Analysis of the evolution of granule associated serine proteases of immune defence (GASPIDs) suggests a revised nomenclature

2014 ◽  
Vol 395 (10) ◽  
pp. 1253-1262 ◽  
Author(s):  
Jamshaid Ahmad ◽  
Phillip Ian Bird ◽  
Dion Kaiserman
Keyword(s):  
Serine Proteases ◽  
Cartilaginous Fish ◽  
Evolutionary Analysis ◽  
Immune Defence ◽  
Evolutionary Path ◽  
Functional Roles ◽  
Single Precursor ◽  
Vertebrate Immune System ◽  
Mutation Analyses

Abstract GASPIDs (granule associated serine protease of immune defence) are a family of serine proteases intimately involved with the function of the vertebrate immune system. With the availability of a large and growing set of assembled genomes, we undertook an evolutionary analysis to plot the development of this protein family from a single precursor to the modern mammalian cohort of 12 genes, in an attempt to define and systematically classify subgroups or clades within this family, which are implied by the conventional gene designations. We identified a primordial GASPID gene as either GzmA or GzmK in cartilaginous fish and reconstructed an evolutionary path through to humans. Apart from historic value, the current sub-designations (granzymes, mast cell proteases and neutrophil serine proteases) serve no useful purpose and are increasingly misleading. We therefore used our phylogenetic and point mutation analyses to separate GASPIDs into three clades. These could form the basis of a simple nomenclature that allows effective classification of GASPIDs without implying functional roles.

Classification of hepatitis C virus into major types and subtypes based on molecular evolutionary analysis

1995 ◽  
Vol 36 (2-3) ◽  
pp. 201-214 ◽  
Author(s):  
Ken-ichi Ohba ◽  
Masashi Mizokami ◽  
Tomoyoshi Ohno ◽  
Kaoru Suzuki ◽  
Etsuro Orito ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Evolutionary Analysis ◽  
Molecular Evolutionary Analysis

scholarly journals The testis-specific serine proteases PRSS44, PRSS46, and PRSS54 are dispensable for male mouse fertility†

2019 ◽  
Author(s):  
Richard J Holcomb ◽  
Seiya Oura ◽  
Kaori Nozawa ◽  
Katarzyna Kent ◽  
Zhifeng Yu ◽  
...  
Keyword(s):  
Serine Proteases ◽  
Sperm Morphology ◽  
Homozygous Deletion ◽  
Developmental Expression ◽  
Sperm Function ◽  
Deletion Mutants ◽  
Es Cell ◽  
Functional Roles ◽  
Functional Genetics ◽  
The Individual

Abstract High-throughput transcriptomics and proteomics approaches have recently identified a large number of germ cell–specific genes with many that remain to be studied through functional genetics approaches. Serine proteases (PRSS) constitute nearly one-third of all proteases, and, in our bioinformatics screens, we identified many that are testis specific. In this study, we chose to focus on Prss44, Prss46, and Prss54, which we confirmed as testis specific in mouse and human. Based on the analysis of developmental expression in the mouse, expression of all four genes is restricted to the late stage of spermatogenesis concomitant with a potential functional role in spermiogenesis, spermiation, or sperm function. To best understand the male reproductive requirement and functional roles of these serine proteases, each gene was individually ablated by CRISPR/Cas9-mediated ES cell or zygote approach. Homozygous deletion mutants for each gene were obtained and analyzed for phenotypic changes. Analyses of testis weights, testis and epididymis histology, sperm morphology, and fertility revealed no significant differences in Prss44, Prss46, and Prss54 knockout mice in comparison to controls. Our results thereby demonstrate that these genes are not required for normal fertility in mice, although do not preclude the possibility that these genes may function in a redundant manner. Elucidating the individual functional requirement or lack thereof of these novel genes is necessary to build a better understanding of the factors underlying spermatogenesis and sperm maturation, which has implications in understanding the etiology of male infertility and the development of male contraceptives.

