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RNA-seq of Oligotropha carboxidovorans strain OM5, a promising candidate for the aerobic utilization of synthesis gas, heterotrophically (acetate) and autotrophically (syngas) grown.

ABSTRACT: RNA-seq of Oligotropha carboxidovorans strain OM5, a promising candidate for the aerobic utilization of synthesis gas, heterotrophically (acetate) and autotrophically (syngas) grown.

PROVIDER: PRJEB36726 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR3895460_1.fastq.gz	Fastqsanger.gz
	ERR3895460_2.fastq.gz	Fastqsanger.gz
	ERR3895470_1.fastq.gz	Fastqsanger.gz
	ERR3895470_2.fastq.gz	Fastqsanger.gz
	ERR3895461_1.fastq.gz	Fastqsanger.gz

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RNA-seq of Oligotropha carboxidovorans strain OM5, a promising candidate for the aerobic utilization of synthesis gas, heterotrophically (acetate) and autotrophically (syngas) grown.

Project description:Oligotropha carboxidovorans strain OM5 is an aerobic carboxidotrophic bacterium and potentially a promising candidate for such processes. We here performed RNA-Seq analysis comparing cells of this organism grown heterotrophically with acetate or autotrophically with CO2, CO and H2 as carbon and energy source and found a variety of chromosomally and of native plasmid-encoded genes to be highly differentially expressed. For RNA extraction and RNA-Seq, respectively, six aliquots of the sample of each culture replicate were pooled to gain enough cell mass and RNA, accordingly, while four biological replicates were processed for the RNA-Seq analysis. Total RNA was isolated from four biological replicates using Zymo Quick-RNA Miniprep Plus kit with bead beating and DNase-treatment (Zymo Research, Freiburg, Germany). Initially RNA quality was checked by Trinean Xpose (Gentbrugge,Belgium) and Agilent RNA Nano 6000 kit on Agilent 2100 Bioanalyzer (Agilent Technologies, Böblingen, Germany). Samples contaminated with DNA were treated with DNase again, cleaned as described above and rechecked by Xpose and Agilent Bioanalyzer. Finally RNA was free of DNA with an RNA Integrity Number (RIN) > 9 and rRNA Ratio [23s / 16s] > 1.5. Ribo-Zero rRNA Removal Kit (Bacteria) from Illumina (San Diego, CA, USA) was used to remove the ribosomal RNA molecules from the isolated total RNA. Removal of rRNA was checked by Agilent RNA Pico 6000 kit on Agilent 2100 Bioanalyzer (Agilent Technologies, Böblingen, Germany). RNA was free of detectable rRNA. TruSeq Stranded mRNA Library Prep Kit from Illumina (San Diego, CA, USA) was used to prepare cDNA libraries. TruSeq stranded cDNAs were sequenced paired end on an Illumina HiSeq1500 system, rapid mode using 70 bp read length.

2020-02-21 | E-MTAB-8786 | biostudies-arrayexpress

Afipia carboxidovorans

Project description:Oligotropha carboxidovorans overview

| PRJNA36857 | ENA

Afipia carboxidovorans OM5

Project description:Oligotropha carboxidovorans OM5 Genome sequencing

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Afipia carboxidovorans OM4

Project description:Oligotropha carboxidovorans OM4 genome sequencing

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Nitrosomonas oligotropha

Project description:Nitrosomonas oligotropha overview

| PRJNA342872 | ENA

Complete genome sequences of the chemolithoautotrophic Oligotropha carboxidovorans strains OM4 and OM5.

Project description:We report on genome sequencing of Oligotropha carboxidovorans strain OM4 and resequencing of strain OM5. The genomes of both are composed of one chromosome and two plasmids. The presence of two plasmids in the OM5 genome is inconsistent with the previously published sequence, for which only one plasmid was described (D. Paul, S. Bridges, S. Burgess, Y. Dandass, and M. Lawrence, BMC Genomics 11:511, 2010).

| S-EPMC3165685 | biostudies-literature

Complete genome and comparative analysis of the chemolithoautotrophic bacterium Oligotropha carboxidovorans OM5.

Project description:BACKGROUND: Oligotropha carboxidovorans OM5 T. (DSM 1227, ATCC 49405) is a chemolithoautotrophic bacterium capable of utilizing CO (carbon monoxide) and fixing CO2 (carbon dioxide). We previously published the draft genome of this organism and recently submitted the complete genome sequence to GenBank. RESULTS: The genome sequence of the chemolithoautotrophic bacterium Oligotropha carboxidovorans OM5 consists of a 3.74-Mb chromosome and a 133-kb megaplasmid that contains the genes responsible for utilization of carbon monoxide, carbon dioxide, and hydrogen. To our knowledge, this strain is the first one to be sequenced in the genus Oligotropha, the closest fully sequenced relatives being Bradyrhizobium sp. BTAi and USDA110 and Nitrobacter hamburgiensis X14. Analysis of the O. carboxidovorans genome reveals potential links between plasmid-encoded chemolithoautotrophy and chromosomally-encoded lipid metabolism. Comparative analysis of O. carboxidovorans with closely related species revealed differences in metabolic pathways, particularly in carbohydrate and lipid metabolism, as well as transport pathways. CONCLUSION: Oligotropha, Bradyrhizobium sp and Nitrobacter hamburgiensis X14 are phylogenetically proximal. Although there is significant conservation of genome organization between the species, there are major differences in many metabolic pathways that reflect the adaptive strategies unique to each species.

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Project description:Nitrosomonas oligotropha Nm76 genome sequencing

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