Biotin biosynthesis, transport and utilization in rhizobia

Guillén-Navarro, Karina; Encarnación, Sergio; Dunn, Michael F.

doi:10.1016/j.femsle.2005.04.020

Cited by 28 publications

(32 citation statements)

References 48 publications

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“…In MM serial growth, most of the rhizobia, which are biotin auxotrophs, synthesize the polymer PHB and, in doing so, limit growth and determine the capability for nitrogen fixation in symbiosis. Strains of S. meliloti, R. etli, and R. phaseoli are biotin auxotrophs, because several genes of this pathway are lacking, and show growth decline (46,47). The R. phaseoli strain CCGM1 is also a biotin auxotroph that showed similar growth behavior and accumulated PHB.…”

Section: Discussionmentioning

confidence: 99%

Nitrogen-Fixing Rhizobial Strains Isolated from Common Bean Seeds: Phylogeny, Physiology, and Genome Analysis

Mora

Dı́az

Vargas-Lagunas

et al. 2014

Appl Environ Microbiol

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Rhizobial bacteria are commonly found in soil but also establish symbiotic relationships with legumes, inhabiting the root nodules, where they fix nitrogen. Endophytic rhizobia have also been reported in the roots and stems of legumes and other plants. We isolated several rhizobial strains from the nodules of noninoculated bean plants and looked for their provenance in the interiors of the seeds. Nine isolates were obtained, covering most known bean symbiont species, which belong to the Rhizobium and Sinorhizobium groups. The strains showed several large plasmids, except for a Sinorhizobium americanum isolate. Two strains, one Rhizobium phaseoli and one S. americanum strain, were thoroughly characterized. Optimal symbiotic performance was observed for both of these strains. The S. americanum strain showed biotin prototrophy when subcultured, as well as high pyruvate dehydrogenase (PDH) activity, both of which are key factors in maintaining optimal growth. The R. phaseoli strain was a biotin auxotroph, did not grow when subcultured, accumulated a large amount of poly-␤-hydroxybutyrate, and exhibited low PDH activity. The physiology and genomes of these strains showed features that may have resulted from their lifestyle inside the seeds: stress sensitivity, a ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) complex, a homocitrate synthase (usually present only in free-living diazotrophs), a hydrogenase uptake cluster, and the presence of prophages. We propose that colonization by rhizobia and their presence in Phaseolus seeds may be part of a persistence mechanism that helps to retain and disperse rhizobial strains. Bacteria can populate diverse environments, from soil to water, even in the most extreme sites on the earth. These organisms can also be found on and inside other organisms, such as fungi, animals, and plants. The microbiome is a recently developed concept used to define the prokaryotic populations in close relationship with more-complex organisms (1, 2). Bacteria can flourish as endophytes inside plant roots, stems, leaves, and seeds (3) in crops (e.g., wheat, rice, maize, sorghum, and sugarcane), legumes (e.g., clover, common bean, and alfalfa), trees (e.g., Populus), grasses (e.g., switchgrass), and model plants (e.g., Arabidopsis) (4). Most common endophytic bacterial species have been described as members of the phyla Firmicutes and Proteobacteria (5).Legumes are economically valuable plants in agriculture and establish symbiotic relationships with rhizobial bacteria (6). These bacteria contribute to the formation of plant root nodules, colonizing them and fixing atmospheric nitrogen. This phenomenon has been studied intensively (7). Endophytic rhizobia, in tissues other than nodules, have also been isolated from clover and pea (e.g., Rhizobium phaseoli and Rhizobium leguminosarum bv. trifolii) (8). Several nonrhizobial bacterial species have been isolated from Phaseolus tissues (roots, stems, and seeds); these include Acinetobacter, Bacillus, Enterococcus, Nocardioides, Paracoccus, Phyll...

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Section: Discussionmentioning

confidence: 99%

Nitrogen-Fixing Rhizobial Strains Isolated from Common Bean Seeds: Phylogeny, Physiology, and Genome Analysis

Mora

Dı́az

Vargas-Lagunas

et al. 2014

Appl Environ Microbiol

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“…This requirement of biotin has long been recognized in a class of important biotin-dependent enzymes involved in central metabolism, such as carboxylases and decarboxylases (2). Generally, bacterial biotin metabolism encompasses the following three processes: transport/uptake, de novo synthesis, and utilization (1,3,4). In microorganisms with a full capability of synthesizing biotin, four universal genes (bioF, bioA, bioD, and bioB) appear to constitute the majority of the biotin biosynthetic pathway (1,5).…”

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confidence: 99%

“…Finally, BioB (biotin synthase) converts dethiobiotin into biotin. In contrast, the microorganisms that possess only an incomplete biotin synthesis pathway (e.g., Lactococcus probiotic bacteria and human pathogen Streptococcus species) seem likely to have evolved an alternative mechanism of biotin scavenging to fulfill their metabolic requirements (2,3,11) (Fig. 1A).…”

