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Algora-Gallardo L, Schniete JK, Mark DR, Hunter IS, Herron PR. Bilateral symmetry of linear streptomycete chromosomes. Microb Genom 2021; 7. [PMID: 34779763 PMCID: PMC8743542 DOI: 10.1099/mgen.0.000692] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Here, we characterize an uncommon set of telomeres from Streptomyces rimosus ATCC 10970, the parental strain of a lineage of one of the earliest-discovered antibiotic producers. Following the closure of its genome sequence, we compared unusual telomeres from this organism with the other five classes of replicon ends found amongst streptomycetes. Closed replicons of streptomycete chromosomes were organized with respect to their phylogeny and physical orientation, which demonstrated that different telomeres were not associated with particular clades and are likely shared amongst different strains by plasmid-driven horizontal gene transfer. Furthermore, we identified a ~50 kb origin island with conserved synteny that is located at the core of all streptomycete chromosomes and forms an axis around which symmetrical chromosome inversions can take place. Despite this chromosomal bilateral symmetry, a bias in parS sites to the right of oriC is maintained across the family Streptomycetaceae and suggests that the formation of ParB/parS nucleoprotein complexes on the right replichore is a conserved feature in streptomycetes. Consequently, our studies reveal novel features of linear bacterial replicons that, through their manipulation, may lead to improvements in growth and productivity of this important industrial group of bacteria.
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Affiliation(s)
- Lis Algora-Gallardo
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK
| | - Jana K Schniete
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK.,Department of Biology, Edge Hill University, Ormskirk L39 4QP, UK
| | - David R Mark
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK
| | - Iain S Hunter
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK
| | - Paul R Herron
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK
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2
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Tidjani AR, Bontemps C, Leblond P. Telomeric and sub-telomeric regions undergo rapid turnover within a Streptomyces population. Sci Rep 2020; 10:7720. [PMID: 32382084 PMCID: PMC7205883 DOI: 10.1038/s41598-020-63912-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 04/07/2020] [Indexed: 11/09/2022] Open
Abstract
Genome dynamics was investigated within natural populations of the soil bacterium Streptomyces. The exploration of a set of closely related strains isolated from micro-habitats of a forest soil exhibited a strong diversity of the terminal structures of the linear chromosome, i.e. terminal inverted repeats (TIRs). Large insertions, deletions and translocations could be observed along with evidence of transfer events between strains. In addition, the telomere and its cognate terminal protein complexes required for terminal replication and chromosome maintenance, were shown to be variable within the population probably reflecting telomere exchanges between the chromosome and other linear replicons (i.e., plasmids). Considering the close genetic relatedness of the strains, these data suggest that the terminal regions are prone to a high turnover due to a high recombination associated with extensive horizontal gene transfer.
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Affiliation(s)
| | - Cyril Bontemps
- Université de Lorraine, INRAE, DynAMic, F-54000, Nancy, France.
| | - Pierre Leblond
- Université de Lorraine, INRAE, DynAMic, F-54000, Nancy, France.
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3
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Ramijan K, Zhang Z, van Wezel GP, Claessen D. Genome rearrangements and megaplasmid loss in the filamentous bacterium Kitasatospora viridifaciens are associated with protoplast formation and regeneration. Antonie van Leeuwenhoek 2020; 113:825-837. [PMID: 32060816 PMCID: PMC7188733 DOI: 10.1007/s10482-020-01393-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 02/05/2020] [Indexed: 12/13/2022]
Abstract
Filamentous Actinobacteria are multicellular bacteria with linear replicons. Kitasatospora viridifaciens DSM 40239 contains a linear 7.8 Mb chromosome and an autonomously replicating plasmid KVP1 of 1.7 Mb. Here we show that lysozyme-induced protoplast formation of the multinucleated mycelium of K. viridifaciens drives morphological diversity. Characterisation and sequencing of an individual revertant colony that had lost the ability to differentiate revealed that the strain had not only lost most of KVP1 but also carried deletions in the right arm of the chromosome. Strikingly, the deletion sites were preceded by insertion sequence elements, suggesting that the rearrangements may have been caused by replicative transposition and homologous recombination between both replicons. These data indicate that protoplast formation is a stressful process that can lead to profound genetic changes.
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Affiliation(s)
- Karina Ramijan
- Molecular Biotechnology, Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
| | - Zheren Zhang
- Molecular Biotechnology, Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
| | - Dennis Claessen
- Molecular Biotechnology, Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands.
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4
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Hashimoto Y, Taniguchi M, Uesaka K, Nomura T, Hirakawa H, Tanimoto K, Tamai K, Ruan G, Zheng B, Tomita H. Novel Multidrug-Resistant Enterococcal Mobile Linear Plasmid pELF1 Encoding vanA and vanM Gene Clusters From a Japanese Vancomycin-Resistant Enterococci Isolate. Front Microbiol 2019; 10:2568. [PMID: 31798546 PMCID: PMC6863802 DOI: 10.3389/fmicb.2019.02568] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 10/23/2019] [Indexed: 11/13/2022] Open
Abstract
Vancomycin-resistant enterococci are troublesome pathogens in clinical settings because of few treatment options. A VanA/VanM-type vancomycin-resistant Enterococcus faecium clinical isolate was identified in Japan. This strain, named AA708, harbored five plasmids, one of which migrated during agarose gel electrophoresis without S1 nuclease treatment, which is indicative of a linear topology. We named this plasmid pELF1. Whole genome sequencing (WGS) analysis of the AA708 strain revealed that the complete sequence of pELF1 was 143,316 bp long and harbored both the vanA and vanM gene clusters. Furthermore, mfold analysis and WGS data show that the left end of pELF1 presumably forms a hairpin structure, unlike its right end. The pELF1 plasmid was not digested by lambda exonuclease, indicating that terminal proteins were bound to the 5′ end of the plasmid, similar to the Streptomyces linear plasmids. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis results were also consistent with the exonuclease assay results. In retardation assays, DNAs containing the right end of proteinase K-untreated pELF1 did not appear to move as well as the proteinase K-treated pELF1, suggesting that terminal proteins might be attached to the right end of pELF1. Palindromic sequences formed hairpin structures at the right terminal sequence of pELF1; however, sequence similarity with the well-known linear plasmids of Streptomyces spp. was not high. pELF1 was unique as it possessed two different terminal structures. Conjugation experiments revealed that pELF1 could be transferred to E. faecalis, E. faecium, E. casseliflavus, and E. hirae. These transconjugants exhibited not only high resistance levels to vancomycin, but also resistance to streptomycin, kanamycin, and erythromycin. These results indicate that pELF1 has the ability to confer multidrug resistance to Enterococcus spp. simultaneously, which might lead to clinical hazards.
