(1/667) Physical and functional heterogeneity in TYMV RNA: evidence for the existence of an independent messenger coding for coat protein.

Turnip yellow mosaic virus RNA can be separated into two distinct components of 2 times 10(6) and 300 000 daltons molecular weight after moderate heat treatment in the presence of SDS or EDTA. The two species cannot have arisen by accidental in vitro degradation of a larger RNA, as they both possess capped 5' ends. Analysis of the newly synthesized proteins resulting from translation of each RNA by a wheat germ extract shows that the 300 000 molecular weight RNA can be translated very efficiently into coat protein. When translated in vitro the longer RNA gave a series of high molecular weight polypeptides but only very small amounts of a polypeptide having about the same mass as the coat protein. Thus our results suggest that the small RNA is the functional messenger for coat protein synthesis in infected cells.  (+info)

(2/667) Complete sequence and genome properties of Chinese wheat mosaic virus, a new furovirus from China.

The complete nucleotide sequence of a virus infecting winter wheat in Shandong province, China has been determined. This was previously thought to be soil-borne wheat mosaic virus but, while the two viruses are related, they are only 75% (RNA1) and 63% (RNA2) identical at the nucleotide level, while the amino acid sequences share from 62% (19 kDa RNA2 product) to 84% (RNA1 replicase) identity. The analysis shows that the Chinese virus should be considered a new member of the genus Furovirus and has been named Chinese wheat mosaic virus (CWMV). A Cys-Gly ... Cys-Gly-X-X-His amino acid pattern was identified in the cysteine-rich protein of CWMV and those of several other plant virus genera, which seems likely to have some functional significance.  (+info)

(3/667) The sCYMV1 hairpin ribozyme: targeting rules and cleavage of heterologous RNA.

The catalytic center of the RNA from the negative strand of the satellite RNA of chicory yellow mottle virus type 1 (sCYMV1) is in the hairpin ribozyme family, has catalytic activity, and cleaves substrates before a preferred GUA sequence. This is different from that of the satellite RNA from the negative strand of tobacco ringspot virus (sTRSV) which prefers a GUC sequence at the site of cleavage. The sCYMV1 hairpin ribozyme has now been developed for cleaving heterologous RNA substrates. When helix 1 was extended from the native 5 bp to 6 bp with a newly added A:U base pair, catalytic activity increased three-fold. The preferred sequence for the substrate loop was the native A*GUA sequence where * is the site of cleavage. When each nucleotide in this sequence was changed to each of the other three nucleotides, catalytic activity decreased 66-100%. RNA targets, containing this A*GUA sequence, were located in both human papillomavirus and HIV-1. Ribozymes were developed which efficiently cleaved these targets in vitro. These results identify a new class of hairpin ribozymes capable of cleaving substrates before a preferred GUA sequence rather than the GUC preferred by the sTRSV hairpin ribozyme. This expands the repertoire of target sites available for gene therapy using the hairpin ribozyme.  (+info)

(4/667) Rapid generation of genetic heterogeneity in progenies from individual cDNA clones of peach latent mosaic viroid in its natural host.

Viroids, small single-stranded circular RNAs endowed with autonomous replication, are unique systems to conduct evolutionary studies of complete RNA genomes. The primary structure of 36 progeny variants of peach latent mosaic viroid (PLMVd), evolved from inoculations of the peach indicator GF-305 with four individual PLMVd cDNAs differing in their pathogenicity, has been determined. Most progeny variants had unique sequences, revealing that the extremely heterogeneous character of PLMVd natural isolates most probably results from the intrinsic ability of this RNA to accumulate changes, rather than from repeated inoculations of the same individual trees under field conditions. The structure of the populations derived from single PLMVd sequences differed according to the observed phenotype. Variant gds6 induced a reproducible symptomatic infection and gave rise to a more uniform progeny that preserves some parental features, whereas variant gds15, which induced a variable phenotype, showed a more complex behaviour, generating two distinct progenies in symptomatic and asymptomatic individual plants. Progenies derived from variants esc10 and Is11, which incited latent infections, followed a similar evolutionary pattern, leading to a population structure consisting of two main groups of variants, one of which was formed by variants closely related to the parental sequence. The evolution rate exhibited by PLMVd, considerably higher than that reported for potato spindle tuber viroid, may contribute to the fluctuating symptomatology of the severe PLMVd natural isolates. However, the polymorphism observed in PLMVd progenies does preserve some structural and functional elements previously proposed for this viroid, supporting the fact that they act as constraints limiting the genetic divergence of PLMVd quasispecies generated de novo.  (+info)

(5/667) Sequences of European wheat mosaic virus and oat golden stripe virus and genome analysis of the genus furovirus.

