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Biomedical subjects

S K Zavriev

Publications and source records attributed to S K Zavriev.

At least 19 recordsLinked to original sources
PubMed2004

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.

Capsid Proteins↗
PubMed2001

Detection of infectious viral particles in plant protoplasts inoculated with transcripts of full-length shallot virus X cDNA.

Flexible filamentous shallot virus X (ShVX) particles were detected in extracts of Beta vulgaris protoplasts inoculated with transcripts from a full-length ShVX cDNA. Extracts from ShVX-infected protoplast were infectious for ShVX-healthy shallot seedlings. Western blot analysis of inoculated plants revealed the accumulation of the ShVX coat protein, while electron microscopy confirmed the presence of ShVX virions. The results suggest that the in vitro RNA transcripts from full-length ShVX cDNA give rise to infectious viral particles.

Allium↗
PubMed1996

Mapping of the red clover necrotic mosaic virus subgenomic RNA.

The red clover necrotic mosaic dianthovirus capsid protein is expressed in vivo from a subgenomic RNA (sgRNA) identical to the 3'-terminal 1.5 kb of RNA-1. The 5' leader sequence of the capsid protein sgRNA is 62 nucleotides, contains a 14-nucleotide putative promoter sequence homologous to the RNA-1 5' terminus, and exhibits a high level of similarity with the tobacco mosaic virus 5' leader translational enhancer element omega. Analysis of the RNA-1 secondary structure, in the region adjacent to the position where the 5' end of the sgRNA was mapped, predicts a stable stem-loop which includes the putative sgRNA promoter element. It is suggested that this structure is important for recognition of the sgRNA transcriptional initiation from the full-length negative-sense RNA-1.

Base Sequence↗
PubMed1995

Use of highly conserved motifs in plant virus RNA polymerases as the tags for specific detection of carmovirus-related RNA-dependent RNA polymerase genes.

Two highly degenerate primers for sequence-specific amplification and cloning of a 510-nucleotide-long segment of RNA-dependent RNA-polymerase (RdRp) genes were selected and synthesized on the basis of available plant carmovirus-like viral RdRp sequences. These primers were shown to be efficient in PCR screening of different RdRp genes including those of carmoviruses, dianthoviruses, and tombusviruses. In particular, they were used for amplification, cloning, and sequencing of an RdRp gene fragment of an isometric plant virus with unknown evolutionary relationships, pelargonium flower break virus (PFBV). Alignment of the respective nucleotide and amino acid sequences indicates a very close similarity between PFBV and carnation mottle virus, the type member of carmoviruses.

Amino Acid Sequence↗
PubMed1994

Nucleotide sequence of carnation ringspot dianthovirus RNA-1.

The nucleotide sequence of carnation ringspot virus (CRSV) RNA-1, the type member of the dianthovirus genus, has been determined. The 3756 nucleotide genomic RNA-1 contains three large open reading frames (ORFs), capable of encoding 27K, 54K and 38K polypeptides. In addition, a small ORF encoding a 10K polypeptide at the 3' terminus of the RNA has been identified. The gene organization of CRSV RNA-1 is similar to those of red clover necrotic mosaic (RCNMV) and sweet clover necrotic mosaic (SCNMV) dianthoviruses with the exception that CRSV RNA-1 contains the additional 3'-terminal ORF. The 27K and 54K proteins possess significant sequence similarity to corresponding polypeptides of the other dianthoviruses. The 54K protein also contains the conserved RNA-dependent RNA polymerase motif. The identification of a shifty heptanucleotide preceding the p27 ORF termination codon and a predicted secondary structure following the terminator suggest that a translational frameshifting event allows translation to continue past the p27 ORF into the p54 ORF, which is in the -1 frame, generating an 88K fusion protein. Amino acid sequence alignment of the 38K protein with the corresponding RCNMV and SCNMV polypeptides indicate that this is the viral capsid protein.

Amino Acid Sequence↗
PubMed1992

Nucleotide sequence of shallot virus X RNA reveals a 5'-proximal cistron closely related to those of potexviruses and a unique arrangement of the 3'-proximal cistrons.

