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Halgasova N, Javorova R, Bocanova L, Krajcikova D, Bauer JA, Bukovska G. Characterization of a newly discovered putative DNA replication initiator from Paenibacillus polymyxa phage phiBP. Microbiol Res 2023; 274:127437. [PMID: 37327604 DOI: 10.1016/j.micres.2023.127437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/08/2023] [Accepted: 06/10/2023] [Indexed: 06/18/2023]
Abstract
The bacteriophage phiBP contains a newly discovered putative replisome organizer, a helicase loader, and a beta clamp, which together may serve to replicate its DNA. Bioinformatics analysis of the phiBP replisome organizer sequence showed that it belongs to a recently identified family of putative initiator proteins. We prepared and isolated a wild type-like recombinant protein, gpRO-HC, and a mutant protein gpRO-HCK8A, containing a lysine to alanine substitution at position 8. gpRO-HC had low ATPase activity regardless of the presence of DNA, while the ATPase activity of the mutant was significantly higher. gpRO-HC bound to both single- and double-stranded DNA substrates. Different methods showed that gpRO-HC forms higher oligomers containing about 12 subunits. This work provides the first information about another group of phage initiator proteins, which trigger DNA replication in phages infecting low GC Gram-positive bacteria.
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Affiliation(s)
- Nora Halgasova
- Department of Genomics and Biotechnology, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, 845 51 Bratislava, Slovakia.
| | - Rachel Javorova
- Department of Genomics and Biotechnology, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, 845 51 Bratislava, Slovakia.
| | - Lucia Bocanova
- Department of Genomics and Biotechnology, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, 845 51 Bratislava, Slovakia.
| | - Daniela Krajcikova
- Department of Microbial Genetics, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, 845 51 Bratislava, Slovakia.
| | - Jacob A Bauer
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, 845 51 Bratislava, Slovakia.
| | - Gabriela Bukovska
- Department of Genomics and Biotechnology, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, 845 51 Bratislava, Slovakia.
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McGrath AE, Martyn AP, Whittell LR, Dawes FE, Beck JL, Dixon NE, Kelso MJ, Oakley AJ. Crystal structures and biochemical characterization of DNA sliding clamps from three Gram-negative bacterial pathogens. J Struct Biol 2018; 204:396-405. [DOI: 10.1016/j.jsb.2018.10.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 10/20/2018] [Accepted: 10/22/2018] [Indexed: 12/19/2022]
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Wegrzyn KE, Gross M, Uciechowska U, Konieczny I. Replisome Assembly at Bacterial Chromosomes and Iteron Plasmids. Front Mol Biosci 2016; 3:39. [PMID: 27563644 PMCID: PMC4980987 DOI: 10.3389/fmolb.2016.00039] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 07/25/2016] [Indexed: 11/13/2022] Open
Abstract
The proper initiation and occurrence of DNA synthesis depends on the formation and rearrangements of nucleoprotein complexes within the origin of DNA replication. In this review article, we present the current knowledge on the molecular mechanism of replication complex assembly at the origin of bacterial chromosome and plasmid replicon containing direct repeats (iterons) within the origin sequence. We describe recent findings on chromosomal and plasmid replication initiators, DnaA and Rep proteins, respectively, and their sequence-specific interactions with double- and single-stranded DNA. Also, we discuss the current understanding of the activities of DnaA and Rep proteins required for replisome assembly that is fundamental to the duplication and stability of genetic information in bacterial cells.
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Affiliation(s)
- Katarzyna E Wegrzyn
- Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk Gdansk, Poland
| | - Marta Gross
- Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk Gdansk, Poland
| | - Urszula Uciechowska
- Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk Gdansk, Poland
| | - Igor Konieczny
- Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk Gdansk, Poland
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Abstract
Iteron-containing plasmids are model systems for studying the metabolism of extrachromosomal genetic elements in bacterial cells. Here we describe the current knowledge and understanding of the structure of iteron-containing replicons, the structure of the iteron plasmid encoded replication initiation proteins, and the molecular mechanisms for iteron plasmid DNA replication initiation. We also discuss the current understanding of control mechanisms affecting the plasmid copy number and how host chaperone proteins and proteases can affect plasmid maintenance in bacterial cells.
