The Transcription and Translation Landscapes during Human Cytomegalovirus Infection Reveal Novel Host-Pathogen Interactions

Abstract

Viruses are by definition fully dependent on the cellular translation machinery, and develop diverse mechanisms to co-opt this machinery for their own benefit. Unlike many viruses, human cytomegalovirus (HCMV) does suppress the host translation machinery, and the extent to which translation machinery contributes to the overall pattern of viral replication and pathogenesis remains elusive. Here, we combine RNA sequencing and ribosomal profiling analyses to systematically address this question. By simultaneously examining the changes in transcription and translation along HCMV infection, we uncover extensive transcriptional control that dominates the response to infection, but also diverse and dynamic translational regulation for subsets of host genes. We were also able to show that, at late time points in infection, translation of viral mRNAs is higher than that of cellular mRNAs. Lastly, integration of our translation measurements with recent measurements of protein abundance enabled comprehensive identification of dozens of host proteins that are targeted for degradation during HCMV infection. Since targeted degradation indicates a strong biological importance, this approach should be applicable for discovering central host functions during viral infection. Our work provides a framework for studying the contribution of transcription, translation and degradation during infection with any virus.

Long and Short Isoforms of the Human Cytomegalovirus UL138 Protein Silence IE Transcription and Promote Latency

“…No transcriptional start sites within the UL138 cds have been mapped (11,33,37), and inhibiting translation initiation at codon 1 by mutation does not preclude the production of pUL138-S (Fig. 2C).…”

“…Our current study demonstrates that the two protein isoforms of pUL138 may have both overlapping and distinct functions during HCMV infection. In recent years, many studies have contributed to a body of work that begins to effectively demonstrate the power and function of increased coding capacity in HCMV through transcriptional, translational, and posttranslational mechanisms (9,15,32,33,37,58,59). Further, many examples of viral protein isoforms that have similar or unique functions exist (60)(61)(62)(63)(64)(65)(66)(67), but these examples likely only begin to scratch the surface of the important roles that protein isoforms play in viral infection and virus-host interactions.…”

“…Genomic approaches have also cataloged previously undetected transcribed and translated sequences during both lytic and latent infections (34)(35)(36)(37). The UL136 gene described above generates a series of coterminal protein isoforms with both overlapping and distinct functions (9,15), illustrating the functional impact of previously unrecognized viral coding capacity.…”

Restriction of Human Cytomegalovirus Replication by ISG15, a Host Effector Regulated by cGAS-STING Double-Stranded-DNA Sensing

“…Attempts to distinguish discrete roles for conjugated versus unconjugated ISG15 have so far been equivocal in HCMV-infected cells (33; C. Bianco and I. Mohr, unpublished observations). Finally, because ISGylation occurs cotranslationally (10), HCMV might further influence host proteins targeted for ISG15 conjugation by regulating which host mRNAs are associated with polyribosomes (22,29). Excluding mRNAs from polyribosomes that code for antiviral proteins whose activities might be augmented by cotranslational ISGylation would limit the impact of ISG15 conjugation on HCMV replication.…”

Ribosome Profiling Reveals Translational Upregulation of Cellular Oxidative Phosphorylation mRNAs during Vaccinia Virus-Induced Host Shutoff

“…Importantly, ribosome profiling can also simultaneously reveal the translation of host mRNAs during a viral infection. In a recent study, translational changes in host genes upon HCMV infection were studied by simultaneous transcriptome sequencing (RNA-Seq) and ribosome profiling (17). That study revealed many host genes translationally activated or repressed by HCMV, which does not induce a host shutoff.…”