1
|
Luchetti A, Castellani LG, Toscani AM, Lagares A, Del Papa MF, Torres Tejerizo G, Pistorio M. Characterization of an accessory plasmid of Sinorhizobium meliloti and its two replication-modules. PLoS One 2023; 18:e0285505. [PMID: 37200389 DOI: 10.1371/journal.pone.0285505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 04/25/2023] [Indexed: 05/20/2023] Open
Abstract
Rhizobia are Gram-negative bacteria known for their ability to fix atmospheric N2 in symbiosis with leguminous plants. Current evidence shows that rhizobia carry in most cases a variable number of plasmids, containing genes necessary for symbiosis or free-living, a common feature being the presence of several plasmid replicons within the same strain. For many years, we have been studying the mobilization properties of pSmeLPU88b from the strain Sinorhizobium meliloti LPU88, an isolate from Argentina. To advance in the characterization of pSmeLPU88b plasmid, the full sequence was obtained. pSmeLPU88b is 35.9 kb in size, had an average GC % of 58.6 and 31 CDS. Two replication modules were identified in silico: one belonging to the repABC type, and the other to the repC. The replication modules presented high DNA identity to the replication modules from plasmid pMBA9a present in an S. meliloti isolate from Canada. In addition, three CDS presenting identity with recombinases and with toxin-antitoxin systems were found downstream of the repABC system. It is noteworthy that these CDS present the same genetic structure in pSmeLPU88b and in other rhizobial plasmids. Moreover, in all cases they are found downstream of the repABC operon. By cloning each replication system in suicide plasmids, we demonstrated that each of them can support plasmid replication in the S. meliloti genetic background, but with different stability behavior. Interestingly, while incompatibility analysis of the cloned rep systems results in the loss of the parental module, both obtained plasmids can coexist together.
Collapse
Affiliation(s)
- Abril Luchetti
- Proteome and Metabolome Research, Faculty of Biology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Universidad Nacional de La Plata, La Plata, Argentina
| | - Lucas G Castellani
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Universidad Nacional de La Plata, La Plata, Argentina
| | - Andrés Martin Toscani
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Universidad Nacional de La Plata, La Plata, Argentina
| | - Antonio Lagares
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Universidad Nacional de La Plata, La Plata, Argentina
| | - María Florencia Del Papa
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Universidad Nacional de La Plata, La Plata, Argentina
| | - Gonzalo Torres Tejerizo
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Universidad Nacional de La Plata, La Plata, Argentina
| | - Mariano Pistorio
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Universidad Nacional de La Plata, La Plata, Argentina
| |
Collapse
|
2
|
Wathugala ND, Hemananda KM, Yip CB, Hynes MF. Defining the requirements for the conjugative transfer of Rhizobium leguminosarum plasmid pRleVF39b. MICROBIOLOGY-SGM 2020; 166:318-331. [PMID: 31935189 DOI: 10.1099/mic.0.000885] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Rhizobium leguminosarum strain VF39 contains a plasmid, pRleVF39b, which encodes a distinctive type of conjugation system (rhizobial type IVa) that is relatively widespread among rhizobial genomes. The cluster of genes encoding the transfer functions lacks orthologs to genes such as traCD, traF and traB, but contains 15 conserved genes of unknown function. We determined the importance of these genes in conjugation by constructing marked and unmarked mutations in each gene, and established that six genes, now designated trcA-F, played a significant role in plasmid transfer. Like the relaxase gene, traA, and the genes encoding the MPF system (trb genes), five of these genes, located in two divergently transcribed operons, are regulated by the Xre family repressor TrbR. The other gene, trcF encodes a protein with similarity to histidinol phosphatases, and its role in conjugation is unclear, but mutations in trcF are severely impaired for conjugation. TrcF does not play a role in regulation of other conjugation genes.
