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Biomedical subjects

J F Antoniw

Publications and source records attributed to J F Antoniw.

At least 19 recordsLinked to original sources
PubMed2001

Plant virus transmission by plasmodiophorid fungi is associated with distinctive transmembrane regions of virus-encoded proteins.

Computer analysis of published sequence data has consistently identified two complementary transmembrane domains in the coat protein readthrough domains of benyviruses, furoviruses and pomoviruses and in the P2 proteins of bymoviruses. These viruses differ in genome organisation but are all transmitted by plasmodiophorid fungi. The second domain is absent or disrupted in naturally-occurring deletion mutants that cannot be fungally-transmitted. In a non-transmissible substitution mutant of Beet necrotic yellow vein virus [Tamada et al. (1996) J Gen Virol 77: 1359-1367], the alignment of the helices is disrupted. From conserved patterns detected in transmembrane helix sequences and calculated relative helix tilts, structural arrangements consistent with tight packing of transmembrane helices were identified. These included ridge/groove arrangements between the two helices and strong electrostatic associations at the interfacial regions of the membrane. The data strongly suggest that these transmembrane helices facilitate the movement of virus particles across the fungal membrane.

Amino Acid Sequence↗
PubMed2001

TMCompare: transmembrane region sequence and structure.

UNLABELLED: TMCompare is an alignment and visualization tool for comparison of sequence information for membrane proteins contained in SWISS-PROT entries, with structural information contained in PDB files. The program can be used for: detection of breaks in alpha helical structure of transmembrane regions; examination of differences in coverage between PDB and SWISS-PROT files; examination of annotation differences between PDB files and associated SWISS-PROT files; examination and comparison of assigned PDB alpha helix regions and assigned SWISS-PROT transmembrane regions in linear sequence (one letter code) format; examination of these differences in 3D using the CHIME plugin, allowing; analysis of the alpha and non-alpha content of transmembrane regions. AVAILABILITY: TMCompare is available for use through selection of a query protein via the internet (http://www.membraneproteins.org/TMCompare) CONTACT: tmcompare@membraneproteins.org

Binding Sites↗
PubMed1999

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.

Amino Acid Sequence↗
PubMed1999

Molecular analysis of barley yellow mosaic virus isolates from China.

The complete sequences of both RNAs of an isolate of barley yellow mosaic virus from Yancheng, Jiangsu province, China, were determined. The sequences resembled those of an isolate from Japan (96.8% identical nucleotides for RNA1; 95.7% for RNA2) more closely than one from Germany (93.9 and 91.0%, respectively). The greatest differences between the Chinese and Japanese isolates were in the 5'-UTRs of RNAs 1 and 2 (88.9 and 91.6% identical nucleotides, respectively) and there were also some other regions of difference in P1 (RNA2) and P3, CI, NIa and the 5' end of the coat protein (CP) (RNA1). Molecular differences between isolates from ten sites widely distributed in Eastern China were studied by sequencing RNA regions coding for the CP (RNA1) and the N-terminus of the P2 protein (RNA2). The P2 fragment was more variable than the CP, and phylogenetic analysis of both regions showed that Asian and European isolates formed distinct clusters. Differences between isolates were also revealed by single-strand conformation polymorphism of reverse transcription-polymerase chain reaction products, spanning the full lengths of both RNA1 and RNA2. However, molecular variations between isolates could not be linked to earlier results showing differences in cultivar response.

Base Sequence↗
PubMed1999

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.

Amino Acid Sequence↗
PubMed1997

A large duplication in the 3'-untranslated region of a subpopulation of RNA2 of the UK-M isolate of barley mild mosaic bymovirus.

The UK-M isolate of the bipartite barley mild mosaic bymovirus (BaMMV UK-M) cannot be fungally transmitted, and has previously been shown to have a 1092 nt deletion in the coding region of RNA2. We now report, using sequence and reverse transcriptase-polymerase chain reaction (RT-PCR) data, that a subpopulation of BaMMV UK-M RNA2 contains a direct imperfect sequence repeat of 552 nt in the 3' untranslated region. The secondary structure of the 3' end of RNA2, and its possible effects on replication of the virus, are also discussed.

