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At least 19 recordsLinked to original sources

PubMed1998

Sequences around the fragmentation sites of the large subunit ribosomal RNA in the family Rhizobiaceae. 23S-like rRNAs in Rhizobiaceae.

We demonstrated that the representatives of the family Rhizobiaceae possess, instead of one single 23S rRNA molecule, three different sets of 23S-like rRNA fragments with sizes of about: 135 b and 2.6 kb (set 1); 135 b, 400 b, and 2.2 kb (set 2); 135 b and two molecules of about 1.3 kb (set 3). In two of the fragmentations, intervening sequences--IVS I and IVS II--are involved. The IVS I is connected to a cleavage of the 23S rRNA primary transcript into two modules (135 b and 2.6 kb large). The IVS II is located at position 543 of the gene, and it leads to an additional processing of the 2.6 kb rRNA species into two molecules with sizes of about 400 b and 2.2 kb. In contrast to the IVS I, which is a common feature of all rhizobia, the IVS II is present in a limited number of strains only. The primary and secondary structures of the regions of the unmatured 23S rRNA transcript possessing IVS I (helix 9) and IVS II (helix 25) were analysed. On the basis of our analyses we propose secondary structure models of the parts of the matured 23S rRNA-like molecules of rhizobia corresponding to the helices 9 and 25. The third fragmentation of the rhizobial 23S rRNA represents a break in the central part of the 2.6 kb-large rRNA and it leads to an occurrence of two fragments with approximately equal size of about 1.3 kb. We have demonstrated that the central fragmentation is not connected to the presence of IVSs but probably to a minor change in the nucleotide sequence in the central part of the 2.6 rRNA.

Base Sequence↗

PubMed1989

Purification and partial characterization of the Rhizobium leguminosarum biovar viciae Ca2+-dependent adhesin, which mediates the first step in attachment of cells of the family Rhizobiaceae to plant root hair tips.

The Ca2+-dependent adhesin which mediates the first step in attachment of bacteria of the family Rhizobiaceae to plant root hair tips was isolated from the surface of Rhizobium leguminosarum biovar viciae cells; its ability to inhibit attachment of R. leguminosarum to pea root hair tips was used as a bioassay. Isolated adhesin was found to be able to inhibit attachment of both carbon-limited and manganese-limited R. leguminosarum cells. A multicolumn purification procedure was developed which resulted in pure adhesin, as judged from silver staining of isoelectric focusing and sodium dodecyl sulfate-polyacrylamide gel electropherograms. The crucial step in purification was the elution of rhizobial proteins by a CaCl2 gradient from a hydroxyapatite matrix. The specific activity increased 1,250 times during purification. The isoelectric point of the adhesin was determined to be 5.1, and the molecular mass was 14 kilodaltons (kDa), as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. By using gel filtration in the presence and absence of Ca2+, the molecular mass of the adhesin was determined to be 15 and 6 kDa, respectively. The adhesin appeared to be a calcium-binding protein. The purified adhesin inhibited attachment of various other rhizobia to pea root hair tips. Also, cell surface preparations of several other rhizobial strains, including Agrobacterium, Bradyrhizobium, and Phyllobacterium spp., showed adhesin activity, suggesting that a common plant receptor is used for attachment of Rhizobiaceae cells and that the adhesin is common among Rhizobiaceae. No attachment-inhibiting activity was detected in cell surface preparations from various other bacterial strains tested. Cell surface preparations from Sym or Ti plasmid-cured Rhizobium and Agrobacterium strains, respectively, also showed adhesin activity, indicating that Sym or Ti plasmid-borne genes are not required for the synthesis and biogenesis of the adhesin. The adhesin was also found to be involved in the attachment of rhizobia to the root hairs of various other legumes and nonlegume plants, including monocotyledonous ones. Since the adhesin appears to be specific for Rhizobiaceae and is Ca2+ dependent, we propose to designate it rhicadhesin. A more detailed model for rhizobial attachment to plant root hairs is discussed.

