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Review
. 2020 Sep 18;9(9):765.
doi: 10.3390/pathogens9090765.

Long Noncoding RNAs in Plant Viroids and Viruses: A Review

Nipin Shrestha  1 , Józef J Bujarski  1
Affiliations
Review

Long Noncoding RNAs in Plant Viroids and Viruses: A Review

Nipin Shrestha et al. Pathogens. .

Abstract

Infectious long-noncoding (lnc) RNAs related to plants can be of both viral and non-viral origin. Viroids are infectious plant lncRNAs that are not related to viruses and carry the circular, single-stranded, non-coding RNAs that replicate with host enzymatic activities via a rolling circle mechanism. Viroids interact with host processes in complex ways, emerging as one of the most productive tools for studying the functions of lncRNAs. Defective (D) RNAs, another category of lnc RNAs, are found in a variety of plant RNA viruses, most of which are noncoding. These are derived from and are replicated by the helper virus. D RNA-virus interactions evolve into mutually beneficial combinations, enhancing virus fitness via competitive advantages of moderated symptoms. Yet the satellite RNAs are single-stranded and include either large linear protein-coding ss RNAs, small linear ss RNAs, or small circular ss RNAs (virusoids). The satellite RNAs lack sequence homology to the helper virus, but unlike viroids need a helper virus to replicate and encapsidate. They can attenuate symptoms via RNA silencing and enhancement of host defense, but some can be lethal as RNA silencing suppressor antagonists. Moreover, selected viruses produce lncRNAs by incomplete degradation of genomic RNAs. They do not replicate but may impact viral infection, gene regulation, and cellular functions. Finally, the host plant lncRNAs can also contribute during plant-virus interactions, inducing plant defense and the regulation of gene expression, often in conjunction with micro and/or circRNAs.

Keywords: RNA interference; RNA viruses; defective RNAs; long noncoding RNAs; satellite RNAs; subviral RNAs; viroids.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Schematic illustration of five types of subviral/virus-associated long non-coding RNAs (lncRNAs) related to plant pathogenesis and their basic attributes. ssRNA—single-stranded RNA, HV—Helper virus, RdRp—RNA dependent RNA polymerase, CP—Coat protein.
Figure 2
Figure 2
Rolling circle replication (RCR) in the Pospiviroidae and the Avsunviroidae. The members of Pospiviroidae replicate by the asymmetric RCR mechanism (A) inside the host nucleus with the help of the host enzymes. The circular + strand (Red) of viroid RNA is copied into the–strand (Blue) by the RCR, which is linearized by the host RNases, and the linear RNA is then used as the template for the synthesis of the + strand. Finally, the host ligases circularize the viroid RNAs. As shown in panel (B), the members of Avsunviroidae replicate by the symmetric rolling circle mechanism using the nuclear-encoded polymerase (NEP) in the chloroplast. Replication of RNA strands with both polarities are completed by the RCR mechanism. In this family, the viroid RNAs have autocatalytic ribozymes that catalyze the cleavage of the circular oligomeric form of the viroid RNAs into monomers (Diagram adapted from the Flores et al. FEBS Letters 567, 2004).
Figure 3
Figure 3
The schematic representation of mechanisms of the generation of defective viral RNAs. (a) Either altered RdRp fidelity due to mutations or effects of virus-encoded co-factors, such as the influenza A virus (IAV) NEP or the paramyxovirus C protein, can favor the generation of D RNAs. (b) Variants of the nucleoprotein with altered binding to viral RNA can promote D RNA generation. (c) Altered structural proteins, such as the PPXY domain in the matrix protein of arenaviruses, can lead to encapsidation of the D RNAs. (d) Inter- and intra-recombination events using homologous sequences (red) can lead to the formation of D RNAs. (Courtesy Vignuzzi and Lopez, 2019, Nat. Micro.)
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