scholarly journals Phenoloxidases in Plants—How Structural Diversity Enables Functional Specificity

2021 ◽  
Vol 12 ◽  
Author(s):  
Leonard Blaschek ◽  
Edouard Pesquet
Keyword(s):  
Protein Structure ◽  
Environmental Changes ◽  
Meta Analysis ◽  
Structural Diversity ◽  
Gene Families ◽  
Homologous Gene ◽  
Functional Roles ◽  
Link Functions ◽  
Primary And Secondary Metabolism ◽  
Evolutionary Trajectories

The metabolism of polyphenolic polymers is essential to the development and response to environmental changes of organisms from all kingdoms of life, but shows particular diversity in plants. In contrast to other biopolymers, whose polymerisation is catalysed by homologous gene families, polyphenolic metabolism depends on phenoloxidases, a group of heterogeneous oxidases that share little beyond the eponymous common substrate. In this review, we provide an overview of the differences and similarities between phenoloxidases in their protein structure, reaction mechanism, substrate specificity, and functional roles. Using the example of laccases (LACs), we also performed a meta-analysis of enzyme kinetics, a comprehensive phylogenetic analysis and machine-learning based protein structure modelling to link functions, evolution, and structures in this group of phenoloxidases. With these approaches, we generated a framework to explain the reported functional differences between paralogs, while also hinting at the likely diversity of yet undescribed LAC functions. Altogether, this review provides a basis to better understand the functional overlaps and specificities between and within the three major families of phenoloxidases, their evolutionary trajectories, and their importance for plant primary and secondary metabolism.

scholarly journals Meta-analysis of liver and heart transcriptomic data for functional annotation transfer in mammalian orthologs

2017 ◽  
Author(s):  
Pía Francesca Loren Reyes ◽  
Tom Michoel ◽  
Anagha Joshi ◽  
Guillaume Devailly
Keyword(s):  
Functional Annotation ◽  
Expression Profiles ◽  
Meta Analysis ◽  
Gene Families ◽  
Homologous Gene ◽  
Orthologous Genes ◽  
Transcriptomic Data ◽  
Genome Wide ◽  
Genome Wide Expression ◽  
Functional Orthologs

AbstractFunctional annotation transfer across multi-gene family orthologs can lead to functional misannotations. We hypothesised that co-expression network will help predict functional orthologs amongst complex homologous gene families. To explore the use of transcriptomic data available in public domain to identify functionally equivalent ones from all predicted orthologs, we collected genome wide expression data in mouse and rat liver from over 1500 experiments with varied treatments. We used a hyper-graph clustering method to identify clusters of orthologous genes co-expressed in both mouse and rat. We validated these clusters by analysing expression profiles in each species separately, and demonstrating a high overlap. We then focused on genes in 18 homology groups with one-to-many or many-to-many relationships between two species, to discriminate between functionally equivalent and non-equivalent orthologs. Finally, we further applied our method by collecting heart transcriptomic data (over 1400 experiments) in rat and mouse to validate the method in an independent tissue.

scholarly journals Expression of a gene duplication encoding conserved sperm tail proteins is translationally regulated in Drosophila melanogaster.

1993 ◽  
Vol 13 (3) ◽  
pp. 1708-1718 ◽  
Author(s):  
M Schäfer ◽  
D Börsch ◽  
A Hülster ◽  
U Schäfer
Keyword(s):  
Drosophila Melanogaster ◽  
Gene Family ◽  
Translational Control ◽  
Germ Line ◽  
Gene Families ◽  
Homologous Gene ◽  
Male Sterile ◽  
Sperm Tail ◽  
Repetitive Motif ◽  
Carboxy Terminal

We have analyzed a locus of Drosophila melanogaster located at 98C on chromosome 3, which contains two tandemly arranged genes, named Mst98Ca and Mst98Cb. They are two additional members of the Mst(3)CGP gene family by three criteria. (i) Both genes are exclusively transcribed in the male germ line. (ii) Both transcripts encode a protein with a high proportion of the repetitive motif Cys-Gly-Pro. (iii) Their expression is translationally controlled; while transcripts can be detected in diploid stages of spermatogenesis, association with polysomes can be shown only in haploid stages of sperm development. The genes differ markedly from the other members of the gene family in structure; they do not contain introns, they are of much larger size, and they have the Cys-Gly-Pro motifs clustered at the carboxy-terminal end of the encoded proteins. An antibody generated against the Mst98Ca protein recognizes both Mst98C proteins in D. melanogaster. In a male-sterile mutation in which spermiogenesis is blocked before individualization of sperm, both of these proteins are no longer synthesized. This finding provides proof of late translation for the Mst98C proteins and thereby independent proof of translational control of expression. Northern (RNA) and Western immunoblot analyses indicate the presence of homologous gene families in many other Drosophila species. The Mst98C proteins share sequence homology with proteins of the outer dense fibers in mammalian spermatozoa and can be localized to the sperm tail by immunofluorescence with an anti-Mst98Ca antibody.

