Reiteration of nitrogen fixation gene sequences in Rhizobium phaseoli

Quinto, Carmen; Vega, Humberto de la; Flores, Margarita Avilés; Fernández, Leonor; Ballado, Teresa; Soberón, Gloria; Palacios, Rafael

doi:10.1038/299724a0

Cited by 156 publications

(75 citation statements)

References 18 publications

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“…Reiteration of nitrogenase structural genes and other genomic regions is a common feature not only in R. phaseoli strains (9,22,23,33,34) but also in other Rhizobium species (3,9,13,14,16,18,28,32,35,42). Therefore, we believe that rearrangements similar to these may occur in other Rhizobium strains.…”

Section: Discussionmentioning

confidence: 95%

“…2b). A third nifH gene (nif region c) (33,34) as well as sequences hybridizing with nodB-, nodC-, nodD-, and nifA-specific gene probes is located within this region. The orientation of nif region c is inverse to that of the other two nif regions (lla).…”

Section: Resultsmentioning

confidence: 99%

“…The complete physical map of this 390-kb plasmid as well as the localization of some nodulation and nitrogen fixation gene sequences has been determined recently in our laboratory (lla). This plasmid contains two nifHDK operons (nif region a and nif region b) (33,34) in direct orientation, separated by 120 kb (Fig. 2b).…”

Section: Resultsmentioning

confidence: 99%

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Amplification and deletion of a nod-nif region in the symbiotic plasmid of Rhizobium phaseoli

et al. 1991

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One remarkable characteristic of the genomes of some Rhizobium species is the frequent occurrence of rearrangements. In some instances these rearrangements alter the symbiotic properties of the strains. However, no detailed molecular mechanisms have been proposed for the generation of these rearrangements. To understand the mechanisms involved in the formation of rearrangements in the genome of Rhizobium phaseoli, we have designed a system which allows the positive selection for amplification and deletion events. We have applied this system to investigate the stability of the symbiotic plasmid of R. phaseoli. High-frequency amplification events were detected which increase the copy number of a 120-kb region carrying nodulation and nitrogen fixation genes two to eight times. Deletion events that affect the same region were also found, albeit at a lower frequency. Both kinds of rearrangements are generated by recombination between reiterated nitrogenase (nifHDK) operons flanking the 120-kb region.Rhizobium spp. are gram-negative soil bacteria studied primarily for their ability to establish nitrogen-fixing symbioses with leguminous plants. Intensive genetic analysis during the past decade has led to the identification of genes essential for the nodulation (nod genes) and nitrogen fixation (nif and fix genes) processes. In all the fast-growing Rhizobium species, these genes are carried on large plasmids, the so-called Sym plasmids or pSym (20,24).One interesting characteristic of the Rhizobium genome is the presence of a large number of reiterated DNA sequences. For Rhizobium phaseoli, the symbiont of the common bean (Phaseolus vulgaris L.), we have estimated the presence of about 700 reiterated elements, belonging to 200 different families (9). This high degree of reiteration is not restricted to R. phaseoli; other members of the Rhizobiaceae family, including the closely related bacteria Agrobacterium tumefaciens, possess a large amount of reiterated DNA (9, 24). For other organisms, it has been shown that recombination between pairs of repeated elements may lead to different kinds of genomic rearrangements, including additions, amplifications, deletions, and inversions (2, 31).Frequent genomic rearrangements (in the range of 10-2 to 10-3) have been commonly observed in different Rhizobium species, including Bradyrhizobium japonicum, Rhizobium trifolii, and R. phaseoli. These rearrangements, which are frequently deletions, may affect the symbiotic properties of the strain, either for nodulation or for nitrogen fixation (4,7,10,14,18,39,44). Unfortunately, the mechanisms involved in the generation of genetic instability in these species have been poorly analyzed.In order to understand the mechanisms involved in the genetic instability of R. phaseoli, we have developed an experimental approach for the general selection of genomic rearrangements. This system allows the positive selection of different kinds of rearrangements, including amplifications, deletions, insertions, and loss of plasmids. We have used this sys...

