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Toro N, Martínez-Abarca F, Molina-Sánchez MD, García-Rodríguez FM, Nisa-Martínez R. Contribution of Mobile Group II Introns to Sinorhizobium meliloti Genome Evolution. Front Microbiol 2018; 9:627. [PMID: 29670598 PMCID: PMC5894124 DOI: 10.3389/fmicb.2018.00627] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 03/19/2018] [Indexed: 12/26/2022] Open
Abstract
Mobile group II introns are ribozymes and retroelements that probably originate from bacteria. Sinorhizobium meliloti, the nitrogen-fixing endosymbiont of legumes of genus Medicago, harbors a large number of these retroelements. One of these elements, RmInt1, has been particularly successful at colonizing this multipartite genome. Many studies have improved our understanding of RmInt1 and phylogenetically related group II introns, their mobility mechanisms, spread and dynamics within S. meliloti and closely related species. Although RmInt1 conserves the ancient retroelement behavior, its evolutionary history suggests that this group II intron has played a role in the short- and long-term evolution of the S. meliloti genome. We will discuss its proposed role in genome evolution by controlling the spread and coexistence of potentially harmful mobile genetic elements, by ectopic transposition to different genetic loci as a source of early genomic variation and by generating sequence variation after a very slow degradation process, through intron remnants that may have continued to evolve, contributing to bacterial speciation.
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Affiliation(s)
- Nicolás Toro
- Structure, Dynamics and Function of Rhizobacterial Genomes (Grupo de Ecología Genética de la Rizosfera), Department of Soil Microbiology and Symbiotic Systems, Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Granada, Spain
| | - Francisco Martínez-Abarca
- Structure, Dynamics and Function of Rhizobacterial Genomes (Grupo de Ecología Genética de la Rizosfera), Department of Soil Microbiology and Symbiotic Systems, Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Granada, Spain
| | - María D Molina-Sánchez
- Structure, Dynamics and Function of Rhizobacterial Genomes (Grupo de Ecología Genética de la Rizosfera), Department of Soil Microbiology and Symbiotic Systems, Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Granada, Spain
| | - Fernando M García-Rodríguez
- Structure, Dynamics and Function of Rhizobacterial Genomes (Grupo de Ecología Genética de la Rizosfera), Department of Soil Microbiology and Symbiotic Systems, Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Granada, Spain
| | - Rafael Nisa-Martínez
- Structure, Dynamics and Function of Rhizobacterial Genomes (Grupo de Ecología Genética de la Rizosfera), Department of Soil Microbiology and Symbiotic Systems, Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Granada, Spain
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2
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Inactivation of group II intron RmInt1 in the Sinorhizobium meliloti genome. Sci Rep 2015; 5:12036. [PMID: 26156864 PMCID: PMC4496777 DOI: 10.1038/srep12036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 06/15/2015] [Indexed: 11/10/2022] Open
Abstract
Group II introns are self-splicing catalytic RNAs that probably originated in bacteria and act as mobile retroelements. The dispersal and dynamics of group II intron spread within a bacterial genome are thought to follow a selection-driven extinction model. Likewise, various studies on the evolution of group II introns have suggested that they are evolving toward an inactive form by fragmentation, with the loss of the intron 3′-terminus, but with some intron fragments remaining and continuing to evolve in the genome. RmInt1 is a mobile group II intron that is widespread in natural populations of Sinorhizobium meliloti, but some strains of this species have no RmInt1 introns. We studied the splicing ability and mobility of the three full-length RmInt1 copies harbored by S. meliloti 1021, and obtained evidence suggesting that specific mutations may lead to the impairment of intron splicing and retrohoming. Our data suggest that the RmInt1 copies in this strain are undergoing a process of inactivation.
