1
|
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: 0.7] [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]
|
2
|
Moldovan MA. Prokaryotic and Mitochondrial Linear Genomes: Their Genesis, Evolutionary Significance, and the Problem of Replicating Chromosome Ends. Mol Biol 2019. [DOI: 10.1134/s0026893319020122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
3
|
Raftis EJ, Forde BM, Claesson MJ, O'Toole PW. Unusual genome complexity in Lactobacillus salivarius JCM1046. BMC Genomics 2014; 15:771. [PMID: 25201645 PMCID: PMC4165912 DOI: 10.1186/1471-2164-15-771] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 08/26/2014] [Indexed: 12/31/2022] Open
Abstract
Background Lactobacillus salivarius strains are increasingly being exploited for their probiotic properties in humans and animals. Dissemination of antibiotic resistance genes among species with food or probiotic-association is undesirable and is often mediated by plasmids or integrative and conjugative elements. L. salivarius strains typically have multireplicon genomes including circular megaplasmids that encode strain-specific traits for intestinal survival and probiotic activity. Linear plasmids are less common in lactobacilli and show a very limited distribution in L. salivarius. Here we present experimental evidence that supports an unusually complex multireplicon genome structure in the porcine isolate L. salivarius JCM1046. Results JCM1046 harbours a 1.83 Mb chromosome, and four plasmids which constitute 20% of the genome. In addition to the known 219 kb repA-type megaplasmid pMP1046A, we identified and experimentally validated the topology of three additional replicons, the circular pMP1046B (129 kb), a linear plasmid pLMP1046 (101 kb) and pCTN1046 (33 kb) harbouring a conjugative transposon. pMP1046B harbours both plasmid-associated replication genes and paralogues of chromosomally encoded housekeeping and information-processing related genes, thus qualifying it as a putative chromid. pLMP1046 shares limited sequence homology or gene synteny with other L. salivarius plasmids, and its putative replication-associated protein is homologous to the RepA/E proteins found in the large circular megaplasmids of L. salivarius. Plasmid pCTN1046 harbours a single copy of an integrated conjugative transposon (Tn6224) which appears to be functionally intact and includes the tetracycline resistance gene tetM. Conclusion Experimental validation of sequence assemblies and plasmid topology resolved the complex genome architecture of L. salivarius JCM1046. A high-coverage draft genome sequence would not have elucidated the genome complexity in this strain. Given the expanding use of L. salivarius as a probiotic, it is important to determine the genotypic and phenotypic organization of L. salivarius strains. The identification of Tn6224-like elements in this species has implications for strain selection for probiotic applications. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-771) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | | | | | - Paul W O'Toole
- School of Microbiology University College Cork, Cork, Ireland.
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
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
| |
Collapse
|
6
|
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
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Wang T, Chen Z, Cheng Q, Zhou M, Tian X, Xie P, Zhong L, Shen M, Qin Z. Characterization of replication and conjugation of plasmid pWTY27 from a widely distributed Streptomyces species. BMC Microbiol 2012; 12:253. [PMID: 23134842 PMCID: PMC3583192 DOI: 10.1186/1471-2180-12-253] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2012] [Accepted: 10/26/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Streptomyces species are widely distributed in natural habitats, such as soils, lakes, plants and some extreme environments. Replication loci of several Streptomyces theta-type plasmids have been reported, but are not characterized in details. Conjugation loci of some Streptomyces rolling-circle-type plasmids are identified and mechanism of conjugal transferring are described. RESULTS We report the detection of a widely distributed Streptomyces strain Y27 and its indigenous plasmid pWTY27 from fourteen plants and four soil samples cross China by both culturing and nonculturing methods. The complete nucleotide sequence of pWTY27 consisted of 14,288 bp. A basic locus for plasmid replication comprised repAB genes and an adjacent iteron sequence, to a long inverted-repeat (ca. 105 bp) of which the RepA protein bound specifically in vitro, suggesting that RepA may recognize a second structure (e.g. a long stem-loop) of the iteron DNA. A plasmid containing the locus propagated in linear mode when the telomeres of a linear plasmid were attached, indicating a bi-directional replication mode for pWTY27. As for rolling-circle plasmids, a single traA gene and a clt sequence (covering 16 bp within traA and its adjacent 159 bp) on pWTY27 were required for plasmid transfer. TraA recognized and bound specifically to the two regions of the clt sequence, one containing all the four DC1 of 7 bp (TGACACC) and one DC2 (CCCGCCC) and most of IC1, and another covering two DC2 and part of IC1, suggesting formation of a high-ordered DNA-protein complex. CONCLUSIONS This work (i) isolates a widespread Streptomyces strain Y27 and sequences its indigenous theta-type plasmid pWTY27; (ii) identifies the replication and conjugation loci of pWTY27 and; (iii) characterizes the binding sequences of the RepA and TraA proteins.
Collapse
Affiliation(s)
- Tao Wang
- Key Laboratory of Synthetic Biology, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Terminal protein-primed amplification of heterologous DNA with a minimal replication system based on phage Phi29. Proc Natl Acad Sci U S A 2011; 108:18655-60. [PMID: 22065756 DOI: 10.1073/pnas.1114397108] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The DNA amplification performed by terminal protein-primed replication systems has not yet been developed for its general use to produce high amounts of DNA linked to terminal protein (TP). Here we present a method to amplify in vitro heterologous DNAs using the Φ29 DNA replication machinery and producing DNA with TP covalently attached to the 5' end. The amplification requires four Φ29 proteins, DNA polymerase, TP, single-stranded DNA binding protein and double-stranded DNA binding protein (p6). The DNA to be amplified is inserted between two sequences that are the Φ29 DNA replication origins, consisting of 191 and 194 bp from the left and right ends of the phage genome, respectively. The replication origins do not need to have TP covalently attached beforehand to be functional in amplification and they can be joined to the DNA to be amplified by cloning or ligation. The facts that two functional origins were required at the ends of a linear template DNA and that the kinetics of DNA synthesis was very similar to that obtained using the TP-containing Φ29 genome as template support the proposal that genuine amplification is taking place. Amplification factors of 30-fold have been obtained. Possible applications of DNAs produced by this method are discussed.
Collapse
|
10
|
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: 1.1] [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.
Collapse
Affiliation(s)
- Peng Guo
- Key Laboratory of Synthetic Biology, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | | | | | | | | | | |
Collapse
|
11
|
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.
Collapse
Affiliation(s)
- Martin Wagenknecht
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstr. 3, D-48149 Münster, Germany
| | | |
Collapse
|
12
|
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.
