Synthesis of double-stranded RNA. II. Partial purification and characterization of an RNA-dependent RNA polymerase in healthy tobacco leaves

N. S, Pachamuthu K, Chenna S, Nair A, Shivaprasad PV. Essential role of γ-clade RNA-dependent RNA polymerases in rice development and yield-related traits is linked to their atypical polymerase activities regulating specific genomic regions

RNA-dependent RNA polymerases (RDR) generate double-stranded (ds)RNA triggers for RNA silencing across eukaryotes. Among the three clades, α-clade and β-clade members are key components of RNA silencing and mediators of stress responses across eukaryotes. However, γ-clade members are unusual in that they are represented in phylogenetically distant plants and fungi, and their functions are unknown. Using genetic, bioinformatic and biochemical methods, we show that γ-clade RDRs from Oryza sativa L. are involved in plant development as well as regulation of expression of coding and noncoding RNAs. Overexpression of γ-clade RDRs in transgenic rice and tobacco plants resulted in robust growth phenotype, whereas their silencing in rice displayed strong inhibition of growth. Small (s)RNA and RNA-seq analysis of OsRDR3 mis-expression lines suggested that it is specifically involved in the regulation of repeat-rich regions in the genome. Biochemical analysis confirmed that OsRDR3 has robust polymerase activities on both single stranded (ss)RNA and ssDNA templates similar to the activities reported for α-clade RDRs such as AtRDR6. Our results provide the first evidence of the importance of γ-clade RDRs in plant development, their atypical biochemical activities and their contribution to the regulation of gene expression.

Isolation and analysis of plant RNA-dependent RNA polymerases

RNA-dependent RNA polymerases (RDRPs) are encoded by RNA viruses as well as eukaryotic organisms such as plants. The function of these cellular RDRPs has been associated with the synthesis of short interfering RNAs (siRNAs), which are essential regulators of genomic integrity and plant viral defense. The multiple gene copies, and functional diversities, of the plant RDRPs raise the question of whether their intrinsic properties differ. This chapter describes protocols to extract and test in vitro, the activity of plant RDRPs.

Purification of cowpea mosaic virus RNA replication complex: Identification of a virus-encoded 110,000-dalton polypeptide responsible for RNA chain elongation

An endogenous cowpea mosaic virus (CPMV) RNA-protein complex (CPMV replication complex) capable of elongating in vitro preexisting nascent chains to full-length viral RNAs has been solubilized from the membrane fraction of CPMV-infected cowpea leaves using Triton X-100 and purified by Sepharose 2B chromatography and glycerol gradient centrifugation in the presence of Triton X-100. Analysis of the polypeptide composition of the complex by NaDod-SO(4)/PAGE and silver staining revealed major polypeptides with molecular masses of 110, 68, and 57 kilodaltons (kDa), among which the 110-kDa polypeptide was consistently found to cosediment precisely with the RNA polymerase activity. Using antisera to specific viral proteins, we found the 110-kDa polypeptide to be the only known viral polypeptide associated with the RNA replication complex, the 68- and 57-kDa polypeptides being most probably host-specific. The host-encoded 130-kDa monomeric RNA-dependent RNA polymerase, which is known to be stimulated in CPMV-infected cowpea leaves, did not copurify with the virus-specific RNA polymerase complex. Our results dispute the hypothesis that plant viral RNA replication may be mediated by the RNA-dependent RNA polymerase of uninfected plants. We tentatively conclude that the 110-kDa polypeptide encoded by the bottom component RNA of CPMV constitutes the core of the CPMV RNA replication complex.

NgRDR1, an RNA-dependent RNA polymerase isolated from Nicotiana glutinosa, was involved in biotic and abiotic stresses

