Complete nucleotide sequence and affinities of the genomic RNA of Narcissus common latent virus (genus Carlavirus)

The complete sequence of an isolate of Narcissus common latent virus (NCLV) from Zhangzhou city, Fujian, China was determined from amplified fragments of purified viral RNA. Excluding the poly(A) tail, the genomic RNA of NCLV was 8539 nucleotides (nt) long and had the typical organization for a member of the genus Carlavirus. The most closely related species were Potato virus M, Hop latent virus and Aconitum latent virus, which had 58-59% nt identity to NCLV in their entire genomes. These relationships were confirmed by a phylogenetic analysis using a composite nucleotide alignment of all the open reading frames.

Interactive effects of dietary resistant starch and fish oil on short-chain fatty acid production and agonist-induced contractility in ileum of young rats

We have shown independently that dietary fiber and n-3 fatty acids can affect gut function. This study investigated the interactive effects of resistant starch (RS) (as high amylose maize starch [HAMS]) and tuna fish oil on ileal contractility. Four-week-old male Sprague Dawley rats were fed 4 diets that contained 100 g/kg fat as sunflower oil or tuna fish oil, with 10% fiber supplied as alpha -cellulose or HAMS for 6 weeks. Fish oil feeding led to higher ileal n-3 fatty acid levels (mainly as DHA) and higher agonist-induced maximal contractility with an RS effect noted for carbachol. HAMS-containing diets resulted in lower colonic pH and higher total short-chain fatty acids (SCFA), but not for butyrate with fish oil. Low prostanoid responses in young rats were enhanced by fish oil independent of RS. The order of muscarinic receptor subtype responses were different compared to older rats; fish oil feeding altered the sensitivity of the M(1) receptor subtype. Although little interactive effects were demonstrated, these data suggest developmental changes in ileal receptor systems with independent effects of RS and fish oil on some bowel properties in juvenile rats.

Detection and characterisation of a second potyvirus from Thunberg fritillary in China

Plants of Thunberg fritillary (Fritillaria thunbergii Miq.) from Zhejiang Province, were found to be co-infected with two distinct potyviruses. One was an isolate of the recently reported Thunberg fritillary mosaic virus (TFMV; Wei et al., (2005) Arch Virol 150: 1271-1280), while the other was a distinct virus that did not react with TFMV antiserum nor with antisera to 17 other potyviruses, except for a weak reaction with antibodies produced to soybean mosaic virus (SMV) Pinellia strain. Both viruses could be transmitted mechanically to their original host but not to any of a range of commonly used indicator plants. No local lesion host was identified that would enable the viruses to be propagated independently. The complete sequences of both viruses were determined; that of the new virus (9656 nt) had the typical genome organisation and recognised sequence motifs of a potyvirus, encoding a putative polyprotein of 351 kDa. Phylogenetic analysis, sequence comparisons, and the pattern of polyprotein cleavage sites all indicated that it was a member of the Bean common mosaic virus subgroup. The most closely related species are Soybean mosaic virus and Wisteria vein mosaic virus, with 68-69% amino acid identity between their polyproteins. This is sufficiently different for the new virus to be regarded as a distinct species, which we have tentatively named Fritillary virus Y.

Overview and analysis of the polyprotein cleavage sites in the family Potyviridae

SUMMARY The genomes of plant viruses in the family Potyviridae encode large polyproteins that are cut by virus-encoded proteases into ten mature proteins. Three different types of protease have been identified, each of which cuts at sites with a distinctive sequence pattern. The experimental evidence for this specificity is reviewed and the cleavage site patterns are compiled for all sequenced species within the family. Seven of the nine cleavage sites in each species are cut by the viral NIa-Pro and patterns around these sites are related where possible to the active site-substrate interactions recently deduced following the resolution of the crystal structure of Tobacco etch virus (TEV) NIa-Pro (Phan et al., 2002. J. Biol. Chem. 277, 50564-50572). In particular, a revised series of cleavage sites for Sweet potato mild mottle virus (genus Ipomovirus) is proposed with a conserved His at the P1 position. This is supported by homology modelling studies using the TEV structure as a template. The data also provide a standard to correct the annotation of some other published sequences and to help predict these sites in further virus sequences as they become available. Comprehensive data for all sequences of each virus in the family, together with some summaries, have been made available at http://www.rothamsted.bbsrc.ac.uk/ppi/links/pplinks/potycleavage/index.html.