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Affiliation(s)
- Yusuke Hashimoto
- Department of Bacteriology, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Makoto Taniguchi
- Oral Microbiome Center, Taniguchi Dental Clinic, Takamatsu, Japan
| | - Kazuma Uesaka
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Takahiro Nomura
- Department of Bacteriology, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Hidetada Hirakawa
- Department of Bacteriology, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Koichi Tanimoto
- Laboratory of Bacterial Drug Resistance, Gunma University Graduate School of Medicine, Maebashi, Japan
| | | | - Genjie Ruan
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China
| | - Bo Zheng
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China
| | - Haruyoshi Tomita
- Department of Bacteriology, Gunma University Graduate School of Medicine, Maebashi, Japan.,Laboratory of Bacterial Drug Resistance, Gunma University Graduate School of Medicine, Maebashi, Japan
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Pan HY, Chen CW, Huang CH. A highly efficient targeted recombination system for engineering linear chromosomes of industrial bacteria Streptomyces. J GEN APPL MICROBIOL 2018; 64:167-173. [PMID: 29669960 DOI: 10.2323/jgam.2017.11.004] [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] [Indexed: 11/03/2022]
Abstract
Soil bacteria Streptomyces are the most important producers of secondary metabolites, including most known antibiotics. These bacteria and their close relatives are unique in possessing linear chromosomes, which typically harbor 20 to 30 biosynthetic gene clusters of tens to hundreds of kb in length. Many Streptomyces chromosomes are accompanied by linear plasmids with sizes ranging from several to several hundred kb. The large linear plasmids also often contain biosynthetic gene clusters. We have developed a targeted recombination procedure for arm exchanges between a linear plasmid and a linear chromosome. A chromosomal segment inserted in an artificially constructed plasmid allows homologous recombination between the two replicons at the homology. Depending on the design, the recombination may result in two recombinant replicons or a single recombinant chromosome with the loss of the recombinant plasmid that lacks a replication origin. The efficiency of such targeted recombination ranges from 9 to 83% depending on the locations of the homology (and thus the size of the chromosomal arm exchanged), essentially eliminating the necessity of selection. The targeted recombination is useful for the efficient engineering of the Streptomyces genome for large-scale deletion, addition, and shuffling.
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Affiliation(s)
- Hung-Yin Pan
- Graduate Institution of Engineering Technology, National Taipei University of Technology
| | - Carton W Chen
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University
| | - Chih-Hung Huang
- Institute of Biochemical and Biomedical Engineering, National Taipei University of Technology
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Yang CC, Tseng SM, Pan HY, Huang CH, Chen CW. Telomere associated primase Tap repairs truncated telomeres of Streptomyces. Nucleic Acids Res 2017; 45:5838-5849. [PMID: 28369604 PMCID: PMC5449611 DOI: 10.1093/nar/gkx189] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 03/11/2017] [Indexed: 01/01/2023] Open
Abstract
Replication of the linear chromosomes of soil bacteria Streptomyces proceeds from an internal origin towards the telomeres, followed by patching of the resulting terminal single-strand overhangs by DNA synthesis using terminal proteins as the primer, which remains covalently bound to the 5΄ ends of the DNA. In most Streptomyces chromosomes, the end patching requires the single-strand overhangs, terminal protein Tpg, and terminal associated protein Tap. The telomere overhangs contain several palindromic sequences capable of forming stable hairpins. Previous in vitro deoxynucleotidylation studies indicated that Tap adds the Palindrome I sequence to Tpg, which is extended by a polymerase to fill the gap. In this study, the stringency of Palindrome I sequence was examined by an in vitro deoxynucleotidylation system and in vivo replication. Several nt in Palindrome I were identified to be critical for priming. While the first 3 G on the template were required for deoxynucleotidylation in vitro, deletions of them could be suppressed by the presence of dGTP. In vivo, deletions of these G were also tolerated, and the telomere sequence was restored in the linear plasmid DNA. Our results indicated that the truncated telomeres were repaired by extension synthesis by Tap on the foldback Palindrome I sequence.
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Affiliation(s)
- Chien-Chin Yang
- Department of Chemistry, Chung-Yuan Christian University, Chung-li, Taiwan
- To whom correspondence should be addressed. Tel: +886 3 2653303; Fax: +886 3 2653399;
| | - Shu-Min Tseng
- Department of Chemistry, Chung-Yuan Christian University, Chung-li, Taiwan
| | - Hung-Yin Pan
- Institute of Biochemical and Biomedical Engineering, National Taipei University of Technology, Taipei, Taiwan
| | - Chih-Hung Huang
- Institute of Biochemical and Biomedical Engineering, National Taipei University of Technology, Taipei, Taiwan
| | - Carton W. Chen
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
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Hoff G, Bertrand C, Piotrowski E, Thibessard A, Leblond P. Implication of RuvABC and RecG in homologous recombination in Streptomyces ambofaciens. Res Microbiol 2016; 168:26-35. [PMID: 27424811 DOI: 10.1016/j.resmic.2016.07.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 07/04/2016] [Accepted: 07/04/2016] [Indexed: 10/21/2022]
Abstract
Most bacterial organisms rely on homologous recombination to repair DNA double-strand breaks and for the post-replicative repair of DNA single-strand gaps. Homologous recombination can be divided into three steps: (i) a pre-synaptic step in which the DNA 3'-OH ends are processed, (ii) a recA-dependent synaptic step allowing the invasion of an intact copy and the formation of Holliday junctions, and (iii) a post-synaptic step consisting of migration and resolution of these junctions. Currently, little is known about factors involved in homologous recombination, especially for the post-synaptic step. In Escherichia coli, branch migration and resolution are performed by the RuvABC complex, but could also rely on the RecG helicase in a redundant manner. In this study, we show that recG and ruvABC are well-conserved among Streptomyces. ΔruvABC, ΔrecG and ΔruvABC ΔrecG mutant strains were constructed. ΔruvABC ΔrecG is only slightly affected by exposure to DNA damage (UV). We also show that conjugational recombination decreases in the absence of RuvABC and RecG, but that intra-chromosomal recombination is not affected. These data suggest that RuvABC and RecG are indeed involved in homologous recombination in Streptomyces ambofaciens and that alternative factors are able to take over Holliday junction in Streptomyces.
