Bioinformatic Analysis Predicts a Novel Genetic Module Related to Triple Gene and Binary Movement Blocks of Plant Viruses: Tetra-Cistron Movement Block

Abstract

Previous studies have shown that the RNA genomes of some plant viruses encode two related genetic modules required for virus movement over the host body, containing two or three genes and named the binary movement block (BMB) and triple gene block (TGB), respectively. In this paper, we predict a novel putative-related movement gene module, called the tetra-cistron movement block (TCMB), in the virus-like transcriptome assemblies of the moss Dicranum scoparium and the Antarctic flowering plant Colobanthus quitensis. These TCMBs are encoded by smaller RNA components of putative two-component viruses related to plant benyviruses. Similar to the RNA2 of benyviruses, TCMB-containing RNAs have the 5′-terminal coat protein gene and include the RNA helicase gene which is followed by two small overlapping cistrons encoding hydrophobic proteins with a distant sequence similarity to the TGB2 and TGB3 proteins. Unlike TGB, TCMB also includes a fourth 5′-terminal gene preceding the helicase gene and coding for a protein showing a similarity to the double-stranded RNA-binding proteins of the DSRM AtDRB-like superfamily. Additionally, based on phylogenetic analysis, we suggest the involvement of replicative beny-like helicases in the evolution of the BMB and TCMB movement genetic modules.

Predicted Membrane-Associated Domains in Proteins Encoded by Novel Monopartite Plant RNA Viruses Related to Members of the Family Benyviridae

“…Our analysis revealed that a number Reclovirids encode non-replicative proteins with other types of putative zinc-finger motifs. In particular, the ORF2 protein of Atriplex prostrata VLRA (Supplementary Table S1) contains the hexa-cysteine motif C(X6)C(X)C(XX)CXC(X12)C, which resembles unconventional hexa-cysteine motifs like those found in proteins of Hepatitis virus E and viruses of the genus Pestivirus [16,17], and in the small protein encoded by the ORF preceding TCMB in Colobanthus quitensis VLRA [7].…”

“…It also contains a recently described group of "Tetra-cistron movement block (TCMB)-containing viruses" (Tecimovirids) coding for the TCMB movement gene module instead of the triple gene block (TGB) of movement genes found in members of the family Benyviridae. [2,7] (Figure 1). The latter branch contains exclusively monopartite viruses and, in particular, includes Goji berry chlorosis virus (GBCV), which encodes six polypeptides and has no close relatives with similar genome organization [8].…”

“…The latter branch contains exclusively monopartite viruses and, in particular, includes Goji berry chlorosis virus (GBCV), which encodes six polypeptides and has no close relatives with similar genome organization [8]. Four additional benyvirus-like members of this brunch are predicted to encode a binary movement block (BMB), which is also found in multipartite viruses of the family Kitaviridae [7,[9][10][11] (Figure 1). In the course of recent studies on the phylogeny of benyvirus-like RNA polymerases, we found that phylogenetically close monopartite viruses include a new, previously In the course of recent studies on the phylogeny of benyvirus-like RNA polymerases, we found that phylogenetically close monopartite viruses include a new, previously un-described group of viruses related to members of the family Benyviridae.…”

Properties of Plant Virus Protein Encoded by the 5′-Proximal Gene of Tetra-Cistron Movement Block

“…Virus-like sequences are often found in plant transcriptomes, as plant tissue samples collected for new-generation sequencing may have been obtained from virus-infected plants [ 15 ]. Another TGB-related gene module, the “tetra-cistron movement block” (TCMB), has recently been discovered in the transcriptomic contigs of the moss Dicranum scoparium and the flowering plant Colobanthus quitensis ; these contigs correspond to a genomic segment, termed RNA2, of novel viruses with two-component RNA genomes provisionally assigned to the Tecimovirids group related to the family Benyviridae [ 16 ]. Sequence analysis indicates that the second TCMB gene encodes a helicase domain-containing protein related to TGB1 and BMB1, whereas the proteins encoded by the third and fourth TCMB genes are similar to TGB2 and TGB3, respectively [ 14 , 16 ].…”

“…Another TGB-related gene module, the “tetra-cistron movement block” (TCMB), has recently been discovered in the transcriptomic contigs of the moss Dicranum scoparium and the flowering plant Colobanthus quitensis ; these contigs correspond to a genomic segment, termed RNA2, of novel viruses with two-component RNA genomes provisionally assigned to the Tecimovirids group related to the family Benyviridae [ 16 ]. Sequence analysis indicates that the second TCMB gene encodes a helicase domain-containing protein related to TGB1 and BMB1, whereas the proteins encoded by the third and fourth TCMB genes are similar to TGB2 and TGB3, respectively [ 14 , 16 ]. Interestingly, the protein encoded by the fourth TCMB gene also shows similarity to TGB2, suggesting that the 5′-distal gene in TGB and TCMB may have originated by a duplication of the TGB2/BMB2 gene of an ancestral BMB-like gene module [ 14 ].…”