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Raw genome sequence data for Acinetobacter baumannii AB5075 and the gene deletion strains SurA+Skp, SurA+DegPm Skp+DegP and SurA+Skp+DegP

ABSTRACT: The role of the periplasmic chaperones SurA, Skp and DegP for fitness, outer membrane integrity and virulence of Acinetobacter baumannii AB5075: same-same, but different?

PROVIDER: PRJEB40766 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR4674870_1.fastq.gz	Fastqsanger.gz
	ERR4674870_2.fastq.gz	Fastqsanger.gz
	ERR4674871_1.fastq.gz	Fastqsanger.gz
	ERR4674871_2.fastq.gz	Fastqsanger.gz
	ERR4674872_1.fastq.gz	Fastqsanger.gz

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The role of the periplasmic chaperones SurA, Skp and DegP for fitness, outer membrane integrity, antibiotic susceptibility and virulence of Acinetobacter baumannii AB5075: same-same, but different?

Project description:The outer membrane (OM) of Gram-negative bacteria efficiently protects from harmful environmental stresses such as antibiotics, disinfectants or dryness. Main constituents of the OM are integral OM β-barrel proteins (OMPs). In Gram-negative bacteria such as Escherichia coli (Ec), Yersinia enterocolitica (Ye) and Pseudomonas aeruginosa (Pa), the insertion of OMPs depends on a sophisticated biogenesis pathway. This comprises the SecYEG translocon, which enables inner membrane (IM) passage, the chaperones SurA, Skp and DegP, which facilitate the passage of β-barrel OMPs through the periplasm, and the β-barrel assembly machinery (BAM) which facilitates insertion into the OM. In Ec, Ye and Pa the deletion of SurA is particularly detrimental and leads to a loss of OM integrity, sensitization to antibiotics, and hypovirulence. In search of targets that could be exploited to develop compounds that interfere with OM integrity in Acinetobacter baumannii (Ab), we employed the multidrug-resistant strain AB5075 to generate single gene knockout strains lacking individual periplasmic chaperones. In contrast to Ec, Ye and Pa, AB5075 tolerates the lack of SurA, Skp or DegP with only weak mutant phenotypes. While the double knockout strains surAskp and surAdegP are conditionally lethal in Ec, all double deletions were well tolerated by AB5075. Strikingly, even a triple knockout strain of AB5075, lacking surA, skp and degP, was viable. Our findings underline the extreme adaptibility of Ab and suggest the existence of mechanisms bypassing or acting redundantly to the known OMP biogenesis pathway comprising SurA, Skp and DegP.

2022-08-29 | PXD022004 | Pride

Role of proteins belonging to the OMP biogenesis machinery for virulence of Yersinia enterocolitica

Project description:The outer membrane (OM) of Gram-negative bacteria acts as a physical barrier protecting Gram-negative species from harmful environmental influences. At the same time it facilitates the import of nutrients, the export of proteins, the passage of signaling molecules and also harbors proteins associated with virulence. Transmembrane traffic particularly is facilitated by membrane-integral proteins. In order to insert these into the OM, an essential oligomeric membrane-associated protein complex, the beta-barrel assembly machinery (BAM) is required. Being essential for the biogenesis of outer membrane proteins (OMPs) the BAM and also periplasmic chaperones (termed the OMP biogenesis machinery as an entity herein) may serve as attractive targets to develop novel antimicrobial or antiinfective agents. We aimed to elucidate which proteins belonging to the OMP biogenesis machinery have the most important function in granting bacterial fitness, facilitating biogenesis of dedicated virulence factors and determination of overall virulence. To this end we used the enteropathogen Yersinia enterocolitica (Ye) as a model system. We individually knocked out all non-essential components of the BAM (BamB, C and E) as well as the periplasmic chaperones DegP, SurA and Skp. In summary, we found that the most profound phenotypes were produced by the loss of BamB or SurA with both knockouts resulting in significant attenuation or even avirulence of Ye in a mouse infection model. Thus, both BamB and SurA are promising targets for the development of new antimicrobials in the future.

