scholarly journals Variation and Selection in the Putative Sperm-Binding Region of ZP3 in Muroid Rodents: A Comparison between Cricetids and Murines

Genes ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1450
Author(s):  
Margarida Alexandra Duarte ◽  
Carlos Rodríguez Fernandes ◽  
Gerald Heckel ◽  
Maria da Luz Mathias ◽  
Cristiane Bastos-Silveira
Keyword(s):  
Amino Acid ◽  
Acid Sites ◽  
Amino Acid Sequences ◽  
Binding Region ◽  
Sperm Binding ◽  
Glycosylation Sites ◽  
Muroid Rodents ◽  
Taxonomic Groups ◽  
Variation And Selection ◽  
Positively Selected Sites

In mammals, the zona pellucida glycoprotein 3 (ZP3) is considered a primary sperm receptor of the oocyte and is hypothesized to be involved in reproductive isolation. We investigated patterns of diversity and selection in the putative sperm-binding region (pSBR) of mouse ZP3 across Cricetidae and Murinae, two hyperdiverse taxonomic groups within muroid rodents. In murines, the pSBR is fairly conserved, in particular the serine-rich stretch containing the glycosylation sites proposed as essential for sperm binding. In contrast, cricetid amino acid sequences of the pSBR were much more variable and the serine-rich motif, typical of murines, was generally substantially modified. Overall, our results suggest a general lack of species specificity of the pSBR across the two muroid families. We document statistical evidence of positive selection acting on exons 6 and 7 of ZP3 and identified several amino acid sites that are likely targets of selection, with most positively selected sites falling within or adjacent to the pSBR.

scholarly journals Cloning and sequence analysis of cDNAs encoding the α1, α2 and α3 chains of mouse collagen VI

1993 ◽  
Vol 291 (3) ◽  
pp. 787-792 ◽  
Author(s):  
R Z Zhang ◽  
T C Pan ◽  
R Timpl ◽  
M L Chu
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequences ◽  
Untranslated Regions ◽  
Cdna Libraries ◽  
Cdna Clones ◽  
Collagen Vi ◽  
Central Segment ◽  
Glycosylation Sites ◽  
Key Features ◽  
Triple Helical Domain

cDNA clones encoding the alpha 1, alpha 2 and alpha 3 chains of mouse collagen VI have been isolated by screening cDNA libraries with the corresponding human probes. The composite cDNAs for the alpha 1, alpha 2, and alpha 3 chains are 2.5, 1.6 and 2.9 kb in size respectively. The alpha 1 and alpha 2 cDNAs encode the C-terminal portions of the chains as well as the entire 3′-untranslated regions, while the alpha 3 cDNAs encode a central segment of 959 amino acids flanking the triple-helical domain. The deduced amino acid sequences share 86-88% identity with the human counterparts and 67-73% identity with the chicken equivalents. Alignment of the deduced amino acid sequences of mouse, human and chicken collagens reveal that the key features of the protein, including the cysteine residues, imperfections in the Gly-Xaa-Xaa regions, Arg-Gly-Asp sequences and potential N-glycosylation sites, are mostly conserved.

ISOLATION AND CHARACTERIZATION OF THE GENES FOR THE a AND b SUBUNITS OF HUMAN COAGULATION FACTOR XIII

1987 ◽  
Author(s):  
A Ichinose ◽  
R E Bottenus ◽  
K R Loeb ◽  
E W Davie
Keyword(s):  
Amino Acid ◽  
Factor Xiii ◽  
Coagulation Factor ◽  
Amino Acid Sequences ◽  
Binding Region ◽  
Recombinant Phage ◽  
B Subunit ◽  
Isolation And Characterization ◽  
A Subunit ◽  
B Subunits

Factor XIII (plasma transglutaminase, fibrin stabilizing factor) is a plasma protein that plays an important role in the final stages of blood coagulation and fibrinolysis. The molecule occurs in blood as a tetramer (a2b2) consisting of two a. subunits and two b subunits. Recently, we have determined the amino acid sequences for both the a. and b subunits of human factor XIII by a combination of cDNA cloning and amino acid sequence analysis. cDNAs coding for the a (3.8 Kb) and b (2.2 Kb) subunits were used for the screening of human genomic DNA libraries. Among 12 × 106 recombinant phage, ∼30 have been shown to contain the sequences for the a subunit and ∼10 have been shown to contain the gene for the b subunit of factor XIII. The clones coding for the a. subunit span ∼90 Kb and have been characterized by restriction mapping. Southern blotting, and DNA sequencing. Both 5’ and 3’ ends of the genomic clones correspond to the 5’ and 3’portions of the cDNA for the a.subunit of factor XIII. The DNA sequence revealed that the activation peptide released ^thrombin (amino acid residues 137), the first putative Ca2+ binding region (around residue 251), the active Site Cys (amino acid residue 314), and the second putative Ca2+ binding region (around residue 473) are encoded by separate exons. Accordingly, the intervening sequences may separate the a subunit into functional and structural domains. The gene organization for the b subunit will also be presented. (Supported by NIH Grant HL 16919.)