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Affiliation(s)
- Grégory Hoff
- Université de Lorraine, Dynamique des Génomes et Adaptation Microbienne, UMR 1128, Vandœuvre-lès-Nancy, F-54506, France; INRA, Dynamique des Génomes et Adaptation Microbienne, UMR 1128, Vandœuvre-lès-Nancy, F-54506, France.
| | - Claire Bertrand
- Université de Lorraine, Dynamique des Génomes et Adaptation Microbienne, UMR 1128, Vandœuvre-lès-Nancy, F-54506, France; INRA, Dynamique des Génomes et Adaptation Microbienne, UMR 1128, Vandœuvre-lès-Nancy, F-54506, France.
| | - Emilie Piotrowski
- Université de Lorraine, Dynamique des Génomes et Adaptation Microbienne, UMR 1128, Vandœuvre-lès-Nancy, F-54506, France; INRA, Dynamique des Génomes et Adaptation Microbienne, UMR 1128, Vandœuvre-lès-Nancy, F-54506, France.
| | - Annabelle Thibessard
- Université de Lorraine, Dynamique des Génomes et Adaptation Microbienne, UMR 1128, Vandœuvre-lès-Nancy, F-54506, France; INRA, Dynamique des Génomes et Adaptation Microbienne, UMR 1128, Vandœuvre-lès-Nancy, F-54506, France.
| | - Pierre Leblond
- Université de Lorraine, Dynamique des Génomes et Adaptation Microbienne, UMR 1128, Vandœuvre-lès-Nancy, F-54506, France; INRA, Dynamique des Génomes et Adaptation Microbienne, UMR 1128, Vandœuvre-lès-Nancy, F-54506, France.
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Abstract
Telomerase is the eukaryotic solution to the ‘end-replication problem’ of linear chromosomes by synthesising the highly repetitive DNA constituent of telomeres, the nucleoprotein cap that protects chromosome termini. Functioning as a ribonucleoprotein (RNP) enzyme, telomerase is minimally composed of the highly conserved catalytic telomerase reverse transcriptase (TERT) and essential telomerase RNA (TR) component. Beyond merely providing the template for telomeric DNA synthesis, TR is an innate telomerase component and directly facilitates enzymatic function. TR accomplishes this by having evolved structural elements for stable assembly with the TERT protein and the regulation of the telomerase catalytic cycle. Despite its prominence and prevalence, TR has profoundly diverged in length, sequence, and biogenesis pathway among distinct evolutionary lineages. This diversity has generated numerous structural and mechanistic solutions for ensuring proper RNP formation and high fidelity telomeric DNA synthesis. Telomerase provides unique insights into RNA and protein coevolution within RNP enzymes.
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Affiliation(s)
- Joshua D Podlevsky
- a School of Molecular Sciences, Arizona State University , Tempe , AZ , USA
| | - Julian J-L Chen
- a School of Molecular Sciences, Arizona State University , Tempe , AZ , USA
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9
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Yang CC, Tseng SM, Chen CW. Telomere-associated proteins add deoxynucleotides to terminal proteins during replication of the telomeres of linear chromosomes and plasmids in Streptomyces. Nucleic Acids Res 2015; 43:6373-83. [PMID: 25883134 PMCID: PMC4513846 DOI: 10.1093/nar/gkv302] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 03/17/2015] [Accepted: 03/25/2015] [Indexed: 12/15/2022] Open
Abstract
Typical telomeres of linear chromosomes and plasmids of soil bacteria Streptomyces consist of tightly packed palindromic sequences with a terminal protein ('TP') covalently attached to the 5' end of the DNA. Replication of these linear replicons is initiated internally and proceeds bidirectionally toward the telomeres, which leaves single-strand overhangs at the 3' ends. These overhangs are filled by DNA synthesis using the TPs as the primers ('end patching'). The gene encoding for typical TP, tpg, forms an operon with tap, encoding an essential telomere-associated protein, which binds TP and the secondary structures formed by the 3' overhangs. Previously one of the two translesion synthesis DNA polymerases, DinB1 or DinB2, was proposed to catalyze the protein-primed synthesis. However, using an in vitro end-patching system, we discovered that Tpg and Tap alone could carry out the protein-primed synthesis to a length of 13 nt. Similarly, an 'atypical' terminal protein, Tpc, and its cognate telomere-associated protein, Tac, of SCP1 plasmid, were sufficient to achieve protein-primed synthesis in the absence of additional polymerase. These results indicate that these two telomere-associated proteins possess polymerase activities alone or in complex with the cognate TPs.
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Affiliation(s)
- Chien-Chin Yang
- Department of Chemistry, Chung-Yuan Christian University, Chung-li 32023, Taiwan
| | - Shu-Min Tseng
- Department of Chemistry, Chung-Yuan Christian University, Chung-li 32023, Taiwan
| | - Carton W Chen
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Shih-Pai, Taipei 11221, Taiwan
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10
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Shintani M, Sanchez ZK, Kimbara K. Genomics of microbial plasmids: classification and identification based on replication and transfer systems and host taxonomy. Front Microbiol 2015; 6:242. [PMID: 25873913 PMCID: PMC4379921 DOI: 10.3389/fmicb.2015.00242] [Citation(s) in RCA: 206] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 03/12/2015] [Indexed: 12/21/2022] Open
Abstract
Plasmids are important "vehicles" for the communication of genetic information between bacteria. The exchange of plasmids transmits pathogenically and environmentally relevant traits to the host bacteria, promoting their rapid evolution and adaptation to various environments. Over the past six decades, a large number of plasmids have been identified and isolated from different microbes. With the revolution of sequencing technology, more than 4600 complete sequences of plasmids found in bacteria, archaea, and eukaryotes have been determined. The classification of a wide variety of plasmids is not only important to understand their features, host ranges, and microbial evolution but is also necessary to effectively use them as genetic tools for microbial engineering. This review summarizes the current situation of the classification of fully sequenced plasmids based on their host taxonomy and their features of replication and conjugative transfer. The majority of the fully sequenced plasmids are found in bacteria in the Proteobacteria, Firmicutes, Spirochaetes, Actinobacteria, Cyanobacteria and Euryarcheota phyla, and key features of each phylum are included. Recent advances in the identification of novel types of plasmids and plasmid transfer by culture-independent methods using samples from natural environments are also discussed.
