fluctuation. In addition, we show that RecA does not polymerize on S-DNA, a recently identified novel base-paired elongated DNA structure that was previously proposed to be a possible binding substrate for RecA. Overall, our studies have helped to resolve several previous single-molecule studies that reported contradictory and inconsistent results on RecA nucleation, polymerization and stability. Furthermore, our findings also provide insights into the regulatory mechanisms of RecA filament formation and stability in vivo.
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Affiliation(s)
- Hongxia Fu
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
- Department of Physics, National University of Singapore, Singapore, Singapore
| | - Shimin Le
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Kalappa Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Jie Yan
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
- Department of Physics, National University of Singapore, Singapore, Singapore
- Centre for Bioimaging Sciences, National University of Singapore, Singapore, Singapore
- * E-mail:
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25
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Chung C, Li HW. Direct observation of RecBCD helicase as single-stranded DNA translocases. J Am Chem Soc 2013; 135:8920-5. [PMID: 23718269 DOI: 10.1021/ja401626t] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The heterotrimeric Escherichia coli RecBCD enzyme comprises two helicase motors with different polarities: RecB (3'-to-5') and RecD (5'-to-3'). This superfamily I helicase is responsible for initiating DNA double-strand-break (DSB) repair in the homologous recombination pathway. We used single-molecule tethered particle motion (TPM) experiments to visualize the RecBCD helicase translocation over long single-stranded (ss) DNA (>200 nt) with no apparent secondary structure. The bead-labeled RecBCD helicases were found to bind to the surface-immobilized blunt-end DNA, and translocate along the DNA substrates containing an ssDNA gap, resulting in a gradual decrease in the bead Brownian motion. Successful observation of RecBCD translocation over a long gap in either 3'-to-5' or 5'-to-3' ssDNA direction indicates that RecBCD helicase possesses ssDNA translocase activities in both polarities. Most RecBCD active tethers showed full translocation across the ssDNA to the dsDNA region, with about 19% of enzymes dissociated from the ss/dsDNA junction after translocating across the ssDNA region. In addition, we prepared DNA substrates containing two opposite polarities (5'-to-3' and 3'-to-5') of ssDNA regions intermitted by duplex DNA. RecBCD was able to translocate across both ssDNA regions in either ssDNA orientation orders, with less than 40% of tethers dissociating when entering into the second ssDNA region. These results suggest a model that RecBCD is able to switch between ssDNA translocases and rethread the other strand of ssDNA.
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Affiliation(s)
- Cinya Chung
- Department of Chemistry, National Taiwan University, Taiwan
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26
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Ngo KV, Molzberger ET, Chitteni-Pattu S, Cox MM. Regulation of Deinococcus radiodurans RecA protein function via modulation of active and inactive nucleoprotein filament states. J Biol Chem 2013; 288:21351-21366. [PMID: 23729671 DOI: 10.1074/jbc.m113.459230] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The RecA protein of Deinococcus radiodurans (DrRecA) has a central role in genome reconstitution after exposure to extreme levels of ionizing radiation. When bound to DNA, filaments of DrRecA protein exhibit active and inactive states that are readily interconverted in response to several sets of stimuli and conditions. At 30 °C, the optimal growth temperature, and at physiological pH 7.5, DrRecA protein binds to double-stranded DNA (dsDNA) and forms extended helical filaments in the presence of ATP. However, the ATP is not hydrolyzed. ATP hydrolysis of the DrRecA-dsDNA filament is activated by addition of single-stranded DNA, with or without the single-stranded DNA-binding protein. The ATPase function of DrRecA nucleoprotein filaments thus exists in an inactive default state under some conditions. ATPase activity is thus not a reliable indicator of DNA binding for all bacterial RecA proteins. Activation is effected by situations in which the DNA substrates needed to initiate recombinational DNA repair are present. The inactive state can also be activated by decreasing the pH (protonation of multiple ionizable groups is required) or by addition of volume exclusion agents. Single-stranded DNA-binding protein plays a much more central role in DNA pairing and strand exchange catalyzed by DrRecA than is the case for the cognate proteins in Escherichia coli. The data suggest a mechanism to enhance the efficiency of recombinational DNA repair in the context of severe genomic degradation in D. radiodurans.
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Affiliation(s)
- Khanh V Ngo
- From the Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Eileen T Molzberger
- From the Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Sindhu Chitteni-Pattu
- From the Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Michael M Cox
- From the Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706.
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27
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Assaying the binding strength of G-quadruplex ligands using single-molecule TPM experiments. Anal Biochem 2013; 436:101-8. [DOI: 10.1016/j.ab.2013.01.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 01/10/2013] [Accepted: 01/18/2013] [Indexed: 01/31/2023]
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28
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Bakhlanova IV, Dudkina AV, Baitin DM. Enzymatic control of homologous recombination and hyperrecombination in Escherichia coli. Mol Biol 2013. [DOI: 10.1134/s0026893313020039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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