Variability of non-structural proteins of equine arteritis virus during persistent infection of the stallion

2015 ◽  
Vol 18 (2) ◽  
pp. 255-259 ◽  
Author(s):  
W. Socha ◽  
J. Rola ◽  
J.F. Żmudziński
Keyword(s):  
Amino Acid ◽  
Sequence Analysis ◽  
Amino Acid Identity ◽  
Equine Arteritis Virus ◽  
The Other ◽  
Structural Proteins ◽  
Amino Acid Substitutions ◽  
Synonymous Substitutions ◽  
Acid Identity ◽  
Synonymous Mutations

AbstractThe genetic stability of ORF1a encoding non-structural proteins nsp1, nsp2, nsp3 and nsp4 of equine arteritis virus (EAV) has been analysed for nearly seven years in a persistently infected stallion of the Malopolska breed. Between November 2004 and June 2011, 11 semen samples were collected. Viral RNA extracted from semen of this carrier stallion was amplified, sequenced and compared with the sequences of the other known strains of EAV. Sequence analysis of ORF1a showed 84 synonymous and 16 non-synonymous mutations. The most variable part of ORF1a was the region encoding nsp2 protein with 13 non-synonymous substitutions. The degree of amino acid identity between isolates ranged from 98.91 to 100%. Only single non-synonymous mutations were detected in nsp1 (one substitution) and nsp4 (two substitutions). The most stable was nsp3 in which no amino acid substitutions were observed during the whole period of observation.

scholarly journals Characterization of the hrpC and hrpRSOperons of Pseudomonas syringae Pathovars Syringae, Tomato, and Glycinea and Analysis of the Ability of hrpF,hrpG, hrcC, hrpT, and hrpVMutants To Elicit the Hypersensitive Response and Disease in Plants

1998 ◽  
Vol 180 (17) ◽  
pp. 4523-4531 ◽  
Author(s):  
Wen-Ling Deng ◽  
Gail Preston ◽  
Alan Collmer ◽  
Chun-Jung Chang ◽  
Hsiou-Chen Huang
Keyword(s):  
Amino Acid ◽  
Outer Membrane ◽  
Pseudomonas Syringae ◽  
Hypersensitive Response ◽  
Amino Acid Identity ◽  
The Other ◽  
Wild Type ◽  
Acid Identity ◽  
Type Iii ◽  
Group I

The species Pseudomonas syringae encompasses plant pathogens with differing host specificities and corresponding pathovar designations. P. syringae requires the Hrp (type III protein secretion) system, encoded by a 25-kb cluster ofhrp and hrc genes, in order to elicit the hypersensitive response (HR) in nonhosts or to be pathogenic in hosts. DNA sequence analysis of the hrpC and hrpRSoperons of P. syringae pv. syringae 61 (brown spot of beans), P. syringae pv. glycinea U1 (bacterial blight of soybeans), and P. syringae pv. tomato DC3000 (bacterial speck of tomatos) revealed that the 13 genes comprising the right half of the hrp cluster (including those in the previously sequenced hrpZ operon) are conserved and identically arranged. The hrpC operon is comprised of hrpF,hrpG, hrcC, hrpT, and hrpV. hrcC encodes a putative outer membrane protein that is conserved in all type III secretion systems. The other four genes appear to be characteristic of group I Hrp systems, such as those possessed byP. syringae and Erwinia amylovora. The predicted products of these four genes in P. syringae pv. syringae 61 are HrpF (8 kDa), HrpG (15.4 kDa), HrpT (7.5 kDa), and HrpV (13.4 kDa). HrpT is a putative outer membrane lipoprotein. HrpF, HrpG, and HrpV are all hydrophilic proteins lacking N-terminal signal peptides. The HrpG, HrcC, HrpT, and HrpV proteins of P. syringae pathovars syringae and tomato (the two most divergent pathovars) had at least 76% amino acid identity with each other, whereas the HrpF proteins of these two pathovars had only 36% amino acid identity. The HrpF proteins of P. syringae pathovars syringae and glycinea also showed significant similarity to the HrpA pilin protein of P. syringae pathovar tomato. Functionally nonpolar mutations were introduced into each of the genes in thehrpC operon of P. syringae pv. syringae 61 by insertion of an nptII cartridge lacking a transcription terminator. The mutants were assayed for their ability to elicit the HR in nonhost tobacco leaves or to multiply and cause disease in host bean leaves. Mutations in hrpF, hrcC, andhrpT abolished or greatly reduced the ability of P. syringae pv. syringae 61 to elicit the HR in tobacco. ThehrpG mutant had only weakly reduced HR activity, and the activity of the hrpV mutant was indistinguishable from that of the wild type. Each of the mutations could be complemented, but surprisingly, the hrpV subclone caused a reduction in the HR elicitation ability of the ΔhrpV::nptIImutant. The hrpF and hrcC mutants caused no disease in beans, whereas the hrpG, hrpT, and hrpV mutants had reduced virulence. Similarly, thehrcC mutant grew little in beans, whereas the other mutants grew to intermediate levels in comparison with the wild type. These results indicate that HrpC and HrpF have essential functions in the Hrp system, that HrpG and HrpT contribute quantitatively but are not essential, and that HrpV is a candidate negative regulator of the Hrp system.

