Acinetobacter baylyi
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA183988 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR635231.fastq.gz | Fastqsanger.gz | |||
| SRR635232.fastq.gz | Fastqsanger.gz | |||
| SRR635233.fastq.gz | Fastqsanger.gz | |||
| SRR635234.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 4 of 4 |
Similar Datasets
Project description:Acinetobacter baylyi ADP1 is naturally competent and proficient at homologous recombination, so it can be transformed without restriction digests or ligation reactions. Expression vectors for this system, however, are not yet widely available. Here we describe the construction and characterization of inducible expression vectors that replicate as plasmids in A. baylyi or integrate into a nonessential part of its chromosome. These tools will facilitate the engineering of genes and genomes in this promising model organism.
| S-EPMC3255645 | biostudies-literature
Project description:We report the effect of the deletion of novel RNA polymerase binding protein AtfA on genome-wide transcription in Acinetobacter baylyi ADP1. Compared the transcription profile of wt vs atfA knockout in Acinetobacter baylyi ADP1 using RNA-seq.
2014-07-28 | E-GEOD-42973 | biostudies-arrayexpress
Project description:We report the effect of the deletion of novel RNA polymerase binding protein AtfA on genome-wide transcription in Acinetobacter baylyi ADP1.
2014-07-28 | GSE42973 | GEO
Project description:There are no previous reports of human infection due to Acinetobacter baylyi. In this study, we report on six patients with bacteremia due to A. baylyi, based on analysis of the 16S-23S rRNA intergenic spacer and the 16S rRNA gene. All six patients had multiple underlying diseases. The infection was nosocomially acquired in five patients. The six clinical isolates had similar ribopatterns, suggesting a clonal relationship. Compared to the reference strain, the clinical isolates were more resistant to antimicrobial agents, especially beta-lactam antibiotics. In three of the isolates, they may have undetermined plasmid mediated class C type beta-lactamases because of the positive results in a double-disk synergy test using 3-aminophenylboronic acid. Two of the clinical isolates retained a level of natural transformability similar to that of the reference strain. None of the patients died, although only three of them received appropriate antimicrobial therapy. This study demonstrates that A. baylyi is a potential human pathogen that can cause nosocomial infection in immunocompromised patients.
| S-EPMC2546726 | biostudies-literature
Project description:Genome wide transcriptional changes induced by various types of oxidative stresses as well as salt stress were studied in a DatfA mutant and the appropriate control A. nidulans strains. Although a significant number of stereotypically regulated genes was identified (Core Oxidative Stress Response or COSR genes) when the global transcriptional effects of five different oxidative stress conditions were compared the number of co-regulated genes decreased to 13 when NaCl stress was included into the analyses. The appearance of only a few co-regulated genes and the great number of genes regulated merely by one certain type of stress do not support the existence of a S. cerevisiae-type Environmental Stress Response in A. nidulans. Deletion of atfA, a true functional ortholog of fission yeast’s “all-purpose” stress response transcription factor, increased the oxidative stress sensitivity of A. nidulans and affected the transcription of several genes under both unstressed and stressed conditions. The number of genes under AtfA control was quite stress-type dependent; e.g. deletion of atfA altered the transcription of a wide spectrum of genes under menadione sodium bisulfite stress but had only a minor effect on the transcriptome profiles when A. nidulans cultures were exposed to H2O2, tBOOH, NaCl and, especially, to diamide stress. These observations suggest that the function of AtfA in the regulation of various stress responses is much smaller than we thought before or other transcription factors can take over a number of AtfA’s functions when the atfA gene is deleted. It is noteworthy that both oxidative and salt stress induced the transcription of some secondary metabolite gene clusters and the deletion of atfA enhanced the stress responsiveness of further clusters. Surprisingly, certain clusters were down-regulated by the stress conditions tested and the majority of them were not stress-responsive at all. Therefore, stress dependent regulation seems to be a frequent but far not a general feature of the regulation of secondary metabolism in A. nidulans.
