Bradyrhizobium diazoefficiens USDA 110
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Similar Datasets
Project description:Bradyrhizobium diazoefficiens USDA 110 Epigenomics
| PRJNA243968 | ENA
Project description:Bradyrhizobium diazoefficiens USDA 110 Epigenomics
| PRJNA242419 | ENA
Project description:Bradyrhizobium diazoefficiens LP USDA 110 Genome sequencing and assembly
| PRJNA634817 | ENA
Project description:Using an integrated systems approach, the expressed proteome of B. diazoefficiens strain 110scp4 was measured under i) normal, oxic growth, and ii) microoxic growth condtions. This included, as a first step, the sequencing and de novo assembly of the genome of this widely used rhizobial model strain, which turned out to harbor several deletions and insertions compared to the B. diazoefficiens USDA 110 NCBI reference genome. With this optimal basis in hand, a shotgun proteomics approach relying on a slightly adapated FASP protocol was carried out, allowing to identify 2900 (oxia) and 2826 (microoxia) proteins, respectively, thereby largely expanding the proteome known to be expressed under microoxic conditions.
2019-05-30 | PXD012491 | Pride
Project description:Bradyrhizobium diazoefficiens USDA 122 genome sequencing and assembly
| PRJNA686127 | ENA
Project description:Bradyrhizobium diazoefficiens strain:USDA 122 Genome sequencing and assembly
| PRJNA162997 | ENA
Project description:Purpose: Identification of genes regulated by NasT during denitrifying growth in B. diazoefficiens. Methods: Two biological replications were processed for each strain (wild-type USDA 110 and ΔnasT mutant). Sequencing was performed in an Illumina HiSeq 2000 Sequencing System in paired-end mode running 100x2 cycles (performed by Hokkaido System Science Co., Ltd.). Mapping of reads to the reference genome, read counting, normalization to RPKM (reads per kilobase per million mapped reads), and calculations of expression values were performed with default values with the CLC Genomic Workbench software 9.5.3. From the total reads that were generated, ~85% were trimmed, and from those, ~42% could be mapped onto the B. diazoefficiens genome. Genes with fewer than 10 reads per 1 million mRNA reads were omitted from the following analysis. A gene with a fold change ≥2 or ≤‒2 and a q value (estimate of false discovery rate) ≤0.05 was considered up- or down- regulated, respectively. The results were validated by qRT–PCR. Conclusion: A total of 77 genes were differentially expressed in the ∆nasT mutant compared to those of the wild-type strain, with 38 genes decreased and 37 genes increased in the ∆nasT mutant. Most of these genes were related to nitrogen metabolism.
2019-04-26 | GSE130301 | GEO
Project description:The ability of Bradyrhizobium japonicum and B. elkanii strains to utilize alkane and aromatic sulfonates as sole sources of sulfur for growth was investigated. All of the strains tested were able to utilize alkane sulfonates, but not aromatic sulfonates for growth. Whole-genome transcriptional profiling was used to assess B. japonicum USDA 110 genes involved in growth on alkane sulfonates, as compared to growth on sulfate and cysteine. Two sets of genes, bll7007 to bll7011 and bll6449 to 6456 were highly expressed during growth with sulfate and sulfonates. These genes were predicted to encode alkanesulfonate monooxygenases and ABC transporter components. Reverse transcription-PCR (RT-PCR) analyses showed that these genes were organized in two operon-like structures and expressed as polycistronic messages. The sulfonate monooxygenase encoded by bll7010 (ssuD) complemented an E. coli mutant defective in utilization of sulfonates. The expression of many genes that were induced during growth on cysteine and taurine were under the control of the FixLJ-FixK2-FixK1 symbiotic nitrogen fixation cascade, indicating there is a novel linkage between sulfur metabolism and nitrogen fixation. Taken together, results of this study indicate that Bradyrhizobium sp. strains are metabolically diverse and likely use organosulfur compounds for growth and survival, and for legume nodulation and nitrogen fixation in soil systems.
2009-11-17 | GSE19039 | GEO
Project description:The ability of Bradyrhizobium japonicum and B. elkanii strains to utilize alkane and aromatic sulfonates as sole sources of sulfur for growth was investigated. All of the strains tested were able to utilize alkane sulfonates, but not aromatic sulfonates for growth. Whole-genome transcriptional profiling was used to assess B. japonicum USDA 110 genes involved in growth on alkane sulfonates, as compared to growth on sulfate and cysteine. Two sets of genes, bll7007 to bll7011 and bll6449 to 6456 were highly expressed during growth with sulfate and sulfonates. These genes were predicted to encode alkanesulfonate monooxygenases and ABC transporter components. Reverse transcription-PCR (RT-PCR) analyses showed that these genes were organized in two operon-like structures and expressed as polycistronic messages. The sulfonate monooxygenase encoded by bll7010 (ssuD) complemented an E. coli mutant defective in utilization of sulfonates. The expression of many genes that were induced during growth on cysteine and taurine were under the control of the FixLJ-FixK2-FixK1 symbiotic nitrogen fixation cascade, indicating there is a novel linkage between sulfur metabolism and nitrogen fixation. Taken together, results of this study indicate that Bradyrhizobium sp. strains are metabolically diverse and likely use organosulfur compounds for growth and survival, and for legume nodulation and nitrogen fixation in soil systems. Three independent biological materials were prepared for sulfate or sulfonate supplemented cells. Total 12 arrays including dye swap were analyzed.
2010-06-19 | E-GEOD-19039 | biostudies-arrayexpress
Project description:Bradyrhizobium diazoefficiens genome sequencing
| PRJNA298974 | ENA