Phylogenetic Analysis of PDV Movement Protein Compared to Bromoviridae Members as Justification of Possible Intercellular Movement

Abstract Prune dwarf virus (PDV) is a member of the Ilarvirus genus which is widely spread all over the world and causes considerable economic losses in nurseries and orchards. The virus is transmitted via seeds and pollen and through vegetative reproduction. However, the mechanisms of cell-to-cell and systemic transport of the virus are still not known. For the first time this study presents phylogenetic characterization of the movement protein (MP) of PDV isolates from the GenBank database in the context of geographic origin. The prepared analyses were based on a comparison of the whole amino acid sequence of the MP-PDV, the RNA-binding domain (RBD) in MP of PDV and MPs of four viruses from the Bromoviridae family with known transport mechanisms. Two different bioinformatic programs ClustalW and Jalview were used, and MP sequence variability up to 8% at the amino acid level among PDV isolates was confirmed. In the constructed phylogenetic trees the isolate sequences clustered in three conserved groups. Further analyses revealed similarity of the MP amino acid sequence of PDV and Alfalfa mosaic virus (AMV) of up to 34% and a 40% similarity of RBD between these viruses which suggested that the PDV transport mechanism may be on some level the same as that for AMV.

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First detection and characterisation of porcine hemagglutinating encephalomyelitis virus in the Czech Republic

Veterinární Medicína ◽

10.17221/95/2018-vetmed ◽

2019 ◽

Vol 64 (No. 02) ◽

pp. 60-66

Author(s):

R Moutelikova ◽

J Prodelalova

Keyword(s):

Czech Republic ◽

Amino Acid ◽

Amino Acid Sequence ◽

Phylogenetic Analyses ◽

Economic Losses ◽

The Czech Republic ◽

Nucleocapsid Gene ◽

Nasal Swabs ◽

Encephalomyelitis Virus ◽

Porcine Hemagglutinating Encephalomyelitis Virus

Porcine hemagglutinating encephalomyelitis virus (PHEV) is a highly neurovirulent coronavirus that invades the central nervous system in piglets. The incidence of PHEV among pigs in many countries is rising, and the economic losses to the pig industry may be significant. Serological studies suggest that PHEV is spread worldwide. However, no surveillance has been carried out in the Czech Republic. In this study, eight pig farms were screened for the presence of members of the Coronaviridae family with the use of reverse transcription PCR. A collection of 123 faecal samples and 151 nasal swabs from domestic pigs were analysed. In PHEV-positive samples, almost the complete coding sequence of the nucleocapsid gene was amplified and the acquired sequences were compared to those of geographically dispersed PHEV strains; phylogenetic analyses were also performed. PHEV was present in 7.9% of nasal swabs taken from different age categories of pigs. No other swine coronaviruses were detected. The amino acid sequence of the Czech PHEV strains showed 95.8–98.1% similarity to other PHEV reference strains in GenBank. PHEV strains collected from animals on the same farm were identical; however, strains from different farms have only exhibited only 96.7–98.7% amino acid sequence identity. Our study demonstrates the presence of PHEV in pigs in the Czech Republic. The Czech PHEV strains were evolutionarily closest to the Belgium strain VW572.

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Molecular Characterization of Genes Coding for Wild-Type and Sulfonylurea-Resistant Acetolactate Synthase in the Cyanobacterium Synechococcus PC C7942

Zeitschrift für Naturforschung C ◽

10.1515/znc-1990-0541 ◽

1990 ◽

Vol 45 (5) ◽

pp. 538-543 ◽

Cited By ~ 6

Author(s):