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Affiliation(s)
- Masaki Shintani
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University Shizuoka, Japan ; Department of Bioscience, Graduate School of Science and Technology, Shizuoka University Shizuoka, Japan
| | - Zoe K Sanchez
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University Shizuoka, Japan
| | - Kazuhide Kimbara
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University Shizuoka, Japan
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Nindita Y, Cao Z, Yang Y, Arakawa K, Shiwa Y, Yoshikawa H, Tagami M, Lezhava A, Kinashi H. The tap-tpg gene pair on the linear plasmid functions to maintain a linear topology of the chromosome in Streptomyces rochei. Mol Microbiol 2015; 95:846-58. [PMID: 25495952 DOI: 10.1111/mmi.12904] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2014] [Indexed: 11/30/2022]
Abstract
Streptomyces rochei 7434AN4 carries three linear plasmids, pSLA2-L (211 kb), pSLA2-M (113 kb) and pSLA2-S (18 kb), their complete nucleotide sequences having been determined. Restriction and sequencing analysis revealed that the telomere sequences at both ends of the linear chromosome are identical to each other, are 98.5% identical to the right end sequences of pSLA2-L and pSLA2-M up to 3.1 kb from the ends and have homology to those of typical Streptomyces species. Mutant 2-39, which lost all the three linear plasmids, was found to carry a circularized chromosome. Sequence comparison of the fusion junction and both deletion ends revealed that chromosomal circularization occurred by terminal deletions followed by nonhomologous recombination. Curing of pSLA2-L from strain 51252, which carries only pSLA2-L, also resulted in terminal deletions in newly obtained mutants. The tap-tpg gene pair, which encodes a telomere-associated protein and a terminal protein for end patching, is located on pSLA2-L and pSLA2-M but has not hitherto been found on the chromosome. These results led us to the idea that the tap-tpg of pSLA2-L or pSLA2-M functions to maintain a linear chromosome in strain 7434AN4. This hypothesis was finally confirmed by complementation and curing experiments of the tap-tpg of pSLA2-M.
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Affiliation(s)
- Yosi Nindita
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, 739-8530, Japan
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12
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Gella P, Salas M, Mencía M. Improved artificial origins for phage Φ29 terminal protein-primed replication. Insights into early replication events. Nucleic Acids Res 2014; 42:9792-806. [PMID: 25081208 PMCID: PMC4150772 DOI: 10.1093/nar/gku660] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The replication machinery of bacteriophage Φ29 is a paradigm for protein-primed replication and it holds great potential for applied purposes. To better understand the early replication events and to find improved origins for DNA amplification based on the Φ29 system, we have studied the end-structure of a double-stranded DNA replication origin. We have observed that the strength of the origin is determined by a combination of factors. The strongest origin (30-fold respect to wt) has the sequence CCC at the 3' end of the template strand, AAA at the 5' end of the non-template strand and 6 nucleotides as optimal unpairing at the end of the origin. We also show that the presence of a correctly positioned displaced strand is important because origins with 5' or 3' ssDNA regions have very low activity. Most of the effect of the improved origins takes place at the passage between the terminal protein-primed and the DNA-primed modes of replication by the DNA polymerase suggesting the existence of a thermodynamic barrier at that point. We suggest that the template and non-template strands of the origin and the TP/DNA polymerase complex form series of interactions that control the critical start of terminal protein-primed replication.
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Affiliation(s)
- Pablo Gella
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid), Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain
| | - Margarita Salas
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid), Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain
| | - Mario Mencía
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid), Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain
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13
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Peng S, Zeng A, Zhong L, Zhang R, Zhou M, Cheng Q, Zhao L, Wang T, Tan H, Qin Z. Three functional replication origins of the linear and artificially circularized plasmid SCP1 of Streptomyces coelicolor. Microbiology (Reading) 2013; 159:2127-2140. [DOI: 10.1099/mic.0.067363-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Shiyuan Peng
- Key Laboratory of Synthetic Biology, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, PR China
| | - Ana Zeng
- Key Laboratory of Synthetic Biology, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, PR China
| | - Li Zhong
- Key Laboratory of Synthetic Biology, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, PR China
| | - Ran Zhang
- Key Laboratory of Synthetic Biology, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, PR China
| | - Min Zhou
- Key Laboratory of Synthetic Biology, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, PR China
| | - Qiuxiang Cheng
- Key Laboratory of Synthetic Biology, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, PR China
| | - Liqian Zhao
- Key Laboratory of Synthetic Biology, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, PR China
| | - Tao Wang
- Key Laboratory of Synthetic Biology, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, PR China
| | - Huarong Tan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Zhongjun Qin
- Key Laboratory of Synthetic Biology, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, PR China
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Huang TW, Hsu CC, Yang HY, Chen CW. Topoisomerase IV is required for partitioning of circular chromosomes but not linear chromosomes in Streptomyces. Nucleic Acids Res 2013; 41:10403-13. [PMID: 23999094 PMCID: PMC3905888 DOI: 10.1093/nar/gkt757] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Filamentous bacteria of the genus Streptomyces possess linear chromosomes and linear plasmids. Theoretically, linear replicons may not need a decatenase for post-replicational separation of daughter molecules. Yet, Streptomyces contain parC and parE that encode the subunits for the decatenase topoisomerase IV. The linear replicons of Streptomyces adopt a circular configuration in vivo through telomere–telomere interaction, which would require decatenation, if the circular configuration persists through replication. We investigated whether topoisomerase IV is required for separation of the linear replicons in Streptomyces. Deletion of parE from the Streptomyces coelicolor chromosome was achieved, when parE was provided on a plasmid. Subsequently, the plasmid was eliminated at high temperature, and ΔparE mutants were obtained. These results indicated that topoisomerase IV was not essential for Streptomyces. Presumably, the telomere–telomere association may be resolved during or after replication to separate the daughter chromosomes. Nevertheless, the mutants exhibited retarded growth, defective sporulation and temperature sensitivity. In the mutants, circular plasmids could not replicate, and spontaneous circularization of the chromosome was not observed, indicating that topoisomerase IV was required for decatenation of circular replicons. Moreover, site-specific integration of a plasmid is impaired in the mutants, suggesting the formation of DNA knots during integration, which must be resolved by topoisomerase IV.
