Small regulatory RNAs in lambdoid bacteriophages and phage-derived plasmids: Not only antisense

Nejman-Faleńczyk, Bożena; Bloch, Sylwia; Licznerska, Katarzyna; Felczykowska, Agnieszka; Dydecka, Aleksandra; Węgrzyn, Alicja; Węgrzyn, Grzegorz

doi:10.1016/j.plasmid.2014.07.006

Cited by 10 publications

(7 citation statements)

References 49 publications

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“…Since polyadenylated oop RNA is rapidly degraded in E. coli cells (Szalewska-Pałasz et al, 1998), impaired modification of this transcript would result in its stabilization, more effective inhibition of cII expression, less efficient production of the cI repressor and difficulties in lysogenization. Such a mechanism could also operate in Stx phages as oop RNA has been reported for W24 B , 933W and some other lambdoid phages (Nejman-Faleń czyk et al, 2015). However, if modification of oop RNA is the only cause of polyadenylation-facilitated lysogenization, it must be more effective than in l.…”

Section: Discussionmentioning

confidence: 91%

Defects in RNA polyadenylation impair both lysogenization by and lytic development of Shiga toxin-converting bacteriophages

Nowicki

Bloch

Nejman-Faleńczyk

et al. 2015

Journal of General Virology

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In Escherichia coli, the major poly(A) polymerase (PAP I) is encoded by the pcnB gene. In this report, a significant impairment of lysogenization by Shiga toxin-converting (Stx) bacteriophages (W24 B , 933W, P22, P27 and P32) is demonstrated in host cells with a mutant pcnB gene. Moreover, lytic development of these phages after both infection and prophage induction was significantly less efficient in the pcnB mutant than in the WT host. The increase in DNA accumulation of the Stx phages was lower under conditions of defective RNA polyadenylation. Although shortly after prophage induction, the levels of mRNAs of most phage-borne early genes were higher in the pcnB mutant, at subsequent phases of the lytic development, a drastically decreased abundance of certain mRNAs, including those derived from the N, O and Q genes, was observed in PAP I-deficient cells. All of these effects observed in the pcnB cells were significantly more strongly pronounced in the Stx phages than in bacteriophage l. Abundance of mRNA derived from the pcnB gene was drastically increased shortly (20 min) after prophage induction by mitomycin C and decreased after the next 20 min, while no such changes were observed in non-lysogenic cells treated with this antibiotic. This prophage induction-dependent transient increase in pcnB transcript may explain the polyadenylation-driven regulation of phage gene expression.

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Section: Discussionmentioning

confidence: 91%

Defects in RNA polyadenylation impair both lysogenization by and lytic development of Shiga toxin-converting bacteriophages

Nowicki

Bloch

Nejman-Faleńczyk

et al. 2015

Journal of General Virology

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“…Although cis -antisense RNAs appear to be a common form of regulation in bacterial genomes, they have not been extensively described in phage genomes. Beside the regulatory oop RNA reported over 40 years ago (reviewed in [ 26 ]), no other asRNAs were reported until recently [ 27 ] and exclusively in lambdoid phages. Moreover, such asRNAs have never been reported for virulent phages until 2014 [ 28 ].…”

Section: Discussionmentioning

confidence: 99%

Next-Generation “-omics” Approaches Reveal a Massive Alteration of Host RNA Metabolism during Bacteriophage Infection of Pseudomonas aeruginosa

et al. 2016

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As interest in the therapeutic and biotechnological potentials of bacteriophages has grown, so has value in understanding their basic biology. However, detailed knowledge of infection cycles has been limited to a small number of model bacteriophages, mostly infecting Escherichia coli. We present here the first analysis coupling data obtained from global next-generation approaches, RNA-Sequencing and metabolomics, to characterize interactions between the virulent bacteriophage PAK_P3 and its host Pseudomonas aeruginosa. We detected a dramatic global depletion of bacterial transcripts coupled with their replacement by viral RNAs over the course of infection, eventually leading to drastic changes in pyrimidine metabolism. This process relies on host machinery hijacking as suggested by the strong up-regulation of one bacterial operon involved in RNA processing. Moreover, we found that RNA-based regulation plays a central role in PAK_P3 lifecycle as antisense transcripts are produced mainly during the early stage of infection and viral small non coding RNAs are massively expressed at the end of infection. This work highlights the prominent role of RNA metabolism in the infection strategy of a bacteriophage belonging to a new characterized sub-family of viruses with promising therapeutic potential.

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“…Furthermore, based on the bioinformatics analysis it is assumed that the intragenic sRNA can be targeting a host mRNA, likely being an element of phage-host interaction strategy. Hitherto, the presence of phage sRNA and host RNA interactions were described mainly for ncRNA encoded by the prophages (reviewed in [ 49 ]).…”

Section: Discussionmentioning

confidence: 99%

RNA-Sequencing Reveals the Progression of Phage-Host Interactions between φR1-37 and Yersinia enterocolitica

Leskinen

Blasdel

Lavigne

et al. 2016

Viruses

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Despite the expanding interest in bacterial viruses (bacteriophages), insights into the intracellular development of bacteriophage and its impact on bacterial physiology are still scarce. Here we investigate during lytic infection the whole-genome transcription of the giant phage vB_YecM_φR1-37 (φR1-37) and its host, the gastroenteritis causing bacterium Yersinia enterocolitica. RNA sequencing reveals that the gene expression of φR1-37 does not follow a pattern typical observed in other lytic bacteriophages, as only selected genes could be classified as typically early, middle or late genes. The majority of the genes appear to be expressed constitutively throughout infection. Additionally, our study demonstrates that transcription occurs mainly from the positive strand, while the negative strand encodes only genes with low to medium expression levels. Interestingly, we also detected the presence of antisense RNA species, as well as one non-coding intragenic RNA species. Gene expression in the phage-infected cell is characterized by the broad replacement of host transcripts with phage transcripts. However, the host response in the late phase of infection was also characterized by up-regulation of several specific bacterial gene products known to be involved in stress response and membrane stability, including the Cpx pathway regulators, ATP-binding cassette (ABC) transporters, phage- and cold-shock proteins.

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Small regulatory RNAs in lambdoid bacteriophages and phage-derived plasmids: Not only antisense

Cited by 10 publications

References 49 publications

Defects in RNA polyadenylation impair both lysogenization by and lytic development of Shiga toxin-converting bacteriophages

Defects in RNA polyadenylation impair both lysogenization by and lytic development of Shiga toxin-converting bacteriophages

Next-Generation “-omics” Approaches Reveal a Massive Alteration of Host RNA Metabolism during Bacteriophage Infection of Pseudomonas aeruginosa

RNA-Sequencing Reveals the Progression of Phage-Host Interactions between φR1-37 and Yersinia enterocolitica

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