Base Sequence↗
PubMed1997

Complete RNA1 sequences of two UK isolates of barley mild mosaic virus: a wild-type fungus-transmissible isolate and a non-fungus-transmissible derivative.

The complete RNA1 sequences of two isolates (fungus transmissible and non-fungus transmissible) of barley mild mosaic virus (BaMMV) were obtained. The two isolates' RNA1 sequences had very high sequence identity (99.3%), and of the 15 amino acid differences (out of 2258) between the putative polyproteins, 11 were conservative and unlikely to affect the structure or function of the protein. The remaining amino acid differences were thought unlikely to affect fungus transmission because they occur in the CI- and NIb-coding regions. This strongly suggests that the P73 protein of RNA2 (which has a 364-aa deletion in the non-fungus-transmissible isolate) is involved in fungus transmission of BaMMV.

Amino Acid Sequence↗
PubMed1996

The complete nucleotide sequence of RNA-2 of a fungally-transmitted UK isolate of barley mild mosaic bymovirus and identification of amino acid combinations possibly involved in fungus transmission.

The complete nucleotide sequence of RNA-2 of a fungally-transmitted UK isolate of barley mild mosaic bymovirus (BaMMV isolate UK-F) was determined and compared with other published sequences, particularly UK-M, an isolate derived from the same source but which has been mechanically passaged for several years, has a deletion of about 1 kb and cannot be fungally transmitted. From an alignment of the BaMMV RNA-2 encoded protein with that for barley yellow mosaic bymovirus (BaYMV), several regions of consistent homology were identified and extensive searches made for similarities with the proteins of other fungally-transmitted viruses, especially amongst the furovirus capsid readthrough proteins which seem especially prone to deletion and which have already been implicated in fungus transmission. The amino acid combinations ER (glutamic acid-arginine) or QR (glutamine-arginine) were found consistently in all of the viruses. They occurred in positions predicted to be on the outside of the protein, and therefore available for interaction with the fungus vector, and were also within the regions prone to spontaneous deletion. In view of the lack of other structural or sequence homologies, it is suggested that these motifs are strong candidates for involvement in fungus transmission.

Amino Acid Sequence↗
PubMed1996

Sequence analysis of wheat and oat furovirus capsid protein genes suggests that oat golden stripe virus is a strain of soil-borne wheat mosaic virus.

In northern blots, cDNA probes prepared to soil-borne wheat mosaic virus (SBWMV) RNA-1 and RNA-2 hybridized to RNA-1 and RNA-2, respectively, from a UK isolate of oat golden stripe virus (OGSV), as well as to their homologous RNAs. RT-PCR was used to amplify, clone and sequence a region of about 750 nucleotides spanning the capsid protein gene and part of the readthrough protein on RNA-2 from OGSV, a French isolate of SBWMV and two stable deletion mutants (Lab1 and Okl-7) of SBWMV isolates from Nebraska and Oklahoma respectively. There was very high (96.7-99.1%) nucleotide homology between all these sequences and the wild-type SBWMV sequences from Nebraska and Oklahoma. OGSV was more similar to SBWMV from France and Nebraska than were any of the isolates to SBWMV from Oklahoma. Of the few differences in the deduced amino acid sequences of the capsid proteins from the different isolates, OGSV differed from all SBWMV isolates only in one amino acid (isoleucine for valine at position 88). The high degree of similarity suggests that OGSV may best be classified as an oat strain of SBWMV.

Avena↗
PubMed1996

Single-strand conformation polymorphism analysis of RT-PCR products of UK isolates of barley yellow mosaic virus.

Single-strand conformation polymorphism (SSCP) analysis of the bipartite genomes of several UK isolates of barley yellow mosaic virus (Ba YMV) was done using fragments of cDNA amplified by RT-PCR. Isolates differed in their SSCP patterns in several regions, but in no case was the pattern able to distinguish between common and resistance-breaking strains. In regions where the nucleotide sequences of UK isolates had been determined, there was no simple relationship between numbers of nucleotide differences and SSCP patterns: differences of only 2 or 3 nucleotides (nt) gave different SSCP patterns, whereas differences of as many as 29 nt did not. Although SSCP analysis has some potential as a rapid and sensitive tool for distinguishing virus isolates, differences detected do not necessarily relate to biological properties and the results are highly dependent on gel conditions.