scholarly journals Analysis of rodent platelet glycoprotein IIb: evidence for evolutionarily conserved domains and alternative proteolytic processing

Blood ◽  
1990 ◽  
Vol 75 (6) ◽  
pp. 1282-1289 ◽  
Author(s):  
M Poncz ◽  
PJ Newman
Keyword(s):  
Amino Acid ◽  
Sequence Analysis ◽  
Dna Sequence ◽  
Genomic Dna ◽  
Amino Acid Identity ◽  
Dna Sequence Analysis ◽  
Amino Acid Residues ◽  
Acid Identity ◽  
Heavy Chains ◽  
Genomic Dna Sequence

Abstract Recently, the full-length primary amino acid sequence for human glycoproteins (GP) IIb and IIIa have been derived from their respective cDNAs. Potential functional domains within these proteins have been proposed based primarily on homology with similar domains in other proteins having known biologic function. To further understand the relationship between structure and function of the platelet fibrinogen receptor, we have begun comparative studies of the human GPIIb/IIIa receptor with the corresponding rodent receptor. The rodent rGPIIb/IIIa receptor differs from the human receptor, having low affinity for R.G.D- containing oligopeptides and not binding at all to the C-terminus of the gamma chain of human fibrinogen. We describe the structure of rodent platelet GPIIb derived from a combination of peptide sequencing, and cDNA and partial genomic DNA sequence analysis. The initial transcript is 1037 amino acid residues, having 78% amino acid identity with its 1039 residue human analog. Both heavy chains have the N- terminal sequence L.N.L.D, agreeing with the consensus derived from other integrin family alpha heavy chains. All 18 cysteine residues occur at positions conserved in human GPIIb and the vitronectin receptor alpha subunit VNR alpha. The putative calcium-binding domains of the GPIIbs have a high level of amino acid identity (92%), supporting the supposition that these regions have a critical biologic role. The final 48 C-terminal amino acid residues of the heavy chain of rodent GPIIb share only 56% identity with its human counterpart, and the proposed cleavage site of human GPIIb into its heavy and light chains is not present in the rodent sequence. Although we demonstrate that rodent GPIIb is split into two subunits during its maturation, this process either involves a different recognition sequence in the rodent or occurs at a different site. Finally, partial genomic DNA sequence analysis indicates that there are at least two rodent GPIIb genes: a normal gene, containing introns in positions similar to those in the human gene, and a processed pseudogene. The human haploid genome contains only a single GPIIb gene.

Cloning of cDNA for goldfish activin βB subunit, and the expression of its mRNA in gonadal and non-gonadal tissues

1997 ◽  
Vol 19 (1) ◽  
pp. 37-45 ◽  
Author(s):  
W Ge ◽  
T Miura ◽  
H Kobayashi ◽  
R E Peter ◽  
Y Nagahama
Keyword(s):  
Amino Acid ◽  
Sequence Analysis ◽  
Chinese Hamster Ovary ◽  
Cho Cells ◽  
Culture Medium ◽  
Specific Activity ◽  
Chinese Hamster ◽  
Amino Acid Identity ◽  
Acid Identity ◽  
Wide Range