Structural diversity of band 4.1 superfamily members

1994 ◽  
Vol 107 (7) ◽  
pp. 1921-1928 ◽  
Author(s):  
K. Takeuchi ◽  
A. Kawashima ◽  
A. Nagafuchi ◽  
S. Tsukita
Keyword(s):  
Plasma Membrane ◽  
Tyrosine Kinases ◽  
Plasma Membranes ◽  
Structural Diversity ◽  
Gene Families ◽  
Cdna Clones ◽  
New Members ◽  
F9 Cells ◽  
Novel Proteins ◽  
Cellular Events

Several proteins contain the domain homologous to the N-terminal half of band 4.1 protein, indicating the existence of a superfamily. The members of this ‘band 4.1’ superfamily are thought to play crucial roles in the regulation of cytoskeleton-plasma membrane interaction just beneath plasma membranes. We examined the structural diversity of this superfamily by means of the polymerase chain reaction using synthesized mixed primers. We thus identified many members of the band 4.1 superfamily that were expressed in mouse teratocarcinoma F9 cells and mouse brain tissue. In total, 15 cDNA clones were obtained; 8 were identical to the corresponding parts of cDNAs for the known members, while 7 appeared to encode novel proteins (NBL1-7: novel band 4.1-like proteins). Sequence analyses of these clones revealed that the band 4.1 superfamily can be subdivided into 5 gene families; band 4.1 protein, ERM (ezrin/radixin/moesin/merlin/NBL6/NBL7+ ++), talin, PTPH1 (PTPH1/PTPMEG/NBL1-3), and NBL4 (NBL4/NBL5) families. The NBL4 family was first identified here, and the full-length cDNA encoding NBL4 was cloned. The deduced amino acid sequence revealed a myristoylation site, as well as phosphorylation sites for A-kinase and tyrosine kinases in its N-terminal half, suggesting its involvement in the phosphorylation-dependent regulation of cellular events just beneath the plasma membrane. In this study, we describe the initial characterization of these new members and discuss the evolution of the band 4.1 superfamily.

scholarly journals The DNA methylation landscape of multiple myeloma shows extensive inter- and intrapatient heterogeneity that fuels transcriptomic variability

2020 ◽  
Author(s):  
Jennifer Derrien ◽  
Catherine Guérin-Charbonnel ◽  
Victor Gaborit ◽  
Loïc Campion ◽  
Magali Devic ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Multiple Myeloma ◽  
Environmental Changes ◽  
Cpg Island ◽  
Entropy Change ◽  
Tumor Evolution ◽  
Cancer Evolution ◽  
High Entropy ◽  
Evolutionary Trajectories ◽  
Poor Outcomes

AbstractBackgroundCancer evolution depends on epigenetic and genetic diversity. Historically, in multiple myeloma (MM), subclonal diversity and tumor evolution have been investigated mostly from a genetic perspective.ResultsHere, we combined the notions of epipolymorphism and epiallele switching to analyze DNA methylation heterogeneity in MM patients. We show that MM is characterized by the continuous accumulation of stochastic methylation at the promoters of development-related genes. High entropy change is associated with poor outcomes and depends predominantly on partially methylated domains (PMDs). These PMDs, which represent the major source of inter- and intrapatient DNA methylation heterogeneity in MM, are linked to other key epigenetic aberrations, such as CpG island (CGI)/transcription start site (TSS) hypermethylation and H3K27me3 redistribution as well as 3D organization alterations. In addition, transcriptome analysis revealed that intratumor methylation heterogeneity was associated with low-level expression and high variability.ConclusionWe propose that disordered methylation in MM is responsible for high epigenetic and transcriptomic instability allowing tumor cells to adapt to environmental changes by tapping into a pool of evolutionary trajectories.

scholarly journals GeneRax: A tool for species tree-aware maximum likelihood based gene family tree inference under gene duplication, transfer, and loss

2019 ◽  
Author(s):  
Benoit Morel ◽  
Alexey M. Kozlov ◽  
Alexandros Stamatakis ◽  
Gergely J. Szöllősi
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Trees ◽  
Large Scale ◽  
Simulated Data ◽  
Gene Families ◽  
Species Tree ◽  
Homologous Gene ◽  
Sequence Alignments ◽  
Full Likelihood ◽  
True Tree

