Integrative omics analysis of Pseudomonas aeruginosa virus PA5oct highlights the molecular complexity of jumbo phages.

Environmental Microbiology
Cédric LoodRob Lavigne

Abstract

Pseudomonas virus vB_PaeM_PA5oct is proposed as a model jumbo bacteriophage to investigate phage-bacteria interactions and is a candidate for phage therapy applications. Combining hybrid sequencing, RNA-Seq and mass spectrometry allowed us to accurately annotate its 286,783 bp genome with 461 coding regions including four non-coding RNAs (ncRNAs) and 93 virion-associated proteins. PA5oct relies on the host RNA polymerase for the infection cycle and RNA-Seq revealed a gradual take-over of the total cell transcriptome from 21% in early infection to 93% in late infection. PA5oct is not organized into strictly contiguous regions of temporal transcription, but some genomic regions transcribed in early, middle and late phases of infection can be discriminated. Interestingly, we observe regions showing limited transcription activity throughout the infection cycle. We show that PA5oct upregulates specific bacterial operons during infection including operons pncA-pncB1-nadE involved in NAD biosynthesis, psl for exopolysaccharide biosynthesis and nap for periplasmic nitrate reductase production. We also observe a downregulation of T4P gene products suggesting mechanisms of superinfection exclusion. We used the proteome of PA5oct to posit...Continue Reading

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Citations

Sep 2, 2020·Journal of Bacteriology·Jingwen Guan, Joseph Bondy-Denomy
Nov 14, 2020·Current Opinion in Biotechnology·Michela Gambino, Lone Brøndsted
Mar 26, 2021·Frontiers in Microbiology·Yoona LeeSangryeol Ryu
Oct 6, 2021·Critical Reviews in Food Science and Nutrition·Md Rashedul IslamHany Anany

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Datasets Mentioned

BETA
PRJNA516157
GSE130190

Methods Mentioned

BETA
dissection
electron microscopy

Software Mentioned

ARNold
TopHat
sniffles browser ribbonviewer
InterPro
mem
HHpred
Phyre2
R
Samtools
vConTACT

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