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Genome-wide transcription start sites mapping in Methylorubrum grown using dichloromethane and methanol

ABSTRACT: Genome-wide transcription start sites mapping in Methylorubrum grown using dichloromethane and methanol

PROVIDER: PRJEB52788 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR9717320.fastq.gz	Fastqsanger.gz
	ERR9717321.fastq.gz	Fastqsanger.gz
	ERR9717322.fastq.gz	Fastqsanger.gz
	ERR9717323.fastq.gz	Fastqsanger.gz
	ERR9717324.fastq.gz	Fastqsanger.gz

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Genome-wide transcription start sites mapping in Methylorubrum grown using dichloromethane and methanol

2022-06-27 | E-MTAB-11726 | biostudies-arrayexpress

Genome-Wide Transcription Start Sites Mapping in <i>Methylorubrum</i> Grown with Dichloromethane and Methanol.

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 suggests a sustainable decontamination strategy of polluted sites. Among methylotrophic bacteria able to use DCM as a sole source of carbon and energy for growth, Methylorubrum extorquens DM4 is a longstanding reference strain. Here, the primary 5'-ends of transcripts were 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 or methanol. In total, 7231 putative TSSs were annotated and classified with respect to their localization to coding sequences (CDSs). TSSs on the opposite strand of CDS (antisense TSS) account for 31% of all identified TSSs. One-third of the detected TSSs were located at a distance to the start codon inferior to 250 nt (average of 84 nt) with 7% of leaderless mRNA. Taken together, the global TSS map for bacterial growth using DCM or methanol will facilitate future studies in which transcriptional regulation is crucial, and efficient DCM removal at polluted sites is limited by regulatory processes.

| S-EPMC9320726 | biostudies-literature

Methylorubrum extorquens DM4

Project description:Genome-wide identification of genes essential for growth with dichloromethane or methanol in Methylorubrum extorquens DM4

| PRJNA940386 | ENA

Comparative proteomics of Desulfotomaculum kuznetsovii grown on methanol and ethanol

Project description:The aim of this study was to unravel the methanol metabolism of Desulfotomaculum kuznetsovii. Anaerobic methylotrophs, such as methanogens and acetogens, use a pathway initiated by a cobalamine-containing methanol methyltransferase, whereas aerobic methylotrophs generally oxidize methanol to formaldehyde through a pathway initiated by a methanol dehydrogenase. Sulfate-respiring cells grown with methanol in the presence and absence of cobalt and vitamin B12 were analyzed and compared with cells grown with lactate or ethanol. Proteome analysis showed the presence of two methanol degrading pathways in D. kuznetsovii: a cobalt-dependent methanol methyltransferase and a cobalt-independent alcohol dehydrogenase. This is the first time that two methanol pathways have been shown to be present in a single microorganism, and we hypothesize this can give D. kuznetsovii a competitive advantage.

2018-01-22 | PXD006899 | Pride

Differential analysis of Methylobacterium extorquens DM4 in methanol versus dichloromethane condition

Project description:Differential analysis of Methylobacterium extorquens DM4 in methanol versus dichloromethane condition using shotgun label free MS1 quantification approach

2018-04-25 | PXD006838 | Pride

Pichia angusta cells glucose- vs methanol-grown

Project description:Transcriptional profiling of Pichia angusta NCYC 495 leu1.1 cells growing exponentially on mineral medium containing 0.5% glucose versus a shift for 2 hours to mineral medium containing 0.5% methanol. Two-conditions experiment, 4 individual glucose-grown cultures were shifted at OD660nm 2.3 to fresh mineral medium OD 0.2 containing 0.5% methanol for 2 hours. Transcriptional profiling was performed using total RNA from the glucose-grown cells at the moment of the shift versus cells adapted to methanol for 2 hours.

2010-06-19 | E-GEOD-19036 | biostudies-arrayexpress

Pichia pastoris Glucose/Methanol comparison

Project description:Comparison of transcription profile of Pichia pastoris cells grown on Glucose medium with Pichia pastoris cells grown on Methanol/Glycerol medium, the fermentations were done in a chemostat.

2015-08-31 | GSE67690 | GEO

Methylorubrum extorquens supernatant extract use case

Project description:Three independent cultures of Methylorubrum extorquens PA1 delta cel were grown on ammonium mineral salts with either methanol or succinate provided as the sole carbon and energy source. The supernatant was subsequently extracted with acidified ethyl acetate and analyzed by LC-MS.

2021-02-10 | MSV000086834 | MassIVE

Pichia angusta cells glucose- vs methanol-grown

2009-11-17 | GSE19036 | GEO

Proteogenomics of Hyphomicrobium sp. MC8b strain

Project description:This project is a proteomic comparison of Hyphomicrobium sp. MC8b grown with dichloromethane or with methanol. The datasets were obtained using the annotated genome of Hyphomicrobium sp. MC8b.

2021-09-09 | PXD021817 | Pride

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