1
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Burguera S, Sahu AK, Chávez Romero MJ, Biswal HS, Bauzá A. Manganese matere bonds in biological systems: PDB inspection and DFT calculations. Phys Chem Chem Phys 2024; 26:18606-18613. [PMID: 38919033 DOI: 10.1039/d4cp01701c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
A Protein Data Bank (PDB) survey has revealed noncovalent contacts involving Mn centres and protein residues. Their geometrical features are in line with the interaction between low electron density sites located along the Mn-O/N coordination bonds (σ-holes) and the lone pairs belonging to TYR, SER or HIS residues, known as a matere bond (MaB). Calculations at the PBE0-D3/def2-TZVP level of theory were used to investigate the strength and shed light on the physical nature of the interaction. We expect the results presented herein will be useful for those scientists working in the fields of bioinorganic chemistry, particulary in protein-metal docking, by providing new insights into transition metal⋯Lewis base interactions as well as a retrospective point of view to further understand the structural and functional implications of this key transition metal ion.
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Affiliation(s)
- Sergi Burguera
- Department of Chemistry, Universitat de les Illes Balears, Ctra. de Valldemossa km 7.5, 07122 Palma de Mallorca, Baleares, Spain.
| | - Akshay Kumar Sahu
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni, Khurda, 752050, Bhubaneswar, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Michael Jordan Chávez Romero
- Department of Chemistry, Universitat de les Illes Balears, Ctra. de Valldemossa km 7.5, 07122 Palma de Mallorca, Baleares, Spain.
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Via-Jatni, Khurda, 752050, Bhubaneswar, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Antonio Bauzá
- Department of Chemistry, Universitat de les Illes Balears, Ctra. de Valldemossa km 7.5, 07122 Palma de Mallorca, Baleares, Spain.
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2
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Jaiswal R, Santosh V, Braud B, Washington A, Escalante CR. Cryo-EM Structure of AAV2 Rep68 bound to integration site AAVS1: Insights into the mechanism of DNA melting. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.02.587759. [PMID: 38617369 PMCID: PMC11014581 DOI: 10.1101/2024.04.02.587759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
The Rep68 protein from Adeno-Associated Virus (AAV) is a multifunctional SF3 helicase that performs most of the DNA transactions required for the viral life cycle. During AAV DNA replication, Rep68 assembles at the origin and catalyzes the DNA melting and nicking reactions during the hairpin rolling replication process to complete the second-strand synthesis of the AAV genome. Here, we report the Cryo-EM structures of Rep68 bound to double-stranded DNA (dsDNA) containing the sequence of the AAVS1 integration site in different nucleotide-bound states. In the apo state, Rep68 forms a heptameric complex around DNA, with three Origin Binding Domains (OBDs) bound to the Rep Binding Site (RBS) sequence and three other OBDs forming transient dimers with them. The AAA+ domains form an open ring with no interactions between subunits and with DNA. We hypothesize the heptameric quaternary structure is necessary to load onto dsDNA. In the ATPγS-bound state, a subset of three subunits binds the nucleotide, undergoing a large conformational change, inducing the formation of intersubunit interactions interaction and interaction with three consecutive DNA phosphate groups. Moreover, the induced conformational change positions three phenylalanine residues to come in close contact with the DNA backbone, producing a distortion in the DNA. We propose that the phenylalanine residues can potentially act as a hydrophobic wedge in the DNA melting process.
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Affiliation(s)
- R. Jaiswal
- Department of Physiology and Biophysics, Virginia Commonwealth University, School of Medicine, Richmond VA, 23298
- Current address: Department of Biochemistry and Molecular Biology, University of Arkansas for the Medical Sciences, Little Rock AR 72205
| | - V. Santosh
- Department of Physiology and Biophysics, Virginia Commonwealth University, School of Medicine, Richmond VA, 23298
- Current address: US Army DEVCOM Chemical Biological Center, Gunpowder MD
| | - B. Braud
- Department of Physiology and Biophysics, Virginia Commonwealth University, School of Medicine, Richmond VA, 23298
| | - A. Washington
- Department of Physiology and Biophysics, Virginia Commonwealth University, School of Medicine, Richmond VA, 23298
- Current address: Mayo Clinic Graduate School of Biomedical Research, Department of Biochemistry and Molecular Biology, Rochester, MN 55905
| | - Carlos R. Escalante
- Department of Physiology and Biophysics, Virginia Commonwealth University, School of Medicine, Richmond VA, 23298
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3
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Du J, Kong Y, Wen Y, Shen E, Xing H. HUH Endonuclease: A Sequence-specific Fusion Protein Tag for Precise DNA-Protein Conjugation. Bioorg Chem 2024; 144:107118. [PMID: 38330720 DOI: 10.1016/j.bioorg.2024.107118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 01/01/2024] [Accepted: 01/09/2024] [Indexed: 02/10/2024]
Abstract
Synthetic DNA-protein conjugates have found widespread applications in diagnostics and therapeutics, prompting a growing interest in developing chemical biology methodologies for the precise and site-specific preparation of covalent DNA-protein conjugates. In this review article, we concentrate on techniques to achieve precise control over the structural and site-specific aspects of DNA-protein conjugates. We summarize conventional methods involving unnatural amino acids and self-labeling proteins, accompanied by a discussion of their potential limitations. Our primary focus is on introducing HUH endonuclease as a novel generation of fusion protein tags for DNA-protein conjugate preparation. The detailed conjugation mechanisms and structures of representative endonucleases are surveyed, showcasing their advantages as fusion protein tag in sequence selectivity, biological orthogonality, and no requirement for DNA modification. Additionally, we present the burgeoning applications of HUH-tag-based DNA-protein conjugates in protein assembly, biosensing, and gene editing. Furthermore, we delve into the future research directions of the HUH-tag, highlighting its significant potential for applications in the biomedical and DNA nanotechnology fields.
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Affiliation(s)
- Jiajun Du
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, School of Chemistry and Chemical Engineering Hunan University Changsha, Hunan 410082, PR China
| | - Yuhan Kong
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, School of Chemistry and Chemical Engineering Hunan University Changsha, Hunan 410082, PR China
| | - Yujian Wen
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, School of Chemistry and Chemical Engineering Hunan University Changsha, Hunan 410082, PR China
| | - Enxi Shen
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, School of Chemistry and Chemical Engineering Hunan University Changsha, Hunan 410082, PR China
| | - Hang Xing
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, School of Chemistry and Chemical Engineering Hunan University Changsha, Hunan 410082, PR China.
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4
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Komiya E, Takamatsu S, Miura D, Tsukakoshi K, Tsugawa W, Sode K, Ikebukuro K, Asano R. Exploration and Application of DNA-Binding Proteins to Make a Versatile DNA-Protein Covalent-Linking Patch (D-Pclip): The Case of a Biosensing Element. J Am Chem Soc 2024; 146:4087-4097. [PMID: 38295327 PMCID: PMC10870700 DOI: 10.1021/jacs.3c12668] [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: 11/11/2023] [Revised: 01/06/2024] [Accepted: 01/08/2024] [Indexed: 02/02/2024]
Abstract
DNA-protein complexes are attractive components with broad applications in various research fields, such as DNA aptamer-enzyme complexes as biosensing elements. However, noncovalent DNA-protein complexes often decrease detection sensitivity because they are highly susceptible to environmental conditions. In this study, we developed a versatile DNA-protein covalent-linking patch (D-Pclip) for fabricating covalent and stoichiometric DNA-protein complexes. We comprehensively explored the database to determine the DNA-binding ability of the candidates and selected UdgX as the only uracil-DNA glycosylase known to form covalent bonds with DNA via uracil, with a binding efficiency >90%. We integrated a SpyTag/SpyCatcher protein-coupling system into UdgX to create a universal and convenient D-Pclip. The usability of D-Pclip was shown by preparing a stoichiometric model complex of a hemoglobin (Hb)-binding aptamer and glucose oxidase (GOx) by mixing at 4 °C. The prepared aptamer-GOx complexes detected Hb in a dose-dependent manner within the clinically required detection range in buffer and human serum without any washing procedures. D-Pclip covalently connects any uracil-inserted DNA sequence and any SpyCatcher-fused protein stoichiometrically; therefore, it has a high potential for various applications.
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Affiliation(s)
- Erika Komiya
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Shouhei Takamatsu
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Daimei Miura
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Kaori Tsukakoshi
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Wakako Tsugawa
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Koji Sode
- Joint
Department of Biomedical Engineering, University
of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, North Carolina 27599, United States
- Institute
of Global Innovation Research, Tokyo University
of Agriculture and Technology, 3-8-1 Harumi-cho, Fuchu, Tokyo 183-8509, Japan
| | - Kazunori Ikebukuro
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Ryutaro Asano
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
- Institute
of Global Innovation Research, Tokyo University
of Agriculture and Technology, 3-8-1 Harumi-cho, Fuchu, Tokyo 183-8509, Japan
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5
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Tejero M, Duzenli OF, Caine C, Kuoch H, Aslanidi G. Bioengineered Hybrid Rep 2/6 Gene Improves Encapsulation of a Single-Stranded Expression Cassette into AAV6 Vectors. Genes (Basel) 2023; 14:1866. [PMID: 37895215 PMCID: PMC10606878 DOI: 10.3390/genes14101866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/18/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
The production of clinical-grade recombinant adeno-associated viral (AAV) vectors for gene therapy trials remains a major hurdle in the further advancement of the gene therapy field. During the past decades, AAV research has been predominantly focused on the development of new capsid modifications, vector-associated immunogenicity, and the scale-up vector production. However, limited studies have examined the possibility to manipulate non-structural components of AAV such as the Rep genes. Historically, naturally isolated, or recombinant library-derived AAV capsids have been produced using the AAV serotype 2 Rep gene to package ITR2-flanked vector genomes. In the current study, we mutated four variable amino acids in the conservative part of the binding domain in AAV serotype 6 Rep to generate a Rep2/6 hybrid gene. This newly generated Rep2/6 hybrid had improved packaging ability over wild-type Rep6. AAV vectors produced with Rep2/6 exhibited similar in vivo activity as standard AAV6 vectors. Furthermore, we show that this Rep2/6 hybrid also improves full/empty capsid ratios, suggesting that Rep bioengineering can be used to improve the ratio of fully encapsulated AAV vectors during upstream manufacturing processes.