Evidence that the recessive bymovirus resistance locus rym4 in barley corresponds to the eukaryotic translation initiation factor 4E gene

SUMMARY Recent studies have shown that resistance in several dicotyledonous plants to viruses in the genus Potyvirus is controlled by recessive alleles of the plant translation initiation factor eIF4E or eIF(iso)4E genes. Here we provide evidence that the barley rym4 gene locus, controlling immunity to viruses in the genus Bymovirus, corresponds to eIF4E. A molecular marker based on the sequence of eIF4E was developed and used to demonstrate that eIF4E and rym4 map to the same genetic interval on chromosome 3HL in barley. Another genetic marker was developed that detects a polymorphism in the coding sequence of eIF4E and consistently distinguishes between rym4 and susceptible barley cultivars of diverse parentage. The eIF4E gene product from barley genotypes carrying rym4 and allelic rym5 and rym6 genes, originating from separate exotic germplasm, and a novel resistant allele that we identified through a reverse genetics approach all contained unique amino acid substitutions compared with the wild-type protein. Three-dimensional models of the barley eIF4E protein revealed that the polymorphic residues identified are all located at or near the mRNA cap-binding pocket, similarly to recent findings from studies on recessive potyvirus resistance in dicotyledonous plants. These new data complement our earlier observations that specific mutations in bymovirus VPg are responsible for overcoming rym4/5-controlled resistance. Because the potyviral VPg is known to interact with eIF4E in dicotyledonous plants, it appears that monocotyledonous and dicotyledonous plants have evolved a similar strategy to combat VPg-encoding viruses in the family Potyviridae.

Characterisation of the welsh onion isolate of Shallot yellow stripe virus from China

The host range and nucleotide sequence of shallot yellow stripe virus (SYSV) from welsh onion in Shandong province, China is described. Of the plants tested, only shallot and welsh onion became infected but most shallot plants were symptomless. The complete sequence of one isolate (10429 nt) and the 3'-terminal 3540 nts of a second isolate were determined. They had c. 90% nt identity to one another and to published (partial) sequences of SYSV. SYSV was most closely related to onion yellow dwarf virus (OYDV) and resembled it in having a much larger P3 protein than other species in the genus.

A new potyvirus from Thunberg fritillary (Fritillaria thunbergii Miq.) in Zhejiang, China

A potyvirus causing mosaic symptoms in Thunberg fritillary (Fritillaria thunbergii) was found at two sites in Zhejiang province, China. The virus was readily mechanically transmitted to its original host but not to any of 17 other widely used plant virus indicators. A polyclonal antiserum raised to purified virus particles reacted with its homologous virus but not with a range of other viruses (including 16 potyvirus species). In electron microscopy, virus particles and inclusion bodies typical of a potyvirus were seen. The complete nucleotide sequence of an isolate from Ningbo was determined. It was 9723 nt long and sequence analyses predicted the standard potyvirus organisation. The partial sequence (1664 nts at the 3'-terminus) of an isolate from Panan was also determined; the two sequences had 96.9% nt identity. In sequence comparisons and phylogenetic analyses with completely sequenced potyviruses, the new virus was most closely related to Lily mottle virus (53.0% aa identity) and Leek yellow stripe virus. The most closely related incomplete sequence in the international databases was for Lycoris mild mottle virus (72.8% nt identity in their coat proteins). These results suggest that the virus studied is a new species in the genus Potyvirus, which we have tentatively named Thunberg fritillary mosaic virus.

