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Acinetobacter baumannii

ABSTRACT: RNA-sequencing of Acinetobacter baumannii LPS-deficient strain

PROVIDER: PRJDB16719 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	DRR505186_1.fastq.gz	Fastqsanger.gz
	DRR505186_2.fastq.gz	Fastqsanger.gz
	DRR505187.fastq.gz	Fastqsanger.gz
	DRR505187_1.fastq.gz	Fastqsanger.gz
	DRR505187_2.fastq.gz	Fastqsanger.gz

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Determining the transcriptome of an AdeRS deletion mutant in Acinetobacter baumannii AYE

Project description:RNA sequencing was carried out by ARK genomics, Edinburgh on an Illumina HiSeq platform to compare gene expression in Acinetobacter baumannii strain AYE and an adeRS deletion mutant in this strain.

2016-04-04 | E-MTAB-4047 | biostudies-arrayexpress

Determining the transcriptome of an AdeAB deletion mutant in Acinetobacter baumannii S1

Project description:RNA sequencing was carried out at BGI, Hong Kong on an Illumina HiSeq platform to compare gene expression in Acinetobacter baumannii strain S1 and an adeAB deletion mutant in this strain.

2016-04-04 | E-MTAB-4071 | biostudies-arrayexpress

Determining the transcriptome of an AdeB deletion mutant in Acinetobacter baumannii AYE

Project description:RNA sequencing was carried out at the University of Birmingham on an Illumina MiSeq platform to compare gene expression in Acinetobacter baumannii strain AYE and an adeB deletion mutant in this strain.

2016-04-04 | E-MTAB-4049 | biostudies-arrayexpress

Colistin-resistant, lipopolysaccharide-deficient Acinetobacter baumannii responds to lipopolysaccharide loss through increased expression of genes involved in the synthesis and transport of lipoproteins, phospholipids and poly-beta-1,6-N-acetylglucosamine

Project description:We recently demonstrated that colistin resistance in Acinetobacter baumannii can result from mutational inactivation of genes essential for lipid A biosynthesis. Consequently, strains harboring these mutations are unable to produce the major Gram negative bacterial surface component, lipopolysaccharide (LPS). To understand how A. baumannii compensates for the lack of LPS, we compared the transcriptional profile of the A. baumannii type strain ATCC19606, to that of an isogenic, LPS-deficient, lpxA mutant strain. Analysis of the expression profiles indicated that the LPS-deficient strain showed increased expression of many genes involved in cell envelope and membrane biogenesis. In particular, up-regulated genes included those involved in the Lol lipoprotein transport system and the Mla-retrograde phospholipid transport system. In addition, genes involved in the synthesis and transport of poly-beta-1,6-N-acetylglucosamine (PNAG) were also up-regulated and a corresponding increase in PNAG production was observed. The LPS-deficient strain also exhibited reduced expression of genes predicted to encode the fimbrial subunit FimA and a type VI secretion system (T6SS). The reduced expression of genes involved in T6SS correlated with the detection of the T6SS-effector protein, AssC, in culture supernatants of the A. baumannii wild-type strain, but not in the LPS-deficient strain. Taken together, these data show that, in response to total LPS loss, A. baumannii alters the expression of critical transport and biosynthesis systems associated with modulating the composition and structure of the bacterial surface. Comparison of a gene expression in biological duplicate samples derived from parent bacterial strain to an isogenic mutant strain.

2011-08-11 | E-GEOD-31206 | biostudies-arrayexpress

2011-08-11 | GSE31206 | GEO

ppGpp signal plays critical role in pathogenesis of Acinetobacter baumannii 17978

Project description:Acinetobacter baumannii is a major cause of nosocomial infections which can survive in different hospital environments and its multidrug-resistant capacity is major concern now-a-days. ppGpp dependent stringent response mediates reprogramming of gene expression with diverse function in many bacteria. A baumannii A1S_0579 gene is responsible for ppGpp production. Transcriptome analysis of early stationary phase cultures represents several differentially expressed genes in ppGpp deficient strain (∆A1S_0579). We found that the expression of csu operon, which is important in pili biosynthesis for early biofilm formation, was significantly reduced in the ppGpp-deficient strain. Our findings showed that ppGpp signaling plays critical role in biofilm formation, surface motility, adherence and virulence of A baumannii. This study is the first demonstration of the association between ppGpp and pathogenicity of A. baumannii.

2021-05-01 | GSE173627 | 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

Tn-seq of desiccated Acinetobacter baumannii

Project description:A major reservoir for spread of the emerging pathogen Acinetobacter baumannii is hopsital surfaces, where bacteria persist in a desiccated state. To identify gene products influencing desiccation survival, a transposon sequencing (Tn-seq) screen was performed. Using this approach, we identified genes both positively and negatively impacting the desiccation tolerance of A. baumannii.

2022-03-09 | GSE198004 | GEO

Towards the complete small RNome of Acinetobacter baumannii

Project description:In recent years, the Gram-negative bacterium Acinetobacter baumannii has garnered considerable attention for its unprecedented capacity to rapidly develop resistance to antibacterial therapeutics. This is coupled with the seemingly epidemic emergence of new hyper-virulent strains. Although strain-specific differences for A. baumannii isolates have been well described, these studies have primarily focused on proteinaceous factors. At present, only limited publications have investigated the presence and role of small regulatory RNA (sRNA) transcripts. Herein, we perform such an analysis, describing the RNA-seq-based identification of 78 A. baumannii sRNAs in the AB5075 background. Together with six previously identified elements, we include each of these in a new genome annotation file, which will serve as a tool to investigate regulatory events in this organism. Our work reveals that the sRNAs display high expression, accounting for >50 % of the 20 most strongly expressed genes. Through conservation analysis we identified six classes of similar sRNAs, with one found to be particularly abundant and homologous to regulatory, C4 antisense RNAs found in bacteriophages. These elements appear to be processed from larger transcripts in an analogous manner to the phage C4 molecule and are putatively controlled by two further sRNAs that are strongly antisense to them. Collectively, this study offers a detailed view of the sRNA content of A. baumannii, exposing sequence and structural conservation amongst these elements, and provides novel insight into the potential evolution, and role, of these understudied regulatory molecules. This study is based on the annotation of novel sRNAs on basis of an Acinetobacter baumannii RNA sequencing dataset. Each sample was generated by pooling three independent biological replicate RNA preps

2016-03-30 | E-GEOD-75708 | biostudies-arrayexpress

Transcription profiling of Acinetobacter baumannii multi-drug resistant strain and a susceptible reference strain - Abefflux

Project description:Transcriptomic comparison of a multidrug resistant Acinetobacter baumannii strain and a susceptible reference strain.

2009-11-20 | E-MEXP-2254 | biostudies-arrayexpress