scholarly journals Sequence of the 3′-terminal end (8·1 kb) of the genome of porcine haemagglutinating encephalomyelitis virus: comparison with other haemagglutinating coronaviruses

2002 ◽  
Vol 83 (10) ◽  
pp. 2411-2416 ◽  
Author(s):  
A. Marie-Josée Sasseville ◽  
Martine Boutin ◽  
Anne-Marie Gélinas ◽  
Serge Dea
Keyword(s):  
Amino Acid ◽  
Field Isolate ◽  
Prototype Strain ◽  
Amino Acid Sequences ◽  
Structural Proteins ◽  
Sequencing Data ◽  
Pig Farms ◽  
Encephalomyelitis Virus ◽  
Respiratory Coronavirus ◽  
Orf4 Gene

A cytopathogenic coronavirus, serologically identified as porcine haemagglutinating encephalomyelitis virus (HEV), has recently been associated with acute outbreaks of wasting and encephalitis in nursing piglets from pig farms in southern Québec and Ontario, Canada. The 3′-terminal end of the genome of the prototype HEV-67N strain and that of the recent Québec IAF-404 field isolate, both propagated in HRT-18 cells, were sequenced. Overall, sequencing data indicated that HEV has remained antigenically and genetically stable since its first isolation in North America in 1962. Compared with the prototype strain of bovine enteropathogenic coronavirus (BCoV), HEV, as well as the human respiratory coronavirus (HCoV-OC43) showed a major deletion in their ORF4 gene. Deduced amino acid sequences for both HEV strains revealed 89/88, 80, 93/92 and 95/94% identities with the structural proteins HE, S, M and N of BCoV and HCoV-OC43, respectively. Major variations were observed in the S1 portion of the S gene of both HEV strains, with only 73/71% amino acid identities compared with those of the two other haemagglutinating coronaviruses.

scholarly journals Amino acid sequences of α-helical segments from S-carbosymethylkerateine-A. Complete sequence of a type-I segment

1978 ◽  
Vol 173 (2) ◽  
pp. 373-385 ◽  
Author(s):  
K H Gough ◽  
A S Inglis ◽  
W G Crewther
Keyword(s):  
Amino Acid ◽  
Sequence Data ◽  
Coiled Coil ◽  
Alpha Helix ◽  
Protein S ◽  
Amino Acid Sequences ◽  
Type I ◽  
Type Ii ◽  
Sequencing Data ◽  
Helical Segment

The amino acid sequence of a type-I helical segment from the low-sulphur protein (S-carboxymethylkerateine-A) of wool was determined by combining automatic and manual-sequencing data. Whereas in the type-II helical segment most of the cationic groups occur in pairs, 11 of the 22 anionic residues in the sequence of the type-I segment were situated next to a second anionic residue. This suggests possible interactions between type-I and type-II helical segments in alpha-keratin. As observed with the sequence of a type-II helical segment a model constructed on 3.6 residues per turn of helix shows a line of hydrophobic residues along the helix, thereby supporting the physicochemical evidence that the molecule is predominantly helical and forms part of a coiled-coil structure. Examination of the sequence data by predictive methods indicates the possibilty of extensive sections of alpha-helix interspersed with discontinuities. The molecule contains a number of regions with peptide sequences identical with those found by other workers after enzymic digestion of fractions from oxidized wool.

scholarly journals Genome-Wide Identification and Characterization of bZIP Transcription Factors inBrassica oleraceaunder Cold Stress

2016 ◽  
Vol 2016 ◽  
pp. 1-18 ◽  
Author(s):  
Indeok Hwang ◽  
Ranjith Kumar Manoharan ◽  
Jong-Goo Kang ◽  
Mi-Young Chung ◽  
Young-Wook Kim ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Amino Acid ◽  
Cold Stress ◽  
Stress Responses ◽  
Sequence Similarity ◽  
Amino Acid Sequences ◽  
Amino Acid Sequence Similarity ◽  
Sequencing Data ◽  
Cold Response ◽  
Bzip Transcription Factors