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Chillón I, Molina-Sánchez MD, Fedorova O, García-Rodríguez FM, Martínez-Abarca F, Toro N. In vitro characterization of the splicing efficiency and fidelity of the RmInt1 group II intron as a means of controlling the dispersion of its host mobile element. RNA (NEW YORK, N.Y.) 2014; 20:2000-2010. [PMID: 25336586 PMCID: PMC4238363 DOI: 10.1261/rna.047407.114] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 09/29/2014] [Indexed: 06/04/2023]
Abstract
Group II introns are catalytic RNAs that are excised from their precursors in a protein-dependent manner in vivo. Certain group II introns can also react in a protein-independent manner under nonphysiological conditions in vitro. The efficiency and fidelity of the splicing reaction is crucial, to guarantee the correct formation and expression of the protein-coding mRNA. RmInt1 is an efficient mobile intron found within the ISRm2011-2 insertion sequence in the symbiotic bacterium Sinorhizobium meliloti. The RmInt1 intron self-splices in vitro, but this reaction generates side products due to a predicted cryptic IBS1* sequence within the 3' exon. We engineered an RmInt1 intron lacking the cryptic IBS1* sequence, which improved the fidelity of the splicing reaction. However, atypical circular forms of similar electrophoretic mobility to the lariat intron were nevertheless observed. We analyzed a run of four cytidine residues at the 3' splice site potentially responsible for a lack of fidelity at this site leading to the formation of circular intron forms. We showed that mutations of residues base-pairing in the tertiary EBS3-IBS3 interaction increased the efficiency and fidelity of the splicing reaction. Our results indicate that RmInt1 has developed strategies for decreasing its splicing efficiency and fidelity. RmInt1 makes use of unproductive splicing reactions to limit the transposition of the insertion sequence into which it inserts itself in its natural context, thereby preventing potentially harmful dispersion of ISRm2011-2 throughout the genome of its host.
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Affiliation(s)
- Isabel Chillón
- Grupo de Ecología Genética, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - María Dolores Molina-Sánchez
- Grupo de Ecología Genética, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
| | - Olga Fedorova
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
| | - Fernando Manuel García-Rodríguez
- Grupo de Ecología Genética, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
| | - Francisco Martínez-Abarca
- Grupo de Ecología Genética, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
| | - Nicolás Toro
- Grupo de Ecología Genética, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
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4
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Biondi EG, Toro N, Bazzicalupo M, Martínez-Abarca F. Spread of the group II intron RmInt1 and its insertion sequence target sites in the plant endosymbiont Sinorhizobium meliloti. Mob Genet Elements 2014; 1:2-7. [PMID: 22016840 DOI: 10.4161/mge.1.1.15316] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Accepted: 02/22/2011] [Indexed: 11/19/2022] Open
Abstract
RmInt1 is a mobile group II intron from Sinorhizobium meliloti that is exceptionally abundant in this bacterial species. We compared the presence of RmInt1 and two of its insertion sequence homing sites (ISRm2011-2 and ISRm10-2) in two phylogenetic clusters (I and II) identified by AFLP analysis in a collection of S. meliloti field isolates from Italy. Both clusters contained several copies of the ISRm2011-2 element, which is present at high copy number in almost all S. meliloti isolates. By contrast, isolates from cluster I harbored no copies of ISRm10-2 and only a truncated copy of RmInt1, despite the absence of constraints on intron mobility in this genetic background, whereas cluster II strains harbored several copies of this intron. The absence of ISRm10-2 from one of the strains of this cluster suggests that this element was acquired more recently than the other two elements. Furthermore, studies of insertional polymorphisms in cluster II strains revealed the acquisition of ISRm10-2 and subsequent retrohoming of RmInt1 to this homing site. These results highlight the role of intron homing sites (ISs) in facilitating intron dispersal and the dynamic and ongoing nature of the spread of the group II intron RmInt1 in S. meliloti.
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Affiliation(s)
- Emanuele G Biondi
- Department of Evolutionary Biology; University of Florence; Florence, Italy
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Complete Genome Sequence of the RmInt1 Group II Intronless Sinorhizobium meliloti Strain RMO17. GENOME ANNOUNCEMENTS 2014; 2:2/5/e01001-14. [PMID: 25301650 PMCID: PMC4192382 DOI: 10.1128/genomea.01001-14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We report the complete genome sequence of the RmInt1 group II intronless Sinorhizobium meliloti strain RMO17 isolated from Medicago orbicularis nodules from Spanish soil. The genome consists of 6.73 Mb distributed between a single chromosome and two megaplasmids (the chromid pSymB and pSymA).
