Coat protein of potyviruses. 7. Amino acid sequence of peanut stripe virus

Potyviral coat protein and genomic RNA: A striking partnership leading virion assembly and more

Potyvirus genus clusters a significant and expanding number of widely distributed plant viruses, responsible for large losses impacting most crops of economic interest. The potyviral genome is a single-stranded, linear, positive-sense RNA of around 10kb that is encapsidated in flexuous rod-shaped filaments, mostly made up of a helically arranged coat protein (CP). Beyond its structural role of protecting the viral genome, the potyviral CP is a multitasking protein intervening in practically all steps of the virus life cycle. In particular, interactions between the CP and the viral RNA must be tightly controlled to allow the correct assignment of the RNA to each of its functions through the infection process. This review attempts to bring together the most relevant available information regarding the architecture and modus operandi of potyviral CP and virus particles, highlighting significant discoveries, but also substantial gaps in the existing knowledge on mechanisms orchestrating virion assembly and disassembly. Biotechnological applications based on potyvirus nanoparticles is another important topic addressed here.

Identificação e caracterização de um potyvírus isolado de Zinnia elegans

O presente trabalho teve como objetivo a identificação e caracterização de um potyvírus isolado de Zinnia elegans, na Região Noroeste do Estado de São Paulo. O potyvírus foi transmitido por inoculação mecânica e apresentou uma gama restrita de hospedeiras sendo que as espécies mais afetadas pertencem à família Asteraceae. Em SDS-PAGE, a massa molecular da proteína capsidial (CP) foi estimada em 33 kDa e, em "Western-blot", reagiu com anti-soro para o Bidens mosaic virus (BiMV). Um fragmento de aproximadamente 820 pb foi amplificado por RT/PCR, clonado e seqüenciado. O fragmento, que inclui o gene da proteína capsidial, mostrou similaridade de aminoácidos do "core" da CP variando de 55% (Tobacco vein mottling virus, TVMV) a 95% (Sunflower chlorotic mottle virus, SuCMoV) e da CP completa de 55% (TVMV) a 91% (SuCMoV). Na região N-terminal, o potyvírus de Zinnia tem uma deleção de quatro aminoácidos (posições 9 a 12 após o sítio de clivagem entre a proteína NIb e a CP) quando comparada com a seqüência do SuCMoV. A análise filogenética agrupou o potyvírus de Zinnia e o SuCMoV em um mesmo ramo em 100% das réplicas, mostrando uma relação de parentesco muito próxima entre esses dois vírus. Os resultados obtidos no presente trabalho demonstraram que o potyvírus de Zinnia e o SuCMoV são estirpes do mesmo vírus. Sugere-se o nome Sunflower chlorotic mottle virus, isolado Zinnia (SuCMoV-Zi), ao potyvírus encontrado em Z. elegans no Brasil.

The complete nucleotide sequences of the coat protein cistron and the 3' non-coding region of a newly-identified potyvirus infecting sweetpotato, as compared to those of sweetpotato feathery mottle virus

Complementary DNA representing 728 nucleotides of the 3' end of the genomic RNA of sweetpotato virus G (SPV-G) a newly-identified potyvirus infecting sweetpotato, was cloned and sequenced. This sequence was combined with that previously determined for the 5' terminal part of the coat protein cistron of the virus. The whole sequence contained a single open reading frame (ORF) of 1065 nucleotide, with the capacity to encode a coat protein of 355 amino acids, significantly larger than that of other potyviruses. The ORF was followed by an untranslated region of 222 nucleotides and a poly (A) tail. The coat protein of SPV-G was only distantly related to that of known potyviruses, with the exception of sweetpotato feathery mottle virus (SPFMV). Indeed, sequence identity in the C-terminal three quarters of the coat protein (more than 80%) and in the 3' untranslated region (more than 70%) indicate that SPV-G should be considered as closely related to, though distinct from SPFMV. This subset relationship is similar to that previously reported for members of the bean yellow mosaic virus subgroup or the bean common mosaic virus subgroup.

Cowpea aphid borne mosaic virus-Morocco and South African Passiflora virus are strains of the same potyvirus

High performance liquid chromatography (HPLC) profiles of tryptic peptides and partial amino acid sequence analysis have been employed to establish the taxonomic status of the Moroccan isolate of cowpea aphid-borne mosaic virus (CABMV). Some previous reports have suggested CABMV to be very closely related to blackeye cowpea mosaic virus (B1CMV) while other reports have concluded that this relationship is distant. In this report a tryptic digest of the coat protein of CABMV-Morocco was compared with those of the coat proteins of B1CMV-Type, B1CMV-W, the mild mottle strain of peanut stripe virus (PStV-MM) and the NY15 strain of bean common mosaic virus (BCMV-NY15), all of which are now recognised as strains of BCMV. The comparisons also included the NL-3 strain of bean necrosis mosaic virus (BNMV-NL3), which had previously been classified as a strain of BCMV. The HPLC peptide profiles indicated that CABMV-Morocco was distinct from BCMV and BNMV. Amino acid sequence analysis of peptides accounting for more than half of the coat protein confirmed that CABMV-Morocco was not a strain of BNMV or BCMV but was a distinct member of the BCMV subset of viruses that previously has been shown to include BCMV, BNMV, soybean mosaic virus, zucchini yellow mosaic virus, passionfruit woodiness virus and South African Passiflora virus (SAPV). Comparison of the partial sequence data with these and other published sequences revealed that the coat protein of CABMV-Morocco is very similar to that of SAPV suggesting that they are strains of the same virus. Since CABMV was described over 25 years earlier than SAPV, the name CABMV should take precedence and SAPV should be renamed CABMV-SAP, the South African Passiflora strain of CABMV.

