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Characterization of a Cryptic Rolling-Circle Replication Plasmid pMK8 from Enterococcus durans 1-8. Curr Microbiol 2018; 75:1198-1205. [PMID: 29777339 DOI: 10.1007/s00284-018-1509-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 05/12/2018] [Indexed: 10/16/2022]
Abstract
A novel cryptic plasmid from Enterococcus durans 1-8, designated as pMK8, was sequenced and analyzed in this study. It consists of 3337 bp with a G + C content of 33.11%. Sequence analysis of pMK8 revealed three putative open reading frames (ORFs). Based on homology, two of them were identified as genes encoding replication initiation (RepC) and mobilization (Mob) protein, respectively. Sequence analysis revealed a pT181 family double-strand origin (dso) and a putative single-strand origin (sso) located upstream of the repC gene. Sequence homology analysis indicated that the sso belongs to the ssoW family. Southern hybridization confirmed the presence of single-strand DNA (ssDNA) intermediates, suggesting that pMK8 replicates via the RCR mechanism. Furthermore, the relative copy number of pMK8 was estimated by real-time PCR to be 175 ± 14 copies in each cell.
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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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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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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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Construction of a shuttle vector based on the small cryptic plasmid pJY33 from Weissella cibaria 33. Plasmid 2015; 79:30-6. [DOI: 10.1016/j.plasmid.2015.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 03/24/2015] [Accepted: 03/30/2015] [Indexed: 11/21/2022]
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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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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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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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Analysis of pYC2, a cryptic plasmid in Lactobacillus sakei BM5 isolated from kimchi. Biotechnol Lett 2008; 31:123-30. [DOI: 10.1007/s10529-008-9842-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2008] [Revised: 08/21/2008] [Accepted: 08/27/2008] [Indexed: 10/21/2022]
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Murray KD, Aronstein KA, de León JH. Analysis of pMA67, a predicted rolling-circle replicating, mobilizable, tetracycline-resistance plasmid from the honey bee pathogen, Paenibacillus larvae. Plasmid 2007; 58:89-100. [PMID: 17363055 DOI: 10.1016/j.plasmid.2007.02.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2005] [Revised: 01/31/2007] [Accepted: 02/01/2007] [Indexed: 11/23/2022]
Abstract
This work characterizes a recently discovered natural tetracycline-resistance plasmid called pMA67 from Paenibacillus larvae--a Gram-positive bacterial pathogen of honey bees. We provide evidence that pMA67 replicates by the rolling-circle mechanism, and sequence comparisons place it in the pMV158 family of rolling-circle replicons. The plasmid contains predicted rep, cop, and rnaII genes for control of replication initiating at a predicted double-strand origin. The plasmid has an ssoT single-strand origin, which is efficient enough to allow only very small amounts of the single-stranded DNA intermediate to accumulate. The overall efficiency of replication is sufficient to render the plasmid segregationally stable without selection in P. larvae and in Bacillus megaterium, but not in Escherichia coli. The plasmid is expected to be mobilizable due to the presence of a mob gene and an oriT site. The plasmid contains a tetL gene, whose predicted amino acid sequence implies a relatively ancient divergence from all previously known plasmid-encoded tetL genes. We confirm that the tetL gene alone is sufficient for conferring resistance to tetracyclines. Sequence comparisons, mostly with the well-characterized pMV158, allow us to predict promoters, DNA and RNA secondary structures, DNA and protein motifs, and other elements.
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Affiliation(s)
- K Daniel Murray
- USDA-ARS, Honey Bee Research Unit, Kika de la Garza Subtropical Agricultural Center, 2413 E. Hwy 83, Weslaco, TX 78596, USA.
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Ruiz-Masó JA, Lurz R, Espinosa M, del Solar G. Interactions between the RepB initiator protein of plasmid pMV158 and two distant DNA regions within the origin of replication. Nucleic Acids Res 2007; 35:1230-44. [PMID: 17267412 PMCID: PMC1851628 DOI: 10.1093/nar/gkl1099] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Plasmids replicating by the rolling circle mode usually possess a single site for binding of the initiator protein at the origin of replication. The origin of pMV158 is different in that it possesses two distant binding regions for the initiator RepB. One region was located close to the site where RepB introduces the replication-initiating nick, within the nic locus; the other, the bind locus, is 84 bp downstream from the nick site. Binding of RepB to the bind locus was of higher affinity and stability than to the nic locus. Contacts of RepB with the bind and nic loci were determined through high-resolution footprinting. Upon binding of RepB, the DNA of the bind locus follows a winding path in its contact with the protein, resulting in local distortion and bending of the double-helix. On supercoiled DNA, simultaneous interaction of RepB with both loci favoured extrusion of the hairpin structure harbouring the nick site while causing a strong DNA distortion around the bind locus. This suggests interplay between the two RepB binding sites, which could facilitate loading of the initiator protein to the nic locus and the acquisition of the appropriate configuration of the supercoiled DNA substrate.
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Affiliation(s)
- José A. Ruiz-Masó
- Centro de Investigaciones Biológicas, CSIC. Ramiro de Maeztu, 9. E-28040-Madrid, Spain and Max Planck Institute for Molecular Genetics. Ihnestrasse 73, D-14195 Berlin, Germany
| | - Rudi Lurz
- Centro de Investigaciones Biológicas, CSIC. Ramiro de Maeztu, 9. E-28040-Madrid, Spain and Max Planck Institute for Molecular Genetics. Ihnestrasse 73, D-14195 Berlin, Germany
| | - Manuel Espinosa
- Centro de Investigaciones Biológicas, CSIC. Ramiro de Maeztu, 9. E-28040-Madrid, Spain and Max Planck Institute for Molecular Genetics. Ihnestrasse 73, D-14195 Berlin, Germany
| | - Gloria del Solar
- Centro de Investigaciones Biológicas, CSIC. Ramiro de Maeztu, 9. E-28040-Madrid, Spain and Max Planck Institute for Molecular Genetics. Ihnestrasse 73, D-14195 Berlin, Germany
- * To whom correspondence should be addressed. Tel: +34 918373112; Fax: +34 915360432; E-mail:
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