Collapse
|
13
|
Wang J, Pettis GS. The tra locus of streptomycete plasmid pIJ101 mediates efficient transfer of a circular but not a linear version of the same replicon. MICROBIOLOGY-SGM 2010; 156:2723-2733. [PMID: 20522498 DOI: 10.1099/mic.0.036467-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Conjugal transfer of circular plasmids in Streptomyces involves a unique mechanism employing few plasmid-encoded loci and the transfer of double-stranded DNA by an as yet uncharacterized intercellular route. Efficient transfer of the circular streptomycete plasmid pIJ101 requires only two plasmid loci: the pIJ101 tra gene, and as a cis-acting function known as clt. Here, we compared the ability of the pIJ101 transfer apparatus to promote conjugal transfer of circular versus linear versions of the same replicon. While the pIJ101 tra locus readily transferred the circular form of the replicon, the linear version was transferred orders of magnitude less efficiently and all plasmids isolated from the transconjugants were circular, regardless of their original configuration in the donor. Additionally, relatively rare circularization of linear plasmids was detectable in the donor cells, which is consistent with the notion that this event was a prerequisite for transfer by TraB(pIJ101). Linear versions of this same replicon did transfer efficiently, in that configuration, from strains containing the conjugative linear plasmid SLP2. Our data indicate that functions necessary and sufficient for transfer of circular DNA were insufficient for transfer of a related linear DNA molecule. The results here suggest that the conjugation mechanisms of linear versus circular DNA in Streptomyces spp. are inherently different and/or that efficient transfer of linear DNA requires additional components.
Collapse
Affiliation(s)
- Jing Wang
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Gregg S Pettis
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| |
Collapse
|
14
|
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.
Collapse
Affiliation(s)
- Hsiu-Hui Tsai
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Shih-Pai, Taipei 112, Taiwan
| | | | | | | |
Collapse
|
15
|
Characterization of replication and conjugation of Streptomyces circular plasmids pFP1 and pFP11 and their ability to propagate in linear mode with artificially attached telomeres. Appl Environ Microbiol 2008; 74:3368-76. [PMID: 18390681 DOI: 10.1128/aem.00402-08] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Many Streptomyces species harbor circular plasmids (8 to 31 kb) as well as linear plasmids (12 to 1,700 kb). We report the characterization of two newly detected circular plasmids, pFP11 (35,139 bp) and pFP1 (39,360 bp). As on linear plasmids, their replication loci comprise repA genes and adjacent iterons, to which RepA proteins bind specifically in vitro. Plasmids containing the minimal iterons plus the repA locus of pFP11 were inherited extremely unstably; par and additional loci were required for stable inheritance. Surprisingly, plasmids containing replication loci from pFP11 or Streptomyces circular plasmid SCP2 but not from pFP1, SLP1, or pIJ101 propagated in a stable linear mode when the telomeres of a linear plasmid were attached. These results indicate bidirectional replication for pFP11 and SCP2. Both pFP11 and pFP1 contain, for plasmid transfer, a major functional traB gene (encoding a DNA translocase typical for Streptomyces plasmids) as well as, surprisingly, a putative traA gene (encoding a DNA nickase, characteristic of single-stranded DNA transfer of gram-negative plasmids), but this did not appear to be functional, at least in isolation.
Collapse
|
16
|
Huang CH, Tsai HH, Tsay YG, Chien YN, Wang SL, Cheng MY, Ke CH, Chen CW. The telomere system of the Streptomyces linear plasmid SCP1 represents a novel class. Mol Microbiol 2007; 63:1710-8. [PMID: 17367390 DOI: 10.1111/j.1365-2958.2007.05616.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Linear plasmids and chromosomes of Streptomyces carry terminal proteins (TPs) covalently attached to the 5' ends of the DNA. Most known telomeres are conserved in primary sequence and in the potential secondary structures formed during replication. The TP that caps these telomeres is also highly conserved and its coding gene, tpg, is present in all Streptomyces chromosomes and some linear plasmids. Linear plasmid SCP1 contains atypical telomere sequences and no tpg homologue, and can replicate in the absence of tpg, suggesting that it carries a novel TP gene. To isolate the TP on the SCP1 telomeres, we constructed a multicopy mini-SCP1 plasmid. The TP capping the plasmid was isolated and subjected to tryptic digestion and mass spectrometric analysis, and the results indicated that the TP was encoded by an open reading frame (ORF), SCP1.127 (tpc), on SCP1. Of the two ORFs upstream of tpc, SCP1.125 (tac) but not SCP1.126 was essential for replication of mini-SCP1. The Tac-Tpc system of SCP1 represents a convergently evolved novel telomere-capping system of Streptomyces linear replicons.
Collapse
Affiliation(s)
- Chih-Hung Huang
- Institute of Biotechnology, National Taipei University of Technology, Taipei 106, Taiwan
| | | | | | | | | | | | | | | |
Collapse
|
17
|
Parschat K, Overhage J, Strittmatter AW, Henne A, Gottschalk G, Fetzner S. Complete nucleotide sequence of the 113-kilobase linear catabolic plasmid pAL1 of Arthrobacter nitroguajacolicus Rü61a and transcriptional analysis of genes involved in quinaldine degradation. J Bacteriol 2007; 189:3855-67. [PMID: 17337569 PMCID: PMC1913324 DOI: 10.1128/jb.00089-07] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2007] [Accepted: 02/27/2007] [Indexed: 11/20/2022] Open
Abstract
The nucleotide sequence of the linear catabolic plasmid pAL1 from the 2-methylquinoline (quinaldine)-degrading strain Arthrobacter nitroguajacolicus Rü61a comprises 112,992 bp. A total of 103 open reading frames (ORFs) were identified on pAL1, 49 of which had no annotatable function. The ORFs were assigned to the following functional groups: (i) catabolism of quinaldine and anthranilate, (ii) conjugation, and (iii) plasmid maintenance and DNA replication and repair. The genes for conversion of quinaldine to anthranilate are organized in two operons that include ORFs presumed to code for proteins involved in assembly of the quinaldine-4-oxidase holoenzyme, namely, a MobA-like putative molybdopterin cytosine dinucleotide synthase and an XdhC-like protein that could be required for insertion of the molybdenum cofactor. Genes possibly coding for enzymes involved in anthranilate degradation via 2-aminobenzoyl coenzyme A form another operon. These operons were expressed when cells were grown on quinaldine or on aromatic compounds downstream in the catabolic pathway. Single-stranded 3' overhangs of putative replication intermediates of pAL1 were predicted to form elaborate secondary structures due to palindromic and superpalindromic terminal sequences; however, the two telomeres appear to form different structures. Sequence analysis of ORFs 101 to 103 suggested that pAL1 codes for one or two putative terminal proteins, presumed to be covalently bound to the 5' termini, and a multidomain telomere-associated protein (Tap) comprising 1,707 amino acids. Even if the putative proteins encoded by ORFs 101 to 103 share motifs with the Tap and terminal proteins involved in telomere patching of Streptomyces linear replicons, their overall sequences and domain structures differ significantly.