ABSTRACT We have cloned a full length cDNA coding for activin βB subunit from the goldfish ovary. Sequence analysis of the goldfish activin βB shows that this peptide is extremely conserved across vertebrates. The mature region of goldfish activin βB has 93 and 98% amino acid identity with that of human and zebrafish βB subunit respectively. The identity of the cloned goldfish activin βB was further confirmed by expressing the protein in the Chinese hamster ovary (CHO) cells followed by detection of the specific activity of activin in the culture medium using F5-5 cell assay. mRNA of goldfish activin βB is expressed in a variety of goldfish tissues including ovary, testis, brain, pituitary, kidney and liver, suggesting a wide range of physiological roles for activin in the goldfish.

scholarly journals Analysis of rodent platelet glycoprotein IIb: evidence for evolutionarily conserved domains and alternative proteolytic processing

Blood ◽  
1990 ◽  
Vol 75 (6) ◽  
pp. 1282-1289 ◽  
Author(s):  
M Poncz ◽  
PJ Newman
Keyword(s):  
Amino Acid ◽  
Sequence Analysis ◽  
Dna Sequence ◽  
Genomic Dna ◽  
Amino Acid Identity ◽  
Dna Sequence Analysis ◽  
Amino Acid Residues ◽  
Acid Identity ◽  
Heavy Chains ◽  
Genomic Dna Sequence

Recently, the full-length primary amino acid sequence for human glycoproteins (GP) IIb and IIIa have been derived from their respective cDNAs. Potential functional domains within these proteins have been proposed based primarily on homology with similar domains in other proteins having known biologic function. To further understand the relationship between structure and function of the platelet fibrinogen receptor, we have begun comparative studies of the human GPIIb/IIIa receptor with the corresponding rodent receptor. The rodent rGPIIb/IIIa receptor differs from the human receptor, having low affinity for R.G.D- containing oligopeptides and not binding at all to the C-terminus of the gamma chain of human fibrinogen. We describe the structure of rodent platelet GPIIb derived from a combination of peptide sequencing, and cDNA and partial genomic DNA sequence analysis. The initial transcript is 1037 amino acid residues, having 78% amino acid identity with its 1039 residue human analog. Both heavy chains have the N- terminal sequence L.N.L.D, agreeing with the consensus derived from other integrin family alpha heavy chains. All 18 cysteine residues occur at positions conserved in human GPIIb and the vitronectin receptor alpha subunit VNR alpha. The putative calcium-binding domains of the GPIIbs have a high level of amino acid identity (92%), supporting the supposition that these regions have a critical biologic role. The final 48 C-terminal amino acid residues of the heavy chain of rodent GPIIb share only 56% identity with its human counterpart, and the proposed cleavage site of human GPIIb into its heavy and light chains is not present in the rodent sequence. Although we demonstrate that rodent GPIIb is split into two subunits during its maturation, this process either involves a different recognition sequence in the rodent or occurs at a different site. Finally, partial genomic DNA sequence analysis indicates that there are at least two rodent GPIIb genes: a normal gene, containing introns in positions similar to those in the human gene, and a processed pseudogene. The human haploid genome contains only a single GPIIb gene.

scholarly journals Human Norovirus Evolution in a Chronically Infected Host

mSphere ◽  
2017 ◽  
Vol 2 (2) ◽  
Author(s):  
Sylvie Y. Doerflinger ◽  
Stefan Weichert ◽  
Anna Koromyslova ◽  
Martin Chan ◽  
Christian Schwerk ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Identity ◽  
Amino Acid Substitutions ◽  
Genotype 4 ◽  
Binding Interactions ◽  
Acid Identity ◽  
The Past ◽  
Genetic Types ◽  
Novel Variants