AbstractInferring phylogenetic trees for individual homologous gene families is difficult because alignments are often too short, and thus contain insufficient signal, while substitution models inevitably fail to capture the complexity of the evolutionary processes. To overcome these challenges species tree-aware methods also leverage information from a putative species tree. However, only few methods are available that implement a full likelihood framework or account for horizontal gene transfers. Furthermore, these methods often require expensive data pre-processing (e.g., computing bootstrap trees), and rely on approximations and heuristics that limit the degree of tree space exploration. Here we present GeneRax, the first maximum likelihood species tree-aware phylogenetic inference software. It simultaneously accounts for substitutions at the sequence level as well as gene level events, such as duplication, transfer, and loss relying on established maximum likelihood optimization algorithms. GeneRax can infer rooted phylogenetic trees for multiple gene families, directly from the per-gene sequence alignments and a rooted, yet undated, species tree. We show that compared to competing tools, on simulated data GeneRax infers trees that are the closest to the true tree in 90% of the simulations in terms of relative Robinson-Foulds distance. On empirical datasets, GeneRax is the fastest among all tested methods when starting from aligned sequences, and it infers trees with the highest likelihood score, based on our model. GeneRax completed tree inferences and reconciliations for 1099 Cyanobacteria families in eight minutes on 512 CPU cores. Thus, its parallelization scheme enables large-scale analyses. GeneRax is available under GNU GPL at https://github.com/BenoitMorel/GeneRax.

scholarly journals Distinct evolutionary trajectories of V1R clades across mouse species

2020 ◽  
Author(s):  
Caitlin H Miller ◽  
Polly Campbell ◽  
Michael J Sheehan
Keyword(s):  
Positive Selection ◽  
House Mouse ◽  
Gene Family Evolution ◽  
Specific Gene ◽  
Receptor Subtypes ◽  
Gene Repertoire ◽  
Social Signals ◽  
Functional Roles ◽  
Wide Range ◽  
Evolutionary Trajectories

Abstract BACKGROUND: Many animals rely heavily on olfaction to navigate their environment. Among rodents, olfaction is crucial for a wide range of social behaviors. The vomeronasal olfactory system in particular plays an important role in mediating social communication, including the detection of pheromones and recognition signals. In this study we examine patterns of vomeronasal type-1 receptor (V1R) evolution in the house mouse and related species within the genus Mus . We report the extent of gene repertoire turnover and conservation among species and clades, as well as the prevalence of positive selection on gene sequences across the V1R tree. By exploring the evolution of these receptors, we provide insight into the functional roles of receptor subtypes as well as the dynamics of gene family evolution. RESULTS: We generated transcriptomes from the vomeronasal organs of 5 Mus species, and produced high quality V1R repertoires for each species. We find that V1R clades in the house mouse and relatives exhibit distinct evolutionary trajectories. We identify putative species-specific gene expansions, including a large clade D expansion in the house mouse. While gene gains are abundant, we detect very few gene losses. We describe a novel V1R clade and highlight candidate receptors for future study. We find evidence for distinct evolutionary processes across different clades, from largescale turnover to highly conserved repertoires. Patterns of positive selection are similarly variable, as some clades exhibit abundant positive selection while others display high gene sequence conservation. Based on clade-level evolutionary patterns, we identify receptor families that are strong candidates for detecting social signals and predator cues. Our results reveal clades with receptors detecting female reproductive status are among the most conserved across species, suggesting an important role in V1R chemosensation. CONCLUSION: Analysis of clade-level evolution is critical for understanding species’ chemosensory adaptations. This study provides clear evidence that V1R clades are characterized by distinct evolutionary trajectories. As receptor evolution is shaped by ligand identity, these results provide a framework for examining the functional roles of receptors.

scholarly journals A review of length-weight relationships of freshwater fishes in Malaysia

2018 ◽  
Vol 20 (1) ◽  
pp. 55-68 ◽  
Author(s):  
Amonodin Mohamad Radhi ◽  
Mohd-Fadzil Nurul Fazlinda ◽  
Mohammad Noor Azmai Amal ◽  
Hashim Rohasliney
Keyword(s):  
Freshwater Fish ◽  
Fish Species ◽  
Environmental Changes ◽  
Meta Analysis ◽  
Freshwater Fishes ◽  
Clarias Batrachus ◽  
Ecological Health ◽  
Allometric Growth ◽  
Freshwater Fish Species

Abstract This manuscript reviews the length-weight relationships (LWRs) of freshwater fishes in Malaysia. A total of 102 LWRs of fishes gathered from literature pertaining to 64 freshwater fish species were analysed. A meta-analysis from 13 previous reports showed that the b values was ranged from 2.19 (Clarias batrachus) to 4.106 (Barbodes binotatus). Out of 64 observed species, 47 species (11 families) experienced positive allometric growth, while another 23 species (eight families) and 31 species (12 families) were recorded under isometric and negative allometric growth, respectively. The fish LWRs observed can be used as an indicator of environmental changes and fish ecological health for freshwater fishes in Malaysia.