Acrylic Resins↗
PubMed1995

Cloning and sequence analysis of RNA-2 of a mechanically transmitted UK isolate of barley mild mosaic bymovirus (BaMMV).

A mutant of the 'Streatley' isolate of barley mild mosaic bymovirus was selected from the original field isolate by repeated mechanical inoculation. Unlike the wild-type barley mild mosaic virus, which is transmitted by the soilborne fungus Polymyxa graminis, the mutant could not be transmitted by this vector. RNA-2 of the mutant virus was shorter than that of the wild-type virus suggesting that a deletion of part of the genome segment had occurred. The nucleotide sequence of the mutant RNA-2 was determined and revealed a high degree of homology with the RNA-2 of a German BaMMV field isolate. The deletion comprises 1092 nucleotides and is located in the 3'-terminal part of the coding region. The 34-kDa truncated form of the C-terminal protein is less than half the size of the corresponding protein of full-length BaMMV RNA-2. Taken together, the sequence data and results of biological experiments suggest an essential role of the C-terminal protein for fungus transmission of BaMMV.

Amino Acid Sequence↗
PubMed1995

Molecular characterisation of UK isolates of barley yellow mosaic bymovirus.

Several isolates of barley yellow mosaic virus (BaYMV) from different sites in the UK, including some that were virulent on European resistant winter barley cultivars (resistance-breaking strain: BaYMV-2) and some that were not, were examined by RT-PCR, restriction mapping and sequencing of selected parts of the virus genome. Nucleotide and predicted amino acid sequences were determined for the 5'-terminal region, part of the NIa coding region and the coat protein coding region on RNA 1 and an area at the N-terminus of the 70-kDa protein coding region on RNA 2. The sequences differed from those previously reported for a BaYMV isolate from Japan and for two German isolates, one of which was of the BaYMV-2 strain. There were no strain-specific amino acid differences and the few, non-consecutive, nucleotide differences detected were probably not significant and were insufficient to develop a rapid diagnostic test to distinguish BaYMV-2 from other isolates. Restriction mapping of RNA 2 cDNA again showed no consistent strain-related differences. The differences previously reported between the two German isolates are probably not strain-related.

Base Sequence↗
PubMed1993

Nucleotide sequence of beet cryptic virus 3 dsRNA2 which encodes a putative RNA-dependent RNA polymerase.

The nucleotide sequence of a DNA copy of beet cryptic virus 3 double-stranded RNA2 was determined, and one strand was found to contain a single long open reading frame of 1431 nucleotides which encoded a putative polypeptide containing 478 amino acid residues with an M(r) of 54.9K. This polypeptide contained conserved amino acid sequence motifs found in the genes that encode putative RNA-dependent RNA polymerases of other RNA viruses.

Amino Acid Sequence↗
PubMed1991

Isolation and characterization of a cDNA clone encoding the anti-viral protein from Phytolacca americana.

Phytolacca anti-viral protein (PAP) was purified from Phytolacca leaves and the N-terminal was sequenced. A cDNA library was made from mRNAs isolated from Phytolacca leaves and cDNA clones for PAP were identified using oligonucleotide probes derived from the N-terminal amino acid sequence. The PAP-cDNA clone was sequenced from both directions. The predicted amino acid sequence of PAP was compared with the amino acid sequences of other ribosome-inactivating proteins. The identities of these proteins to PAP ranged from 29 to 38%, and a region was found in each with a sequence similar to the PAP sequence (AIQMVSEAARFKYI). Southern blot analysis indicates that PAP is encoded by a multi-gene family.

Amino Acid Sequence↗
PubMed1986

The chemical induction of PR (b) proteins and resistance to TMV infection in tobacco.

Aspirin injected into Xanthi-nc tobacco leaves induces the production of PR protein and resistance to TMV. The concentration of PR protein and resistance increases with increasing aspirin concentration, up to a plateau. 2-Thiouracil and dioxohexahydrotriazine also induce PR protein when injected into tobacco leaves. Barium and manganese salts induced PR protein, but those of eight other cations did not. Certain salts were phytotoxic but did not induce PR protein, confirming that the production of PR protein is not a non-specific stress response.

Aspirin↗