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Affiliation(s)
- Marcos Tejero
- Hormel Institute, University of Minnesota, 801 16th Avenue NE, Austin, MN 55455, USA; (M.T.)
| | - Ozgun F. Duzenli
- Hormel Institute, University of Minnesota, 801 16th Avenue NE, Austin, MN 55455, USA; (M.T.)
| | - Colin Caine
- Hormel Institute, University of Minnesota, 801 16th Avenue NE, Austin, MN 55455, USA; (M.T.)
| | - Hisae Kuoch
- Hormel Institute, University of Minnesota, 801 16th Avenue NE, Austin, MN 55455, USA; (M.T.)
| | - George Aslanidi
- Hormel Institute, University of Minnesota, 801 16th Avenue NE, Austin, MN 55455, USA; (M.T.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Institute Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
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6
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Machón C, Ruiz-Masó JA, Amodio J, Boer DR, Bordanaba-Ruiseco L, Bury K, Konieczny I, del Solar G, Coll M. Structures of pMV158 replication initiator RepB with and without DNA reveal a flexible dual-function protein. Nucleic Acids Res 2023; 51:1458-1472. [PMID: 36688326 PMCID: PMC9943647 DOI: 10.1093/nar/gkac1271] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 12/20/2022] [Accepted: 01/03/2023] [Indexed: 01/24/2023] Open
Abstract
DNA replication is essential to all living organisms as it ensures the fidelity of genetic material for the next generation of dividing cells. One of the simplest replication initiation mechanisms is the rolling circle replication. In the streptococcal plasmid pMV158, which confers antibiotic resistance to tetracycline, replication initiation is catalysed by RepB protein. The RepB N-terminal domain or origin binding domain binds to the recognition sequence (bind locus) of the double-strand origin of replication and cleaves one DNA strand at a specific site within the nic locus. Using biochemical and crystallographic analyses, here we show how the origin binding domain recognises and binds to the bind locus using structural elements removed from the active site, namely the recognition α helix, and a β-strand that organises upon binding. A new hexameric structure of full-length RepB that highlights the great flexibility of this protein is presented, which could account for its ability to perform different tasks, namely bind to two distinct loci and cleave one strand of DNA at the plasmid origin.
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Affiliation(s)
| | | | - Juliana Amodio
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10-12, 08028 Barcelona, Spain,Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - D Roeland Boer
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10-12, 08028 Barcelona, Spain,Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Lorena Bordanaba-Ruiseco
- Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Katarzyna Bury
- Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | - Igor Konieczny
- Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | - Gloria del Solar
- Correspondence may also be addressed to Gloria del Solar. Tel: +34 918373112 (Ext 4413); Fax: +34 915360432;
| | - Miquel Coll
- To whom correspondence should be addressed. Tel: +34 93 4034951; Fax: +34 93 4034979;
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7
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Thomsen J, Schmitz RA. Generating a Small Shuttle Vector for Effective Genetic Engineering of Methanosarcina mazei Allowed First Insights in Plasmid Replication Mechanism in the Methanoarchaeon. Int J Mol Sci 2022; 23:ijms231911910. [PMID: 36233214 PMCID: PMC9569500 DOI: 10.3390/ijms231911910] [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: 09/08/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 11/16/2022] Open
Abstract
Due to their role in methane production, methanoarchaea are of high ecological relevance and genetic systems have been ever more established in the last two decades. The system for protein expression in Methanosarcina using a comprehensive shuttle vector is established; however, details about its replication mechanism in methanoarchaea remain unknown. Here, we report on a significant optimisation of the rather large shuttle vector pWM321 (8.9 kbp) generated by Metcalf through a decrease in its size by about 35% by means of the deletion of several non-coding regions and the ssrA gene. The resulting plasmid (pRS1595) still stably replicates in M. mazei and—most likely due to its reduced size—shows a significantly higher transformation efficiency compared to pWM321. In addition, we investigate the essential gene repA, coding for a rep type protein. RepA was heterologously expressed in Escherichia coli, purified and characterised, demonstrating the significant binding and nicking activity of supercoiled plasmid DNA. Based on our findings we propose that the optimised shuttle vector replicates via a rolling circle mechanism with RepA as the initial replication protein in Methanosarcina. On the basis of bioinformatic comparisons, we propose the presence and location of a double-strand and a single-strand origin, which need to be further verified.
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8
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A Structural Perspective of Reps from CRESS-DNA Viruses and Their Bacterial Plasmid Homologues. Viruses 2021; 14:v14010037. [PMID: 35062241 PMCID: PMC8780604 DOI: 10.3390/v14010037] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 11/17/2022] Open
Abstract
Rolling circle replication (RCR) is ubiquitously used by cellular and viral systems for genome and plasmid replication. While the molecular mechanism of RCR has been described, the structural mechanism is desperately lacking. Circular-rep encoded single stranded DNA (CRESS-DNA) viruses employ a viral encoded replicase (Rep) to initiate RCR. The recently identified prokaryotic homologues of Reps may also be responsible for initiating RCR. Reps are composed of an endonuclease, oligomerization, and ATPase domain. Recent structural studies have provided structures for all these domains such that an overall mechanism of RCR initiation can begin to be synthesized. However, structures of Rep in complex with its various DNA substrates and/or ligands are lacking. Here we provide a 3D bioinformatic review of the current structural information available for Reps. We combine an excess of 1590 sequences with experimental and predicted structural data from 22 CRESS-DNA groups to identify similarities and differences between Reps that lead to potentially important functional sites. Experimental studies of these sites may shed light on how Reps execute their functions. Furthermore, we identify Rep-substrate or Rep-ligand structures that are urgently needed to better understand the structural mechanism of RCR.
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9
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The Facts and Family Secrets of Plasmids That Replicate via the Rolling-Circle Mechanism. Microbiol Mol Biol Rev 2021; 86:e0022220. [PMID: 34878299 DOI: 10.1128/mmbr.00222-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Plasmids are self-replicative DNA elements that are transferred between bacteria. Plasmids encode not only antibiotic resistance genes but also adaptive genes that allow their hosts to colonize new niches. Plasmid transfer is achieved by conjugation (or mobilization), phage-mediated transduction, and natural transformation. Thousands of plasmids use the rolling-circle mechanism for their propagation (RCR plasmids). They are ubiquitous, have a high copy number, exhibit a broad host range, and often can be mobilized among bacterial species. Based upon the replicon, RCR plasmids have been grouped into several families, the best known of them being pC194 and pUB110 (Rep_1 family), pMV158 and pE194 (Rep_2 family), and pT181 and pC221 (Rep_trans family). Genetic traits of RCR plasmids are analyzed concerning (i) replication mediated by a DNA-relaxing initiator protein and its interactions with the cognate DNA origin, (ii) lagging-strand origins of replication, (iii) antibiotic resistance genes, (iv) mobilization functions, (v) replication control, performed by proteins and/or antisense RNAs, and (vi) the participating host-encoded functions. The mobilization functions include a relaxase initiator of transfer (Mob), an origin of transfer, and one or two small auxiliary proteins. There is a family of relaxases, the MOBV family represented by plasmid pMV158, which has been revisited and updated. Family secrets, like a putative open reading frame of unknown function, are reported. We conclude that basic research on RCR plasmids is of importance, and our perspectives contemplate the concept of One Earth because we should incorporate bacteria into our daily life by diminishing their virulence and, at the same time, respecting their genetic diversity.
