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ABSTRACT: Obligate methanotroph Methylotuvimicrobium alcaliphilum 20Z-3E as a fumarate producer

PROVIDER: PRJNA1149720 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR30296607_1.fastq.gz	Fastqsanger.gz
	SRR30296608_1.fastq.gz	Fastqsanger.gz
	SRR30296609_1.fastq.gz	Fastqsanger.gz
	SRR30296610_1.fastq.gz	Fastqsanger.gz
	SRR30296611_1.fastq.gz	Fastqsanger.gz

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Project description:Methylotuvimicrobium alcaliphilum whole genome sequencing

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Methylotuvimicrobium alcaliphilum 20Z

Project description:Methylotuvimicrobium alcaliphilum 20Z Genome sequencing

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RNA-seq profiling of Methylotuvimicrobium alcaliphilum 20ZR grown with or without La-supplementation

Project description:In this study we investigated the steady-state growth of Methylotuvimicrobium alcaliphilum 20ZR in media containing calcium (Ca) or lanthanum (La, a REE element). RNA-seq profiling of Methylomicrobium alcaliphilum strain 20ZR in bioreactor on methane. Sample cultures, La-optimum, La-CH4 limited, Ca-optimum and Ca-CH4 limited, were collected and immediately transferred into tubes containing 5 ml of the stop solution (5% water-equilibrated phenol in ethanol). It was found, that cells supplemented with La show a higher growth rate compared to Ca-cultures; however, the efficiency of carbon conversion, estimated as biomass yield, is higher in cells grown with Ca. The study was financially supported by DOE under FOA DE-FOA-0001085 and by NSF-CBET award 1605031

2024-02-02 | GSE253414 | GEO

A methanotrophic bacterium to enable direct methane capture for climate mitigation

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

Adaptive evolution of Methylotuvimicrobium alcaliphilum to grow in the presence of rhamnolipids improves fatty acid and rhamnolipid production from CH4

Project description:Rhamnolipids (RL) are well-studied biosurfactants naturally produced by pathogenic strains of P. aeruginosa. Current methods to produce RLs in native and heterologous hosts have focused on carbohydrates as production substrate; however CH4 provides an intriguing alternative as a substrate for RL production because it is low-cost and may mitigate greenhouse gas emissions. Here we demonstrate RL production from CH4 by Methylotuvimicrobium alcaliphilum 20Z. RLs were inhibitory to M. alcaliphilum growth at low concentrations (<0.05 g/L), so adaptive evolution was performed by growing M. alcaliphilum in increasing concentrations of RLs, producing a strain that grew in the presence of 5 g/L of RLs. Metabolomics and proteomics of the adapted strain grown on CH4 in the absence of RLs revealed metabolic changes increase in fatty acid production and secretion, alterations in gluconeogenesis, and increased secretion of lactate and osmolyte products compared to the parent strain. Expression of plasmid-borne RL production genes in the parent M. alcaliphilum strain resulted in cessation of growth and cell death. In contrast, the adapted strain transformed with the RL production genes showed no growth inhibition and produced up to 1 M of RLs, a 600-fold increase compared to the parent strain. This work has promise for developing technologies to produce fatty acid-derived bioporducts, including biosurfactants, from CH4.

2022-09-19 | PXD029605 | Pride

RNA-seq profiling of Methylotuvimicrobium alcaliphilum 20ZR grown with or without La-supplementation

Project description:RNA-seq profiling of Methylotuvimicrobium alcaliphilum 20ZR grown with or without La-supplementation

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Project description:Transcriptional and metabolic adaptations of the methanotroph Methylomicrobium alcaliphilum to high salinity conditions

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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

Methylotuvimicrobium alcaliphilum

Project description:Methylomicrobium alcaliphilum overview

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Engineered methanotrophic platform for biomanufacturing of non-oxidative ribulose monophosphate pathway-derived products from methane and xylose

Project description:Comparative transcriptomic analysis between methane- and methane plus xylose- grown cultures revealed different transcriptional responses of pXyl M. alcaliphilum 20Z strain on diffirent growth modes.

2021-12-31 | GSE150282 | GEO

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