scholarly journals Molecular Evolution and Structural Features of IRAK Family Members

PLoS ONE ◽  
2012 ◽  
Vol 7 (11) ◽  
pp. e49771 ◽  
Author(s):  
Vijayakumar Gosu ◽  
Shaherin Basith ◽  
Prasannavenkatesh Durai ◽  
Sangdun Choi
Keyword(s):  
Molecular Evolution ◽  
Family Members ◽  
Structural Features

scholarly journals Beyond gene ontology (GO): using biocuration approach to improve the gene nomenclature and functional annotation of rice S-domain kinase subfamily

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11052
Author(s):  
Sushma Naithani ◽  
Daemon Dikeman ◽  
Priyanka Garg ◽  
Noor Al-Bader ◽  
Pankaj Jaiswal
Keyword(s):  
Gene Ontology ◽  
Abiotic Stress ◽  
Differential Expression ◽  
Functional Annotation ◽  
Expression Profiles ◽  
Abiotic Stress Tolerance ◽  
Family Members ◽  
Gene Families ◽  
Structural Features ◽  
Response Expression

The S-domain subfamily of receptor-like kinases (SDRLKs) in plants is poorly characterized. Most members of this subfamily are currently assigned gene function based on the S-locus Receptor Kinase from Brassica that acts as the female determinant of self-incompatibility (SI). However, Brassica like SI mechanisms does not exist in most plants. Thus, automated Gene Ontology (GO) pipelines are not sufficient for functional annotation of SDRLK subfamily members and lead to erroneous association with the GO biological process of SI. Here, we show that manual bio-curation can help to correct and improve the gene annotations and association with relevant biological processes. Using publicly available genomic and transcriptome datasets, we conducted a detailed analysis of the expansion of the rice (Oryza sativa) SDRLK subfamily, the structure of individual genes and proteins, and their expression.The 144-member SDRLK family in rice consists of 82 receptor-like kinases (RLKs) (67 full-length, 15 truncated),12 receptor-like proteins, 14 SD kinases, 26 kinase-like and 10 GnK2 domain-containing kinases and RLKs. Except for nine genes, all other SDRLK family members are transcribed in rice, but they vary in their tissue-specific and stress-response expression profiles. Furthermore, 98 genes show differential expression under biotic stress and 98 genes show differential expression under abiotic stress conditions, but share 81 genes in common.Our analysis led to the identification of candidate genes likely to play important roles in plant development, pathogen resistance, and abiotic stress tolerance. We propose a nomenclature for 144 SDRLK gene family members based on gene/protein conserved structural features, gene expression profiles, and literature review. Our biocuration approach, rooted in the principles of findability, accessibility, interoperability and reusability, sets forth an example of how manual annotation of large-gene families can fill in the knowledge gap that exists due to the implementation of automated GO projections, thereby helping to improve the quality and contents of public databases.

scholarly journals The concept of family in Hausa

2021 ◽  
Vol 33 ◽  
pp. 49
Author(s):  
Nina Pawlak
Keyword(s):  
Popular Culture ◽  
Family Members ◽  
Structural Features ◽  
Religious Discourse ◽  
Traditional Model ◽  
African Language ◽  
European Context ◽  
Specific Concept

The paper attempts to define the notion of family in Hausa, an African language which is very distant, both geographically and culturally, from the European context. With reference to the universal features of the notion family, the culture-specific concept of family is discussed, focusing on traditional model of the Hausa family and relations between family members. The main features of the concept are identified through the analysis of the lexicon, phraseology, and structural features. The discussion includes some specific profiles of the concept of family in Hausa, manifested in religious discourse and in the language of popular culture.

scholarly journals Molecular Evolution of APP family proteins: Rapid Evolution of the Mammalian APLP1 as a Synaptic Adhesion Molecule

