Project description:A total gene expression approach was applied to study the methylotrophic nature of B. methanolicus by comparing the gene expression in bacteria grown methylotropic compared to non-methylotrophic. Genes of interest with different gene expression were quantified in the same RNA samples by real-time PCR, confirming the results found in the microarray experiment. Genes of special interest that are expressed higher when grown methylotrophic, were the RuMP pathway genes located on the pBM19.
Project description:A total gene expression approach was applied to study the methylotrophic nature of B. methanolicus by comparing the gene expression in bacteria grown methylotropic compared to non-methylotrophic. Genes of interest with different gene expression were quantified in the same RNA samples by real-time PCR, confirming the results found in the microarray experiment. Genes of special interest that are expressed higher when grown methylotrophic, were the RuMP pathway genes located on the pBM19. Bacillus methanolicus was grown in minimal media with either methanol or mannitol as carbon source. The experiment was preformed in triplicate, with bacterial cultures grown on 3 different days.
Project description:The recent discovery of the lanthanide(Ln)-dependent methanol dehydrogenase (MDH) XoxF has expanded the spectrum of bacteria recognized for methylotrophic metabolism. Many bacteria, including rhizobia, have long escaped being categorized as methylotrophs because they exclusively produce XoxF-type Ln-dependent MDH and entirely lack the long-studied calcium-dependent MDH MxaFI. We report that the XoxF-type Ln-dependent MDH encoded by the smb20173 gene is the sole MDH that supports methylotrophic growth of Sinorhizobium meliloti. The Ln that consistently supported growth of S. meliloti in minimal media with methanol included lanthanum, cerium, praseodymium, and neodymium. Based on genome, whole-transcriptome, and mutant phenotype analyses, we propose a metabolic model for Ln-dependent methylotrophy in S. meliloti wherein oxidation of one-carbon compounds such as methanol generates the reducing power needed to assimilate carbon via the Calvin-Benson-Bassham cycle. By investigating how these newfound insights about Ln reshape our understanding of the methylotrophic capabilities of rhizobia, we explored how methanol produced by plants has the potential to create a nutritional niche in the rhizosphere. Using a Medicago sativa (alfalfa) nodule occupation assay, we found that the xoxF mutant strain was outcompeted by the wild-type strain only when Ln were available, suggesting that Ln-dependent methylotrophy is a potential nutritional mediator of the rhizobia-legume symbiosis.
Project description:Bacteria use different strategies to sense and respond to reduced sulfur compounds such as sulfide or thiosulfate. In the methylotrophic Alphaproteobacterium Hyphomicrobium denitrificans, which uses thiosulfate as an accessory electron donor, this involves two distinct but related ArsR-type transcriptional repressors, sHdrR and SoxR. Here, we focused on identifying target genes regulated by these repressors. This was achieved by generating individual deletions of each regulator gene, and performing comparative RNA-seq analysis.
Project description:Dichloromethane (DCM, methylene chloride) is a toxic halogenated volatile organic compound massively used for industrial applications, and consequently often detected in the environment as a major pollutant. DCM biotransformation offers a sustainable decontamination strategy of polluted sites. Among methylotrophic bacteria able to use DCM as sole source of carbon and energy for growth, Methylorubrum extorquens DM4 (formerly named Methyobacterium extorquens) is a longstanding reference Alphaproteobacteria strain. Here, its primary transcriptome was obtained using a differential RNA-seq (dRNA-seq) approach to provide the first transcription start site (TSS) genome-wide landscape of a methylotroph using DCM.