Collapse
Affiliation(s)
- N Dulmini Wathugala
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Kasuni M Hemananda
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Cynthia B Yip
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Michael F Hynes
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| |
Collapse
|
3
|
Li X, Wang H, Tong W, Feng L, Wang L, Rahman SU, Wei G, Tao S. Exploring the evolutionary dynamics of Rhizobium plasmids through bipartite network analysis. Environ Microbiol 2019; 22:934-951. [PMID: 31361937 DOI: 10.1111/1462-2920.14762] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 06/24/2019] [Accepted: 07/25/2019] [Indexed: 10/26/2022]
Abstract
The genus Rhizobium usually has a multipartite genome architecture with a chromosome and several plasmids, making these bacteria a perfect candidate for plasmid biology studies. As there are no universally shared genes among typical plasmids, network analyses can complement traditional phylogenetics in a broad-scale study of plasmid evolution. Here, we present an exhaustive analysis of 216 plasmids from 49 complete genomes of Rhizobium by constructing a bipartite network that consists of two classes of nodes, the plasmids and homologous protein families that connect them. Dissection of the network using a hierarchical clustering strategy reveals extensive variety, with 34 homologous plasmid clusters. Four large clusters including one cluster of symbiotic plasmids and two clusters of chromids carrying some truly essential genes are widely distributed among Rhizobium. In contrast, the other clusters are quite small and rare. Symbiotic clusters and rare accessory clusters are exogenetic and do not appear to have co-evolved with the common accessory clusters; the latter ones have a large coding potential and functional complementarity for different lifestyles in Rhizobium. The bipartite network also provides preliminary evidence of Rhizobium plasmid variation and formation including genetic exchange, plasmid fusion and fission, exogenetic plasmid transfer, host plant selection, and environmental adaptation.
Collapse
Affiliation(s)
- Xiangchen Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China.,Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Hao Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China.,Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Wenjun Tong
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Li Feng
- College of Enology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Lina Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China.,Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Siddiq Ur Rahman
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China.,Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi, 712100, China.,Department of Computer Science and Bioinformatics, Khushal Khan Khattak University, Karak, Khyber Pakhtunkhwa, 27200, Pakistan
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Shiheng Tao
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China.,Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi, 712100, China
| |
Collapse
|
4
|
Nelson M, Guhlin J, Epstein B, Tiffin P, Sadowsky MJ. The complete replicons of 16 Ensifer meliloti strains offer insights into intra- and inter-replicon gene transfer, transposon-associated loci, and repeat elements. Microb Genom 2018; 4. [PMID: 29671722 PMCID: PMC5994717 DOI: 10.1099/mgen.0.000174] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Ensifer meliloti (formerly Rhizobium meliloti and Sinorhizobium meliloti) is a model bacterium for understanding legume–rhizobial symbioses. The tripartite genome of E. meliloti consists of a chromosome, pSymA and pSymB, and in some instances strain-specific accessory plasmids. The majority of previous sequencing studies have relied on the use of assemblies generated from short read sequencing, which leads to gaps and assembly errors. Here we used PacBio-based, long-read assemblies and were able to assemble, de novo, complete circular replicons. In this study, we sequenced, de novo-assembled and analysed 10 E. meliloti strains. Sequence comparisons were also done with data from six previously published genomes. We identified genome differences between the replicons, including mol% G+C and gene content, nucleotide repeats, and transposon-associated loci. Additionally, genomic rearrangements both within and between replicons were identified, providing insight into evolutionary processes at the structural level. There were few cases of inter-replicon gene transfer of core genes between the main replicons. Accessory plasmids were more similar to pSymA than to either pSymB or the chromosome, with respect to gene content, transposon content and G+C content. In our population, the accessory plasmids appeared to share an open genome with pSymA, which contains many nodulation- and nitrogen fixation-related genes. This may explain previous observations that horizontal gene transfer has a greater effect on the content of pSymA than pSymB, or the chromosome, and why some rhizobia show unstable nodulation phenotypes on legume hosts.
Collapse
Affiliation(s)
- Matthew Nelson
- 1Biotechnology Institute and Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN 55108, USA
| | - Joseph Guhlin
- 2Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108, USA
| | - Brendan Epstein
- 2Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108, USA
| | - Peter Tiffin
- 2Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108, USA
| | - Michael J Sadowsky
- 1Biotechnology Institute and Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN 55108, USA
| |
Collapse
|
5
|
Döhlemann J, Wagner M, Happel C, Carrillo M, Sobetzko P, Erb TJ, Thanbichler M, Becker A. A Family of Single Copy repABC-Type Shuttle Vectors Stably Maintained in the Alpha-Proteobacterium Sinorhizobium meliloti. ACS Synth Biol 2017; 6:968-984. [PMID: 28264559 PMCID: PMC7610768 DOI: 10.1021/acssynbio.6b00320] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
![]()
A considerable
share of bacterial species maintains segmented genomes.