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6
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Kuhn S, Stiens M, Pühler A, Schlüter A. Prevalence of pSmeSM11a-like plasmids in indigenous Sinorhizobium meliloti strains isolated in the course of a field release experiment with genetically modified S. meliloti strains. FEMS Microbiol Ecol 2008; 63:118-31. [DOI: 10.1111/j.1574-6941.2007.00399.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Costa M, Michel F, Molina-Sánchez MD, Martinez-Abarca F, Toro N. An alternative intron-exon pairing scheme implied by unexpected in vitro activities of group II intron RmInt1 from Sinorhizobium meliloti. Biochimie 2006; 88:711-7. [PMID: 16460862 DOI: 10.1016/j.biochi.2005.12.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2005] [Accepted: 12/27/2005] [Indexed: 11/16/2022]
Abstract
RmInt1 is a mobile group II intron which interrupts ISRm2011-2, another mobile element from the bacterium Sinorhizobium meliloti. Ribozyme constructs derived from intron RmInt1 self-splice in vitro when incubated under permissive conditions, but the excised intron and ligated exons are largely replaced by unconventional products. These include a slightly shorter, 5'-end truncated 3' exon, truncated variants of the linear and lariat forms of the intron-3' exon reaction intermediate, as well as presumably circular molecules derived from the latter. Two factors explain the abundance of these products: (i) nucleotides 5-11 of the 3' exon (IBS1*) provide a better match to the EBS1 5'-exon-binding site than the authentic IBS1 sequence in the 5' exon; (ii) exon ligation is unusually inefficient, and especially so when the 5' exon is truncated close to the second (IBS2) intron-binding site. We propose that reactions at the IBS1* site play a part in the regulation of the intron ISRm2011-2 host in vivo.
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Affiliation(s)
- María Costa
- Centre de Genétique Moléculaire du CNRS, Avenue de la Terrasse, 91190 Gif-sur-Yvette, France
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8
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Giuntini E, Mengoni A, De Filippo C, Cavalieri D, Aubin-Horth N, Landry CR, Becker A, Bazzicalupo M. Large-scale genetic variation of the symbiosis-required megaplasmid pSymA revealed by comparative genomic analysis of Sinorhizobium meliloti natural strains. BMC Genomics 2005; 6:158. [PMID: 16283928 PMCID: PMC1298293 DOI: 10.1186/1471-2164-6-158] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2005] [Accepted: 11/10/2005] [Indexed: 12/21/2022] Open
Abstract
Background Sinorhizobium meliloti is a soil bacterium that forms nitrogen-fixing nodules on the roots of leguminous plants such as alfalfa (Medicago sativa). This species occupies different ecological niches, being present as a free-living soil bacterium and as a symbiont of plant root nodules. The genome of the type strain Rm 1021 contains one chromosome and two megaplasmids for a total genome size of 6 Mb. We applied comparative genomic hybridisation (CGH) on an oligonucleotide microarrays to estimate genetic variation at the genomic level in four natural strains, two isolated from Italian agricultural soil and two from desert soil in the Aral Sea region. Results From 4.6 to 5.7 percent of the genes showed a pattern of hybridisation concordant with deletion, nucleotide divergence or ORF duplication when compared to the type strain Rm 1021. A large number of these polymorphisms were confirmed by sequencing and Southern blot. A statistically significant fraction of these variable genes was found on the pSymA megaplasmid and grouped in clusters. These variable genes were found to be mainly transposases or genes with unknown function. Conclusion The obtained results allow to conclude that the symbiosis-required megaplasmid pSymA can be considered the major hot-spot for intra-specific differentiation in S. meliloti.
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Affiliation(s)
- Elisa Giuntini
- Dipartimento di Biologia Animale e Genetica, Università di Firenze, via Romana 17, I-50125 Firenze, Italy
| | - Alessio Mengoni
- Dipartimento di Biologia Animale e Genetica, Università di Firenze, via Romana 17, I-50125 Firenze, Italy
| | - Carlotta De Filippo
- Dipartimento di Farmacologia, Università di Firenze, Viale Pieraccini 6, 50139 Firenze, Italy
| | - Duccio Cavalieri
- Dipartimento di Farmacologia, Università di Firenze, Viale Pieraccini 6, 50139 Firenze, Italy
| | - Nadia Aubin-Horth
- Bauer Center for Genomics Research, Harvard University, 7 Divinity Avenue, Cambridge, Massachusetts, 02138, USA
| | - Christian R Landry
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts, 02138, USA
| | - Anke Becker
- Lehrstuhl fur Genetik, Universitat Bielefeld, 33594 Bielefeld, Germany
| | - Marco Bazzicalupo
- Dipartimento di Biologia Animale e Genetica, Università di Firenze, via Romana 17, I-50125 Firenze, Italy
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Pettinari JM, Chaneton L, Vazquez G, Steinbüchel A, Méndez BS. Insertion sequence-like elements associated with putative polyhydroxybutyrate regulatory genes in Azotobacter sp. FA8. Plasmid 2003; 50:36-44. [PMID: 12826056 DOI: 10.1016/s0147-619x(03)00009-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The genes phaR, phaP, and phaF, encoding putative regulatory proteins, were found in the poly (3-hydroxybutyrate) (PHB) gene cluster of the free nitrogen-fixing bacteria Azotobacter sp. FA8. These genes were flanked by the insertion sequence ISAzsp1, belonging to the IS3 family, and a region highly homologous to insertion sequences of the IS630 family. These are the first site-specific recombination elements to be described in association with genes involved in the metabolism of polyhydroxyalkanoates (PHAs). A possible role for ISs in the assembly of pha genes is presented.