Adhesins, Bacterial↗

PubMed1984

Comparative study of the DNA-binding HU-type proteins from slow growing and fast growing strains of Rhizobiaceae.

The DNA-binding HU-type proteins have been isolated from two very different strains of Rhizobiaceae : Agrobacterium tumefaciens and Rhizobium japonicum. These proteins have been called HAt and HRj respectively. Their electrophoretic mobility on polyacrylamide gel, amino acid composition and crossed immunoreactivity have been compared to that of the homologous protein isolated from Rhizobium meliloti: the protein HRm . The proteins HAt and HRm show close similarities whereas the protein HRj differs markedly from the two others. The physico-chemical characteristics of the HU-type proteins from these Rhizobiaceae are in good agreement with the respective position of these bacteria in the taxonomy.

Amino Acids↗

PubMed1993

Phylogenetic analysis of the family Rhizobiaceae and related bacteria by sequencing of 16S rRNA gene using PCR and DNA sequencer.

The 16S rRNA gene sequences of 19 strains covering 97% of the molecules were determined for the members of the family Rhizobiaceae and related bacteria by PCR and DNA sequencer. The three biovars of Agrobacterium were located separately, whereas Agrobacterium rubi clustered with A. tumefaciens. Phylogenetic locations for the species of the genera Rhizobium, Sinorhizobium, Agrobacterium, Phylobacterium, Mycoplana (M. dimorpha), Ochrobactrum, Brucella and Rochalimaea (a rickettsia) were intermingled with each other with the similarity values higher than 92%. The family Rhizobiaceae should be redefined including the above-mentioned genera despite the ability for plant association and nitrogen fixation. Bradyrhizobium japonicum and Mycoplana bullata were far remote from the other species and should be excluded from this family.

Base Sequence↗

PubMed1998

Analysis of stable low-molecular-weight RNA profiles of members of the family Rhizobiaceae.

Staircase electrophoresis in polyacrylamide gels was used to analyze the stable low-molecular-weight (LMW) RNA profiles of 24 type strains belonging to the family Rhizobiaceae. This new electrophoretic technique results in good separation of the molecules forming the LMW RNA profiles. Differences in the number and distribution of the RNA bands in these profiles allowed us to identify differences among the 24 strains assayed. Species assignments based on LMW RNAs proved to be consistent with the established taxonomic classification. Analysis of the data obtained and the corresponding dendrograms revealed relationships between genera and species; these relationships were essentially the same as those obtained with other techniques, such as DNA hybridization and 16S rRNA sequencing. Use of the technique described here, with which it is possible to analyze a large number of strains in a short time, permits rapid identification of species belonging to the family Rhizobiaceae and should in the future facilitate biodiversity studies and detection of new species.

Bacterial Typing Techniques↗

PubMed1991

The genomes of the family Rhizobiaceae: size, stability, and rarely cutting restriction endonucleases.

The lack of high-resolution genetic or physical maps for the family Rhizobiaceae limits our understanding of this agronomically important bacterial family. On the basis of statistical analyses of DNA sequences of the Rhizobiaceae and direct evaluation by pulsed-field agarose gel electrophoresis (PFE), five restriction endonucleases with AT-rich target sites were identified as the most rarely cutting: AseI (5'-ATTAAT-3'), DraI (5'-TTTAAA-3'), SpeI (5'-ACTAGT-3'), SspI (5'-AATAAT-3'), and XbaI (5'-TCTAGA-3'). We computed the sizes of the genomes of Bradyrhizobium japonicum USDA 424 and Rhizobium meliloti 1021 by adding the sizes of DNA fragments generated by SpeI digests. The genome sizes of R. meliloti 1021 and B. japonicum USDA 424 were 5,379 +/- 282.5 kb and 6,195 +/- 192.4 kb, respectively. We also compared the organization of the genomes of free-living and bacteroid forms of B. japonicum. No differences between the PFE-resolved genomic fingerprints of free-living and mature (35 days after inoculation) bacteroids of B. japonicum USDA 123 and USDA 122 were observed. Also, B. japonicum USDA 123 genomic fingerprints were unchanged after passage through nodules and after maintenance on a rich growth medium for 100 generations. We conclude that large-scale DNA rearrangements are not seen in mature bacteroids or during free-living growth on rich growth media under laboratory conditions.