The complete nucleotide sequences of both RNAs of oat golden stripe virus (OGSV) and a wheat-infecting furovirus isolate from France, previously thought to be soil-borne wheat mosaic virus (SBWMV), have been determined. Both viruses had a similar genomic organisation to SBWMV and Chinese wheat mosaic virus, the two other furoviruses previously sequenced but had <70% nucleotides identical to them. The French isolate has been named European wheat mosaic virus (EWMV). Phylogenetic analyses supported the recognition of these isolates as distinct viruses in the genus Furovirus. Analysis of the coat protein readthrough domain on RNA2 of all furoviruses strongly predicts two mutually compatible conserved transmembrane domains that may be significant for fungus transmission. The second of these regions is eliminated by a deletion in the isolate of OGSV studied. Leaky opal (UGA) stop codons occur on both RNAs of all four furoviruses characterised and, in common with most other leaky opal codons identified in plant viruses, they are followed by a CGG codon.  (+info)

(6/667) Structural fingerprinting: subgrouping of comoviruses by structural studies of red clover mottle virus to 2.4-A resolution and comparisons with other comoviruses.

Red clover mottle virus (RCMV) is a member of the comoviruses, a group of picornavirus-like plant viruses. The X-ray structure of RCMV strain S has been determined and refined to 2.4 A. The overall structure of RCMV is similar to that of two other comoviruses, Cowpea mosaic virus (CPMV) and Bean pod mottle virus (BPMV). The sequence of the coat proteins of RCMV strain O were modeled into the capsid structure of strain S without causing any distortion, confirming the close resemblance between the two strains. By comparing the RCMV structure with that of other comoviruses, a structural fingerprint at the N terminus of the small subunit was identified which allowed subgrouping of comoviruses into CPMV-like and BPMV-like viruses.  (+info)

(7/667) Quasi-elastic behavior of solutions of viral capsid and RNA at very low shearing stresses.

By the application of shearing stresses on the order of 10(-3) dyne cm-2 (10(-2) muN cm-2), via the magnetic viscodensimeter, extremely high relative viscosities (greater than 500) were observed when turnip yellow mosaic virus was degraded in alkali into its capsid and RNA. The solutions, however, possessed a watery consistency at this stage and exhibited a quasi-elastic character by rotor-recoil experiments. The development of this curious behavior was concentration and temperature dependent; it was not seen less than 0.5% nor at 8 degrees, and appeared sooner at 30 degrees than at 20 degrees. The time of appearance was delayed as the pH was lowered; however, the effect was still observed when the pH was as low as 9. Whereas reversibility was demonstrated when the shearing stresses exceeded the elastic resistance [0.17 dyne cm-2 (1.7 muN CM-2)], thorough mixing usually resulted in a normal behavior of the solutions thereafter. Values for the modulus of rigidity at 20 degrees for about 1% virus concentration was less than 2 X 10(-2) dyne cm-2 rad-1 (0.2 muN cm-2 rad-1), which, while extremely small, was reproducible. A porous structure, possibly involving a capsid and RNA complex, is envisioned.  (+info)

(8/667) A gene cluster encoded by panicum mosaic virus is associated with virus movement.

A subgenomic RNA (sgRNA) of about 1500 nucleotides has been detected in millet plants and protoplasts infected with panicum mosaic virus (PMV). This sgRNA expressed p8, p6.6, p15, and the 26-kDa capsid protein (CP) genes during in vitro translation assays, as determined by using mutants inactivated for expression of each open reading frame. Abolishing expression of p8 and p6.6, the two 5'-proximal genes on the sgRNA, did not affect the replication of PMV in millet protoplasts, but obstructed spread in plants. As predicted for a typical cell-to-cell movement protein, p8 localized to the cell wall fraction of PMV-infected millet plants. The introduction of premature stop codons downstream of the PMV p15 start codon (p15*) abolished infectivity in planta, but did not impair replication in protoplasts. However, a delayed systemic infection in millet plants was supported by the p15aug(-) start codon mutant, which may reflect very low levels of expression from a suboptimal start codon context and/or leaky scanning to a second inframe AUG codon to express the C-terminal portion of the 15-kDa protein. PMV CP mutants had little effect on sgRNA accumulation, but were correlated with a reduction of the gRNA and the decreased expression of the 8-kDa protein in protoplasts as well as abolishment of cell-to-cell spread in plants. These results imply that the successful establishment of a PMV systemic infection in millet host plants appears to be dependent on the concerted expression of the p8, p6.6, p15, and CP genes.  (+info)