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.

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 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

scholarly journals Structural and functional characterization of buffalo oviduct-specific glycoprotein (OVGP1) expressed during estrous cycle

2019 ◽  
Vol 39 (12) ◽  
Author(s):  
Suman Choudhary ◽  
Jagadeesh Janjanam ◽  
Sudarshan Kumar ◽  
Jai K. Kaushik ◽  
Ashok K. Mohanty
Keyword(s):  
Estrous Cycle ◽  
Structural Model ◽  
Structural Characteristics ◽  
Functional Characterization ◽  
Carbohydrate Binding ◽  
Evolutionary Analysis ◽  
Binding Assays ◽  
Sugar Binding ◽  
Tim Barrel

Abstract Oviduct-specific glycoprotein (OVGP1) is a high molecular weight chitinase-like protein belonging to GH18 family. It is secreted by non-ciliated epithelial cells of oviduct during estrous cycle providing an essential milieu for fertilization and embryo development. The present study reports the characterization of buffalo OVGP1 through structural modeling, carbohydrate-binding properties and evolutionary analysis. Structural model displayed the typical fold of GH18 family members till the boundary of chitinase-like domain further consisting of a large (β/α)8 TIM barrel sub-domain and a small (α+β) sub-domain. Two critical catalytic residues were found substituted in the catalytic centre (Asp to Phe118, Glu to Leu120) compared with the active chitinase. The carbohydrate-binding groove in TIM barrel was lined with various conserved aromatic residues. Molecular docking with different sugars revealed the involvement of various residues in hydrogen-bonding and non-bonded contacts. Most of the substrate-binding residues were conserved except for a few replacements (Ser13, Lys48, Asp49, Pro50, Asp167, Glu199, Gln272 and Phe275) in comparison with other GH18 members. The residues Trp10, Trp79, Asn80, Gln272, Phe275 and Trp334 were involved in recognition of all six ligands. The α+β sub-domain participated in sugar-binding through Thr270, Gln272, Tyr242 and Phe275. The binding assays revealed significant sugar-binding with purified native and recombinant OVGP1. Phylogenetic analysis revealed that OVGP1 was closely related to AMCases followed by other CLPs and evolution of OVGP1 occurred through several gene duplications. This is the first study describing the structural characteristics of OVGP1 that will further help to understand its interaction with gametes to perform crucial reproductive functions.

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.

On the Nature of Nucleobase Stacking in RNA: A Comprehensive Survey of Its Structural Variability and a Systematic Classification of Associated Interactions

2021 ◽  
Vol 61 (3) ◽  
pp. 1470-1480
Author(s):  
Ayush Jhunjhunwala ◽  
Zakir Ali ◽  
Sohini Bhattacharya ◽  
Antarip Halder ◽  
Abhijit Mitra ◽  
...  
Keyword(s):  
Systematic Classification ◽  
Structural Variability ◽  
Comprehensive Survey

scholarly journals Transcriptome-Wide Identification, Evolutionary Analysis, and GA Stress Response of the GRAS Gene Family in Panax ginseng C. A. Meyer

Plants ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 190
Author(s):  
Nan Wang ◽  
Kangyu Wang ◽  
Shaokun Li ◽  
Yang Jiang ◽  
Li Li ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Stress Response ◽  
Panax Ginseng ◽  
Perennial Herb ◽  
Evolutionary Analysis ◽  
Physiological Processes ◽  
Variation Function ◽  
Plant Signal Transduction ◽  
Gras Gene

GRAS transcription factors are a kind of plant-specific transcription factor that have been found in a variety of plants. According to previous studies, GRAS proteins are widely involved in the physiological processes of plant signal transduction, stress, growth and development. The Jilin ginseng (Panax ginseng C.A. Meyer) is a heterogeneous tetraploid perennial herb of the Araliaceae family, ginseng genus. Important information regarding the GRAS transcription factors has not been reported in ginseng. In this study, 59 Panax ginseng GRAS (PgGRAS) genes were obtained from the Jilin ginseng transcriptome data and divided into 13 sub-families according to the classification of Arabidopsis thaliana. Through systematic evolution, structural variation, function and gene expression analysis, we further reveal GRAS’s potential function in plant growth processes and its stress response. The expression of PgGRAS genes responding to gibberellin acids (GAs) suggests that these genes could be activated after application concentration of GA. The qPCR analysis result shows that four PgGRAS genes belonging to the DELLA sub-family potentially have important roles in the GA stress response of ginseng hairy roots. This study provides not only a preliminary exploration of the potential functions of the GRAS genes in ginseng, but also valuable data for further exploration of the candidate PgGRAS genes of GA signaling in Jilin ginseng, especially their roles in ginseng hairy root development and GA stress response.

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.

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