scholarly journals On the diversity of F420-dependent oxidoreductases: a sequence- and structure-based classification

2020 ◽  
Author(s):  
María Laura Mascotti ◽  
Maximiliano Juri Ayub ◽  
Marco W. Fraaije
Keyword(s):  
Evolutionary Analysis ◽  
Structural Homology ◽  
Structural Variability ◽  
Rossmann Fold ◽  
Tim Barrel

AbstractThe F420 deazaflavin cofactor is an intriguing molecule as it structurally resembles the canonical flavin cofactor, although biochemically behaves as a nicotinamide cofactor. Since its discovery, numerous enzymes relying on it have been described. The known deazaflavoproteins are taxonomically restricted to Archaea and Bacteria. The biochemistry of the deazaflavoenzymes is diverse and they exhibit some degree of structural variability as well. In this study a thorough sequence and structural homology evolutionary analysis was performed in order to generate an overarching classification of all known F420-dependent oxidoreductases. Five different superfamilies are described: Superfamily I, TIM-barrel F420-dependent enzymes; Superfamily II, Rossmann fold F420-dependent enzymes; Superfamily III, β-roll F420-dependent enzymes; Superfamily IV, SH3 barrel F420-dependent enzymes and Superfamily V, 3 layer ββα sandwich F420-dependent enzymes. This classification aims to be the framework for the identification, the description and the understanding the biochemistry of novel deazaflavoenzymes.

scholarly journals Framework Phylogeny, Evolution and Complex Diversification of Chinese Oaks

Plants ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 1024
Author(s):  
Jia Yang ◽  
Yu-Fan Guo ◽  
Xiao-Dan Chen ◽  
Xiao Zhang ◽  
Miao-Miao Ju ◽  
...  
Keyword(s):  
Sequence Data ◽  
Late Eocene ◽  
Tectonic Activity ◽  
Evolutionary Analysis ◽  
Species Radiation ◽  
Species Evolution ◽  
Phylogenetic Framework ◽  
Nuclear Loci ◽  
Lineage Diversification

Oaks (Quercus L.) are ideal models to assess patterns of plant diversity. We integrated the sequence data of five chloroplast and two nuclear loci from 50 Chinese oaks to explore the phylogenetic framework, evolution and diversification patterns of the Chinese oak’s lineage. The framework phylogeny strongly supports two subgenera Quercus and Cerris comprising four infrageneric sections Quercus, Cerris, Ilex and Cyclobalanopsis for the Chinese oaks. An evolutionary analysis suggests that the two subgenera probably split during the mid-Eocene, followed by intergroup divergence within the subgenus Cerris around the late Eocene. The initial diversification of sections in the subgenus Cerris was dated between the mid-Oligocene and the Oligocene–Miocene boundary, while a rapid species radiation in section Quercus started in the late Miocene. Diversification simulations indicate a potential evolutionary shift on section Quercus, while several phenotypic shifts likely occur among all sections. We found significant negative correlations between rates of the lineage diversification and phenotypic turnover, suggesting a complex interaction between the species evolution and morphological divergence in Chinese oaks. Our infrageneric phylogeny of Chinese oaks accords with the recently proposed classification of the genus Quercus. The results point to tectonic activity and climatic change during the Tertiary as possible drivers of evolution and diversification in the Chinese oak’s lineage.

scholarly journals Recent Molecular Evolution of Human Metapneumovirus (HMPV): Subdivision of HMPV A2b Strains

2020 ◽  
Vol 8 (9) ◽  
pp. 1280
Author(s):  
Naganori Nao ◽  
Miwako Saikusa ◽  
Ko Sato ◽  
Tsuyoshi Sekizuka ◽  
Shuzo Usuku ◽  
...  
Keyword(s):  
Respiratory Infections ◽  
Epidemiological Studies ◽  
Human Metapneumovirus ◽  
Evolutionary Relationships ◽  
Acute Respiratory Infections ◽  
Evolutionary Analysis ◽  
The Novel ◽  
Genome Wide ◽  
A Genome