Cabbages (Brassica oleraceaL.) are an important vegetable crop around world, and cold temperature is among the most significant abiotic stresses causing agricultural losses, especially in cabbage crops. Plant bZIP transcription factors play diverse roles in biotic/abiotic stress responses. In this study, 119 putative BolbZIP transcription factors were identified using amino acid sequences from several bZIP domain consensus sequences. The BolbZIP members were classified into 63 categories based on amino acid sequence similarity and were also compared with BrbZIP and AtbZIP transcription factors. Based on this BolbZIP identification and classification, cold stress-responsiveBolbZIPgenes were screened in inbred lines,BN106andBN107, using RNA sequencing data and qRT-PCR. The expression level of the 3 genes,Bol008071,Bol033132, andBol042729, was significantly increased inBN107under cold conditions and was unchanged inBN106. The upregulation of these genes inBN107, a cold-susceptible inbred line, suggests that they might be significant components in the cold response. Among three identified genes,Bol033132has 97% sequence similarity toBra020735, which was identified in a screen for cold-related genes inB. rapaand a protein containing N-rich regions in LCRs. The results obtained in this study provide valuable information for understanding the potential function of BolbZIP transcription factors in cold stress responses.

scholarly journals Sequence Conservation and Antigenic Variation of the Structural Proteins of Equine Rhinitis A Virus

2001 ◽  
Vol 75 (21) ◽  
pp. 10550-10556 ◽  
Author(s):  
Annalisa Varrasso ◽  
Heidi E. Drummer ◽  
Jin-an Huang ◽  
Rachel A. Stevenson ◽  
Nino Ficorilli ◽  
...  
Keyword(s):  
Monoclonal Antibodies ◽  
Amino Acid ◽  
Antigenic Variation ◽  
Amino Acid Sequences ◽  
Sequence Conservation ◽  
Structural Proteins ◽  
Serum Neutralization ◽  
Prototype Virus

ABSTRACT The nucleotide and deduced amino acid sequences of the P1 region of the genomes of 10 independent equine rhinitis A virus (ERAV) isolates were determined and found to be very closely related. A panel of seven monoclonal antibodies to the prototype virus ERAV.393/76 that bound to nonneutralization epitopes conserved among all 10 isolates was raised. In serum neutralization assays, rabbit polyclonal sera and sera from naturally and experimentally infected horses reacted in a consistent and discriminating manner with the 10 isolates, which indicated the existence of variation in the neutralization epitopes of these viruses.

scholarly journals Expression and characterisation of the ryegrass mottle virus non-structural proteins

2010 ◽  
Vol 64 (5-6) ◽  
pp. 215-222
Author(s):  
Ina Baļķe ◽  
Gunta Resēviča ◽  
Dace Skrastiņa ◽  
Andris Zeltiņš
Keyword(s):  
Amino Acid ◽  
Expression System ◽  
Protein Structures ◽  
Amino Acid Sequences ◽  
Host Cells ◽  
Structural Proteins ◽  
Mottle Virus ◽  
Expression Vectors ◽  
Structural Protein ◽  
E Coli

Expression and characterisation of the ryegrass mottle virus non-structural proteins The Ryegrass mottle virus (RGMoV) single-stranded RNA genome is organised into four open reading frames (ORF) which encode several proteins: ORF1 encodes protein P1, ORF2a contains the membrane-associated 3C-like serine protease, genome-linked protein VPg and a P16 protein gene. ORF2b encodes replicase RdRP and the only structural protein, coat protein, is synthesised from ORF3. To obtain the non-structural proteins in preparative quantities and to characterise them, the corresponding RGMoV gene cDNAs were cloned in pET- and pColdI-derived expression vectors and overexpressed in several E. coli host cells. For protease and RdRP, the best expression system containing pColdI vector and E. coli WK6 strain was determined. VPg and P16 proteins were obtained from the pET- or pACYC- vectors and E. coli BL21 (DE3) host cells and purified using Ni-Sepharose affinity chromatography. Attempts to crystallize VPg and P16 were unsuccessful, possibly due to non-structured amino acid sequences in both protein structures. Methods based on bioinformatic analysis indicated that the entire VPg domain and the C-terminal part of the P16 contain unstructured amino acid stretches, which possibly prevented the formation of crystals.

scholarly journals Complete nucleotide sequence of chikungunya virus and evidence for an internal polyadenylation site

2002 ◽  
Vol 83 (12) ◽  
pp. 3075-3084 ◽  
Author(s):  
Afjal Hossain Khan ◽  
Kouichi Morita ◽  
Maria del Carmen Parquet ◽  
Futoshi Hasebe ◽  
Edward G. M. Mathenge ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Chikungunya Virus ◽  
Genomic Sequence ◽  
Adenine Nucleotides ◽  
Repeated Sequence ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Structural Proteins ◽  
Sequence Elements