2021 ◽  
Author(s):  
Wataru Onodera ◽  
Toru Asahi ◽  
Naoya Sawamura
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Evolution ◽  
Rapid Evolution ◽  
Family Members ◽  
Docking Simulation ◽  
Brain Evolution ◽  
Mammalian Brain ◽  
Heparin Binding ◽  
Family Based ◽  
App Gene

Abstract Amyloid precursor protein (APP) family members are involved in essential neuronal activities, and dysfunction of APP family members leads to neurodegenerative diseases such as Alzheimer’s disease. Among the APP gene family members, amyloid precursor-like protein 1 (APLP1) is selectively expressed in neurons and has specialized functions during synaptogenesis. Although a potential role for APLP1 in neuronal evolution has been indicated, its precise evolutionary and functional contributions are unknown. This study shows the molecular evolution of the vertebrate APP family based on phylogenetic analysis, while contrasting the evolutionary differences within the APP family. Phylogenetic analysis showed 15 times higher substitution rate that is driven by positive selection at the stem branch of the mammalian APLP1, resulting in dissimilar protein sequences compared to APP/APLP2. Docking simulation identified one positively selected site in APLP1 that alters the heparin-binding site, which could affect its function, and dimerization rate. Furthermore, the evolutionary rate covariation between the mammalian APP family and synaptic adhesion molecules (SAMs) was confirmed, indicating that only APLP1 has evolved to gain synaptic adhesion property. Overall, our results suggest that the enhanced synaptogenesis property of APLP1 as one of the SAMs may have played a role in mammalian brain evolution.

scholarly journals Molecular evolution of NASP and conserved histone H3/H4 transport pathway

2021 ◽  
Author(s):  
Syed Nabeel-Shah ◽  
Kanwal Ashraf ◽  
Ronald E Pearlman ◽  
Jeffrey Fillingham
Keyword(s):  
Molecular Evolution ◽  
Functional Diversity ◽  
Protein Level ◽  
Family Members ◽  
Gc Content ◽  
Purifying Selection ◽  
Crown Group ◽  
Transport Pathway ◽  
Critical Function ◽  
Transport Pathways

Background: NASP is an essential protein in mammals that functions in histone transport pathways and maintenance of a soluble reservoir of histones H3/H4. NASP has been studied exclusively in Opisthokonta lineages where some functional diversity has been reported. In humans, growing evidence implicates NASP miss-regulation in the development of a variety of cancers. Although a comprehensive phylogenetic analysis is lacking, NASP-family proteins that possess four TPR motifs are thought to be widely distributed across eukaryotes. Results: We characterize the molecular evolution of NASP by systematically identifying putative NASP orthologs across diverse eukaryotic lineages ranging from excavata to those of the crown group. We detect extensive silent divergence at the nucleotide level suggesting the presence of strong purifying selection acting at the protein level. We also observe a selection bias for high frequencies of acidic residues which we hypothesize is a consequence of their critical function(s), further indicating the role of functional constraints operating on NASP evolution. Our data indicate that TPR1 and TPR4 constitute the most rapidly evolving functional units of NASP and may account for the functional diversity observed among well characterized family members. We also show that NASP paralogs in ray-finned fish have different genomic environments with clear differences in their GC content and have undergone significant changes at the protein level suggesting functional diversification. Conclusion: We draw four main conclusions from this study. First, wide distribution of NASP throughout eukaryotes suggests that it was likely present in the last eukaryotic common ancestor (LECA) possibly as an important innovation in the transport of H3/H4. Second, strong purifying selection operating at the protein level has influenced the nucleotide composition of NASP genes. Further, we show that selection has acted to maintain a high frequency of functionally relevant acidic amino acids in the region that interrupts TPR2. Third, functional diversity reported among several well characterized NASP family members can be explained in terms of quickly evolving TPR1 and TPR4 motifs. Fourth, NASP fish specific paralogs have significantly diverged at the protein level with NASP2 acquiring a NNR domain.

scholarly journals Nanobody generation and structural characterization of Plasmodium falciparum 6-cysteine protein Pf12p

