Dataset Information

Transcriptomic Analysis Reveals the Dependency of Pseudomonas aeruginosa Genes for Double-Stranded RNA Bacteriophage phiYY Infection Cycle.

ABSTRACT: Bacteriophage phiYY is currently the only double-stranded RNA (dsRNA) phage that infects Pseudomonas aeruginosa and is a potential candidate for phage therapy. Here we applied RNA-seq to investigate the lytic cycle of phiYY infecting P. aeruginosa strain PAO1r. About 12.45% (651/5,229) of the host genes were determined to be differentially expressed genes. Moreover, oxidative stress response genes katB and ahpB are upregulated 64- to 128-fold after phage infection, and the single deletion of each gene blocked phiYY infection, indicating that phiYY is extremely sensitive to oxidative stress. On the contrary, another upregulated gene PA0800 might constrain phage infection, because the deletion of PA0800 resulted in a 3.5-fold increase of the efficiency of plating. Our study highlights a complicated dsRNA phage-phage global interaction and raises new questions toward the host defense mechanisms against dsRNA phage and dsRNA phage-encoded hijacking mechanisms.

SUBMITTER: Zhong Q

PROVIDER: S-EPMC7452160 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

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Transcriptomic Analysis Reveals the Dependency of Pseudomonas aeruginosa Genes for Double-Stranded RNA Bacteriophage phiYY Infection Cycle.

Zhong Qiu Q Yang Lan L Li Linlin L Shen Wei W Li Yang Y Xu Huan H Zhong Zhuojun Z Chen Ming M Le Shuai S

iScience 20200806 9

Bacteriophage phiYY is currently the only double-stranded RNA (dsRNA) phage that infects Pseudomonas aeruginosa and is a potential candidate for phage therapy. Here we applied RNA-seq to investigate the lytic cycle of phiYY infecting P. aeruginosa strain PAO1r. About 12.45% (651/5,229) of the host genes were determined to be differentially expressed genes. Moreover, oxidative stress response genes katB and ahpB are upregulated 64- to 128-fold after phage infection, an ...[more]

PMID: 32827855

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Project description:Significance Hfq is a key posttranscriptional regulator that modulates base-pairing interactions between sRNAs and their target mRNAs. Although there are more than 100 different sRNAs in Pseudomonas aeruginosa, information on their regulatory targets was available for only a few. Here, we identify the targets of 89 Hfq-associated sRNAs in this important opportunistic pathogen. Furthermore, we show that a single sRNA called PhrS dominates the RNA–RNA interaction landscape in this organism by pairing with approximately 800 targets. Our study therefore provides insight into the potential regulatory roles for many sRNAs in P. aeruginosa and identifies an sRNA with an acutely outsized influence on the RNA–RNA interactions occurring on Hfq in this bacterium. The RNA chaperone Hfq plays important regulatory roles in many bacteria by facilitating the base pairing between small RNAs (sRNAs) and their cognate mRNA targets. In the gram-negative opportunistic pathogen Pseudomonas aeruginosa, over a hundred putative sRNAs have been identified but for most, their regulatory targets remained unknown. Using RIL-seq with Hfq in P. aeruginosa, we identified the mRNA targets for dozens of previously known and unknown sRNAs. Strikingly, hundreds of the RNA–RNA interactions we discovered involved PhrS. This sRNA was thought to mediate its effects by pairing with a single target mRNA and regulating the abundance of the transcription regulator MvfR required for the synthesis of the quorum sensing signal PQS. We present evidence that PhrS controls many transcripts by pairing with them directly and employs a two-tiered mechanism for governing PQS synthesis that involves control of an additional transcription regulator called AntR. Our findings in P. aeruginosa expand the repertoire of targets for previously known sRNAs, reveal potential regulatory targets for previously unknown sRNAs, and suggest that PhrS may be a keystone sRNA with the ability to pair with an unusually large number of transcripts in this organism.

Dataset Information

Transcriptomic Analysis Reveals the Dependency of Pseudomonas aeruginosa Genes for Double-Stranded RNA Bacteriophage phiYY Infection Cycle.

Publications

Transcriptomic Analysis Reveals the Dependency of <i>Pseudomonas aeruginosa</i> Genes for Double-Stranded RNA Bacteriophage phiYY Infection Cycle.

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