D. Friedberg ◽

J. Seijffers

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Amino Acid Sequence ◽

Molecular Characterization ◽

Amino Acid Level ◽

Acetolactate Synthase ◽

Mutant Gene ◽

Wild Type ◽

E Coli

We present here the isolation and molecular characterization of acetolactate synthase (ALS) genes from the cyanobacterium Synechococcus PCC7942 which specify a sulfonylurea-sensitive enzyme and from the sulfonylurea-resistant mutant SM3/20, which specify resistance to sulfonylurea herbicides. The ALS gene was cloned and mapped by complementation of an Escherichia coli ilv auxotroph that requires branched-chain amino acids for growth and lacks ALS activity. The cyanobacterial gene is efficiently expressed in this heterologous host. The ALS gene codes for 612 amino acids and shows high sequence homology (46%) at the amino acid level with ALS III of E. coli and with the tobacco ALS. The resistant phenotype is a consequence of proline to serine substitution in residue 115 of the deduced amino acid sequence. Functional expression of the mutant gene in wild-type Synechococcus and in E. coli confirmed that this amino-acid substitution is responsible for the resistance. Yet the deduced amino-acid sequence as compared with othjer ALS proteins supports the notion that the amino-acid context of the substitution is important for the resistance.

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Prediction of RNA binding sites in proteins from amino acid sequence

RNA ◽

10.1261/rna.2197306 ◽

2006 ◽

Vol 12 (8) ◽

pp. 1450-1462 ◽

Cited By ~ 119

Author(s):

M. Terribilini

Keyword(s):

Amino Acid ◽

Amino Acid Sequence ◽

Binding Sites ◽

Rna Binding ◽

Rna Binding Sites

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Evidence against use of bacterial amino acid sequence data for construction of all-inclusive phylogenetic trees.

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.83.2.217 ◽

1986 ◽

Vol 83 (2) ◽

pp. 217-220 ◽

Cited By ~ 60

Author(s):

T. E. Meyer ◽

M. A. Cusanovich ◽

M. D. Kamen

Keyword(s):

Amino Acid ◽

Amino Acid Sequence ◽

Phylogenetic Trees ◽

Sequence Data ◽

Amino Acid Sequence Data

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Population Genetics Based Phylogenetics Under Stabilizing Selection for an Optimal Amino Acid Sequence: A Nested Modeling Approach

10.1101/120238 ◽

2017 ◽

Author(s):

Jeremy M. Beaulieu ◽

Brian C. O’Meara ◽

Russell Zaretzki ◽

Cedric Landerer ◽

Juanjuan Chai ◽

...

Keyword(s):

Population Genetics ◽

Protein Synthesis ◽

Amino Acid ◽

Amino Acid Sequence ◽

Phylogenetic Trees ◽

Cost Benefit ◽

Specific Protein ◽

Substitution Matrix ◽

Stabilizing Selection ◽

Protein Coding

AbstractWe present a new phylogenetic approach SelAC (Selection on Amino acids and Codons), whose substitution rates are based on a nested model linking protein expression to population genetics. Unlike simpler codon models which assume a single substitution matrix for all sites, our model more realistically represents the evolution of protein coding DNA under the assumption of consistent, stabilizing selection using cost-benefit approach. This cost-benefit approach allows us generate a set of 20 optimal amino acid specific matrix families using just a handful of parameters and naturally links the strength of stabilizing selection to protein synthesis levels, which we can estimate. Using a yeast dataset of 100 orthologs for 6 taxa, we find SelAC fits the data much better than popular models by 104–105 AICc units. Our results indicate there is great potential for more accurate inference of phylogenetic trees and branch lengths from already existing data through the use of nested, mechanistic models. Additional parameters estimated by SelAC indicate that a large amount of non-phylogenetic, but biologically meaningful, information can be inferred from exisiting data. For example, SelAC prediction of gene specific protein synthesis rates correlates well with both empirical (r=0.33−0.48) and other theoretical predictions (r=0.45−0.64) for multiple yeast species. SelAC also provides estimates of the optimal amino acid at each site. Finally, because SelAC is a nested approach based on clearly stated biological assumptions, future modifications, such as including shifts in the optimal amino acid sequence within or across lineages, are possible.

