Aliivibrio
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA934681 | ENA |
REPOSITORIES: ENA
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Project description:Aliivibrio salmonicida causes “cold-water vibriosis” (or “Hitra disease”) in fish, including marine-reared Atlantic salmon. During development of the disease the bacterium will encounter macrophages with antibacterial activities such as production of damaging reactive oxygen species (ROS). To defend itself the bacterium will presumably start producing detoxifying enzymes, reducing agents, and proteins involved in DNA and protein repair systems. Even though responses to oxidative stress are well studied for a few model bacteria, little work has been done in general to explain how important groups of pathogens, like members of the Vibrionaceae family, can survive at high levels of ROS. We have used bioinformatic tools and an –omics approach to study how A. salmonicida responds to hydrogen peroxide (H2O2). First, we used the recently published genome sequence to predict potential binding sites for OxyR (H2O2 response regulator). The computer-based search identified OxyR sites associated with 20 single genes and 8 operons, and these predictions were compared to experimental data from Northern blot analysis, microarray analysis and 2D gel electrophoresis. In general, OxyR binding site predictions and experimental results are in agreement. Up- and down-regulated genes are distributed among all functional gene categories, but a striking number of ≥2 fold up-regulated genes encode proteins involved in detoxification or DNA protection and repair, are part of reduction systems, or are involved in carbon metabolism and regeneration of NADH/NADPH. Our predictions and –omics data corroborates well with findings from other model bacteria, but also suggest species-specific gene regulation.
2010-03-01 | GSE20082 | GEO
Project description:Aliivibrio (Vibrio) salmonicida is the causative agent of cold-water vibriosis in salmonids (Oncorhynchus mykiss and Salmo salar L.) and gadidae (Gadus morhua L.). Virulence-associated factors that are essential for the full spectrum of Al. salmonicida pathogenicity are largely unknown. Chitin-active lytic polysaccharide monooxygenases (LPMOs) have been indicated to play roles in both chitin degradation and virulence in a variety of pathogenic bacteria. In the present study we investigated the role of LPMOs in the pathogenicity of Al. salmonicida LFI238 in Atlantic salmon (Salmo salar L.). In vivo challenge experiments using isogenic deletion mutants of the two LPMOs encoding genes AsLPMO10A and AsLPMO10B, showed that both LPMOs, and in particular AsLPMO10B, were important in the invasive phase of cold-water vibriosis. Crystallographic analysis of the AsLPMO10B AA10 LPMO domain (to 1.4 Å resolution) revealed high structural similarity to viral fusolin, an LPMO known to enhance the virulence of insecticidal agents. Finally, exposure to Atlantic salmon serum resulted in substantial proteome re-organization of the Al. salmonicida LPMO deletion variants compared to the wild type strain, indicating the struggle of the bacterium to adapt to the host immune components.
2022-10-13 | PXD031437 | Pride
Project description:Aliivibrio salmonicida causes âcold-water vibriosisâ (or âHitra diseaseâ) in fish, including marine-reared Atlantic salmon. During development of the disease the bacterium will encounter macrophages with antibacterial activities such as production of damaging reactive oxygen species (ROS). To defend itself the bacterium will presumably start producing detoxifying enzymes, reducing agents, and proteins involved in DNA and protein repair systems. Even though responses to oxidative stress are well studied for a few model bacteria, little work has been done in general to explain how important groups of pathogens, like members of the Vibrionaceae family, can survive at high levels of ROS. We have used bioinformatic tools and an âomics approach to study how A. salmonicida responds to hydrogen peroxide (H2O2). First, we used the recently published genome sequence to predict potential binding sites for OxyR (H2O2 response regulator). The computer-based search identified OxyR sites associated with 20 single genes and 8 operons, and these predictions were compared to experimental data from Northern blot analysis, microarray analysis and 2D gel electrophoresis. In general, OxyR binding site predictions and experimental results are in agreement. Up- and down-regulated genes are distributed among all functional gene categories, but a striking number of â¥2 fold up-regulated genes encode proteins involved in detoxification or DNA protection and repair, are part of reduction systems, or are involved in carbon metabolism and regeneration of NADH/NADPH. Our predictions and âomics data corroborates well with findings from other model bacteria, but also suggest species-specific gene regulation. Two-condition experiment, cells grown in LB medium (control samples) vs. cells grown under oxidative stress (H2O2) (stimulated samples). Samples collected from three different timepoints (15, 30 and 60 min). Technical replicates for each timepoint: 3 control, 3 stimulated, independently grown and harvested. One replicate per array.
2010-05-06 | E-GEOD-20082 | biostudies-arrayexpress
Project description:Aliivibrio finisterrensis Genome sequencing and assembly
| PRJNA515947 | ENA
Project description:Aliivibrio fischeri Genome sequencing and assembly
| PRJNA311605 | ENA
Project description:Aliivibrio fischeri Genome sequencing and assembly
| PRJNA785243 | ENA
Project description:This SuperSeries is composed of the following subset Series: GSE25545: Prediction, microarray and Northern blot analyses identify new intergenic small RNAs in Aliivibrio salmonicida (LB medium vs. iron-limited condition) GSE25546: Prediction, microarray and Northern blot analyses identify new intergenic small RNAs in Aliivibrio salmonicida (wild type vs. LitR mutant) Refer to individual Series
2010-12-01 | E-GEOD-25558 | biostudies-arrayexpress
Project description:The availability of a reference genome assembly for Atlantic salmon, Salmo salar, SNP genotyping platforms and low cost sequencing is enhancing the understanding of both life history and production-related traits in this important commercial species. We collected and analysed transcriptomes from selected tissues of Atlantic salmon to inform future functional and comparative genomics studies. Messenger RNA (mRNA) was isolated from brain, pituitary, ovary and liver before Illumina sequencing produced a total of 640 million 150-bp paired-end reads. Following read mapping, feature counting and normalization, cluster analysis identified genes highly expressed in a tissue-specific manner. Functional profiling identified gene clusters describing the unique functions of each tissue. Moreover, highly-expressed transcription factors present in each tissue-specific gene cluster were identified. The data and analysis presented are relevant to the emerging Functional Annotation of All Salmonid Genomes (FAASG) initiative that is seeking to develop a detailed understanding of both salmonid evolution and the genomic elements that drive gene expression and regulation.
2018-08-22 | GSE114247 | GEO
Project description:Aliivibrio fischeri JRM200 Genome sequencing and assembly
| PRJNA212807 | ENA
Project description:Aliivibrio fischeri EM17 Genome sequencing and assembly
| PRJNA212806 | ENA