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S Loss

Publications and source records attributed to S Loss.

10 recordsLinked to original sources
PubMed2006

NMR in the SPINE Structural Proteomics project.

This paper describes the developments, role and contributions of the NMR spectroscopy groups in the Structural Proteomics In Europe (SPINE) consortium. Focusing on the development of high-throughput (HTP) pipelines for NMR structure determinations of proteins, all aspects from sample preparation, data acquisition, data processing, data analysis to structure determination have been improved with respect to sensitivity, automation, speed, robustness and validation. Specific highlights are protonless (13)C-direct detection methods and inferential structure determinations (ISD). In addition to technological improvements, these methods have been applied to deliver over 60 NMR structures of proteins, among which are five that failed to crystallize. The inclusion of NMR spectroscopy in structural proteomics pipelines improves the success rate for protein structure determinations.

Algorithms↗
PubMed2006

Zygocactus virus X-based expression vectors and formation of rod-shaped virus-like particles in plants by the expressed coat proteins of Beet necrotic yellow vein virus and Soil-borne cereal mosaic virus.

Expression vectors were constructed from 35S promoter-containing full-length cDNA clones of Zygocactus virus X (ZVX). The expression of foreign genes was driven by the ZVX coat protein (cp) subgenomic promoter. It was successful only when the variable region downstream of the conserved putative promoter region GSTTAAGTT(X(12-13))GAA was retained. Most of the ZVX cp gene, except for a short 3' part, was replaced by the corresponding sequence of the related Schlumbergera virus X (SVX) and its cp subgenomic promoter to enable encapsidation of the transcribed RNA by an SVX/ZVX hybrid cp. Vector-expressed cp of Beet necrotic yellow vein virus (BNYVV) assembled in Chenopodium quinoa, Tetragonia expansa and Beta vulgaris leaves into particles resembling true BNYVV particles. The virus produced from these constructs retained its ability to express BNYVV cp in local infections during successive passages on C. quinoa. This ability was lost, however, in the rarely occurring systemic infections.

Capsid Proteins↗
PubMed2005

Molecular characterization of isolates of anagyris vein yellowing virus, plantago mottle virus and scrophularia mottle virus -- comparison of various approaches for tymovirus classification.

The complete nucleotide sequences were determined for the genomic RNAs of three tymoviruses, i.e. isolates of anagyris vein yellowing virus (AVYV), plantago mottle virus (PlMoV) and scrophularia mottle virus (SrMV) which are all serologically closely related to ononis yellow mosaic virus (ibid) and to Nemesia ring necrosis virus (NeRNV), a recently described recombinant virus which is widely spread in commercially grown ornamental plant species belonging to the Scrophulariaceae. Total nucleotide and coat protein amino acid sequence identities revealed similar groupings in the genus tymovirus as serological studies did. The latter, however, tended to suggest much closer relationships than the molecular data and may fail to recognise the distinctiveness of new tymovirus species. The usefulness of various species demarcation criteria for the classification of tymoviruses is discussed.

Genome, Viral↗
PubMed2005

Nemesia ring necrosis virus: a new tymovirus with a genomic RNA having a histidylatable tobamovirus-like 3' end.

The complete nucleotide sequence of the genomic RNA of the new virus Nemesia ring necrosis virus (NeRNV), which is widespread in various ornamental plant species belonging to the Scrophulariaceae and Verbenaceae, has been determined. Based on its gene content, the folding properties of its 5'-untranslated region and in vitro translation experiments, NeRNV RNA is a typical tymovirus RNA. Its 3' end, however, differs greatly from those of the valine-specific tymoviral RNAs that have been analysed previously. It can be folded into an upstream pseudoknot domain and a histidine-specific tRNA-like structure, a combination that, so far, has been found only in tobamoviral RNAs. The identity elements found in NeRNV RNA for recognition by yeast histidyl-tRNA synthetase are more similar to those of yeast tRNAHis than the ones found in tobacco mosaic virus RNA. As a result NeRNV RNA can be charged with histidine even more efficiently than tobacco mosaic virus RNA.

3' Flanking Region↗
PubMed2004

Molecular characterisation of potexviruses isolated from three different genera in the family Cactaceae.