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Affiliation(s)
- Julia M Pettinari
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, 1428 Buenos Aires, Argentina
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10
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Andronov EE, Terefework Z, Roumiantseva ML, Dzyubenko NI, Onichtchouk OP, Kurchak ON, Dresler-Nurmi A, Young JPW, Simarov BV, Lindström K. Symbiotic and genetic diversity of Rhizobium galegae isolates collected from the Galega orientalis gene center in the Caucasus. Appl Environ Microbiol 2003; 69:1067-74. [PMID: 12571030 PMCID: PMC143604 DOI: 10.1128/aem.69.2.1067-1074.2003] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2002] [Accepted: 11/13/2002] [Indexed: 11/20/2022] Open
Abstract
This paper explores the relationship between the genetic diversity of rhizobia and the morphological diversity of their plant hosts. Rhizobium galegae strains were isolated from nodules of wild Galega orientalis and Galega officinalis in the Caucasus, the center of origin for G. orientalis. All 101 isolates were characterized by genomic amplified fragment length polymorphism fingerprinting and by PCR-restriction fragment length polymorphism (RFLP) of the rRNA intergenic spacer and of five parts of the symbiotic region adjacent to nod box sequences. By all criteria, the R. galegae bv. officinalis and R. galegae bv. orientalis strains form distinct clusters. The nod box regions are highly conserved among strains belonging to each of the two biovars but differ structurally to various degrees between the biovars. The findings suggest varying evolutionary pressures in different parts of the symbiotic genome of closely related R. galegae biovars. Sixteen R. galegae bv. orientalis strains harbored copies of the same insertion sequence element; all were isolated from a particular site and belonged to a limited range of chromosomal genotypes. In all analyses, the Caucasian R. galegae bv. orientalis strains were more diverse than R. galegae bv. officinalis strains, in accordance with the gene center theory.
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Affiliation(s)
- E E Andronov
- Research Institute of Agricultural Microbiology, St. Petersburg, Pushkin 196608, Russia.
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11
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Toro N, Martínez-Abarca F, Fernández-López M, Muñoz-Adelantado E. Diversity of group II introns in the genome of Sinorhizobium meliloti strain 1021: splicing and mobility of RmInt1. Mol Genet Genomics 2003; 268:628-36. [PMID: 12589437 DOI: 10.1007/s00438-002-0778-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2002] [Accepted: 10/25/2002] [Indexed: 10/25/2022]
Abstract
The number and diversity of known group II introns in eubacteria are continually increasing with the addition of new data from sequencing projects, but the significance of these introns in the evolution of bacterial genomes is unknown. We analyzed the main features of the group II introns present in the genome of the soil microorganism Sinorhizobium meliloti (strain 1021), the nitrogen-fixing symbiont of alfalfa, the DNA sequence of which was recently determined. Strain 1021 harbors three different classes of group II introns: RmInt1, of bacterial class D; SMb2147/SMb21167, which cluster within bacterial class C; and SMa1875, the phylogenetic class of which is uncertain. The group II introns SMb2147/SMb21167 and SMa1875 are widely distributed in S. meliloti, but are present in lower copy numbers than RmInt1. Strain 1021 harbors three copies of RmInt1, which is pSym-specific. Although RmInt1 is spliced in strain 1021, mobility assays suggested that, in contrast to other S. meliloti strains, the genetic background of strain 1021 does not support intron homing events.
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Affiliation(s)
- N Toro
- Grupo de Ecología Genética, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Calle Profesor Albareda 1, 18008, Granada, Spain.