Cloning and sequence analysis of the coat protein genes of an Australian strain of peanut mottle and an Indonesian 'blotch' strain of peanut stripe potyviruses

We have analysed the coat protein gene sequences of two potyviruses infecting peanut. The 3' terminal 1247 nucleotides (nt) of an Australian strain of peanut mottle virus (PeMoV-AU) and the 3' terminal 1388 nt of an Indonesian 'blotch' strain of peanut stripe virus (PStV-Ib) were cloned and sequenced. Those regions included the 861 and 864 nt encoding the respective putative coat proteins as well as the 285 and 253 nt, respectively of 3' non-coding sequences. Comparison of the nucleotide sequences of PeMoV-AU and PStV-Ib revealed a sequence similarity of 64.4% for the coat protein gene and 34.6% for the 3' non-coding region. The deduced amino acid sequences of PeMoV-AU and PStV-Ib coat proteins are 66.7% identical. These results provide further evidence that PeMoV and PStV are distinct viruses. Comparisons of the 3' terminal sequences of PeMoV-AU and PStV-Ib with those of the genomic RNA of other strains of PeMoV and PStV and with other potyviruses are discussed.

Evolutionary relationships among bean common mosaic virus strains and closely related potyviruses

Bean common mosaic virus (BCMV) consists of a large number of strains with complex and controversial relationships among them and with other potyviruses that infect legumes. In order to elucidate the BCMV taxonomic pattern and its evolutionary implications, a phylogenetic analysis has been carried out. The analysis of the coat protein gene and 3' non-coding region (NCR) sequences recently obtained by us and other currently available potyviral sequences confirms the clustering of viruses comprised in BCMV strains with other closely related potyviruses and reveals the great informative content of 3' NCR, suggesting a more relevant role for this region in phylogenetic analysis.

Cloning of the capsid protein gene from a blotch isolate of peanut stripe virus

The 3' terminal 1,367 nucleotides (nts) of a blotch isolate of the potyvirus, peanut stripe virus (PStV), were cloned and sequenced. This region included the 861 nts (287 amino acids) of the PStV capsid protein (CP). The amino acid sequence of the predicted proteinase cleavage site was identified. This region shared limited homology with other potyvirus proteinase cleavage sites. The viral CP gene sequence was followed by 254 nucleotides of 3' nontranslated sequence and a poly-A tail. Based on computer modeling, the 3' nontranslated region could form two lengthy stem-loop structures and two pseudoknot structures. Subclones containing the coding sequences of the CP (amino acids 1-287, 17-287, 17-113 and 106-287) were constructed and expressed in Escherichia coli. These polypeptides were detected using polyclonal antibodies in Western blots.

Purification of hydrophilic and hydrophobic peptide fragments on a single reversed phase high performance liquid chromatographic column

Hydrophilic peptides generated from enzymic fragmentation of proteins are difficult to purify because they are either weakly bound or unretained by the reversed phase C18 columns favoured for liquid chromatographic separation of peptide mixtures. To overcome this difficulty, peptides that were not bound or only weakly bound by a C18 RP column were reacted with phenyl isothiocyanate (PITC), as used in the initial step in Edman sequencing. The hydrophobic phenylthiocarbamyl (PTC) peptide derivatives produced by the reaction were rechromatographed on the same column. Peptides generated by tryptic digestion of equine cytochrome C were used as a model system to test whether a complete set of peptide fragments could be purified by this method using just one column and solvent system. All the expected hydrophobic tryptic peptides bound to the RP column and were resolved by elution with acetonitrile, but no hydrophilic peptides were recovered as pure fractions. The column breakthrough fraction was reacted with PITC and rechromatographed on the same column, producing a profile consisting of 19 bound peaks. Further rechromatography of some of the fractions at different column temperatures enabled all six of the expected hydrophilic peptides to be purified and identified. The technique has also been applied to the sequence determination of coat protein from peanut stripe potyvirus protein, eight hydrophilic tryptic peptides being recovered and identified as PTC derivatives.

Watermelon mosaic virus-Morocco is a distinct potyvirus

The relationship of the Morocco isolate of watermelon mosaic virus (WMV) to WMV2, soybean mosaic virus (a virus closely related to WMV2) and the W strain of papaya ringspot virus (PRSV-W), formerly WMV1, was examined by comparing tryptic peptide profiles using high performance liquid chromatography. The profiles indicated that the coat protein sequence of WMV-Morocco differed substantially from those of the other potyviruses. This conclusion was supported by sequence data from five tryptic peptides from the coat protein of WMV-Morocco, which showed only 61-68% identity to equivalent sequences in PRSV-W, WMV2 and zucchini yellow mosaic, another potyvirus infecting cucurbits. Based on the above data, and on known correlations between coat protein sequence similarities and potyvirus relationship, it is concluded that WMV-Morocco should be regarded as a distinct potyvirus.