In this study, the complete genomic sequence of chikungunya virus (CHIK; S27 African prototype) was determined and the presence of an internal polyadenylation [I-poly(A)] site was confirmed within the 3′ non-translated region (NTR) of this strain. The complete genome was 11805 nucleotides in length, excluding the 5′ cap nucleotide, an I-poly(A) tract and the 3′ poly(A) tail. It comprised two long open reading frames that encoded the non-structural (2474 amino acids) and structural polyproteins (1244 amino acids). The genetic location of the non-structural and structural proteins was predicted by comparing the deduced amino acid sequences with the known cleavage sites of other alphaviruses, located at the C-terminal region of their virus-encoded proteins. In addition, predicted secondary structures were identified within the 5′ NTR and repeated sequence elements (RSEs) within the 3′ NTR. Amino acid sequence homologies, phylogenetic analysis of non-structural and structural proteins and characteristic RSEs revealed that although CHIK is closely related to o’nyong-nyong virus, it is in fact a distinct virus. The existence of I-poly(A) fragments with different lengths (e.g. 19, 36, 43, 91, 94 and 106 adenine nucleotides) at identical initiation positions for each clone strongly suggests that the polymerase of the alphaviruses has a capacity to create poly(A) by a template-dependant mechanism such as ‘polymerase slippage’, as has been reported for vesicular stomatitis virus.

scholarly journals The Coronavirus SARS-Cov-2: the Characteristics of Structural Proteins, Contagiousness, and Possible Immune Collisions

2020 ◽  
Vol 19 (2) ◽  
pp. 13-30
Author(s):  
E. Р. Kharchenko
Keyword(s):  
Amino Acid ◽  
Close Contact ◽  
Amino Acid Content ◽  
Infection Process ◽  
Amino Acid Sequences ◽  
Surface Proteins ◽  
Structural Proteins ◽  
Subunit Structure ◽  
S Protein ◽  
Immune Epitope

Relevance. Coronavirus SARS-Cov-2 is a novel virus demonstrating the ability to be trans¬mitted from human-to-human, via respiratory droplets or close contact, and cause the severe acute respiratory syndrome (SARS). The role of its structural proteins in the SARS pathogenesis is unknown.Aim is to characterize the features of the SARS-Cov-2 structural proteins and their changes associated with acquiring other way of transmission and analyze the possibility of heterologous immunity emergence in its infection. Materials and method. For the computer analysis and alignment, the gene sequences of SARS-Cov-2 , SARS-CoV , MERS-CoV и bat CoV HKU3 reference strains were used from the Internet. From the primary structure of their genes it were translated their structural proteins: spike (S), envelope (E),membrane (M), and nucleocapsid (N). The genetic code of structural proteins was also defined. The search of homologous sequences in the SARS-Cov-2 S-protein, surface proteins of other viruses, and human proteins was made to find immune epitope continuum of protein relationships.Results. In the SARS-Cov-2 structural proteins amino acid sequences of M, E, and N-proteins are conservative. The S1 subunit of the S-protein contains some large insertions, significant changes of the amino acid content with the predominance of arginine and lysine which is typical for the surface glycoproteins in the viruses possessing high contagiousness. The S2 subunit is rather conservative and retain negative polarity. The S-protein exhibits the immune epitope relationships with many proteins of viruses and human which may be associated with immune collisions.Conclusion: The SARSCov-2 features are determined by marked changes of the S1 subunit structure in the S-protein which may be responsible for its contagiousness and many immune collisions aggravating infection process.

