scholarly journals Sequence Characterization of matrix protein (M1) in influenza A viruses (H1, H3 and H5)

2011 ◽  
Vol 2 (1) ◽  
pp. 16
Author(s):  
Jun Zhang ◽  
Xiao Ling Yu ◽  
Lei Xu ◽  
Fang Zhi Li ◽  
Yong Gang Li
Keyword(s):  
Amino Acid ◽  
Nuclear Localization Signal ◽  
Influenza A ◽  
Matrix Protein ◽  
Amino Acid Sequences ◽  
Influenza A Viruses ◽  
Sequence Characterization ◽  
Matrix Protein M1 ◽  
Localization Signal

<p><strong> </strong>This study brings the analysis of amino acid sequences of matrix protein (M1) from the influenza virus A (H1N1, H3N2 and H5N1) during 2007-2208. 741 sequences of M1 were compared, of them, H1N1 388; H3N2 251 and H5N1 102. Even though, the M1 is relatively conserved among the influenza A viruses, we found some variations in the M1 among the viruses, H1N1, H3N2 and H5N1. The nuclear localization signal at amino acid 101 to 105 is RKLKR for H1N1 and H3N2, but for H5N1 is KKLKR. All differences of amino acid in M1 of H1, H3 and H5 were listed. 80 sequences of M1 of H1N1 H3N2 and H5N1 were used for phylogenetic analysis. There is no reasontantment found in the M1 among these subtypes. Further study is needed to study the differences of the function of M1 among H1N1, H3N2 and H5N1. The M1 of H5N1 may contribute to the high pathogenesis to this virus.</p>

Co-evolution analysis to predict protein–protein interactions within influenza virus envelope

2014 ◽  
Vol 12 (02) ◽  
pp. 1441008 ◽  
Author(s):  
Ramil R. Mintaev ◽  
Andrei V. Alexeevski ◽  
Larisa V. Kordyukova
Keyword(s):  
Amino Acid ◽  
Protein Interactions ◽  
Influenza A ◽  
Matrix Protein ◽  
Amino Acid Sequences ◽  
Viral Envelope ◽  
Research Database ◽  
Virus Envelope ◽  
Physical Constraints ◽  
Matrix Protein M1

Interactions between integral membrane proteins hemagglutinin (HA), neuraminidase (NA), M2 and membrane-associated matrix protein M1 of influenza A virus are thought to be crucial for assembly of functionally competent virions. We hypothesized that the amino acid residues located at the interface of two different proteins are under physical constraints and thus probably co-evolve. To predict co-evolving residue pairs, the EvFold ( http://evfold.org ) program searching the (nontransitive) Direct Information scores was applied for large samplings of amino acid sequences from Influenza Research Database ( http://www.fludb.org/ ). Having focused on the HA, NA, and M2 cytoplasmic tails as well as C-terminal domain of M1 (being the less conserved among the protein domains) we captured six pairs of correlated positions. Among them, there were one, two, and three position pairs for HA–M2, HA–M1, and M2–M1 protein pairs, respectively. As expected, no co-varying positions were found for NA–HA, NA–M1, and NA–M2 pairs obviously due to high conservation of the NA cytoplasmic tail. The sum of frequencies calculated for two major amino acid patterns observed in pairs of correlated positions was up to 0.99 meaning their high to extreme evolutionary sustainability. Based on the predictions a hypothetical model of pair-wise protein interactions within the viral envelope was proposed.

scholarly journals Characterization of H9N2 influenza A viruses isolated from chicken products imported into Japan from China

2006 ◽  
Vol 135 (3) ◽  
pp. 386-391 ◽  
Author(s):  
M. MASE ◽  
M. ETO ◽  
K. IMAI ◽  
K. TSUKAMOTO ◽  
S. YAMAGUCHI
Keyword(s):  
Influenza Virus ◽  
Amino Acid ◽  
Avian Influenza ◽  
Avian Influenza Virus ◽  
Influenza A ◽  
H9n2 Virus ◽  
Amino Acid Substitutions ◽  
Influenza A Viruses ◽  
Potential Sources

We characterized eleven H9N2 influenza A viruses isolated from chicken products imported from China. Genetically they were classified into six distinct genotypes, including five already known genotypes and one novel genotype. This suggested that such multiple genotypes of the H9N2 virus have possibly already become widespread and endemic in China. Two isolates have amino-acid substitutions that confer resistance to amantadine in the M2 region, and this supported the evidence that this mutation might be a result of the wide application of amantadine for avian influenza treatment in China. These findings emphasize the importance of surveillance for avian influenza virus in this region, and of quarantining imported chicken products as potential sources for the introduction of influenza virus.

scholarly journals Genetic and Antigenic Evolution of European Swine Influenza A Viruses of HA-1C (Avian-Like) and HA-1B (Human-Like) Lineages in France from 2000 to 2018

