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Tsaplina O, Khaitlina S, Chukhontseva K, Karaseva M, Demidyuk I, Bakhlanova I, Baitin D, Artamonova T, Vedyaykin A, Khodorkovskii M, Vishnyakov I. Protealysin Targets the Bacterial Housekeeping Proteins FtsZ and RecA. Int J Mol Sci 2022; 23:ijms231810787. [PMID: 36142700 PMCID: PMC9505478 DOI: 10.3390/ijms231810787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/09/2022] [Accepted: 09/13/2022] [Indexed: 12/04/2022] Open
Abstract
Serratia proteamaculans synthesizes the intracellular metalloprotease protealysin. This work was aimed at searching for bacterial substrates of protealysin among the proteins responsible for replication and cell division. We have shown that protealysin unlimitedly cleaves the SOS response protein RecA. Even 20% of the cleaved RecA in solution appears to be incorporated into the polymer of uncleaved monomers, preventing further polymerization and inhibiting RecA ATPase activity. Transformation of Escherichia coli with a plasmid carrying the protealysin gene reduces the bacterial UV survival up to 10 times. In addition, the protealysin substrate is the FtsZ division protein, found in both E. coli and Acholeplasma laidlawii, which is only 51% identical to E. coli FtsZ. Protealysin cleaves FtsZ at the linker between the globular filament-forming domain and the C-terminal peptide that binds proteins on the bacterial membrane. Thus, cleavage of the C-terminal segment by protealysin can lead to the disruption of FtsZ’s attachment to the membrane, and thereby inhibit bacterial division. Since the protealysin operon encodes not only the protease, but also its inhibitor, which is typical for the system of interbacterial competition, we assume that in the case of penetration of protealysin into neighboring bacteria that do not synthesize a protealysin inhibitor, cleavage of FtsZ and RecA by protealysin may give S. proteamaculans an advantage in interbacterial competition.
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Affiliation(s)
- Olga Tsaplina
- Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia
- Correspondence: ; Tel.: +7-812-297-42-96
| | - Sofia Khaitlina
- Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia
| | - Ksenia Chukhontseva
- Institute of Molecular Genetics of National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Maria Karaseva
- Institute of Molecular Genetics of National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Ilya Demidyuk
- Institute of Molecular Genetics of National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Irina Bakhlanova
- Kurchatov Genome Center—PNPI, Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of National Research Centre ‘‘Kurchatov Institute”, 188300 Gatchina, Russia
| | - Dmitry Baitin
- Kurchatov Genome Center—PNPI, Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of National Research Centre ‘‘Kurchatov Institute”, 188300 Gatchina, Russia
| | - Tatiana Artamonova
- Department of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
| | - Alexey Vedyaykin
- Department of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
| | - Mikhail Khodorkovskii
- Department of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
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Puig J, Knödlseder N, Quera J, Algara M, Güell M. DNA Damage Protection for Enhanced Bacterial Survival Under Simulated Low Earth Orbit Environmental Conditions in Escherichia coli. Front Microbiol 2022; 12:789668. [PMID: 34970246 PMCID: PMC8713957 DOI: 10.3389/fmicb.2021.789668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/23/2021] [Indexed: 11/13/2022] Open
Abstract
Some organisms have shown the ability to naturally survive in extreme environments, even outer space. Some of these have natural mechanisms to resist severe DNA damage from conditions such as ionizing and non-ionizing radiation, extreme temperatures, and low pressures or vacuum. A good example can be found in Deinococcus radiodurans, which was exposed to severe conditions such as those listed in the Exposure Facility of the International Space Station (ISS) for up to three years. Another example are tardigrades (Ramazzottius varieornatus) which are some of the most resilient animals known. In this study, the survival under simulated Low earth Orbit (LEO) environmental conditions was tested in Escherichia coli. The radiation resistance of this bacteria was enhanced using the Dsup gene from R. varieornatus, and two more genes from D. radiodurans involved in DNA damage repair, RecA and uvrD. The enhanced survival to wide ranges of temperatures and low pressures was then tested in the new strains. This research constitutes a first step in the creation of new bacterial strains engineered to survive severe conditions and adapting existing species for their survival in remote environments, including extra-terrestrial habitats. These strains could be key for the development of environments hospitable to life and could be of use for ecological restoration and space exploration. In addition, studying the efficacy and the functioning of the DNA repair mechanisms used in this study could be beneficial for medical and life sciences engineering.
