scholarly journals Accelerated Evolution of Limb-Related Gene Hoxd11 in the Common Ancestor of Cetaceans and Ruminants (Cetruminantia)

2019 ◽  
Vol 10 (2) ◽  
pp. 515-524
Author(s):  
Jun Li ◽  
Songyang Shang ◽  
Na Fang ◽  
Yubo Zhu ◽  
Junpeng Zhang ◽  
...  
Keyword(s):  
Amino Acid ◽  
Limb Development ◽  
Common Ancestor ◽  
Statistical Tests ◽  
Molecular Evidence ◽  
Amino Acid Substitutions ◽  
Evolutionary Pattern ◽  
Accelerated Evolution ◽  
Tarsal Bones ◽  
The Common

Reduced numbers of carpal and tarsal bones (wrist and ankle joints) are extensively observed in the clade of Cetacea and Ruminantia (Cetruminantia). Homebox D11 (Hoxd11) is one of the important genes required for limb development in mammals. Mutations in Hoxd11 can lead to defects in particular bones of limbs, including carpus and tarsus. To test whether evolutionary changes in Hoxd11 underlie the loss of these bones in Cetruminantia, we sequenced and analyzed Hoxd11 coding sequences and compared them with other 5′ HoxA and HoxD genes in a taxonomic coverage of Cetacea, Ruminantia and other mammalian relatives. Statistical tests on the Hoxd11 sequences found an accelerated evolution in the common ancestor of cetaceans and ruminants, which coincided with the reduction of carpal and tarsal bones in this clade. Five amino acid substitutions (G222S, G227A, G229S, A240T and G261V) and one amino acid deletion (G254Del) occurred in this lineage. In contrast, other 5′ HoxA and HoxD genes do not show this same evolutionary pattern, but instead display a highly conserved pattern of evolution in this lineage. Accelerated evolution of Hoxd11, but not other 5′ HoxA and HoxD genes, is probably related to the reduction of the carpal and tarsal bones in Cetruminantia. Moreover, we found two amino acid substitutions (G110S and D223N) in Hoxd11 that are unique to the lineage of Cetacea, which coincided with hindlimb loss in the common ancestor of cetaceans. Our results give molecular evidence of Hoxd11 adaptive evolution in cetaceans and ruminants, which could be correlated with limb morphological adaptation.

scholarly journals Amino acid synthesis loss in parasitoid wasps and other hymenopterans

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Xinhai Ye ◽  
Shijiao Xiong ◽  
Ziwen Teng ◽  
Yi Yang ◽  
Jiale Wang ◽  
...  
Keyword(s):  
Amino Acid ◽  
Common Ancestor ◽  
Gene Loss ◽  
Acid Synthesis ◽  
Parasitoid Wasps ◽  
Amino Acid Synthesis ◽  
The Common ◽  
Multiple Loss ◽  
Lysine Synthesis ◽  
Cotesia Chilonis

Insects utilize diverse food resources which can affect the evolution of their genomic repertoire, including leading to gene losses in different nutrient pathways. Here, we investigate gene loss in amino acid synthesis pathways, with special attention to hymenopterans and parasitoid wasps. Using comparative genomics, we find that synthesis capability for tryptophan, phenylalanine, tyrosine, and histidine was lost in holometabolous insects prior to hymenopteran divergence, while valine, leucine, and isoleucine were lost in the common ancestor of Hymenoptera. Subsequently, multiple loss events of lysine synthesis occurred independently in the Parasitoida and Aculeata. Experiments in the parasitoid Cotesia chilonis confirm that it has lost the ability to synthesize eight amino acids. Our findings provide insights into amino acid synthesis evolution, and specifically can be used to inform the design of parasitoid artificial diets for pest control.

scholarly journals First Molecular Evidence and Genetic Characterization of Ovine Herpesvirus 2 in Multiple Animal Species in India

2021 ◽  
Vol 8 ◽  
Author(s):  
Naveen Kumar ◽  
Richa Sood ◽  
Atul K. Pateriya ◽  
E. Venkatesakumar ◽  
R. Ramprabhu ◽  
...  
Keyword(s):  
Amino Acid ◽  
Membrane Fusion ◽  
Genetic Characterization ◽  
Phylogenetic Analyses ◽  
Ovis Aries ◽  
Capra Hircus ◽  
Dimensional Structure ◽  
Molecular Evidence ◽  
Amino Acid Substitutions ◽  
Molecular Flexibility

