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RNA-seq of Arcobacter butzleri RM4018 wild-type and Abu0127 deletion mutant under microaerophilic and paraquat stress conditions

ABSTRACT: RNA-seq of Arcobacter butzleri RM4018 wild-type and Abu0127 deletion mutant under microaerophilic and paraquat stress conditions

PROVIDER: PRJEB71434 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR12380067_1.fastq.gz	Fastqsanger.gz
	ERR12380067_2.fastq.gz	Fastqsanger.gz
	ERR12380068_1.fastq.gz	Fastqsanger.gz
	ERR12380068_2.fastq.gz	Fastqsanger.gz
	ERR12380069_1.fastq.gz	Fastqsanger.gz

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RNA-seq of Arcobacter butzleri RM4018 wild-type and Abu0127 deletion mutant under microaerophilic and paraquat stress conditions

Project description:We performed transcriptome (RNA-seq) analyses for Arcobacter butzleri RM4018 wild-type (WT) and Abu0127 deletion mutant (ΔAbu0127::aphA-3) under oxidative stress and optimal microaerobic growth conditions. The expression of 290 genes was affected by oxidative stress in stressed wild-type cells (WTS) compared to non-stressed cells (WT). A comparison of genes expressed in the ΔAbu0127 and WT strains under optimal growth conditions revealed 779 differently expressed genes. Moreover, transcriptional changes and overall final protein levels correlated across multiple genes. The data were validated through RT-qPCR and phenotype experiments for selected processes.

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The complete genome sequence and analysis of the human pathogen Arcobacter butzleri.

Project description:Background: The human pathogen Arcobacter butzleri is a member of the epsilon subdivision of the Proteobacteria and a close taxonomic relative of other established pathogens, such as Campylobacter jejuni and Helicobacter pylori. Here we present the complete genome sequence of the human clinical isolate, A. butzleri strain RM4018. Results: Arcobacter butzleri is a member of the Campylobacteraceae, but the majority of its proteome is most similar to those of Thiomicrospira denitrificans and Wolinella succinogenes, both members of the Helicobacteraceae. In addition, many of the genes and pathways described here, e.g. those involved in signal transduction and sulfur metabolism, have been identified previously within the epsilon subdivision only in T. denitrificans and/or W. succinogenes, or are unique to the subdivision. The analyses indicated also that a large proportion of the A. butzleri genome is devoted to growth and survival under diverse environmental conditions, with a large number of respiration-associated proteins, signal transduction and chemotaxis proteins and proteins involved in DNA repair and adaptation. To investigate the genomic diversity of A. butzleri strains, we constructed an A. butzleri DNA microarray comprising 2238 genes from strain RM4018. Comparative genomic indexing analysis of 12 additional A. butzleri strains identified both the core genes of A. butzleri and intraspecies hypervariable regions, where < 70% of the genes were present in at least two strains. Conclusion: The presence of environmentally-associated pathways and loci, as well as genes associated with virulence indicates that this free-living, water-borne organism A. butzleri can be classified rightfully as an emerging pathogen. Keywords: comparative genomic hybridization

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Regulation of Energy Metabolism by the Extracytoplasmic Function (ECF) σ factors of Arcobacter butzleri

Project description:The extracytoplasmic function (ECF) σ factors are fundamental for bacterial adaptation to distinct environments and for survival under different stress conditions. The emerging pathogen Arcobacter butzleri possesses seven putative pairs of σ/anti-σ factors belonging to the ECF family. Here, we report the identification of the genes regulated by five out of the seven A. butzleri ECF σ factors. Three of the ECF σ factors play an apparent role in transport, energy generation and the maintainance of redox balance. Several genes like the nap, sox and tct genes are regulated by more than one ECF σ factor indicating that the A. butzleri ECF σ factors form a network of overlapping regulons. In contrast to other eubacteria, these A. butzleri ECF regulons appear to primarily regulate responses to changing environments in order to meet metabolic needs instead of an obvious role in stress adaptation.

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Regulation of Energy Metabolism by the Extracytoplasmic Function (ECF) ? factors of Arcobacter butzleri

Project description:The extracytoplasmic function (ECF) ? factors are fundamental for bacterial adaptation to distinct environments and for survival under different stress conditions. The emerging pathogen Arcobacter butzleri possesses seven putative pairs of ?/anti-? factors belonging to the ECF family. Here, we report the identification of the genes regulated by five out of the seven A. butzleri ECF ? factors. Three of the ECF ? factors play an apparent role in transport, energy generation and the maintainance of redox balance. Several genes like the nap, sox and tct genes are regulated by more than one ECF ? factor indicating that the A. butzleri ECF ? factors form a network of overlapping regulons. In contrast to other eubacteria, these A. butzleri ECF regulons appear to primarily regulate responses to changing environments in order to meet metabolic needs instead of an obvious role in stress adaptation. Eleven condition experiment, wild-type A. butzleri and 10 mutants. Three replicates for isolates RM4810, RM4810?A?1::Km, RM4018??1/A?1::Km, RM4810?A?2::Km, RM4018??2/A?2::Km, RM4018?A?4::Km, RM4018??4/A?4::Km, RM4018?A?5::Km, RM4018??5/A?5::Km, RM4018?A?7::Km, and RM4018??7/A?7::Km independently grown in BHI and incubated at 30°C on a shaking platform set at 150 rpm. RNA was isolated from 5 ml of mid-logarithmic phase cultures (OD550 of approximately 0.5). A type 2 gene expression experimental design was used, with fluorescently labeled genomic DNA as a reference channel in each experiment as described by Lucchini, S., et al. 2005. Infect Immun 73:88-102.

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