Subfunctionalization of Duplicate mitf Genes Associated With Differential Degeneration of Alternative Exons in Fish

Genetics ◽  
2002 ◽  
Vol 161 (1) ◽  
pp. 259-267 ◽  
Author(s):  
Joachim Altschmied ◽  
Jacqueline Delfgaauw ◽  
Brigitta Wilde ◽  
Jutta Duschl ◽  
Laurence Bouneau ◽  
...  
Keyword(s):  
Danio Rerio ◽  
Evolutionary History ◽  
Single Gene ◽  
Regulatory Elements ◽  
Fugu Rubripes ◽  
Gene Encoding ◽  
Tetraodon Nigroviridis ◽  
Mammalian Lineage ◽  
History Of ◽  
Fish Proteins

Abstract The microphthalmia-associated transcription factor (MITF) exists in at least four isoforms. These are generated in higher vertebrates using alternative 5′ exons and promoters from a single gene. Two separate genes (mitf-m and mitf-b), however, are present in different teleost fish species including the poeciliid Xiphophorus, the pufferfishes Fugu rubripes and Tetraodon nigroviridis, and the zebrafish Danio rerio. Fish proteins MITF-m and MITF-b correspond at both the structural and the expression levels to one particular bird/mammalian MITF isoform. In the teleost lineage subfunctionalization of mitf genes after duplication at least 100 million years ago is associated with the degeneration of alternative exons and, probably, regulatory elements and promoters. For example, a remnant of the first exon specific for MITF-m is detected within the pufferfish gene encoding MITF-b. Retracing the evolutionary history of mitf genes in vertebrates uncovered the differential recruitment of new introns specific for either the teleost or the bird/mammalian lineage.

scholarly journals Functional analyses of the horizontally acquired Phytophaga glycoside hydrolase family 45 (GH45) proteins reveal distinct functional characteristics

2018 ◽  
Author(s):  
André Busch ◽  
Etienne G.J. Danchin ◽  
Yannick Pauchet
Keyword(s):  
Glycoside Hydrolase ◽  
Evolutionary History ◽  
Plant Cell Wall ◽  
Glycoside Hydrolase Family ◽  
Last Common Ancestor ◽  
Gene Encoding ◽  
Amorphous Cellulose ◽  
History Of ◽  
Functional Analyses ◽  
Hydrolase Family

AbstractCellulose, a major polysaccharide of the plant cell wall, consists of β-1,4-linked glucose moieties forming a molecular network recalcitrant to enzymatic breakdown. Although cellulose is potentially a rich source of energy, the ability to degrade it is rare in animals and was believed to be present only in cellulolytic microbes. Recently, it has become clear that some animals encode endogenous cellulases belonging to several glycoside hydrolase families (GHs), including GH45. GH45s are distributed patchily among the Metazoa and, in insects, are encoded only by the genomes of Phytophaga beetles. This study aims to understand both the enzymatic properties and the evolutionary history of GH45s in these beetles. To this end, we tested the enzymatic abilities of 37 GH45s derived from five species of Phytophaga beetles and learned that beetle-derived GH45s degrade three different substrates: amorphous cellulose, xyloglucan and glucomannan. Our phylogenetic and gene structure analyses indicate that at least one gene encoding a putative cellulolytic GH45 was present in the last common ancestor of the Phytophaga, and that GH45 xyloglucanases evolved several times independently in these beetles. The most closely related clade to Phytophaga GH45s contained fungal sequences, suggesting this GH family was acquired by horizontal gene transfer from fungi. Other than in insects, arthropod GH45s do not share a common origin and appear to have emerged at least three times independently.

scholarly journals Complex evolutionary history of translation Elongation Factor 2 and diphthamide biosynthesis in Archaea and parabasalids

2018 ◽  
Author(s):  
Adrienne B. Narrowe ◽  
Anja Spang ◽  
Courtney W. Stairs ◽  
Eva F. Caceres ◽  
Brett J. Baker ◽  
...  
Keyword(s):  
Functional Divergence ◽  
Single Gene ◽  
Elongation Factor ◽  
Single Copy ◽  
Compensatory Mechanisms ◽  
Gene Encoding ◽  
Elongation Factor 2 ◽  
Eukaryotic Elongation Factor ◽  
History Of ◽  
Key Residues

ABSTRACTDiphthamide is a modified histidine residue which is uniquely present in archaeal and eukaryotic elongation factor 2 (EF-2), an essential GTPase responsible for catalyzing the coordinated translocation of tRNA and mRNA through the ribosome. In part due to the role of diphthamide in maintaining translational fidelity, it was previously assumed that diphthamide biosynthesis genes (dph) are conserved across all eukaryotes and archaea. Here, comparative analysis of new and existing genomes reveals that some archaea (i.e., members of the Asgard superphylum,Geoarchaea, andKorarchaeota) and eukaryotes (i.e., parabasalids) lackdph. In addition, while EF-2 was thought to exist as a single copy in archaea, many of thesedph-lacking archaeal genomes encode a second EF-2 paralog missing key-residues required for diphthamide modification and for normal translocase function, perhaps suggesting functional divergence linked to loss of diphthamide biosynthesis. Interestingly, some Heimdallarchaeota previously suggested to be most closely related to the eukaryotic ancestor maintaindphgenes and a single gene encoding canonical EF-2. Our findings reveal that the ability to produce diphthamide, once thought to be a universal feature in archaea and eukaryotes, has been lost multiple times during evolution, and suggest that anticipated compensatory mechanisms evolved independently.

