Single-Molecule Insights into ATP-Dependent Conformational Dynamics of Nucleoprotein Filaments of Deinococcus radiodurans RecA
Abstract
:1. Introduction
2. Results
2.1. Assembly of DrRecA Filament on Single-Stranded DNA
2.2. Interconvertibility of Active and Compressed States of DrRecA–ssDNA Filament
2.3. Force–Extension Behavior of Two States of DrRecA–ssDNA Filament
2.4. Dynamics of DrRecA Filament on Double-Stranded DNA
2.5. Compression of DrRecA Filaments Is Induced by ATP Hydrolysis
3. Discussion
4. Materials and Methods
4.1. DNA Construct and Proteins
4.2. Optical Tweezers Setup
4.3. Single-Molecule Assay
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
Abbreviations
DrRecA EcRecA dsDNA | Deinococcus radiodurans RecA E. coli RecA Double-stranded DNA |
ssDNA | Single-stranded DNA |
ESDSA | Extended synthesis-dependent strand annealing |
References
- Minton, K.W. DNA repair in the extremely radioresistant bacterium Deinococcus radiodurans. Mol. Microbiol. 1994, 13, 9–15. [Google Scholar] [CrossRef] [PubMed]
- Battista, J.R. Against all odds: The survival strategies of Deinococcus radiodurans. Annu. Rev. Microbiol. 1997, 51, 203–224. [Google Scholar] [CrossRef] [PubMed]
- Cox, M.M.; Battista, J.R. Deinococcus radiodurans—The consummate survivor. Nat. Rev. Microbiol. 2005, 3, 882–892. [Google Scholar] [CrossRef] [PubMed]
- de Groot, A.; Chapon, V.; Servant, P.; Christen, R.; Saux, M.F.; Sommer, S.; Heulin, T. Deinococcus deserti sp. nov., a gamma-radiation-tolerant bacterium isolated from the Sahara Desert. Int. J. Syst. Evol. Microbiol. 2005, 55, 2441–2446. [Google Scholar] [CrossRef] [Green Version]
- Makarova, K.S.; Omelchenko, M.V.; Gaidamakova, E.K.; Matrosova, V.Y.; Vasilenko, A.; Zhai, M.; Lapidus, A.; Copeland, A.; Kim, E.; Land, M.; et al. Deinococcus geothermalis: The pool of extreme radiation resistance genes shrinks. PLoS ONE 2007, 2, e955. [Google Scholar] [CrossRef]
- Slade, D.; Radman, M. Oxidative stress resistance in Deinococcus radiodurans. Microbiol. Mol. Biol. Rev. 2011, 75, 133–191. [Google Scholar] [CrossRef] [Green Version]
- Daly, M.J.; Gaidamakova, E.K.; Matrosova, V.Y.; Kiang, J.G.; Fukumoto, R.; Lee, D.-Y.; Wehr, N.B.; Viteri, G.A.; Berlett, B.S.; Levine, R.L. Small-molecule antioxidant proteome-shields in Deinococcus radiodurans. PLoS ONE 2010, 5, e12570. [Google Scholar] [CrossRef]
- Slade, D.; Lindner, A.B.; Paul, G.; Radman, M. Recombination and replication in DNA repair of heavily irradiated Deinococcus radiodurans. Cell 2009, 136, 1044–1055. [Google Scholar] [CrossRef] [Green Version]
- Bentchikou, E.; Servant, P.; Coste, G.; Sommer, S. A major role of the RecFOR pathway in DNA double-strand-break repair through ESDSA in Deinococcus radiodurans. PLoS Genet. 2010, 6, e1000774. [Google Scholar] [CrossRef] [Green Version]
- Cox, M.M. Motoring along with the bacterial RecA protein. Nat. Rev. Mol. Cell Biol. 2007, 8, 127–138. [Google Scholar] [CrossRef]
- del Val, E.; Nasser, W.; Abaibou, H.; Reverchon, S. RecA and DNA recombination: A review of molecular mechanisms. Biochem. Soc. Trans. 2019, 47, 1511–1531. [Google Scholar] [CrossRef] [PubMed]
- Gutman, P.D.; Carroll, J.D.; lan Masters, C.; Minton, K.W. Sequencing, targeted mutagenesis and expression of a recA gene required for the extreme radioresistance of Deinococcus radiodurans. Gene 1994, 141, 31–37. [Google Scholar] [CrossRef]
