scholarly journals Nucleotide and amino acid sequences of a coat protein of an Ukrainian isolate of Potato virus Y: comparison with homologous sequences of other isolates and phylogenetic analysis

2014 ◽  
Vol 30 (2) ◽  
pp. 141-148
Author(s):  
I. G. Budzanivska ◽  
L. P. Ovcharenko ◽  
A. V. Kharina ◽  
I. I. Boubriak ◽  
V. P. Polischuk
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Coat Protein ◽  
Potato Virus ◽  
Potato Virus Y ◽  
Amino Acid Sequences ◽  
Homologous Sequences

Detection of the Na+-translocating NADH-quinone reductase in marine bacteria using a PCR technique

2000 ◽  
Vol 46 (4) ◽  
pp. 325-332 ◽  
Author(s):  
Sanae Kato ◽  
Isao Yumoto
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
16S Rrna ◽  
Marine Bacteria ◽  
Genomic Dna ◽  
Screening Method ◽  
Quinone Reductase ◽  
Amino Acid Sequences ◽  
Homologous Sequences ◽  
Simple Screening

To examine the distribution of the Na+-translocating NADH-quinone reductase (Na+-NQR) among marine bacteria, we developed a simple screening method for the detection of this enzyme. By reference to the homologous sequences of the Na+-NQR operons from Vibrio alginolyticus and Haemophilus influenzae, a pair of primers was designed for amplification of a part of the sixth ORF (nqr6) of the Na+-NQR operon. When PCR was performed using genomic DNA from 13 marine bacteria, a 0.9-kbp fragment corresponding to nqr6 was amplified in 10 strains. Although there were three PCR-negative strains phylogenetically, based on the sequence of the 16S rRNA, these were placed far from the PCR-positive strains. No product was observed in the case of nonmarine bacteria. The nucleotide and predicted amino acid sequences of nqr6 were highly conserved among the PCR-positive marine bacteria. A phylogenetic analysis of marine bacteria, based on nqr6 sequencing, was performed.Key words: Na+-translocating, NADH-quinone reductase, marine bacteria, PCR.

scholarly journals A Single Amino Acid Change in Viral Genome-Associated Protein of Potato Virus Y Correlates with Resistance Breaking in ‘Virgin A Mutant’ Tobacco

1999 ◽  
Vol 89 (2) ◽  
pp. 118-123 ◽  
Author(s):  
Chikara Masuta ◽  
Mitsuyo Nishimura ◽  
Hiroshi Morishita ◽  
Tatsuji Hataya
Keyword(s):  
Amino Acid ◽  
Potato Virus ◽  
Viral Genome ◽  
Potato Virus Y ◽  
Cell Movement ◽  
Amino Acid Sequences ◽  
Single Amino Acid ◽  
Viral Gene ◽  
Resistance Breaking ◽  
Single Amino Acid Change

Tobacco cultivar Virgin A Mutant (VAM) is reported to have the recessive potyvirus resistance gene va. Varied levels of resistance were observed in VAM plants inoculated with Japanese potato virus Y (PVY) isolates. VAM was highly resistant to most of the PVY isolates tested and tolerant to three necrotic strain isolates of PVY-T. Based on data obtained from tissue printing and press blotting, the resistance appeared to be mainly at the level of cell-to-cell movement. PVY replicated in VAM proto-plasts, but the replication was 30% lower than in susceptible tobacco, suggesting that impairment of replication also contributes to resistance. To identify the viral gene product or products involved in VAM resistance, we isolated spontaneous resistance-breaking mutants by passing vein-banding (O strain) isolates several times through VAM plants. By comparing the amino acid sequences of the mutants with their original isolates, we identified a single amino acid substitution in the viral genome-associated protein (VPg) domain that is correlated with VAM resistance breaking. Together, these results suggest that, in addition to its role in replication, VPg plays an important role in the cell-to-cell movement of PVY.

scholarly journals Mapping antigenic epitopes of potato virus Y with antibodies affinity-purified by using overlapping synthetic peptides

1994 ◽  
Vol 3 (2) ◽  
pp. 207-211
Author(s):  
Maija Vihanen-Rantanen ◽  
Reijo Sironen ◽  
Matti Vuento
Keyword(s):  
Amino Acid ◽  
Coat Protein ◽  
Amino Acid Sequence ◽  
Potato Virus ◽  
Synthetic Peptides ◽  
Potato Virus Y ◽  
Detection Methods ◽  
Polyclonal Antisera ◽  
Antigenic Epitopes

Synthetic, overlapping peptides representing the entire amino acid sequence of potato virus Y (PVY) coat protein were used to affinity-purify antibodies from polyclonal antisera to PVY. In testing the binding of the purified antibodies to PVY particles, antigenic epitopes were identified. The N-terminal and C-terminal regions of the PVY coat protein were found to contain most of the antigenic epitopes. The results will facilitate the development of detection methods for PVY based on synthetic peptides.