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10
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Valdelvira R, Bordanaba-Ruiseco L, Martín-Huestamendía C, Ruiz-Masó JA, Del Solar G. Acidic pH Decreases the Endonuclease Activity of Initiator RepB and Increases the Stability of the Covalent RepB-DNA Intermediate while Has Only a Limited Effect on the Replication of Plasmid pMV158 in Lactococcus lactis. Front Mol Biosci 2021; 8:634461. [PMID: 33889596 PMCID: PMC8056398 DOI: 10.3389/fmolb.2021.634461] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 01/27/2021] [Indexed: 11/28/2022] Open
Abstract
Plasmid vectors constitute a valuable tool for homologous and heterologous gene expression, for characterization of promoter and regulatory regions, and for genetic manipulation and labeling of bacteria. During the last years, a series of vectors based on promiscuous replicons of the pMV158 family have been developed for their employment in a variety of Gram-positive bacteria and proved to be useful for all above applications in lactic acid bacteria. A proper use of the plasmid vectors requires detailed knowledge of their main replicative features under the changing growth conditions of the studied bacteria, such as the acidification of the culture medium by lactic acid production. Initiation of pMV158 rolling-circle replication is catalyzed by the plasmid-encoded RepB protein, which performs a sequence-specific cleavage on one of the parental DNA strands and, as demonstrated in this work, establishes a covalent bond with the 5′-P end generated in the DNA. This covalent adduct must last until the leading-strand termination stage, where a new cleavage on the regenerated nick site and a subsequent strand-transfer reaction result in rejoining of the ends of the cleaved parental strand, whereas hydrolysis of the newly-generated adduct would release the protein from a nicked double-stranded DNA plasmid form. We have analyzed here the effect of pH on the different in vitro reactions catalyzed by RepB and on the in vivo replication ability of plasmid pMV158. We show that acidic pH greatly impairs the catalytic activity of the protein and reduces hydrolysis of the covalent RepB-DNA adduct, as expected for the nucleophilic nature of these reactions. Conversely, the ability of pMV158 to replicate in vivo, as monitored by the copy number and segregational stability of the plasmid in Lactococcus lactis, remains almost intact at extracellular pHs ranging from 7.0 to 5.0, and a significant reduction (by ∼50%) in the plasmid copy number per chromosome equivalent is only observed at pH 4.5. Moreover, the RepB to pMV158 molar ratio is increased at pH 4.5, suggesting the existence of compensatory mechanisms that operate in vivo to allow pMV158 replication at pH values that severely disturb the catalytic activity of the initiator protein.
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Affiliation(s)
- Rafael Valdelvira
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Lorena Bordanaba-Ruiseco
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Cristina Martín-Huestamendía
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - José Angel Ruiz-Masó
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Gloria Del Solar
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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11
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Heilers JH, Reiners J, Heller EM, Golzer A, Smits SHJ, van der Does C. DNA processing by the MOBH family relaxase TraI encoded within the gonococcal genetic island. Nucleic Acids Res 2019; 47:8136-8153. [PMID: 31276596 PMCID: PMC6736028 DOI: 10.1093/nar/gkz577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 06/18/2019] [Accepted: 06/26/2019] [Indexed: 11/26/2022] Open
Abstract
Relaxases of the MOBH family are often found on large plasmids, genetic islands and integrative conjugative elements. Many members of this family contain an N-terminal relaxase domain (TraI_2) followed by a disordered middle part and a C-terminal domain of unknown function (TraI_2_C). The TraI_2 domain contains two putative metal-binding motifs, an HD domain motif and an alternative 3H motif. TraI, encoded within the gonococcal genetic island of Neisseria gonorrhoeae, is the prototype of the MOBH family. SAXS experiments showed that TraI_2 and TraI_2_C form globular structures separated by an extended middle domain. The TraI_2 domain cleaves oriT-ssDNA in a site-specific Mn2+ or Co2+ dependent manner. The minimal oriT encompasses 50 nucleotides, requires an inverted repeat 3′ of the nic-site and several nucleotides around nic for efficient cleavage. Surprisingly, no stable covalent relaxase-DNA intermediate was observed. Mutagenesis of conserved tyrosines showed that cleavage was abolished in the Y212A mutant, whereas the Y212F and Y212H mutants retained residual activity. The HD and the alternative 3H motifs were essential for cleavage and the HD domain residues D162 and D267 for metal ion binding. We propose that the active site binds two metal ions, one in a high-affinity and one in a low-affinity site.
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Affiliation(s)
- Jan-Hendrik Heilers
- Institute for Biology II, Microbiology, Albert Ludwig University Freiburg, 79104 Freiburg, Germany
| | - Jens Reiners
- Biochemie I, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany.,Center for Structural Studies, Heinrich Heine University, 40225 Düsseldorf, Germany
| | | | - Annika Golzer
- Institute for Biology II, Microbiology, Albert Ludwig University Freiburg, 79104 Freiburg, Germany
| | - Sander H J Smits
- Biochemie I, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany.,Center for Structural Studies, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Chris van der Does
- Institute for Biology II, Microbiology, Albert Ludwig University Freiburg, 79104 Freiburg, Germany
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12
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Lorenzo-Diaz F, Moreno-Córdoba I, Espinosa M. Complete labelling of pneumococcal DNA-binding proteins with seleno-L-methionine. J Microbiol Methods 2019; 166:105720. [PMID: 31518592 DOI: 10.1016/j.mimet.2019.105720] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 09/06/2019] [Accepted: 09/09/2019] [Indexed: 10/26/2022]
Abstract
Streptococcus pneumoniae is a pathogenic and opportunistic Gram-positive bacterium that is the leading cause of community-acquired respiratory diseases, varying from mild- to deathly- infections. The appearance of antibiotic-resistant isolates has prompted the search for novel strategies and targets to tackle the bacterial resistances. One of the most promising approaches is the structure-based knowledge of possible targets in conjunction with rational design and docking of inhibitors of the chosen targets. A useful technique that helps to solve protein structures is to label them with an amino acid derivative like seleno-methionine that facilitates tracing of some of the amino acid residues. We have chosen two pneumococcal DNA-binding proteins, namely the relaxase domain of MobM protein from plasmid pMV158, and the RelB-RelE antitoxin-toxin protein complex. Through several changes that improve substantially a previous protocol (Budisa et al., 1995), we have used seleno-L-methionine to incorporate selenium into the amino acid sequence of the selected proteins. We have achieved 100% labelling of the proteins and could demonstrate that the labelled proteins retained full activity as judged from the relaxation of supercoiled plasmid DNA and from gel-retardation assays.
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Affiliation(s)
- Fabián Lorenzo-Diaz
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Inmaculada Moreno-Córdoba
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu, 9, 28040 Madrid, Spain
| | - Manuel Espinosa
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu, 9, 28040 Madrid, Spain.
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13
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Oke M, Agbalajobi R, Osifeso M, Muhammad B, Lawal H, Mai M, Adegunle Q. Design and implementation of structural bioinformatics projects for biological sciences undergraduate students. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2018; 46:547-554. [PMID: 30369034 DOI: 10.1002/bmb.21169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/21/2018] [Accepted: 09/03/2018] [Indexed: 06/08/2023]
Abstract
Contemporary biology is currently undergoing a revolution, driven by the availability of high-throughput technologies and a wide variety of bioinformatics tools. However, bioinformatics education and practice is still in its infancy in most of the African continent. Consequently, concerted efforts have been made in recent years to incorporate bioinformatics modules into biological sciences curriculum of African Universities. Despite this, one aspect of bioinformatics that is yet to be incorporated is structural bioinformatics. In this article, we report on a structural bioinformatics project carried out by final year project students in a Nigerian university. The target protein was the thermoacidophilic Sulfolobus islandicus rod-shaped virus 1 (SIRV1) Rep protein, which was further characterized using various free, user-friendly and online sequence-based and structure-based bioinformatics tools. This exercise gave students the opportunity to generate new data, interpret the data, and acquire collaborative research skills. In this report, emphasis is placed on analysis of the data generated to further encourage analytical skills. By sharing this experience, it is anticipated that other similar institutions would adopt parallel strategies to expose undergraduate students to structural biology, and increase awareness of freely available bioinformatics tools for tackling pertinent biological questions. © 2018 International Union of Biochemistry and Molecular Biology, 46(5):547-554, 2018.
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Affiliation(s)
- Muse Oke
- Department of Biological Sciences, Fountain University, Oke-Osun, Osogbo, Nigeria
| | - Ramon Agbalajobi
- Department of Biological Sciences, Fountain University, Oke-Osun, Osogbo, Nigeria
| | | | - Babagana Muhammad
- Department of Biological Sciences, Fountain University, Oke-Osun, Osogbo, Nigeria
| | - Halimat Lawal
- Department of Biological Sciences, Fountain University, Oke-Osun, Osogbo, Nigeria
| | - Muhammad Mai
- Department of Biological Sciences, Fountain University, Oke-Osun, Osogbo, Nigeria
| | - Quadri Adegunle
- Department of Biological Sciences, Fountain University, Oke-Osun, Osogbo, Nigeria
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14
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Ruiz-Masó JÁ, Luengo LM, Moreno-Córdoba I, Díaz-Orejas R, Del Solar G. Successful Establishment of Plasmids R1 and pMV158 in a New Host Requires the Relief of the Transcriptional Repression of Their Essential rep Genes. Front Microbiol 2017; 8:2367. [PMID: 29250051 PMCID: PMC5717011 DOI: 10.3389/fmicb.2017.02367] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/16/2017] [Indexed: 11/13/2022] Open
Abstract
Although differing in size, encoded traits, host range, and replication mechanism, both narrow-host-range theta-type conjugative enterobacterial plasmid R1 and promiscuous rolling-circle-type mobilizable streptococcal plasmid pMV158 encode a transcriptional repressor protein, namely CopB in R1 and CopG in pMV158, involved in replication control. The gene encoding CopB or CopG is cotranscribed with a downstream gene that encodes the replication initiator Rep protein of the corresponding plasmid. However, whereas CopG is an auto-repressor that inhibits transcription of the entire copG-repB operon, CopB is expressed constitutively and represses a second, downstream promoter that directs transcription of repA. As a consequence of the distinct regulatory pathways implied by CopB and CopG, these repressor proteins play a different role in control of plasmid replication during the steady state: while CopB has an auxiliary role by keeping repressed the regulated promoter whenever the plasmid copy number is above a low threshold, CopG plays a primary role by acting coordinately with RNAII. Here, we have studied the role of the regulatory circuit mediated by these transcriptional repressors during the establishment of these two plasmids in a new host cell, and found that excess Cop repressor molecules in the recipient cell result in a severe decrease in the frequency and/or the velocity of appearance of transformant colonies for the cognate plasmid but not for unrelated plasmids. Using the pMV158 replicon as a model system, together with highly sensitive real-time qPCR and inverse PCR methods, we have also analyzed the effect of CopG on the kinetics of repopulation of the plasmid in Streptococcus pneumoniae. We show that, whereas in the absence of CopG pMV158 repopulation occurs mainly during the first 45 min following plasmid transfer, the presence of the transcriptional repressor in the recipient cell severely impairs the replicon repopulation and makes the plasmid replicate at approximately the same rate as the chromosome at any time after transformation, which results in maximal plasmid loss rate in the absence of selection. Overall, these findings indicate that unrepressed activity of the Cop-regulated promoter is crucial for the successful colonization of the recipient bacterial cells by the plasmid.
