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

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.

Susceptibility Genes to Plant Viruses

“…Antiviral defense restricts viral RNA translation, virus replication, movement, or virion assembly, resulting in reduced virus accumulation and/or a delay in virus movement with or without a hypersensitive response [ 26 , 27 , 28 ]. Antiviral defense mechanisms are reviewed in [ 26 , 29 ].…”

Translational gene regulation in plants: A green new deal

“…The mechanism of reinitiation is not fully understood in any organism (Gunisova, Hronova, Mohammad, Hinnebusch, & Valasek, 2018), but it is clear that spontaneous reinitiation is common only after short ORFs, typically uORFs in the 5' leader (von Arnim et al, 2014). In the exceptional case of cauliflower mosaic virus (CaMV), reinitiation after long coding sequences is boosted by the viral transactivator protein, TAV, a scaffold that coordinates with initiation factors such as eIF3 and eIF4B, other host proteins, and the ribosome (Pooggin & Ryabova, 2018). Extensive work on the 5' leader of CaMV and related pararetroviruses has suggested that the reinitiating 40S has different properties from a cap-dependent 40S.…”

“…Extensive work on the 5' leader of CaMV and related pararetroviruses has suggested that the reinitiating 40S has different properties from a cap-dependent 40S. For example, even in the absence of TAV, the reinitiating 40S is capable of "shunting" past a 500 nt secondary structure in the CaMV 5' leader ( Figure 3b), and its ability to distinguish authentic from near-cognate start codons may be reduced (Pooggin & Ryabova, 2018).…”

“…Interestingly, in nearly every virus examined, the capacity to shunt requires a short uORF right upstream of the shunt take-off site. Apparently, some property specific to the posttermination (40S) ribosome makes it permissive to skip past the hairpin structure, possibly because the prior translation event stripped helicase activities from the 40S subunit (Pooggin & Ryabova, 2018).…”

Conservation of Translation Initiation Between Prokaryotes and Eukaryotes

“…In both cases, the 5'-proximal sORF within the leader is translated prior to encountering the hairpin structure, which then forces the ribosome to shunt to a downstream portion of the mRNA sequence (pairing ribosome shunting and reinitiation, which is mentioned below). While identified in plant viruses, ribosomal shunting also occurs in animal viruses and in cellular mRNAs (Pooggin and Ryabova, 2018).…”