The 8890 nucleotide RNA sequence of shallot virus X (ShVX), a new virus isolated from shallot, has been determined. The sequence contains six open reading frames (ORFs) which encode putative proteins (in the 5' to 3' direction) of M(r) 194528 (ORF1), 26333 (ORF2), 11245 (ORF3), 42209 (ORF4), 28486 (ORF5) and 14741 (ORF6). The ORF1 protein was found to be highly homologous to the putative potexvirus RNA replicases; ORF2, -3, -5 and -6 proteins also have analogues among the potex- and/or carlavirus-encoded proteins. ORF3 is followed by an AUG-lacking frame coding for an amino acid sequence homologous to that of the 7K to 8K proteins of the triple gene block of the above-mentioned viruses. The putative ORF4 protein has no reliable homology with proteins in the database. The results obtained testify that, except for the unique 42K protein gene, the ShVX genome combines a number of elements typical of both carla- and potexviruses.

Amino Acid Sequence↗
PubMed1991

The genome organization of potato virus M RNA.

The 8534 nucleotide sequence of the genome of the carlavirus, potato virus M (PVM), has been determined. The sequence contains six large open reading frames (ORFs) and non-coding regions consisting of 75 nucleotides at the 5' end, 70 nucleotides followed by a poly(A) tail at the 3' end and 38 and 21 nucleotides between three large blocks of coding sequences. The ORF beginning at the first initiation codon at nucleotide 76 encodes a polypeptide of 223K which, according to its primary sequence analysis, seems to be a virus RNA replicase. The next coding block consists of three ORFs encoding polypeptides of 25K, 12K and 7K. The third block consists of two ORFs encoding polypeptides of 34K (PVM coat protein) and 11K. The 11K polypeptide contains a pattern resembling the consensus for a metal-binding nucleic acid-binding 'finger'.

Amino Acid Sequence↗
PubMed1990

The putative RNA replicase of potato virus M: obvious sequence similarity with potex- and tymoviruses.

On the basis of comparison of the protein sequences of the putative virus-specific replicases, carlaviruses can be placed in the "Sindbis-like" supergroup of plus-stranded RNA viruses. Among these, the amino acid sequences of the replication proteins of potex- and tymoviruses showed the highest similarity to potato virus M. The possible functions of conserved domains are suggested to be methyltransferase, nucleotide-binding domain, and RNA polymerase.

Amino Acid Sequence↗
PubMed1989

Partial nucleotide sequence of potato virus M RNA shows similarities to protexviruses in gene arrangement and the encoded amino acid sequences.

The nucleotide sequence of the 3'-proximal 2630 nucleotides of potato virus M (PVM) genomic RNA was determined. The sequenced region contained five long open reading frames (ORFs). The ORF nearest to the 3'-terminal pol(A) tail corresponds to a polypeptide of Mr 10,848. This ORF is preceded by one which encodes a protein of Mr 33,906 (34K) which has an amino acid sequence that is very similar in its carboxyterminal part to that of the coat proteins of some potexviruses. Three other ORFs encoding polypeptides of Mr 24,615, 11,983 and 6739 are present in the region 5' to the 34K protein gene. There is extensive similarity between these proteins and the corresponding proteins encoded by the conserved triple gene block in the RNA of potexviruses.

Amino Acid Sequence↗
PubMed1982

RNA polymerase-dependent mechanism for the stepwise T7 phage DNA transport from the virion into E. coli.

The influence of rifampicin, streptolydigin, tetracycline and chloramphenicol on phage DNA transport from the T7 virion into the E. coli cell was studied. It has been found that the DNA transport proceeds in at least three stages. During the initial stage the phage injects into the host cell the left approximately 10 per cent of its DNA molecule. The entrance of the next 50 per cent of 17 DNA molecule is blocked by inhibitors which block transcription but not translation. Moreover, the entrance time of this part of the T7 DNA increases in the case of the T7 mutant D111 (which contains a deletion of the A2 and A3 promoters) and decreases in the case of the D53 mutant (which contains a deletion in the region of the early gene transcription terminator). It would appear, that the second stage of the phage DNA transport is tightly coupled with its transcription and that a mechanical function is carried out by RNA polymerase. The translation inhibitors completely block the entrance of the remaining 40 per cent of the 17 DNA molecule (class III genes) into the host cell. It would appear that some class I and (or) II gene product(s) are obligatory components of the final stage of 17 DNA transport. Some probable consequences of this virus DNA transport model as well as its agreement with the functional structure of T7 chromosome and with T7 development are discussed.