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Affiliation(s)
- José Á Ruiz-Masó
- Molecular Microbiology and Infection Biology Department, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Luis M Luengo
- Molecular Microbiology and Infection Biology Department, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Inmaculada Moreno-Córdoba
- Molecular Microbiology and Infection Biology Department, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Ramón Díaz-Orejas
- Molecular Microbiology and Infection Biology Department, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Gloria Del Solar
- Molecular Microbiology and Infection Biology Department, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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15
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Wawrzyniak P, Płucienniczak G, Bartosik D. The Different Faces of Rolling-Circle Replication and Its Multifunctional Initiator Proteins. Front Microbiol 2017; 8:2353. [PMID: 29250047 PMCID: PMC5714925 DOI: 10.3389/fmicb.2017.02353] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 11/15/2017] [Indexed: 11/13/2022] Open
Abstract
Horizontal gene transfer (HGT) contributes greatly to the plasticity and evolution of prokaryotic and eukaryotic genomes. The main carriers of foreign DNA in HGT are mobile genetic elements (MGEs) that have extremely diverse genetic structures and properties. Various strategies are used for the maintenance and spread of MGEs, including (i) vegetative replication, (ii) transposition (and other types of recombination), and (iii) conjugal transfer. In many MGEs, all of these processes are dependent on rolling-circle replication (RCR). RCR is one of the most well characterized models of DNA replication. Although many studies have focused on describing its mechanism, the role of replication initiator proteins has only recently been subject to in-depth analysis, which indicates their involvement in multiple biological process associated with RCR. In this review, we present a general overview of RCR and its impact in HGT. We focus on the molecular characteristics of RCR initiator proteins belonging to the HUH and Rep_trans protein families. Despite analogous mechanisms of action these are distinct groups of proteins with different catalytic domain structures. This is the first review describing the multifunctional character of various types of RCR initiator proteins, including the latest discoveries in the field. Recent reports provide evidence that (i) proteins initiating vegetative replication (Rep) or mobilization for conjugal transfer (Mob) may also have integrase (Int) activity, (ii) some Mob proteins are capable of initiating vegetative replication (Rep activity), and (iii) some Rep proteins can act like Mob proteins to mobilize plasmid DNA for conjugal transfer. These findings have significant consequences for our understanding of the role of RCR, not only in DNA metabolism but also in the biology of many MGEs.
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Affiliation(s)
- Paweł Wawrzyniak
- Department of Bioengineering, Institute of Biotechnology and Antibiotics, Warsaw, Poland.,Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Grażyna Płucienniczak
- Department of Bioengineering, Institute of Biotechnology and Antibiotics, Warsaw, Poland
| | - Dariusz Bartosik
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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16
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Kwong SM, Ramsay JP, Jensen SO, Firth N. Replication of Staphylococcal Resistance Plasmids. Front Microbiol 2017; 8:2279. [PMID: 29218034 PMCID: PMC5703833 DOI: 10.3389/fmicb.2017.02279] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 11/06/2017] [Indexed: 11/16/2022] Open
Abstract
The currently widespread and increasing prevalence of resistant bacterial pathogens is a significant medical problem. In clinical strains of staphylococci, the genetic determinants that confer resistance to antimicrobial agents are often located on mobile elements, such as plasmids. Many of these resistance plasmids are capable of horizontal transmission to other bacteria in their surroundings, allowing extraordinarily rapid adaptation of bacterial populations. Once the resistance plasmids have been spread, they are often perpetually maintained in the new host, even in the absence of selective pressure. Plasmid persistence is accomplished by plasmid-encoded genetic systems that ensure efficient replication and segregational stability during cell division. Staphylococcal plasmids utilize proteins of evolutionarily diverse families to initiate replication from the plasmid origin of replication. Several distinctive plasmid copy number control mechanisms have been studied in detail and these appear conserved within plasmid classes. The initiators utilize various strategies and serve a multifunctional role in (i) recognition and processing of the cognate replication origin to an initiation active form and (ii) recruitment of host-encoded replication proteins that facilitate replisome assembly. Understanding the detailed molecular mechanisms that underpin plasmid replication may lead to novel approaches that could be used to reverse or slow the development of resistance.
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Affiliation(s)
- Stephen M Kwong
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Joshua P Ramsay
- School of Biomedical Sciences, Curtin University, Perth, WA, Australia
| | - Slade O Jensen
- Antimicrobial Resistance and Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, NSW, Australia
| | - Neville Firth
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
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17
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Structural basis of a histidine-DNA nicking/joining mechanism for gene transfer and promiscuous spread of antibiotic resistance. Proc Natl Acad Sci U S A 2017; 114:E6526-E6535. [PMID: 28739894 DOI: 10.1073/pnas.1702971114] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Relaxases are metal-dependent nucleases that break and join DNA for the initiation and completion of conjugative bacterial gene transfer. Conjugation is the main process through which antibiotic resistance spreads among bacteria, with multidrug-resistant staphylococci and streptococci infections posing major threats to human health. The MOBV family of relaxases accounts for approximately 85% of all relaxases found in Staphylococcus aureus isolates. Here, we present six structures of the MOBV relaxase MobM from the promiscuous plasmid pMV158 in complex with several origin of transfer DNA fragments. A combined structural, biochemical, and computational approach reveals that MobM follows a previously uncharacterized histidine/metal-dependent DNA processing mechanism, which involves the formation of a covalent phosphoramidate histidine-DNA adduct for cell-to-cell transfer. We discuss how the chemical features of the high-energy phosphorus-nitrogen bond shape the dominant position of MOBV histidine relaxases among small promiscuous plasmids and their preference toward Gram-positive bacteria.
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18
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Lovendahl KN, Hayward AN, Gordon WR. Sequence-Directed Covalent Protein-DNA Linkages in a Single Step Using HUH-Tags. J Am Chem Soc 2017; 139:7030-7035. [PMID: 28481515 DOI: 10.1021/jacs.7b02572] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We present a robust strategy to covalently link proteins and DNA using HUH-endonuclease domains as fusion partners (HUH-tags). We show that HUH-tags react robustly with specific sequences of unmodified single-stranded DNA, and we have identified five tags that react orthogonally with distinct DNA sequences. We demonstrate the versatility of HUH-tags as fusion partners in Cas9-mediated gene editing and the construction of doubly DNA-tethered proteins for single-molecule studies. Finally we demonstrate application to cellular imaging in live and fixed cells.
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Affiliation(s)
- Klaus N Lovendahl
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Amanda N Hayward
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Wendy R Gordon
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota , Minneapolis, Minnesota 55455, United States
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19
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Ruiz-Masó JA, Bordanaba-Ruiseco L, Sanz M, Menéndez M, Del Solar G. Metal-Induced Stabilization and Activation of Plasmid Replication Initiator RepB. Front Mol Biosci 2016; 3:56. [PMID: 27709114 PMCID: PMC5030251 DOI: 10.3389/fmolb.2016.00056] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 09/02/2016] [Indexed: 02/02/2023] Open
Abstract
Initiation of plasmid rolling circle replication (RCR) is catalyzed by a plasmid-encoded Rep protein that performs a Tyr- and metal-dependent site-specific cleavage of one DNA strand within the double-strand origin (dso) of replication. The crystal structure of RepB, the initiator protein of the streptococcal plasmid pMV158, constitutes the first example of a Rep protein structure from RCR plasmids. It forms a toroidal homohexameric ring where each RepB protomer consists of two domains: the C-terminal domain involved in oligomerization and the N-terminal domain containing the DNA-binding and endonuclease activities. Binding of Mn2+ to the active site is essential for the catalytic activity of RepB. In this work, we have studied the effects of metal binding on the structure and thermostability of full-length hexameric RepB and each of its separate domains by using different biophysical approaches. The analysis of the temperature-induced changes in RepB shows that the first thermal transition, which occurs at a range of temperatures physiologically relevant for the pMV158 pneumococcal host, represents an irreversible conformational change that affects the secondary and tertiary structure of the protein, which becomes prone to self-associate. This transition, which is also shown to result in loss of DNA binding capacity and catalytic activity of RepB, is confined to its N-terminal domain. Mn2+ protects the protein from undergoing this detrimental conformational change and the observed protection correlates well with the high-affinity binding of the cation to the active site, as substituting one of the metal-ligands at this site impairs both the protein affinity for Mn2+and the Mn2+-driven thermostabilization effect. The level of catalytic activity of the protein, especially in the case of full-length RepB, cannot be explained based only on the high-affinity binding of Mn2+ at the active site and suggests the existence of additional, lower-affinity metal binding site(s), missing in the separate catalytic domain, that must also be saturated for maximal activity. The molecular bases of the thermostabilizing effect of Mn2+ on the N-terminal domain of the protein as well as the potential location of additional metal binding sites in the entire RepB are discussed.
