Hybrid Gene Origination Creates Human-Virus Chimeric Proteins during Infection

Jessica Ho ,Christopher Benner,Zeyu Zhu,Adam M Dinan,Maria João Amorim,Joshua D Jones,Alessandro Vannini,Emily R Miraldi,Nerea Irigoyen,Vladimir Roudko,Elizabeth Sloan,Guojun Wang,Yesai Fstkchyan,Laura Campisi,Jiajie Wei,Zuleyma Peralta,Marta Alenquer,Edward Hutchinson,Justine Noel,Bo Wang,Marta Łuksza,Ivan Marazzi,Slobodan Paessler,Léa Meyer,Sara Clohisey,Ingeborg Van Knippenberg,Yixuan Ma,Andrew E Firth,Cheng Huang,Quan Gu,Natasha Moshkina,Harm Van Bakel,Paul Digard,Ian Brierley,Matthew Angel,Nan Zhao,Jonathan W Yewdell,Liliane Chung,Simin Zheng,Rong Shen,Jeffrey R Johnson ,Megan K L Macleod ,James S Gibbs ,Adolfo Garcı́a-Sastre ,Robert J Gifford ,J Kenneth Baillie ,Max W Chang ,Helen Wise ,Robyn M Kaake ,Benjamin Greenbaum ,Brad R Rosenberg ,Nevan J Krogan ,Veronica V Rezelj ,Carles Martínez-Romero

doi:10.1016/j.cell.2020.05.035

Abstract

SummaryRNA viruses are a major human health threat. The life cycles of many highly pathogenic RNA viruses like influenza A virus (IAV) and Lassa virus depends on host mRNA, because viral polymerases cleave 5′-m7G-capped host transcripts to prime viral mRNA synthesis (“cap-snatching”). We hypothesized that start codons within cap-snatched host transcripts could generate chimeric human-viral mRNAs with coding potential. We report the existence of this mechanism of gene origination, which we named “start-snatching.” Depending on the reading frame, start-snatching allows the translation of host and viral “untranslated regions” (UTRs) to create N-terminally extended viral proteins or entirely novel polypeptides by genetic overprinting. We show that both types of chimeric proteins are made in IAV-infected cells, generate T cell responses, and contribute to virulence. Our results indicate that during infection with IAV, and likely a multitude of other human, animal and plant viruses, a host-dependent mechanism allows the genesis of hybrid genes.

Highlights

In eukaryotes, ribosomes typically recognize mRNAs with a terminal 50 cap structure followed by an untranslated region (UTR), which can be tens to hundreds of nucleotides in length (Decroly et al, 2011; Kochetov et al, 2008; Leppek et al, 2018)
A growing body of work has shown that translation can initiate in the 50 UTRs of a large proportion of eukaryotic mRNAs, sometimes extremely close to the 50 cap, resulting in upstream open reading frames (Andreev et al, 2015; Calvo et al, 2009; Dikstein, 2012; Elfakess and Dikstein, 2008; Haimov et al, 2017; Johnstone et al, 2016; Kochetov et al, 2008; Young and Wek, 2016)
influenza A virus (IAV) Cap-Snatches Sequences Containing uAUGs IAV gene transcription is initiated by cap-snatching from a host mRNA (Figure 1A)

Summary

Introduction

Ribosomes typically recognize mRNAs with a terminal 50 cap structure followed by an untranslated region (UTR), which can be tens to hundreds of nucleotides in length (Decroly et al, 2011; Kochetov et al, 2008; Leppek et al, 2018). A growing body of work has shown that translation can initiate in the 50 UTRs of a large proportion of eukaryotic mRNAs, sometimes extremely close to the 50 cap, resulting in upstream open reading frames (uORFs) (Andreev et al, 2015; Calvo et al, 2009; Dikstein, 2012; Elfakess and Dikstein, 2008; Haimov et al, 2017; Johnstone et al, 2016; Kochetov et al, 2008; Young and Wek, 2016). In sNSVs, viral mRNA synthesis is primed using short 50 methyl-7-guanosine (m7G) capped RNA sequences, which the viral polymerase cleaves from host RNA polymerase II (RNAPII) transcripts in a process known as ‘‘capsnatching’’ (Dias et al, 2009; Plotch et al, 1981; Reich et al, 2014; Rialdi et al, 2017). Viral mRNAs are translated by the host machinery

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Conclusion