The RNA-dependent RNA polymerases (RDRs) play a key role in RNA silencing, heterochromatin formation and natural gene regulation. Here, a novel RDR gene was isolated from Nicotiana glutinosa, designated as NgRDR1. The full-length cDNA of NgRDR1 encodes a 1117-amino acid protein which harbors the five conserved regions in plant RDRs, including the most remarkable motif DbDGD (b is a bulky residue). Amino acid sequence alignment revealed that NgRDR1 exhibited a high degree of identity with other higher plant RDR genes. Five exons were detected in the genomic DNA sequence, and the fourth exon is 151bp, the location and the length of which are conserved among different plant species. From the phylogenetic tree constructed with different kinds of plant RDRs, it is determined that NgRDR1 falls into group I, and is closely associated with the dicotyledons RDRs. The analysis of the 5'-flanking region of NgRDR1 revealed a group of putative cis-acting elements. The results of expression analysis showed that the transcripts of NgRDR1 can be induced by biotic stresses, such as exogenous signaling molecules including salicylic acid (SA), SA analogues, hydrogen peroxide (H(2)O(2)), and methyl jasmonate (MeJA). Furthermore, NgRDR1 expression can be up-regulated by potato virus Y (PVY), tobacco mosaic virus (TMV) and cucumber mosaic virus (CMV), but not by potato virus X (PVX). Besides, different kinds of fungi can also induce NgRDR1 expression. These results indicate that NgRDR1 may play an important role in response to biotic and abiotic stresses.

Biochemical activities of Arabidopsis RNA-dependent RNA polymerase 6

In Arabidopsis, genetic evidence demonstrates that RNA-dependent RNA polymerase 6 (RDR6) plays a fundamental role in at least four RNA silencing pathways whose functions range from defense against transgenes or viruses to endogene regulation in development and in stress responses. Despite its critical role in RNA silencing, the biochemical activities of RDR6 have yet to be characterized. In this study, we transiently expressed Arabidopsis RDR6 in Nicotiana benthamiana and investigated the biochemical activities of immunopurified RDR6 in vitro. We showed that RDR6 possesses terminal nucleotidyltransferase activity as well as primer-independent RNA polymerase activity on single-stranded RNAs. We found that RDR6 cannot distinguish RNAs with or without a cap or poly(A) tail. We also demonstrated that RDR6 has strong polymerase activity on single-stranded DNA. All these activities require the conserved catalytic Asp(867) residue. Our findings have important implications on the processes involving RDR6 in vivo and provide new biochemical insights into the mechanisms of RNA silencing in Arabidopsis.

Molecular cloning and characterization of an inducible RNA-dependent RNA polymerase gene, GhRdRP, from cotton (Gossypium hirsutum L.)

The RNA-dependent RNA polymerase (RdRP) cDNA, designated as Gossypium hirsutum RdRP (GhRdRP) was cloned from cotton by rapid amplification of cDNA ends-polymerase chain reaction (RACE-PCR). The full-length cDNA was 3,672 bp in size and encoded an open reading frame (ORF) of 1,110 amino acids which contained the RdRP conserved functional domain and the signature motif DbDGD. Amino acid sequence alignment indicated that GhRdRP shared the highest identity (66.37%) with AtRdRP1 and had homology with other plant, fungal, yeast and nematode RdRPs. The corresponding genomic DNA containing five exons and four introns, was isolated and analyzed. Also a 5'-flanking region was cloned, and a group of putative cis-acting elements were identified. Southern blot analysis revealed a single copy of the GhRdRP gene in cotton genome. The expression analysis by semi-quantitative RT-PCR showed that GhRdRP was induced by salicylic acid (SA), 5-chloroSA (5-CSA) and fungal infection of Rhizoctonia solani Kuhn. The cloning and characterization of the GhRdRP gene will be useful for further studies of biological roles of GhRdRP in plants.

Analysis of the involvement of an inducible Arabidopsis RNA-dependent RNA polymerase in antiviral defense

RNA-dependent RNA polymerases (RdRPs) have been implicated in posttranscriptional gene silencing (PTGS) and antiviral defense. An Arabidopsis RdRP (SDE1/SGS2) has been previously shown to be required for transgene-induced PTGS but has no general role in antiviral defense. On the other hand, we have recently shown that transgenic tobacco deficient in an inducible RdRP (NtRdRP1) activity became more susceptible to both Tobacco mosaic virus and Potato virus X. Thus, different RdRPs may have distinct roles in closely related PTGS and antiviral defense. In the present study, we analyzed roles of a newly identified Arabidopsis RdRP gene (AtRdRP1) in plant antiviral defense. AtRdRP1 encodes an RdRP closely related structurally to NtRdRP1 and is also induced by salicylic acid treatment and virus infection. A T-DNA insertion mutant for AtRdRP1 has been isolated and analyzed for possible alterations in response to viral infection. When infected by a tobamovirus and a tobravirus, the knockout mutant accumulated higher and more persistent levels of viral RNAs in both the lower, inoculated and in upper, systemically infected leaves than did wild-type plants. These results suggest that the inducible AtRdRP1 is the Arabidopsis ortholog of NtRdRP1 and plays a role in antiviral defense. Examination of short viral RNAs and silencing studies using a viral vector harboring an endogenous plant gene suggest that, while not required for virus-induced PTGS, AtRdRP1 can apparently promote turnover of viral RNAs in infected plants.