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Tobamovirus Replicase Coding Region Is Involved in Cell-to-Cell Movement

Journal of Virology ◽

10.1128/jvi.75.18.8831-8836.2001 ◽

2001 ◽

Vol 75 (18) ◽

pp. 8831-8836 ◽

Cited By ~ 72

Author(s):

Kyotaro Hirashima ◽

Yuichiro Watanabe

Keyword(s):

Amino Acid ◽

Amino Acid Sequence ◽

Tobacco Mosaic Virus ◽

Host Range ◽

Mosaic Virus ◽

Movement Protein ◽

Cell Movement ◽

Coding Region ◽

Replicase Proteins ◽

Viral Movement

ABSTRACT Tobacco mosaic virus (TMV) encodes a 30-kDa movement protein (MP) which enables viral movement from cell to cell. It is, however, unclear whether the 126- and 183-kDa replicase proteins are involved in the cell-to-cell movement of TMV. In the course of our studies into TMV-R, a strain with a host range different from that of TMV-U1, we have obtained an interesting chimeric virus, UR-hel. The amino acid sequence differences between UR-hel and TMV-U1 are located only in the helicase-like domain of the replicase. Interestingly, UR-hel has a defect in its cell-to-cell movement. The replication of UR-hel showed a level of replication of the genome, synthesis, and accumulation of MP similar to that observed in TMV-U1-inoculated protoplasts. Such observations support the hypothesis that the replicase coding region may in some fashion be involved in cell-to-cell movement of TMV.

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Molecular characterisation and hormone-dependent expression of the porcine whey acidic protein gene

Journal of Molecular Endocrinology ◽

10.1677/jme.0.0200027 ◽

1998 ◽

Vol 20 (1) ◽

pp. 27-35 ◽

Cited By ~ 46

Author(s):

KJ Simpson ◽

P Bird ◽

D Shaw ◽

K Nicholas

Keyword(s):

Gene Expression ◽

Mammary Gland ◽

Amino Acid ◽

Amino Acid Sequence ◽

Amino Acid Level ◽

Whey Acidic Protein ◽

Acidic Protein ◽

Northern Analysis ◽

Major Protein ◽

Sds Page

A 17.5 kDa protein was isolated from porcine whey by reverse phase HPLC and identified as a putative whey acidic protein (WAP) homologue by sequencing 35 and 40 amino acid residues of the amino- and carboxy-terminus respectively. Degenerate oligonucleotides to both of these amino acid sequences were designed and used in reverse transcriptase PCR with RNA from lactating porcine mammary gland as a template. A 162 bp PCR fragment was detected and sequenced. Compilation of the deduced and determined amino acid sequence revealed a protein of 111 amino acids, which had approximately 75, 50, 40 and 35% similarity at amino acid level to camel, rabbit, rat and mouse WAP respectively. It also included the four-disulphide core characteristic of all WAP proteins and most Kunitz-type protease inhibitors. This provides the first unequivocal evidence for WAP secretion in the pig. SDS PAGE analysis of the whey fraction showed that WAP is secreted as a major protein in sow's milk from farrowing to weaning. The molecular mass of WAP in SDS PAGE was significantly greater than the 11.7 kDa determined from amino acid sequence, indicating that porcine WAP is possibly glycosylated. Northern analysis detected a single mRNA transcript of approximately 600 bp in porcine RNA from the mammary gland of lactating sows. To examine the hormone-regulated expression of the WAP gene the mammary glands of sows at day 90 of pregnancy were biopsied and explants cultured for 3 days in the presence of various combinations of porcine insulin (I), cortisol (F) and porcine prolactin (P). Northern analysis of RNA extracted from the tissue indicated that WAP gene expression was barely detectable in the mammary gland prior to culture and there was no increment in explants cultured in the presence of I and F. However, a significant increase in the accumulation of WAP mRNA was observed in explants cultured in I, F and P. A similar result was observed for beta-casein and alpha-lactalbumin gene expression.