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Affiliation(s)
- Jaume Puig
- Translational Synthetic Biology Laboratory, Experimental and Health Sciences Department, Universitat Pompeu Fabra, Barcelona, Spain.,Experimental and Health Sciences Department, Universitat Pompeu Fabra, Barcelona, Spain
| | - Nastassia Knödlseder
- Translational Synthetic Biology Laboratory, Experimental and Health Sciences Department, Universitat Pompeu Fabra, Barcelona, Spain.,Experimental and Health Sciences Department, Universitat Pompeu Fabra, Barcelona, Spain
| | - Jaume Quera
- Experimental and Health Sciences Department, Universitat Pompeu Fabra, Barcelona, Spain.,Radiation Oncology Department, Hospital del Mar, Parc de Salut Mar, Barcelona, Spain.,IMIM Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - Manuel Algara
- Experimental and Health Sciences Department, Universitat Pompeu Fabra, Barcelona, Spain.,Radiation Oncology Department, Hospital del Mar, Parc de Salut Mar, Barcelona, Spain.,IMIM Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - Marc Güell
- Translational Synthetic Biology Laboratory, Experimental and Health Sciences Department, Universitat Pompeu Fabra, Barcelona, Spain.,Experimental and Health Sciences Department, Universitat Pompeu Fabra, Barcelona, Spain
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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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RecA and DNA recombination: a review of molecular mechanisms. Biochem Soc Trans 2020; 47:1511-1531. [PMID: 31654073 DOI: 10.1042/bst20190558] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/18/2019] [Accepted: 09/25/2019] [Indexed: 11/17/2022]
Abstract
Recombinases are responsible for homologous recombination and maintenance of genome integrity. In Escherichia coli, the recombinase RecA forms a nucleoprotein filament with the ssDNA present at a DNA break and searches for a homologous dsDNA to use as a template for break repair. During the first step of this process, the ssDNA is bound to RecA and stretched into a Watson-Crick base-paired triplet conformation. The RecA nucleoprotein filament also contains ATP and Mg2+, two cofactors required for RecA activity. Then, the complex starts a homology search by interacting with and stretching dsDNA. Thanks to supercoiling, intersegment sampling and RecA clustering, a genome-wide homology search takes place at a relevant metabolic timescale. When a region of homology 8-20 base pairs in length is found and stabilized, DNA strand exchange proceeds, forming a heteroduplex complex that is resolved through a combination of DNA synthesis, ligation and resolution. RecA activities can take place without ATP hydrolysis, but this latter activity is necessary to improve and accelerate the process. Protein flexibility and monomer-monomer interactions are fundamental for RecA activity, which functions cooperatively. A structure/function relationship analysis suggests that the recombinogenic activity can be improved and that recombinases have an inherently large recombination potential. Understanding this relationship is essential for designing RecA derivatives with enhanced activity for biotechnology applications. For example, this protein is a major actor in the recombinase polymerase isothermal amplification (RPA) used in point-of-care diagnostics.
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Leite WC, Galvão CW, Saab SC, Iulek J, Etto RM, Steffens MBR, Chitteni-Pattu S, Stanage T, Keck JL, Cox MM. Structural and Functional Studies of H. seropedicae RecA Protein - Insights into the Polymerization of RecA Protein as Nucleoprotein Filament. PLoS One 2016; 11:e0159871. [PMID: 27447485 PMCID: PMC4957752 DOI: 10.1371/journal.pone.0159871] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/08/2016] [Indexed: 11/18/2022] Open
Abstract
The bacterial RecA protein plays a role in the complex system of DNA damage repair. Here, we report the functional and structural characterization of the Herbaspirillum seropedicae RecA protein (HsRecA). HsRecA protein is more efficient at displacing SSB protein from ssDNA than Escherichia coli RecA protein. HsRecA also promotes DNA strand exchange more efficiently. The three dimensional structure of HsRecA-ADP/ATP complex has been solved to 1.7 Å resolution. HsRecA protein contains a small N-terminal domain, a central core ATPase domain and a large C-terminal domain, that are similar to homologous bacterial RecA proteins. Comparative structural analysis showed that the N-terminal polymerization motif of archaeal and eukaryotic RecA family proteins are also present in bacterial RecAs. Reconstruction of electrostatic potential from the hexameric structure of HsRecA-ADP/ATP revealed a high positive charge along the inner side, where ssDNA is bound inside the filament. The properties of this surface may explain the greater capacity of HsRecA protein to bind ssDNA, forming a contiguous nucleoprotein filament, displace SSB and promote DNA exchange relative to EcRecA. Our functional and structural analyses provide insight into the molecular mechanisms of polymerization of bacterial RecA as a helical nucleoprotein filament.