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12
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Bloem JF, Botha WJ, Law IJ, Steyn PL. Colony variation in Sinorhizobium meliloti inoculant strain U 45. Microbiol Res 2003; 157:283-92. [PMID: 12501992 DOI: 10.1078/0944-5013-00158] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A culture of Sinorhizobium meliloti strain U 45, maintained on yeast extract-mannitol (YM) agar, produced a mixture of Congo red-absorbing (R1) and non-absorbing (W1) colonies when grown on YM medium containing Congo red. The original freeze-dried (FD) culture formed gummy (G), white (W2) and small red (R2) colony types on the above medium. All colonies were stable except G, which segregated into G and W2-like types. Immune diffusion patterns of all colony types were identical. The W1 colony type dominated R1 when a 1:1 combination was sub-cultured on YM agar. The parent cultures and their variants exhibited a range of N2-fixing effectiveness and competitiveness when inoculated onto two cultivars of Medicago sativa. Variant R2 from the FD culture was ineffective on both cultivars. Genomic DNA fingerprinting with insertion elements ISRm3 and ISRm2011-2 suggested that transposition of these elements was not a cause of variation, but a DNA band was absent in the profiles of two out of three W2-like colonies. Protein profile comparisons showed high similarity (r = 0.98) between the colony types when grown in YM broth. When grown on Tryptone-Yeast extract medium, variants from the FD and agar-maintained cultures formed separate clusters with r = 0.79. Polymerase chain reaction fingerprinting using repetitive, site-directed and arbitrary primers failed to differentiate the variants. The results emphasize the need to monitor culture variability to maintain the quality of legume inoculants.
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Affiliation(s)
- J F Bloem
- ARC-Plant Protection Research Institute, Private Bag X 134, Pretoria 0001, Republic of South Africa
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13
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Muñoz E, Villadas PJ, Toro N. Ectopic transposition of a group II intron in natural bacterial populations. Mol Microbiol 2001; 41:645-52. [PMID: 11532132 DOI: 10.1046/j.1365-2958.2001.02540.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Self-splicing group II introns are thought to be the evolutionary progenitors of eukaryotic spliceosomal introns. The invasion of novel (ectopic) sites by group II introns is considered to be a key mechanism by which spliceosomal introns may have become widely dispersed. However, the dynamics of these events in populations are unknown. In bacteria, only two group II introns have been shown to splice and to be mobile in vivo. One of these introns, RmInt1 from Sinorhizobium meliloti, which encodes a protein with no endonuclease domain, has been shown to invade the ectopic oxi1 site independently of recombinase. In this study, we analysed ectopic transposition of the RmInt1 intron in a natural population of S. meliloti. We characterized S. meliloti isolates by polymerase chain reaction amplification of a gene, dapB, which is found only on the pRmeGR4b plasmid diagnostic of GR4-type strains. The diversity within this specific field population of bacteria was analysed by restriction fragment length polymorphism using ISRm2011-2 (homing site of RmInt1) and RmInt1 as probes. We found that ectopic transposition of RmInt1 to the oxi1 site occurred in this natural bacterial population. This ectopic transposition was also the most frequent genetic event observed. This work provides further evidence that the ectopic transposition of group II introns is an important mechanism for their spread in natural bacterial populations.
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Affiliation(s)
- E Muñoz
- Grupo de Ecología Genética, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Calle Profesor Albareda 1, 18008 Granada, Spain
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14
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Martínez-Abarca F, Toro N. RecA-independent ectopic transposition in vivo of a bacterial group II intron. Nucleic Acids Res 2000; 28:4397-402. [PMID: 11058141 PMCID: PMC113133 DOI: 10.1093/nar/28.21.4397] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
RmInt1 is a group II intron of Sinorhizobium meliloti which was initially found within the insertion sequence ISRm2011-2. Although the RmInt1 intron-encoded protein lacks a recognizable endonuclease domain, it is able to mediate insertion of RmInt1 at an intron-specific location in intronless ISRm2011-2 recipient DNA, a phenomenon termed homing. Here we have characterized three additional insertion sites of RmInt1 in the genome of S.meliloti. Two of these sites are within IS elements closely related to ISRm2011-2, which appear to form a characteristic group within the IS630-Tc1 family. The third site is in the oxi1 gene, which encodes a putative oxide reductase. The newly identified integration sites contain conserved intron-binding site (IBS1 and IBS2) and delta' sequences (14 bp). The RNA of the intron-containing oxi1 gene is able to splice and the oxi1 site is a DNA target for RmInt1 transposition in vivo. Ectopic transposition of RmInt1 into the oxi1 gene occurs at 20-fold lower efficiency than into the homing site (ISRm2011-2) and is independent of the major RecA recombination pathway. The possibility that transposition of RmInt1 to the oxi1 site occurs by reverse splicing into DNA is discussed.