2018-10-17 | PXD004429 | Pride

Acinetobacter baumannii AB5075

Project description:Acinetobacter baumannii AB5075 Genome sequencing

| PRJNA1074270 | ENA

Acinetobacter baumannii AB5075

Project description:Acinetobacter baumannii AB5075 Genome sequencing and assembly

| PRJNA168474 | ENA

Alteration of global transcription by the phytochemical Kaempferol in Acinetobacter baumannii AB5075

Project description:We perform RNA-seq comparing a treatment with 0.375 mM Kaempferol to a mock treatment (DMSO) in A. baumannii AB5075 in order to describe the alterations in global transcription produced by this phytochemical. A. baumannii AB5075 cultures were grown in LB medium in the presence of 0.375 mM Kaempferol or a DMSO control (3 biological replicates per condition) until reaching mid-exponential phase. At this point, cells were harvested, treated with RNAlater for preservation of total RNA and stored at -80 C. After that, total RNA was extracted from each sample. As a result, 99 genes appeared upregulated in the presence of Kaempferol whereas 18 were downregulated. In highlights, the gene functional groups showing the strongest transcriptional alterations were those related to iron acquisition, siderophore biosynthesis and iron transport genes.

2023-09-20 | GSE212989 | GEO

native Tn-seq analysis of ISAba13 in Acinetobacter baumannii AB5075

Project description:The experiment contains native Tn-seq data for Acinetobacter baumannii strain AB5075 with different genetic alterations. The strain was grown at 37 degrees in LB medium and genomic DNA was isolated. We then used PCR to select for DNA regions containing a junction between ISAba13 and chromosomal DNA. Libraries were then prepared using these DNA fragments.

2024-07-15 | E-MTAB-13792 | biostudies-arrayexpress

Transcription regulation by CavA cyclase in Acinetobacter baumannii AB5075

Project description:We perform RNA-seq for comparison of deleted cavA wiht empty vector and complemented strains in A. baumannii AB5075 in order to assess the transcription regulation uder the control of this cyclase. A. baumannii AB5075 ΔcavA EV and ΔcavA+cavA cultures were grown in LB medium with 1mM IPTG (3 biological replicates per strain) until reaching mid-exponential phase. At this point, cells were harvested, treated with RNAlate for preservation of total RNA and stored at -80 C. After that, total RNA was extracted from each sample. The results showed 234 differentially expressed genes of which 143 were upregulated and 91 were downregulated in the ΔcavA+cavA complemented strain compared to the deleted cavA mutant harbouring empty vector (ΔcavA EV). The gene functional groups showing the strongest transcriptional alterations were those related to twitching motility (upregulation of genes involves in biogenesis and control of Type IV pili and com genes) as well as biofilm formation, exopolysaccharides production and fimbriae biogenesis (downregulation of csu operon, pga operon and ABUW_2052-2055). Also, genes related to inter- and intracellular signalling were differentially expressed. Cyclic AMP response regulator vfr and genes involved in c-di-GMP synthesis (ABUW_2135) and degradation (ABUW_1138) were upregulated while another gene linked to c-di-GMP degradation (ABUW_2631) and autoinducer synthase encoding gene abaI (part of the quorum sensing signalling system) were downregulated.

2024-08-30 | GSE250425 | GEO

Acinetobacter baumannii strain:AB5075-UW

Project description:Acinetobacter baumannii strain:AB5075-UW Genome sequencing

| PRJNA243297 | ENA

ChIP-seq analysis of H-NS in Acinetobacter baumannii AB5075

Project description:The experiment contains ChIP-seq data for Acinetobacter baumannii strain AB5075 encoding 3xFLAG tagged H-NS. Experiments were done with or without ectopic expression of the truncated H-NS-39 protein (corresponding to the H-NS multimerization surface). The strain was grown at 37 degrees in LB medium and crosslinked with 1 % (v/v) formaldehyde. After sonication, to break open cells and fragment DNA, immunoprecipitations were done using anti-FLAG antibodies against. Libraries were prepared using DNA remaining after immunoprecipitation.

2024-07-15 | E-MTAB-13790 | biostudies-arrayexpress

Alteration of global transcription by the artificial sweetener acesulfame K in Acinetobacter baumannii AB5075

Project description:We perform RNA-seq comparing a treatment with 1.33% acesulfame K to a mock treatment in A. baumannii AB5075 in order to describe the alterations in global transcription produced by this artificial sweetener. A. baumannii AB5075 cultures were grown in LB medium in the presence of 1.33% acesulfame K or a water control (3 biological replicates per condition) until reaching mid-exponential phase. At this point, cells were harvested, treated with RNAlate for preservation of total RNA and stored at -80 C. After that, total RNA was extracted from each sample. As a result, 212 genes appeared upregulated in the presence of acesulfame K, whereas 252 were downregulated. In highlights, the gene functional groups showing the strongest transcriptional alterations were those related to twtching motility and natural transformation (downregulation of genes involves in biogenesis and control of Type IV pili and com genes), as well as genes involved in iron acquisition and siderophore biosynthesis and an uncharacterised gene cluster that might be involved in detoxification of sulfonamide compounds.

2022-10-27 | GSE199706 | GEO

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