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Species Specificity of Macaque Rhadinovirus Glycoprotein B Sequences

Journal of Virology ◽

10.1128/jvi.74.1.584-590.2000 ◽

2000 ◽

Vol 74 (1) ◽

pp. 584-590 ◽

Cited By ~ 17

Author(s):

Marcy R. Auerbach ◽

Susan C. Czajak ◽

Welkin E. Johnson ◽

Ronald C. Desrosiers ◽

Louis Alexander

Keyword(s):

Amino Acid ◽

Phylogenetic Trees ◽

New World ◽

Amino Acid Level ◽

Kaposi Sarcoma ◽

Macaca Nemestrina ◽

Herpesvirus Saimiri ◽

Glycoprotein B ◽

Close Relatedness ◽

Distinct Branch

ABSTRACT All members of the Herpesviridae family contain sequences for a highly conserved glycoprotein B (gB) gene. We investigated the phylogenetic relationships of gB sequences from eight independent rhadinovirus isolates obtained from three species: rhesus (Macaca mulatta), cynomologus (Macaca fasicularis), and pig-tailed (Macaca nemestrina) macaques. Samples were derived from monkeys housed at four separate facilities. Analysis of these eight independent gB sequences revealed five regions of heterogeneity within the 823- to 829-amino-acid polypeptides: residues 1 to 65, 120 to 185, 255 to 300, 352 to 393, and 412 to 457. The remaining regions of gB were highly conserved among the different macaque isolates. Overall divergence among these gene sequences ranged from 0.1 to 7.2% at the amino acid level. Phylogenetic trees constructed with our macaque rhadinovirus gB sequences and those derived from additional subfamilies or genera (alpha, beta, gamma-1, and gamma-2) revealed that the macaque gB sequences branched with other gamma-2 herpesvirus gB sequences and that within the gamma-2 genera, the macaque gB sequences clustered as a distinct branch. The eight macaque rhadinovirus gB sequences were all approximately equidistant from Kaposi sarcoma-associated herpesvirus (KSHV) gB sequences and had a shorter evolutionary distance to KSHV gB sequences than to any other herpesvirus, including the gamma-2 herpesvirus saimiri (HVS) of New World squirrel monkeys. The macaque gB sequences did not cluster according to the facility of origin, but did cluster according to the species of origin, displaying less intraspecies divergence (0.1 to 2.9%) than interspecies divergence (3.3 to 7.2%). These results demonstrate a close relatedness of rhadinovirus isolates from different macaque species.

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COMPARISON OF FOUR MOLECULAR TYPING METHODS FOR RIEMERELLA ANATIPESTIFER

Taiwan Veterinary Journal ◽

10.1142/s1682648515500080 ◽

2015 ◽

Vol 41 (03) ◽

pp. 177-185 ◽

Cited By ~ 3

Author(s):

Chiou-Lin Chen ◽

Sin-Tian Wang ◽

Chishih Chu ◽

Shao-Hung Wang

Keyword(s):

Amino Acid ◽

Amino Acid Sequence ◽

Molecular Typing ◽

Biofilm Formation ◽

Phylogenetic Trees ◽

Its Region ◽

Genetic Variations ◽

Typing Method ◽

Riemerella Anatipestifer ◽

16S Rdna Sequence Analysis

The pathogen causing septicaemiae and infectious serositis in waterfowl, Riemerella anatipestifer has been categorized as a member of Flavobacteriaceae by 16S rDNA sequence analysis and at least 21 serotypes have been characterized through serum agglutination test. So far, the molecular determinants for R. anatipestifer serotyping are not clear; moreover, serotype analysis is time-consuming and labor-intensive. To find a better molecular typing method for R. anatipestifer, 58 field isolates collected from sick birds in central Taiwan from 2006 to 2008 were investigated by molecular methods to determine serotype-associated genetic variations. Genetic variations were determined by the methods of ITS nucleotide sequence, OmpA amino acid sequence, pulsed-field gel electrophoresis (PFGE), and repetitive-sequence PCR (Rep-PCR). The phylogenetic trees constructed by the ITS region showed nine clusters, while the amino acid sequence of OmpA clustered into seven clusters. OmpA sequence correlated much better with serotyping than ITS, PFGE, and Rep-PCR. Meanwhile, the biofilm formation activity was also tested for serotypes 2 and 8, which were the two largest groups in the study. Serotype 2 isolates showed a higher degree of biofilm formation than serotype 8 isolates. In conclusion, we demonstrated that phylogenetic analysis with OmpA amino acid sequence is an effective tool in epidemiology and may be a candidate method substituting serotyping for R. anatipestifer. Moreover, the biofilm forming activity may play an important role in field transmission of R. anatipestifer.

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