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Prediction, microarray and Northern blot analyses identify new intergenic small RNAs in Aliivibrio salmonicida (LB medium vs. iron-limited condition)

ABSTRACT: Bacterial small RNAs (sRNAs) are trans-encoded regulatory RNAs that typically bind mRNAs by short sequence complementarities and change the expression of the corresponding proteins. Some of the well characterized sRNAs serve critical steps in the regulation of important cellular processes, such as quorum sensing (Qrr), iron homeostasis (RyhB), oxidative stress (OxyS) and carbon metabolism (Spot42). However, many sRNAs remains to be identified, and the functional roles of sRNAs are known for only a small fraction. For example, of the hundreds of candidate sRNAs from members of the bacterial family Vibrionaceae the function is known for only nine. We have in this study significantly contributed to the discovery and verification of new sRNAs in a representative of Vibrioneceae, i.e., the A. salmonicida which causes severe disease in farmed Atlantic salmon and other fishes. A computational search for intergenic non-coding (nc) RNAs in the 4.6 Mb genome identified a total of 233 potential sRNAs and 19 other types of ncRNAs with homologs in Rfam. Depending on a set threshold value our microarray approach identified 50-80 sRNAs that are expressed under different growth conditions, twelve of which were verified by Northern blot analysis. In total our data identify nine previously unrecognized sRNAs.

ORGANISM(S): Aliivibrio salmonicida LFI1238 Aliivibrio salmonicida

PROVIDER: GSE25545 | GEO | 2010/12/01

SECONDARY ACCESSION(S): PRJNA142437

REPOSITORIES: GEO

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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.

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Prediction, microarray and Northern blot analyses identify new intergenic small RNAs in Aliivibrio salmonicida (LB medium vs. iron-limited condition)

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