Anti-Bacterial Agents↗
PubMed1980

On the promoter complex formation rate of E. coli RNA polymerases with T7 phage DNA.

Influence of ionic strength on the kinetics of the promoter complex formation between E. coli RNA polymerase and T7 phage DNA was investigated using a membrane filter assay. The enzyme-promoter association rate constant was determined. It varies from 10(9) to 3 x 10(7) M-1 sec-1 when the ionic strength is changed from zero to 0.15 M NaCl. Basing on the theoretical analysis of experimental data obtained the model for the promoter site selection assuming the enzyme sliding along the DNA is discussed.

DNA, Viral↗
PubMed1979

Circular dichroism anisotrophy of DNA with different modifications at N7 of guanine.

The complexex DNA-Ag1+, DNA-Cu1+, protonated DNA and DNA methylated at N7 of guanine were oriented by pumping the solutions through a multicapillary cell in the direction of a light beam. The CD components along the DNA axis, delta epsilon parallel, and normal to it, 2 delta epsilon perpendicular, were calculated from the CD spectra of the oriented samples by the method of Chung and Holzwarth, (1975) J. Mol. Biol. 92, 449--466. It was shown that in most cases, except that of the protonated DNA, the degree of orientation was only slightly less than that for pure DNA. This demonstrated the absence of aggregation and of appreciable denaturation. In all cases the modifications of DNA give rise to a negative component 2 delta epsilon perpendicular, whose magnitude increased as the extent of modification increased. From both the CD spectra of non-oriented samples and the absorption spectra, an inference is drawn that Ag1+ and Cu1+ are attached to the same site as CH3 groups i.e., to the N7 atom of guanine. Proton transfer along the H-bond from the N1 atom of G to the N3 atom of the complementary cytosine is suggested to be a result of the modifications, although the case of H+-DNA may differ from the others. Based on the CD spectra for the anisotropic components, delta epsilon parallel and 2 delta epsilon perpendicular, it is proposed that ligand binding is accompanied by winding of the DNA helix.

Animals↗
PubMed1978

On the flexibility of the boundaries between the A-form and B-form sections in DNA molecule.

The degree of orientation of DNA in a flow has been studied within the interval of the B - A transition induced by ethanol. The orientation of the B DNA (60-65% ethanol, v/v) and that of the A DNA (80-82% ethanol) are nearly identical. This means that both conformations have similar persistence lengths and that there is no aggregation in the course of formation of the A form. Within the transition range (65-78% ethanol) the orientation attains a sharp minimum which coincides with the half-transition point (73% ethanol). The cooperative character of the B - A transition presupposes the existence of boundaries between the alternating sections of the A and B conformations that may entail an increased flexibility of the DNA molecule and a corresponding drop of orientation. Theory predicts an elliptical dependence of the number of boundaries on the proportion of the A form. The experimental degree of orientation follows the same pattern. Quantitative evaluation shows that the flexibility of a boundary is small, so that several dozen of boundaries are required to simulate free rotation.

Chemical Phenomena↗
PubMed1976

Circular dichroism of DNA--proflavine, DNA--ethidium and DNA--distamycine flow--oriented complexes.

The circular dichroism (CD) spectra of flow-oriented complexes of DNA with proflavine (PF), ethidium (ET) and distamycine (DS) have been studied in the ultraviolet region. The CD spectra with light propagating in parallel to the flow direction were measured by the method of Chung and Holzwarth [1]. Delta epsilon and delta epsilon values have been obtained by this method. It was shown that all the complexes studied exhibit a strong CD anisotropy so that "isotropic" CD spectra measured with a conventional procedure can be attributed to the mutual compensation of the two components of opposite signs.

Acridines↗