2015-12-31 | GSE63019 | GEO
Project description:Genome wide transcriptional changes induced by various types of oxidative stresses as well as salt stress were studied in a DatfA mutant and the appropriate control A. nidulans strains. Although a significant number of stereotypically regulated genes was identified (Core Oxidative Stress Response or COSR genes) when the global transcriptional effects of five different oxidative stress conditions were compared the number of co-regulated genes decreased to 13 when NaCl stress was included into the analyses. The appearance of only a few co-regulated genes and the great number of genes regulated merely by one certain type of stress do not support the existence of a S. cerevisiae-type Environmental Stress Response in A. nidulans. Deletion of atfA, a true functional ortholog of fission yeastâs âall-purposeâ stress response transcription factor, increased the oxidative stress sensitivity of A. nidulans and affected the transcription of several genes under both unstressed and stressed conditions. The number of genes under AtfA control was quite stress-type dependent; e.g. deletion of atfA altered the transcription of a wide spectrum of genes under menadione sodium bisulfite stress but had only a minor effect on the transcriptome profiles when A. nidulans cultures were exposed to H2O2, tBOOH, NaCl and, especially, to diamide stress. These observations suggest that the function of AtfA in the regulation of various stress responses is much smaller than we thought before or other transcription factors can take over a number of AtfAâs functions when the atfA gene is deleted. It is noteworthy that both oxidative and salt stress induced the transcription of some secondary metabolite gene clusters and the deletion of atfA enhanced the stress responsiveness of further clusters. Surprisingly, certain clusters were down-regulated by the stress conditions tested and the majority of them were not stress-responsive at all. Therefore, stress dependent regulation seems to be a frequent but far not a general feature of the regulation of secondary metabolism in A. nidulans. 14 samples, 7 with the control strain and 7 with an DatfA strain (each series contains samples from untreated as well as menadione, low concentration hidrogen-peroxide, high concentration hidrogen-peroxide, tert-butylhydroperoxide, diamide and NaCl treated cultures)
2015-12-31 | E-GEOD-63019 | biostudies-arrayexpress
Project description:The bZIP transcription factors (TFs) govern regulation of development, secondary metabolism and various stress responses in filamentous fungi. In this work, we carried out genome-wide expression studies employing Illumina RNAseq to understand the roles of the two bZIP transcription factors AtfA and AtfB in Aspergillus nidulans. Comparative analyses of transcriptomes of vegetatively grown cells (mycelia) and asexual spores (conidia) obtained from the surface cultures of control, DatfA, DatfB, DatfADatfB mutant strains with/without menadione sodium bisulfite (MSB) treatment were performed. Probable AtfA and AtfB dependent gene sets were determined by comparing transcriptomes of both single gene deletion mutants with the reference strain, and the double gene deletion mutant with the appropriate single gene deletion mutants. As AtfA is the primary bZip TF governing stress-response in A. nidulans, a significantly higher number was differentially expressed genes (DEGs) by DatfA than DatfB in both mycelial and conidial samples, and most of the AtfB dependent genes showed AtfA dependence, too. Moreover, a low number of genes showing AtfB dependence only can be a consequence of that DatfA leading to downregulation of atfB expression. The abundance of atfA and atfB mRNAs and, concurring with it the number of AtfA and AtfB affected genes were much higher in conidial than in mycelial samples. The number of AtfB- (but not of AtfA-) affected DEGs decreased markedly in the presence of MSB, which was accompanied with decreased mRNA levels of atfB in MSB treated mycelial (reference strain) and conidial (DatfA mutant) samples. The overlap between the AtfA dependent DEGs in the case of MSB treated and untreated mycelial samples was low demonstrating that distinct genes can be under AtfA control in different cell types. The AtfA-dependent DEGs were enriched with carbohydrate metabolism genes. Among them, AtfA-dependence of glycolytic genes in the case of the conidial samples was the most notable. Levels of transcripts of certain secondary metabolitic gene clusters, like the Emericellamide cluster also showed AtfA-dependent regulation. The AtfA affected DEGs under all experimental conditions include those encoding catalase and histidine-containing phosphotransfer proteins. The 23 DEGs that solely dependent on AtfB considering all transcriptomics data sets, included a putative a -glucosidase (agdB), a putative a-amylase, calA involved in early conidial germination and an alternative oxidase. In summary, there is a complex interaction between the two b-Zip TFs in which the main function of AtfB is supporting the regulatory role of the primary b-Zip TF AtfA in A. nidulans.