Base Sequence↗

PubMed1994

Cyclic beta-glucans of members of the family Rhizobiaceae.

Cyclic beta-glucans are low-molecular-weight cell surface carbohydrates that are found almost exclusively in bacteria of the Rhizobiaceae family. These glucans are major cellular constituents, and under certain culture conditions their levels may reach up to 20% of the total cellular dry weight. In Agrobacterium and Rhizobium species, these molecules contain between 17 and 40 glucose residues linked solely by beta-(1,2) glycosidic bonds. In Bradyrhizobium species, the cyclic beta-glucans are smaller (10 to 13 glucose residues) and contain glucose linked by both beta-(1,6) and beta-(1,3) glycosidic bonds. In some rhizobial strains, the cyclic beta-glucans are unsubstituted, whereas in other rhizobia these molecules may become highly substituted with moieties such as sn-1-phosphoglycerol. To date, two genetic loci specifically associated with cyclic beta-glucan biosynthesis have been identified in Rhizobium (ndvA and ndvB) and Agrobacterium (chvA and chvB) species. Mutants with mutations at these loci have been shown to be impaired in their ability to grow in hypoosmotic media, have numerous alterations in their cell surface properties, and are also impaired in their ability to infect plants. The present review will examine the structure and occurrence of the cyclic beta-glucans in a variety of species of the Rhizobiaceae. The possible functions of these unique molecules in the free-living bacteria as well as during plant infection will be discussed.

ATP-Binding Cassette Transporters↗

PubMedDate not supplied

[Lipopolysaccharides of rhizobiaceae: structure and biosynthesis].

The lipopolysaccharides (LPS) are major components of the outer membrane of Gram negative bacteria and, because of their location, are important mediators in the interaction between these bacteria and their environment and other organisms. The alpha-Proteobacterial family Rhizobiaceae includes the rhizobia and agrobacteria, microorganisms which establish symbiotic or parasitic relationships with plants. Mutants deficient in LPS biosynthesis show anomalous interactions with their hosts. The agronomical relevance of the relationship between rhizobia and agrobacteria with plants has promoted a large number of studies on the LPS from these bacteria. The complete structures of one or several domains of LPS from Rhizobiaceae have been determined in the last years. Additionally, several metabolic steps in the biosynthesis of these molecules have been elucidated. This review aims at the description of the more recent findings on the structure and biosynthesis of LPS in Rhizobium, Sinorhizobium and Agrobacterium.

Carbohydrate Sequence↗

PubMed1991

Degradation of the Herbicide Glyphosate by Members of the Family Rhizobiaceae.

Several strains of the family Rhizobiaceae were tested for their ability to degrade the phosphonate herbicide glyphosate (isopropylamine salt of N-phosphonomethylglycine). All organisms tested (seven Rhizobium meliloti strains, Rhizobium leguminosarum, Rhizobium galega, Rhizobium trifolii, Agrobacterium rhizogenes, and Agrobacterium tumefaciens) were able to grow on glyphosate as the sole source of phosphorus in the presence of the aromatic amino acids, although growth on glyphosate was not as fast as on P(i). These results suggest that glyphosate degradation ability is widespread in the family Rhizobiaceae. Uptake and metabolism of glyphosate were studied by using R. meliloti 1021. Sarcosine was found to be the immediate breakdown product, indicating that the initial cleavage of glyphosate was at the C-P bond. Therefore, glyphosate breakdown in R. meliloti 1021 is achieved by a C-P lyase activity.

Journal Article↗

PubMed2001

The complete nucleotide sequence of a plant root-inducing (Ri) plasmid indicates its chimeric structure and evolutionary relationship between tumor-inducing (Ti) and symbiotic (Sym) plasmids in Rhizobiaceae.