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Affiliation(s)
| | | | | | - Carton W. Chen
- *To whom correspondence should be addressed. Tel: +886 2 28267040;
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15
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Zhang R, Xia H, Xu Q, Dang F, Qin Z. Recombinational cloning of the antibiotic biosynthetic gene clusters in linear plasmid SCP1 ofStreptomyces coelicolorA3(2). FEMS Microbiol Lett 2013; 345:39-48. [DOI: 10.1111/1574-6968.12183] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 04/19/2013] [Accepted: 05/17/2013] [Indexed: 11/30/2022] Open
Affiliation(s)
- Ran Zhang
- Key laboratory of Synthetic Biology; Shanghai Institute of Plant Physiology and Ecology; Shanghai Institutes for Biological Sciences; the Chinese Academy of Sciences; Shanghai; China
| | - Haiyang Xia
- Key laboratory of Synthetic Biology; Shanghai Institute of Plant Physiology and Ecology; Shanghai Institutes for Biological Sciences; the Chinese Academy of Sciences; Shanghai; China
| | - Qingyu Xu
- Key laboratory of Synthetic Biology; Shanghai Institute of Plant Physiology and Ecology; Shanghai Institutes for Biological Sciences; the Chinese Academy of Sciences; Shanghai; China
| | - Fujun Dang
- Key laboratory of Synthetic Biology; Shanghai Institute of Plant Physiology and Ecology; Shanghai Institutes for Biological Sciences; the Chinese Academy of Sciences; Shanghai; China
| | - Zhongjun Qin
- Key laboratory of Synthetic Biology; Shanghai Institute of Plant Physiology and Ecology; Shanghai Institutes for Biological Sciences; the Chinese Academy of Sciences; Shanghai; China
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16
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Yang CC, Sun WC, Wang WY, Huang CH, Lu FS, Tseng SM, Chen CW. Mutational analysis of the terminal protein Tpg of Streptomyces chromosomes: identification of the deoxynucleotidylation site. PLoS One 2013; 8:e56322. [PMID: 23457549 PMCID: PMC3572947 DOI: 10.1371/journal.pone.0056322] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 01/08/2013] [Indexed: 11/23/2022] Open
Abstract
The linear chromosomes and linear plasmids of Streptomyces are capped by terminal proteins (TPs) covalently bound to the 5' ends of the DNA. The TPs serve as primers for DNA synthesis that patches in the single-stranded gaps at the telomeres resulting from the bi-directional replication ('end patching'). Typical Streptomyces TPs, designated Tpgs, are conserved in sequence and size (about 185 amino acids), and contain a predicted helix-turn-helix domain and a functional nuclear localization signal. The Tpg-encoding gene (tpg) is often accompanied by an upstream gene tap that encodes an essential telomere-associating protein. Five lone tpg variants (not accompanied by tap) from various Streptomyces species were tested, and three were found to be pseudogenes. The lone tpg variant on the SLP2 plasmid, although functional, still requires the presence of tap on the chromosome for end patching. Using a combination of in vitro deoxynucleotidylation, physical localization, and genetic analysis, we identified the threonine at position 114 (T114) in Tpg of Streptomyces lividans chromosome as the deoxynucleotidylated site. Interestingly, T114 could be substituted by a serine without destroying the priming activity of Tpg in vitro and in vivo. Such T114S substitution is seen in and a number of pseudogenes as well as functional Tpgs. T114 lies in a predicted coil flanked by two short helixes in a highly hydrophilic region. The location and structural arrangement of the deoxynucleotidylated site in Tpg is similar to those in the TPs of phage ø 29 and adenoviruses. However, these TPs are distinct in their sequences and sizes, indicating that they have evolved independently during evolution. Using naturally occurring and artificially created tpg variants, we further identified several amino acid residues in the N-terminus and the helix-turn-helix domain that were important for functionality.
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Affiliation(s)
- Chien-Chin Yang
- Department of Chemistry, Chung-Yuan Christian University, Chung-li, Taiwan
| | - We-Chi Sun
- Department of Chemistry, Chung-Yuan Christian University, Chung-li, Taiwan
| | - Wan-Yu Wang
- Department of Chemistry, Chung-Yuan Christian University, Chung-li, Taiwan
| | - Chi-Hung Huang
- Institute of Biotechnology, National Taipei University of Technology, Taipei, Taiwan
| | - Fang-Shy Lu
- Department of Chemistry, Chung-Yuan Christian University, Chung-li, Taiwan
| | - Shu-Min Tseng
- Department of Chemistry, Chung-Yuan Christian University, Chung-li, Taiwan
| | - Carton W. Chen
- Department of Life Sciences, Institute of Genome Sciences, National Yang-Ming University, Shih-Pai, Taipei, Taiwan
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17
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Deng Z, Wang Z, Lieberman PM. Telomeres and viruses: common themes of genome maintenance. Front Oncol 2012; 2:201. [PMID: 23293769 PMCID: PMC3533235 DOI: 10.3389/fonc.2012.00201] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 12/08/2012] [Indexed: 12/14/2022] Open
Abstract
Genome maintenance mechanisms actively suppress genetic instability associated with cancer and aging. Some viruses provoke genetic instability by subverting the host's control of genome maintenance. Viruses have their own specialized strategies for genome maintenance, which can mimic and modify host cell processes. Here, we review some of the common features of genome maintenance utilized by viruses and host chromosomes, with a particular focus on terminal repeat (TR) elements. The TRs of cellular chromosomes, better known as telomeres, have well-established roles in cellular chromosome stability. Cellular telomeres are themselves maintained by viral-like mechanisms, including self-propagation by reverse transcription, recombination, and retrotransposition. Viral TR elements, like cellular telomeres, are essential for viral genome stability and propagation. We review the structure and function of viral repeat elements and discuss how they may share telomere-like structures and genome protection functions. We consider how viral infections modulate telomere regulatory factors for viral repurposing and can alter normal host telomere structure and chromosome stability. Understanding the common strategies of viral and cellular genome maintenance may provide new insights into viral-host interactions and the mechanisms driving genetic instability in cancer.