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Affiliation(s)
- José A Ruiz-Masó
- Molecular Biology of Gram-Positive Bacteria, Molecular Microbiology and Infection Biology, Centro de Investigaciones Biológicas (Consejo Superior de Investigaciones Científicas) Madrid, Spain
| | - Lorena Bordanaba-Ruiseco
- Molecular Biology of Gram-Positive Bacteria, Molecular Microbiology and Infection Biology, Centro de Investigaciones Biológicas (Consejo Superior de Investigaciones Científicas) Madrid, Spain
| | - Marta Sanz
- Molecular Biology of Gram-Positive Bacteria, Molecular Microbiology and Infection Biology, Centro de Investigaciones Biológicas (Consejo Superior de Investigaciones Científicas) Madrid, Spain
| | - Margarita Menéndez
- Biological Physical Chemistry, Protein Structure and Thermodynamics, Instituto de Química-Física Rocasolano (Consejo Superior de Investigaciones Científicas)Madrid, Spain; CIBER of Respiratory DiseasesMadrid, Spain
| | - Gloria Del Solar
- Molecular Biology of Gram-Positive Bacteria, Molecular Microbiology and Infection Biology, Centro de Investigaciones Biológicas (Consejo Superior de Investigaciones Científicas) Madrid, Spain
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20
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Characterization of a Rolling-Circle Replication Plasmid pM411 from Lactobacillus plantarum 1-3. Curr Microbiol 2016; 73:820-826. [PMID: 27592105 DOI: 10.1007/s00284-016-1124-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 08/13/2016] [Indexed: 10/21/2022]
Abstract
A cryptic plasmid pM411 isolated from Lactobacillus plantarum 1-3 consisted of a 2303-bp circular molecule with a G + C content 32.96 %. Sequence analysis of pM411 revealed four putative open reading frames (ORFs). ORF1 shared 99 and 94 % similarities, respectively, with the Rep proteins of plasmids pLC2 and pYC2, which belong to the rolling-circle replication pMV158 family. A typical pMV158 family double-strand origin (dso) and a putative single-strand origin (sso) located upstream of the rep gene. Southern hybridization confirmed the presence of single-strand DNA (ssDNA) intermediates, suggesting that pM411 belongs to the RCR pMV158 family. Sequence homology analysis indicated that the sso belongs to the ssoW family. Furthermore, the relative copy number of pM411 was about 88 copies in each cell by real-time PCR.
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21
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Identification of a Functionally Relevant Adeno-Associated Virus Rep68 Oligomeric Interface. J Virol 2016; 90:6612-6624. [PMID: 27170758 PMCID: PMC4944284 DOI: 10.1128/jvi.00356-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/01/2016] [Indexed: 12/11/2022] Open
Abstract
The life cycle of the human parvovirus adeno-associated virus (AAV) is orchestrated by four Rep proteins. The large Rep proteins, Rep78 and Rep68, are remarkably multifunctional and display a range of biochemical activities, including DNA binding, nicking, and unwinding. Functionally, Rep78 and Rep68 are involved in transcriptional regulation, DNA replication, and genomic integration. Structurally, the Rep proteins share an AAA+ domain characteristic of superfamily 3 helicases, with the large Rep proteins additionally containing an N-terminal origin-binding domain (OBD) that specifically binds and nicks DNA. The combination of these domains, coupled with dynamic oligomerization properties, is the basis for the remarkable multifunctionality displayed by Rep68 and Rep78 during the AAV life cycle. In this report, we describe an oligomeric interface formed by Rep68 and demonstrate how disruption of this interface has drastic effects on both the oligomerization and functionality of the Rep proteins. Our results support a role for the four-helix bundle in the helicase domain of Rep68 as a bona fide oligomerization domain (OD). We have identified key residues in the OD that are critical for the stabilization of the Rep68-Rep68 interface; mutation of these key residues disrupts the enzymatic activities of Rep68, including DNA binding and nicking, and compromises viral DNA replication and transcriptional regulation of the viral promoters. Taken together, our data contribute to our understanding of the dynamic and substrate-responsive Rep78/68 oligomerization that is instrumental in the regulation of the DNA transitions that take place during the AAV life cycle.
IMPORTANCE The limited genome size of small viruses has driven the evolution of highly multifunctional proteins that integrate different domains and enzymatic activities within a single polypeptide. The Rep68 protein from adeno-associated virus (AAV) combines a DNA binding and endonuclease domain with a helicase-ATPase domain, which together support DNA replication, transcriptional regulation, and site-specific integration. The coordination of the enzymatic activities of Rep68 remains poorly understood; however, Rep68 oligomerization and Rep68-DNA interactions have been suggested to play a crucial role. We investigated the determinants of Rep68 oligomerization and identified a hydrophobic interface necessary for Rep68 activity during the AAV life cycle. Our results provide new insights into the molecular mechanisms underlying the regulation of the versatile Rep proteins. Efficient production of AAV-based gene therapy vectors requires optimal Rep expression levels, and studies such as the one presented here could contribute to further optimization of AAV production schemes.
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22
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Sagredo S, de la Cruz F, Moncalián G. Design of Novel Relaxase Substrates Based on Rolling Circle Replicases for Bioconjugation to DNA Nanostructures. PLoS One 2016; 11:e0152666. [PMID: 27027740 PMCID: PMC4814116 DOI: 10.1371/journal.pone.0152666] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 03/17/2016] [Indexed: 11/28/2022] Open
Abstract
During bacterial conjugation and rolling circle replication, HUH endonucleases, respectively known as relaxases and replicases, form a covalent bond with ssDNA when they cleave their target sequence (nic site). Both protein families show structural similarity but limited amino acid identity. Moreover, the organization of the inverted repeat (IR) and the loop that shape the nic site differs in both proteins. Arguably, replicases cleave their target site more efficiently, while relaxases exert more biochemical control over the process. Here we show that engineering a relaxase target by mimicking the replicase target, results in enhanced formation of protein-DNA covalent complexes. Three widely different relaxases, which belong to MOBF, MOBQ and MOBP families, can properly cleave DNA sequences with permuted target sequences. Collaterally, the secondary structure that the permuted targets acquired within a supercoiled plasmid DNA resulted in poor conjugation frequencies underlying the importance of relaxase accessory proteins in conjugative DNA processing. Our results reveal that relaxase and replicase targets can be interchangeable in vitro. The new Rep substrates provide new bioconjugation tools for the design of sophisticated DNA-protein nanostructures.
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Affiliation(s)
- Sandra Sagredo
- Departamento de Biología Molecular e Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-Consejo Superior de Investigaciones Científicas-SODERCAN, C/ Albert Einstein 22, 39011, Santander, Spain
| | - Fernando de la Cruz
- Departamento de Biología Molecular e Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-Consejo Superior de Investigaciones Científicas-SODERCAN, C/ Albert Einstein 22, 39011, Santander, Spain
- * E-mail: (FC); (GM)
| | - Gabriel Moncalián
- Departamento de Biología Molecular e Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-Consejo Superior de Investigaciones Científicas-SODERCAN, C/ Albert Einstein 22, 39011, Santander, Spain
- * E-mail: (FC); (GM)
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23
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Abstract
Plasmids are DNA entities that undergo controlled replication independent of the chromosomal DNA, a crucial step that guarantees the prevalence of the plasmid in its host. DNA replication has to cope with the incapacity of the DNA polymerases to start de novo DNA synthesis, and different replication mechanisms offer diverse solutions to this problem. Rolling-circle replication (RCR) is a mechanism adopted by certain plasmids, among other genetic elements, that represents one of the simplest initiation strategies, that is, the nicking by a replication initiator protein on one parental strand to generate the primer for leading-strand initiation and a single priming site for lagging-strand synthesis. All RCR plasmid genomes consist of a number of basic elements: leading strand initiation and control, lagging strand origin, phenotypic determinants, and mobilization, generally in that order of frequency. RCR has been mainly characterized in Gram-positive bacterial plasmids, although it has also been described in Gram-negative bacterial or archaeal plasmids. Here we aim to provide an overview of the RCR plasmids' lifestyle, with emphasis on their characteristic traits, promiscuity, stability, utility as vectors, etc. While RCR is one of the best-characterized plasmid replication mechanisms, there are still many questions left unanswered, which will be pointed out along the way in this review.