The Ri (root-inducing) plasmid in Agrobacterium rhizogenes and Ti (tumor-inducing) plasmid in Agrobacterium tumefaciens have provided the fundamental basis for the construction of plant vectors and transgenic plants. Recently, the determination of the first complete nucleotide sequence of the Ti plasmid (pTi-SAKURA) has been successful. To understand the general structure of these oncogenic T-DNA transfer plasmids, the whole nucleotide sequence of a mikimopine-type Ri plasmid, pRi1724, was analyzed. The plasmid is 217,594 bp in size, and has 173 open reading frames (ORFs) in total, which are asymmetrically distributed. Except for 27 ORFs, which are unknown, 173 ORFs were classified into 12 groups as follows: three for DNA replication, nine for plasmid modification, 22 for conjugation, 26 for virulence, 11 for T-DNA gene, 19 for mikimopine/mikimopine-lactam transport, ten for an unknown opine metabolism, seven for transcriptional regulator, five for sugar transport, five for glycerol metabolism, four for chemoreceptor and 32 for others. The elucidated chimeric structure of pRi1724 interestingly indicates that the evolution of Rhizobiaceae plasmids seems to have kept interactions among the plasmids; especially, the genes and elements for a conjugal transfer of pRi1724 had clearly closer kinship to those of a Sym (symbiotic) plasmid, pNGR234a in Rhizobium sp. than those of Ti plasmids. By using sequencing and Northern analysis, we examined the metabolic pathway and gene expression of mikimopine, which is probably an Ri-specific opine.

ATP-Binding Cassette Transporters↗

PubMed2000

Sequence diversity of the plasmid replication gene repC in the Rhizobiaceae.

The repABC operon is essential for stable maintenance of some Rhizobiaceae plasmids and of pTAV320 from Paracoccus versutus. These plasmids are the largest described family of homologous, yet compatible replicons. The repC gene is essential for plasmid replication, and previous work identified four distinct sequence groups (repC1, repC2, repC3, and repC4) that appear to define different compatibility classes. Probes for these different groups were used to characterize plasmids in Rhizobium leguminosarum population studies and three new repC sequence groups, repC5, repC6, and repC7 were identified. The general repC primers were modified to amplify a wider range of repC sequences and repC sequences were identified in Sinorhizobium and Mesorhizobium type strains. We also showed that the repC3 group-specific primers described previously do not amplify all repC3 sequences and developed a new repC3 amplification strategy.

Bacterial Proteins↗

PubMed1990

Isolation of the replication DNA region from a Rhizobium plasmid and examination of its potential as a replicon for Rhizobiaceae cloning vectors.

The DNA region essential for replication and stability of a native plasmid (pTM5) from Rhizobium sp. (Hedysarum) has been identified and isolated within a 5.4-kb PstI restriction fragment. The isolation of this region was accomplished by cloning endonuclease-restricted pTM5 DNA into a ColE1-type replicon and selecting the recombinant plasmids containing the pTM5 replicator (pTM5 derivative plasmids) by their ability to replicate in Rhizobium. DNA homology studies revealed that pTM5-like replicons are present in cryptic plasmids from some Rhizobium sp. (Hedysarum) strains but not in plasmids from strains of other Rhizobium species or Agrobacterium tumefaciens. The pTM5 derivative plasmids were able to replicate in Escherichia coli and A. tumefaciens and in a wide range of Rhizobium species. On the basis of stability assays in the absence of antibiotic selective pressure, the pTM5 derivative plasmids were shown to be highly stable in both free-living and symbiotic cells of Rhizobium sp. (Hedysarum). The stability of these plasmids in other species of Rhizobium and in A. tumefaciens varied depending on the host and on the plasmid. Most pTM5 derivative plasmids tested showed significantly higher symbiotic stability than RK2 derivative plasmids pRK290 and pAL618 in Rhizobium sp. (Hedysarum), R. meliloti, and R. leguminosarum by. phaseoli. Consequently, we consider that the constructed pTM5 derivative plasmids are potentially useful as cloning vectors for Rhizobiaceae.