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Affiliation(s)
- Zhong Deng
- The Wistar Institute Philadelphia, PA, USA
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18
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Tsai HH, Shu HW, Yang CC, Chen CW. Translesion-synthesis DNA polymerases participate in replication of the telomeres in Streptomyces. Nucleic Acids Res 2011; 40:1118-30. [PMID: 22006845 PMCID: PMC3273824 DOI: 10.1093/nar/gkr856] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Linear chromosomes and linear plasmids of Streptomyces are capped by terminal proteins that are covalently bound to the 5′-ends of DNA. Replication is initiated from an internal origin, which leaves single-stranded gaps at the 3′-ends. These gaps are patched by terminal protein-primed DNA synthesis. Streptomyces contain five DNA polymerases: one DNA polymerase I (Pol I), two DNA polymerases III (Pol III) and two DNA polymerases IV (Pol IV). Of these, one Pol III, DnaE1, is essential for replication, and Pol I is not required for end patching. In this study, we found the two Pol IVs (DinB1 and DinB2) to be involved in end patching. dinB1 and dinB2 could not be co-deleted from wild-type strains containing a linear chromosome, but could be co-deleted from mutant strains containing a circular chromosome. The resulting ΔdinB1 ΔdinB2 mutants supported replication of circular but not linear plasmids, and exhibited increased ultraviolet sensitivity and ultraviolet-induced mutagenesis. In contrast, the second Pol III, DnaE2, was not required for replication, end patching, or ultraviolet resistance and mutagenesis. All five polymerase genes are relatively syntenous in the Streptomyces chromosomes, including a 4-bp overlap between dnaE2 and dinB2. Phylogenetic analysis showed that the dinB1-dinB2 duplication occurred in a common actinobacterial ancestor.
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Affiliation(s)
- Hsiu-Hui Tsai
- Department of Life Sciences and Institute of Genome Sciences, Institute of Biotechnology in Medicine, National Yang-Ming University, Shih-Pai, Taipei 11221, Taiwan
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Zhou Z, Gu J, Du YL, Li YQ, Wang Y. The -omics Era- Toward a Systems-Level Understanding of Streptomyces. Curr Genomics 2011; 12:404-16. [PMID: 22379394 PMCID: PMC3178909 DOI: 10.2174/138920211797248556] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2011] [Revised: 06/28/2011] [Accepted: 07/03/2011] [Indexed: 11/22/2022] Open
Abstract
Streptomyces is a group of soil bacteria of medicinal, economic, ecological, and industrial importance. It is renowned for its complex biology in gene regulation, antibiotic production, morphological differentiation, and stress response. In this review, we provide an overview of the recent advances in Streptomyces biology inspired by -omics based high throughput technologies. In this post-genomic era, vast amounts of data have been integrated to provide significant new insights into the fundamental mechanisms of system control and regulation dynamics of Streptomyces.
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Affiliation(s)
- Zhan Zhou
- College of Life Sciences, Zhejiang University, Hangzhou 310058, P.R. China
- Department of Biology, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Jianying Gu
- Department of Biology, College of Staten Island, City University of New York, Staten Island, NY 10314, USA
| | - Yi-Ling Du
- College of Life Sciences, Zhejiang University, Hangzhou 310058, P.R. China
| | - Yong-Quan Li
- College of Life Sciences, Zhejiang University, Hangzhou 310058, P.R. China
| | - Yufeng Wang
- Department of Biology, University of Texas at San Antonio, San Antonio, TX 78249, USA
- South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX 78249, USA
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20
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Guo P, Cheng Q, Xie P, Fan Y, Jiang W, Qin Z. Characterization of the multiple CRISPR loci on Streptomyces linear plasmid pSHK1. Acta Biochim Biophys Sin (Shanghai) 2011; 43:630-9. [PMID: 21705768 DOI: 10.1093/abbs/gmr052] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The complete nucleotide sequence including the novel telomere sequence of Streptomyces linear plasmid pSHK1 consists of 187,263-bp, 158 genes, in which 51 genes resemble those of the linear plasmid SCP1 of Streptomyces coelicolor A3(2), and 20 genes encode transposases. Strikingly, the repetitive CRISPRs (clustered regularly interspaced short palindromic repeats) and cas (CRISPR-associated) genes were found, including a cluster of eight cas genes, in the order cas2B-cas1B-cas3B-cas5-cas4-cas2A-cas1A-cas3A, bracketed by a pair of divergent CRISPRs, and five other dispersed CRISPRs. The cas2B-cas1B-cas3B-cas5 or cas4-cas2A-cas1A genes were co-transcribed. Protein-protein interactions between Cas5 and Cas1A, 2A, 2B, 3B were detected by yeast two-hybrids, indicating a critical role of Cas5 for the formation of protein complexes. By polymerase chain reaction and Southern hybridization, 12 cas4 genes including three on linear plasmids were found among 75 newly isolated Streptomyces strains. The paired-CRISPRs and bracketed cas were also conserved in several other Streptomyces or actinomycete species. However, unlike other bacteria, the CRISPRs-cas in pSHK1 could not provide immunity against introduction of phage ΦC31 and plasmid containing the particular spacers in Streptomyces.
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Affiliation(s)
- Peng Guo
- Key Laboratory of Synthetic Biology, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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21
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Abstract
Many chromosomes from Actinomycetales, an order within the Actinobacteria, have been sequenced over the last 10 years and the pace is increasing. This group of Gram-positive and high G+C% bacteria is economically and medically important. However, this group of organisms also is just about the only order in the kingdom Bacteria to have a relatively high proportion of linear chromosomes. Chromosome topology varies within the order according to the genera. Streptomyces, Kitasatospora and Rhodococcus, at least as chromosome sequencing stands at present, have a very high proportion of linear chromosomes, whereas most other genera seem to have circular chromosomes. This review examines chromosome topology across the Actinomycetales and how this affects our concepts of chromosome evolution.
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Affiliation(s)
- Ralph Kirby
- Department of Life Sciences, Institute of Genome Science, National Yang-Ming University, Taipei, Taiwan.