The use of conventional and quantitative real-time PCR assays for Polymyxa graminis to examine host plant resistance, inoculum levels and intraspecific variation

* A real-time PCR protocol based on 18S rDNA sequences was developed to provide a specific, sensitive and quantitative assay for the root-infecting virus vector Polymyxa graminis. * The assay was calibrated with zoospore suspensions and inoculated roots and then shown to work with naturally infected plant roots and infested soil. Both the temperate P. graminis ribotypes previously described are detected but are not distinguished. DNA from related plasmodiophorids and from a range of fungi and plants was not detected. * Different genotypes of Triticum were grown in a soil infested with P. graminis and Soil-borne cereal mosaic virus (SBCMV). The genotypes differed in susceptibility to P. graminis, the least susceptible being the Triticum monococcum accession K-58505. * Conventional PCR assays and sequencing of amplified rDNA fragments showed that P. graminis isolates infecting wheat were mostly, but not exclusively, of ribotype II. Ribotype II was clearly associated with SBCMV transmission and seems to occur preferentially on wheat whereas ribotype I is mostly associated with barley.

Structure of 6-phosphogluconate dehydrogenase refined at 2 A resolution

The X-ray unliganded structure of 6-phosphogluconate dehydrogenase (E.C. 1.1.1.44) (6-PGDH) from sheep liver has been determined at 2A resolution and refined to a final R-factor of 19.8% for 35 031 unique reflections. The enzyme is dimeric, each subunit being comprised of an N-terminal coenzyme-binding domain with a Rossmann fold, a large all-helical domain and a small C-terminal tail. The model contains 473 residues, three sulfate ions and 346 water molecules; the two best defined sulfates are found in the active site. This structure, based on improved diffraction data, is an extension of the 2.5 A, resolution model reported earlier. It has good geometry with 92% of the residues falling in the most favoured areas of the Ramachandran plot. Several unusual features are discussed: the incorporation of an alanine in place of the second conserved glycine of the dinucleotide-binding fingerprint; a duplicated five-helix motif which is unique to this enzyme; an extended water network at the dimer interface and a C-terminal tail which is incorporated within the second subunit, forming not only a major part of the dimer interface but also part of the active site.

Restoration of depressed prostanoid-induced ileal contraction in spontaneously hypertensive rats by dietary fish oil

We have reported that dietary fish oil (FO) rich in n-3 PUFA modulates gut contractility. It was further demonstrated that the gut of spontaneously hypertensive rats (SHR) has a depressed contractility response to prostaglandins (PG) compared with normotensive Wistar-Kyoto (WKY) rats. We investigated whether feeding diets supplemented with n-3 PUFA increased gut contractility and restored the depressed prostanoid response in SHR gut. Thirteen-week-old SHR were fed diets containing fat at 5 g/100 g as coconut oil (CO), lard, canola oil containing 10% (w/w) n-3 FA as alpha-linolenic acid (1 8:3n-3), or FO (as HiDHA, 22:6n-3) for 12 wk. A control WKY group was fed 5 g/100 g CO in the diet. As confirmed, the SHR CO group had a significantly lower gut response to PGE2 and PGF2alpha compared with the WKY CO group. Feeding FO increased the maximal contraction response to acetylcholine in the ileum compared with all diets and in the colon compared with lard, and restored the depressed response to PGE2 and PGF2alpha in the ileum but not the colon of SHR. FO feeding also led to a significant increase in gut total phospholipid n-3 PUFA as DHA (22:6n-3) with lower n-6 PUFA as arachidonic acid (20:4n-6). Canola feeding led to a small increase in ileal EPA (20:5n-3) and DHA and in colonic DHA without affecting contractility. However, there was no change in ileal membrane muscarinic binding properties due to FO feeding. This report confirms that dietary FO increases muscarinic- and eicosanoid receptor-induced contractility in ileum and that the depressed prostanoid response in SHR ileum, but not colon, is restored by tissue incorporation of DHA as the active nutrient.

