Vibrio harveyi strain:345
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PROVIDER: PRJNA801904 | ENA |
REPOSITORIES: ENA
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Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare the gene (including sRNA) expression of the Wild Type Vibrio harveyi 345 and hfq mutant 345∆hfq, thus to figure out the effect of hfq on the gene expression of V. harveyi Methods:The mid-log bacterial cells (OD600 = 3.5) of wild type strain V. harveyi 345 and the hfq mutant strain 345∆hfq were collected to extract the total RNA. TruSeqTM RNA sample preparation Kit (Illumina, San Diego, CA)) was used to prepare RNA-seq transcriptome library using 2μg of total RNA. The Illumina HiSeq×TEN was performed to sequence the paired-end RNA-seq sequencing library (2 × 150bp read length). A Perl program was written to remove low-quality sequences, reads with more than 5% of N bases (unknown bases) and reads containing adaptor sequences, obtaining clean reads. The high quality reads in each sample were mapped to the referent V. harveyi (PRJNA418027) genome by Bowtie2 (Langmead and Salzberg, 2012). Transcript per million (TPM) mapped reads was calculated by RSEM (Dewey and Li, 2011) to assessment the gene expression. The different expressed genes (DEGs) were identified by using the edgeR, DESeq2, or DESeq packages (Anders, 2010; Love et al., 2014; Smyth, 2020). The cluster Profiler software KOBAS 2.0 (Chen et al., 2011) was used to perform KEGG pathway enrichment analysis of DGEs. The adjusted P-value (padj) ≤ 0.05 was the threshold for significant enrichment.The software Rockhopper (Ryan et al., 2013) was used to predict sRNAs basing on base sequencing coverage. Then the sRNAs were annotated by Blast, sRNAMap, sRNATarBase, SIPHT, and Rfam (Hsi-Yuan et al., 2008; Cao et al., 2010). RNAfold (Denman, 1993) was performed to predicted sRNAs second structure. RNAphybrid and RNAplex were used to predicted sRNAs targets (Jan and Marc, 2006; Tafer and Hofacker, 2008). Results: There were total 883 genes significantly differential expressed in 345Δhfq compared with the wild type strain V. harveyi 345, accounting for 16.39% of the total genes on V. harveyi 345 with 538 were up-regulated and 345 were down-regulated. The up-regulated genes were enriched mainly in the pathways those involved into metabolism, including biosynthesis of siderophore group nonribosomal peptides, phosphotransferase system (PTS), starch and sucrose metabolism, amino sugar and nucleotide sugar metabolism, fructose and mannose metabolism, naphthalene degradation, chloroalkane and chloroalkene degradation, ascorbate and aldarate metabolism, fatty acid degradation, retinol metabolism, and histidine metabolism. The down-regulated genes were mainly enriched in shigellosis (fliC), NOD-like receptor signaling pathway (fliC), Salmonella infection (gapA, fliC), legionellosis (fliC), plant-pathogen interaction (fliC), apoptosis, flagellar assembly (flgI, fliD, fliS, motY, and fliC), bacterial chemotaxis (malE, cheV, cheW, and mcp), and microRNAs in cancer (dcm) which were involved into bacterial virulence. In addition, a total of 434 sRNAs were obtained in the transcriptome data, and 11 sRNAs were significantly down-regulated (padjust>0.05, fold change >8, and at least one the strains Transcripts Per Million reads tpm >50) without hfq. The RNAfold indicated that all the sRNAs were stem-loop structures. Conclusions: Our study represents the first detailed analysis of the effect of hfq on gene expression of Vibrio harveyi by RNA-seq technology. We conclude that Hfq played variable roles in bacterial metabolism, cell mobility, bacterial chemotaxis, biofilm formation, and secretion which are associated with bacterial virulence.
2022-06-01 | GSE195758 | GEO
Project description:Objectives: determination of transcription start sites in Vibrio harveyi genome and discovery of new transcripts Methods: we performed differential seqencing of total RNA isolated from o.n. control Vibrio harveyi cultures. Sample treatment with Terminator EXonuclease (TEX) allowed differenciation of primary and secondary transcripts, helping in the definition of transcription start sites (TSS) Results: by data-mining RNA-seq data and performing some Northern Blot experiments we were able to detect new putative small-RNAs, along with these results, a more deep analisys of our RNA-seq data will give futher insight into genetic organization of Vibrio harveyi genome to help in its investigation
2018-03-27 | GSE105060 | GEO
Project description:Vibrio harveyi Genome sequencing and assembly
| PRJNA418027 | ENA
Project description:Vibrio harveyi is a major bacterial pathogen that can cause fatal vibriosis in Chinese tongue sole (Cynoglossus semilaevis). To comprehend the molecular mechanisms of C. semilaevis host response against V. harveyi infection, we performed transcriptome (RNA-seq) analysis of C. semilaevis from resistant family and susceptible family.
2019-02-26 | GSE126995 | GEO
Project description:In this research, we used RNA-sequencing technology to detect genome-wide differentially expressed genes in spleen and gill of Vibrio harveyi -infected Takifugu rubripes.This high-throughput sequencing could help us to understand new mechanisms of action of V. harveyi induced aquaculture fish disease.
2022-02-23 | GSE155911 | GEO
Project description:Vibrio species represent one of the most diverse genera of marine bacteria known for their ubiquitous presence in natural aquatic systems. Several members of this genus including Vibrio harveyi are receiving increasing attention lately because they are becoming a source of health problems, especially for some marine organisms widely used in sea food industry. To learn about adaptation changes triggered by V. harveyi during its long-term persistence at elevated temperatures, we studied adaptation of this marine bacterium in sea water microcosms at 30 oC that closely mimicks the upper limits of sea surface temperatures recorded around the globe.
2019-02-05 | GSE113564 | GEO
Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type Vibrio harveyi 345 and hfq mutant 345∆hfq Transcriptomes
| PRJNA802111 | ENA
Project description:Quorum sensing controls hundreds of genes in vibrios required for cell density-specific behaviors, including bioluminescence, biofilm formation, competence, secretion, and motility. The central regulator in the quorum sensing pathway in vibrios is LuxR/HapR, which directly regulates >100 genes in the 625-gene regulon of Vibrio harveyi. Among these directly regulated genes are 15 transcription factors, which we predicted would comprise the second tier in the hierarchy of the quorum sensing regulon. To better study the mechanism of regulation of the quorum sensing network, we mapped all transcriptional start sites in V. harveyi using dRNA-seq. From these data, we determined the relative position of LuxR binding sites in the promoters of genes directly regulated by LuxR. We confirmed that LuxR directly binds to the promoters of the genes encoding transcription factors and quantified the extent of LuxR activation or repression of transcript levels. Finally, we determined the individual regulons for a subset of transcription factors that have not been previously studied. For regulators such as LysR- or AsnC/Lrp-type transcription factors, the regulons contained >100 genes that contained both unique and overlapping genes with the LuxR regulon. These data support a model in which LuxR directly regulates other transcription factors, which act to further alter the second tier of the gene expression cascade producing cell density behaviors in V. harveyi.
2020-05-15 | GSE144017 | GEO
Project description:Draft genome sequence of Vibrio harveyi strain GAN1807
| PRJDB8137 | ENA