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Li P, Zhang J, Deng Z, Gao F, Ou HY. Identification and characterization of a central replication origin of the mega-plasmid pSCATT of Streptomyces cattleya. Microbiol Res 2022; 257:126975. [DOI: 10.1016/j.micres.2022.126975] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 01/17/2022] [Accepted: 01/20/2022] [Indexed: 11/25/2022]
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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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Mingyar E, Novakova R, Knirschova R, Feckova L, Bekeova C, Kormanec J. Unusual features of the large linear plasmid pSA3239 from Streptomyces aureofaciens CCM 3239. Gene 2017; 642:313-323. [PMID: 29155332 DOI: 10.1016/j.gene.2017.11.046] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 11/13/2017] [Accepted: 11/15/2017] [Indexed: 11/17/2022]
Abstract
We previously identified the aur1 gene cluster, responsible for the production of the angucycline antibiotic auricin in Streptomyces aureofaciens CCM 3239. Pulse-field gel electrophoresis showed a single, 241kb linear plasmid, pSA3239, in this strain, and several approaches confirmed the presence of the aur1 cluster in this plasmid. We report here the nucleotide sequence of this 241,076-bp plasmid. pSA3239 contains an unprecedentedly small (13bp) telomeric sequence CCCGCGGAGCGGG, which is identical to the conserved Palindrome I sequence involved in the priming of end-patching replication. A bioinformatics analysis revealed 234 open reading frames with high number (28) of regulatory genes from various families. In contrast to most other linear plasmids, pSA3239 contains a pair of replication initiation genes (sa76 and sa75) located at its extreme left end, adjacent to the telomere. Together with similar proteins from several other linear plasmids (pFRL2, pSLA2-M, pSV2, pSDA1, and SAP1), they constitute a new family of replication initiation proteins. This left end also contains two genes, tpgSa and tapSa, encoding the terminal protein and the telomere associated-protein involved in telomere end-patching replication. pSA3239 also contains two genes homologous to the parAB partitioning system, and deletion of the parA homologue (sa43) affects structural stability of the plasmid. pSA3239 carries five potential secondary metabolite gene clusters. In addition to aur1 and a non-ribosomal peptide synthase (NRPS) gene cluster for the blue pigment indigoidine, it also contains a partial type II polyketide synthase (PKS) gene cluster, a partial type I PKS gene cluster, and a NRPS/PKSI gene cluster for unknown secondary metabolites. The last gene cluster contains a subcluster of seven genes (sa91-sa97), highly similar to part of the valanimycin biosynthetic cluster vlm. A S. aureofaciens strain lacking pSA3239 was prepared. This deletion did not substantially affect growth and differentiation. A comparative analysis of secondary metabolites between both strains did not identify any product, except auricin and indigoidine, which is dependent upon pSA3239. Thus, the other three identified gene clusters are likely silent under these conditions.
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Affiliation(s)
- Erik Mingyar
- Institute of Molecular Biology, Slovak Academy of Sciences, 845 51 Bratislava, Slovak Republic
| | - Renata Novakova
- Institute of Molecular Biology, Slovak Academy of Sciences, 845 51 Bratislava, Slovak Republic
| | - Renata Knirschova
- Institute of Molecular Biology, Slovak Academy of Sciences, 845 51 Bratislava, Slovak Republic
| | - Lubomira Feckova
- Institute of Molecular Biology, Slovak Academy of Sciences, 845 51 Bratislava, Slovak Republic
| | - Carmen Bekeova
- Institute of Molecular Biology, Slovak Academy of Sciences, 845 51 Bratislava, Slovak Republic
| | - Jan Kormanec
- Institute of Molecular Biology, Slovak Academy of Sciences, 845 51 Bratislava, Slovak Republic.