- Daly, M.J.; Minton, K.W. Interchromosomal recombination in the extremely radioresistant bacterium Deinococcus radiodurans. J. Bacteriol. 1995, 177, 5495–5505. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Zahradka, K.; Slade, D.; Bailone, A.; Sommer, S.; Averbeck, D.; Petranovic, M.; Lindner, A.B.; Radman, M. Reassembly of shattered chromosomes in Deinococcus radiodurans. Nature 2006, 443, 569–573. [Google Scholar] [CrossRef]
- Tempest, P.R.; Moseley, B.E. Lack of ultraviolet mutagenesis in radiation-resistant bacteria. Mutat. Res. 1982, 104, 275–280. [Google Scholar] [CrossRef]
- Dulermo, R.; Fochesato, S.; Blanchard, L.; De Groot, A. Mutagenic lesion bypass and two functionally different RecA proteins in Deinococcus deserti. Mol. Microbiol. 2009, 74, 194–208. [Google Scholar] [CrossRef]
- Rajan, R.; Bell, C.E. Crystal structure of RecA from Deinococcus radiodurans: Insights into the structural basis of extreme radioresistance. J Mol. Biol. 2004, 344, 951–963. [Google Scholar] [CrossRef]
- Carroll, J.D.; Daly, M.J.; Minton, K.W. Expression of recA in Deinococcus radiodurans. J. Bacteriol. 1996, 178, 130–135. [Google Scholar] [CrossRef] [Green Version]
- Ogawa, T.; Yu, X.; Shinohara, A.; Egelman, E.H. Similarity of the yeast RAD51 filament to the bacterial RecA filament. Science 1993, 259, 1896–1899. [Google Scholar] [CrossRef]
- Yu, X.; Jacobs, S.A.; West, S.C.; Ogawa, T.; Egelman, E.H. Domain structure and dynamics in the helical filaments formed by RecA and Rad51 on DNA. Proc. Natl. Acad. Sci. USA 2001, 98, 8419–8424. [Google Scholar] [CrossRef] [Green Version]
- Sheridan, S.D.; Yu, X.; Roth, R.; Heuser, J.E.; Sehorn, M.G.; Sung, P.; Egelman, E.H.; Bishop, D.K. A comparative analysis of Dmc1 and Rad51 nucleoprotein filaments. Nucleic Acids Res. 2008, 36, 4057–4066. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Chen, Z.; Yang, H.; Pavletich, N.P. Mechanism of homologous recombination from the RecA–ssDNA/dsDNA structures. Nature 2008, 453, 489–494. [Google Scholar] [CrossRef] [PubMed]
- Seitz, E.M.; Brockman, J.P.; Sandler, S.J.; Clark, A.J.; Kowalczykowski, S.C. RadA protein is an archaeal RecA protein homolog that catalyzes DNA strand exchange. Genes Dev. 1998, 12, 1248–1253. [Google Scholar] [CrossRef] [PubMed]
- Bell, J.C.; Kowalczykowski, S.C. RecA: Regulation and mechanism of a molecular search engine. Trends Biochem. Sci. 2016, 41, 491–507. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Kim, J.-I.; Cox, M.M. The RecA proteins of Deinococcus radiodurans and Escherichia coli promote DNA strand exchange via inverse pathways. Proc. Natl. Acad. Sci. USA 2002, 99, 7917–7921. [Google Scholar] [CrossRef] [Green Version]
- Warfel, J.D.; LiCata, V.J. Enhanced DNA binding affinity of RecA protein from Deinococcus radiodurans. DNA Repair 2015, 31, 91–96. [Google Scholar] [CrossRef]
- Liu, J.; Ehmsen, K.T.; Heyer, W.-D.; Morrical, S.W. Presynaptic filament dynamics in homologous recombination and DNA repair. Crit. Rev. Biochem. Mol. Biol. 2011, 46, 240–270. [Google Scholar] [CrossRef] [Green Version]
- DiCapua, E.; Schnarr, M.; Ruigrok, R.W.; Lindner, P.; Timmins, P.A. Complexes of reca protein in solution: A study by small angle neutron scattering. J. Mol. Biol. 1990, 214, 557–570. [Google Scholar] [CrossRef]
- Lebedev, D.; Baitin, D.; Islamov, A.K.; Kuklin, A.; Shalguev, V.K.; Lanzov, V.; Isaev-Ivanov, V. Analytical model for determination of parameters of helical structures in solution by small angle scattering: Comparison of RecA structures by SANS. FEBS Lett. 2003, 537, 182–186. [Google Scholar] [CrossRef] [Green Version]