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22
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Wagenknecht M, Meinhardt F. Replication-involved genes of pAL1, the linear plasmid of Arthrobacter nitroguajacolicus Rü61a--phylogenetic and transcriptional analysis. Plasmid 2010; 65:176-84. [PMID: 21185858 DOI: 10.1016/j.plasmid.2010.12.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Revised: 12/16/2010] [Accepted: 12/17/2010] [Indexed: 11/28/2022]
Abstract
The 113-kb pAL1 is the only Arthrobacter linear plasmid known; it has terminal inverted repeats and 5' covalently attached terminal proteins (TPs). The latter and a telomere-associated protein (Tap) are encoded by plasmid ORFs 102 and 101, respectively. As for Streptomyces linear replicons, in which both above proteins are instrumental in telomere patching, they are involved in pAL1 replication as well. However, the alignment of actinobacterial Taps and TPs revealed that pAL1 and the linear elements from Rhodococci comprise a discrete phylogenetic group, clearly delineated from the streptomycetes linear plasmids. In line with such findings is the same genetic arrangement of ORF 101 and 102 counterparts in the rhodococcal elements. Furthermore, the adjacent gene (ORF100) has matches in the rhodococcal plasmids as well. In linear elements of Streptomyces there is no ORF100 homolog. Two alternative annotations are possible for ORF100 gene products. As RT-PCR revealed cotranscription of ORFs 100-102, the ORF100 gene product is presumably involved in replicative processes. Taken also into consideration the likely absence of an internal replication origin (other than in Streptomyces linear elements), we assume a distinct replication/telomere patching mechanism for pAL1 type replicons.
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Affiliation(s)
- Martin Wagenknecht
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstr. 3, D-48149 Münster, Germany
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23
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Giant linear plasmids in Streptomyces: a treasure trove of antibiotic biosynthetic clusters. J Antibiot (Tokyo) 2010; 64:19-25. [DOI: 10.1038/ja.2010.146] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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24
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Tsai HH, Huang CH, Tessmer I, Erie DA, Chen CW. Linear Streptomyces plasmids form superhelical circles through interactions between their terminal proteins. Nucleic Acids Res 2010; 39:2165-74. [PMID: 21109537 PMCID: PMC3064793 DOI: 10.1093/nar/gkq1204] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Linear chromosomes and linear plasmids of Streptomyces possess covalently bound terminal proteins (TPs) at the 5′ ends of their telomeres. These TPs are proposed to act as primers for DNA synthesis that patches the single-stranded gaps at the 3′ ends during replication. Most (‘archetypal’) Streptomyces TPs (designated Tpg) are highly conserved in size and sequence. In addition, there are a number of atypical TPs with heterologous sequences and sizes, one of which is Tpc that caps SCP1 plasmid of Streptomyces coelicolor. Interactions between the TPs on the linear Streptomyces replicons have been suggested by electrophoretic behaviors of TP-capped DNA and circular genetic maps of Streptomyces chromosomes. Using chemical cross-linking, we demonstrated intramolecular and intermolecular interactions in vivo between Tpgs, between Tpcs and between Tpg and Tpc. Interactions between the chromosomal and plasmid telomeres were also detected in vivo. The intramolecular telomere interactions produced negative superhelicity in the linear DNA, which was relaxed by topoisomerase I. Such intramolecular association between the TPs poses a post-replicational complication in the formation of a pseudo-dimeric structure that requires resolution by exchanging TPs or DNA.
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Affiliation(s)
- Hsiu-Hui Tsai
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Shih-Pai, Taipei 112, Taiwan
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25
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Dib JR, Wagenknecht M, Hill RT, Farías ME, Meinhardt F. Novel linear megaplasmid from Brevibacterium sp. isolated from extreme environment. J Basic Microbiol 2010; 50:280-4. [PMID: 20473959 DOI: 10.1002/jobm.200900332] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Brevibacterium sp. Ap13, isolated from flamingo's feces in Laguna Aparejos, a high-altitude lake located at approximately 4,200 m in the northwest of Argentina was previously found to be resistant to multiple antibiotics, and was therefore screened for plasmids that may be implicated in antibiotic resistance. Brevibacterium sp. Ap13 was found to contain two plasmids of approximately 87 and 436 kb, designated pAP13 and pAP13c, respectively. Only pAP13 was stably maintained and was extensively characterized by pulsed-field gel electrophoresis to reveal that this plasmid is linear and likely has covalently linked terminal proteins associated with its 5' ends. This is the first report of a linear plasmid in the genus Brevibacterium and may provide a new tool for genetic manipulation of this commercially important genus.
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Affiliation(s)
- Julián Rafael Dib
- Planta Piloto de Procesos Industriales Microbiológicos-CONICET, Tucumán, Argentina
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26
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A novel replicative enzyme encoded by the linear Arthrobacter plasmid pAL1. J Bacteriol 2010; 192:4935-43. [PMID: 20675469 DOI: 10.1128/jb.00614-10] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The soil bacterium Arthrobacter nitroguajacolicus Rü61a contains the linear plasmid pAL1, which codes for the degradation of 2-methylquinoline. Like other linear replicons of actinomycetes, pAL1 is characterized by short terminal inverted-repeat sequences and terminal proteins (TPpAL1) covalently attached to its 5' ends. TPpAL1, encoded by the pAL1.102 gene, interacts in vivo with the protein encoded by pAL1.101. Bioinformatic analysis of the pAL1.101 protein, which comprises 1,707 amino acids, suggested putative zinc finger and topoisomerase-primase domains and part of a superfamily 2 helicase domain in its N-terminal and central regions, respectively. Sequence motifs characteristic of the polymerization domain of family B DNA polymerases are partially conserved in a C-terminal segment. The purified recombinant protein catalyzed the deoxycytidylation of TPpAL1 in the presence of single-stranded DNA templates comprising the 3'-terminal sequence (5'-GCAGG-3'), which in pAL1 forms the terminal inverted repeat, but also at templates with 5'-(G/T)CA(GG/GC/CG)-3' ends. Enzyme assays suggested that the protein exhibits DNA topoisomerase, DNA helicase, and DNA- and protein-primed DNA polymerase activities. The pAL1.101 protein, therefore, may act as a replicase of pAL1.