Plant symbiotic α-proteobacterial rhizobia contain up to six repABC-type replicons in addition to the primary chromosome.
These low or unit-copy replicons, classified as secondary chromosomes,
chromids, or megaplasmids, are exclusively found in α-proteobacteria.
Replication and faithful partitioning of these replicons to the daughter
cells is mediated by the repABC region. The importance
of α-rhizobial symbiotic nitrogen fixation for sustainable agriculture
and Agrobacterium-mediated plant transformation as
a tool in plant sciences has increasingly moved biological engineering
of these organisms into focus. Plasmids are ideal DNA-carrying vectors
for these engineering efforts. On the basis of repABC regions collected from α-rhizobial secondary replicons, and
origins of replication derived from traditional cloning vectors, we
devised the versatile family of pABC shuttle vectors propagating in Sinorhizobium meliloti, related members of the Rhizobiales, and Escherichia coli. A modular plasmid library
providing the elemental parts for pABC vector assembly was founded.
The standardized design of these vectors involves five basic modules:
(1) repABC cassette, (2) plasmid-derived origin of
replication, (3) RK2/RP4 mobilization site (optional), (4) antibiotic
resistance gene, and (5) multiple cloning site flanked by transcription
terminators. In S. meliloti, pABC vectors showed
high propagation stability and unit-copy number. We demonstrated stable
coexistence of three pABC vectors in addition to the two indigenous
megaplasmids in S. meliloti, suggesting combinability
of multiple compatible pABC plasmids. We further devised an in vivo cloning strategy involving Cre/lox-mediated translocation of large DNA fragments to an autonomously
replicating repABC-based vector, followed by conjugation-mediated
transfer either to compatible rhizobia or E. coli.
Collapse
Affiliation(s)
- Johannes Döhlemann
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
- Faculty of Biology, Philipps-Universität Marburg, Marburg, 35043, Germany
| | - Marcel Wagner
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
- Faculty of Biology, Philipps-Universität Marburg, Marburg, 35043, Germany
| | - Carina Happel
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
- Faculty of Biology, Philipps-Universität Marburg, Marburg, 35043, Germany
| | - Martina Carrillo
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
- Biochemistry and Synthetic Biology of Microbial Metabolism Group, Max Planck Institute for Terrestrial Microbiology, Marburg, 35043, Germany
| | - Patrick Sobetzko
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
| | - Tobias J. Erb
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
- Biochemistry and Synthetic Biology of Microbial Metabolism Group, Max Planck Institute for Terrestrial Microbiology, Marburg, 35043, Germany
| | - Martin Thanbichler
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
- Faculty of Biology, Philipps-Universität Marburg, Marburg, 35043, Germany
| | - Anke Becker
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
- Faculty of Biology, Philipps-Universität Marburg, Marburg, 35043, Germany
| |
Collapse
|
6
|
Baltrus DA, Dougherty K, Arendt KR, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Ngan CY, Daum C, Shapiro N, Markowitz V, Ivanova N, Kyrpides N, Woyke T, Arnold AE. Absence of genome reduction in diverse, facultative endohyphal bacteria. Microb Genom 2017; 3:e000101. [PMID: 28348879 PMCID: PMC5361626 DOI: 10.1099/mgen.0.000101] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 12/04/2016] [Indexed: 01/03/2023] Open
Abstract
Fungi interact closely with bacteria, both on the surfaces of the hyphae and within their living tissues (i.e. endohyphal bacteria, EHB). These EHB can be obligate or facultative symbionts and can mediate diverse phenotypic traits in their hosts. Although EHB have been observed in many lineages of fungi, it remains unclear how widespread and general these associations are, and whether there are unifying ecological and genomic features can be found across EHB strains as a whole. We cultured 11 bacterial strains after they emerged from the hyphae of diverse Ascomycota that were isolated as foliar endophytes of cupressaceous trees, and generated nearly complete genome sequences for all. Unlike the genomes of largely obligate EHB, the genomes of these facultative EHB resembled those of closely related strains isolated from environmental sources. Although all analysed genomes encoded structures that could be used to interact with eukaryotic hosts, pathways previously implicated in maintenance and establishment of EHB symbiosis were not universally present across all strains. Independent isolation of two nearly identical pairs of strains from different classes of fungi, coupled with recent experimental evidence, suggests horizontal transfer of EHB across endophytic hosts. Given the potential for EHB to influence fungal phenotypes, these genomes could shed light on the mechanisms of plant growth promotion or stress mitigation by fungal endophytes during the symbiotic phase, as well as degradation of plant material during the saprotrophic phase. As such, these findings contribute to the illumination of a new dimension of functional biodiversity in fungi.
