The enigmatic genome of Chara australis virus

Abstract

Most of the genomic sequence of Chara australis virus (CAV), previously called Chara corallina virus, has been determined. It is a ssRNA molecule of 9065 nt with at least four ORFs. At its 59 end is an ORF encoding a protein of 227 kDa, distantly homologous to the multifunctional replicases of benyviruses and rubiviruses. Next is an ORF encoding a protein of 44 kDa, homologous to the helicases of pestiviruses. The third ORF encodes an unmatched protein of 38 kDa that is probably a movement protein. The fourth and 39-terminal ORF encodes a protein of 17.7 kDa homologous to the coat proteins of tobamoviruses. The short methyltransferase region of the CAV replicase matches only the C-terminal motif of benyvirus methyltransferases. This and other clues indicate that approximately 11 % and 2 % of the 59 and 39 termini of the complete CAV genome, respectively, are missing from the sequence. The aligned amino acid sequences of the CAV proteins and their nearest homologues contain many gaps but relationships inferred from them were little affected by removal of these gaps. Sequence comparisons show that three of the CAV genes may have diverged from the most closely related genes of other viruses 250-450 million years ago, and the sister relationship between the genes of CAV and those of benyviruses and tobamoviruses, mirroring the ancient sister relationship between charophytes (i.e. the algal host of CAV) and embryophytes (i.e. the plant hosts of tobamoviruses and benyviruses), is congruent with this possibility. INTRODUCTIONA large charophyte alga growing in the Murrumbidgee River near Canberra, Australia was reported to be infected with a tobamovirus (Gibbs et al., 1975;Skotnicki et al., 1976). The host was identified as Chara corallina var. corallina K. ex Willd., but more recently this species has been reclassified and named Chara australis var. nobilis (A. Braun) R. D. Wood (http://data.gbif.org/search/chara%20australis; http://www. algaebase.org/search/species/detail/?species_id=27145). This species is rightly called 'nobilis' as individual plants are up to 2 m in length, and their coenocytic internodal cells are up to 100 mm in length! The virus was reported to be a tobamovirus as its virions closely resembled those of tobacco mosaic tobamovirus (Zaitlin, 2000) except that their modal length was approximately 530 nm, rather than the 300 nm of all reported tobamoviruses. Moreover, preparations of its virions reacted with high-titre antisera prepared against the virions of tobacco mosaic and odontoglossum ringspot viruses, but not those of several other tobamoviruses. The new virus was named Chara corallina virus, but with the updated nomenclature of the host, we now call it Chara australis virus (CAV).Up to 22 % of the naturally infected Chara plants first found contained CAV virions, and some infected cells contained birefringent inclusions, like those found in tobacco mosaic virus (TMV)-infected plants (Sheffield, 1934;Steere & Williams, 1953). Healthy C. australis plants became infected when injected with viri...

Tobamoviruses have probably co-diverged with their eudicotyledonous hosts for at least 110 million years

“…This timing has since been supported by several lines of circumstantial evidence (Gibbs 1999; Gibbs et al. 2008, 2010, 2011), notably the possibility of co-divergence with their long-term eudicotyledonous hosts, because the relationships of the genomes of different tobamovirus species reflects the relationships of their hosts (Lartey, Voss, and Melcher 1996; Gibbs 1999), and as the relevant host clades diverged at least 100 million years ago (Magallón and Castillo 2009; Magallón, Hilu, and Quandt 2013), it suggests that the tobamoviruses did too.…”

Did Silencing Suppression Counter-Defensive Strategy Contribute to Origin and Evolution of the Triple Gene Block Coding for Plant Virus Movement Proteins?

“…This is Chara australis virus (CAV; Gibbs et al, 2011), the largest encoded protein of which shows the relationship with RNA polymerases of benyviruses, while the coat protein – with the coat protein of tobamoviruses, thus reflecting the ancient sister relationship between hosts of these viruses, charophytes and land plants. Two additional CAV ORFs code for non-replicative RNA helicase and a protein of unknown function.…”

Characterization of burdock mottle virus, a novel member of the genus Benyvirus, and the identification of benyvirus-related sequences in the plant and insect genomes

“…BdMoV CP has 31-39% identity to benyvirus CPs (Table 1). The CP of CAV is closely related to those of tobamoviruses, although the CAV replicase is more similar to benyvirus replicase (Gibbs et al, 2011) (Fig. 4A).…”

“…As shown in Table 1, three distinct domains (MTR, HEL and RdRp) of the BdMoV replicase are 44-81% identical to the corresponding domains of three other benyviruses, and 30-35% identical to those of CAV excluding its MTR domain which is undetermined (Gibbs et al, 2011). The BdMoV Pro domain shows 33-44% identity with that of three benyviruses.…”

“…RSNV is transmitted by Polymyxa graminis (Morales et al, 1999). Furthermore, two benyvirus-related rod-shaped viruses are known: Nicotiana velutina mosaic virus (NVMV) that was isolated from Nicotiana velutina plants in Australia having a bipartite genome (Randles and Rohde, 1990) and Chara australis virus (CAV) that was isolated from fresh water algae (Chara australis) in Australia having a monopartite genome, whose replicase is most closely related to that of benyviruses (Gibbs et al, 2011). This implies wide distribution of benyvirus-like species in various eukaryotic organisms.…”