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27
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Medema MH, Trefzer A, Kovalchuk A, van den Berg M, Müller U, Heijne W, Wu L, Alam MT, Ronning CM, Nierman WC, Bovenberg RAL, Breitling R, Takano E. The sequence of a 1.8-mb bacterial linear plasmid reveals a rich evolutionary reservoir of secondary metabolic pathways. Genome Biol Evol 2010; 2:212-24. [PMID: 20624727 PMCID: PMC2997539 DOI: 10.1093/gbe/evq013] [Citation(s) in RCA: 156] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Plasmids are mobile genetic elements that play a key role in the evolution of bacteria by mediating genome plasticity and lateral transfer of useful genetic information. Although originally considered to be exclusively circular, linear plasmids have also been identified in certain bacterial phyla, notably the actinomycetes. In some cases, linear plasmids engage with chromosomes in an intricate evolutionary interplay, facilitating the emergence of new genome configurations by transfer and recombination or plasmid integration. Genome sequencing of Streptomyces clavuligerus ATCC 27064, a Gram-positive soil bacterium known for its production of a diverse array of biotechnologically important secondary metabolites, revealed a giant linear plasmid of 1.8 Mb in length. This megaplasmid (pSCL4) is one of the largest plasmids ever identified and the largest linear plasmid to be sequenced. It contains more than 20% of the putative protein-coding genes of the species, but none of these is predicted to be essential for primary metabolism. Instead, the plasmid is densely packed with an exceptionally large number of gene clusters for the potential production of secondary metabolites, including a large number of putative antibiotics, such as staurosporine, moenomycin, β-lactams, and enediynes. Interestingly, cross-regulation occurs between chromosomal and plasmid-encoded genes. Several factors suggest that the megaplasmid came into existence through recombination of a smaller plasmid with the arms of the main chromosome. Phylogenetic analysis indicates that heavy traffic of genetic information between Streptomyces plasmids and chromosomes may facilitate the rapid evolution of secondary metabolite repertoires in these bacteria.
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Affiliation(s)
- Marnix H Medema
- Department of Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
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28
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Two internal origins of replication in Streptomyces linear plasmid pFRL1. Appl Environ Microbiol 2010; 76:5676-83. [PMID: 20601502 DOI: 10.1128/aem.02905-09] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Previous reports showed that Streptomyces linear plasmids usually contain one internal replication locus. Here, we identified two new replication loci on pFRL1, one (rep1A-ncs1) next to a telomere and another (rep2A-ncs2) approximately 10 kb from it. The rep1A-ncs1 locus was able to direct replication independently in both linear and circular modes, whereas rep2A-ncs2 required an additional locus, rlrA-rorA, in order to direct propagation in linear mode. Rep1A protein bound to ncs1 in vitro. By quantitative reverse transcription-PCR and Northern hybridization, we showed that transcription of rep1A and rep2A varied during development and that each dominated at different time points. pFRL1-derived linear plasmids were inherited through spores more stably than circular plasmids and were more stable with pSLA2 telomeres than with pFRL1 telomeres in Streptomyces lividans.
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29
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Dib JR, Wagenknecht M, Hill RT, Farías ME, Meinhardt F. First report of linear megaplasmids in the genus Micrococcus. Plasmid 2010; 63:40-5. [DOI: 10.1016/j.plasmid.2009.10.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2009] [Revised: 10/05/2009] [Accepted: 10/12/2009] [Indexed: 11/26/2022]
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30
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Tsai HH, Huang CH, Lin AM, Chen CW. Terminal proteins of Streptomyces chromosome can target DNA into eukaryotic nuclei. Nucleic Acids Res 2008; 36:e62. [PMID: 18480119 PMCID: PMC2425503 DOI: 10.1093/nar/gkm1170] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Streptomyces species are highly abundant soil bacteria that possess linear chromosomes (and linear plasmids). The 5′ ends of these molecules are covalently bound by terminal proteins (TPs), that are important for integrity and replication of the telomeres. There are at least two types of TPs, both of which contain a DNA-binding domain and a classical eukaryotic nuclear localization signal (NLS). Here we show that the NLS motifs on these TPs are highly efficient in targeting the proteins along with covalently bound plasmid DNA into the nuclei of human cells. The TP-mediated nuclear targeting resembles the inter-kingdom gene transfer mediated by Ti plasmids of Agrobacterium tumefaciens, in which a piece of the Ti plasmid DNA is targeted to the plant nuclei by a covalently bound NLS-containing protein. The discovery of the nuclear localization functions of the Streptomyces TPs not only suggests possible inter-kingdom gene exchanges between Streptomyces and eukaryotes in soil but also provides a novel strategy for gene delivery in humans and other eukaryotes.
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Affiliation(s)
- Hsiu-Hui Tsai
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Shih-Pai, Taipei 112, Taiwan
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31
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Genome sequence of the streptomycin-producing microorganism Streptomyces griseus IFO 13350. J Bacteriol 2008; 190:4050-60. [PMID: 18375553 DOI: 10.1128/jb.00204-08] [Citation(s) in RCA: 454] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We determined the complete genome sequence of Streptomyces griseus IFO 13350, a soil bacterium producing an antituberculosis agent, streptomycin, which is the first aminoglycoside antibiotic, discovered more than 60 years ago. The linear chromosome consists of 8,545,929 base pairs (bp), with an average G+C content of 72.2%, predicting 7,138 open reading frames, six rRNA operons (16S-23S-5S), and 66 tRNA genes. It contains extremely long terminal inverted repeats (TIRs) of 132,910 bp each. The telomere's nucleotide sequence and secondary structure, consisting of several palindromes with a loop sequence of 5'-GGA-3', are different from those of typical telomeres conserved among other Streptomyces species. In accordance with the difference, the chromosome has pseudogenes for a conserved terminal protein (Tpg) and a telomere-associated protein (Tap), and a novel pair of Tpg and Tap proteins is instead encoded by the TIRs. Comparisons with the genomes of two related species, Streptomyces coelicolor A3(2) and Streptomyces avermitilis, clarified not only the characteristics of the S. griseus genome but also the existence of 24 Streptomyces-specific proteins. The S. griseus genome contains 34 gene clusters or genes for the biosynthesis of known or unknown secondary metabolites. Transcriptome analysis using a DNA microarray showed that at least four of these clusters, in addition to the streptomycin biosynthesis gene cluster, were activated directly or indirectly by AdpA, which is a central transcriptional activator for secondary metabolism and morphogenesis in the A-factor (a gamma-butyrolactone signaling molecule) regulatory cascade in S. griseus.
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