Molecular criteria for genus and species discrimination within the family Potyviridae

A phylogenetic analysis of the optimised nucleotide (nt) alignment of the entire ORFs of a representative of each fully-sequenced species in the family Potyviridae provided strong support for several subgroups within the genus Potyvirus. A complete set of two-way comparisons was done between the sequences for the entire ORF and for each gene amongst all the 187 complete sequences from the family. Most species had 50-55% nt identity to other members of their genus in their ORFs but there were significant groups of more closely related species and species demarcation criteria were <76% nt identity and <82% amino acid identity. The corresponding thresholds for species demaracation using nt identity values for the individual genes ranged from 58% (P1 gene) to 74-78% (other genes) although a few comparisons between different species exceeded these values. For the entire ORF, genus demarcation criteria were <46% nt identity but this did not separate rymoviruses from potyviruses. Comparisons in the CI gene most accurately reflected those for the complete ORF and this region would therefore be the best for diagnostic and taxonomic studies if only a sub-portion of the genome is to be sequenced. Further comparisons were then made using all the 1220 complete capsid protein (CP) genes. These studies suggest that 76-77% nt identity is the optimal species demarcation criterion for the CP. The study has also helped to allocate the correct virus name to some sequences from the international databases that currently have incorrect or redundant names. The taxonomic status of the current genus Rymovirus and of three unassigned species in the family is discussed. Significant discontinuities in the distributions within and between the currently defined species suggest that the continuum of variation that is theoretically available is constrained or disrupted by molecular barriers that must have some biological significance.

The complete sequence of the genomic RNA of an isolate of Lily virus X (genus Potexvirus)

The complete sequence of the genomic RNA of an isolate of Lily virus X (LVX) has been determined for the first time. The isolate from the Netherlands was 5823 nucleotide (nt) long excluding the 3'-poly(A) tail, making it the shortest reported potexvirus sequence. The 5'-non-coding region begins with GGAAAA like that of Scallion virus X (ScaVX) and some isolates of Cymbidium mosaic virus (CymMV), whereas those of other sequenced potexviruses probably all begin with GAAAA. The genome organisation was similar to that of other members of the genus except that a TGBp3-like region lacked a normal AUG start codon. A phylogenetic analysis based on the entire coding sequence showed that LVX was most closely related to Strawberry mild yellow edge virus and belonged in a subgroup of the genus that also contains CymMV, Narcissus mosaic virus, ScaVX, Pepino mosaic virus, Potato aucuba mosaic virus and White clover mosaic virus.

Depressed prostanoid-induced contractility of the gut in spontaneously hypertensive rats (SHR) is not affected by the level of dietary fat

Dietary saturated fat (SF) has adverse effects on cardiac and vascular smooth muscle (VSM) contractility. Furthermore, VSM of spontaneously hypertensive rats (SHR) is overreactive to various biological stimuli. The aim of this study was to investigate the effects of increasing dietary fat as lard on gut contractility in SHR. Control Wistar-Kyoto (WKY) rats and SHR (13 wk old) were fed for 12 wk a diet containing 3% sunflower oil [low fat (LF), 3% total fat] or diets supplemented with 7% lard [medium fat (MF), 10% total fat] or 27% lard [high fat (HF), 30% total fat]. For ileal and colonic tissues (WKY and SHR), there was a lower total phospholipid PUFA (n-6)/(n-3) ratio with increased dietary SF (P < 0.003). For WKY, increasing SF led to lower levels of the major SCFA and lower total SCFA levels in cecal digesta (P < 0.01). This trend was evident in SHR but significant only for butyrate (P < 0.01). Contractility responses were unaltered in ileum. In colon, there was a change of sensitivity (50% effective concentration) to angiotensin II in WKY (P < 0.05) due to increased SF and a change of sensitivity to prostaglandin (PG)E(2) and carbachol in SHR (P < 0.05). When the 3 dietary groups were combined, there was lower sensitivity (P < 0.01) and lower maximal contraction (P < 0.05) in ileum and lower maximal contraction in colon of SHR in response to PGF(2alpha) (P < 0.05) and PGE(2) (P < 0.01) compared with WKY. Unlike (n-3) PUFA, dietary SF had little overall effect on gut contractility. However, this is the first report of a defect in PG responsiveness from gut tissue from hypertensive rats.