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Affiliation(s)
- Wellington C. Leite
- Department of Physics, Ponta Grossa State University (UEPG), Av. Carlos Cavalcanti, 4748, CEP. 84.030–900, Ponta Grossa, PR, Brazil
- * E-mail: (MC); (WL)
| | - Carolina W. Galvão
- Department of Structural and Molecular Biology and Genetics, Ponta Grossa State University (UEPG), CEP 84030–900, Ponta Grossa, PR, Brazil
| | - Sérgio C. Saab
- Department of Physics, Ponta Grossa State University (UEPG), Av. Carlos Cavalcanti, 4748, CEP. 84.030–900, Ponta Grossa, PR, Brazil
| | - Jorge Iulek
- Department of Chemistry, Ponta Grossa State University (UEPG), CEP 84030–900, Ponta Grossa, PR, Brazil
| | - Rafael M. Etto
- Department of Chemistry, Ponta Grossa State University (UEPG), CEP 84030–900, Ponta Grossa, PR, Brazil
| | - Maria B. R. Steffens
- Department of Biochemistry and Molecular Biology, Federal University of Parana, CEP 81531–980 Curitiba, Brazil
| | - Sindhu Chitteni-Pattu
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI, 53706–1544, United States of America
| | - Tyler Stanage
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI, 53706–1544, United States of America
| | - James L. Keck
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53706, United States of America
| | - Michael M. Cox
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI, 53706–1544, United States of America
- * E-mail: (MC); (WL)
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Bakhlanova IV, Dudkina AV, Wood EA, Lanzov VA, Cox MM, Baitin DM. DNA Metabolism in Balance: Rapid Loss of a RecA-Based Hyperrec Phenotype. PLoS One 2016; 11:e0154137. [PMID: 27124470 PMCID: PMC4849656 DOI: 10.1371/journal.pone.0154137] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 04/09/2016] [Indexed: 12/04/2022] Open
Abstract
The RecA recombinase of Escherichia coli has not evolved to optimally promote DNA pairing and strand exchange, the key processes of recombinational DNA repair. Instead, the recombinase function of RecA protein represents an evolutionary compromise between necessary levels of recombinational DNA repair and the potentially deleterious consequences of RecA functionality. A RecA variant, RecA D112R, promotes conjugational recombination at substantially enhanced levels. However, expression of the D112R RecA protein in E. coli results in a reduction in cell growth rates. This report documents the consequences of the substantial selective pressure associated with the RecA-mediated hyperrec phenotype. With continuous growth, the deleterious effects of RecA D112R, along with the observed enhancements in conjugational recombination, are lost over the course of 70 cell generations. The suppression reflects a decline in RecA D112R expression, associated primarily with a deletion in the gene promoter or chromosomal mutations that decrease plasmid copy number. The deleterious effects of RecA D112R on cell growth can also be negated by over-expression of the RecX protein from Neisseria gonorrhoeae. The effects of the RecX proteins in vivo parallel the effects of the same proteins on RecA D112R filaments in vitro. The results indicate that the toxicity of RecA D112R is due to its persistent binding to duplex genomic DNA, creating barriers for other processes in DNA metabolism. A substantial selective pressure is generated to suppress the resulting barrier to growth.
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Affiliation(s)
- Irina V. Bakhlanova
- Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, 188300, Russia
- Peter the Great St. Petersburg Polytechnic University, Saint-Petersburg, 195251, Russia
| | - Alexandra V. Dudkina
- Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, 188300, Russia
| | - Elizabeth A. Wood
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706–1544, United States of America
| | - Vladislav A. Lanzov
- Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, 188300, Russia
| | - Michael M. Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706–1544, United States of America
| | - Dmitry M. Baitin
- Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, 188300, Russia
- Peter the Great St. Petersburg Polytechnic University, Saint-Petersburg, 195251, Russia
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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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Dudkina AV, Schvetsov AV, Bakhlanova IV, Baitin DM. Change of filamentation dynamics of RecA protein induced by D112R Amino acid substitution or ATP to dATP replacement; results in filament resistance to RecX protein action. Mol Biol 2011. [DOI: 10.1134/s0026893311030046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Bakhlanova IV, Dudkina AV, Baitin DM, Knight KL, Cox MM, Lanzov VA. Modulating cellular recombination potential through alterations in RecA structure and regulation. Mol Microbiol 2010; 78:1523-38. [PMID: 21143322 DOI: 10.1111/j.1365-2958.2010.07424.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The wild-type Escherichia coli RecA protein is a recombinase platform with unrealized recombination potential. We have explored the factors affecting recombination during conjugation with a quantitative assay. Regulatory proteins that affect RecA function have the capacity to increase or decrease recombination frequencies by factors up to sixfold. Autoinhibition by the RecA C-terminus can affect recombination frequency by factors up to fourfold. The greatest changes in recombination frequency measured here are brought about by point mutations in the recA gene. RecA variants can increase recombination frequencies by more than 50-fold. The RecA protein thus possesses an inherently broad functional range. The RecA protein of E. coli (EcRecA) is not optimized for recombination function. Instead, much of the recombination potential of EcRecA is structurally suppressed, probably reflecting cellular requirements. One point mutation in EcRecA with a particularly dramatic effect on recombination frequency, D112R, exhibits an enhanced capacity to load onto SSB-coated ssDNA, overcome the effects of regulatory proteins such as PsiB and RecX, and to pair homologous DNAs. Comparisons of key RecA protein mutants reveal two components to RecA recombination function - filament formation and the inherent DNA pairing activity of the formed filaments.
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Dudkina AV, Bakhlanova IV, Baitin DM. The new mechanism of the frequency of recombination exchanges increase by improving the synaptase activity of the RecA protein from Escherichia coli. DOKL BIOCHEM BIOPHYS 2010; 432:120-2. [DOI: 10.1134/s1607672910030075] [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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Williams JA, Luke J, Hodgson C. Strain Engineering by Genome Mass Transfer: Efficient Chromosomal Trait Transfer Method Utilizing Donor Genomic DNA and Recipient Recombineering Hosts. Mol Biotechnol 2009; 43:41-51. [DOI: 10.1007/s12033-009-9177-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2009] [Accepted: 04/24/2009] [Indexed: 11/24/2022]
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