Viruses ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 1304
Author(s):  
Amélie Chastagner ◽  
Séverine Hervé ◽  
Stéphane Quéguiner ◽  
Edouard Hirchaud ◽  
Pierrick Lucas ◽  
...  
Keyword(s):  
Amino Acid ◽  
Influenza A ◽  
Phylogenetic Analyses ◽  
Swine Influenza ◽  
Amino Acid Sequences ◽  
Antigenic Drift ◽  
Influenza A Viruses ◽  
Double Deletion ◽  
Antigenic Evolution ◽  
Amino Acid Mutations

This study evaluated the genetic and antigenic evolution of swine influenza A viruses (swIAV) of the two main enzootic H1 lineages, i.e., HA-1C (H1av) and -1B (H1hu), circulating in France between 2000 and 2018. SwIAV RNAs extracted from 1220 swine nasal swabs were hemagglutinin/neuraminidase (HA/NA) subtyped by RT-qPCRs, and 293 virus isolates were sequenced. In addition, 146 H1avNy and 105 H1huNy strains were submitted to hemagglutination inhibition tests. H1avN1 (66.5%) and H1huN2 (25.4%) subtypes were predominant. Most H1 strains belonged to HA-1C.2.1 or -1B.1.2.3 clades, but HA-1C.2, -1C.2.2, -1C.2.3, -1B.1.1, and -1B.1.2.1 clades were also detected sporadically. Within HA-1B.1.2.3 clade, a group of strains named “Δ146-147” harbored several amino acid mutations and a double deletion in HA, that led to a marked antigenic drift. Phylogenetic analyses revealed that internal segments belonged mainly to the “Eurasian avian-like lineage”, with two distinct genogroups for the M segment. In total, 17 distinct genotypes were identified within the study period. Reassortments of H1av/H1hu strains with H1N1pdm virus were rarely evidenced until 2018. Analysis of amino acid sequences predicted a variability in length of PB1-F2 and PA-X proteins and identified the appearance of several mutations in PB1, PB1-F2, PA, NP and NS1 proteins that could be linked to virulence, while markers for antiviral resistance were identified in N1 and N2. Altogether, diversity and evolution of swIAV recall the importance of disrupting the spreading of swIAV within and between pig herds, as well as IAV inter-species transmissions.

Comparison of complete amino acid sequences and receptor-binding properties among 13 serotypes of hemagglutinins of influenza A viruses

Virology ◽  
1991 ◽  
Vol 182 (2) ◽  
pp. 475-485 ◽  
Author(s):  
E. Nobusawa ◽  
T. Aoyama ◽  
H. Kato ◽  
Y. Suzuki ◽  
Y. Tateno ◽  
...  
Keyword(s):  
Amino Acid ◽  
Receptor Binding ◽  
Influenza A ◽  
Amino Acid Sequences ◽  
Influenza A Viruses ◽  
Binding Properties

Evolutionary characterization of the six internal genes of H5N1 human influenza A virus

Microbiology ◽  
2000 ◽  
Vol 81 (5) ◽  
pp. 1293-1303 ◽  
Author(s):  
Yasuaki Hiromoto ◽  
Yoshinao Yamazaki ◽  
Tatsunobu Fukushima ◽  
Takehiko Saito ◽  
Stephen E. Lindstrom ◽  
...  
Keyword(s):  
Amino Acid ◽  
Influenza A ◽  
Phylogenetic Trees ◽  
Geographical Location ◽  
Amino Acid Sequences ◽  
Point Of View ◽  
Influenza A Viruses ◽  
Evolutionary Patterns ◽  
H5n1 Influenza ◽  
Human H5n1

The entire nucleotide sequences of all six internal genes of six human H5N1 influenza A viruses isolated in Hong Kong in 1997 were analysed in detail from a phylogenetic point of view and compared with the evolutionary patterns of the haemagglutinin and neuraminidase genes. Despite being isolated within a single year in the same geographical location, human H5N1 viruses were characterized by a variety of amino acid substitutions in the ribonucleoprotein complex [PB2, PB1, PA and nucleoprotein (NP)] as well as the matrix (M) proteins 1 and 2 and nonstructural (NS) proteins 1 and 2. The presence of previously reported amino acid sequences specific for human strains was confirmed in the PB2, PA, NP and M2 proteins. Nucleotide and amino acid sequence identities of the six internal genes of H5N1 viruses examined here were separated into at least two variant groups. In agreement with the above result, phylogenetic trees of the six internal genes of human H5N1 viruses were generally composed of two minor clades. Additionally, variable dendrogram topologies suggested that reassortment among viruses contributed further to the genetic variability of these viruses. As a result, it became clear that human H5N1 viruses are characterized by divergent gene constellations, suggesting the possible occurrence of genetic reassortment between viruses of the two evolutionary lineages.