- Ruigrok, R.; Bohrmann, B.; Hewat, E.; Engel, A.; Kellenberger, E.; Di Capua, E. The inactive form of recA protein: The ‘compact’structure. EMBO J. 1993, 12, 9–16. [Google Scholar] [CrossRef]
- Chang, C.-F.; Rankert, D.A.; Jeng, T.-W.; Morgan, D.G.; Schmid, M.F.; Chiu, W. Cryo electron microscopy of unstained, unfixed RecA-cssDNA complexes. J. Ultrastruct. Mol. Struct. Res. 1988, 100, 166–172. [Google Scholar] [CrossRef]
- Rajpurohit, Y.S.; Bihani, S.C.; Waldor, M.K.; Misra, H.S. Phosphorylation of Deinococcus radiodurans RecA regulates its activity and may contribute to radioresistance. J. Biol. Chem. 2016, 291, 16672–16685. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Sharma, D.K.; Siddiqui, M.Q.; Gadewal, N.; Choudhary, R.K.; Varma, A.K.; Misra, H.S.; Rajpurohit, Y.S. Phosphorylation of deinococcal RecA affects its structural and functional dynamics implicated for its roles in radioresistance of Deinococcus radiodurans. J. Biomol. Struct. Dyn. 2020, 38, 114–123. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- van Loenhout, M.T.; van der Heijden, T.; Kanaar, R.; Wyman, C.; Dekker, C. Dynamics of RecA filaments on single-stranded DNA. Nucleic Acids Res. 2009, 37, 4089–4099. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Nishinaka, T.; Doi, Y.; Hara, R.; Yashima, E. Elastic behavior of RecA-DNA helical filaments. J. Mol. Biol. 2007, 370, 837–845. [Google Scholar] [CrossRef] [PubMed]
- Robertson, R.B.; Moses, D.N.; Kwon, Y.; Chan, P.; Chi, P.; Klein, H.; Sung, P.; Greene, E.C. Structural transitions within human Rad51 nucleoprotein filaments. Proc. Natl. Acad. Sci. USA 2009, 106, 12688–12693. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Kim, S.H.; Ragunathan, K.; Park, J.; Joo, C.; Kim, D.; Ha, T. Cooperative conformational transitions keep RecA filament active during ATPase cycle. J. Am. Chem. Soc. 2014, 136, 14796–14800. [Google Scholar] [CrossRef] [Green Version]
- Volodin, A.A.; Bocharova, T.N.; Smirnova, E.A.; Camerini-Otero, R.D. Reversibility, equilibration, and fidelity of strand exchange reaction between short oligonucleotides promoted by RecA protein from escherichia coli and human Rad51 and Dmc1 proteins. J. Biol. Chem. 2009, 284, 1495–1504. [Google Scholar] [CrossRef] [Green Version]
- Lee, J.Y.; Qi, Z.; Greene, E.C. ATP hydrolysis promotes duplex DNA release by the RecA presynaptic complex. J. Biol. Chem. 2016, 291, 22218–22230. [Google Scholar] [CrossRef] [Green Version]
- Danilowicz, C.; Hermans, L.; Coljee, V.; Prévost, C.; Prentiss, M. ATP hydrolysis provides functions that promote rejection of pairings between different copies of long repeated sequences. Nucleic Acids Res. 2017, 45, 8448–8462. [Google Scholar] [CrossRef] [Green Version]
- Hsu, H.-F.; Ngo, K.V.; Chitteni-Pattu, S.; Cox, M.M.; Li, H.-W. Investigating Deinococcus radiodurans RecA protein filament formation on double-stranded DNA by a real-time single-molecule approach. Biochemistry 2011, 50, 8270–8280. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- 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, 426–430. [Google Scholar] [CrossRef] [PubMed]
- Brouwer, I.; Moschetti, T.; Candelli, A.; Garcin, E.B.; Modesti, M.; Pellegrini, L.; Wuite, G.J.; Peterman, E.J. Two distinct conformational states define the interaction of human RAD51-ATP with single-stranded DNA. EMBO J. 2018, 37, e98162. [Google Scholar] [CrossRef] [PubMed]