scholarly journals Insights into the Selective Pressures Restricting Pelargonium Flower Break Virus Genome Variability: Evidence for Host Adaptation

2006 ◽  
Vol 80 (16) ◽  
pp. 8124-8132 ◽  
Author(s):  
Patricia Rico ◽  
Pilar Ivars ◽  
Santiago F. Elena ◽  
Carmen Hernández
Keyword(s):  
Amino Acid ◽  
Leucine Zipper ◽  
Critical Role ◽  
Chenopodium Quinoa ◽  
Virus Genome ◽  
Acid Sites ◽  
Genomic Region ◽  
Amino Acid Sequences ◽  
Nucleotide Substitutions ◽  
Selective Pressures

ABSTRACT The molecular diversity of Pelargonium flower break virus (PFBV) was assessed using a collection of isolates from different geographical origins, hosts, and collecting times. The genomic region examined was 1,828 nucleotides (nt) long and comprised the coding sequences for the movement (p7 and p12) and the coat (CP) proteins, as well as flanking segments including the entire 3′ untranslated region (3′ UTR). Some constraints limiting viral heterogeneity could be inferred from sequence analyses, such as the conservation of the amino acid sequences of p7 and of the shell domain of the CP, the maintenance of a leucine zipper motif in p12, and the preservation of a particular folding in the 3′ UTR. A remarkable covariation, involving five specific amino acid sites, was found in the CP of isolates largely propagated in the local lesion host Chenopodium quinoa and in the progeny of a PFBV variant subjected to serial passages in this host. Concomitant with this covariation, up to 30 nucleotide substitutions in a 1,428-nt region of the viral RNA could be attributable to C. quinoa-specific adaptation, representing one of the most outstanding cases of host-driven genome variation for a plant virus. Globally, the results indicate that the selective pressures exerted by the host play a critical role in shaping PFBV populations and that these populations are likely being selected for at both protein and RNA levels.

scholarly journals ADOPS - Automatic Detection Of Positively Selected Sites

2012 ◽  
Vol 9 (3) ◽  
pp. 18-32 ◽  
Author(s):  
David Reboiro-Jato ◽  
Miguel Reboiro-Jato ◽  
Florentino Fdez-Riverola ◽  
Cristina P. Vieira ◽  
Nuno A. Fonseca ◽  
...  
Keyword(s):  
Amino Acid ◽  
Maximum Likelihood ◽  
Dna Sequences ◽  
Sequence Data ◽  
Automatic Detection ◽  
Acid Sites ◽  
Nucleotide Sequence Data ◽  
Software Applications ◽  
Codon Substitution ◽  
Positively Selected Sites

Summary Maximum-likelihood methods based on models of codon substitution have been widely used to infer positively selected amino acid sites that are responsible for adaptive changes. Nevertheless, in order to use such an approach, software applications are required to align protein and DNA sequences, infer a phylogenetic tree and run the maximum-likelihood models. Therefore, a significant effort is made in order to prepare input files for the different software applications and in the analysis of the output of every analysis. In this paper we present the ADOPS (Automatic Detection Of Positively Selected Sites) software. It was developed with the goal of providing an automatic and flexible tool for detecting positively selected sites given a set of unaligned nucleotide sequence data. An example of the usefulness of such a pipeline is given by showing, under different conditions, positively selected amino acid sites in a set of 54 Coffea putative S-RNase sequences. ADOPS software is freely available and can be downloaded from http://sing.ei.uvigo.es/ADOPS.

scholarly journals Senescence and entrenchment in evolution of amino acid sites

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
A. V. Stolyarova ◽  
E. Nabieva ◽  
V. V. Ptushenko ◽  
A. V. Favorov ◽  
A. V. Popova ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Adaptive Evolution ◽  
Protein Evolution ◽  
Environmental Changes ◽  
Acid Sites ◽  
Analytical Modelling ◽  
Site Change ◽  
A Site ◽  
Positively Selected Sites

Abstract Amino acid propensities at a site change in the course of protein evolution. This may happen for two reasons. Changes may be triggered by substitutions at epistatically interacting sites elsewhere in the genome. Alternatively, they may arise due to environmental changes that are external to the genome. Here, we design a framework for distinguishing between these alternatives. Using analytical modelling and simulations, we show that they cause opposite dynamics of the fitness of the allele currently occupying the site: it tends to increase with the time since its origin due to epistasis (“entrenchment”), but to decrease due to random environmental fluctuations (“senescence”). By analysing the genomes of vertebrates and insects, we show that the amino acids originating at negatively selected sites experience strong entrenchment. By contrast, the amino acids originating at positively selected sites experience senescence. We propose that senescence of the current allele is a cause of adaptive evolution.

