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  • 1
    Electronic Resource
    Electronic Resource
    Group II introns in the bacterial world (2000)
    Oxford, UK : Blackwell Publishing Ltd
    Molecular microbiology 38 (2000), S. 0 
    Details
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: Group II introns are large catalytic RNA molecules that act as mobile genetic elements. They were initially identified in the organelle genomes of lower eukaryotes and plants, and it has been suggested that they are the progenitors of nuclear spliceosomal introns. Group II self-splicing introns were shown to be present in bacteria in 1993, since when the various bacterial genome sequencing projects have led to a significant increase in the number of group II intron sequences present in databases. However, few of these introns have been characterized, and most were identified on the basis of their intron-encoded protein (IEP), with little data available concerning their ribozyme/RNA structure. Their frequency in prokaryotes is also unknown. We attempt here to provide a first comprehensive review of bacterial group II introns based on recent genome sequencing data and mechanistic studies.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1046/j.1365-2958.2000.02197.x
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  • 2
    Electronic Resource
    Electronic Resource
    Ectopic transposition of a group II intron in natural bacterial populations (2001)
    Oxford, UK : Blackwell Science Ltd
    Molecular microbiology 41 (2001), S. 0 
    Details
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: 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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1046/j.1365-2958.2001.02540.x
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  • 3
    Electronic Resource
    Electronic Resource
    Characterization and splicing in vivo of a Sinorhizobium meliloti group II intron associated with particular insertion sequences of the IS630-Tc1/IS3 retroposon superfamily (1998)
    Oxford BSL : Blackwell Science Ltd
    Molecular microbiology 28 (1998), S. 0 
    Details
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: 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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1046/j.1365-2958.1998.00894.x
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  • 4
    Electronic Resource
    Electronic Resource
    The Rhizobium meliloti putA gene: its role in the establishment of the symbiotic interaction with alfalfa (1997)
    Oxford BSL : Blackwell Science Ltd
    Molecular microbiology 23 (1997), S. 0 
    Details
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: Little is known about the energy sources used by rhizobia during colonization, invasion and root nodule formation on leguminous plants. We have recently reported that an impaired proline metabolism in Rhizobium meliloti leads to a reduced nodulation efficiency and competitiveness on alfalfa roots. In the present study we have characterized the R. meliloti proline dehydrogenase gene (putA) and addressed the question of its role in symbiosis. This rhizobial gene encodes a 1224-amino-acid-long polypeptide which is homologous to enteric bacteria, Rhodobacter capsulatus and Bradyrhizobium japonicum PutA proteins.Like the situation in these bacteria, sequence analysis identified the proline dehydrogenase (PDH) and pyrroline-5-carboxylate dehydrogenase (P5CDH) domains in the R. meliloti putA-encoded protein. Beta-galactosidase assays performed with free-living cells carrying a putA–lacZ transcriptional fusion revealed that R. meliloti putA gene expression is induced by proline, autoregulated by its encoded product, and independent of the general nitrogen regulatory system (Ntr). In addition, analysis of putA expression during the different steps of the symbiotic interaction with alfalfa showed that expression of this gene is turned on by the root exudates (RE), during root invasion and nodule formation, but not in differentiated nitrogen-fixing bacteroids. Furthermore, we show that the PutA− phenotype leads to a significant reduction of alfalfa root colonization by R. meliloti.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1046/j.1365-2958.1997.1861555.x
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  • 5
    Electronic Resource
    Electronic Resource
    The Sinorhizobium meliloti insertion sequence (IS) elements ISRm102F34-1/ISRm7 and ISRm220-13-5 belong to a new family of insertion sequence elements (1999)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 172 (1999), S. 0 
    Details
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: The Sinorhizobium meliloti insertion sequence (IS) elements ISRm102F34-1 and ISRm220-13-5 are 1481 and 1550 base pairs (bp) in size, respectively. ISRm102F34-1 is bordered by 15 bp imperfect terminal inverted repeat sequences (two mismatches), whereas the terminal inverted repeat of ISRm220-13-5 has a length of 16 bp (two mismatches). Both insertion sequence elements generate a 6-bp target duplication upon transposition. The putative transposase enzymes of ISRm102F34-1 and ISRm220-13-5 consist of 449 or 448 amino acid residues with predicted molecular weights of 50.7 or 51.3 kDa and theoretical isoelectric points of 10.8 or 11.1, respectively. ISRm102F34-1 is identical in 98.9% of its nucleotide sequence to an apparently inactive copy of an insertion sequence element, designated ISRm7, which flanks the left-end of the nodule formation efficiency (nfe) region of plasmid pRmeGR4b of S. meliloti strain GR4. ISRm102F34-1 and ISRm220-13-5 are closely related since they show an overall identity of 57.0% at the nucleotide sequence level and of 47.3% at the deduced amino acid level of their putative transposases. Both insertion sequence elements displayed significant similarity to the Xanthomonas campestris ISXc6 and its homolog IS1478a. Since none of these insertion sequence elements could be allocated to existing families of insertion sequence elements, a new family is proposed. Analysis of the distribution of ISRm102F34-1/ISRm7 in various local S. meliloti populations sampled from Medicago sativa, Medicago sphaerocarpa and Melilotus alba host plants at different locations in Spain revealed its presence in 35% of the isolates with a copy number ranging from 1 to 5. Furthermore, ISRm102F34-1/ISRm7 homologs were identified in other rhizobial species.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6968.1999.tb13441.x
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  • 6
    Electronic Resource
    Electronic Resource
    A new insertion sequence from Sinorhizobium meliloti with homology to IS1357 from Methylobacterium sp. and IS1452 from Acetobacter pasteurianus (1998)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 158 (1998), S. 0 
    Details