Ovine herpesvirus 2 (OvHV-2) is the causative agent of sheep-associated malignant catarrhal fever (SA-MCF), a highly fatal disease syndrome that predominantly affects susceptible hosts of the order Artiodactyla. In this study, an in-depth clinico-molecular investigation of SA-MCF disease in a morbid 50-days-old cattle calf (Bos taurus indicus) and asymptomatic infection in the in-contact reservoir hosts, sheep (Ovis aries), and goat (Capra hircus) housed on a farm located in the Southern India is reported. An OIE recommended SA-MCF type-specific PCR confirmed the etiological agent as OvHV-2. The genetic characterization and phylogenetic analyses based on the glycoprotein B (gB) gene indicate that three genetic variants of OvHV-2 had infected the animal cluster of this study. As the OvHV-2 infection eventually lead to the death of the cattle calf, and the fact that its gB sequence carried four unique amino acid substitutions (N169S, L594P, I645V, and V730A), an investigation of these substitutions impact on its stability and molecular flexibility was carried out. The mapping of these amino acid substitutions on the three-dimensional structure of gB coupled with supplementary investigations showed that these substitutions conveyed the molecular flexibility to the gB, at the cost of its stability. Future studies would be to investigate whether these gB substitutions have any impact on membrane fusion activity using a virus-free cell-to-cell membrane fusion assay. The study also highlights the importance of adopting stringent biosecurity measures where mixed animal farming is a common practice.

2. The evolution of amphibians

2021 ◽  
pp. 25-47
Author(s):  
T. S. Kemp
Keyword(s):  
Dna Sequence ◽  
Common Ancestor ◽  
Evolutionary Tree ◽  
Monophyletic Group ◽  
Evolutionary Origin ◽  
Molecular Evidence ◽  
The Common

‘The evolution of amphibians’ traces the evolutionary origin of living amphibians: anurans, urodeles, and caecilians. The comparison of the DNA sequence of their genes shows that the living amphibians taken together are a monophyletic group. This means that they all go back to a single common ancestor that had already separated from the common ancestor of the amniotes in the evolutionary tree. However, molecular evidence is little help in discovering which of the ancient tetrapod groups are related to the modern groups. Moreover, the earliest fossils of the three modern groups do not occur until far later, tens of millions years later, than any plausible relatives amongst the Carboniferous and Permian tetrapods.

scholarly journals How Bacterial Chemoreceptors Evolve Novel Ligand Specificities

mBio ◽  
2020 ◽  
Vol 11 (1) ◽  
Author(s):  
José Antonio Gavira ◽  
Vadim M. Gumerov ◽  
Miriam Rico-Jiménez ◽  
Marharyta Petukh ◽  
Amit A. Upadhyay ◽  
...  
Keyword(s):  
Amino Acid ◽  
Ligand Binding ◽  
Common Ancestor ◽  
Protein Structures ◽  
Binding Pocket ◽  
Comparative Sequence Analysis ◽  
Content Type ◽  
The Common ◽  
Dynamics Simulations ◽  
Amino Acid Sensing

ABSTRACT Chemoreceptor-based signaling pathways are among the major modes of bacterial signal transduction, and Pseudomonas aeruginosa PAO1 is an important model to study their function. Of the 26 chemoreceptors of this strain, PctA has a broad ligand range and responds to most of the proteinogenic amino acids, whereas PctB and PctC have a much narrower range and show strong ligand preference for l-glutamine and γ-aminobutyrate, respectively. Using several comparative genomics approaches, we show that these receptors are paralogs: pctA gene duplication in the common ancestor of the genus Pseudomonas led to pctC, whereas pctB originated through another, independent pctA duplication in the common ancestor of P. aeruginosa. Thus, the broad-range amino acid chemoreceptor was evolutionarily older, and chemoreceptors that complemented “missing” amino acid sensing abilities arose later in specific Pseudomonas lineages. Using comparative sequence analysis, newly solved crystal structures of PctA, PctB, and PctC ligand-binding domains, and their molecular dynamics simulations, we identified a conserved amino acid recognition motif and changes in the ligand-binding pocket that led to novel ligand specificities. In addition, we determined major forces driving the evolution of this group of chemoreceptors. IMPORTANCE Many bacteria possess a large number of chemoreceptors that recognize a variety of different compounds. More than 60% of the genomes analyzed in this study contain paralogous chemoreceptors, suggesting that they emerge with high frequency. We provide first insight on how paralogous receptors have evolved and show that two chemoreceptors with a narrow ligand range have evolved from an ancestral protein with a broad chemoeffector spectrum. Protein structures show that multiple changes in the ligand-binding site account for the differences in the ligand spectrum. This work lays the ground for further studies aimed at establishing whether the principles of ligand-binding evolution reported here can be generalized for a wider spectrum of sensory proteins in bacteria.

