Characterization of sub-genomic double-stranded RNAs from virus-infected plants

Double-stranded RNAs of cucumber mosaic virus and its satellite contain an unpaired terminal guanosine: implications for replication

Terminal sequences of the double-stranded (ds) forms of RNAs 3 and 4 and the satellite RNA (CARNA 5) of cucumber mosaic virus (CMV) have been determined. The ds forms of both CARNA 5 and RNA 3 contain an unpaired guanosine (G) at the 3' end of the minus (-) strand, a feature also present in the replicative forms (RFs) of several animal alphaviruses. The unpaired G present in the CMV-related ds RNAs suggests that these molecules represent RFs and that viral and satellite RNAs share common replicative machinery. The 3' terminus of the (-) strand of ds RNA 4 is heterogeneous, with and without the added G. The existence of these two ds RNA 4 molecules suggests that replication of the subgenomic RNA 4 proceeds through a mechanism different from that of the genomic RNAs. The plus (+) strands of the ds forms of RNAs 3 and 4 and CARNA 5 are uncapped at the 5' termini and all end with a 3'-terminal cytosine (C. The 3'-terminal adenosine (A) present on most single-stranded (ss), encapsidated, CMV RNAs 3 and 4 is therefore added post-transcriptionally, and a possible control function for such a 3' terminus is discussed. The lack of an added 3'-terminal A on ss, encapsidated, CARNA 5 could result in its high replicative efficiency through escape from such a control.

Investigative proteomics: identification of an unknown plant virus from infected plants using mass spectrometry

We describe the identification of a previously uncharacterized plant virus that is capable of infecting Nicotiana spp. and Arabidopsis thaliana. Protein extracts were first prepared from leaf tissue of uninfected tobacco plants, and the proteins were visualized with two-dimensional electrophoresis (2-DE). Matching gels were then run using protein extracts of a tobacco plant infected with tobacco mosaic virus (TMV). After visual comparison, the proteins spots that were differentially expressed in infected plant tissues were cut from the gels and analyzed by high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). Tandem mass spectrometry data of individual peptides was searched with SEQUEST. Using this approach we demonstrated a successful proof-of-concept experiment by identifying TMV proteins present in the total protein extract. The same procedure was then applied to tobacco plants infected with a laboratory viral isolate of unknown identity. Several of the differentially expressed protein spots were identified as proteins of potato virus X (PVX), thus successfully identifying the causative agent of the uncharacterized viral infection. We believe this demonstrates that HPLC-MS/MS can be used to successfully characterize unknown viruses in infected plants.

The p23 protein of citrus tristeza virus controls asymmetrical RNA accumulation

Citrus tristeza virus (CTV), a member of the Closteroviridae, has a 19.3-kb positive-stranded RNA genome that is organized into 12 open reading frames (ORFs) with the 10 3' genes expressed via a nested set of nine or ten 3'-coterminal subgenomic mRNAs (sgRNAs). Relatively large amounts of negative-stranded RNAs complementary to both genomic and sgRNAs accumulate in infected cells. As is characteristic of RNA viruses, wild-type CTV produced more positive than negative strands, with the plus-to-minus ratios of genomic and sgRNAs estimated at 10 to 20:1 and 40 to 50:1, respectively. However, a mutant with all of the 3' genes deleted replicated efficiently, but produced plus to minus strands at a markedly decreased ratio of 1 to 2:1. Deletion analysis of 3'-end genes revealed that the p23 ORF was involved in asymmetric RNA accumulation. A mutation which caused a frameshift after the fifth codon resulted in nearly symmetrical RNA accumulation, suggesting that the p23 protein, not a cis-acting element within the p23 ORF, controls asymmetric accumulation of CTV RNAs. Further in-frame deletion mutations in the p23 ORF suggested that amino acid residues 46 to 180, which contained RNA-binding and zinc finger domains, were indispensable for asymmetrical RNA accumulation, while the N-terminal 5 to 45 and C-terminal 181 to 209 amino acid residues were not absolutely required. Mutation of conserved cysteine residues to alanines in the zinc finger domain resulted in loss of activity of the p23 protein, suggesting involvement of the zinc finger in asymmetric RNA accumulation. The absence of p23 gene function was manifested by substantial increases in accumulation of negative-stranded RNAs and only modest decreases in positive-stranded RNAs. Moreover, the substantial decrease in the accumulation of negative-stranded coat protein (CP) sgRNA in the presence of the functional p23 gene resulted in a 12- to 15-fold increase in the expression of the CP gene. Apparently the excess negative-stranded sgRNA reduces the availability of the corresponding positive-stranded sgRNA as a messenger. Thus, the p23 protein controls asymmetric accumulation of CTV RNAs by downregulating negative-stranded RNA accumulation and indirectly increases expression of 3' genes.

Functions of the 126- and 183-kDa proteins of tobacco mosaic virus

Tobacco mosaic virus produces two proteins that contain domains similar to the methyltransferase (MT) and helicase (HEL)-like domains of the replicase-associated proteins of other RNA viruses. The more abundant 126-kDa protein contains only the MT and HEL-like domains, whereas the 183-kDa readthrough protein additionally contains the polymerase domain. We examined the functions of these proteins by constructing a bipartite system to express the 126- and 183-kDa proteins from separate RNAs. Mutants expressing the 183-kDa protein recognized promoters for negative- and positive-stranded RNA synthesis, transcribed subgenomic mRNAs, capped RNAs, synthesized proteins, moved cell to cell within the plant, and replicated defective RNAs (dRNAs). The principal function of the 126-kDa protein was to increase the rate of replication approximately tenfold. The 126-kDa protein appeared to function primarily in cis, and production of the 126-kDa protein in trans did not enhance replication of the helper virus. dRNAs producing a functional 126-kDa protein were replicated efficiently by helper viruses that produced only the 183-kDa protein but not by wild-type virus, suggesting that efficient replication required the 183-kDa protein to form a heterodimer with the 126-kDa protein already bound to the target dRNA.

Tobacco mosaic virus protein synthesis is correlated with double-stranded RNA synthesis and not single-stranded RNA synthesis

The synthesis rates of three proteins of tobacco mosaic virus (TMV), 160, 110, and 17.5 kDa, were monitored at intervals after interruption of synthesis of TMV RNA. Following inhibition of synthesis of both single-stranded and double-stranded RNAs by shifting wild type TMV to 40 degrees or ts mutant III2-35 to 35 degrees, the synthesis rates of viral proteins declined sequentially, with that of the larger proteins declining faster. When viral RNA synthesis was prevented with cordycepin, synthesis rates of the 110 and 160-kDa proteins declined rapidly, while the 17.5-kDa protein decreased more slowly. These data imply that the functional mRNA is transitory, probably nascent RNA, and that each protein is produced independently. The process of translation of viral mRNA was not temperature sensitive and occurred normally for brief periods after shift to restrictive temperatures. When single-stranded RNA synthesis was inhibited differentially from double-stranded RNA synthesis, protein synthesis was correlated with double-stranded RNA synthesis and not single-stranded RNA synthesis. Following a shift of ts mutant IV-35 to 35 degrees, a shift that immediately stopped single-stranded RNA synthesis without inhibiting double-stranded RNA synthesis, all three viral proteins continued to be produced normally. Also, after return of wild type TMV to 25 degrees after a 1-hr incubation at 40 degrees, viral protein and double-stranded RNA synthesis recovered in parallel to the normal rate after 8 hr whereas single-stranded RNA synthesis, which had been reduced more drastically, recovered more slowly after 16 hr.