Collapse
Affiliation(s)
- Katja Parschat
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, D-48149 Münster, Germany
| | | | | | | | | | | |
Collapse
|
18
|
Zhang R, Yang Y, Fang P, Jiang C, Xu L, Zhu Y, Shen M, Xia H, Zhao J, Chen T, Qin Z. Diversity of telomere palindromic sequences and replication genes among Streptomyces linear plasmids. Appl Environ Microbiol 2006; 72:5728-33. [PMID: 16957187 PMCID: PMC1563600 DOI: 10.1128/aem.00707-06] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Streptomyces sp. linear plasmids and linear chromosomes usually contain conserved terminal palindromic sequences bound by the conserved telomeric proteins Tap and Tp, encoded by the tap and tpg genes, respectively, as well as plasmid loci required for DNA replication in circular mode when the telomeres are deleted. These consist of iterons and an adjacent rep gene. By using PCR, we found that 8 of 17 newly detected linear plasmids in Streptomyces strains lack typical telomeric tap and tpg sequences. Instead, two novel telomeres in plasmids pRL1 and pRL2 from the eight strains and one conserved telomere in pFRL1 from the other strains were identified, while multiple short palindromes were also found in the plasmids. The complete nucleotide sequence of pRL2 revealed a gene encoding a protein containing two domains, resembling Tap of Streptomyces and a helicase of Thiobacillus, and an adjacent gene encoding a protein similar to Tpg of Streptomyces and a portion of the telomere terminal protein pTP of adenoviruses. No typical iterons-rep loci were found in the three plasmids. These results indicate an unexpected diversity of telomere palindromic sequences and replication genes among Streptomyces linear plasmids.
Collapse
Affiliation(s)
- Ran Zhang
- Shanghai Institute of Plant Physiology, Shanghai Institutes of Biological Science, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, People's Republic of China
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Xu M, Zhu Y, Zhang R, Shen M, Jiang W, Zhao G, Qin Z. Characterization of the genetic components of Streptomyces lividans linear plasmid SLP2 for replication in circular and linear modes. J Bacteriol 2006; 188:6851-7. [PMID: 16980488 PMCID: PMC1595531 DOI: 10.1128/jb.00873-06] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The nucleotide sequence of Streptomyces lividans linear plasmid SLP2 consists of 50,410 bp (C. H. Huang, C. Y. Chen, H. H. Tsai, C. Chen, Y. S. Lin, and C. W. Chen, Mol. Microbiol. 47:1563-1576, 2003). Here we report that the basic SLP2 locus for plasmid replication in circular mode resembles that of Streptomyces linear plasmids pSLA2 and SCP1 and comprises iterons(SLP2) and the adjacent rep(SLP2) gene. More efficient replication additionally required the 47-bp sequence between bp 581 and 628 upstream of the iterons. Replacement of either the iterons or the rep gene of SLP2 by the corresponding genes of pSLA2 or SCP1 still allows propagation in Streptomyces, although the transformation frequencies were 3 orders of magnitude lower than the original plasmids, suggesting that these plasmids share similar replication mechanisms. To replicate SLP2 in linear mode, additional SLP2 loci--either mtap(SLP2)/tpg(SLP2) or mtap(SLP2)/ilrA(SLP2)--were required. IlrA(SLP2) protein binds specifically to the iterons(SLP2) in vitro. Interactions were detected between these SLP2-borne replication proteins (Mtap(SLP2), Tpg(SLP2), and IlrA(SLP2)) and the telomeric replication proteins (TpgL, TapL, and TpgL) of the S. lividans chromosome, respectively, but the SLP2 proteins failed to interact. These results suggest that SLP2 recruits chromosomally encoded replication proteins for its telomere replication.
Collapse
Affiliation(s)
- Mingxuan Xu
- Shanghai Institute of Plant Physiology, Shanghai Institutes of Biological Sciences, The Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032 People's Republic of China
| | | | | | | | | | | | | |
Collapse
|
20
|
McLeod MP, Warren RL, Hsiao WWL, Araki N, Myhre M, Fernandes C, Miyazawa D, Wong W, Lillquist AL, Wang D, Dosanjh M, Hara H, Petrescu A, Morin RD, Yang G, Stott JM, Schein JE, Shin H, Smailus D, Siddiqui AS, Marra MA, Jones SJM, Holt R, Brinkman FSL, Miyauchi K, Fukuda M, Davies JE, Mohn WW, Eltis LD. The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse. Proc Natl Acad Sci U S A 2006; 103:15582-7. [PMID: 17030794 PMCID: PMC1622865 DOI: 10.1073/pnas.0607048103] [Citation(s) in RCA: 450] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rhodococcus sp. RHA1 (RHA1) is a potent polychlorinated biphenyl-degrading soil actinomycete that catabolizes a wide range of compounds and represents a genus of considerable industrial interest. RHA1 has one of the largest bacterial genomes sequenced to date, comprising 9,702,737 bp (67% G+C) arranged in a linear chromosome and three linear plasmids. A targeted insertion methodology was developed to determine the telomeric sequences. RHA1's 9,145 predicted protein-encoding genes are exceptionally rich in oxygenases (203) and ligases (192). Many of the oxygenases occur in the numerous pathways predicted to degrade aromatic compounds (30) or steroids (4). RHA1 also contains 24 nonribosomal peptide synthase genes, six of which exceed 25 kbp, and seven polyketide synthase genes, providing evidence that rhodococci harbor an extensive secondary metabolism. Among sequenced genomes, RHA1 is most similar to those of nocardial and mycobacterial strains. The genome contains few recent gene duplications. Moreover, three different analyses indicate that RHA1 has acquired fewer genes by recent horizontal transfer than most bacteria characterized to date and far fewer than Burkholderia xenovorans LB400, whose genome size and catabolic versatility rival those of RHA1. RHA1 and LB400 thus appear to demonstrate that ecologically similar bacteria can evolve large genomes by different means. Overall, RHA1 appears to have evolved to simultaneously catabolize a diverse range of plant-derived compounds in an O(2)-rich environment. In addition to establishing RHA1 as an important model for studying actinomycete physiology, this study provides critical insights that facilitate the exploitation of these industrially important microorganisms.
