Figure 1 - uploaded by Peter Sarin
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Schematic overview of selected RNA components utilized by viruses to further their replication and suppress host immune responses. Abbreviations: PTM = post-transcriptional chemical modification of ribonucleosides; tRNA = transfer RNA; tRF = tRNA-derived fragment; vgRNA, vmRNA, vtRNA = virus-encoded genomic, messenger, or transfer RNA. Figure created with BioRender.
Source publication
Viruses feature an evolutionary shaped minimal genome that is obligately dependent on the cellular transcription and translation machinery for propagation. To suppress host cell immune responses and ensure efficient replication, viruses employ numerous tactics to favor viral gene expression and protein synthesis. This necessitates a carefully balan...
Contexts in source publication
Context 1
... is often achieved via an intricate network of viral and host factors. The focus here is on the role of selected RNA components, on what we can learn about protein synthesis control by studying how viruses use these RNA components to interact with the translation machinery (Figure 1). ...
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... is often achieved via an intricate network of viral and host factors. The focus here is on the role of selected RNA components, on what we can learn about protein synthesis control by studying how viruses use these RNA components to interact with the translation machinery (Figure 1). ...
Citations
... Viruses are obligate intracellular parasites that entirely rely on the transcription and translation machinery of the host cell for their replication. As outlined in the perspective by Sarin [7], RNA-based regulatory mechanisms have emerged as a focal point for infection studies. Viruses employ a number of these, including the post-transcriptional chemical modification of ribonucleosides, codon usage, and virusencoded transfer RNAs, as the means to further their replication and evade host immune responses [7]. ...
... As outlined in the perspective by Sarin [7], RNA-based regulatory mechanisms have emerged as a focal point for infection studies. Viruses employ a number of these, including the post-transcriptional chemical modification of ribonucleosides, codon usage, and virusencoded transfer RNAs, as the means to further their replication and evade host immune responses [7]. These RNA-based regulatory mechanisms not only play a crucial role in viral infection, but also provide opportunities for studying host-virus interactions and present potential targets for antiviral strategies. ...
... Recent studies have revealed that eukaryotic and prokaryotic viruses alike cause alterations at post-transcriptional ribonucleoside modification (PTM) levels, with specific changes being linked to codon recognition and preferential translation of viral transcripts over host mRNAs [7,9]. In their research article, Lampi et al. [10] investigate the dynamics of the transfer RNA (tRNA) modification landscape during Shewanella phage 1/4 infection in the cold-active marine bacterium, Shewanella glacialimarina. ...
For the better part of the century, microbes have been a treasure trove for deciphering the inner workings of the cell, from early insights into DNA replication and restriction-enzyme-mediated antiviral responses, to unravelling the complexities of metabolic pathways and understanding gene expression and its regulatory mechanisms [...]
... Table S1). Hence, as tRNA CCU Gly is only sparingly utilized, it is possible that the virus-encoded copy has a role in controlling co-translational folding and translation rate, or that it partakes in non-canonical regulatory functions in the cell [32]. ...
... Phage 1/4 does not encode for RNA modification enzymes of its own [16], but it is nonetheless plausible that cellular metabolites and enzymes may be potential targets during phage 1/4 infection, as modulating their availability and activity would have a direct impact on tRNA modification levels. Hence, it is conceivable that tRNA modifications play interconnected roles in regulating the translation of host-and virus-derived proteins, as well as in other non-canonical regulatory functions [32]. Moreover, we uncovered a surprising codon usage bias for a set of late viral genes (Table 1), which ought to hamper their translation. ...
Viruses are obligate intracellular parasites that, throughout evolution, have adapted numerous strategies to control the translation machinery, including the modulation of post-transcriptional modifications (PTMs) on transfer RNA (tRNA). PTMs are critical translation regulators used to further host immune responses as well as the expression of viral proteins. Yet, we lack critical insight into the temporal dynamics of infection-induced changes to the tRNA modification landscape (i.e., 'modificome'). In this study, we provide the first comprehensive quantitative characterization of the tRNA modificome in the marine bacterium Shewanella glacialimarina during Shewanella phage 1/4 infection. Specifically, we show that PTMs can be grouped into distinct categories based on modification level changes at various infection stages. Furthermore, we observe a preference for the UAC codon in viral transcripts expressed at the late stage of infection, which coincides with an increase in queuosine modification. Queuosine appears exclusively on tRNAs with GUN anticodons, suggesting a correlation between phage codon usage and PTM modification. Importantly, this work provides the basis for further studies into RNA-based regulatory mechanisms employed by bacteriophages to control the prokaryotic translation machinery.