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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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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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Novakova R, Knirschova R, Farkasovsky M, Feckova L, Rehakova A, Mingyar E, Kormanec J. The gene clusteraur1for the angucycline antibiotic auricin is located on a large linear plasmid pSA3239 inStreptomyces aureofaciensCCM 3239. FEMS Microbiol Lett 2013; 342:130-7. [DOI: 10.1111/1574-6968.12095] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 01/28/2013] [Indexed: 11/28/2022] Open
Affiliation(s)
- Renata Novakova
- Institute of Molecular Biology; Slovak Academy of Sciences; Bratislava; Slovak Republic
| | - Renata Knirschova
- Institute of Molecular Biology; Slovak Academy of Sciences; Bratislava; Slovak Republic
| | - Marian Farkasovsky
- Institute of Molecular Biology; Slovak Academy of Sciences; Bratislava; Slovak Republic
| | - Lubomira Feckova
- Institute of Molecular Biology; Slovak Academy of Sciences; Bratislava; Slovak Republic
| | - Alena Rehakova
- Institute of Molecular Biology; Slovak Academy of Sciences; Bratislava; Slovak Republic
| | - Erik Mingyar
- Institute of Molecular Biology; Slovak Academy of Sciences; Bratislava; Slovak Republic
| | - Jan Kormanec
- Institute of Molecular Biology; Slovak Academy of Sciences; Bratislava; Slovak Republic
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Chen W, Qin Z. Development of a gene cloning system in a fast-growing and moderately thermophilic Streptomyces species and heterologous expression of Streptomyces antibiotic biosynthetic gene clusters. BMC Microbiol 2011; 11:243. [PMID: 22032628 PMCID: PMC3212956 DOI: 10.1186/1471-2180-11-243] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Accepted: 10/28/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Streptomyces species are a major source of antibiotics. They usually grow slowly at their optimal temperature and fermentation of industrial strains in a large scale often takes a long time, consuming more energy and materials than some other bacterial industrial strains (e.g., E. coli and Bacillus). Most thermophilic Streptomyces species grow fast, but no gene cloning systems have been developed in such strains. RESULTS We report here the isolation of 41 fast-growing (about twice the rate of S. coelicolor), moderately thermophilic (growing at both 30°C and 50°C) Streptomyces strains, detection of one linear and three circular plasmids in them, and sequencing of a 6996-bp plasmid, pTSC1, from one of them. pTSC1-derived pCWH1 could replicate in both thermophilic and mesophilic Streptomyces strains. On the other hand, several Streptomyces replicons function in thermophilic Streptomyces species. By examining ten well-sporulating strains, we found two promising cloning hosts, 2C and 4F. A gene cloning system was established by using the two strains. The actinorhodin and anthramycin biosynthetic gene clusters from mesophilic S. coelicolor A3(2) and thermophilic S. refuineus were heterologously expressed in one of the hosts. CONCLUSIONS We have developed a gene cloning and expression system in a fast-growing and moderately thermophilic Streptomyces species. Although just a few plasmids and one antibiotic biosynthetic gene cluster from mesophilic Streptomyces were successfully expressed in thermophilic Streptomyces species, we expect that by utilizing thermophilic Streptomyces-specific promoters, more genes and especially antibiotic genes clusters of mesophilic Streptomyces should be heterologously expressed.
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Affiliation(s)
- Weihua Chen
- Key Laboratory of Synthetic Biology, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, the Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 20032, People's Republic of China
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pSLA2-M of Streptomyces rochei is a composite linear plasmid characterized by self-defense genes and homology with pSLA2-L. Biosci Biotechnol Biochem 2011; 75:1147-53. [PMID: 21670526 DOI: 10.1271/bbb.110054] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The 113,463-bp nucleotide sequence of the linear plasmid pSLA2-M of Streptomyces rochei 7434AN4 was determined. pSLA2-M had a 69.7% overall GC content, 352-bp terminal inverted repeats with 91% (321/352) identity at both ends, and 121 open reading frames. The rightmost 14.6-kb sequence was almost (14,550/14,555) identical to that of the coexisting 211-kb linear plasmid pSLA2-L. Adjacent to this homologous region an 11.8-kb CRISPR cluster was identified, which is known to function against phage infection in prokaryotes. This cluster region as well as another one containing two large membrane protein genes (orf78 and orf79) were flanked by direct repeats of 194 and 566 bp respectively. Hence the insertion of circular DNAs containing each cluster by homologous recombination was suggested. In addition, the orf71 encoded a Ku70/Ku80-like protein, known to function in the repair of double-strand DNA breaks in eukaryotes, but disruption of it did not affect the radiation sensitivity of the mutant. A pair of replication initiation genes (orf1-orf2) were identified at the extreme left end. Thus, pSLA2-M proved to be a composite linear plasmid characterized by self-defense genes and homology with pSLA2-L that might have been generated by multiple recombination events.
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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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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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Structural peculiarities of linear megaplasmid, pLMA1, from Micrococcus luteus interfere with pyrosequencing reads assembly. Biotechnol Lett 2010; 32:1853-62. [PMID: 20652620 PMCID: PMC2974207 DOI: 10.1007/s10529-010-0357-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Accepted: 07/09/2010] [Indexed: 11/16/2022]
Abstract
Different strains of Micrococcus luteus, isolated from high-altitude Argentinean wetlands, were recently reported to harbour the linear plasmids pLMA1, pLMH5 and pLMV7, all of which with 5′-covalently attached terminal proteins. The link between pLMA1 and the host’s erythromycin resistance as well as further presumptive qualities prompted us to perform a detailed characterization. When the 454 technology was applied for direct sequencing of gel-purified pLMA1, assembly of the reads was impossible. However, combined Sanger/454 sequencing of cloned pLMA1 fragments, covering altogether 23 kb of the 110-kb spanning plasmid, allowed numerous sequence repeats of varying in lengths to be identified thus rendering an explanation for the above 454 assembly failure. A large number of putative transposase genes were identified as well. Furthermore, a region with five putative iteron sequences is possibly involved in pLMA1 replication.
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