Collapse
Affiliation(s)
- Michael P. McLeod
- *Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - René L. Warren
- Michael Smith Genome Sciences Centre, Vancouver, BC, Canada V5Z 1L3
| | - William W. L. Hsiao
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada V5A 1S6; and
| | - Naoto Araki
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka 940-2118, Japan
| | - Matthew Myhre
- *Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Clinton Fernandes
- *Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Daisuke Miyazawa
- *Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Wendy Wong
- *Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Anita L. Lillquist
- *Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Dennis Wang
- *Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Manisha Dosanjh
- *Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Hirofumi Hara
- *Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Anca Petrescu
- Michael Smith Genome Sciences Centre, Vancouver, BC, Canada V5Z 1L3
| | - Ryan D. Morin
- Michael Smith Genome Sciences Centre, Vancouver, BC, Canada V5Z 1L3
| | - George Yang
- Michael Smith Genome Sciences Centre, Vancouver, BC, Canada V5Z 1L3
| | - Jeff M. Stott
- Michael Smith Genome Sciences Centre, Vancouver, BC, Canada V5Z 1L3
| | | | - Heesun Shin
- Michael Smith Genome Sciences Centre, Vancouver, BC, Canada V5Z 1L3
| | - Duane Smailus
- Michael Smith Genome Sciences Centre, Vancouver, BC, Canada V5Z 1L3
| | - Asim S. Siddiqui
- Michael Smith Genome Sciences Centre, Vancouver, BC, Canada V5Z 1L3
| | - Marco A. Marra
- Michael Smith Genome Sciences Centre, Vancouver, BC, Canada V5Z 1L3
| | | | - Robert Holt
- Michael Smith Genome Sciences Centre, Vancouver, BC, Canada V5Z 1L3
| | - Fiona S. L. Brinkman
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada V5A 1S6; and
| | - Keisuke Miyauchi
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka 940-2118, Japan
| | - Masao Fukuda
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka 940-2118, Japan
| | - Julian E. Davies
- *Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - William W. Mohn
- *Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Lindsay D. Eltis
- *Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
- To whom correspondence should be addressed. E-mail:
| |
Collapse
|
21
|
Wu W, Leblanc SKD, Piktel J, Jensen SE, Roy KL. Prediction and functional analysis of the replication origin of the linear plasmid pSCL2 inStreptomyces clavuligerus. Can J Microbiol 2006; 52:293-300. [PMID: 16699579 DOI: 10.1139/w05-126] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
pSCL2 (120 kb), one of the linear plasmids found in Streptomyces clavuligerus NRRL3585, was isolated and partially sequenced. Computational analysis of the central region of pSCL2 revealed the presence of two open reading frames that appear to encode proteins highly homologous to RepL1 and RepL2, replication proteins from pSLA2-L, the large linear plasmid in Streptomyces rochei. The S. clavuligerus open reading frames were designated repC1 and repC2, encoding the proteins RepC1 (150 amino acids) and RepC2 (102 amino acids), respectively. The RepC and RepL proteins have identical translation features and very similar predicted secondary and tertiary structures. Functional analysis confirmed that RepC1 is essential for replication initiation of pSCL2, whereas RepC2 is dispensable but may play a role in copy number control. The RepC and RepL proteins do not show similarity to any other bacterial plasmid replication proteins. Three regions of DNA sequence, Box 1 (1050–850 bp), Box 2 (723–606 bp), and Box 3 (224–168 bp), located upstream of repC1, were also shown to be essential or very important for replication of pSCL2.Key words: pSCL2, Streptomyces clavuligerus, replication origin.
Collapse
Affiliation(s)
- Wei Wu
- Department of Biological Sciences, CW 405 Biological Sciences Bldg., University of Alberta, Edmonton, Canada
| | | | | | | | | |
Collapse
|
22
|
Warren R, Hsiao WWL, Kudo H, Myhre M, Dosanjh M, Petrescu A, Kobayashi H, Shimizu S, Miyauchi K, Masai E, Yang G, Stott JM, Schein JE, Shin H, Khattra J, Smailus D, Butterfield YS, Siddiqui A, Holt R, Marra MA, Jones SJM, Mohn WW, Brinkman FSL, Fukuda M, Davies J, Eltis LD. Functional characterization of a catabolic plasmid from polychlorinated- biphenyl-degrading Rhodococcus sp. strain RHA1. J Bacteriol 2004; 186:7783-95. [PMID: 15516593 PMCID: PMC524921 DOI: 10.1128/jb.186.22.7783-7795.2004] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rhodococcus sp. strain RHA1, a potent polychlorinated-biphenyl (PCB)-degrading strain, contains three linear plasmids ranging in size from 330 to 1,100 kb. As part of a genome sequencing project, we report here the complete sequence and characterization of the smallest and least-well-characterized of the RHA1 plasmids, pRHL3. The plasmid is an actinomycete invertron, containing large terminal inverted repeats with a tightly associated protein and a predicted open reading frame (ORF) that is similar to that of a mycobacterial rep gene. The pRHL3 plasmid has 300 putative genes, almost 21% of which are predicted to have a catabolic function. Most of these are organized into three clusters. One of the catabolic clusters was predicted to include limonene degradation genes. Consistent with this prediction, RHA1 grew on limonene, carveol, or carvone as the sole carbon source. The plasmid carries three cytochrome P450-encoding (CYP) genes, a finding consistent with the high number of CYP genes found in other actinomycetes. Two of the CYP genes appear to belong to novel families; the third belongs to CYP family 116 but appears to belong to a novel class based on the predicted domain structure of its reductase. Analyses indicate that pRHL3 also contains four putative "genomic islands" (likely to have been acquired by horizontal transfer), insertion sequence elements, 19 transposase genes, and a duplication that spans two ORFs. One of the genomic islands appears to encode resistance to heavy metals. The plasmid does not appear to contain any housekeeping genes. However, each of the three catabolic clusters contains related genes that appear to be involved in glucose metabolism.
Collapse
|
23
|
Hosted TJ, Wang T, Horan AC. Characterization of the Streptomyces lavendulae IMRU 3455 linear plasmid pSLV45. Microbiology (Reading) 2004; 150:1819-1827. [PMID: 15184568 DOI: 10.1099/mic.0.26994-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Streptomyces lavendulae IMRU 3455 contains two large linear plasmids designated pSLV45 (45 kb) and pSLV195 (195 kb). A cosmid, pSPRX604, containing 42 kb from pSLV45 was cloned and sequenced. pSLV45 was tagged with a hygromycin-resistance marker by homologous recombination to generate the derivatives pSLV45.680 and pSLV45.681. An apramycin-resistance marker was introduced into S. lavendulae IMRU 467 using the pSPR910 integration vector to yield the recipient strain SPW910. The self-transmissible nature of pSLV45 was determined by transfer of pSLV45.680 and pSLV45.681 from the donor strains SPW680 and SPW681 into the recipient strain SPW910. Southern analysis indicated the presence of hygromycin- and pSLV45-hybridizing sequences within SPW910 exconjugants. PFGE analysis confirmed pSLV45.680 and pSLV45.681 were transferred intact and formed freely replicating linear plasmids. Sequence analysis of pSPRX604 revealed genes predicted to be involved in plasmid transfer, partitioning and regulation. The transfer of the linear plasmid pSLV45 from S. lavendulae IMRU 3455 into S. lavendulae IMRU 467 may allow the development of pSLV45 as an actinomycete-to-actinomycete conjugative shuttle vector.
Collapse
Affiliation(s)
- Thomas J Hosted
- New Lead Discovery, Schering Plough Research Institute, 2015 Galloping Hill Road, K15-C321-MS3600, Kenilworth, NJ 07033, USA
| | - Tim Wang
- New Lead Discovery, Schering Plough Research Institute, 2015 Galloping Hill Road, K15-C321-MS3600, Kenilworth, NJ 07033, USA
| | - Ann C Horan
- New Lead Discovery, Schering Plough Research Institute, 2015 Galloping Hill Road, K15-C321-MS3600, Kenilworth, NJ 07033, USA
| |
Collapse
|
24
|
Qin Z, Shen M, Cohen SN. Identification and characterization of a pSLA2 plasmid locus required for linear DNA replication and circular plasmid stable inheritance in Streptomyces lividans. J Bacteriol 2003; 185:6575-82. [PMID: 14594830 PMCID: PMC262113 DOI: 10.1128/jb.185.22.6575-6582.2003] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Streptomyces linear plasmids and linear chromosomes can replicate also in a circular form when their telomeres are deleted. The 17-kb linear plasmid pSLA2 has been a useful model in studies of such replicons. Here we report that the minimal origin initiating replication of pSLA2-derived plasmids as circular molecules cannot propagate these plasmids in a linear mode unless they also contain a novel plasmid-encoded locus, here named rlrA (required for linear replication). In contrast with the need for rlrA to accomplish replication of telomere-containing linear plasmids, expression of rlrA, which encodes two LuxR family regulatory domains, interferes with the establishment of pSLA2 in circular form in Streptomyces lividans transformants. The additional presence of an adjacent divergently transcribed locus, rorA (rlrA override), which strongly resembles the kor (kil override) transcription control genes identified previously on Streptomyces plasmids, reversed the detrimental effects of rlrA on plasmid establishment and additionally stabilized circular plasmid inheritance by spores during the S. lividans life cycle. While the effects of the rlrA/rorA locus of pSLA2 were seen also on linear plasmids derived from the unrelated SLP2 replicon, they did not extend to plasmids whose replication was initiated at a cloned chromosomal origin. Our results establish the existence of, and provide the initial description of, a novel plasmid-borne regulatory system that differentially affects the propagation of linear and circular plasmids in Streptomyces.
