scholarly journals Evolutionary Analysis of Functional Divergence among Chemokine Receptors, Decoy Receptors, and Viral Receptors

2012 ◽  
Vol 3 ◽  
Author(s):  
Hiromi Daiyasu ◽  
Wataru Nemoto ◽  
Hiroyuki Toh
Keyword(s):  
Chemokine Receptors ◽  
Functional Divergence ◽  
Evolutionary Analysis ◽  
Decoy Receptors ◽  
Viral Receptors

P450ome of the white rot fungus Phanerochaete chrysosporium: structure, evolution and regulation of expression of genomic P450 clusters

2006 ◽  
Vol 34 (6) ◽  
pp. 1165-1169 ◽  
Author(s):  
J.S. Yadav ◽  
H. Doddapaneni ◽  
V. Subramanian
Keyword(s):  
Phanerochaete Chrysosporium ◽  
Functional Divergence ◽  
Carbon Sources ◽  
White Rot ◽  
White Rot Fungus ◽  
Structure Evolution ◽  
Gene Clustering ◽  
Evolutionary Analysis ◽  
Regulation Of Expression ◽  
Genome Wide

The model white rot fungus Phanerochaete chrysosporium has the extraordinary ability to degrade (to CO2) lignin and detoxify a variety of chemical pollutants. Whole genome sequencing of this fungus has revealed the presence of the largest P450ome in fungi comprising approx. 150 P450 genes, most of which have unknown function. On the basis of our genome-wide structural and evolutionary analysis, these P450 genes could be classified into 12 families and 23 subfamilies and under 11 fungal P450 clans. The analysis further revealed an extensive gene clustering with a total of 16 P450 clusters constituted of up to 11 members per cluster. In particular, evidence and role of gene duplications and horizontal gene transfer in the evolution of these P450 clusters have been discussed using two of the P450 families [CYP63 and CYP505 (where CYP is cytochrome P450)] as examples. In addition, the observed differential transcriptional induction of the clustered members of the CYP63 gene family, in response to different xenobiotic chemicals and carbon sources, indicated functional divergence within the P450 clusters, of this basidiomycete fungus.

Evolutionary Analysis for the Functional Divergence of the Spo0A Protein: The Key Sporulation Control Element

2009 ◽  
Vol 9 (4) ◽  
pp. 149-162 ◽  
Author(s):  
Andrés Julián Gutiérrez Escobar ◽  
Dolly Montoya Casta�o
Keyword(s):  
Functional Divergence ◽  
Control Element ◽  
Evolutionary Analysis

scholarly journals Adaptation and Constraint in the Atypical Chemokine Receptor Family in Mammals

2018 ◽  
Vol 2018 ◽  
pp. 1-9 ◽  
Author(s):  
Li Pan ◽  
Jianliang Lv ◽  
Zhongwang Zhang ◽  
Yongguang Zhang
Keyword(s):  
Ligand Binding ◽  
Chemokine Receptors ◽  
Homo Sapiens ◽  
Mammalian Species ◽  
Evolutionary Analysis ◽  
Amino Acid Residues ◽  
Mammal Species ◽  
And Function ◽  
G Protein Coupled ◽  
Receptor Family

Atypical chemokine receptors (ACKRs) are a subclass of G protein-coupled receptors characterized by promiscuity of ligand binding and an obvious inability to signal after ligand binding. Although some discoveries regarding this family in Homo sapiens and other species have been reported in some studies, the evolution and function of multiple ACKR in mammals have not yet been clearly understood. We performed an evolutionary analysis of ACKR genes (ACKR1, ACKR2, ACKR3, and ACKR4) in mammals. Ninety-two full-length ACKR genes from 27 mammal species were retrieved from the Genbank and Ensemble databases. Phylogenetic analysis showed that there were four well-conserved subfamilies in mammals. Synteny analysis revealed that ACKR genes formed conserved linkage groups with their adjacent genes across mammalian species, facilitating the identification of ACKRs in as yet unannotated genome datasets. Analysis of the site-specific profiles established by posterior probability revealed the positive-selection sites to be distributed mainly in the ligand binding region of ACKR1. This study highlights the molecular evolution of the ACKR gene family in mammals and identifies the critical amino acid residues likely to be relevant to ligand binding. Further experimental verification of these findings may provide valuable information regarding the ACKR’s biochemical and physiological functions.