2021 ◽  
Vol 478 (3) ◽  
pp. 579-595
Author(s):  
Melanie H. Dietrich ◽  
Li-Jin Chan ◽  
Amy Adair ◽  
Sravya Keremane ◽  
Phillip Pymm ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Life Cycle ◽  
Vaccine Development ◽  
Structural Information ◽  
Family Members ◽  
Structural Features ◽  
Protein Family ◽  
Parasite Life Cycle ◽  
D2 Domain

Surface-associated proteins play critical roles in the Plasmodium parasite life cycle and are major targets for vaccine development. The 6-cysteine (6-cys) protein family is expressed in a stage-specific manner throughout Plasmodium falciparum life cycle and characterized by the presence of 6-cys domains, which are β-sandwich domains with conserved sets of disulfide bonds. Although several 6-cys family members have been implicated to play a role in sexual stages, mosquito transmission, evasion of the host immune response and host cell invasion, the precise function of many family members is still unknown and structural information is only available for four 6-cys proteins. Here, we present to the best of our knowledge, the first crystal structure of the 6-cys protein Pf12p determined at 2.8 Å resolution. The monomeric molecule folds into two domains, D1 and D2, both of which adopt the canonical 6-cys domain fold. Although the structural fold is similar to that of Pf12, its paralog in P. falciparum, we show that Pf12p does not complex with Pf41, which is a known interaction partner of Pf12. We generated 10 distinct Pf12p-specific nanobodies which map into two separate epitope groups; one group which binds within the D2 domain, while several members of the second group bind at the interface of the D1 and D2 domain of Pf12p. Characterization of the structural features of the 6-cys family and their associated nanobodies provide a framework for generating new tools to study the diverse functions of the 6-cys protein family in the Plasmodium life cycle.

scholarly journals The crystal structure of phosphorylated MAPK13 reveals common structural features and differences in p38 MAPK family activation

2015 ◽  
Vol 71 (4) ◽  
pp. 790-799 ◽  
Author(s):  
Zeynep Yurtsever ◽  
Suzanne M. Scheaffer ◽  
Arthur G. Romero ◽  
Michael J. Holtzman ◽  
Tom J. Brett
Keyword(s):  
Family Member ◽  
P38 Mapk ◽  
Map Kinases ◽  
Sequence Similarity ◽  
Family Members ◽  
Structural Features ◽  
P38 Map Kinase ◽  
Structural Basis ◽  
Structure Based Drug Design ◽  
Specific Inhibitors

The p38 MAP kinases (p38 MAPKs) represent an important family centrally involved in mediating extracellular signaling. Recent studies indicate that family members such as MAPK13 (p38δ) display a selective cellular and tissue expression and are therefore involved in specific diseases. Detailed structural studies of all p38 MAPK family members are crucial for the design of specific inhibitors. In order to facilitate such ventures, the structure of MAPK13 was determined in both the inactive (unphosphorylated; MAPK13) and active (dual phosphorylated; MAPK13/pTpY) forms. Here, the first preparation, crystallization and structure determination of MAPK13/pTpY are presented and the structure is compared with the previously reported structure of MAPK13 in order to facilitate studies for structure-based drug design. A comprehensive analysis of inactiveversusactive structures for the p38 MAPK family is also presented. It is found that MAPK13 undergoes a larger interlobe configurational rearrangement upon activation compared with MAPK14. Surprisingly, the analysis of activated p38 MAPK structures (MAP12/pTpY, MAPK13/pTpY and MAPK14/pTpY) reveals that, despite a high degree of sequence similarity, different side chains are used to coordinate the phosphorylated residues. There are also differences in the rearrangement of the hinge region that occur in MAPK14 compared with MAPK13 which would affect inhibitor binding. A thorough examination of all of the active (phosphorylated) and inactive (unphosphorylated) p38 MAPK family member structures was performed to reveal a common structural basis of activation for the p38 MAP kinase family and to identify structural differences that may be exploited for developing family member-specific inhibitors.

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