N-Terminal Amino Acid Sequences of Vaccinia Virus Structural Proteins

Virology ◽  
1994 ◽  
Vol 202 (2) ◽  
pp. 844-852 ◽  
Author(s):  
Tetsuya Takahashi ◽  
Masayasu Oie ◽  
Yasuo Ichihashi
Keyword(s):  
Amino Acid ◽  
Vaccinia Virus ◽  
Amino Acid Sequences ◽  
Structural Proteins ◽  
Terminal Amino Acid ◽  
Terminal Amino

Genomic and phylogenetic analysis of a single-stranded RNA virus infecting Rhizosolenia setigera (Stramenopiles: Bacillariophyceae)

2006 ◽  
Vol 86 (3) ◽  
pp. 475-483 ◽  
Author(s):  
Y. Shirai ◽  
Y. Takao ◽  
H. Mizumoto ◽  
Y. Tomaru ◽  
D. Honda ◽  
...  
Keyword(s):  
Amino Acid ◽  
Rna Virus ◽  
Rna Helicase ◽  
Amino Acid Sequences ◽  
Marine Diatom ◽  
Structural Proteins ◽  
Ssrna Virus ◽  
Gene Coding ◽  
Positive Sense ◽  
Rhizosolenia Setigera

We report the first complete genome sequence of the marine diatom-infecting, positive-sense single-stranded RNA (ssRNA) virus, Rhizosolenia setigera RNA virus (RsRNAV). The genome is 8877 nucleotides (nt), polyadenylated, lacking a cap structure, and has two large open reading frames (ORFs): ORF-1 (4818 nt), a polyprotein gene coding for replicases, e.g. RNA helicase, RNA-dependent RNA polymerase (RdRp); and ORF-2 (2883 nt), a polyprotein gene coding for structural proteins. The ORFs are separated by a 323 nt intergenic region (IGR), flanked by a 624 nt 5′-untranslated region (UTR) and a 229 nt 3′-UTR. The deduced amino acid sequences for ORF-1 and ORF-2 respectively show considerable similarities to the non-structural and structural proteins of a marine raphidophyte-infecting virus HaRNAV (Heterosigma akashiwo RNA virus). Phylogenetic analyses of concatenated amino acid sequences of RNA helicase and RdRp domains supported the monophyly of RsRNAV, HaRNAV and a marine protist-infecting virus SssRNAV (Schizochytrium single-stranded RNA virus) with moderate bootstrap values of 79–83%, but not at the family level, whilst their monophyly was only weakly supported (50–55%) in the phylogenetic tree based on RdRp whole domain. As a result, comparison of the genome organization and sequence suggests RsRNAV is not a member of any currently defined virus family. In the RdRp tree, the positive-sense ssRNA viruses infecting Stramenopiles (RsRNAV, HaRNAV and SssRNAV) and Alveolata (HcRNAV (Heterocapsa circularisquama RNA virus)) were categorized into phylogenetically distant clades, which suggests a host/virus coevolution. Our study supports the hypothesis that a diverse array of ssRNA viruses exists in marine environments.

scholarly journals Spritz: A Proteogenomic Database Engine

2020 ◽  
Author(s):  
Anthony J. Cesnik ◽  
Rachel M. Miller ◽  
Khairina Ibrahim ◽  
Lei Lu ◽  
Robert J. Millikin ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Amino Acid ◽  
Cell Line ◽  
Rna Sequencing ◽  
Amino Acid Sequences ◽  
Osteosarcoma Cell ◽  
Sequencing Data ◽  
Protein Database ◽  
Bottom Up ◽  
Sequence Variations

AbstractProteoforms are the workhorses of the cell, and subtle differences between their amino acid sequence or post-translational modifications (PTMs) can change their biological function. To most effectively identify and quantify proteoforms in genetically diverse samples by mass spectrometry (MS), it is advantageous to search the MS data against a sample-specific protein database that is tailored to the sample being analyzed, in that it contains the correct amino acid sequences and relevant PTMs for that sample. To this end, we have developed Spritz (https://smith-chem-wisc.github.io/Spritz/), an open-source software tool for generating protein databases annotated with sequence variations and PTMs. We provide a simple graphical user interface (GUI) for Windows and scripts that can be run on any operating system. Spritz automatically sets up and executes approximately 20 tools, which enable construction of a proteogenomic database from only raw RNA sequencing data. Sequence variations that are discovered in RNA sequencing data upon comparison to the Ensembl reference genome are annotated on proteins in these databases, and PTM annotations are transferred from UniProt. Modifications can also be discovered and added to the database using bottom-up mass spectrometry data and global PTM discovery in MetaMorpheus. We demonstrate that such sample-specific databases allow the identification of variant peptides, modified variant peptides, and variant proteoforms by searching bottom-up and top-down proteomic data from the Jurkat human T lymphocyte cell line and demonstrate the identification of phosphorylated variant sites with phosphoproteomic data from the U2OS human osteosarcoma cell line.

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