Collapse
Affiliation(s)
- Zhongjun Qin
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305-5120, USA
| | | | | |
Collapse
|
25
|
Stewart PE, Chaconas G, Rosa P. Conservation of plasmid maintenance functions between linear and circular plasmids in Borrelia burgdorferi. J Bacteriol 2003; 185:3202-9. [PMID: 12730180 PMCID: PMC154063 DOI: 10.1128/jb.185.10.3202-3209.2003] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Lyme disease agent Borrelia burgdorferi maintains both linear and circular plasmids that appear to be essential for mammalian infection. Recent studies have characterized the circular plasmid regions that confer autonomous replication, but the genetic elements necessary for linear plasmid maintenance have not been experimentally identified. Two vectors derived from linear plasmids lp25 and lp28-1 were constructed and shown to replicate autonomously in B. burgdorferi. These vectors identify internal regions of linear plasmids necessary for autonomous replication in B. burgdorferi. Although derived from linear plasmids, the vectors are maintained in circular form in B. burgdorferi, indicating that plasmid maintenance functions are conserved, regardless of DNA form. Finally, derivatives of these vectors indicate that paralogous gene family 49 is apparently not required for either circular or linear plasmid replication.
Collapse
Affiliation(s)
- Philip E Stewart
- Laboratory of Human Bacterial Pathogenesis, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana 59840, USA.
| | | | | |
Collapse
|
26
|
Bao K, Cohen SN. Recruitment of terminal protein to the ends of Streptomyces linear plasmids and chromosomes by a novel telomere-binding protein essential for linear DNA replication. Genes Dev 2003; 17:774-85. [PMID: 12651895 PMCID: PMC196017 DOI: 10.1101/gad.1060303] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Bidirectional replication of Streptomyces linear plasmids and chromosomes from a central origin produces unpaired 3'-leading-strand overhangs at the telomeres of replication intermediates. Filling in of these overhangs leaves a terminal protein attached covalently to the 5' DNA ends of mature replicons. We report here the essential role of a novel 80-kD DNA-binding protein (telomere-associated protein, Tap) in this process. Biochemical studies, yeast two-hybrid analysis, and immunoprecipitation/immunodepletion experiments indicate that Tap binds tightly to specific sequences in 3' overhangs and also interacts with Tpg, bringing Tpg to telomere termini. Using DNA microarrays to analyze the chromosomes of tap mutant bacteria, we demonstrate that survivors of Tap ablation undergo telomere deletion, chromosome circularization, and amplification of subtelomeric DNA. Microarray-based chromosome mapping at single-ORF resolution revealed common endpoints for independent deletions, identified amplified chromosomal ORFs adjacent to these endpoints, and quantified the copy number of these ORFs. Sequence analysis confirmed chromosome circularization and revealed the insertion of adventitious DNA between joined chromosome ends. Our results show that Tap is required for linear DNA replication in Streptomyces and suggest that it functions to recruit and position Tpg at the telomeres of replication intermediates. They also identify hotspots for the telomeric deletions and subtelomeric DNA amplifications that accompany chromosome circularization.
Collapse
Affiliation(s)
- Kai Bao
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5120, USA
| | | |
Collapse
|
27
|
Huang CH, Chen CY, Tsai HH, Chen C, Lin YS, Chen CW. Linear plasmid SLP2 of Streptomyces lividans is a composite replicon. Mol Microbiol 2003; 47:1563-76. [PMID: 12622812 DOI: 10.1046/j.1365-2958.2003.03403.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
SLP2 is a 50 kb linear plasmid in Streptomyces lividans that contains short (44 bp) terminal inverted repeats and covalently bound terminal proteins. The nucleotide sequence of SLP2 was determined. The rightmost 15.4 kb sequence is identical to that of the host chromosome, including the Tn4811 sequence at the border, which is interrupted by an insertion sequence (IS) element in SLP2. Examination of the flanking target sequences of Tn4811 suggests a previous recombinational event there. The 43 putative protein coding sequences contained many involved in replication (including two terminal protein homologues), partitioning, conjugal transfer and intramycelial spread. The terminally located helicase-like gene ttrA was necessary for conjugal transfer. The two telomeres diverge significantly in primary sequence, while preserving similar secondary structures. Mini-linear plasmids containing these telomeres replicated in S. lividans using the chromosomally encoded terminal protein. In addition, two pseudotelomere sequences are present near the left telomere. The G+C content and GC or AT skew profiles exhibit complex distributions. These, plus the inferred recombination at the right arm, indicate that SLP2 has evolved through rounds of exchanges involving at least three replicons.
Collapse
Affiliation(s)
- Chih-Hung Huang
- Institute of Genetics, National Yang-Ming University, Shih-Pai, Taipei 112, Taiwan
| | | | | | | | | | | |
Collapse
|
28
|
Goshi K, Uchida T, Lezhava A, Yamasaki M, Hiratsu K, Shinkawa H, Kinashi H. Cloning and analysis of the telomere and terminal inverted repeat of the linear chromosome of Streptomyces griseus. J Bacteriol 2002; 184:3411-5. [PMID: 12029061 PMCID: PMC135112 DOI: 10.1128/jb.184.12.3411-3415.2002] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cloning and sequencing of the telomere of Streptomyces griseus revealed five palindromic sequences in the terminal 116 nucleotides, all of which can make a hairpin loop structure. However, the end sequence cannot form the foldback secondary structure that is common in Streptomyces telomeres and is suggested to be necessary for terminal replication. Both inside ends of the terminal inverted repeat (TIR) were also cloned and sequenced. The results confirmed the size of the TIR to be 24 kb and identified two almost identical open reading frames that might have been involved in the formation of the TIR.