Collapse
Affiliation(s)
- David A Baltrus
- 1School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Kevin Dougherty
- 1School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Kayla R Arendt
- 1School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | | | - Alicia Clum
- 2Joint Genome Institute, Walnut Creek, CA, USA
| | | | | | | | | | | | - T B K Reddy
- 2Joint Genome Institute, Walnut Creek, CA, USA
| | | | - Chris Daum
- 2Joint Genome Institute, Walnut Creek, CA, USA
| | | | | | | | | | - Tanja Woyke
- 2Joint Genome Institute, Walnut Creek, CA, USA
| | - A Elizabeth Arnold
- 1School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA.,3Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| |
Collapse
|
7
|
Platt TG, Morton ER, Barton IS, Bever JD, Fuqua C. Ecological dynamics and complex interactions of Agrobacterium megaplasmids. FRONTIERS IN PLANT SCIENCE 2014; 5:635. [PMID: 25452760 PMCID: PMC4231840 DOI: 10.3389/fpls.2014.00635] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Accepted: 10/27/2014] [Indexed: 05/15/2023]
Abstract
As with many pathogenic bacteria, agrobacterial plant pathogens carry most of their virulence functions on a horizontally transmissible genetic element. The tumor-inducing (Ti) plasmid encodes the majority of virulence functions for the crown gall agent Agrobacterium tumefaciens. This includes the vir genes which drive genetic transformation of host cells and the catabolic genes needed to utilize the opines produced by infected plants. The Ti plasmid also encodes, an opine-dependent quorum sensing system that tightly regulates Ti plasmid copy number and its conjugal transfer to other agrobacteria. Many natural agrobacteria are avirulent, lacking the Ti plasmid. The burden of harboring the Ti plasmid depends on the environmental context. Away from diseased hosts, plasmid costs are low but the benefit of the plasmid is also absent. Consequently, plasmidless genotypes are favored. On infected plants the costs of the Ti plasmid can be very high, but balanced by the opine benefits, locally favoring plasmid bearing cells. Cheating derivatives which do not incur virulence costs but can benefit from opines are favored on infected plants and in most other environments, and these are frequently isolated from nature. Many agrobacteria also harbor an At plasmid which can stably coexist with a Ti plasmid. At plasmid genes are less well characterized but in general facilitate metabolic activities in the rhizosphere and bulk soil, such as the ability to breakdown plant exudates. Examination of A. tumefaciens C58, revealed that harboring its At plasmid is much more costly than harboring it's Ti plasmid, but conversely the At plasmid is extremely difficult to cure. The interactions between these co-resident plasmids are complex, and depend on environmental context. However, the presence of a Ti plasmid appears to mitigate At plasmid costs, consistent with the high frequency with which they are found together.