Phylogenetics and evolution of Trx SET genes in fully sequenced land plants

Genome ◽  
2012 ◽  
Vol 55 (4) ◽  
pp. 269-280 ◽  
Author(s):  
Xinyu Zhu ◽  
Caoyi Chen ◽  
Baohua Wang
Keyword(s):  
Gene Family ◽  
Physcomitrella Patens ◽  
Functional Divergence ◽  
Experimental Studies ◽  
Land Plants ◽  
Orthologous Group ◽  
Evolutionary Stage ◽  
Evolutionary Analysis ◽  
Genes Encoding ◽  
Gene Structures

Plant Trx SET proteins are involved in H3K4 methylation and play a key role in plant floral development. Genes encoding Trx SET proteins constitute a multigene family in which the copy number varies among plant species and functional divergence appears to have occurred repeatedly. To investigate the evolutionary history of the Trx SET gene family, we made a comprehensive evolutionary analysis on this gene family from 13 major representatives of green plants. A novel clustering (here named as cpTrx clade), which included the III-1, III-2, and III-4 orthologous groups, previously resolved was identified. Our analysis showed that plant Trx proteins possessed a variety of domain organizations and gene structures among paralogs. Additional domains such as PHD, PWWP, and FYR were early integrated into primordial SET–PostSET domain organization of cpTrx clade. We suggested that the PostSET domain was lost in some members of III-4 orthologous group during the evolution of land plants. At least four classes of gene structures had been formed at the early evolutionary stage of land plants. Three intronless orphan Trx SET genes from the Physcomitrella patens (moss) were identified, and supposedly, their parental genes have been eliminated from the genome. The structural differences among evolutionary groups of plant Trx SET genes with different functions were described, contributing to the design of further experimental studies.

scholarly journals Delineation of the Crucial Evolutionary Amino Acid Sites in Trehalose-6-Phosphate Synthase From Higher Plants

2020 ◽  
Vol 16 ◽  
pp. 117693432091014
Author(s):  
Rong Wang ◽  
Congfen He ◽  
Kun Dong ◽  
Xin Zhao ◽  
Yaxuan Li ◽  
...  
Keyword(s):  
Amino Acid ◽  
Positive Selection ◽  
Higher Plants ◽  
Functional Divergence ◽  
Acid Sites ◽  
Evolutionary Analysis ◽  
Codon Substitution ◽  
Bioinformatics Tools ◽  
Amino Acid Properties ◽  
Phosphate Synthase

Trehalose-6-phosphate synthase (TPS) is a key enzyme in the biosynthesis of trehalose, with its direct product, trehalose-6-phosphate, playing important roles in regulating whole-plant carbohydrate allocation and utilization. Genes encoding TPS constitute a multigene family in which functional divergence appears to have occurred repeatedly. To identify the crucial evolutionary amino acid sites of TPS in higher plants, a series of bioinformatics tools were applied to investigate the phylogenetic relationships, functional divergence, positive selection, and co-evolution of TPS proteins. First, we identified 150 TPS genes from 13 higher plant species. Phylogenetic analysis placed these TPS proteins into 2 clades: clades A and B, of which clade B could be further divided into 4 subclades (B1-B4). This classification was supported by the intron-exon structures, with more introns present in clade A. Next, detection of the critical functionally divergent amino acid sites resulted in the isolation of a total of 286 sites reflecting nonredundant radical shifts in amino acid properties with a high posterior probability cutoff among subclades. In addition, positively selected sites were identified using a codon substitution model, from which 46 amino acid sites were isolated as exhibiting positive selection at a significant level. Moreover, 18 amino acid sites were highlighted both for functional divergence and positive selection; these may thus potentially represent crucial evolutionary sites in the TPS family. Further co-evolutionary analysis revealed 3 pairs of sites: 11S and 12H, 33S and 34N, and 109G and 110E as demonstrating co-evolution. Finally, the 18 crucial evolutionary amino acid sites were mapped in the 3-dimensional structure. A total of 77 sites harboring functionally and structurally important residues of TPS proteins were found by using the CLIPS-4D online tool; notably, no overlap was observed with the identified crucial evolutionary sites, providing positive evidence supporting their designation. A total of 18 sites were isolated as key amino acids by using multiple bioinformatics tools based on their concomitant functional divergence and positive selection. Almost all these key sites are located in 2 domains of this protein family where they exhibit no overlap with the structurally and functionally conserved sites. These results will provide an improved understanding of the complexity of the TPS gene family and of its function and evolution in higher plants. Moreover, this knowledge may facilitate the exploitation of these sites for protein engineering applications.

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