Collapse
Affiliation(s)
- Kohei Goshi
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima 739-8530, Japan
| | | | | | | | | | | | | |
Collapse
|
29
|
Bao K, Cohen SN. Terminal proteins essential for the replication of linear plasmids and chromosomes in Streptomyces. Genes Dev 2001; 15:1518-27. [PMID: 11410532 PMCID: PMC312717 DOI: 10.1101/gad.896201] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Linear plasmids and chromosomes of the bacterial genus Streptomyces have proteins of unknown characteristics and function linked covalently to their 5' DNA termini. We purified protein attached to the end of the pSLA2 linear plasmid of Streptomyces rochei, determined the N-terminal amino acid sequence, and used this information to clone corresponding genes from a S. rochei cosmid library. Three separate terminal protein genes (here designated as tpgR1, tpgR2, and tpgR3), which map to the S. rochei chromosome and to 100-kb and 206-kb linear plasmids contained in S. rochei, were isolated and found to encode a family of similar but distinct 21-kD proteins. Using tpgR1 to probe a genomic DNA library of Streptomyces lividans ZX7, whose linear chromosome can undergo transition to a circular form, we isolated a S. lividans chromosomal gene (tpgL) that we found specifies a protein closely related to, and functionally interchangeable with, TpgR proteins for pSLA2 maintenance in S. lividans. Mutation of tpgL precluded propagation of the pSLA2 plasmid in a linear form and also prevented propagation of S. lividans cells that contain linear, but not circular, chromosomes, indicating a specific and essential role for tpg genes in linear DNA replication. Surprisingly, Tpg proteins were observed to contain a reverse transcriptase-like domain rather than sequences in common with proteins that attach covalently to the termini of linear DNA replicons.
Collapse
Affiliation(s)
- K Bao
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305-5120, USA
| | | |
Collapse
|
30
|
Picardeau M, Lobry JR, Hinnebusch BJ. Analyzing DNA strand compositional asymmetry to identify candidate replication origins of Borrelia burgdorferi linear and circular plasmids. Genome Res 2000; 10:1594-604. [PMID: 11042157 PMCID: PMC310945 DOI: 10.1101/gr.124000] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The Lyme disease agent Borrelia burgdorferi has a genome composed of a linear chromosome and a series of linear and circular plasmids. We previously mapped the oriC of the linear chromosome to the center of the molecule, where a pronounced switch in CG skew occurs. In this study, we analyzed B. burgdorferi plasmid sequences for AT and CG skew in an effort to similarly identify plasmid replication origins. Cumulative skew diagrams of the plasmids suggested that they, like the linear chromosome, replicate bidirectionally from an internal origin. The B. burgdorferi linear chromosome contains homologs to partitioning protein genes soj and spoOJ, which are closely linked to oriC at the minimum cumulative skew point of the 1-Mb molecule. A soj/parA homolog also maps to cumulative skew minima of the B. burgdorferi linear and circular plasmids, further suggesting that these regions contain the replication origin. The heterogeneity in these genes and in the nucleotide sequences of the putative origin regions could account for the mutual compatibility of the multiple DNA elements in B. burgdorferi.
Collapse
Affiliation(s)
- M Picardeau
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Laboratory of Human Bacterial Pathogenesis, Hamilton, Montana 59840, USA
| | | | | |
Collapse
|
31
|
Volff JN, Altenbuchner J. A new beginning with new ends: linearisation of circular chromosomes during bacterial evolution. FEMS Microbiol Lett 2000; 186:143-50. [PMID: 10802162 DOI: 10.1111/j.1574-6968.2000.tb09095.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Bacterial circular chromosomes have sporadically become linearised during prokaryote evolution. Unrelated bacteria, including the spirochete Borrelia burgdorferi and the actinomycete Streptomyces, have linear chromosomes. Linear chromosomes may have been formed through integration of linear plasmids. Linear chromosomes use linear plasmid strategies to resolve the 'end-of-replication problem', but they have generally retained from their circular ancestors a central origin of replication. Streptomyces linear chromosomes are very unstable and at high frequency undergo amplifications and large deletions, often removing the telomeres. At least in Streptomyces, chromosome linearity is reversible: circular chromosomes arise spontaneously as products of genetic instability or can be generated artificially by targeted recombination. Streptomyces circularised chromosomes are very unstable as well, indicating that genetic instability is not confined to the linearised chromosomes. Bacterial linear chromosomes may contain telomere-linked regions of enhanced genomic plasticity, which undergo more frequent genetic exchanges and rearrangements and allow differential evolution of genes, depending on their chromosomal location.
Collapse
Affiliation(s)
- J N Volff
- Physiologische Chemie I, Biozentrum der Universität Würzburg, Am Hubland, D-97074, Würzburg, Germany.
| | | |
Collapse
|
32
|
Bey SJ, Tsou MF, Huang CH, Yang CC, Chen CW. The homologous terminal sequence of the Streptomyces lividans chromosome and SLP2 plasmid. MICROBIOLOGY (READING, ENGLAND) 2000; 146 ( Pt 4):911-922. [PMID: 10784050 DOI: 10.1099/00221287-146-4-911] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The chromosome of Streptomyces lividans shares 15.4 kb homology with one end of the linear plasmid SLP2, consisting of a 10.1 kb terminal sequence followed by the 5.3 kb transposable element Tn4811. The 10.1 kb terminal sequence was determined. The mean G+C content of this sequence is 67.9 mol% with a striking G vs C bias in the last kb. The terminal 232 nt contained 10 palindromic sequences with potential to form complex secondary structures. One typical Streptomyces coding sequence (designated ORF1) of 2643 bp was predicted in the determined sequence. The amino acid sequence of the ORF1 product contained a DEAH helicase motif, and exhibited similarity to type I restriction enzyme HsdR subunits in the database, suggesting a possible role in replication of the telomeres. However, all the ORF1 sequences on the chromosome and SLP2 could be simultaneously knocked out by targeted recombination without affecting the viability of the cells and the linearity of the chromosome and SLP2. This ruled out ORF1 as an essential component in the maintenance of the linear chromosome and plasmids.
Collapse
Affiliation(s)
- Shian-Jy Bey
- Institute of Genetics, National Yang-Ming University, Shih-Pai, Taipei 112, Taiwan1
| | - Meng-Fu Tsou
- Institute of Genetics, National Yang-Ming University, Shih-Pai, Taipei 112, Taiwan1
| | - Chih-Hung Huang
- Institute of Genetics, National Yang-Ming University, Shih-Pai, Taipei 112, Taiwan1
| | - Chien-Chin Yang
- Department of Chemistry, Chung-Yuan Christian University, Chung-Li, Taiwan2
| | - Carton W Chen
- Institute of Genetics, National Yang-Ming University, Shih-Pai, Taipei 112, Taiwan1
| |
Collapse
|
33
|
Picardeau M, Le Dantec C, Vincent V. Analysis of the internal replication region of a mycobacterial linear plasmid. MICROBIOLOGY (READING, ENGLAND) 2000; 146 ( Pt 2):305-313. [PMID: 10708369 DOI: 10.1099/00221287-146-2-305] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Linear plasmids have previously been identified by the authors in mycobacteria, the telomeres of which have terminal inverted repeats and covalently attached proteins. In this study, the replication of these unusual molecules was investigated by studying a 25 kb linear plasmid from the slow-growing species Mycobacterium celatum called pCLP. An internal region of pCLP responsible for replication in Mycobacterium smegmatis was identified. The nucleotide sequence of the minimum replication region of pCLP, which was 2.8 kb long, contained a putative replication gene, rep, and a putative origin of replication consisting of an 18 bp direct repeat and an AT-rich region. A short section of the pCLP replication region was also found to have sequence identity with the replication regions of mycobacterial circular plasmids, suggesting that these linear and circular plasmids are related. It was found that pCLP replicated in Mycobacterium bovis BCG and was compatible in M. smegmatis with pAL5000- and pJAZ38-derived plasmids from Mycobacterium fortuitum, which belong to two different compatibility groups. Thus, this new Escherichia coli-mycobacteria shuttle vector may be used in both slow- and fast-growing mycobacteria and in co-transformation experiments with other mycobacterial vectors.