Cloning and nucleotide sequence of the capsid protein and the nuclear inclusion protein (NIb) of potato virus A

The sequence of the 3'-terminal 2597 nucleotides of potato virus A (PVA) genome has been determined from cDNA clones. An open reading frame was identified and potentially encodes a large polyprotein containing 789 amino acid residues. This large open reading frame was found to have a high similarity to the nuclear inclusion protein (NIb) and the capsid protein (CP) genes of several potyviruses. The data suggest that the PVA NIb and CP are products arising from the maturation of the large polyprotein as observed for other potyviruses. Putative cleavage sites corresponded to consensus sequences NIa/NIb and NIb/CP, respectively, of other potyviruses. The NIb (putative RNA polymerase) and CP are expected to be 516 and 269 amino acid residues (M(r) of 58,939 and 30,094), respectively. The non-coding region is 227 nucleotides long, rich in A and U and unlike other viruses. Furthermore, there are two AUG codons in frame in front of the capsid protein gene suggesting an alternative mode for the capsid protein expression.

Coat protein phylogeny and systematics of potyviruses

The feasibility of applying molecular phylogenetic methods of analysis to aligned coat-protein sequences and other molecular data derived from coat proteins or genomic sequences of members of the proposed taxonomic family of Potyviridae, is discussed. We show that comparative sequence analysis of whole coat-protein sequences may be used reliably to differentiate between sequences of closely related strains, and to show groupings of more distantly related viruses; that coat proteins of putative Potyviridae cluster according to the proposed generic divisions, and, even if some are only very distantly related, the members of the family form a cluster distinct from coat proteins of other filamentous and rod-shaped viruses. Taxonomic revisions based on perceived evolutionary relationships, and the lack of feasibility of erecting higher taxa for these viruses, are discussed.

Serotype A and B strains of bean common mosaic virus are two distinct potyviruses

The serological relationships among strains of bean common mosaic virus (BCMV) (genus Potyvirus, family Potyviridae) were investigated by testing 13 isolates of the 10 known BCMV pathotypes with two monoclonal antibodies and six antisera to BCMV strains. In addition, other properties of serologically distinct BCMV strains were compared. Two groups of BCMV strains were obtained by ELISA and Western blot serology: serotype A contained the BCMV strains NL3, NL5, and NL8 and serotype B contained the BCMV strains NL1, NL2, NL4, NL6, US4, NL7, NY15, and Fla. SDS polyacrylamide gel electrophoresis and Western blotting of freshly purified preparations, and of extracts from leaves infected with eleven BCMV strains showed that the apparent molecular mass of the capsid protein of the serotype A isolates NL3, NL5, and NL8 are lower (about M(r) 33,000) than those of the serotype B isolates (M(r) 34,500 to 35,000). The normal lengths of the particles of the serotype A isolates were shorter (810-818 nm) than those of most isolates (except NL6 and NY15) of serotype B (847-886 nm). All isolates studied induced cytoplasmic pinwheel and scroll inclusions. Cells infected with serotype A isolates contained a specific type of proliferated endoplasmic reticulum which was never found in cells infected with serotype B isolates. The capsid protein gene of a representative member of each serotype was cloned and sequenced. Molecular mass calculations based upon nucleotide sequence-derived amino acid sequences yielded M(r) of 29,662 and 32,489 for the capsid proteins of the serotype A isolate NL8 and the serotype B isolate NL4, respectively. Comparison of the coat-protein sequences showed considerable differences at the N-termini whereas the core regions and the C-termini appeared to be highly conserved. Marked differences were also observed within the 3' non-coding regions of cloned cDNAs of NL 4 and NL 8. The striking differences between the two serotypes of BCMV strongly suggest that they be classified as two distinct potyviruses which naturally infect Phaseolus beans.

Strains of bean common mosaic virus consist of at least two distinct potyviruses

Bean common mosaic virus (BCMV) consists of a large number of pathotypes and strains which have largely been identified by their characteristic interactions with a selected number of differential bean cultivars. The relationships among these strains and other potyviruses that infect legumes are complex, with indications that BCMV, blackeye cowpea mosaic virus (BlCMV) and azuki bean mosaic virus (AzMV) may be strains of the one virus. Using high performance liquid chromatographic peptide profiles of coat-protein digests, the NL3 and NY15 strains of BCMV were compared with each other, with the Type and W strains of BlCMV and with the mild mottle strain of peanut stripe virus (PStV). The results suggest that BCMV-NL3 and BCMV-NY15 are distinct potyviruses, not strains of the one virus, and that BCMV-NY15 is a strain of the same potyvirus that includes BlCMV, PStV, AzMV and three potyvirus isolates (74, PM, PN) from soybeans.