scholarly journals Mitochondrial Cytochrome b Gene Analysis of Aspergillus fumigatus and Related Species

2000 ◽  
Vol 38 (4) ◽  
pp. 1352-1358 ◽  
Author(s):  
Li Wang ◽  
Koji Yokoyama ◽  
Makoto Miyaji ◽  
Kazuko Nishimura
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Nucleotide Sequences ◽  
Amino Acid Sequences ◽  
The Other ◽  
Gene Analysis ◽  
Homologous Sequences ◽  
Mitochondrial Cytochrome B ◽  
Mitochondrial Cytochrome B Gene ◽  
Neosartorya Fischeri

Nucleotide sequences of 426 bp from the mitochondrial (mt) cytochrome b genes of six anamorph species and two species of Neosartorya teleomophs of Aspergillussection Fumigati were determined. These sequences were used to build nucleotide- and amino acid-based trees for phylogenetic analysis. Thirteen strains of A. fumigatus including 10 clinical isolates of A. fumigatus, 1 type culture ofA. fumigatus var. fumigatus, 1 type culture ofA. fumigatus var. ellipticus, and 1 strain ofA. fumigatus var. albus, had the same nucleotide sequences. One strain of A. fumisynnematus, two strains labeled A. neoellipticus, two strains of A. viridinutans, and one strain of A. duricaulis had distinct nucleotide and amino acid sequences. Two strains of A. brevipes were divided into two types. One produced a 1,500-bp fragment that included an intron. The nucleotide sequences of its two exons were similar to those of the A. fumigatus, and the derived amino acid sequence was the same as that for A. fumigatus. The other produced a 426-bp fragment and had the same nucleotide and amino acid sequences as A. unilateralis. Neosartorya fischeri var. fischeri and N. stramenia had nucleotide sequences that differed from that ofA. fumigatus. These species possessed their own characteristic nucleotide sequences that differed from each other. In comparisons of homologous sequences from four other pathogenic species of Aspergillus, regions specific to sectionFumigati were found. The mt cytochrome b gene analysis was valuable for the identification, classification, and phylogenetic analysis of isolates of section Fumigati.

Molecular characterization of coat protein genes of serologically distinct isolates of potato virus Y necrotic strain

1997 ◽  
Vol 43 (7) ◽  
pp. 677-683 ◽  
Author(s):  
A. K. Dhar ◽  
R. P. Singh
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Coat Protein ◽  
Potato Virus ◽  
Sequence Comparison ◽  
Potato Virus Y ◽  
Protein Gene ◽  
Hydrophobic Amino Acids ◽  
Amino Acid Levels

The coat protein (CP) genes of two potato virus Y necrotic isolates (N27 and a mutant strain N27-92), which differed in their reactivity to a monoclonal antibody (mab), were characterized. Both isolates could be detected by mab 4E7, but mab VN295.5 selectively reacted to N27 and not to N27-92. The CP genes of both isolates coded for 267 amino acids with ~99.0% identity at both the nucleotide and the amino acid levels. Nucleotide sequence comparison indicated five substitutions in N27-92 compared with N27. Three of these changes resulted in substitution of amino acids. Two transitions (A→G) in N27-92 changed threonine to alanine and lysine to arginine at positions 7 and 55, respectively, whereas a A→T transversion changed asparagine to isoleucine at position 27. The surface probability curves of both the isolates could almost be superimposed, except at amino acid positions 7 and 27. Since amino acid substitution at position 55 is conservative, changes from polar to hydrophobic amino acids (threonine→alanine and asparagine→isoleucine) at positions 7 and 27 might have changed the epitope(s) of N27-92, abolishing its detection by mab VN295.5.Key words: potato virus Y, PVYN, coat protein gene.

Coat protein of potyviruses 2. amino acid sequence of the coat protein of potato virus Y

Virology ◽  
1986 ◽  
Vol 152 (1) ◽  
pp. 118-125 ◽  
Author(s):  
Dharma D. Shukla ◽  
Adam S. Inglis ◽  
Neil M. McKern ◽  
Keith H. Gough
Keyword(s):  
Amino Acid ◽  
Coat Protein ◽  
Amino Acid Sequence ◽  
Potato Virus ◽  
Potato Virus Y

scholarly journals Evidence for diversifying selection in Potato virus Y and in the coat protein of other potyviruses

2002 ◽  
Vol 83 (10) ◽  
pp. 2563-2573 ◽  
Author(s):  
Benoît Moury ◽  
Caroline Morel ◽  
Elisabeth Johansen ◽  
Mireille Jacquemond
Keyword(s):  
Amino Acid ◽  
Coat Protein ◽  
Mosaic Virus ◽  
Potato Virus ◽  
Potato Virus Y ◽  
Yellow Mosaic Virus ◽  
Likelihood Method ◽  
Evolutionary Constraints ◽  
Coat Proteins ◽  
Diversifying Selection