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Affiliation(s)
- F Martínez-Abarca
- Grupo de Ecología Genética, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Profesor Albareda 1, 18008 Granada, Spain
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15
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Barloy-Hubler F, Capela D, Barnett MJ, Kalman S, Federspiel NA, Long SR, Galibert F. High-resolution physical map of the Sinorhizobium meliloti 1021 pSyma megaplasmid. J Bacteriol 2000; 182:1185-9. [PMID: 10648551 PMCID: PMC94401 DOI: 10.1128/jb.182.4.1185-1189.2000] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To facilitate sequencing of the Sinorhizobium meliloti 1021 pSyma megaplasmid, a high-resolution map was constructed by ordering 113 overlapping bacterial artificial chromosome clones with 192 markers. The 157 anonymous sequence tagged site markers (81,072 bases) reveal hypothetical functions encoded by the replicon.
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Affiliation(s)
- F Barloy-Hubler
- Laboratoire de Recombinaisons Génétiques UPR41-CNRS, Faculté de Médecine, F-35043 Rennes Cedex, France
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16
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Biondi EG, Fancelli S, Bazzicalupo M. ISRm10: a new insertion sequence of Sinorhizobium meliloti: nucleotide sequence and geographic distribution. FEMS Microbiol Lett 1999; 181:171-6. [PMID: 10564804 DOI: 10.1111/j.1574-6968.1999.tb08841.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
In this study the description of a new insertion sequence of Sinorhizobium meliloti, ISRm10, is reported. ISRm10 was found in the intergenic region between nodJ and nodQ of a natural isolated strain. ISRm10 was 1047 bp long and showed the typical features of the ISs belonging to the IS630-Tc1/IS3 superfamily. In particular the ISRm10 nucleotide sequence showed the highest homology (62%) with a Sphingomonas aromaticivorans IS. ISRm10 was present in 32% of the analyzed S. meliloti strains while it was not found in the reference strains of other Rhizobium species.
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Affiliation(s)
- E G Biondi
- Dipartimento di Biologia Animale e Genetica, Università di Firenze, Via Romana 19, I-50125, Florence, Italy
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Capela D, Barloy-Hubler F, Gatius MT, Gouzy J, Galibert F. A high-density physical map of Sinorhizobium meliloti 1021 chromosome derived from bacterial artificial chromosome library. Proc Natl Acad Sci U S A 1999; 96:9357-62. [PMID: 10430947 PMCID: PMC17787 DOI: 10.1073/pnas.96.16.9357] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/1999] [Accepted: 05/27/1999] [Indexed: 11/18/2022] Open
Abstract
As part of the European Sinorhizobium meliloti (strain 1021) chromosome sequencing project, four genomic bacterial artificial chromosome (BAC) libraries have been constructed, one of which was mainly used for chromosome mapping. This library consists of 1,824 clones with an average insert size of 80 kilobases and represents approximately 20-fold total genome coverage [6.8 megabases (Mbs)]. PCR screening of 384 BAC clones with 447 chromosomal markers (PCR primer pairs), consisting of 73 markers representing 118 genes (40 individual genes and 78 genes clustered in 23 operons), two markers from the rrn operon (three loci), four markers from insertion sequences (approximately 16 loci) and 368 sequence-tagged sites allowed the identification of 252 chromosomal BAC clones and the construction of a high-density physical map of the whole 3.7-Mb chromosome of S. meliloti. An average of 5.5 overlapping and colinear BAC clones per marker, correlated with a low rate of deleted or rearranged clones (0.8%) indicate a solid BAC contigation and a correct mapping. Systematic BLASTX analysis of sequence-tagged site marker sequences allowed prediction of a biological function for a number of putative ORFs. Results are available at. This map, whose resolution averages one marker every 9 kilobases, should provide a valuable tool for further sequencing, functional analysis, and positional cloning.