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24
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Boer DR, Ruiz-Masó JA, Rueda M, Petoukhov MV, Machón C, Svergun DI, Orozco M, del Solar G, Coll M. Conformational plasticity of RepB, the replication initiator protein of promiscuous streptococcal plasmid pMV158. Sci Rep 2016; 6:20915. [PMID: 26875695 PMCID: PMC4753449 DOI: 10.1038/srep20915] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 01/13/2016] [Indexed: 11/16/2022] Open
Abstract
DNA replication initiation is a vital and tightly regulated step in all replicons and requires an initiator factor that specifically recognizes the DNA replication origin and starts replication. RepB from the promiscuous streptococcal plasmid pMV158 is a hexameric ring protein evolutionary related to viral initiators. Here we explore the conformational plasticity of the RepB hexamer by i) SAXS, ii) sedimentation experiments, iii) molecular simulations and iv) X-ray crystallography. Combining these techniques, we derive an estimate of the conformational ensemble in solution showing that the C-terminal oligomerisation domains of the protein form a rigid cylindrical scaffold to which the N-terminal DNA-binding/catalytic domains are attached as highly flexible appendages, featuring multiple orientations. In addition, we show that the hinge region connecting both domains plays a pivotal role in the observed plasticity. Sequence comparisons and a literature survey show that this hinge region could exists in other initiators, suggesting that it is a common, crucial structural element for DNA binding and manipulation.
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Affiliation(s)
- D Roeland Boer
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain.,Institut de Biologia Molecular de Barcelona (Consejo Superior de Investigaciones Científicas), Barcelona, 08028, Spain
| | - José Angel Ruiz-Masó
- Centro de Investigaciones Biológicas (Consejo Superior de Investigaciones Científicas), Madrid, 28040, Spain
| | - Manuel Rueda
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain
| | - Maxim V Petoukhov
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Hamburg, 22607, Germany
| | - Cristina Machón
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain.,Institut de Biologia Molecular de Barcelona (Consejo Superior de Investigaciones Científicas), Barcelona, 08028, Spain
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Hamburg, 22607, Germany
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain.,Departament de Bioquímica, Facultat de Biologia, Universitat de Barcelona, Barcelona, 08028, Spain
| | - Gloria del Solar
- Centro de Investigaciones Biológicas (Consejo Superior de Investigaciones Científicas), Madrid, 28040, Spain
| | - Miquel Coll
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain.,Institut de Biologia Molecular de Barcelona (Consejo Superior de Investigaciones Científicas), Barcelona, 08028, Spain
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Carr SB, Phillips SEV, Thomas CD. Structures of replication initiation proteins from staphylococcal antibiotic resistance plasmids reveal protein asymmetry and flexibility are necessary for replication. Nucleic Acids Res 2016; 44:2417-28. [PMID: 26792891 PMCID: PMC4797284 DOI: 10.1093/nar/gkv1539] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 12/22/2015] [Indexed: 12/22/2022] Open
Abstract
Antibiotic resistance in pathogenic bacteria is a continual threat to human health, often residing in extrachromosomal plasmid DNA. Plasmids of the pT181 family are widespread and confer various antibiotic resistances to Staphylococcus aureus. They replicate via a rolling circle mechanism that requires a multi-functional, plasmid-encoded replication protein to initiate replication, recruit a helicase to the site of initiation and terminate replication after DNA synthesis is complete. We present the first atomic resolution structures of three such replication proteins that reveal distinct, functionally relevant conformations. The proteins possess a unique active site and have been shown to contain a catalytically essential metal ion that is bound in a manner distinct from that of any other rolling circle replication proteins. These structures are the first examples of the Rep_trans Pfam family providing insights into the replication of numerous antibiotic resistance plasmids from Gram-positive bacteria, Gram-negative phage and the mobilisation of DNA by conjugative transposons.
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Affiliation(s)
- Stephen B Carr
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxfordshire OX11 0FA, UK
| | - Simon E V Phillips
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxfordshire OX11 0FA, UK
| | - Christopher D Thomas
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
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López-Aguilar C, Romero-López C, Espinosa M, Berzal-Herranz A, Del Solar G. The 5'-tail of antisense RNAII of pMV158 plays a critical role in binding to the target mRNA and in translation inhibition of repB. Front Genet 2015; 6:225. [PMID: 26175752 PMCID: PMC4485353 DOI: 10.3389/fgene.2015.00225] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 06/12/2015] [Indexed: 02/05/2023] Open
Abstract
Rolling-circle replication of streptococcal plasmid pMV158 is controlled by the concerted action of two trans-acting elements, namely transcriptional repressor CopG and antisense RNAII, which inhibit expression of the repB gene encoding the replication initiator protein. The pMV158-encoded antisense RNAII exerts its activity of replication control by inhibiting translation of the essential repB gene. RNAII is the smallest and simplest among the characterized antisense RNAs involved in control of plasmid replication. Structure analysis of RNAII revealed that it folds into an 8-bp-long stem containing a 1-nt bulge and closed by a 6-nt apical loop. This hairpin is flanked by a 17-nt-long single-stranded 5′-tail and an 8-nt-long 3′-terminal U-rich stretch. Here, the 3′ and 5′ regions of the 5′-tail of RNAII are shown to play a critical role in the binding to the target mRNA and in the inhibition of repB translation, respectively. In contrast, the apical loop of the single hairpin of RNAII plays a rather secondary role and the upper stem region hardly contributes to the binding or inhibition processes. The entire 5′-tail is required for efficient inhibition of repB translation, though only the 8-nt-long region adjacent to the hairpin seems to be essential for rapid binding to the mRNA. These results show that a “kissing” interaction involving base-pairing between complementary hairpin loops in RNAII and mRNA is not critical for efficient RNA/RNA binding or repB translation inhibition. A singular binding mechanism is envisaged whereby initial pairing between complementary single-stranded regions in the antisense and sense RNAs progresses upwards into the corresponding hairpin stems to form the intermolecular duplex.
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Affiliation(s)
- Celeste López-Aguilar
- Molecular Microbiology and Infection Biology Department, Centro de Investigaciones Biológicas (CIB-CSIC) Madrid, Spain
| | - Cristina Romero-López
- Molecular Biology Department, Instituto de Parasitología y Biomedicina López-Neyra (IPBLN-CSIC) Granada, Spain
| | - Manuel Espinosa
- Molecular Microbiology and Infection Biology Department, Centro de Investigaciones Biológicas (CIB-CSIC) Madrid, Spain
| | - Alfredo Berzal-Herranz
- Molecular Biology Department, Instituto de Parasitología y Biomedicina López-Neyra (IPBLN-CSIC) Granada, Spain
| | - Gloria Del Solar
- Molecular Microbiology and Infection Biology Department, Centro de Investigaciones Biológicas (CIB-CSIC) Madrid, Spain
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Rueda M, Orozco M, Totrov M, Abagyan R. BioSuper: a web tool for the superimposition of biomolecules and assemblies with rotational symmetry. BMC STRUCTURAL BIOLOGY 2013; 13:32. [PMID: 24330655 PMCID: PMC3924234 DOI: 10.1186/1472-6807-13-32] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 12/03/2013] [Indexed: 12/02/2022]
Abstract
Background Most of the proteins in the Protein Data Bank (PDB) are oligomeric complexes consisting of two or more subunits that associate by rotational or helical symmetries. Despite the myriad of superimposition tools in the literature, we could not find any able to account for rotational symmetry and display the graphical results in the web browser. Results BioSuper is a free web server that superimposes and calculates the root mean square deviation (RMSD) of protein complexes displaying rotational symmetry. To the best of our knowledge, BioSuper is the first tool of its kind that provides immediate interactive visualization of the graphical results in the browser, biomolecule generator capabilities, different levels of atom selection, sequence-dependent and structure-based superimposition types, and is the only web tool that takes into account the equivalence of atoms in side chains displaying symmetry ambiguity. BioSuper uses ICM program functionality as a core for the superimpositions and displays the results as text, HTML tables and 3D interactive molecular objects that can be visualized in the browser or in Android and iOS platforms with a free plugin. Conclusions BioSuper is a fast and functional tool that allows for pairwise superimposition of proteins and assemblies displaying rotational symmetry. The web server was created after our own frustration when attempting to superimpose flexible oligomers. We strongly believe that its user-friendly and functional design will be of great interest for structural and computational biologists who need to superimpose oligomeric proteins (or any protein). BioSuper web server is freely available to all users at http://ablab.ucsd.edu/BioSuper.
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Affiliation(s)
| | | | | | - Ruben Abagyan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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28
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Carr SB, Mecia LB, Phillips SEV, Thomas CD. Identification, characterization and preliminary X-ray diffraction analysis of the rolling-circle replication initiator protein from plasmid pSTK1. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1123-6. [PMID: 24100563 PMCID: PMC3792671 DOI: 10.1107/s1744309113023828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 08/23/2013] [Indexed: 11/11/2022]
Abstract
Antibiotic resistance in bacterial pathogens poses an ever-increasing risk to human health. In antibiotic-resistant strains of Staphylococcus aureus this resistance often resides in extra-chromosomal plasmids, such as those of the pT181 family, which replicate via a rolling-circle mechanism mediated by a plasmid-encoded replication initiation protein. Currently, there is no structural information available for the pT181-family Rep proteins. Here, the crystallization of a catalytically active fragment of a homologous replication initiation protein from the thermophile Geobacillus stearothermophilus responsible for the replication of plasmid pSTK1 is reported. Crystals of the RepSTK1 fragment diffracted to a resolution of 2.5 Å and belonged to space group P2₁2₁2₁.