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Felicori L, Jameson KH, Roblin P, Fogg MJ, Garcia-Garcia T, Ventroux M, Cherrier MV, Bazin A, Noirot P, Wilkinson AJ, Molina F, Terradot L, Noirot-Gros MF. Tetramerization and interdomain flexibility of the replication initiation controller YabA enables simultaneous binding to multiple partners. Nucleic Acids Res 2016; 44:449-63. [PMID: 26615189 PMCID: PMC4705661 DOI: 10.1093/nar/gkv1318] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 11/06/2015] [Accepted: 11/10/2015] [Indexed: 11/12/2022] Open
Abstract
YabA negatively regulates initiation of DNA replication in low-GC Gram-positive bacteria. The protein exerts its control through interactions with the initiator protein DnaA and the sliding clamp DnaN. Here, we combined X-ray crystallography, X-ray scattering (SAXS), modeling and biophysical approaches, with in vivo experimental data to gain insight into YabA function. The crystal structure of the N-terminal domain (NTD) of YabA solved at 2.7 Å resolution reveals an extended α-helix that contributes to an intermolecular four-helix bundle. Homology modeling and biochemical analysis indicates that the C-terminal domain (CTD) of YabA is a small Zn-binding domain. Multi-angle light scattering and SAXS demonstrate that YabA is a tetramer in which the CTDs are independent and connected to the N-terminal four-helix bundle via flexible linkers. While YabA can simultaneously interact with both DnaA and DnaN, we found that an isolated CTD can bind to either DnaA or DnaN, individually. Site-directed mutagenesis and yeast-two hybrid assays identified DnaA and DnaN binding sites on the YabA CTD that partially overlap and point to a mutually exclusive mode of interaction. Our study defines YabA as a novel structural hub and explains how the protein tetramer uses independent CTDs to bind multiple partners to orchestrate replication initiation in the bacterial cell.
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Affiliation(s)
- Liza Felicori
- Departamento de Bioquimica e Imunologia, Universidade Federal de Minas Gerais, UFMG, 31270-901, Belo Horizonte, MG, Brazil Sys2Diag FRE3690-CNRS/ALCEDIAG, Montpellier, France
| | - Katie H Jameson
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Pierre Roblin
- Synchrotron SOLEIL-L'Orme des Merisiers Saint-Aubin- BP 48 91192 GIF-sur-YVETTE CEDEX, France
| | - Mark J Fogg
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Transito Garcia-Garcia
- INRA, UMR1319 Micalis, F-78350 Jouy-en-Josas, France AgroParisTech, UMR1319 Micalis, F-78350 Jouy-en-Josas, France
| | - Magali Ventroux
- INRA, UMR1319 Micalis, F-78350 Jouy-en-Josas, France AgroParisTech, UMR1319 Micalis, F-78350 Jouy-en-Josas, France
| | - Mickaël V Cherrier
- CNRS, UMR 5086 Bases Moléculaires et Structurales de Systèmes Infectieux, Institut de Biologie et Chimie des Protéines, 7 Passage du Vercors, F-69367 Lyon, France Université de Lyon, F-69622 Lyon, France Université Claude Bernard Lyon 1, F-69622 Villeurbanne, France
| | - Alexandre Bazin
- CNRS, UMR 5086 Bases Moléculaires et Structurales de Systèmes Infectieux, Institut de Biologie et Chimie des Protéines, 7 Passage du Vercors, F-69367 Lyon, France Université de Lyon, F-69622 Lyon, France Université Claude Bernard Lyon 1, F-69622 Villeurbanne, France
| | - Philippe Noirot
- INRA, UMR1319 Micalis, F-78350 Jouy-en-Josas, France AgroParisTech, UMR1319 Micalis, F-78350 Jouy-en-Josas, France
| | - Anthony J Wilkinson
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | | | - Laurent Terradot
- CNRS, UMR 5086 Bases Moléculaires et Structurales de Systèmes Infectieux, Institut de Biologie et Chimie des Protéines, 7 Passage du Vercors, F-69367 Lyon, France Université de Lyon, F-69622 Lyon, France Université Claude Bernard Lyon 1, F-69622 Villeurbanne, France
| | - Marie-Françoise Noirot-Gros
- INRA, UMR1319 Micalis, F-78350 Jouy-en-Josas, France AgroParisTech, UMR1319 Micalis, F-78350 Jouy-en-Josas, France
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Pierechod M, Nowak A, Saari A, Purta E, Bujnicki JM, Konieczny I. Conformation of a plasmid replication initiator protein affects its proteolysis by ClpXP system. Protein Sci 2009; 18:637-49. [PMID: 19241373 DOI: 10.1002/pro.68] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Proteins from the Rep family of DNA replication initiators exist mainly as dimers, but only monomers can initiate DNA replication by interaction with the replication origin (ori). In this study, we investigated both the activation (monomerization) and the degradation of the broad-host-range plasmid RK2 replication initiation protein TrfA, which we found to be a member of a class of DNA replication initiators containing winged helix (WH) domains. Our in vivo and in vitro experiments demonstrated that the ClpX-dependent activation of TrfA leading to replicationally active protein monomers and mutations affecting TrfA dimer formation, result in the inhibition of TrfA protein degradation by the ClpXP proteolytic system. These data revealed that the TrfA monomers and dimers are degraded at substantially different rates. Our data also show that the plasmid replication initiator activity and stability in E. coli cells are affected by ClpXP system only when the protein sustains dimeric form.
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Affiliation(s)
- Marcin Pierechod
- Department of Molecular and Cellular Biology, Faculty of Biotechnology, University of Gdansk, Gdansk, Poland
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