Project description:We report here a methanotroph, Methylotuvimicrobium buryatense 5GB1C, that consumes methane at 500ppm at rates several times higher than any previously published. Analyses of bioreactor-based performance and RNAseq based transcriptomics suggest that this superior ability to utilize low methane is based at least in part on an extremely low non-growth associated maintenance energy and on a 5-fold higher methane specific affinity than previous reports.

2023-08-02 | GSE221011 | GEO

Methylotuvimicrobium buryatense 5G strain:5G

Project description:Methylotuvimicrobium buryatense 5G strain:5G Genome sequencing and assembly

| PRJNA89087 | ENA

Project description:"Methylotuvimicrobium buryatense" 5GB1C lanthanum-response repressor mutants

| PRJNA535342 | ENA

Project description:Metabolic engineering of artificial CO2 fixation for succinate production in Methylotuvimicrobium buryatense 5GB1S using methane

| PRJNA1103350 | ENA

A computational framework for identifying promoter sequences in non-model organisms using RNA-seq datasets

Project description:We developed a computational framework to discover short DNA sequences that confer strong expression in non-model organisms. The framework relies solely on whole genome and RNA sequencing data types, which are easily accessible to a variety of research groups. The framework proceeds in three main stages: 1) identification of a group of highly expressed loci that maintain high transcript counts across a broad range of experimental conditions, 2) extraction of the corresponding upstream candidate promoter regions of these highly expressed loci while minding nearby annotations and avoiding those that may potentially reside in operons, and 3) application of the motif finding algorithm in BioProspector to these upstream regions to predict the location and sequence of the -35 and -10 hexamers that drive the strong expression of these loci. Ultimately, we report sequences of 27-30 bases in length as candidate -35, -10 signals for each of the top loci and create a consensus motif from these predictions. We apply our framework to 80 RNA-seq datasets collected for the methanotroph Methylotuvimicrobium buryatense 5GB1 and validate our predictions computationally and experimentally. The data deposited here represent all RNA-seq data that, until this study, has not previously been published.

2021-05-24 | GSE162089 | GEO

Core metabolism shifts of methanol vs. methane growth in the methanotroph Methylomicrobium buryatense 5GB1

Project description:Methylomicrobium buryatense 5GB1 is an obligate methylotroph, which grows on methane or methanol with similar growth rates. Core metabolic pathways are similar on both substrates, but recent studies of methane metabolism suggest that growth on methanol might have significant differences from growth on methane. In this study, both a targeted metabolomics approach as well as a 13C tracer approach have been taken to understand core carbon metabolism in M. buryatense 5GB1 during methanol growth, to determine whether such differences occur. Targeted metabolomics analyses were performed on both methane and methanol cultures to identify metabolic nodes with altered fluxes. Several key metabolites showed significant differences in pool size. Noticeably, 2-keto-3-deoxy-6-phosphogluconate (KDPG) showed much larger pools under methanol culture, suggesting the Entner-Doudoroff (ED) pathway was more active. Intermediates in other parts of metabolism also showed differences in pool sizes under methanol growth. A systematic shift of active core metabolism is proposed to explain the changes. In order to distinguish flux partition differences at the C3-C4 node, 13C tracer analysis was also applied to methanol-grown cultures. Using the experimental results as constraints, we applied flux balance analysis to determine the metabolic flux phenotype of M. buryatense 5GB1 growing on methanol. The resulting new insights into core metabolism of this methanotroph provide an improved basis for future strain design.

2019-04-17 | GSE110541 | GEO

Methylotuvimicrobium kenyense strain:AMO

Project description:Methylotuvimicrobium kenyense strain:AMO Genome sequencing

| PRJNA255620 | ENA