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: The insertion sequence ISRm8 was identified by sequence analysis of the cryptic plasmid pRmeGR4b of Sinorhizobium meliloti GR4. ISRm8 is 1451 bp in length and carries 22/24-bp terminal imperfect inverted repeats with seven mismatches and a direct target site duplication of 3 bp. ISRm8 carries a unique open reading frame whose putative protein showed significant similarity to the insertion sequences IS1357 and IS1452, isolated from Methylobacterium sp. and Acetobacter pasteurianus, respectively. Two copies of this IS element were found in strain GR4; one of them is linked to plasmid pRmeGR4b, whereas the other is localized out of the non-pSym plasmids. In S. meliloti field populations ISRm8 shows a limited distribution (50% of the strains tested carry the IS element), with a copy number ranging from 1 to 6.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6968.1998.tb12804.x
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  • 7
    Electronic Resource
    Electronic Resource
    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 (1996)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 21 (1996), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Abstract: Rhizobium meliloti strain GR4, which exhibits a highly competitive ability for alfalfa root nodule occupancy, was used in a field release experiment in Granada, Spain. In order to analyze the ecological impact of the GR4 release, we characterized the R. meliloti indigenous population of the field site by ERIC-(enterobacterial repetitive intergenic consensus) PCR and IS (insertion sequence) fingerprinting. Both fingerprinting methods resulted in the same grouping of the isolates. Data obtained were compared with a previous analysis by plasmid based sequence-specific PCR. Isolates belonging to the major infective group, as defined by dominant plasmid types, were shown to have identical or nearly identical ERIC and IS fingerprint patterns. Hence, we conclude that all three typing methods are suited to characterize the genetic structure of the field population. The possible impact of the introduction of strain GR4 was examined two years after its release in its original environment. No effect on the genetic structure of the indigenous R. meliloti field population was observed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6941.1996.tb00331.x
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  • 8
    Electronic Resource
    Electronic Resource
    Identification of nodule-dominant Rhizobium meliloti strains carrying pRmeGR4b-type plasmid within indigenous soil populations by PCR using primers derived from specific DNA sequences (1995)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 17 (1995), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Abstract: Rhizobium meliloti strain GR4 is a highly infective and competitive bacteria which was isolated in 1975 from a field site in Granada (Spain) and which has a high potential as an inoculant. R. meliloti isolates from alfalfa plants grown in this field site were characterized using polymerase chain reaction. Characterization was based on primers derived from insertion sequence elements (ISRm3 and ISRm4), plasmid origin of replication (pRmeGR4a repC locus) and plasmid pRmeGR4b specific DNA sequences. Soil isolates harbouring plasmid type pRmeGR4b represented the major infective population in this field site. A direct correlation between the presence of pRmeGR4b-like plasmid and the competitiveness of the strains was found. In addition, four different R. meliloti field populations isolated from Spanish soils were analyzed for the presence of pRmeGR4b related plasmids. Our results indicate that this plasmid type is widespread among R. meliloti field populations and that its frequency within the infective isolates depends on the host plant.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6941.1995.tb00139.x
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  • 9
    Electronic Resource
    Electronic Resource
    Characterization of rhizobia homologues of Sinorhizobium meliloti insertion sequences ISRm3 and ISRm4 (1998)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 25 (1998), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Homologues to Sinorhizobium meliloti insertion sequences ISRm3 and ISRm4 were found within Rhizobium leguminosarum bv. viciae field populations. Similarly, homologous sequences to S. meliloti ISRm4 were found in S. fredii strains. Based on the polymerase chain reaction, we cloned and partially sequenced some of these putative insertion sequence elements. DNA sequence comparisons indicate that S. meliloti and R. leguminosarum ISRm3-type elements are closely related whereas the ISRm4 homologues show distinct relationships. In addition, specific primers for PCR recognition of ISRm3 and ISRm4 elements in rhizobia species and S. meliloti ISRm6 were designed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6941.1998.tb00485.x
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  • 10
    Electronic Resource
    Electronic Resource
    Attachment to plant roots and nod gene expression are not affected by pH or calcium in the acid-tolerant alfalfa-nodulating bacteria Rhizobium sp. LPU83 (2004)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 48 (2004), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Soil acidification is one of the environmental factors that more strongly hampers the establishment of an effective symbiotic interaction between rhizobia and leguminous plants. Sinorhizobium meliloti and the acid-tolerant Rhizobium sp. strain LPU83 are able to nodulate alfalfa plants at pH 5.6 but both exhibit a delayed nodulation and a reduction in the number of elicited nodules. We show here that the addition of calcium (Ca) has no positive effect on the nodulation kinetics shown by LPU83 at low pH, but does retrieve the competition capacity of S. meliloti strains in acidic media, likely by improving the ability of these bacteria to attach to plant roots. In contrast, the attachment of the acid-tolerant strain LPU83 to alfalfa roots is not greatly affected by pH or Ca concentration. Media acidification impairs nod gene induction in different S. meliloti strains but not in LPU83. However, the addition of Ca at low pH does not affect neither nod gene expression in alfalfa-nodulating rhizobia (S. meliloti or strain LPU83) nor the quality of nod gene inducers exudated by alfalfa plants, in contrast to what has been reported previously. These data reveal differential features among alfalfa-nodulating rhizobia and point out the adsorption of S. meliloti to alfalfa roots as the major limiting step affecting its symbiotic performance in acidic conditions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1016/j.femsec.2003.12.010
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