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confidence: 99%

Brucella BioR Regulator Defines a Complex Regulatory Mechanism for Bacterial Biotin Metabolism

Feng

Zhang

et al. 2013

J Bacteriol

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eThe enzyme cofactor biotin (vitamin H or B7) is an energetically expensive molecule whose de novo biosynthesis requires 20 ATP equivalents. It seems quite likely that diverse mechanisms have evolved to tightly regulate its biosynthesis. Unlike the model regulator BirA, a bifunctional biotin protein ligase with the capability of repressing the biotin biosynthetic pathway, BioR has been recently reported by us as an alternative machinery and a new type of GntR family transcriptional factor that can repress the expression of the bioBFDAZ operon in the plant pathogen Agrobacterium tumefaciens. However, quite unusually, a closely related human pathogen, Brucella melitensis, has four putative BioR-binding sites (both bioR and bioY possess one site in the promoter region, whereas the bioBFDAZ [bio] operon contains two tandem BioR boxes). This raised the question of whether BioR mediates the complex regulatory network of biotin metabolism. Here, we report that this is the case. The B. melitensis BioR ortholog was overexpressed and purified to homogeneity, and its solution structure was found to be dimeric. Functional complementation in a bioR isogenic mutant of A. tumefaciens elucidated that Brucella BioR is a functional repressor. Electrophoretic mobility shift assays demonstrated that the four predicted BioR sites of Brucella plus the BioR site of A. tumefaciens can all interact with the Brucella BioR protein. In a reporter strain that we developed on the basis of a double mutant of A. tumefaciens (the ⌬bioR ⌬bioBFDA mutant), the ␤-galactosidase (␤-Gal) activity of three plasmid-borne transcriptional fusions (bioBbme-lacZ, bioYbme-lacZ, and bioRbme-lacZ) was dramatically decreased upon overexpression of Brucella bioR. Real-time quantitative PCR analyses showed that the expression of bioBFDA and bioY is significantly elevated upon removal of bioR from B. melitensis. Together, we conclude that Brucella BioR is not only a negative autoregulator but also a repressor of expression of bioY and bio operons that separately function in biotin transport and the biosynthesis pathway.

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“…This regulatory circuit ensures that biotin is not produced in higher amounts than required for protein biotinylation (26). Many prokaryotic and all eukaryotic biotinprotein ligases, in contrast, lack DNA-binding domains, indicating that these organisms use different mechanisms to monitor biotin availability (27,28).…”

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confidence: 99%

Biotin Sensing in Saccharomyces cerevisiae Is Mediated by a Conserved DNA Element and Requires the Activity of Biotin-Protein Ligase

Pirner

Stolz

2006

Journal of Biological Chemistry

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Biotin is a water-soluble vitamin that functions as a prosthetic group in carboxylation reactions. In addition to its role as a cofactor, biotin has multiple roles in gene regulation. We analyzed biotin effects on gene expression in the yeast Saccharomyces cerevisiae and demonstrated by microarray, Northern, and Western analyses that all yeast genes encoding proteins involved in biotin metabolism are up-regulated following biotin depletion. Many of these genes contain a palindromic promoter element that is necessary and sufficient for mediating the biotin response and functions as an upstream-activating sequence. Mutants lacking the plasma membrane biotin transporter Vht1p display constitutively high expression levels of biotin-responsive genes. However, they react normally to biotin precursors that do not require Vht1p for uptake. The biotin-like effect of precursors with regard to gene expression requires their intracellular conversion to biotin. This demonstrates that Vht1p does not act as a sensor for biotin and that intracellular biotin is crucial for gene expression. Mutants with defects in biotin-protein ligase, similar to vht1⌬ mutants, also display aberrantly high expression of biotin-responsive genes. Like vht1⌬ cells, they have reduced levels of protein biotinylation, but unlike vht1⌬ mutants, they possess normal levels of free intracellular biotin. This indicates that free intracellular biotin is irrelevant for gene regulation and identifies biotin-protein ligase as an important element of the biotin-sensing pathway in yeast.

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Biotin biosynthesis, transport and utilization in rhizobia

Cited by 28 publications

References 48 publications

Nitrogen-Fixing Rhizobial Strains Isolated from Common Bean Seeds: Phylogeny, Physiology, and Genome Analysis

Nitrogen-Fixing Rhizobial Strains Isolated from Common Bean Seeds: Phylogeny, Physiology, and Genome Analysis

Brucella BioR Regulator Defines a Complex Regulatory Mechanism for Bacterial Biotin Metabolism

Biotin Sensing in Saccharomyces cerevisiae Is Mediated by a Conserved DNA Element and Requires the Activity of Biotin-Protein Ligase

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