scholarly journals Ensembl 2021

2020 ◽  
Vol 49 (D1) ◽  
pp. D884-D891 ◽  
Author(s):  
Kevin L Howe ◽  
Premanand Achuthan ◽  
James Allen ◽  
Jamie Allen ◽  
Jorge Alvarez-Jarreta ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Evolutionary History ◽  
Genomic Data ◽  
Regulatory Elements ◽  
Vertebrate Species ◽  
Variant Effect Predictor ◽  
Rapid Release ◽  
History Of ◽  
Genome Browsers ◽  
Gene Structures

Abstract The Ensembl project (https://www.ensembl.org) annotates genomes and disseminates genomic data for vertebrate species. We create detailed and comprehensive annotation of gene structures, regulatory elements and variants, and enable comparative genomics by inferring the evolutionary history of genes and genomes. Our integrated genomic data are made available in a variety of ways, including genome browsers, search interfaces, specialist tools such as the Ensembl Variant Effect Predictor, download files and programmatic interfaces. Here, we present recent Ensembl developments including two new website portals. Ensembl Rapid Release (http://rapid.ensembl.org) is designed to provide core tools and services for genomes as soon as possible and has been deployed to support large biodiversity sequencing projects. Our SARS-CoV-2 genome browser (https://covid-19.ensembl.org) integrates our own annotation with publicly available genomic data from numerous sources to facilitate the use of genomics in the international scientific response to the COVID-19 pandemic. We also report on other updates to our annotation resources, tools and services. All Ensembl data and software are freely available without restriction.

scholarly journals Stress-Free Evolution: The Nrf-Coordinated Oxidative Stress Response in Early Diverging Metazoans

2019 ◽  
Vol 59 (4) ◽  
pp. 799-810 ◽  
Author(s):  
Liam B Doonan ◽  
Ashlie Hartigan ◽  
Beth Okamura ◽  
Paul F Long
Keyword(s):  
Oxidative Stress ◽  
Stress Response ◽  
Evolutionary History ◽  
Regulatory Elements ◽  
Oxidative Stress Response ◽  
Last Common Ancestor ◽  
Redox Control ◽  
Functional Responses ◽  
Regulatory Pathways ◽  
History Of

Abstract Environmental stress from ultraviolet radiation, elevated temperatures or metal toxicity can lead to reactive oxygen species in cells, leading to oxidative DNA damage, premature aging, neurodegenerative diseases, and cancer. The transcription factor nuclear factor (erythroid-derived 2)-like 2 (Nrf2) activates many cytoprotective proteins within the nucleus to maintain homeostasis during oxidative stress. In vertebrates, Nrf2 levels are regulated by the Kelch-family protein Keap1 (Kelch-like ECH-associated protein 1) in the absence of stress according to a canonical redox control pathway. Little, however, is known about the redox control pathway used in early diverging metazoans. Our study examines the presence of known oxidative stress regulatory elements within non-bilaterian metazoans including free living and parasitic cnidarians, ctenophores, placozoans, and sponges. Cnidarians, with their pivotal position as the sister phylum to bilaterians, play an important role in understanding the evolutionary history of response to oxidative stress. Through comparative genomic and transcriptomic analysis our results show that Nrf homologs evolved early in metazoans, whereas Keap1 appeared later in the last common ancestor of cnidarians and bilaterians. However, key Nrf–Keap1 interacting domains are not conserved within the cnidarian lineage, suggesting this important pathway evolved with the radiation of bilaterians. Several known downstream Nrf targets are present in cnidarians suggesting that cnidarian Nrf plays an important role in oxidative stress response even in the absence of Keap1. Comparative analyses of key oxidative stress sensing and response proteins in early diverging metazoans thus provide important insights into the molecular basis of how these lineages interact with their environment and suggest a shared evolutionary history of regulatory pathways. Exploration of these pathways may prove important for the study of cancer therapeutics and broader research in oxidative stress, senescence, and the functional responses of early diverging metazoans to environmental change.

Elaborating the role of reflection and individual differences in the study of folk-economic beliefs

2018 ◽  
Vol 41 ◽  
Author(s):  
Kevin Arceneaux
Keyword(s):  
Decision Making ◽  
Individual Differences ◽  
Cognitive Processes ◽  
Evolutionary History ◽  
Behavioral Responses ◽  
History Of ◽  
Economic Beliefs

AbstractIntuitions guide decision-making, and looking to the evolutionary history of humans illuminates why some behavioral responses are more intuitive than others. Yet a place remains for cognitive processes to second-guess intuitive responses – that is, to be reflective – and individual differences abound in automatic, intuitive processing as well.

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