ABSTRACT The norovirus genogroup II genotype 4 (GII.4) variants have approximately 5% divergence in capsid amino acid identity and have dominated over the past decade. The precise reason(s) for the GII.4 emergence and persistence in the human population is still unknown, but some studies have suggested that chronically infected patients might generate novel variants that can cause new epidemics. We examined GII.4 noroviruses isolated from an immunocompromised patient with a long-term infection. Numerous norovirus capsid quasi-species were isolated during the 13-month study. The capsid quasi-species clustered into two genetic and antigenic types. However, the HBGA binding profiles were similar between the two antigenic clusters, indicating that the amino acid substitutions did not alter the HBGA binding interactions. The isolated sequences represented two new GII.4 variants, but similar sequences were not found in the database. These results indicated that chronically infected patients might not generate novel noroviruses that cause outbreaks. Typically, human noroviruses cause symptoms of acute gastroenteritis for 2 to 4 days. Often, the virions are shed in stool for several days after the symptoms recede, which in turn can lead to further contamination and transmission. Moreover, a number of reports have considered that chronic norovirus infections, i.e., lasting months and years, might even function as reservoirs for the generation of novel strains that can escape the herd immunity or have modified binding interactions with histo-blood group antigens (HBGAs). In this study, we analyzed noroviruses isolated from a patient who has presented a chronic infection for more than 6 years. We found that the isolated capsid sequences clustered into two main genetic types (termed A and B), despite a plethora of capsid quasi-sequences. Furthermore, the two genetic types corresponded well with distinct antigenicities. On the other hand, we showed that numerous amino acid substitutions on the capsid surface of genetic types A and B did not alter the HBGA binding profiles. However, divergent binding profiles for types A and B were observed with human milk oligosaccharides (HMOs), which structurally mimic HBGAs and may act as natural antivirals. Importantly, the isolated capsid sequences only had approximately 90% amino acid identity with other known sequences, which suggested that transmission of these chronic noroviruses could be limited. IMPORTANCE The norovirus genogroup II genotype 4 (GII.4) variants have approximately 5% divergence in capsid amino acid identity and have dominated over the past decade. The precise reason(s) for the GII.4 emergence and persistence in the human population is still unknown, but some studies have suggested that chronically infected patients might generate novel variants that can cause new epidemics. We examined GII.4 noroviruses isolated from an immunocompromised patient with a long-term infection. Numerous norovirus capsid quasi-species were isolated during the 13-month study. The capsid quasi-species clustered into two genetic and antigenic types. However, the HBGA binding profiles were similar between the two antigenic clusters, indicating that the amino acid substitutions did not alter the HBGA binding interactions. The isolated sequences represented two new GII.4 variants, but similar sequences were not found in the database. These results indicated that chronically infected patients might not generate novel noroviruses that cause outbreaks.

scholarly journals Molecular and Kinetic Comparison of the Novel Extended-Spectrum β-Lactamases CTX-M-25 and CTX-M-26

2004 ◽  
Vol 48 (12) ◽  
pp. 4829-4834 ◽  
Author(s):  
Craig J. Munday ◽  
David A. Boyd ◽  
Nigel Brenwald ◽  
Mark Miller ◽  
Jennifer M. Andrews ◽  
...  
Keyword(s):  
Amino Acid ◽  
Susceptibility Testing ◽  
Kinetic Studies ◽  
Amino Acid Identity ◽  
Amino Acid Substitutions ◽  
The Novel ◽  
Acid Identity ◽  
The United Kingdom ◽  
Extended Spectrum ◽  
Plasmid Profiling

ABSTRACT CTX-M-25 is a novel extended-spectrum β-lactamase isolated from a single Canadian Escherichia coli isolate. Susceptibility testing demonstrated that this enzyme confers resistance to both cefotaxime and ceftazidime, but the level of resistance was reduced with the addition of β-lactamase inhibitors. The bla CTX-M-25 gene was detected on a 111-kb plasmid. It is a member of the CTX-M-8 group and has the closest amino acid identity (99%; three amino acid substitutions) with CTX-M-26. The bla CTX-M-26 gene was detected on a 100-kb plasmid isolated from a Klebsiella pneumoniae strain from the United Kingdom, and plasmid profiling revealed that it showed some homology to the bla CTX-M-25-harboring plasmid. Both CTX-M genes were located downstream of ISEcp1, although the copy upstream of bla CTX-M-25 was disrupted by IS50-A. Comparative kinetic studies of recombinant CTX-M-25 and CTX-M-26 enzymes showed that CTX-M-25 has a higher level of ceftazidime hydrolysis (k cat values, 33 and 0.005 s−1 for CTX-M-25 and CTX-M-26, respectively).

scholarly journals A50 Whole-genome sequencing of African swine fever isolates from Sardinia