The genome properties of three potexviruses which previously had been isolated from different genera in the family Cactaceae and had been found to be only distantly related serologically have been studied. The sequence of the 3040 3' terminal nucleotides of the genomic RNA of isolate K11 from Schlumbergera bridgesii and the complete RNA sequences of isolates B1 and CC10 from Zygocactus sp. and Opuntia sp., respectively, were determined. Starting sequences were obtained by means of immunocapture reverse transcription PCR using primers derived from highly conserved sequences in other potexviral RNAs. The known parts of the sequences were extended by means of random-primed cDNAs and specific primers derived from the known parts of the sequences. The genome structure of the three viruses resembles that of other potexviruses. The conserved motifs typical for replication-associated proteins, triple gene block (TGB) proteins and coat proteins of potexviruses were readily identified in the translation products of the five open reading frames. The 3' untranslated regions of the three RNAs are folded into secondary structures containing three characteristic hairpins. Rather low percentages of amino acid sequence identities ranging from 62% to 76% for the coat proteins and 41% to 49% for TGB proteins 3 suggest that these viruses should be regarded as distinct virus species for which the names Zygocactus virus X, Schlumbergera virus X and Opuntia virus X are proposed. It is also suggested that the name Cactus virus X which originally was coined for all three virus isolates should no longer be used.

3' Untranslated Regions↗
PubMed2002

A New York isolate of Soil-borne wheat mosaic virus differs considerably from the Nebraska type strain in the nucleotide sequences of various coding regions but not in the deduced amino acid sequences.

A wheat-infecting furovirus found in Tompkins County, New York, U.S.A. was identified as a strain of Soil-borne wheat mosaic virus (SBWMV) by means of sequence analyses of portions of its RNA 1 and 2. The nucleotide sequences of several of its genes differed by c. 9 to 12% from those of the corresponding genome regions of the Nebraska type strain of SBWMV. The deduced amino acid sequences of the putative translation products, however, suggested much closer relationships. Thus, the amino acid sequences of the coat proteins of the two virus strains were 100% identical despite the fact that their coding regions differed in as many as 68 nucleotide positions. The New York (NY) strain of SBWMV is possibly closely related to an isolate from Illinois for which so far only the nucleotide sequences of its coat protein gene and the 5' untranslated region of its RNA 2 are known.

Amino Acid Sequence↗
PubMed1997

Beet soil-borne virus RNA 1: genetic analysis enabled by a starting sequence generated with primers to highly conserved helicase-encoding domains.

The complete sequence of the 5834 nucleotides of RNA 1 of beet soil-borne furovirus (BSBV, Ahlum isolate) was determined using a PCR product obtained with primers to highly conserved coding regions for helicase-like proteins in RNA 1 of furo-, hordei- and tobraviruses as a starting sequence. Unknown parts of the sequence upstream and downstream of this starting sequence were amplified by means of RT-PCR techniques using combinations of specific and random primers. BSBV RNA 1 contains one large ORF for a readthrough protein with a molecular mass of 204 kDa (204K protein) which is interrupted internally by a UAA stop codon terminating the coding region for a protein of 145 kDa (145K protein). The N- and C-terminal parts of the 145K protein and the readthrough domain of the 204K protein contain methyltransferase, helicase and RNA-dependent RNA polymerase motifs, respectively. Unlike other furo- and tobraviruses BSBV contains no further genes on its RNA 1.

Amino Acid Sequence↗
PubMed1997

Beet soil-borne virus RNA 2: similarities and dissimilarities to the coat protein gene-carrying RNAs of other furoviruses.

The complete sequence of the 3454 nt of RNA 2 of the Ahlum isolate of beet soil-borne furovirus (BSBV) has been determined starting with two short stretches of cloned cDNA. Unknown parts of the sequence were amplified by means of RT-PCR techniques using combinations of specific and random primers. BSBV RNA 2 is more similar in its genetic organization to potato mop top virus (PMTV) RNA 3 than to any other furoviral RNA, although it is more than 1100 nt longer. Its 3'-end, unlike that of PMTV RNA 3, has the potential to fold into a tRNA-like structure. It contains one large open reading frame for a readthrough protein with a molecular mass of 104 kDa (104K protein) which is interrupted internally by an amber stop codon terminating the coding region for a protein of 19 kDa (19K), most likely the viral coat protein (CP). The readthrough domain of the 104K protein is much larger than that of PMTV, but the N- and C-proximal portions of these domains are similar for the two viruses. No serological relationships were found between the particles of the two viruses, although more than 50% of the amino acid sequences of the putative CPs are identical.

Amino Acid Sequence↗