Deduced amino acid sequences at the haemagglutinin cleavage site of avian influenza A viruses of H 5 and H 7 subtypes

1993 ◽  
Vol 130 (1-2) ◽  
pp. 209-217 ◽  
Author(s):  
G. W. Wood ◽  
J. W. McCauley ◽  
J. B. Bashiruddin ◽  
D. J. Alexander
Keyword(s):  
Amino Acid ◽  
Avian Influenza ◽  
Cleavage Site ◽  
Influenza A ◽  
Amino Acid Sequences ◽  
Influenza A Viruses

scholarly journals Isolation and characterization of a c-repeat binding factor gene from Tevang-1 maize cultivar

2019 ◽  
Vol 41 (3) ◽  
Author(s):  
Nguyen Thuy Linh ◽  
Luu Han Ly ◽  
Nguyen Thuy Duong ◽  
Huynh Thi Thu Hue
Keyword(s):  
Transcription Factor ◽  
Amino Acid ◽  
Amino Acid Sequences ◽  
Bioinformatic Tools ◽  
Functional Regions ◽  
Isolation And Characterization ◽  
Binding Factor ◽  
Localization Signal ◽  
Ap2 Domain

C-repeat binding factor (CBF) proteins are transcription factors involved in plant response to abiotic stresses, especially low-temperature condition. In this research, a CBF3-coding gene was isolated from a cold-acclimation maize variety, Zea mays var. Tevang-1 and denoted as ZmCBF3tv. The isolated gene shared 96.49% homology with the B73-reference gene and had no intron in the coding sequence. By using bioinformatic tools, a number of variations in the nucleotide and amino acid sequences were identified. An alignment between ZmCBF3tv and other CBF/DREB1 proteins from various species revealed functional regions and typical features, such as nuclear localization signal (NLS), the AP2 DNA-binding domain, and acidic-amino-acid-rich segments. Additionally, a phylogenetic analysis based on the AP2 domain showed that the maize CBF3 transcription factor had the highest similarity with that from rice and closely related to other DREB1/CBF protein of monocots. The function of the ZmCBF3tv product is suggested to be a CBF/DREB1 transcription factor.     

The influenza A virus matrix protein as a marker to monitor initial virus internalisation

2009 ◽  
Vol 390 (5/6) ◽  
Author(s):  
Thorsten Eierhoff ◽  
Stephan Ludwig ◽  
Christina Ehrhardt
Keyword(s):  
Viral Entry ◽  
Influenza A ◽  
Matrix Protein ◽  
Screening Method ◽  
Antiviral Drug ◽  
Influenza A Viruses ◽  
Entry Inhibitors ◽  
Endosomal Acidification ◽  
Matrix Protein M1 ◽  
Virus Strains

AbstractThe uptake of influenza A viruses (IAV) into cells represents an attractive antiviral drug target, e.g., by interfering with essential cellular or viral entry factors. So far, this process could only be studied by time-consuming microscopical methods. Thus, there is a lack of rapid and easy assay systems to monitor viral entry. Here, we describe a rapid procedure to analyse internalisation of IAV via Western blot detection of virion-associated matrix protein (M1), the most abundant protein within the viral particle. The assay is broadly applicable and detects different virus strains of various subtypes. As a proof of principle, treatment of cells with various known or presumed entry inhibitors resulted in reduced M1 levels. Removal of sialic acids, the receptors for IAV, led to a complete loss of the M1 signal, indicating that virus internalisation can be monitored already at the stage of attachment. Prevention of endosomal acidification resulted in a delayed degradation of M1 indicative of IAV particles trapped in endosomes. Thus, early detection of the virus-associated M1 protein is a rapid method to monitor different steps of influenza virus internalisation and has potential for application as a screening method for drugs that interfere with the uptake of IAV.

scholarly journals Isolation and characterization of a c-repeat binding factor gene from Tevang-1 maize cultivar

2019 ◽  
Vol 41 (3) ◽  
Author(s):  
Nguyen Thuy Linh ◽  
Luu Han Ly ◽  
Nguyen Thuy Duong ◽  
Huynh Thi Thu Hue
Keyword(s):  
Transcription Factor ◽  
Amino Acid ◽  
Amino Acid Sequences ◽  
Bioinformatic Tools ◽  
Functional Regions ◽  
Isolation And Characterization ◽  
Binding Factor ◽  
Localization Signal ◽  
Ap2 Domain

C-repeat binding factor (CBF) proteins are transcription factors involved in plant response to abiotic stresses, especially low-temperature condition. In this research, a CBF3-coding gene was isolated from a cold-acclimation maize variety, Zea mays var. Tevang-1 and denoted as ZmCBF3tv. The isolated gene shared 96.49% homology with the B73-reference gene and had no intron in the coding sequence. By using bioinformatic tools, a number of variations in the nucleotide and amino acid sequences were identified. An alignment between ZmCBF3tv and other CBF/DREB1 proteins from various species revealed functional regions and typical features, such as nuclear localization signal (NLS), the AP2 DNA-binding domain, and acidic-amino-acid-rich segments. Additionally, a phylogenetic analysis based on the AP2 domain showed that the maize CBF3 transcription factor had the highest similarity with that from rice and closely related to other DREB1/CBF protein of monocots. The function of the ZmCBF3tv product is suggested to be a CBF/DREB1 transcription factor.     

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