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Affiliation(s)
- D Capela
- Laboratoire Recombinaisons Génétiques, Centre National de la Recherche Scientifique-UPR41, 2 Avenue du Pr Léon Bernard, 35043 Rennes Cedex, France
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Romine MF, Stillwell LC, Wong KK, Thurston SJ, Sisk EC, Sensen C, Gaasterland T, Fredrickson JK, Saffer JD. Complete sequence of a 184-kilobase catabolic plasmid from Sphingomonas aromaticivorans F199. J Bacteriol 1999; 181:1585-602. [PMID: 10049392 PMCID: PMC93550 DOI: 10.1128/jb.181.5.1585-1602.1999] [Citation(s) in RCA: 238] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The complete 184,457-bp sequence of the aromatic catabolic plasmid, pNL1, from Sphingomonas aromaticivorans F199 has been determined. A total of 186 open reading frames (ORFs) are predicted to encode proteins, of which 79 are likely directly associated with catabolism or transport of aromatic compounds. Genes that encode enzymes associated with the degradation of biphenyl, naphthalene, m-xylene, and p-cresol are predicted to be distributed among 15 gene clusters. The unusual coclustering of genes associated with different pathways appears to have evolved in response to similarities in biochemical mechanisms required for the degradation of intermediates in different pathways. A putative efflux pump and several hypothetical membrane-associated proteins were identified and predicted to be involved in the transport of aromatic compounds and/or intermediates in catabolism across the cell wall. Several genes associated with integration and recombination, including two group II intron-associated maturases, were identified in the replication region, suggesting that pNL1 is able to undergo integration and excision events with the chromosome and/or other portions of the plasmid. Conjugative transfer of pNL1 to another Sphingomonas sp. was demonstrated, and genes associated with this function were found in two large clusters. Approximately one-third of the ORFs (59 of them) have no obvious homology to known genes.
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Affiliation(s)
- M F Romine
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA.
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Segundo E, Martinez-Abarca F, Dillewijn P, Fernández-López M, Lagares A, Martinez-Drets G, Niehaus K, Pühler A, Toro N. Characterisation of symbiotically efficient alfalfa-nodulating rhizobia isolated from acid soils of Argentina and Uruguay. FEMS Microbiol Ecol 1999. [DOI: 10.1111/j.1574-6941.1999.tb00572.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Martínez-Abarca F, Zekri S, Toro N. Characterization and splicing in vivo of a Sinorhizobium meliloti group II intron associated with particular insertion sequences of the IS630-Tc1/IS3 retroposon superfamily. Mol Microbiol 1998; 28:1295-306. [PMID: 9680217 DOI: 10.1046/j.1365-2958.1998.00894.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
By sequence analysis of Sinorhizobium meliloti strain GR4 plasmid pRmeGR4b, we have identified a group II intron named RmInt1 inserted within the insertion sequence ISRm2011-2 of the IS630-Tc1/IS3 retroposon superfamily. Like some other group II introns, RmInt1 possesses, in addition to the structurally conserved ribozyme core, an open reading frame (ORF) with homology to reverse transcriptases. Using a T7 expression system in Escherichia coli, we show that the intron is active in splicing in vivo and that splicing efficiency requires the intron-encoded ORF, which suggests that the putative intron encoded protein has a maturase function. DNA hybridization studies indicate that intron RmInt1 is widespread within S. meliloti native populations and appears to be mostly located within this IS element. Nevertheless, some S. meliloti strains harbour one copy of RmInt1 at a different location. DNA sequence analysis of the 5' exon of one of these heterologous intron insertion sites revealed the presence of a putative IS element closely related to insertion sequence ISRm2011-2. The intron-binding sites (IBS1 and IBS2 motifs) are conserved, although a transition of a G-->A in the IBS1 has occurred. Our results demonstrate an association of intron RmInt1 with particular insertion sequences of the IS630-Tc1/IS3 retroposon superfamily that may have ensured the spread and maintenance of this group II intron in S. meliloti.
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Affiliation(s)
- F Martínez-Abarca
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
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Villadas PJ, Burgos P, RodrıÌguez-Navarro DN, Temprano F, Toro N. Characterization of rhizobia homologues of Sinorhizobium meliloti insertion sequences ISRm3 and ISRm4. FEMS Microbiol Ecol 1998. [DOI: 10.1111/j.1574-6941.1998.tb00485.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Zekri S, Soto MJ, Toro N. ISRm4-1 and ISRm9, two novel insertion sequences from Sinorhizobium meliloti. Gene X 1998; 207:93-6. [PMID: 9511748 DOI: 10.1016/s0378-1119(97)00625-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Two novel insertion sequences, ISRm4-1 and ISRm9 have been identified in Sinorhizobium meliloti. ISRm4-1 is 936-bp in length, flanked by 17-bp putative terminal inverted repeats and a putative target duplication of 3-bp. ISRm4-1 is a member of the IS5 family of insertion sequences, closely related to ISRm4. ISRm9 is 2797-bp in length and carries 25-bp inverted repeats with target duplication of 7-bp: ISRm9 belongs to the IS21 family of insertion elements. On the non-pSym plasmid pRmeGR4b from S. meliloti strain GR4, a copy of ISRm4-1 is interrupted at nucleotide 150 from its 5'-end by a copy of ISRm9. Whereas ISRm4-like elements are widespread in S. meliloti, the distribution of ISRm9 appears to be correlated to that of pRmeGR4b-type plasmids.