Cloning, Molecular↗

PubMed1988

Mini-Mulac transposons with broad-host-range origins of conjugal transfer and replication designed for gene regulation studies in Rhizobiaceae.

Novel mini-Mu derivatives were constructed, carrying a truncated lacZYA operon fused to the terminal 117 bp of the Mu S-end, for the isolation of translational lac fusions by mini-Mu-mediated insertion mutagenesis. Different selectable markers (chloramphenicol resistance; gentamycin resistance) were introduced to allow selection for mini-Mu insertions in different replicons and bacterial strains. A mini-Mulac derivative carrying the site for conjugal transfer of plasmid RP4 (oriT) and the origin of replication of the Agrobacterium rhizogenes Ri plasmid (oriRiHRI) was constructed to enable one-step lac-fusion mutagenesis of cloned (plasmid-borne) regions in Escherichia coli and efficient conjugal transfer of gene fusions to to a variety of Gram-negative bacteria. The conjugation frequency, stability and copy number of replicons carrying mini-Mulac derivatives with oriT and oriRiHRI in members of the Rhizobiaceae such as Rhizobium meliloti, Azorhizobium caulinodans ORS571 and Agrobacterium tumefaciens C58 was examined.

Bacteriophage mu↗

PubMed2005

Genes for utilization of deoxyfructosyl glutamine (DFG), an amadori compound, are widely dispersed in the family Rhizobiaceae.

Amadori compounds form spontaneously in decomposing plant material and can be found in the rhizosphere. As such, these compounds could influence microbial populations by serving as sources of carbon, nitrogen and energy to microorganisms expressing suitable catabolic pathways. Two distinct sets of genes for utilization of deoxyfructosyl glutamine (DFG), an Amadori compound, have been identified in isolates of Agrobacterium spp. One, the soc gene set, is encoded by pAtC58, a 543 kb plasmid in A. tumefaciens strain C58. The second, mocD dissimilates DFG formed in the pathway for catabolism of mannopine (MOP) a non-Amadori, imine-type member of the mannityl opine family characteristic of certain Ti and Ri plasmids. To assess the level of dispersal of these two Amadori-utilizing systems, isolates of Agrobacterium spp. and related bacteria in the family Rhizobiaceae were examined by Southern analysis for homologs of socD and mocD. Homologs of mocD were associated only with Ti plasmid-encoded pathways for catabolism of MOP. Homologs of socD were more widely distributed, being detectable in many but not all of the isolates of Agrobacterium, Sinorhizobium, and Rhizobium spp. tested. However, this gene was never associated with the virulence elements, such as the Ti and Ri plasmids, in these strains. Regardless of genus most of the isolates containing socD homologs could utilize DFG as sole source of carbon, nitrogen and energy. Correlation studies suggested that mocD has evolved uniquely as part of the mannityl opine catabolic pathway while socD has evolved for the general utilization of Amadori compounds. Certain isolates of Agrobacterium and Rhizobium that lacked detectable homologs of socD and mocD also could utilize DFG suggesting the existence of additional, unrelated pathways for the catabolism of this Amadori compound. These results suggest that Amadori compounds constitute a source of nutrition that is important to microflora in the rhizosphere.

Biological Evolution↗

PubMed2004

Leech mycetome endosymbionts are a new lineage of alphaproteobacteria related to the Rhizobiaceae.

Mycetomal organs attached to the esophagus of hematophagous leeches which are known to harbor endosymbiotic bacteria were removed from three species in the leech family Glossiphoniidae. Anatomical observations indicated that placobdellid mycetomes are paired and caecate, inserting into the esophagus posterior to the proboscis. Light and electron microscopy demonstrated that there is a single layer of mycetome epithelial cells harboring gram-negative rods and that these epithelial cells are ultrastructurally distinct from neighboring esophageal epithelial cells. Fluorescent in situ hybridization with eubacterial and alphaproteobacterial probes localized the bacteria solely to the mycetomes both in adult and in unfed juvenile leeches whereas a gammaproteobacterial probe did not yield a bound fluorescencent signal. DNA was isolated from these tissues and subjected to PCR amplification using bacteria-specific primers for 16S and 23S rDNA. Results from sequencing the amplification products and phylogenetic analysis with other Alphaproteobacteria revealed that the bacteria resident in these organs comprise a new genus of Alphaproteobacteria, Reichenowia n. gen., closely related to the nitrogen-fixing, nodule-forming Rhizobiaceae. The three bacterial strains, though different from each other were each other's closest relatives, suggesting a history of close coevolution with their leech hosts.