Stejnulxin, a novel snake C-type lectin-like protein from Trimeresurus stejnegeri venom is a potent platelet agonist acting specifically via GPVI

2003 ◽  
Vol 90 (10) ◽  
pp. 662-671 ◽  
Author(s):  
Wen-Hui Lee ◽  
Xiao-Yan Du ◽  
Qiu-Min Lu ◽  
Kenneth Clemetson ◽  
Yun Zhang
Keyword(s):  
Amino Acid ◽  
Platelet Aggregation ◽  
Molecular Mass ◽  
Mass Difference ◽  
Amino Acid Sequences ◽  
Dependent Manner ◽  
Reducing Conditions ◽  
Glycosylation Sites ◽  
Molecular Masses ◽  
Dose Dependent

SummaryStejnulxin, a novel snake C-type lectin-like protein with potent platelet activating activity, was purified and characterized from Trimeresurus stejnegeri venom. Under non-reducing conditions, it migrated on a SDS-polyacrylamide gel with an apparent molecular mass of 120 kDa. On reduction, it separated into three polypeptide subunits with apparent molecular masses of 16 kDa (α), 20 kDa (β1) and 22 kDa (β2), respectively. The complete amino acid sequences of its subunits were deduced from cloned cDNAs. The N-terminal sequencing and cDNA cloning indicated that β1 and β2 subunits of stejnulxin have identical amino acid sequences and each contains two N-glycosylation sites. Accordingly, the molecular mass difference between β1 and β2 is caused by glycosylation heterogenity. The subunit amino acid sequences of stejnulxin are similar to those of convulxin, with sequence identities of 52.6% and 66.4% for the α and β, respectively. Stejnulxin induced human platelet aggregation in a dose-dependent manner. Antibodies against αIIbβ3 inhibited the aggregation response to stejnulxin, indicating that activation of αIIbβ3 and binding of fibrinogen are involved in stejnulxin-induced platelet aggregation. Antibodies against GPIbα or α2β1 as well as echicetin or rhodocetin had no significant effect on stejnulxin-induced platelet aggregation. However, platelet activation induced by stejnulxin was blocked by anti-GPVI antibodies. In addition, stejnulxin induced a tyrosine phosphorylation profile in platelets that resembled that produced by convulxin. Biotinylated stejnulxin bound specifically to platelet membrane GPVI.

scholarly journals Up to date with human thyroglobulin

2001 ◽  
Vol 170 (2) ◽  
pp. 307-321 ◽  
Author(s):  
SA van de Graaf ◽  
C Ris-Stalpers ◽  
E Pauws ◽  
FM Mendive ◽  
HM Targovnik ◽  
...  
Keyword(s):  
Amino Acid ◽  
Additional Data ◽  
Amino Acid Sequences ◽  
Wild Type ◽  
Coding Region ◽  
Tyrosine Residues ◽  
Glycosylation Sites ◽  
Function Relationship ◽  
Receptor Domain ◽  
Antigenic Epitopes

The coding region of the human thyroglobulin (TG) mRNA has been resequenced, and comparison with the TG sequence originally published in 1987 showed many variations. All of the variations were validated in 20--40 other alleles, and this resulted in the revision of 41 nucleotide positions. This review presents the revised wild-type human TG sequence, including all known exon/exon boundaries and additional data on the TG mRNA population, concerning alternative splicing and variability of the polyadenylation cleavage site. The amino acid sequence derived shows one additional, 12 changed, and 10 polymorphic residues. Protein characteristics, such as acceptor and donor tyrosine residues, N-glycosylation sites, cysteine-rich repeats, the proposed receptor domain, and antigenic epitopes, are included, and their relationship to the revised sequence is discussed. Furthermore, all reported TG mutations causing dyshormonogenesis in humans and animals are designated in the nucleotide and amino acid sequences. This up-to-date profile of the human TG molecule presents the features of importance for its complex role in thyroid hormonogenesis, and is the basis for future studies on the structure--function relationship.

scholarly journals Sequence analysis and structure prediction of ABHD16A and the roles of the ABHD family members in human disease

