Transcriptional differences in Bradyrhizobium sp. USDA 3456 during growth on methanol with La versus succinate with La
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PROVIDER: PRJNA1255291 | ENA |
REPOSITORIES: ENA
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Project description:Nodule-forming bacteria play crucial roles in plant health and nutrition by fixing atmospheric nitrogen. Despite the importance of this relationship, how nodule-forming bacteria are affected by plant exudates and soil minerals is not fully characterized. Of particular interest are the effects of plant-derived methanol and lanthanide metals on the growth of nitrogen-fixing Rhizobiales. Prior work has demonstrated that select Bradyrhizobium are able to assimilate methanol only in the presence of lanthanide metals; however, the pathway enabling assimilation remains unknown. Here we characterize Bradyrhizobium sp. USDA 3456 to determine the pathways involved in methanol metabolism. Based on genomic analyses, we hypothesized that methanol assimilation in these organisms occurs via the lanthanide-dependent methanol dehydrogenase XoxF, followed by oxidation of formaldehyde via the glutathione-linked oxidation pathway, subsequent oxidation of formate via formate dehydrogenases, and finally assimilation of CO2 via the Calvin Benson Bassham (CBB) pathway. Transcriptomics revealed upregulation of the aforementioned pathways in Bradyrhizobium sp. USDA 3456 during growth on methanol. Assays demonstrated increased activity of the glutathione-linked oxidation pathway and formate dehydrogenases during growth on methanol compared to succinate. 13C-labeling studies demonstrate the presence of CBB intermediates and label incorporation during growth on methanol. Our findings provide multiple lines of evidence supporting the proposed XoxF-CBB pathway and, combined with genomic analyses, suggest that this metabolism is widespread among Bradyrhizobium and Sinorhizobium species.
2025-06-27 | GSE295604 | GEO
Project description:Ensifer meliloti strains USDA 1021 and USDA 1157 were cultured in succinate minimal media and analyzed for metabolites on LCMS. Analyze extracted with SPE using 80% or 100% methanol.
2024-07-26 | MSV000095449 | MassIVE
Project description:Ensifer meliloti strains USDA 1021 and USDA 1157 were cultured in succinate minimal media (SMM) and then analyzed for metabolites with LCMS and an iron infusion.
2024-07-26 | MSV000095451 | MassIVE
Project description:Ensifer meliloti strains USDA 1021 and USDA 1157 were cultured in succinate minimal media (SMM) with and without 10 micromolar FeCl3. Samples were analyzed for metabolites on LCMS.
2024-07-26 | MSV000095452 | MassIVE
Project description:In order to provide information about the gene expression response that occurs when cells experience a change in carbon source, succinate limited chemostat cultures of Methylobacterium extorquens AM1 were grown to and maintained at an OD of ~0.63, transferred to flasks and methanol was added. Cells were harvested for RNA extraction at time: 0 min, 10 min, 30 min, 1 hr, 2 hr, 4 hr and 6 hr post transition. At 30 min, a no methanol addition sample was extracted as a carbon starvation control. These data were used in conjunction with flux, enzymatic and metabolite measurements to assess the changes in central metabolism during this transition. Abstract from manuscript: When organisms experience environmental change, how does their metabolic network reset and adapt to the new condition? This study focused on the mechanisms of metabolic adaptation occurring during the transition from succinate to methanol growth by the methylotrophic bacterium Methylobacterium extorquens, analyzing changes in carbon flux, gene expression, metabolites and enzymatic activities over time. Initially, cells experienced metabolic imbalance with excretion of metabolites, changes in nucleotide levels and cessation of cell growth. Though assimilatory pathways were induced rapidly, a transient block in carbon flow to biomass synthesis occurred, and enzymatic assays suggested methylenetetrahydrofolate dehydrogenase as one control point. This “downstream priming” mechanism ensures that significant carbon flux through these pathways does not occur until they are fully induced, precluding the buildup of toxic intermediates. Most metabolites that are required for growth on both carbon sources did not change significantly, even though transcripts and enzymatic activities required for their production changed radically, underscoring the concept of metabolic setpoints. Gene expression in succinate limited chemostat cultures was compared to gene expression in cells transferred to flasks before and after methanol addition. As a control, a time = 0 sample (RNA prepared from cells harvested directly from the chemostat) was compared to a time = 0 sample immediately obtained after the cells were transferred to flasks, before methanol was added in order to identify changes due to flask transfer. A carbon starvation control was also done comparing expression from time = 0 (chemostat cells) to cells transferred to flasks for 30 min with no carbon source added. Two biological replicates each with two techinal replicates (dye swap) were analyzed for time = 0 (chemostat) vs 10 min, 30 min, 1 hr and 2 hr after methanol addition. One biological replicate with two technical replicates (dye swap) were analyzed for time = 0 (chemostat) vs time = 0 (flask transfer), and time = 0 (chemostat) vs time = 4 hr, 6 hr and 30 min no methanol addition.
2011-07-31 | E-GEOD-22031 | biostudies-arrayexpress
Project description:In order to provide information about the gene expression response that occurs when cells experience a change in carbon source, succinate limited chemostat cultures of Methylobacterium extorquens AM1 were grown to and maintained at an OD of ~0.63, transferred to flasks and methanol was added. Cells were harvested for RNA extraction at time: 0 min, 10 min, 30 min, 1 hr, 2 hr, 4 hr and 6 hr post transition. At 30 min, a no methanol addition sample was extracted as a carbon starvation control. These data were used in conjunction with flux, enzymatic and metabolite measurements to assess the changes in central metabolism during this transition. Abstract from manuscript: When organisms experience environmental change, how does their metabolic network reset and adapt to the new condition? This study focused on the mechanisms of metabolic adaptation occurring during the transition from succinate to methanol growth by the methylotrophic bacterium Methylobacterium extorquens, analyzing changes in carbon flux, gene expression, metabolites and enzymatic activities over time. Initially, cells experienced metabolic imbalance with excretion of metabolites, changes in nucleotide levels and cessation of cell growth. Though assimilatory pathways were induced rapidly, a transient block in carbon flow to biomass synthesis occurred, and enzymatic assays suggested methylenetetrahydrofolate dehydrogenase as one control point. This “downstream priming” mechanism ensures that significant carbon flux through these pathways does not occur until they are fully induced, precluding the buildup of toxic intermediates. Most metabolites that are required for growth on both carbon sources did not change significantly, even though transcripts and enzymatic activities required for their production changed radically, underscoring the concept of metabolic setpoints.
2011-08-01 | GSE22031 | GEO
Project description:Ensifer meliloti strains USDA 1021 and USDA 1157 were cultured in succinate minimal media and then analyzed for metabolites using untargeted LC-MS with a copper infusion.
2025-03-25 | MSV000097446 | GNPS
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 sp. USDA 223 isolate:USDA 223 Genome sequencing
| PRJNA1115348 | ENA