scholarly journals Seasonal influenza circulation patterns and projections for Sep 2017 to Sep 2018

2017 ◽  
Author(s):  
Trevor Bedford ◽  
Richard A. Neher
Keyword(s):  
Genetic Diversity ◽  
Amino Acid ◽  
Seasonal Influenza ◽  
Common Ancestor ◽  
Amino Acid Deletion ◽  
Circulation Patterns ◽  
Antigenic Evolution ◽  
The Common ◽  
Amino Acid Mutations ◽  
Selection Of

AbstractThis report details current seasonal influenza circulation patterns as of Sep 2017 and makes projections up to Sep 2018 to coincide with selection of the 2018 Southern Hemisphere vaccine strain. This is not meant as a comprehensive report, but is instead intended as particular observations that we’ve made that may be of relevance. Please also note that observed patterns reflect the GISAID database and may not be entirely representative of underlying dynamics. All analyses are based on the nextflu pipeline [1] with continual updates posted to nextflu.org.A/H3N2H3N2 continues to diversify with many coexisting clades, all of which carry several amino acid mutations at previously characterized epitope sites. The majority of viruses fall into the 3c2.a clade which has been dominating globally for >3 years, but 3c3.a viruses continue to persist. The common ancestor of circulating H3N2 viruses is now more than 5 years old, which is rare for H3N2. Despite extensive genetic diversity, serological assays suggest limited, but non-zero, antigenic evolution. We expect multiple competing clades within 3c2.a to persist into the future with no clear immediate winner.A/H1N1pdmA clade comprising mutations S74R and I295V has recently risen to >60% global frequency. Although it shows no antigenic distinction by ferret HI data, the rapidity of its rise suggests a selective origin.B/VicA clade with a two amino acid deletion 162-/163-has altered serological properties and is increasing in frequency, albeit slowly. Two other clades (carrying mutations K209N and V87A/I175V) have increased in frequency moderately.B/YamA clade comprising M251V within clade 3 viruses continues to dominate. The is little genetic differentiation within this clade and no evidence of antigenic evolution.

Recombinant Variants of Tissue-Type Plasminogen Activator Containing Amino Acid Substitutions in the Finger Domain

1992 ◽  
Vol 68 (06) ◽  
pp. 672-677 ◽  
Author(s):  
Hitoshi Yahara ◽  
Keiji Matsumoto ◽  
Hiroyuki Maruyama ◽  
Tetsuya Nagaoka ◽  
Yasuhiro Ikenaka ◽  
...  
Keyword(s):  
Amino Acid ◽  
Plasminogen Activator ◽  
Half Life ◽  
Tissue Type ◽  
Clot Lysis ◽  
Amino Acid Substitutions ◽  
Wild Type ◽  
Plasma Clot ◽  
Tissue Type Plasminogen Activator ◽  
Type Plasminogen Activator

SummaryTissue-type plasminogen activator (t-PA) is a fibrin-specific agent which has been used to treat acute myocardial infarction. In an attempt to clarify the determinants for its rapid clearance in vivo and high affinity for fibrin clots, we produced five variants containing amino acid substitutions in the finger domain, at amino acid residues 7–9, 10–14, 15–19, 28–33, and 37–42. All the variants had a prolonged half-life and a decreased affinity for fibrin of various degrees. The 37–42 variant demonstrated about a 6-fold longer half-life with a lower affinity for fibrin. Human plasma clot lysis assay estimated the fibrinolytic activity of the 37–42 variant to be 1.4-fold less effective than that of the wild-type rt-PA. In a rabbit jugular vein clot lysis model, doses of 1.0 and 0.15 mg/kg were required for about 70% lysis in the wild-type and 37–42 variant, respectively. Fibrinogen was degraded only when the wild-type rt-PA was administered at a dose of 1.0 mg/kg. These findings suggest that the 37–42 variant can be employed at a lower dosage and that it is a more fibrin-specific thrombolytic agent than the wild-type rt-PA.

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