Satellite RNAs and Satellite Viruses of Plants

Abstract

The view that satellite RNAs (satRNAs) and satellite viruses are purely molecular parasites of their cognate helper viruses has changed. The molecular mechanisms underlying the synergistic and/or antagonistic interactions among satRNAs/satellite viruses, helper viruses, and host plants are beginning to be comprehended. This review aims to summarize the recent achievements in basic and practical research, with special emphasis on the involvement of RNA silencing mechanisms in the pathogenicity, population dynamics, and, possibly, the origin(s) of these subviral agents. With further research following current trends, the comprehensive understanding of satRNAs and satellite viruses could lead to new insights into the trilateral interactions among host plants, viruses, and satellites.

Keywords: RNA silencing; pathogenicity; replication; satellite RNA; satellite virus.

Figure 1.

A key illustrating the hierarchical classification of subviral RNAs. Blue boxes describe salient features distinguishing different categories of subviral RNAs, pink boxes show satellite viruses and satRNAs, and green boxes show the other types of RNAs. Abbreviations: ss, single-stranded; ds, double-stranded; vRNA, viral genomic RNA; CP, coat protein.

Figure 2.

A Schematic representation of the complex interaction among host plants, helper viruses, satRNAs and satellite viruses, and the RNA silencing mechanism of the host. T-shaped lines indicate inhibitory effect, whereas the solid arrows represent an enhancing effect. Arrows on dotted lines represent an “uncertainty state,” in which the three participating members (host plants, helper viruses, and satRNAs or satellite viruses) would have to compete for the targeting of host gene silencing mechanisms. B Example scenarios illustrating the consequences of competition among plants, viruses, and satellites for the activation and targeting of the RNA silencing mechanisms. The yellow box indicates the emergence of new satRNAs as a result of an RNA silencing mechanism.

Figure 2.

A Schematic representation of the complex interaction among host plants, helper viruses, satRNAs and satellite viruses, and the RNA silencing mechanism of the host. T-shaped lines indicate inhibitory effect, whereas the solid arrows represent an enhancing effect. Arrows on dotted lines represent an “uncertainty state,” in which the three participating members (host plants, helper viruses, and satRNAs or satellite viruses) would have to compete for the targeting of host gene silencing mechanisms. B Example scenarios illustrating the consequences of competition among plants, viruses, and satellites for the activation and targeting of the RNA silencing mechanisms. The yellow box indicates the emergence of new satRNAs as a result of an RNA silencing mechanism.

Figure 3.

Identification of conserved secondary structures among sequences sharing low similarity of satRNAs. The flow chart outlines the process for the linear comparison of multiple secondary structures. Only the relevant nucleotides participating in base-pairing are indicated. Nucleotides in single-stranded regions are represented by the letter “n”. For each sequence (Seq1–Seq4), secondary structures were predicted by the program Mfold [119], with constraints matching the structures determined by enzymatic or chemical probing experiments. The resulting connect file (“.ct file”) was converted to a linear format according to the rules [74] and subjected to multiple sequence alignment by use of Clustal W [120]. The base-paired regions are represented by letters in lower case, a, b, and c, with dotted lines connecting the corresponding regions. The conserved base-paired regions among different sequences are indicated by stars under the alignment. Consen, consensus secondary structure derived from the multiple alignments.