Juranic Lisnic, V. | bioRxiv Science

bioRxiv2025

Murine cytomegalovirus evolved a cell-cycle regulator (m54.5) within the highly conserved viral DNA polymerase gene

Ribosome profiling (Ribo-seq) coupled with transcription start site profiling time-course analyses recently unveiled hundreds of novel viral gene products in lytic murine cytomegalovirus (MCMV) infection. One of these is the m54.5 open reading frame (ORF) located within the highly conserved viral DNA polymerase locus (M54). Interestingly, the m54.5 ORF is expressed from its own transcript (m54.5 RNA) with early gene expression kinetics, and at much higher levels than M54. In this study, we show that m54.5 encodes a nuclear viral protein (m54.5p) that contributes to cell cycle regulation during lytic MCMV infection. We show that m54.5p interacts with components of the anaphase-promoting complex/cyclosome (APC/C) and the phosphatase-6 (PP6) complex. Nocodazole mitotic arrest assays confirmed G1 cell cycle arrest and dysregulation by m54.5. Serum starvation revealed impaired cell cycle progression to S-phase. Notably, m54.5p is not conserved in other cytomegaloviruses but functionally mimics the UL21a protein of human cytomegalovirus (HCMV), which similarly targets the master cell cycle regulator APC/C to disrupt cell cycle progression. m54.5 thus represents convergent evolution to HCMV UL21a in MCMV within the highly conserved viral DNA polymerase gene. Nevertheless, we found that m54.5p is dispensable for viral replication in cultured mouse fibroblasts, indicative of redundant cell cycle regulation in lytic MCMV infection. These findings highlight a surprising genomic plasticity of herpesviruses, facilitating the evolution of an independent transcript encoding for a >200 aa gene product within a deeply conserved viral gene locus. Author SummarySystems biology approaches have revealed a surprising complexity of herpesvirus gene products. Using advanced sequencing approaches, we discovered a novel gene, m54.5, that independently evolved within a highly conserved region of the murine cytomegalovirus (MCMV) genome. This gene, which shows no conservation in other CMVs, produces a nuclear protein, m54.5p, abundantly expressed early during infection. We show that m54.5p interacts with host cell cycle regulators--the anaphase-promoting complex/cyclosome (APC/C) and phosphatase-6 (PP6)--to arrest cells in G1 phase and block progression into S phase. This function and underlying mechanism are reminiscent of the unrelated UL21a protein in human cytomegalovirus, illustrating how distinct viruses can evolve similar strategies to control host cell division. Despite its role in cell cycle disruption, m54.5p is not required for MCMV replication in cultured cells, suggesting redundant viral mechanisms. Our findings reveal an unexpected plasticity of herpesvirus genomes to evolve new, functional transcripts and proteins even within one of the most highly conserved genomic regions. Our findings thereby reshape our understanding of herpesvirus evolution and virus-host interaction.

microbiology↗

bioRxiv2022

Decoding murine cytomegalovirus

The genomes of both human cytomegalovirus (HCMV) and murine cytomegalovirus (MCMV) were first sequenced over 20 years ago. Similar to HCMV, the MCMV genome had initially been proposed to harbor {approx}170 open reading frames (ORFs). More recently, omics approaches revealed HCMV gene expression to be substantially more complex comprising several hundreds of translated ORFs. Here, we provide a state-of-the art reannotation of lytic MCMV gene expression based on integrative analysis of a large set of omics data. Our data reveal 363 viral transcription start sites (TiSS) that give rise to 380 and 454 viral transcripts and ORFs, respectively. The latter include >200 small ORFs, some of which represented the most highly expressed viral gene products. By combining TiSS profiling with metabolic RNA labelling and chemical nucleotide conversion sequencing (dSLAM-seq), we provide a detailed picture of the expression kinetics of viral transcription. This not only resulted in the identification of a novel MCMV immediate early transcript encoding the m166.5 ORF, which we termed ie4, but also revealed a group of well-expressed viral transcripts that are induced later than canonical true late genes and contain an initiator element (Inr) but no TATA- or TATT-box in their core promoters. We show that viral uORFs tune gene expression of longer viral ORFs expressed in cis at translational level. Finally, we identify a truncated isoform of the viral NK-cell immune evasin m145 arising from a viral TiSS downstream of the canonical m145 mRNA. Despite being {approx}5-fold more abundantly expressed than the canonical m145 protein it was not required for downregulating the NK cell ligand, MULT-I. In summary, our work will pave the way for future mechanistic studies on previously unknown cytomegalovirus gene products in an important virus animal model. Author summaryWe conducted a comprehensive characterization and reannotation of murine cytomegalovirus (MCMV) gene expression during lytic infection in murine fibroblasts using an integrative multi-omics approach. This unveiled hundreds of novel transcripts that explained the expression of close to 300 so far unknown viral open reading frames (ORFs). Interestingly, small viral ORFs (sORFs) were amongst the most highly expressed viral gene products and thus presumably encode for important viral microproteins of unknown function. However, we also show that sORFs located upstream of larger ORFs tune the expression of the downstream ORFs at the level of translation. We classified viral transcription start sites (TiSS) based on their expression kinetics obtained by a new combination of metabolic RNA labelling with transcription start sites profiling. This not only identified a so far unknown viral immediate-early transcript (ie4, m166.5 RNA) but also revealed a novel class of viral late transcripts that are expressed later than canonical true late genes and lack TATA box-like motifs. We exemplify for the m145 locus how so far unknown TiSS give rise to abundantly expressed truncated viral proteins. In summary, we provide a state-of-the-art annotation of an important model virus, which will be instrumental for future studies on CMV biology, immunology and pathogenesis.

microbiology↗