Human metapneumovirus (HMPV) is a major etiological agent of acute respiratory infections in humans. HMPV has been circulating worldwide for more than six decades and is currently divided into five agreed-upon subtypes: A1, A2a, A2b, B1, and B2. Recently, the novel HMPV subtypes A2c, A2b1, and A2b2 have been proposed. However, the phylogenetic and evolutionary relationships between these recently proposed HMPV subtypes are unclear. Here, we report a genome-wide phylogenetic and evolutionary analysis of 161 HMPV strains, including unique HMPV subtype A2b strains with a 180- or 111-nucleotide duplication in the G gene (nt-dup). Our data demonstrate that the HMPV A2b subtype contains two distinct subtypes, A2b1 and A2b2, and that the HMPV subtypes A2c and A2b2 may be different names for the same subtype. HMPV A2b strains with a nt-dup also belong to subtype A2b2. Molecular evolutionary analyses indicate that subtypes A2b1 and A2b2 diverged from subtype A2b around a decade after the subtype A2 was divided into the subtypes A2a and A2b. These data support the A2b1 and A2b2 subtypes proposed in 2012 and are essential for the unified classification of HMPV subtype A2 strains, which is important for future HMPV surveillance and epidemiological studies.

scholarly journals Evolutionary Analysis and Classification of OATs, OCTs, OCTNs, and Other SLC22 Transporters: Structure-Function Implications and Analysis of Sequence Motifs

PLoS ONE ◽  
2015 ◽  
Vol 10 (11) ◽  
pp. e0140569 ◽  
Author(s):  
Christopher Zhu ◽  
Kabir B. Nigam ◽  
Rishabh C. Date ◽  
Kevin T. Bush ◽  
Stevan A. Springer ◽  
...  
Keyword(s):  
Structure Function ◽  
Evolutionary Analysis ◽  
Sequence Motifs

Molecular evolution of serine protease and its inhibitor with special reference to domain evolution

1994 ◽  
Vol 344 (1310) ◽  
pp. 411-415 ◽  
Keyword(s):  
Special Reference ◽  
Serine Protease ◽  
Serine Proteases ◽  
Phylogenetic Trees ◽  
Evolutionary Process ◽  
Life Forms ◽  
Functional Domains ◽  
Functional Domain ◽  
Evolutionary Analysis ◽  
Domain Evolution

The evolution of serine protease and its inhibitor are discussed with special reference to domain evolution. It is now known that most proteins are composed of more than one functional domain. Because serine proteases such as urokinase and plasminogen are made of various functional domains, these proteins are typical examples of the so-called mosaic proteins. When Kringle domains in serine proteases and a Kunitz-type protease inhibitor domain in the amyloid B precursor protein in Alzheimer’s disease patients were examined by the molecular evolutionary analysis, the phylogenetic trees constructed showed that these functional domains had undergone dynamic changes in the evolutionary process. In particular, these domains are evolutionarily movable. Thus, it is concluded that various functional domains evolved independently of each other and that they have been shuffled to create the existent mosaic proteins. This conclusion leads us to the reasonable speculation that those functional domains must have been minigenes possibly at the time of primordial life or the origin of life. We call these minigenes ‘ancestral minigenes’. Every effort should be made to answer the question about the minimum set of ancestral minigenes that must have existed and must have been needed for maintaining life forms. The DNA sequence database is useful for making attempts to answer such difficult but significant questions.

scholarly journals Evolutionary analyses of the gasdermin family suggest conserved roles in infection response despite loss of pore-forming functionality

