Ribosome Shunting, Polycistronic Translation, and Evasion of Antiviral Defenses in Plant Pararetroviruses and Beyond.

Mikhail M Pooggin,Lyubov A Ryabova

doi:10.3389/fmicb.2018.00644

Abstract

Viruses have compact genomes and usually translate more than one protein from polycistronic RNAs using leaky scanning, frameshifting, stop codon suppression or reinitiation mechanisms. Viral (pre-)genomic RNAs often contain long 5′-leader sequences with short upstream open reading frames (uORFs) and secondary structure elements, which control both translation initiation and replication. In plants, viral RNA and DNA are targeted by RNA interference (RNAi) generating small RNAs that silence viral gene expression, while viral proteins are recognized by innate immunity and autophagy that restrict viral infection. In this review we focus on plant pararetroviruses of the family Caulimoviridae and describe the mechanisms of uORF- and secondary structure-driven ribosome shunting, leaky scanning and reinitiation after translation of short and long uORFs. We discuss conservation of these mechanisms in different genera of Caulimoviridae, including host genome-integrated endogenous viral elements, as well as in other viral families, and highlight a multipurpose use of the highly-structured leader sequence of plant pararetroviruses in regulation of translation, splicing, packaging, and reverse transcription of pregenomic RNA (pgRNA), and in evasion of RNAi. Furthermore, we illustrate how targeting of several host factors by a pararetroviral effector protein can lead to transactivation of viral polycistronic translation and concomitant suppression of antiviral defenses. Thus, activation of the plant protein kinase target of rapamycin (TOR) by the Cauliflower mosaic virus transactivator/viroplasmin (TAV) promotes reinitiation of translation after long ORFs on viral pgRNA and blocks antiviral autophagy and innate immunity responses, while interaction of TAV with the plant RNAi machinery interferes with antiviral silencing.

Highlights

Viruses tend to evolve compact genomes with closely spaced or overlapping protein-coding sequences and rather short non-coding sequences stuffed with multiple regulatory cis-acting elements
In genera Tungrovirus and Caulimovirus, positioning of the reverse transcriptase (RT) primer binding site close to the end of the pregenomic RNA (pgRNA) leader, combined with a stable viroid-like secondary structure of 8S RNA, the run-off transcript terminating at the primer binding site and 5 -coterminal with pgRNA, has enabled to express a double-stranded RNA (dsRNA) decoy engaging the RNA interference (RNAi) machinery in massive small interfering RNA Sweet potato pakakuy virus (SPPV) (siRNA) production and thereby strongly reducing siRNA production from other regions of the viral genome
Other genera of Caulimoviridae with the RT binding site located downstream of the structured leader region may have evolved a similar decoy strategy of silencing evasion. Another milestone in the evolution of plant pararetroviruses was the acquisition of a unique gene encoding the transactivator protein TAV, which enabled to translate two and more consecutive large viral ORFs from a single pgRNA or its spliced variant

Summary

INTRODUCTION

Viruses tend to evolve compact genomes with closely spaced or overlapping protein-coding sequences and rather short non-coding sequences stuffed with multiple regulatory cis-acting elements This compactness allows for more efficient replication and encapsidation as well as successful competition with host mRNAs for translation in the cytoplasm and, in the case of DNA. In this review we focus on plant pararetroviruses (family Caulimoviridae) that have evolved (i) short upstream (u)ORFdependent ribosome shunting to regulate sorting of pregenomic RNA (pgRNA) for translation and reverse transcription, and (ii) leaky scanning and virus-activated reinitiation to make ribosomes translate two and more long ORFs from one polycistronic RNA. Likewise, during ribosome shunting in plant pararetroviruses, translation of the 5 -proximal uORF allows the post-terminating ribosomes to overcome the inhibitory effects of multiple downstream short uORFs and stable secondary structure and reinitiate translation of a long ORF downstream of the leader structure (discussed below). By analogy with SIV, uORF-mediated ribosomal sorting was proposed to operate in the human retrovirus HIV-1 for translation of vpu and env proteins from a dicistronic mRNA (van der Velden et al, 2012)

DISCOVERY OF RIBOSOME SHUNTING

RIBOSOME SHUNTING IN ANIMAL VIRUSES

POLYCISTRONIC TRANSLATION IN PLANT PARARETROVIRUSES

TAV ACTIVATES TOR KINASE TO BLOCK ANTIVIRAL AUTOPHAGY

Findings

CONCLUDING REMARKS AND EVOLUTIONARY IMPLICATIONS FOR THE FAMILY CAULIMOVIRIDAE