The modes of evolution of the proteins of Potato virus Y were investigated with a maximum-likelihood method based on estimation of the ratio between non-synonymous and synonymous substitution rates. Evidence for diversifying selection was obtained for the 6K2 protein (one amino acid position) and coat protein (24 amino acid positions). Amino acid sites in the coat proteins of other potyviruses (Bean yellow mosaic virus, Yam mosaic virus) were also found to be under diversifying selection. Most of the sites belonged to the N-terminal domain, which is exposed to the exterior of the virion particle. Several of these amino acid positions in the coat proteins were shared between some of these three potyviruses. Identification of diversifying selection events in these different proteins will help to unravel their biological functions and is essential to an understanding of the evolutionary constraints exerted on the potyvirus genome. The hypothesis of a link between evolutionary constraints due to host plants and occurrence of diversifying selection is discussed.

scholarly journals Phylogenetic Analysis: Basic Concepts and Its Use as a Tool for Virology and Molecular Epidemiology

2018 ◽  
Vol 44 (1) ◽  
pp. 20
Author(s):  
Eloiza Teles Caldart ◽  
Helena Mata ◽  
Cláudio Wageck Canal ◽  
Ana Paula Ravazzolo
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Molecular Epidemiology ◽  
Phylogenetic Analyses ◽  
Phylogenetic Reconstruction ◽  
Evolutionary Process ◽  
Amino Acid Sequences ◽  
Evolutionary Models ◽  
Reconstruction Methods ◽  
Basic Concepts

Background: Phylogenetic analyses are an essential part in the exploratory assessment of nucleic acid and amino acid sequences. Particularly in virology, they are able to delineate the evolution and epidemiology of disease etiologic agents and/or the evolutionary path of their hosts. The objective of this review is to help researchers who want to use phylogenetic analyses as a tool in virology and molecular epidemiology studies, presenting the most commonly used methodologies, describing the importance of the different techniques, their peculiar vocabulary and some examples of their use in virology.Review: This article starts presenting basic concepts of molecular epidemiology and molecular evolution, emphasizing their relevance in the context of viral infectious diseases. It presents a session on the vocabulary relevant to the subject, bringing readers to a minimum level of knowledge needed throughout this literature review. Within its main subject, the text explains what a molecular phylogenetic analysis is, starting from a multiple alignment of nucleotide or amino acid sequences. The different software used to perform multiple alignments may apply different algorithms. To build a phylogeny based on amino acid or nucleotide sequences it is necessary to produce a data matrix based on a model for nucleotide or amino acid replacement, also called evolutionary model. There are a number of evolutionary models available, varying in complexity according to the number of parameters (transition, transversion, GC content, nucleotide position in the codon, among others). Some papers presented herein provide techniques that can be used to choose evolutionary models. After the model is chosen, the next step is to opt for a phylogenetic reconstruction method that best fits the available data and the selected model. Here we present the most common reconstruction methods currently used, describing their principles, advantages and disadvantages. Distance methods, for example, are simpler and faster, however, they do not provide reliable estimations when the sequences are highly divergent. The accuracy of the analysis with probabilistic models (neighbour joining, maximum likelihood and bayesian inference) strongly depends on the adherence of the actual data to the chosen development model. Finally, we also explore topology confidence tests, especially the most used one, the bootstrap. To assist the reader, this review presents figures to explain specific situations discussed in the text and numerous examples of previously published scientific articles in virology that demonstrate the importance of the techniques discussed herein, as well as their judicious use.Conclusion: The DNA sequence is not only a record of phylogeny and divergence times, but also keeps signs of how the evolutionary process has shaped its history and also the elapsed time in the evolutionary process of the population. Analyses of genomic sequences by molecular phylogeny have demonstrated a broad spectrum of applications. It is important to note that for the different available data and different purposes of phylogenies, reconstruction methods and evolutionary models should be wisely chosen. This review provides theoretical basis for the choice of evolutionary models and phylogenetic reconstruction methods best suited to each situation. In addition, it presents examples of diverse applications of molecular phylogeny in virology.

Expression and assembly of the potato virus Y (PVY) coat protein (CP) in Escherichia coli cells

1993 ◽  
Vol 28 (1) ◽  
pp. 29-35 ◽  
Author(s):  
Yehuda Stram ◽  
Ilan Sela ◽  
Orit Edelbaum ◽  
Edna Tanne ◽  
Miri Karchi ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Coat Protein ◽  
Potato Virus ◽  
Potato Virus Y ◽  
Escherichia Coli Cells
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