BMC Biology ◽  
2022 ◽  
Vol 20 (1) ◽  
Author(s):  
Diego Angosto-Bazarra ◽  
Cristina Alarcón-Vila ◽  
Laura Hurtado-Navarro ◽  
María C. Baños ◽  
Jack Rivers-Auty ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Family Members ◽  
Cartilaginous Fish ◽  
Limited Information ◽  
Functional Roles ◽  
Ancestral Lineage ◽  
Wide Range ◽  
History Of ◽  
Infection Response ◽  
Pore Forming Proteins

Abstract Background Gasdermins are ancient (>500million-years-ago) proteins, constituting a family of pore-forming proteins that allow the release of intracellular content including proinflammatory cytokines. Despite their importance in the immune response, and although gasdermin and gasdermin-like genes have been identified across a wide range of animal and non-animal species, there is limited information about the evolutionary history of the gasdermin family, and their functional roles after infection. In this study, we assess the lytic functions of different gasdermins across Metazoa species, and use a mouse model of sepsis to evaluate the expression of the different gasdermins during infection. Results We show that the majority of gasdermin family members from distantly related animal clades are pore-forming, in line with the function of the ancestral proto-gasdermin and gasdermin-like proteins of Bacteria. We demonstrate the first expansion of this family occurred through a duplication of the ancestral gasdermin gene which formed gasdermin E and pejvakin prior to the divergence of cartilaginous fish and bony fish ~475 mya. We show that pejvakin from cartilaginous fish and mammals lost the pore-forming functionality and thus its role in cell lysis. We describe that the pore-forming gasdermin A formed ~320 mya as a duplication of gasdermin E prior to the divergence of the Sauropsida clade (the ancestral lineage of reptiles, turtles, and birds) and the Synapsid clade (the ancestral lineage of mammals). We then demonstrate that the gasdermin A gene duplicated to form the rest of the gasdermin family including gasdermins B, C, and D: pore-forming proteins that present a high variation of the exons in the linker sequence, which in turn allows for diverse activation pathways. Finally, we describe expression of murine gasdermin family members in different tissues in a mouse sepsis model, indicating function during infection response. Conclusions In this study we explored the evolutionary history of the gasdermin proteins in animals and demonstrated that the pore-formation functionality has been conserved from the ancient proto-gasdermin protein. We also showed that one gasdermin family member, pejvakin, lost its pore-forming functionality, but that all gasdermin family members, including pejvakin, likely retained a role in inflammation and the physiological response to infection.

scholarly journals Using Data-Compressors for Classification Hunting Behavioral Sequences in Rodents as “Ethological Texts”

Mathematics ◽  
2020 ◽  
Vol 8 (4) ◽  
pp. 579
Author(s):  
Jan Levenets ◽  
Anna Novikovskaya ◽  
Sofia Panteleeva ◽  
Zhanna Reznikova ◽  
Boris Ryabko
Keyword(s):  
Small Mammals ◽  
Structural Characteristics ◽  
Pairwise Comparisons ◽  
Evolutionary Analysis ◽  
Hunting Behavior ◽  
Homogeneity Testing ◽  
Association Coefficients ◽  
Behavioral Sequences ◽  
Using Data

One of the main problems in comparative studying animal behavior is searching for an adequate mathematical method for evaluating the similarities and differences between behavioral patterns. This study aims to propose a new tool to evaluate ethological differences between species. We developed the new compression-based method for the homogeneity testing and classification to investigate hunting behavior of small mammals. A distinction of this approach is that it belongs to the framework of mathematical statistics and allows one to compare the structural characteristics of any texts in pairwise comparisons. To validate a new method, we compared the hunting behaviors of different species of small mammals as ethological “texts.” To do this, we coded behavioral elements with different letters. We then tested the hypothesis whether the behavioral sequences of different species as “texts” are generated either by a single source or by different ones. Based on association coefficients obtained from pairwise comparisons, we built a new classification of types of hunting behaviors, which brought a unique insight into how particular elements of hunting behavior in rodents changed and evolved. We suggest the compression-based method for homogeneity testing as a relevant tool for behavioral and evolutionary analysis.

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