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Affiliation(s)
- S Zekri
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Consejo Superior de Investigaciones Científicas, Granada, Spain
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Vinardell JM, Ollero FJ, Krishnan HB, del Rosario Espuny M, Villalobo E, Pueppke SG, Ruiz-Sainz JE. ISRf1, a transposable insertion sequence from Sinorhizobium fredii. Gene 1997; 204:63-9. [PMID: 9434166 DOI: 10.1016/s0378-1119(97)00523-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Sinorhizobium fredii strain HH103, a nitrogen-fixing bacterial symbiont of plants, contains an insertion sequence (IS) that can transpose into plasmid pMUS248 and activate a promoterless TcR gene that is normally not expressed. We have cloned and characterized this element, which we designate ISRf1. The IS is 1002 bp in length, contains a single 513-bp open reading frame (ORF), is flanked by imperfect 36-bp terminal inverted repeats, and creates 5-bp target duplications. Two copies of ISRf1 are present in the genome of HH103, but it is absent from 12 other Sinorhizobium and Rhizobium strains. The element transposes at a frequency of 2.7 x 10(-6) per generation per cell.
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Affiliation(s)
- J M Vinardell
- Departamento de Microbiología, Facultad de Biología , Universidad de Sevilla, Spain
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Cassier-Chauvat C, Poncelet M, Chauvat F. Three insertion sequences from the cyanobacterium Synechocystis PCC6803 support the occurrence of horizontal DNA transfer among bacteria. Gene 1997; 195:257-66. [PMID: 9305771 DOI: 10.1016/s0378-1119(97)00165-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Three insertion sequences were characterized from the widely-used cyanobacterium Synechocystis PCC6803. They all harbored a putative transposase sequence flanked by two imperfect inverted repeats, seemed to have duplicated their target insertion site and occurred as multiple copies in the host genome. They exhibited no obvious homology with any other cyanobacterial ISs and were termed IS5S (871 bp), IS4S (1299 bp) and ISS1987 (949 bp) because they were, respectively, homologous to IS5- and IS4-bacterial elements, and to several members of the IS630-Tc1-mariner superfamily of IS elements occurring in a wide range of hosts. This suggests that these IS-elements were spread through horizontal transfer between evolutionary distant organisms. Three IS5S-copies were isolated as a rescue insertion into a replicating plasmid (IS5Sa), or subsequently cloned from a Synechocystis DNA-library probed with IS5Sa (IS5Sb and IS5Sc), and appeared to be almost identical. In the vicinity of IS5Sb, we found the ISS1987 element inserted into the IS4S element. This indicates that the ISS1987 element has been, and could still be, mobile since its transposase sequence is not interrupted with stop codons or translational frameshifts, unlike that which is found in most members of the IS630-Tc1-mariner superfamily of transposable elements.
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MESH Headings
- Amino Acid Sequence
- Base Sequence
- Cloning, Molecular
- Codon, Terminator
- Cyanobacteria/genetics
- DNA Probes
- DNA Transposable Elements/genetics
- DNA, Bacterial/genetics
- Frameshifting, Ribosomal
- Gene Transfer, Horizontal
- Genome, Bacterial
- Molecular Sequence Data
- Mutagenesis, Insertional
- Nucleic Acid Hybridization
- Phylogeny
- Plasmids
- Repetitive Sequences, Nucleic Acid
- Sequence Alignment
- Sequence Homology, Amino Acid
- Sequence Homology, Nucleic Acid
- Transposases/genetics
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Affiliation(s)
- C Cassier-Chauvat
- Service de Biochimie et Génétique Moléculaire, CEA Saclay, URA 2096 CNRS, Gif sur Yvette, France.
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Villadas PJ, Burgos P, Jording D, Selbitschka W, Pühler A, Toro N. Comparative analysis of the genetic structure of a Rhizobium meliloti field population before and after environmental release of the highly competitive R. meliloti strain GR4. FEMS Microbiol Ecol 1996. [DOI: 10.1111/j.1574-6941.1996.tb00331.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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