Alphaproteobacteria↗

PubMed2000

The lipid A region of lipopolysaccharides from Rhizobiaceae activates bone marrow granulocytes from lipopolysaccharide-hyporesponsive C3H/HeJ and C57BL/10ScCr mice.

We established in previous studies that the binding of Salmonella lipopolysaccharide (LPS) to constitutive receptors of low affinity triggers the expression of the inducible LPS-binding molecule CD14 in bone marrow cells (BMC) of C3H/HeOU mice, but not in BMC from C3H/HeJ mice. We show in this study that BMC from C3H/HeJ and C57BL/10ScCr mice do not express CD14 after exposure to LPSs from Salmonella enterica and Bordetella pertussis, but do express this marker when treated with several LPSs from Rhizobiaceae, or their lipid A fragments. This shows that the constitutive LPS receptor in BMC from C3H/HeJ and C57BL/10ScCr mice is fully able to trigger a complete signalling cascade. Results of cross-inhibition of the binding of radiolabelled LPS indicated that active LPSs (from R. species Sin-1 and R. galegae) and inactive LPSs (from S. enterica and B. pertussis) bind to the same site of the constitutive LPS receptor of C3H/HeJ cells. Furthermore, binding of R. species Sin-1 LPS, and signalling induced by this LPS, were both inhibited by pre-exposure of C3H/HeJ cells to B. pertussis lipid A. This correlation between binding and signalling suggests that in C3H/HeJ cells, the constitutive receptor, which recognizes a large panel of LPSs from different origins, appears selectively unable to be activated by some particular LPSs, such as those of Enterobacteria and Bordetella.

Animals↗

PubMed2003

Agrobacterium is a definable genus of the family Rhizobiaceae.

Members of the genus Agrobacterium constitute a diverse group of organisms, all of which, when harbouring the appropriate plasmids, are capable of causing neoplastic growths on susceptible host plants. The agrobacteria, which are members of the family Rhizobiaceae, can be differentiated into at least three biovars, corresponding to species divisions based on differential biochemical and physiological tests. Recently, Young et al. [Int J Syst Evol Microbiol 51 (2003), 89-103] proposed to incorporate all members of the genus Agrobacterium into the genus RHIZOBIUM: We present evidence from classical and molecular comparisons that supports the conclusion that the biovar 1 and biovar 3 agrobacteria are sufficiently different from members of the genus Rhizobium to warrant retention of the genus AGROBACTERIUM: The biovar 2 agrobacteria cluster more closely to the genus Rhizobium, but some studies suggest that these isolates differ from species of Rhizobium with respect to their capacity to interact with plants. We conclude that there is little scientific support for the proposal to group the agrobacteria into the genus Rhizobium and consequently recommend retention of the genus AGROBACTERIUM:

Phenotype↗

PubMed1985

Characterization and primary structures of DNA-binding HU-type proteins from Rhizobiaceae.

The DNA-binding HU-type proteins from several species of Rhizobiaceae including Rhizobium meliloti, two strains of Rhizobium leguminosarum with highly different phenotypic characters and Agrobacterium tumefaciens, were characterized and their amino acid sequences were determined. HU-type proteins isolated from R. leguminosarum L18 and A. tumefaciens are identical and show slight differences with the R. meliloti HU-type protein. On the other hand the R. leguminosarum L53 HU-type protein is quite different from the proteins cited above; several amino acid substitutions encountered in this protein result in significant changes in the folding of the polypeptide chain. The biochemical characteristics of these proteins are in good agreement with the respective position of these bacteria in the phylogeny determined by numerical taxonomy.

Amino Acid Sequence↗