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Affiliation(s)
- Stephen B. Carr
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, Oxfordshire OX11 0FA, England
| | - Lauren B. Mecia
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, England
| | - Simon E. V. Phillips
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, Oxfordshire OX11 0FA, England
| | - Christopher D. Thomas
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, England
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Abstract
HUH endonucleases are numerous and widespread in all three domains of life. The major function of these enzymes is processing a range of mobile genetic elements by catalysing cleavage and rejoining of single-stranded DNA using an active-site Tyr residue to make a transient 5'-phosphotyrosine bond with the DNA substrate. These enzymes have a key role in rolling-circle replication of plasmids and bacteriophages, in plasmid transfer, in the replication of several eukaryotic viruses and in various types of transposition. They have also been appropriated for cellular processes such as intron homing and the processing of bacterial repeated extragenic palindromes. Here, we provide an overview of these fascinating enzymes and their functions, using well-characterized examples of Rep proteins, relaxases and transposases, and we explore the molecular mechanisms used in their diverse activities.
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Characterization of pMRI 5.2, a rolling-circle-type plasmid from Lactobacillus plantarum BFE 5092 which harbours two different replication initiation genes. Plasmid 2013; 69:160-71. [DOI: 10.1016/j.plasmid.2012.11.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 11/28/2012] [Accepted: 11/29/2012] [Indexed: 12/11/2022]
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Espinosa M. Plasmids as models for studying macromolecular interactions: the pMV158 paradigm. Res Microbiol 2013; 164:199-204. [PMID: 23385144 DOI: 10.1016/j.resmic.2013.01.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Manuel Espinosa
- Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu, 9, E-28040 Madrid, Spain.
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32
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Chang YC, Huang JY, Chiou MT, Chung TC, Hsu WL, Lin CF. Characterization of a small cryptic plasmid pK50-2 isolated from Lactobacillus reuteri K50. Plasmid 2013; 69:58-66. [DOI: 10.1016/j.plasmid.2012.08.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 08/28/2012] [Accepted: 08/29/2012] [Indexed: 11/28/2022]
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Zarate-Perez F, Bardelli M, Burgner JW, Villamil-Jarauta M, Das K, Kekilli D, Mansilla-Soto J, Linden RM, Escalante CR. The interdomain linker of AAV-2 Rep68 is an integral part of its oligomerization domain: role of a conserved SF3 helicase residue in oligomerization. PLoS Pathog 2012; 8:e1002764. [PMID: 22719256 PMCID: PMC3375335 DOI: 10.1371/journal.ppat.1002764] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 05/03/2012] [Indexed: 11/24/2022] Open
Abstract
The four Rep proteins of adeno-associated virus (AAV) orchestrate all aspects of its viral life cycle, including transcription regulation, DNA replication, virus assembly, and site-specific integration of the viral genome into the human chromosome 19. All Rep proteins share a central SF3 superfamily helicase domain. In other SF3 members this domain is sufficient to induce oligomerization. However, the helicase domain in AAV Rep proteins (i.e. Rep40/Rep52) as shown by its monomeric characteristic, is not able to mediate stable oligomerization. This observation led us to hypothesize the existence of an as yet undefined structural determinant that regulates Rep oligomerization. In this document, we described a detailed structural comparison between the helicase domains of AAV-2 Rep proteins and those of the other SF3 members. This analysis shows a major structural difference residing in the small oligomerization sub-domain (OD) of Rep helicase domain. In addition, secondary structure prediction of the linker connecting the helicase domain to the origin-binding domain (OBD) indicates the potential to form α-helices. We demonstrate that mutant Rep40 constructs containing different lengths of the linker are able to form dimers, and in the presence of ATP/ADP, larger oligomers. We further identified an aromatic linker residue (Y224) that is critical for oligomerization, establishing it as a conserved signature motif in SF3 helicases. Mutation of this residue critically affects oligomerization as well as completely abolishes the ability to produce infectious virus. Taken together, our data support a model where the linker residues preceding the helicase domain fold into an α-helix that becomes an integral part of the helicase domain and is critical for the oligomerization and function of Rep68/78 proteins through cooperative interaction with the OBD and helicase domains.
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Affiliation(s)
- Francisco Zarate-Perez
- Department of Physiology and Biophysics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, United States of America
| | - Martino Bardelli
- Department of Infectious Diseases, King's College London School of Medicine at Guy's, King's and St. Thomas Hospital, London, United Kingdom
| | - John W. Burgner
- Department of Physiology and Biophysics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, United States of America
| | - Maria Villamil-Jarauta
- Department of Physiology and Biophysics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, United States of America
| | - Kanni Das
- Department of Physiology and Biophysics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, United States of America
| | - Demet Kekilli
- Department of Applied Sciences, University of the West of England, Bristol, United Kingdom
| | - Jorge Mansilla-Soto
- Center for Cell Engineering, Department of Human Genetics, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - R. Michael Linden
- Department of Infectious Diseases, King's College London School of Medicine at Guy's, King's and St. Thomas Hospital, London, United Kingdom
- UCL Gene Therapy Consortium, UCL Cancer Institute, University College London, London, United Kingdom
| | - Carlos R. Escalante
- Department of Physiology and Biophysics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, United States of America
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The amino acid linker between the endonuclease and helicase domains of adeno-associated virus type 5 Rep plays a critical role in DNA-dependent oligomerization. J Virol 2011; 86:3337-46. [PMID: 22205752 DOI: 10.1128/jvi.06775-11] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The adeno-associated virus (AAV) genome encodes four Rep proteins, all of which contain an SF3 helicase domain. The larger Rep proteins, Rep78 and Rep68, are required for viral replication, whereas Rep40 and Rep52 are needed to package AAV genomes into preformed capsids; these smaller proteins are missing the site-specific DNA-binding and endonuclease domain found in Rep68/78. Other viral SF3 helicases, such as the simian virus 40 large T antigen and the papillomavirus E1 protein, are active as hexameric assemblies. However, Rep40 and Rep52 have not been observed to form stable oligomers on their own or with DNA, suggesting that important determinants of helicase multimerization lie outside the helicase domain. Here, we report that when the 23-residue linker that connects the endonuclease and helicase domains is appended to the adeno-associated virus type 5 (AAV5) helicase domain, the resulting protein forms discrete complexes on DNA consistent with single or double hexamers. The formation of these complexes does not require the Rep binding site sequence, nor is it nucleotide dependent. These complexes have stimulated ATPase and helicase activities relative to the helicase domain alone, indicating that they are catalytically relevant, a result supported by negative-stain electron microscopy images of hexameric rings. Similarly, the addition of the linker region to the AAV5 Rep endonuclease domain also confers on it the ability to bind and multimerize on nonspecific double-stranded DNA. We conclude that the linker is likely a key contributor to Rep68/78 DNA-dependent oligomerization and may play an important role in mediating Rep68/78's conversion from site-specific DNA binding to nonspecific DNA unwinding.
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Deldar AA, Yakhchali B. The influence of riboflavin and nicotinic acid on Shigella sonnei colony conversion. IRANIAN JOURNAL OF MICROBIOLOGY 2011; 3:13-20. [PMID: 22347577 PMCID: PMC3279797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND AND OBJECTIVES Shigella, causative of bacillary dysentery, has two colony forms. The loss of large virulence plasmid from virulent Shigella sonnei form I, during cell storage and subculturing, lead to avirulent form II. Environmental factors, e.g. culture media composition, could affect the conversion of the bacterial forms. MATERIALS AND METHODS In this study, some components, i.e., B-complex vitamins, nicotinic acid and riboflavin, were added to the bacterial culture medium and their influence on colony conversion were examined. RESULTS The findings revealed that colony conversion is temperature independent and growth on the SS agar did not stabilize the bacterium in form I. Also, the findings showed that colonies on the minimal media supplemented with nicotinic acid and riboflavin, were stable in form I. In addition, according to the findings, the active OxyR has potential binding sites upstream of two genes involved in the replication of large virulence plasmid and expression of O-polysaccharide, i.e., repB and wbgT, respectively. CONCLUSION Based on the findings of the present study, it is possible that nicotinic acid and riboflavin activate the transcriptional regulatory protein OxyR via dropping off the intracellular reducing power and in this way stabilize the colonies in form I.
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Affiliation(s)
| | - B Yakhchali
- Corresponding author: Dr. Bagher Yakhchali Address: National Institute of Genetic Engineering and Biotechnology (NIGEB), Shahrak-e-Pajoohesh, km 15, Tehran-Karaj Highway, Tehran, Iran. Tel: +98-21-44580353. E-mail:
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Lorenzo-Díaz F, Dostál L, Coll M, Schildbach JF, Menéndez M, Espinosa M. The MobM relaxase domain of plasmid pMV158: thermal stability and activity upon Mn2+ and specific DNA binding. Nucleic Acids Res 2011; 39:4315-29. [PMID: 21296755 PMCID: PMC3105389 DOI: 10.1093/nar/gkr049] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Protein MobM, the relaxase involved in conjugative transfer of the streptococcal plasmid pMV158, is the prototype of the MOBV superfamily of relaxases. To characterize the DNA-binding and nicking domain of MobM, a truncated version of the protein (MobMN199) encompassing its N-terminal region was designed and the protein was purified. MobMN199 was monomeric in contrast to the dimeric form of the full-length protein, but it kept its nicking activity on pMV158 DNA. The optimal relaxase activity was dependent on Mn2+ or Mg2+ cations in a dosage-dependent manner. However, whereas Mn2+ strongly stabilized MobMN199 against thermal denaturation, no protective effect was observed for Mg2+. Furthermore, MobMN199 exhibited a high affinity binding for Mn2+ but not for Mg2+. We also examined the binding-specificity and affinity of MobMN199 for several substrates of single-stranded DNA encompassing the pMV158 origin of transfer (oriT). The minimal oriT was delimited to a stretch of 26 nt which included an inverted repeat located eight bases upstream of the nick site. The structure of MobMN199 was strongly stabilized by binding to the defined target DNA, indicating the formation of a tight protein–DNA complex. We demonstrate that the oriT recognition by MobMN199 was highly specific and suggest that this protein most probably employs Mn2+ during pMV158 transfer.