Further molecular characterisation of potyviruses infecting aroid plants for medicinal use in China

Degenerate primers were used to detect and amplify 3'-terminal genome fragments of potyviruses from medicinal aroid plants growing at 16 sites in China. Virus was detected in 7 samples of which six, all of Pinellia ternata, contained a strain of soybean mosaic virus (SMV) similar to that previously reported from this host in China. The complete sequence of one isolate and the P1 protein coding region of the other isolates were also sequenced. In all cases, the P1 proteins resembled isolates of Dasheen mosaic virus (DsMV) more closely than SMV, confirming earlier suggestions of recombination in this region. In a phylogenetic analysis of SMV, DsMV and related sequences, the aroid sequences of SMV formed a distinct group which also included a sequence published as Zantedeschia symptomless virus (AF469171). One of the P. ternata samples was also infected with a second potyvirus, the 3'-terminal sequence of which was similar to DsMV and to some sequences published as Vanilla mosaic virus. The seventh infected sample was Typhonium flagelliforme and the virus from it was identified from its sequence as zantedeschia mosaic virus (ZaMV), providing the first report of this virus from mainland China.

The new plant virus family Flexiviridae and assessment of molecular criteria for species demarcation

The new plant virus family Flexiviridae is described. The family is named because its members have flexuous virions and it includes the existing genera Allexivirus, Capillovirus, Carlavirus, Foveavirus, Potexvirus, Trichovirus and Vitivirus, plus the new genus Mandarivirus together with some related viruses not assigned to any genus. The family is justified from phylogenetic analyses of the polymerase and coat protein (CP) sequences. To help to define suitable molecular criteria for demarcation of species, a complete set of pairwise comparisons was made using the nucleotide (nt) and amino acid (aa) sequences of each fully-sequenced gene from every available accession in the family. Based on the distributions and on inspection of the data, it was concluded that, as a general rule, distinct species have less than ca. 72% identical nt or 80% identical aa between their entire CP or replication protein genes.

Biological and sequence analysis of a novel European isolate of Barley mild mosaic virus that overcomes the barley rym5 resistance gene

A Barley mild mosaic virus (BaMMV) isolate from France (BaMMV-Sil) capable of overcoming rym5-controlled resistance was inoculated to barley genotypes carrying various genes for resistance to the barley mosaic viruses. BaMMV-Sil was unable to infect genotypes carrying rym1, rym4, rym8, rym9, or rym11 but genotypes carrying rym3, rym5, rym6 or no known bymovirus resistance gene were susceptible. Plants carrying rym7 or rym10 showed partial resistance with delayed virus accumulation. The two genomic RNAs of BaMMV-Sil were sequenced and compared to published sequences and those of a further common strain isolate from the UK. Four amino acid differences were observed between BaMMV-Sil and European common strain isolates in the polypeptide encoded by RNA1, the RNA species which determines pathogenicity on the rym5 genotypes. Only two of these differences are likely to be functionally important (His rather than Gln at position1217 in the VPg cistron; His rather than Asp at position 1776 in the NIb cistron). Comparisons with related viruses in the genera Bymovirus and Potyvirus suggest that the change in the VPg, which occurs within a motif conserved amongst all viruses within the family Potyviridae, is the more likely cause of rym5 resistance-breaking.

A new potyvirus from tuberose ( Polianthes tuberosa) in China

Tuberose plants with mild mottle symptoms, growing in a glasshouse in Hangzhou, China, contained virions and inclusion bodies typical of a potyvirus. The virus was mechanically transmitted to tuberose but not to 14 other test plant species. A fragment of 4607 nucleotides, corresponding to the 3'-half of a typical potyvirus was amplified by RT-PCR using degenerate primers and sequenced. The most similar sequence in the databases was that of Tuberose mild mosaic virus (TuMMV) from Taiwan and this was the only virus significantly related to it in phylogenetic analyses. The new sequence had 71.1% nt and 76.6% aa identity to TuMMV in the coat protein. Western blot analyses using antisera raised to expressed coat protein showed that the two viruses were serologically related. Although there are no substantial biological data to distinguish the Hangzhou isolate from TuMMV, the molecular difference between the two virus isolates is similar to, or slightly greater than, that between several pairs of well-established potyvirus species. These results therefore suggest that the Hangzhou isolate should be regarded as a new member of the genus Potyvirus, and we have tentatively named it Tuberose mild mottle virus.