2023-02-15 | GSE220052 | GEO
Project description:Natural transformation enables acquisition of adaptive traits and drives genome evolution in prokaryotes. Yet, the selective forces responsible for the evolution and maintenance of natural transformation remain elusive since taken-up DNA has also been hypothesized to provide benefits such as nutrients or templates for DNA repair to individual cells.We investigated the immediate effects of DNA uptake and recombination on the naturally competent bacterium Acinetobacter baylyi in both benign and genotoxic conditions. In head-to-head competition experiments between DNA uptake-proficient and -deficient strains, we observed a fitness benefit of DNA uptake independent of UV stress. This benefit was found with both homologous and heterologous DNA and was independent of recombination. Recombination with taken-up DNA reduced survival of transformed cells with increasing levels of UV-stress through interference with nucleotide excision repair, suggesting that DNA strand breaks occur during recombination attempts with taken-up DNA. Consistent with this, we show that absence of RecBCD and RecFOR recombinational DNA repair pathways strongly decrease natural transformation.Our data show a physiological benefit of DNA uptake unrelated to recombination. In contrast, recombination during transformation is a strand break inducing process that represents a previously unrecognized cost of natural transformation.
| S-EPMC5312590 | biostudies-literature
Project description:Bacterial contact-dependent growth inhibition (CDI) systems are two-partner secretion systems in which toxic CdiA proteins are exported on the outer membrane by cognate transporter CdiB proteins. Upon binding to specific receptors, the C-terminal toxic (CT) domain, detached from CdiA, is delivered to neighbouring cells. Contacts inhibit the growth of not-self-bacteria, lacking immunity proteins co-expressed with CdiA, but promote cooperative behaviours in "self" bacteria, favouring the formation of biofilm structures. The Acinetobacter baylyi ADP1 strain features two CdiA, which differ significantly in size and have different CT domains. Homologous proteins sharing the same CT domains have been identified in A. baumannii. The growth inhibition property of the two A. baylyi CdiA proteins was supported by competition assays between wild-type cells and mutants lacking immunity genes. However, neither protein plays a role in biofilm formation or adherence to epithelial cells, as proved by assays carried out with knockout mutants. Inhibitory and stimulatory properties may be similarly uncoupled in A. baumannii proteins.
| S-EPMC6182759 | biostudies-literature
Project description:Bacterial genes defining intrinsic resistance to antibiotics encode proteins that can be targeted by antibiotic potentiators. To find such genes, a transposon insertion library of Acinetobacter baylyi was screened with subinhibitory concentrations of various antibiotics to find supersusceptible mutants. A DNA microarray printer was used to replica plate 10,000 individual library clones to select mutants unable to grow at 1/10 the MICs of 12 different antibiotics. Transposon insertions in 11 genes were found to cause an eightfold or higher hypersusceptibility to at least one antibiotic. Most of the mutants identified exhibited hypersusceptibility to beta-lactam antibiotics. These included mutants with disruptions of genes encoding proteins involved in efflux (acrB and oprM) as well as genes pertaining to peptidoglycan synthesis and modification (ampD, mpl, and pbpG). However, disruptions of genes encoding proteins with seemingly unrelated functions (gph, argH, hisF, and ACIAD0795) can also render cells hypersusceptible to beta-lactam antibiotics. A knockout of gshA, involved in glutathione biosynthesis, enhanced the susceptibility to metronidazole, while a knockout of recD, involved in recombination and repair, made the bacteria hypersusceptible to ciprofloxacin. Disruption of acrB in Escherichia coli rendered the cells hypersusceptible to several antibiotics. However, knockout mutants of other homologous genes in E. coli showed no significant changes in antibiotic MICs, indicating that the intrinsic resistance genes are species specific.
| S-EPMC1635227 | biostudies-literature