Collapse
Affiliation(s)
- Mathieu Picardeau
- Laboratoire de Référence des Mycobactéries, Institut Pasteur, 75724 Paris Cedex 15, France1
| | - Corinne Le Dantec
- Laboratoire de Référence des Mycobactéries, Institut Pasteur, 75724 Paris Cedex 15, France1
| | - Véronique Vincent
- Laboratoire de Référence des Mycobactéries, Institut Pasteur, 75724 Paris Cedex 15, France1
| |
Collapse
|
34
|
Redenbach M, Bibb M, Gust B, Seitz B, Spychaj A. The linear plasmid SCP1 of Streptomyces coelicolor A3(2) possesses a centrally located replication origin and shows significant homology to the transposon Tn4811. Plasmid 1999; 42:174-85. [PMID: 10545260 DOI: 10.1006/plas.1999.1419] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The linear plasmid SCP1 of Streptomyces coelicolor A3(2) is one of the genetically more studied linear streptomycete replicons. Although the genetics of SCP1 and its interaction with the host chromosome have been analyzed for nearly three decades no information exists on its replication. With the help of an ordered cosmid contig for the complete 360-kb element, we have localized a 5439-bp fragment from the central region that confers autonomous replication in Streptomyces lividans. The minimal origin contains two overlapping ORFs which are separated from an AT-rich region which might correspond to the replication start point. ORF1 revealed intensive similarity to a class of DNA-primase/helicases of actinophages and archael plasmids. In addition, we have identified a region in both terminal inverted repeats of SCP1 that shows significant homology to the transposable element Tn4811 located near the ends of the S. lividans 66 chromosome.
Collapse
Affiliation(s)
- M Redenbach
- Genome Research Unit, Kaiserslautern University, Kaiserslautern, 67663, Germany.
| | | | | | | | | |
Collapse
|
35
|
Abstract
The Streptomyces linear plasmid pSLA2 initiates DNA replication bidirectionally towards its telomeres from a site located near the centre of the molecule; at the telomeres, the recessed ends of lagging strands are filled in by non-displacing DNA synthesis. Here, we report experiments that test three proposed mechanisms for lagging-strand fill-in. We present data inconsistent with recombinational or terminal hairpin models for the formation of full-length duplex pSLA2 DNA. Instead, we find that deletions in short, distantly separated homologous palindromes in the leading-strand 3' overhang prevent propagation of linear pSLA2 DNA, implicating a mechanism of palindrome-mediated leading-strand fold-back in telomere replication. We further show that circularized pSLA2 DNA molecules are opened in vivo precisely at the terminal nucleotides of telomeres, generating functional linear replicons containing native telomeres covalently bound to a protein at their 5' DNA termini. Together, our results support a model in which pairing of multiple widely separated pSLA2 palindromes anchors the 3' end of the leading-strand overhang to a site near the overhang's base -- providing a recognition site for terminal-protein-primed DNA synthesis and subsequent endonucleolytic processing. Thus, the replication of Streptomyces plasmid telomeres may have features in common with the mechanism proposed for telomere replication in autonomous parvoviruses.
Collapse
Affiliation(s)
- Z Qin
- Department of Genetics, Stanford University School of Medicine, CA 94305-5120, USA
| | | |
Collapse
|
36
|
Kalkus J, Menne R, Reh M, Schlegel HG. The terminal structures of linear plasmids from Rhodococcus opacus. MICROBIOLOGY (READING, ENGLAND) 1998; 144 ( Pt 5):1271-1279. [PMID: 9611802 DOI: 10.1099/00221287-144-5-1271] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The telomers of several linear plasmids of Rhodococcus opacus (formerly Nocardia opaca) were studied. The plasmids pHG201, pHG204 and pHG205 carry proteins bound to their ends, as shown by gel retardation experiments. A sequence hybridizing with the terminal sequence of pHG207, a recombinant linear plasmid consisting of the left part of pHG204 and the right part of pHG205, which was analysed in a previous study by the authors, could be detected in all linear plasmids of the wild-type R. opacus strains MR11 and MR22. However, only pHG204 and pHG206 carry terminal inverted repeats (TIRs) like pHG207. Cloning and sequencing of the terminal fragment of pHG204 revealed a nearly perfect TIR of 1016 bp. In contrast, the termini of pHG201 and pHG205 share little homology. Sequence analysis of the two end fragments of pHG201 revealed a similarity of only 65% within the terminal 34/32 bp and a perfect TIR of only 3 bp. The results support the assumption that long TIRs are not absolutely necessary for replication and maintenance of linear plasmids.
Collapse
Affiliation(s)
- Jutta Kalkus
- Institut für Mikrobiologie der Georg-August-Universität, Grisebachstrasse 8, D-37077 Göttingen, Germany
| | - Renate Menne
- Institut für Mikrobiologie der Georg-August-Universität, Grisebachstrasse 8, D-37077 Göttingen, Germany
| | - Michael Reh
- Institut für Mikrobiologie der Georg-August-Universität, Grisebachstrasse 8, D-37077 Göttingen, Germany
| | - Hans G Schlegel
- Institut für Mikrobiologie der Georg-August-Universität, Grisebachstrasse 8, D-37077 Göttingen, Germany
| |
Collapse
|
37
|
Netolitzky DJ, Jensen SE, Roy KL. Two small linear plasmids of Streptomyces jumonjinensis. Can J Microbiol 1997. [DOI: 10.1139/m97-090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In a survey of plasmids in a variety of β-lactam antibiotic producing Streptomyces spp., two small linear plasmids (pSJL1 and pSJL2) of approximately 12 and 17.5 kb were detected within Streptomyces jumonjinensis NRRL 5741, in addition to the previously reported giant linear plasmids pSJL3 and pSJL4. Characterization of these plasmids by Southern hybridization indicated that no significant homology exists between the S. jumonjinensis plasmids and plasmids detected in other β-lactam antibiotic producing Streptomyces spp. Single and double restriction endonuclease digestions were performed to generate maps of the two plasmids. The plasmids pSJL1 and pSJL2 have copy numbers of 21–27 and 15–20, respectively.Key words: Streptomyces, linear plasmid, DNA hybridization, DNA homology.