Collapse
Affiliation(s)
| | | | | | | | - Clay Fuqua
- Department of Biology, Indiana UniversityBloomington, IN, USA
| |
Collapse
|
8
|
Stasiak G, Mazur A, Wielbo J, Marczak M, Zebracki K, Koper P, Skorupska A. Functional relationships between plasmids and their significance for metabolism and symbiotic performance of Rhizobium leguminosarum bv. trifolii. J Appl Genet 2014; 55:515-27. [PMID: 24839164 PMCID: PMC4185100 DOI: 10.1007/s13353-014-0220-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 04/11/2014] [Accepted: 04/30/2014] [Indexed: 12/31/2022]
Abstract
Rhizobium leguminosarum bv. trifolii TA1 (RtTA1) is a soil bacterium establishing a highly specific symbiotic relationship with clover, which is based on the exchange of molecular signals between the host plant and the microsymbiont. The RtTA1 genome is large and multipartite, composed of a chromosome and four plasmids, which comprise approximately 65 % and 35 % of the total genome, respectively. Extrachromosomal replicons were previously shown to confer significant metabolic versatility to bacteria, which is important for their adaptation in the soil and nodulation competitiveness. To investigate the contribution of individual RtTA1 plasmids to the overall cell phenotype, metabolic properties and symbiotic performance, a transposon-based elimination strategy was employed. RtTA1 derivatives cured of pRleTA1b or pRleTA1d and deleted in pRleTA1a were obtained. In contrast to the in silico predictions of pRleTA1b and pRleTA1d, which were described as chromid-like replicons, both appeared to be completely curable. On the other hand, for pRleTA1a (symbiotic plasmid) and pRleTA1c, which were proposed to be unessential for RtTA1 viability, it was not possible to eliminate them at all (pRleTA1c) or entirely (pRleTA1a). Analyses of the phenotypic traits of the RtTA1 derivatives obtained revealed the functional significance of individual plasmids and their indispensability for growth, certain metabolic pathways, production of surface polysaccharides, autoaggregation, biofilm formation, motility and symbiotic performance. Moreover, the results allow us to suggest broad functional cooperation among the plasmids in shaping the phenotypic properties and symbiotic capabilities of rhizobia.
Collapse
Affiliation(s)
- Grażyna Stasiak
- Department of Genetics and Microbiology, Maria-Curie Skłodowska University, 19 Akademicka St., 20-033, Lublin, Poland
| | | | | | | | | | | | | |
Collapse
|
9
|
RepA and RepB exert plasmid incompatibility repressing the transcription of the repABC operon. Plasmid 2013; 70:362-76. [PMID: 24016735 DOI: 10.1016/j.plasmid.2013.08.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 08/06/2013] [Accepted: 08/16/2013] [Indexed: 11/22/2022]
Abstract
Rhizobium etli CFN42 has a multipartite genome composed of one chromosome and six large plasmids with low copy numbers, all belonging to the repABC plasmid family. All elements essential for replication and segregation of these plasmids are encoded within the repABC operon. RepA and RepB direct plasmid segregation and are involved in the transcriptional regulation of the operon, and RepC is the initiator protein of the plasmid. Here we show that in addition to RepA (repressor) and RepB (corepressor), full transcriptional repression of the operon located in the symbiotic plasmid (pRetCFN42d) of this strain requires parS, the centromere-like sequence, and the operator sequence. However, the co-expression of RepA and RepB is sufficient to induce the displacement of the parental plasmid. RepA is a Walker-type ATPase that self associates in vivo and in vitro and binds specifically to the operator region in its RepA-ADP form. In contrast, RepA-ATP is capable of binding to non-specific DNA. RepA and RepB form high molecular weight DNA-protein complexes in the presence of ATP and ADP. RepA carrying ATP-pocket motif mutations induce full repression of the repABC operon without the participation of RepB and parS. These mutants specifically bind the operator sequence in their ATP or ADP bound forms. In addition, their expression in trans exerts plasmid incompatibility against the parental plasmid. RepA and RepB expressed in trans induce plasmid incompatibility because of their ability to repress the repABC operon and not only by their capacity to distort the plasmid segregation process.
Collapse
|
10
|
Marek-Kozaczuk M, Leszcz A, Wielbo J, Wdowiak-Wróbel S, Skorupska A. Rhizobium pisi sv. trifolii K3.22 harboring nod genes of the Rhizobium leguminosarum sv. trifolii cluster. Syst Appl Microbiol 2013; 36:252-8. [DOI: 10.1016/j.syapm.2013.01.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 01/09/2013] [Accepted: 01/10/2013] [Indexed: 11/25/2022]
|