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Section: Discussionmentioning

confidence: 95%

Section: Resultsmentioning

confidence: 99%

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Amplification and deletion of a nod-nif region in the symbiotic plasmid of Rhizobium phaseoli

et al. 1991

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“…Usually, the genes involved in nodulation and nitrogen fixation processes are located on a single large plasmid. This plasmid is referred to as the symbiotic plasmid (pSym) (22,34,46).A general characteristic of the Rhizobium genome is the presence of a large number of reiterated DNA sequences (15,31,40). It has been established that genomic rearrangements in Rhizobium leguminosarum bv.…”

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confidence: 99%

Structural complexity of the symbiotic plasmid of Rhizobium leguminosarum bv. phaseoli

et al. 1991

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The complete physical map of the symbiotic plasmid of Rhizobium leguminosarum bv. phaseoli strain CFN42 was established. The data support the concept that Rhizobium symbiotic genes are part of a complex genomic structure which contains a large amount of reiterated DNA sequences. This plasmid is a circular structure of 390 kb with approximately 10 families of internally reiterated DNA sequences of two to three elements each. One family includes two directly oriented nitrogenase operons situated 120 kb apart. We also found several stretches of pSym that are reiterated in other replicons of the cell. Localization of symbiotic gene sequences by heterologous hybridization revealed that nodABC sequences are separated in two regions, each of which contains a nod boxlike element, and it also suggested the presence of two copies of the nifA and nodD gene sequences. We propose that the complex structure of the symbiotic plasmid allows interactions between repeated DNA sequences which, in turn, might result in frequent rearrangements.Bacteria of the genus Rhizobium interact with the roots of leguminous plants to develop a highly specialized structure, the nitrogen-fixing nodule. Many genetic determinants of the symbionts are responsible for this differentiation process. The Rhizobium genome is organized in two different types of replicons, the chromosome and large plasmids. Usually, the genes involved in nodulation and nitrogen fixation processes are located on a single large plasmid. This plasmid is referred to as the symbiotic plasmid (pSym) (22,34,46).A general characteristic of the Rhizobium genome is the presence of a large number of reiterated DNA sequences (15,31,40). It has been established that genomic rearrangements in Rhizobium leguminosarum bv. phaseoli, the symbiont of the common bean plant, Phaseolus vulgaris, occur at high frequency (16,31). DNA rearrangements caused by recombination between repeated sequences might participate in the generation of genomic diversity.Establishment of the physical structure of the Rhizobium genome, in particular, the locations and orientations of reiterated DNA sequences, is of primary importance in elucidating the molecular mechanisms involved in genomic dynamics.As a model structure, we selected pSym of R. leguminosarum bv. phaseoli. Several physical maps of symbiotic regions of different Rhizobium species have been published, including large portions of the R. meliloti and Sinorhizobium fredii symbiotic plasmids (25, 32), as well as the complete physical map of the 240-kb pSym of an R. leguminosarum bv. viciae strain (38). A genetic map of R. meliloti megaplasmid pRmeSU47b has also been reported recently (8). In such studies, emphasis has been put on localization of specific genes and regulatory sequences. The studies reported here were focussed on the underlying structural complexity of pSym with respect to the presence of reiterated DNA Tn5-Mob element and its insertion site are also shown.

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“…leguminosarum biovar phaseoZi are reiterated (Quinto et al, 1982) and the nucleotide sequences of the three copies of the nitrogenase reductase gene (nijH) that are e n d e d by the Sym plasmid are identical (Quinto et aZ., 1985). The involvement of these reiterated sequences in the genetic rearrangements described has not been established.…”

Section: Introductionmentioning

confidence: 99%

Symbiotic Plasmid Rearrangement in a Hyper-recombinant Mutant of Rhizobium leguminosarum biovar phaseoli

Soberón-Chávez

NáJERA

1989

Microbiology

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The symbiotic plasmid of Rhizobium leguminosarum biovar phaseoli strain CFN23 has been previously shown to undergo a series of genetic rearrangements that modify the bacterial symbiotic phenotype. A hyper-recombinant derivative of strain CFN23 was isolated. This derivative (strain CFN2300) has a similar phenotype to that reported for Escherichia coli mutants defective in DNA metabolism. The frequency of CFN23 symbiotic plasmid deletion is increased in the CFN2300 background, suggesting that homologous genetic recombination is involved in the generation of this genetic rearrangement.

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Reiteration of nitrogen fixation gene sequences in Rhizobium phaseoli

Cited by 156 publications

References 18 publications

Amplification and deletion of a nod-nif region in the symbiotic plasmid of Rhizobium phaseoli

Amplification and deletion of a nod-nif region in the symbiotic plasmid of Rhizobium phaseoli

Structural complexity of the symbiotic plasmid of Rhizobium leguminosarum bv. phaseoli

Symbiotic Plasmid Rearrangement in a Hyper-recombinant Mutant of Rhizobium leguminosarum biovar phaseoli

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