Collapse
|
38
|
Abstract
The high level of genetic instability in Streptomyces ambofaciens is related to large scale DNA rearrangements (deletions and DNA amplifications) which occur within a 2 Mb chromosomal region. The genome of several Streptomyces species is linear and the unstable region is present at the chromosomal extremities. This has raised the questions of the role of the unstable region (which is dispensable under laboratory conditions), the functions of the genes present in this area, and the relationships between instability and chromosomal linearity. The unstable region of Streptomyces and the replication termini of several other microorganisms, including Escherichia coli, share numerous common traits. This suggests that the unstable region of Streptomyces includes the replication terminus, and that chromosomal instability is related to the termination process.
Collapse
Affiliation(s)
- P Leblond
- Laboratoire de Génétique et Microbiologie associé I.N.R.A., Faculté des Sciences, Université de Nancy I, Vandoeuvre-lès-Nancy, France
| | | |
Collapse
|
39
|
Chang PC, Cohen SN. Bidirectional replication from an internal origin in a linear streptomyces plasmid. Science 1994; 265:952-4. [PMID: 8052852 DOI: 10.1126/science.8052852] [Citation(s) in RCA: 84] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Commonly, linear replicons that have protein covalently attached to 5' DNA termini replicate by protein-primed, strand-displacing, continuous synthesis of full-length strands. The synthesis of DNA in pSLA2, a 17-kilobase linear plasmid of Streptomyces rochei containing 5' terminal protein, occurs bidirectionally from an internally located replication origin. The replication intermediates are linear duplex molecules that have recessed (approximately 280 nucleotides) 5' ends rather than full-length single strands. The 3' over-hangs may serve as templates for the non-displacing synthesis of the lagging strand terminus primed by the covalently attached 5' DNA binding protein.
Collapse
Affiliation(s)
- P C Chang
- Department of Genetics, Stanford University School of Medicine, CA 94305
| | | |
Collapse
|
40
|
Abstract
Linear plasmids and chromosomes were unknown in prokaryotes until recently but have now been found in spirochaetes, Gram-positive bacteria, and Gram-negative bacteria. Two structural types of bacterial linear DNA have been characterized. Linear plasmids of the spirochaete Borrelia have a covalently closed hairpin loop at each end and linear plasmids of the Gram-positive filamentous Streptomyces have a covalently attached protein at each end. Replicons with similar structures are more frequent in eukaryotic cells than in prokaryotes. Linear genomic structures are probably more common in bacteria than previously recognized, however, and some replicons may interconvert between circular and linear isomers. The molecular biology of these widely dispersed elements provides clues to explain the origin of linear DNA in bacteria, including evidence for genetic exchange between prokaryotes and eukaryotes.
Collapse
Affiliation(s)
- J Hinnebusch
- Laboratory of Vectors and Pathogens, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana 59840
| | | |
Collapse
|
41
|
Abstract
Two copies of a DNA sequence similar or identical to one end of the linear plasmid SLP2 were found on the Streptomyces lividans chromosome. Restriction mapping showed that these sequences represented free ends. Electrophoretic retardation and glass-binding studies indicated that the telomeres carry covalently bound proteins. Moreover, the chromosome migrated as an 8 Mb linear DNA in pulsed-field gel electrophoresis. A similar finding with the chromosomes of six other Streptomyces species suggested that a linear chromosome may be characteristic of the genus. The S. lividans chromosome can be circularized by joining the two ends by artificial targeted recombination or by spontaneous deletions spanning both telomeres. Thus the chromosome appears to be able to exist, in viable bacteria, as a linear or a circular molecule.
Collapse
Affiliation(s)
- Y S Lin
- Institute of Biochemistry, National Yang-Ming Medical College, Taipei, Taiwan
| | | | | | | |
Collapse
|
42
|
Chen CW, Yu TW, Lin YS, Kieser HM, Hopwood DA. The conjugative plasmid SLP2 of Streptomyces lividans is a 50 kb linear molecule. Mol Microbiol 1993; 7:925-32. [PMID: 8387146 DOI: 10.1111/j.1365-2958.1993.tb01183.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The SLP2 plasmid had previously been demonstrated genetically to exist in Streptomyces lividans by its ability to promote conjugation and to elicit 'pocks' on recipient (SLP2-) cultures, but it had not been physically detected. Using pulsed-field gel electrophoresis, a 50 kb linear DNA was isolated from SLP2+ but not SLP2- strains of S. lividans, and from Streptomyces coelicolor and Streptomyces parvulus strains to which SLP2 had been transferred by conjugation or transformation. We conclude that this linear DNA is SLP2. The terminal fragments of SLP2 were cloned. The determined sequences revealed a 44bp imperfect terminal inverted repeat. The terminal 12bp sequence of SLP2 was identical to those of two other Streptomyces linear plasmids, pSLA2 and pSCL, and similar to the terminal sequences of another Streptomyces linear plasmid, SCP1. The termini of SLP2 DNA were resistant to digestion by lambda exonuclease and ExoIII. A truncated (probably crippled) copy of Tn4811 is present on the plasmid. While the SLP2 plasmid exists as a free form in the host, a 15.7 kb sequence corresponding to the segment of SLP2 from Tn4811 to the right terminus is also present (at a copy number similar to the free form) elsewhere in the genome of S. lividans. Furthermore, SLP2 is partially homologous to a newly discovered 650 kb linear plasmid in S. parvulus.
Collapse
Affiliation(s)
- C W Chen
- Institute of Genetics, National Yang-Ming Medical College, Shih-Pai, Taipei, Taiwan, Republic of China
| | | | | | | | | |
Collapse
|
43
|
Wu X, Roy KL. Complete nucleotide sequence of a linear plasmid from Streptomyces clavuligerus and characterization of its RNA transcripts. J Bacteriol 1993; 175:37-52. [PMID: 8416908 PMCID: PMC196095 DOI: 10.1128/jb.175.1.37-52.1993] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The complete nucleotide sequence of a small linear plasmid (pSCL1) from Streptomyces clavuligerus has been determined. This plasmid is 11,696 bp in length, has a 72% G+C content, and has approximately 900-bp inverted terminal repeat sequences. A comparison of the inverted terminal repeats of pSCL1 with those of a linear plasmid from S. rochei shows that the two terminal sequences have a high degree of similarity (approximately 70%). Several small inverted repeats found in the long terminal sequences of both plasmids are also conserved. An analysis of the sequence and codon preferences indicates that pSCL1 has seven or eight highly probable protein-coding open reading frames (ORFs). However, only two RNA species encoded by pSCL1 were detected in S. clavuligerus grown in liquid culture. The larger of these transcripts (900 nucleotides) corresponds to an ORF and is likely to be an mRNA for a protein similar to the KorA protein of pIJ101. The smaller transcript (460 nucleotides) does not correspond to any ORF; however, its 5' end is complementary to the 5' end of a predicted mRNA, suggesting that it may function as an antisense RNA. The larger of the two RNA species was present at a high level during the early stage of growth in liquid medium, and then its apparent rate of transcription decreased and remained at a lower level through the later stages; the level of the smaller RNA species remained relatively constant through all stages of growth.
Collapse
Affiliation(s)
- X Wu
- Department of Microbiology, University of Alberta, Edmonton, Canada
| | | |
Collapse
|