A Novel Strategy for Exploitation of Host RNase E Activity by a Marine Cyanophage

Abstract

Previous studies have shown that infection of Prochlorococcus MED4 by the cyanophage P-SSP7 leads to increased transcript levels of host endoribonuclease (RNase) E. However, it has remained enigmatic whether this is part of a host defense mechanism to degrade phage messenger RNA (mRNA) or whether this single-strand RNA-specific RNase is utilized by the phage. Here we describe a hitherto unknown means through which this cyanophage increases expression of RNase E during phage infection and concomitantly protects its own RNA from degradation. We identified two functionally different RNase E mRNA variants, one of which is significantly induced during phage infection. This transcript lacks the 59 UTR, is considerably more stable than the other transcript, and is likely responsible for increased RNase E protein levels during infection. Furthermore, selective enrichment and in vivo analysis of double-stranded RNA (dsRNA) during infection revealed that phage antisense RNAs (asRNAs) sequester complementary mRNAs to form dsRNAs, such that the phage protein-coding transcriptome is nearly completely covered by asRNAs. In contrast, the host protein-coding transcriptome is only partially covered by asRNAs. These data suggest that P-SSP7 orchestrates degradation of host RNA by increasing RNase E expression while masking its own transcriptome from RNase E degradation in dsRNA complexes. We propose that this combination of strategies contributes significantly to phage progeny production.KEYWORDS antisense RNA; T7-like cyanophage P-SSP7; dsRNA fishing; RNase E; Prochlorococcus A common theme of the lifestyle of viruses is the manipulation of host metabolism for the purpose of viral reproduction. However, different virus types have established different regulatory pathways for the takeover and manipulation of their particular hosts. For example, all genes of T4 and the early genes of T7 Escherichia coli bacteriophages are transcribed by the host RNA polymerase (RNAP) (Ueno and Yonesaki 2004;Molineux 2006). However, expression of middle and late T4 genes is mediated by host RNAP that has been modified by T4-encoded factors (Ueno and Yonesaki 2004). In contrast to T4, the subsequent T7 expression program is coordinated by the activity of a phage RNAP (Maniloff and Ackermann 1998). Nevertheless, direct manipulation of host proteins plays a crucial role for the gene expression program of T7.The gene product of the early T7 0.7 gene codes for a protein kinase (Rahmsdorf et al. 1974) and is responsible for phosphorylation and, thus, functional manipulation of .90 host proteins (Robertson et al. 1994). For example, phosphorylation of host RNAP b9-subunit (Zillig et al. 1975) results in reduced processivity, which is believed to assist in the coordinated transition of expression from T7 cluster 1 to cluster 2 genes (Severinova and Severinov 2006). In addition, phosphorylation of translation factors such as IF1, IF2, and IF3 is required for expression of T7 cluster 3 genes (Robertson and Nicholson 1992).Another protein of particul...

Vibrio Phage KVP40 Encodes a Functional NAD + Salvage Pathway

“…So, it is not surprising that entirely new biochemical processes not previously seen in the T-even phages are being observed. Thus, we encounter the aforementioned psbA and psbD (and hli) photosynthesis-related genes in the cyanomyovirus genomes that appear to be important for phage in the marine environmental niche/ host (22,34) and the novel massive whole-genome antisense RNA suppression of phage mRNA degradation by host RNase E by these same types of phages (35). Interestingly, whenever natV is observed in a phage genome, there is always a nadV in that genome as well (Table 1); the converse is not the case.…”

Synergic Effects of Temperature and Irradiance on the Physiology of the Marine Synechococcus Strain WH7803

“…This abundance, ubiquity and the availability of many genomes and strains in culture make Synechococcus one of the most relevant model microorganisms to study the response to variations of environmental conditions in the marine ecosystem. Quite a few transcriptomic studies have been conducted on Prochlorococcus and Synechococcus strains ( Tolonen et al, 2006 ; Lindell et al, 2007 ; Zinser et al, 2009 ; Tetu et al, 2009 , 2013 ; Blot et al, 2011 ; Thompson et al, 2011 ; Mella-Flores et al, 2012 ; Reistetter et al, 2013 ; Voigt et al, 2014 ; Stazic et al, 2016 ; Lambrecht et al, 2019 ), but they have mainly focused on the effect of single environmental factors. Here, the well-characterized marine Synechococcus strain WH7803, a warm temperature-adapted ecotype, which also has the advantage of being axenic ( Kana and Glibert, 1987a , b ; Kana et al, 1988 ; Garczarek et al, 2008 ; Blot et al, 2011 ; Mella-Flores et al, 2012 ; Pittera et al, 2018 ), was selected to study the effect of various stress conditions, high light (HL), UV, low (LT) and high (HT) temperatures, on cultures previously acclimated to either low light (LL) or HL conditions, as well as to assess the effect of diel variations, as triggered by a modulated light/dark (L/D) cycle.…”

Structural elucidation of a novel mechanism for the bacteriophage-based inhibition of the RNA degradosome

“…Finally, an increase in the expression of RNase E was observed during the infection of Prochlorococcus MED4 by cyanophage P-SSP7, due to elevated levels of an RNase E mRNA variant lacking the 5’UTR responsible for the negative feedback regulation of the gene. In parallel, antisense RNAs derived from the phage sequester the P-SSP7 transcriptome to form dsRNA, which is subsequently protected from degradation by RNase E ( Sesto et al, 2013 ; Stazic et al, 2016 , 2011 ).…”