Open Biology ◽  
2018 ◽  
Vol 8 (5) ◽  
pp. 180017 ◽  
Author(s):  
Jun Xu ◽  
Weizhen Gu ◽  
Kai Ji ◽  
Zhao Xu ◽  
Haihua Zhu ◽  
...  
Keyword(s):  
Amino Acid ◽  
Structure Prediction ◽  
Active Sites ◽  
Metabolic Regulation ◽  
Acid Sites ◽  
Amino Acid Sequences ◽  
The Body ◽  
Gene Location ◽  
Future Research ◽  
Animal Cells

Abhydrolase domain containing 16A (ABHD16A) is a member of the α/β hydrolase domain-containing (ABHD) protein family and is expressed in a variety of animal cells. Studies have shown that ABHD16A has acylglycerol lipase and phosphatidylserine lipase activities. Its gene location in the main histocompatibility complex (MHC) III gene cluster suggests that this protein may participate in the immunomodulation of the body. The results of studies investigating nearly 20 species of ABHDs reveal that the ABHD proteins are key factors in metabolic regulation and disease occurrence and development. In this paper, we summarize the related progress regarding the function of ABHD16A and other ABHD proteins. A prediction of the active sites and structural domains of ABHD16A and an analysis of the amino acid sites are included. Moreover, we analysed the amino acid sequences of the ABHD16A molecules in different species and provide an overview of the related functions and diseases associated with these proteins. The functions and diseases related to ABHD are systematically summarized and highlighted. Future research directions for studies investigating the functions and mechanisms of these proteins are also suggested. Further studies investigating the function of ABHD proteins may further confirm their positions as important determinants of lipid metabolism and related diseases.

scholarly journals Genetic Diversity and Molecular Epidemiology of Circulating Respiratory Syncytial Virus in Central Taiwan, 2008–2017

Viruses ◽  
2021 ◽  
Vol 14 (1) ◽  
pp. 32
Author(s):  
Chun-Yi Lee ◽  
Yu-Ping Fang ◽  
Li-Chung Wang ◽  
Teh-Ying Chou ◽  
Hsin-Fu Liu
Keyword(s):  
Respiratory Syncytial Virus ◽  
Amino Acid ◽  
Temporal Evolution ◽  
Local Level ◽  
Hypervariable Region ◽  
Amino Acid Sequences ◽  
Sequence Alignments ◽  
Glycosylation Sites ◽  
Syncytial Virus ◽  
Central Taiwan

In this study, we investigated the molecular evolution and phylodynamics of respiratory syncytial virus (RSV) over 10 consecutive seasons (2008–2017) and the genetic variability of the RSV genotypes ON1 and BA in central Taiwan. The ectodomain region of the G gene was sequenced for genotyping. The nucleotide and deduced amino acid sequences of the second hypervariable region of the G protein in RSV ON1 and BA were analyzed. A total of 132 RSV-A and 81 RSV-B isolates were obtained. Phylogenetic analysis revealed that the NA1, ON1, and BA9 genotypes were responsible for the RSV epidemics in central Taiwan in the study period. For RSV-A, the NA1 genotype predominated during the 2008–2011 seasons. The ON1 genotype was first detected in 2011 and replaced NA1 after 2012. For RSV-B, the BA9 and BA10 genotypes cocirculated from 2008 to 2010, but the BA9 genotype has predominated since 2012. Amino acid sequence alignments revealed the continuous evolution of the G gene in the ectodomain region. The predicted N-glycosylation sites were relatively conserved in the ON1 (site 237 and 318) and BA9 (site 296 and 310) genotype strains. Our results contribute to the understanding and prediction of the temporal evolution of RSV at the local level.

scholarly journals Dermatan sulphate is located on serine-4 of bovine skin proteodermatan sulphate. Demonstration that most molecules possess only one glycosaminoglycan chain and comparison of amino acid sequences around glycosylation sites in different proteoglycans

1985 ◽  
Vol 232 (1) ◽  
pp. 277-279 ◽  
Author(s):  
R K Chopra ◽  
C H Pearson ◽  
G A Pringle ◽  
D S Fackre ◽  
P G Scott
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequences ◽  
Serine Residue ◽  
Dermatan Sulphate ◽  
Cathepsin C ◽  
Glycosylation Sites ◽  
Different Tissues

Digestions of bovine skin proteodermatan sulphate with cathepsin C proved that the dermatan sulphate was located on Ser-4 in most of the molecules. A Ser-Gly sequence is essential for xylosylation of the serine residue and sulphated galactosaminoglycan synthesis in different proteoglycans. Variations in adjoining sequences may be significant in relation to the glycosylation process in different tissues.

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