A virus related to soybean mosaic virus from Pinellia ternata in China and its comparison with local soybean SMV isolates

A potyvirus isolated from Pinellia ternata in China was characterised and shown to be related to Soybean mosaic virus (SMV). The virus was pathogenic on P. ternata and some soybean cultivars, whereas the local soybean SMV isolate HH5 did not infect P. ternata. Western blot experiments demonstrated a serological relationship between the virus from Pinellia, SMV and Watermelon mosaic virus (WMV). The complete nucleotide sequences of the Pinellia virus (isolate P-1, 9735 nt) and of the Chinese soybean SMV isolates HH5 (9585 nt) and HZ (9588 nt) were determined. A 1733 nt sequence at the 3'-terminus of a second isolate from Pinellia (isolate P-2) was also determined. The predicted polyprotein of isolate P-1 has 83% amino acid (aa) identity with those of published SMV sequences. In many parts of the genome, aa identity was about 90% but it was much lower in the P1 protein region (24-29%), where it more closely resembled Dasheen mosaic virus (62%). The partial sequence of isolate P-2 had 91% nt identity to P-1 and both isolates resembled a recent sequence in the public databases (AF469171) wrongly named Zantedeschia mosaic virus. The two complete SMV soybean sequences had 93-95% nt identity with those of the previously sequenced isolates and >97% amino acid identity. Phylogenetic analysis and comparisons of coat proteins suggest that the Pinellia, WMV and SMV potyviruses should probably be treated as strains of the same species.

Detection and classification of allexiviruses from garlic in China

Degenerate primers for RT-PCR were designed and used to amplify genome fragments ( c. 750 nt in the coat protein-ORF6 region) of allexiviruses from a total of 28 garlic samples from 24 provinces in China. Many samples contained more than one distinct sequence. A total of 60 different sequences were obtained. Phylogenetic analysis and two-way comparisons were used to assess the status of the sequences and to re-examine the criteria for distinguishing species within the genus. Most of the sequences could be allocated to either Garlic virus D or Garlic virus X on the basis of sequence similarity but some appeared to be intermediate between existing species. There were no sequences of Garlic virus C or Shallot virus X. A comparison with the related genera Carlavirus, Foveavirus and Potexvirus suggests that the published allexivirus species demarcation criteria may have been drawn too tightly and should be re-examined.

The ability of a bymovirus to overcome the rym4-mediated resistance in barley correlates with a codon change in the VPg coding region on RNA1

The genome difference(s) that enable the European pathotype 2 isolates of Barley yellow mosaic virus (BaYMV-2) to infect barley genotypes with the rym4 resistance gene were investigated. Stable deletions of different sizes occurred in RNA2 of laboratory isolates of the common pathotype (BaYMV-1) and BaYMV-2. After mechanical inoculation of susceptible or rym4 genotypes with a mixture of both isolates, immunocapture-RT-PCR with RNA2-specific primers flanking stable deletion regions was used to detect and distinguish the two pathotypes. Individual leaves contained RNA2 of either or both isolates, showing that RNA2 of BaYMV-1 can replicate and move systemically in rym4 plants when co-inoculated with BaYMV-2. In contrast, sequences of RNA1-specific RT-PCR fragments showed that in resistant plants these were always BaYMV-2, suggesting that the pathogenicity determinant was on RNA1. The complete ORFs of RNA1 of three BaYMV-1 and four BaYMV-2 isolates from the UK and Germany were sequenced, and the RNA2 sequences of one BaYMV-1 and two BaYMV-2 isolates from the UK were also determined. All sequences were very similar to one another and to the published German BaYMV-1 isolate. The only consistent amino acid difference between the BaYMV-1 and BaYMV-2 isolates was in the RNA1-encoded polyproteins and this was confirmed by sequencing the relevant region of eight further German isolates. All BaYMV-1 isolates had lysine at aa 1307, whereas BaYMV-2 isolates had asparagine (or, in one isolate, histidine). The polymorphism occurred in the central region of VPg, which has been shown to be required for pathogenicity on genotypes carrying recessive resistance genes in several potyvirus/dicotyledonous plant pathosystems.