Expression of a gene duplication encoding conserved sperm tail proteins is translationally regulated in Drosophila melanogaster

1993 ◽  
Vol 13 (3) ◽  
pp. 1708-1718
Author(s):  
M Schäfer ◽  
D Börsch ◽  
A Hülster ◽  
U Schäfer
Keyword(s):  
Drosophila Melanogaster ◽  
Gene Family ◽  
Translational Control ◽  
Germ Line ◽  
Gene Families ◽  
Homologous Gene ◽  
Male Sterile ◽  
Sperm Tail ◽  
Repetitive Motif ◽  
Carboxy Terminal

We have analyzed a locus of Drosophila melanogaster located at 98C on chromosome 3, which contains two tandemly arranged genes, named Mst98Ca and Mst98Cb. They are two additional members of the Mst(3)CGP gene family by three criteria. (i) Both genes are exclusively transcribed in the male germ line. (ii) Both transcripts encode a protein with a high proportion of the repetitive motif Cys-Gly-Pro. (iii) Their expression is translationally controlled; while transcripts can be detected in diploid stages of spermatogenesis, association with polysomes can be shown only in haploid stages of sperm development. The genes differ markedly from the other members of the gene family in structure; they do not contain introns, they are of much larger size, and they have the Cys-Gly-Pro motifs clustered at the carboxy-terminal end of the encoded proteins. An antibody generated against the Mst98Ca protein recognizes both Mst98C proteins in D. melanogaster. In a male-sterile mutation in which spermiogenesis is blocked before individualization of sperm, both of these proteins are no longer synthesized. This finding provides proof of late translation for the Mst98C proteins and thereby independent proof of translational control of expression. Northern (RNA) and Western immunoblot analyses indicate the presence of homologous gene families in many other Drosophila species. The Mst98C proteins share sequence homology with proteins of the outer dense fibers in mammalian spermatozoa and can be localized to the sperm tail by immunofluorescence with an anti-Mst98Ca antibody.

scholarly journals RNA regulons are essential in intestinal homeostasis

2019 ◽  
Vol 316 (1) ◽  
pp. G197-G204 ◽  
Author(s):  
Louis R. Parham ◽  
Patrick A. Williams ◽  
Priya Chatterji ◽  
Kelly A. Whelan ◽  
Kathryn E. Hamilton
Keyword(s):  
Epithelial Cells ◽  
Rna Binding ◽  
Environmental Changes ◽  
Cell Function ◽  
Rna Binding Proteins ◽  
Cell Types ◽  
Intestinal Epithelial ◽  
Cell Dynamics ◽  
Functional Roles ◽  
Proliferating Cell

Intestinal epithelial cells are among the most rapidly proliferating cell types in the human body. There are several different subtypes of epithelial cells, each with unique functional roles in responding to the ever-changing environment. The epithelium’s ability for rapid and customized responses to environmental changes requires multitiered levels of gene regulation. An emerging paradigm in gastrointestinal epithelial cells is the regulation of functionally related mRNA families, or regulons, via RNA-binding proteins (RBPs). RBPs represent a rapid and efficient mechanism to regulate gene expression and cell function. In this review, we will provide an overview of intestinal epithelial RBPs and how they contribute specifically to intestinal epithelial stem cell dynamics. In addition, we will highlight key gaps in knowledge in the global understanding of RBPs in gastrointestinal physiology as an opportunity for future studies.

scholarly journals Meta-Omics Reveals Genetic Flexibility of Diatom Nitrogen Transporters in Response to Environmental Changes

2019 ◽  
Vol 36 (11) ◽  
pp. 2522-2535 ◽  
Author(s):  
Greta Busseni ◽  
Fabio Rocha Jimenez Vieira ◽  
Alberto Amato ◽  
Eric Pelletier ◽  
Juan J Pierella Karlusich ◽  
...  
Keyword(s):  
Environmental Changes ◽  
Seawater Temperature ◽  
Holistic Approach ◽  
Gene Families ◽  
Functional Trait ◽  
Marine Phytoplankton ◽  
Functional Biology ◽  
Key Events ◽  
Diverse Groups ◽  
Shed Light

Abstract Diatoms (Bacillariophyta), one of the most abundant and diverse groups of marine phytoplankton, respond rapidly to the supply of new nutrients, often out-competing other phytoplankton. Herein, we integrated analyses of the evolution, distribution, and expression modulation of two gene families involved in diatom nitrogen uptake (DiAMT1 and DiNRT2), in order to infer the main drivers of divergence in a key functional trait of phytoplankton. Our results suggest that major steps in the evolution of the two gene families reflected key events triggering diatom radiation and diversification. Their expression is modulated in the contemporary ocean by seawater temperature, nitrate, and iron concentrations. Moreover, the differences in diversity and expression of these gene families throughout the water column hint at a possible link with bacterial activity. This study represents a proof-of-concept of how a holistic approach may shed light on the functional biology of organisms in their natural environment.

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