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Affiliation(s)
- Fabián Lorenzo-Díaz
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
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37
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Pan Q, Zhang L, Li J, Chen T, Chen W, Wang G, Yin J. Characterization of pLP18, a novel cryptic plasmid of Lactobacillus plantarum PC518 isolated from Chinese pickle. Plasmid 2011; 65:204-9. [PMID: 21255609 DOI: 10.1016/j.plasmid.2011.01.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Revised: 01/11/2011] [Accepted: 01/12/2011] [Indexed: 11/18/2022]
Abstract
A cryptic plasmid of Lactobacillus plantarum PC518 isolated from Chinese pickle, designated pLP18, was sequenced and characterized. It is a 1806-bp circular molecule with a G+C content of 37.5%. Sequence analysis of pLP18 revealed three putative open reading frames (ORFs), in which ORF1 contained conserved motifs of pMV158-family Rep proteins and showed 60% similarity with the Rep protein of pPSC22, a member of rolling-circle replication (RCR) pMV158 family. The double strand origin (dso) of pMV158 family and the single strand origin A (ssoA) located upstream of the rep gene. The putative cop and rnaII genes were predicted to be regulatory genes controlling copy number of pLP18. The results of Southern hybridization suggested that pLP18 replicate via the RCR mechanism. Furthermore, the relative copy number of pLP18 was estimated to be about 24 copies per chromosome equivalent by quantitative PCR.
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Affiliation(s)
- Qu Pan
- Department of Microbiology, Chengdu Medical College, Chengdu 610083, China.
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38
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Zhang H, Hao Y, Zhang D, Luo Y. Characterization of the cryptic plasmid pTXW from Lactobacillus paracasei TXW. Plasmid 2011; 65:1-7. [DOI: 10.1016/j.plasmid.2010.08.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Revised: 08/07/2010] [Accepted: 08/09/2010] [Indexed: 10/19/2022]
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39
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Dostál L, Shao S, Schildbach JF. Tracking F plasmid TraI relaxase processing reactions provides insight into F plasmid transfer. Nucleic Acids Res 2010; 39:2658-70. [PMID: 21109533 PMCID: PMC3074121 DOI: 10.1093/nar/gkq1137] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Early in F plasmid conjugative transfer, the F relaxase, TraI, cleaves one plasmid strand at a site within the origin of transfer called nic. The reaction covalently links TraI Tyr16 to the 5′-ssDNA phosphate. Ultimately, TraI reverses the cleavage reaction to circularize the plasmid strand. The joining reaction requires a ssDNA 3′-hydroxyl; a second cleavage reaction at nic, regenerated by extension from the plasmid cleavage site, may generate this hydroxyl. Here we confirm that TraI is transported to the recipient during transfer. We track the secondary cleavage reaction and provide evidence it occurs in the donor and F ssDNA is transferred to the recipient with a free 3′-hydroxyl. Phe substitutions for four Tyr within the TraI active site implicate only Tyr16 in the two cleavage reactions required for transfer. Therefore, two TraI molecules are required for F plasmid transfer. Analysis of TraI translocation on various linear and circular ssDNA substrates supports the assertion that TraI slowly dissociates from the 3′-end of cleaved F plasmid, likely a characteristic essential for plasmid re-circularization.
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Affiliation(s)
- Lubomír Dostál
- Department of Biology, Johns Hopkins University, 3400 N. Charles St, Baltimore, MD 21218, USA
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40
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A dimeric Rep protein initiates replication of a linear archaeal virus genome: implications for the Rep mechanism and viral replication. J Virol 2010; 85:925-31. [PMID: 21068244 DOI: 10.1128/jvi.01467-10] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The Rudiviridae are a family of rod-shaped archaeal viruses with covalently closed, linear double-stranded DNA (dsDNA) genomes. Their replication mechanisms remain obscure, although parallels have been drawn to the Poxviridae and other large cytoplasmic eukaryotic viruses. Here we report that a protein encoded in the 34-kbp genome of the rudivirus SIRV1 is a member of the replication initiator (Rep) superfamily of proteins, which initiate rolling-circle replication (RCR) of diverse viruses and plasmids. We show that SIRV Rep nicks the viral hairpin terminus, forming a covalent adduct between an active-site tyrosine and the 5' end of the DNA, releasing a 3' DNA end as a primer for DNA synthesis. The enzyme can also catalyze the joining reaction that is necessary to reseal the DNA hairpin and terminate replication. The dimeric structure points to a simple mechanism through which two closely positioned active sites, each with a single tyrosine residue, work in tandem to catalyze DNA nicking and joining. We propose a novel mechanism for rudivirus DNA replication, incorporating the first known example of a Rep protein that is not linked to RCR. The implications for Rep protein function and viral replication are discussed.
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41
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Bryksin AV, Matsumura I. Rational design of a plasmid origin that replicates efficiently in both gram-positive and gram-negative bacteria. PLoS One 2010; 5:e13244. [PMID: 20949038 PMCID: PMC2951906 DOI: 10.1371/journal.pone.0013244] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2010] [Accepted: 09/08/2010] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Most plasmids replicate only within a particular genus or family. METHODOLOGY/PRINCIPAL FINDINGS Here we describe an engineered high copy number expression vector, pBAV1K-T5, that produces varying quantities of active reporter proteins in Escherichia coli, Acinetobacter baylyi ADP1, Agrobacterium tumefaciens, (all gram-negative), Streptococcus pneumoniae, Leifsonia shinshuensis, Peanibacillus sp. S18-36 and Bacillus subtilis (gram-positive). CONCLUSIONS/SIGNIFICANCE Our results demonstrate the efficiency of pBAV1K-T5 replication in different bacterial species, thereby facilitating the study of proteins that don't fold well in E. coli and pathogens not amenable to existing genetic tools.
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Affiliation(s)
- Anton V. Bryksin
- Center for Fundamental and Applied Molecular Evolution, Department of Biochemistry, Emory University, Atlanta, Georgia, United States of America
| | - Ichiro Matsumura
- Center for Fundamental and Applied Molecular Evolution, Department of Biochemistry, Emory University, Atlanta, Georgia, United States of America
- * E-mail:
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DNA-binding specificity determinants of replication proteins encoded by eukaryotic ssDNA viruses are adjacent to widely separated RCR conserved motifs. Arch Virol 2010; 155:1033-46. [PMID: 20422235 DOI: 10.1007/s00705-010-0674-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Accepted: 03/22/2010] [Indexed: 10/19/2022]
Abstract
Eukaryotic ssDNA viruses encode a rolling-circle replication (RCR) initiation protein, Rep, which binds to iterated DNA elements functioning as essential elements for virus-specific replication. By using the iterons of all known circoviruses, nanoviruses and nanovirus-like satellites as heuristic devices, we have identified certain amino acid residues that presumably determine the DNA-binding specificity of their Rep proteins. These putative "specificity determinants" (SPDs) cluster in two discrete protein regions, which are adjacent to distinct conserved motifs. A comparable distribution of SPDs was uncovered in the Rep protein of geminiviruses. Modeling of the tertiary structure of diverse Rep proteins showed that SPD regions interact to form a small beta-sheet element that has been proposed to be critical for high-affinity DNA-binding of Rep. Our findings indicate that eukaryotic circular ssDNA viruses have a common ancestor and suggest that SPDs present in replication initiators from a huge variety of viral and plasmid RCR systems are associated with the same conserved motifs.
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Characterization of a rolling-circle replication plasmid pXY3 from Lactobacillus plantarum XY3. Plasmid 2010; 64:36-40. [PMID: 20353802 DOI: 10.1016/j.plasmid.2010.03.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Revised: 03/05/2010] [Accepted: 03/18/2010] [Indexed: 11/20/2022]
Abstract
The complete nucleotide sequence of cryptic plasmid pXY3 isolated from Lactobacillus plantarum strain XY3 has been determined. It consisted of a 2968-bp circular molecule with a G+C content of 39%. Sequence analysis of pXY3 revealed three putative open reading frames (ORFs). Based on sequence similarity, the Rep protein shared 89% and 88% identity with Rep proteins of pLF24 and pWCFS102, respectively, which belonged to the rolling-circle replication (RCR) pMV158 family. A ssoT-like single-strand origin (sso) and a typical pMV158 family double-strand origin (dso) located upstream of the rep gene. Southern blot analysis indicated pXY3 replicate via a rolling-circle (RC) mechanism. Furthermore, the relative copy number of pXY3 was estimated to be about 97 copies per chromosome equivalent by real-time PCR.
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