2019 ◽  
Vol 5 (Supplement_1) ◽  
Author(s):  
C Torresi ◽  
F Granberg ◽  
L Bertolotti ◽  
A Oggiano ◽  
B Colitti ◽  
...  
Keyword(s):  
Amino Acid ◽  
Sequence Data ◽  
Temporal Distribution ◽  
African Swine Fever ◽  
Amino Acid Identity ◽  
Genotype I ◽  
Acid Identity ◽  
Wide Range ◽  
Intergenic Sequences ◽  
Genes Encoding

Abstract In order to assess the molecular epidemiology of African swine fever (ASF) in Sardinia, we analyzed a wide range of isolates from wild and domestic pigs over a 31-year period (1978–2009) by genotyping sequence data from the genes encoding the p54 and the p72 proteins and the CVR. On this basis, the analysis of the B602L gene revealed a minor difference, placing the Sardinian isolates into two clusters according to their temporal distribution. As an extension of this study, in order to achieve a higher level of discrimination, three further variable genome regions, namely p30, CD2v, and I73R/I329L, of a large number of isolates collected from outbreaks in the years 2002–14 have been investigated. Sequence analysis of the CD2v region revealed a temporal subdivision of the viruses into two subgroups. These data, together with those from the B602L gene analysis, demonstrated that the viruses circulating in Sardinia belong to p72/genotype I, but since 1990 have undergone minor genetic variations in respect to its ancestor, thus making it impossible to trace isolates, enabling a more accurate assessment of the origin of outbreaks, and extending knowledge of virus evolution. To solve this problem, we have sequenced and annotated the complete genome of nine ASF isolates collected in Sardinia between 1978 and 2012. This was achieved using sequence data determined by next-generation sequencing. The results showed a very high identity with range of nucleotide similarity among isolates of 99.5 per cent to 99.9 per cent. The ASF virus (ASFV) genomes were composed of terminal inverted repeats and conserved and non-conserved ORFs. Among the conserved ORFs, B385R, H339R, and O61R-p12 showed 100 per cent amino acid identity. The same was true for the hypervariable ORFs, with regard to X69R, DP96R, DP60R, EP153R, B407L, I10L, and L60L genes. The EP402R and B602L genes showed, as expected, an amino acid identity range of 98.5 per cent to 100 per cent and 91 per cent to 100 per cent, respectively. In addition, all of the isolates displayed variable intergenic sequences. As a whole, the results from our studies confirmed a remarkable genetic stability of the ASFV/p72 genotype I viruses circulating in Sardinia.

Characterization and Induction of Two Cytochrome P450 Genes, CYP6AE28 and CYP6AE30, in Cnaphalocrocis medinalis: Possible Involvement in Metabolism of Rice Allelochemicals

2010 ◽  
Vol 65 (11-12) ◽  
pp. 719-725 ◽  
Author(s):  
Xiaoli Liu ◽  
Jun Chen ◽  
Zhifan Yang
Keyword(s):  
Amino Acid ◽  
Rice Variety ◽  
Amino Acid Identity ◽  
Cnaphalocrocis Medinalis ◽  
Amino Acid Residues ◽  
Acid Identity ◽  
Rice Leaf Folder ◽  
Cytochrome P450 Genes ◽  
Molecular Masses ◽  
Lepidoptera Pyralidae

Two cDNAs specific for P450 genes, CYP6AE28 and CYP6AE30, have been isolated from the rice leaf folder Cnaphalocrocis medinalis Guenée (Lepidoptera: Pyralidae). Both cDNApredicted proteins have 504 amino acid residues in length, but with molecular masses of 60177 Dalton for CYP6AE28 and 60020 Dalton for CYP6AE30, and theoretical pI values of 8.49 for CYP6AE28 and 8.56 for CYP6AE30, respectively. Both putative proteins contain the conserved structural and functional domains characteristic of all CYP6 members. CYP6AE28 and CYP6AE30 show 52% amino acid identity to each other; both of them have 49 - 56% identities with CYP6AE1, Cyp6ae12, and CYP6AE14. Phylogenetic analysis showed that the two P450s are grouped in the lineage containing some of the CYP6AE members, CYP6B P450s and CYP321A1. The transcripts of CYP6AE28 and CYP6AE30 were found to be induced in response to TKM-6, a rice variety with high resistance to C. medinalis. The results suggest that the two P450s may play important roles in adaptation to the host plant rice. This is the first report of P450 genes cloned in C. medinalis

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