Tobamovirus 3′-Terminal Gene Overlap May be a Mechanism for within-Host Fitness Improvement

Abstract

Overlapping genes (OGs) are a universal phenomenon in all kingdoms, and viruses display a high content of OGs combined with a high rate of evolution. It is believed that the mechanism of gene overlap is based on overprinting of an existing gene. OGs help virus genes compress a maximum amount of information into short sequences, conferring viral proteins with novel features and thereby increasing their within-host fitness. Analysis of tobamovirus 3′-terminal genes reveals at least two modes of OG organization and mechanisms of interaction with the host. Originally isolated from Solanaceae species, viruses (referred to as Solanaceae-infecting) such as tobacco mosaic virus do not show 3′-terminal overlap between movement protein (MP) and coat protein (CP) genes but do contain open reading frame 6 (ORF6), which overlaps with both genes. Conversely, tobamoviruses, originally isolated from Brassicaceae species (referred to as Brassicaceae-infecting) and also able to infect Solanaceae plants, have no ORF6 but are characterized by overlapping MP and CP genes. Our analysis showed that the MP/CP overlap of Brassicaceae-infecting tobamoviruses results in the following: (i) genome compression and strengthening of subgenomic promoters; (ii) CP gene early expression directly from genomic and dicistronic MP subgenomic mRNA using an internal ribosome entry site (IRES) and a stable hairpin structure in the overlapping region; (iii) loss of ORF6, which influences the symptomatology of Solanaceae-infecting tobamoviruses; and (iv) acquisition of an IRES polypurine-rich region encoding an MP nuclear localization signal. We believe that MP/CP gene overlap may constitute a mechanism for host range expansion and virus adjustment to Brassicaceae plants.

Diversity of Plant Virus Movement Proteins: What Do They Have in Common?

“…The decrease in the synthesis of MP:GFP directed by the infectious copy of the TMV is explained by the peculiarity of the functioning of the TMV subgenomic promoters; specifically, their "strength" decrease when the distance between the subgenomic promoter and the 3'-end of the TMV genomic RNA increases [115][116][117]. However, decreased MP:GFP synthesis did not significantly affect the development of infection at fluorescent infection sites on N. tabacum and N. benthamiana leaves [19,118].…”

“…MP self-movement is the basis for the mechanism of cell conditioning [10] or cell "predisposing" [18] that results in creating a favorable environment for the accelerated intercellular movement of genomic vRNA in the leading edge of the viral infection focus [118]. We believe that the cell conditioning occurs as follows: first, early synthesis of MP is likely mediated by an internal ribosome entry site (IRES MP,75 ) that allows translation of the MP gene directly from genomic RNA even before the synthesis of subgenomic RNA [117,[163][164][165][166]. Moreover, direct experiments to restore movement function using the KK6 TMV mutant [167] containing IRES CR MP,75 , confirmed the possibility of early synthesis of MP from the genomic TMV RNA [168].…”

Non-Canonical Translation Initiation Mechanisms Employed by Eukaryotic Viral mRNAs

“…It resembles the above-described IRESs from the 5′ UTR of RhPV and HalV viruses: RNA segments rich in adenine residues seem to form extended single-stranded elements that are capable of providing internal translation initiation not only in plants, but also in yeast and mammalian cells [ 176 ]. On the other hand, like all tobamoviruses, crTMV encodes a separate monocistronic sgRNA CP, and due to this, the bicistronic mRNA contributes only about 3% of the total synthesis of CP [ 177 ]. A similar assessment of the contribution of internal initiation was made for the unstructured IRES from the turnip wrinkle virus (TCV) [ 178 ].…”

The Tobamoviral Movement Protein: A “Conditioner” to Create a Favorable Environment for Intercellular Spread of Infection

“…All the above-mentioned considerations of the mechanisms of early synthesis of MP are based on its synthesis from a dicistronic intermediate length RNA-2 called sgRNA I 2 (Bruening et al, 1976;Higgins et al, 1976;Beachy and Zaitlin, 1977;Goelet et al, 1982). However, another mechanism for the early synthesis of MP, in addition to subgenomic mRNA, has long been known (Skulachev et al, 1999;Dorokhov et al, 2002;Komarova et al, 2003;Dorokhov et al, 2006;Dorokhov et al, 2017). This mechanism involves the direct binding of ribosomes on the 75-nt sequence of the internal ribosome entry site (IRES) as part of the TMV U1 (IRES MP,75 U1 ) genomic RNA (Skulachev et al, 1999).…”

“…Methanol vapors activate methanol-inducible genes (MIGs), including BG and non-cell-autonomous pathway protein (NCAPP), which in turn stimulate intracellular trafficking and create favorable conditions for viral infection (Dorokhov et al, 2018a), especially at the early stages. While the synthesis of BG promotes the removal of callose as a plasmodesmal sphincter, NCAPP is a cellular factor that participates in PME/methanol regulation (Sheshukova et al, 2017) and is indispensable for MP functioning (Lee et al, 2003;Lucas et al, 2009).…”