Comparative sequence analysis and serological and infectivity studies indicate that cocksfoot mild mosaic virus is a member of the genus Panicovirus

Analysis of gene functions in Maize chlorotic mottle virus

Gene functions of strains of Maize chlorotic mottle virus, which comprises the monotypic genus Machlomovirus, have not been previously identified. In this study mutagenesis of the seven genes encoded in maize chlorotic mottle virus (MCMV) showed that the genes with positional and sequence similarity to their homologs in viruses of related tombusvirid genera had similar functions. p50 and its readthrough protein p111 are the only proteins required for replication in maize protoplasts, and they function at a low level in trans. Two movement proteins, p7a and p7b, and coat protein, encoded on subgenomic RNA1, are required for cell-to-cell movement in maize, and p7a and p7b function in trans. A unique protein, p31, expressed as a readthrough extension of p7a, is required for efficient systemic infection. The 5' proximal MCMV gene encodes a unique 32kDa protein that is not required for replication or movement. Transcripts lacking p32 expression accumulate to about 1/3 the level of wild type transcripts in protoplasts and produce delayed, mild infections in maize plants. Additional studies on p32, p31 and the unique amino-terminal region of p50 are needed to further characterize the life cycle of this unique tombusvirid.

The cap-binding translation initiation factor, eIF4E, binds a pseudoknot in a viral cap-independent translation element

Eukaryotic initiation factor eIF4E performs a key early step in translation by specifically recognizing the m⁷GpppN cap structure at the 5' end of cellular mRNAs. Many viral mRNAs lack a 5' cap and thus bypass eIF4E. In contrast, we reported a cap-independent translation element (PTE) in Pea enation mosaic virus RNA2 that binds and requires eIF4E for translation initiation. To understand how this uncapped RNA is bound tightly by eIF4E, we employ SHAPE probing, phylogenetic comparisons with new PTEs discovered in panico- and carmoviruses, footprinting of the eIF4E binding site, and 3D RNA modeling using NAST, MC-Fold, and MC-Sym to predict a compact, 3D structure of the RNA. We propose that the cap-binding pocket of eIF4E clamps around a pseudoknot, placing a highly SHAPE-reactive guanosine in the pocket in place of the normal m⁷GpppN cap. This reveals a new mechanism of mRNA recognition by eIF4E.

Detection of members of the Tombusviridae in the Tallgrass Prairie Preserve, Osage County, Oklahoma, USA

Viruses are most frequently discovered because they cause disease in organisms of importance to humans. To expand knowledge of plant-associated viruses beyond these narrow constraints, non-cultivated plants of the Tallgrass Prairie Preserve, Osage County, Oklahoma, USA were systematically surveyed for evidence of the presence of viruses. This report discusses viruses of the family Tombusviridae putatively identified by the survey. Evidence of two carmoviruses, a tombusvirus, a panicovirus and an unclassifiable tombusvirid was found. The complete genome sequence was obtained for putative TGP carmovirus 1 from the legume Lespedeza procumbens, and the virus was detected in several other plant species including the fern Pellaea atropurpurea. Phylogenetic analysis of the sequence and partial sequence of a related virus supported strongly the placement of these viruses in the genus Carmovirus. Polymorphisms in the sequences suggested existence of two populations of TGP carmovirus 1 in the study area and year-to-year variations in infection by TGP carmovirus 3.

Detection of Cereal yellow dwarf virus using small interfering RNAs and enhanced infection rate with Cocksfoot streak virus in wild cocksfoot grass (Dactylis glomerata)

Small RNA sequences were obtained from leaf extracts of wild Dactylis glomerata (cocksfoot grass) using deep sequencing (454 Life Sciences, Roche Diagnostics), and were screened against virus sequences in GenBank using a local BLASTn search program (BioEdit). Putative small interfering (si)RNAs complementary in sequence to Cereal yellow dwarf virus (CYDV, genus Luteovirus) genomes were identified. Primer sequences were made against the "high scoring" siRNA sequences and RT-PCR was used to amplify a 438 bp CYDV fragment in total RNA extracts from D. glomerata leaves. Sequencing of the RT-PCR product confirmed the occurrence of a previously undescribed CYDV population with phylogenetic affinity to CYDV-RPS. In D. glomerata the CYDV infection rates were 42.3% (n=78) in 2008 and 50.0% (n=48) in 2009. Specific RT-PCR tests also showed that this D. glomerata population harboured Cocksfoot streak virus (CSV, genus Potyvirus). Dual infections by these viruses were observed in 20.5-22.9% of all plants tested in 2008-2009. Interestingly, infections of either CYDV or CSV enhanced the occurrence of the other virus in individual grasses. Opportunities are discussed for using siRNA sequencing approaches in virus survey and other ecology studies under field conditions.