- Candelli, A.; Holthausen, J.T.; Depken, M.; Brouwer, I.; Franker, M.A.; Marchetti, M.; Heller, I.; Bernard, S.; Garcin, E.B.; Modesti, M. Visualization and quantification of nascent RAD51 filament formation at single-monomer resolution. Proc. Natl. Acad. Sci. USA 2014, 111, 15090–15095. [Google Scholar] [CrossRef] [Green Version]
- Forget, A.L.; Kowalczykowski, S.C. Single-molecule imaging of DNA pairing by RecA reveals a three-dimensional homology search. Nature 2012, 482, 423–427. [Google Scholar] [CrossRef] [Green Version]
- Hegner, M.; Smith, S.B.; Bustamante, C. Polymerization and mechanical properties of single RecA–DNA filaments. Proc. Natl. Acad. Sci. USA 1999, 96, 10109–10114. [Google Scholar] [CrossRef] [Green Version]
- Ngo, K.V.; Molzberger, E.T.; Chitteni-Pattu, S.; Cox, M.M. Regulation of Deinococcus radiodurans RecA protein function via modulation of active and inactive nucleoprotein filament states. J. Biol. Chem. 2013, 288, 21351–21366. [Google Scholar] [CrossRef] [Green Version]
- Boyer, B.; Danilowicz, C.; Prentiss, M.; Prévost, C. Weaving DNA strands: Structural insight on ATP hydrolysis in RecA-induced homologous recombination. Nucleic Acids Res. 2019, 47, 7798–7808. [Google Scholar] [CrossRef]
- Horspool, D.R.; Coope, R.J.; Holt, R.A. Efficient assembly of very short oligonucleotides using T4 DNA Ligase. BMC Res. Notes 2010, 3, 291. [Google Scholar] [CrossRef] [Green Version]
- Candelli, A.; Hoekstra, T.P.; Farge, G.; Gross, P.; Peterman, E.J.; Wuite, G.J. A toolbox for generating single-stranded DNA in optical tweezers experiments. Biopolym. Orig. Res. Biomol. 2013, 99, 611–620. [Google Scholar] [CrossRef]
- Kim, J.I.; Sharma, A.K.; Abbott, S.N.; Wood, E.A.; Dwyer, D.W.; Jambura, A.; Minton, K.W.; Inman, R.B.; Daly, M.J.; Cox, M.M. RecA Protein from the extremely radioresistant bacterium Deinococcus radiodurans: Expression, purification, and characterization. J. Bacteriol. 2002, 184, 1649–1660. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Yakimov, A.; Pobegalov, G.; Bakhlanova, I.; Khodorkovskii, M.; Petukhov, M.; Baitin, D. Blocking the RecA activity and SOS-response in bacteria with a short α-helical peptide. Nucleic Acids Res. 2017, 45, 9788–9796. [Google Scholar] [CrossRef] [PubMed]
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Alekseev, A.; Cherevatenko, G.; Serdakov, M.; Pobegalov, G.; Yakimov, A.; Bakhlanova, I.; Baitin, D.; Khodorkovskii, M. Single-Molecule Insights into ATP-Dependent Conformational Dynamics of Nucleoprotein Filaments of Deinococcus radiodurans RecA. Int. J. Mol. Sci. 2020, 21, 7389. https://doi.org/10.3390/ijms21197389
Alekseev A, Cherevatenko G, Serdakov M, Pobegalov G, Yakimov A, Bakhlanova I, Baitin D, Khodorkovskii M. Single-Molecule Insights into ATP-Dependent Conformational Dynamics of Nucleoprotein Filaments of Deinococcus radiodurans RecA. International Journal of Molecular Sciences. 2020; 21(19):7389. https://doi.org/10.3390/ijms21197389
Chicago/Turabian StyleAlekseev, Aleksandr, Galina Cherevatenko, Maksim Serdakov, Georgii Pobegalov, Alexander Yakimov, Irina Bakhlanova, Dmitry Baitin, and Mikhail Khodorkovskii. 2020. "Single-Molecule Insights into ATP-Dependent Conformational Dynamics of Nucleoprotein Filaments of Deinococcus radiodurans RecA" International Journal of Molecular Sciences 21, no. 19: 7389. https://doi.org/10.3390/ijms21197389