An important role of an inducible RNA-dependent RNA polymerase in plant antiviral defense

Plants contain RNA-dependent RNA polymerase (RdRP) activities that synthesize short cRNAs by using cellular or viral RNAs as templates. During studies of salicylic acid (SA)-induced resistance to viral pathogens, we recently found that the activity of a tobacco RdRP was increased in virus-infected or SA-treated plants. Biologically active SA analogs capable of activating plant defense response also induced the RdRP activity, whereas biologically inactive analogs did not. A tobacco RdRP gene, NtRDRP1, was isolated and found to be induced both by virus infection and by treatment with SA or its biologically active analogs. Tobacco lines deficient in the inducible RDRP activity were obtained by expressing antisense RNA for the NtRDRP1 gene in transgenic plants. When infected by tobacco mosaic virus, these transgenic plants accumulated significantly higher levels of viral RNA and developed more severe disease symptoms than wild-type plants. After infection by a strain of potato virus X that does not spread in wild-type tobacco plants, the transgenic NtRDRP1 antisense plants accumulated virus and developed symptoms not only locally in inoculated leaves but also systemically in upper uninoculated leaves. These results strongly suggest that inducible RdRP activity plays an important role in plant antiviral defense.

In vitro transcription of viroid RNA into full-length copies by RNA-dependent RNA polymerase from healthy tomato leaf tissue

RNA-dependent RNA polymerase from healthy tomato plant tissue accepts potato spindle tuber viroid (PSTV) RNA as a template for the in vitro synthesis of full-length RNA copies of the PSTV genome. Viroid transcription requires the presence of Mn2+ and /or Mg2+ ions and is not inhibited by concentrations of 10(-5) M alpha-amanitin. This is the first report of a well-defined product synthesized in vitro by an RNA-dependent RNA polymerase from healthy plants.

Heterogeneous chromatographic behaviour or soluble RNA replicase from healthy and virus-infected tobacco leaves: an improvement of the purification methodology

During purification of soluble RNA replicase from healthy and alfalfa mosaic virus-infected tobacco leaves, crude extracts were chromatographed on DEAE-Sephadex A-25, and three RNA-dependent RNA polymerase activities were obtained; one of these was previously characterized as a true RNA replicase, the remaining two were not studied (Chifflot et al., 1980, Virology 100, 91). We now demonstrate that all of these activities correspond to the same RNA replicase, complexed or not to cellular or viral RNA. Upon chromatography on DEAE-Sephadex A-25, the free replicase did not bind to the gel at low ionic strength, whereas the RNA-replicase complexes were bound to the gel through the medium of RNA. Increasing the ionic strength allowed the dissociation of the complexes and elution of the replicase only. From this observation, a new and rapid purification procedure combining all these activities and yielding large amounts of replicase was developed; the first main step of purification was chromatography on Blue-Sepharose CL6B under conditions conductive to the dissociation of RNA-replicase complexes, and thus maximal adsorption of the replicase. The enzyme was then eluted by increasing the ionic strength and was further purified on coupled DEAE-Sephadex A-25 and phosphocellulose columns. The DEA-Sephadex A-25 was used to bind the remaining RNA, while the replicase passed through, and bound to the cationic ion exchanger. The final replicase preparations which were obtained were very stable and had a purification factor of 1100-1400. The recovery averaged 70% and specific activities were much higher than those already described for similar enzymes from healthy or virus-infected tobacco leaves.

Evolution of RNA viruses

These arguments lead to the suggestion that four independent evolutionary lines exist within the general group of RNA viruses. These are positive strand viruses, negative strand viruses, double stranded viruses, and retroviruses. Three of the viral systems may well have shared genes but the double-stranded RNA viruses appear to represent a very different evolutionary line.