Molecular evolution and expression of oxygen transport genes in livebearing fishes (Poeciliidae) from hydrogen sulfide rich springs

Hydrogen sulfide (H2S) is a natural toxicant in some aquatic environments that has diverse molecular targets. It binds to oxygen transport proteins, rendering them non-functional by reducing oxygen-binding affinity. Hence, organisms permanently inhabiting H2S-rich environments are predicted to exhibit adaptive modifications to compensate for the reduced capacity to transport oxygen. We investigated 10 lineages of fish of the family Poeciliidae that have colonized freshwater springs rich in H2S—along with related lineages from non-sulfidic environments—to test hypotheses about the expression and evolution of oxygen transport genes in a phylogenetic context. We predicted shifts in the expression of and signatures of positive selection on oxygen transport genes upon colonization of H2S-rich habitats. Our analyses indicated significant shifts in gene expression for multiple hemoglobin genes in lineages that have colonized H2S-rich environments, and three hemoglobin genes exhibited relaxed selection in sulfidic compared to non-sulfidic lineages. However, neither changes in gene expression nor signatures of selection were consistent among all lineages in H2S-rich environments. Oxygen transport genes may consequently be predictable targets of selection during adaptation to sulfidic environments, but changes in gene expression and molecular evolution of oxygen transport genes in H2S-rich environments are not necessarily repeatable across replicated lineages.

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A Comparative Study of the Oxygen Transport Proteins of Dendrostomum pyroides

Journal of Biological Chemistry ◽

10.1016/s0021-9258(19)44851-5 ◽

1972 ◽

Vol 247 (18) ◽

pp. 5959-5963

Author(s):

Gerald L. Klippenstein ◽

Dee A. Van Riper ◽

Elizabeth A. Oosterom

Keyword(s):

Comparative Study ◽

Oxygen Transport ◽

Transport Proteins

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Novel germline variant in the histone demethylase and transcription regulator KDM4C induces a multi-cancer phenotype

Journal of Medical Genetics ◽

10.1136/jmedgenet-2021-107747 ◽

2021 ◽

pp. jmedgenet-2021-107747

Author(s):

Riku Katainen ◽

Iikki Donner ◽

Maritta Räisänen ◽

Davide Berta ◽

Anna Kuosmanen ◽

...

Keyword(s):

Gene Expression ◽

Rare Variants ◽

Cancer Susceptibility ◽

Histone Demethylase ◽

Interaction Partner ◽

Transcription Regulator ◽

H3k9 Trimethylation ◽

Mutation Carriers ◽

The Family ◽

Project Data

BackgroundGenes involved in epigenetic regulation are central for chromatin structure and gene expression. Specific mutations in these might promote carcinogenesis in several tissue types.MethodsWe used exome, whole-genome and Sanger sequencing to detect rare variants shared by seven affected individuals in a striking early-onset multi-cancer family. The only variant that segregated with malignancy resided in a histone demethylase KDM4C. Consequently, we went on to study the epigenetic landscape of the mutation carriers with ATAC, ChIP (chromatin immunoprecipitation) and RNA-sequencing from lymphoblastoid cell lines to identify possible pathogenic effects.ResultsA novel variant in KDM4C, encoding a H3K9me3 histone demethylase and transcription regulator, was found to segregate with malignancy in the family. Based on Roadmap Epigenomics Project data, differentially accessible chromatin regions between the variant carriers and controls enrich to normally H3K9me3-marked chromatin. We could not detect a difference in global H3K9 trimethylation levels. However, carriers of the variant seemed to have more trimethylated H3K9 at transcription start sites. Pathway analyses of ChIP-seq and differential gene expression data suggested that genes regulated through KDM4C interaction partner EZH2 and its interaction partner PLZF are aberrantly expressed in mutation carriers.ConclusionsThe apparent dysregulation of H3K9 trimethylation and KDM4C-associated genes in lymphoblastoid cells supports the hypothesis that the KDM4C variant is causative of the multi-cancer susceptibility in the family. As the variant is ultrarare, located in the conserved catalytic JmjC domain and predicted pathogenic by the majority of available in silico tools, further studies on the role of KDM4C in cancer predisposition are warranted.

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Unearthing LTR retrotransposon gag genes co-opted in the deep evolution of eukaryotes

Molecular Biology and Evolution ◽

10.1093/molbev/msab101 ◽

2021 ◽

Author(s):

Jianhua Wang ◽

Guan-Zhu Han

Keyword(s):

Gene Expression ◽

Selective Pressure ◽

Ltr Retrotransposon ◽

Ltr Retrotransposons ◽

Cellular Functions ◽

The Family ◽

Family Level ◽

Gene Expression Analyses ◽

Comprehensive Picture ◽

Gypsy Retrotransposons

Abstract LTR retrotransposons comprise a major component of the genomes of eukaryotes. On occasion, retrotransposon genes can be recruited by their hosts for diverse functions, a process formally referred to as co-option. However, a comprehensive picture of LTR retrotransposon gag gene co-option in eukaryotes is still lacking, with several documented cases exclusively involving Ty3/Gypsy retrotransposons in animals. Here we use a phylogenomic approach to systemically unearth co-option of retrotransposon gag genes above the family level of taxonomy in 2,011 eukaryotes, namely co-option occurring during the deep evolution of eukaryotes. We identify a total of 14 independent gag gene co-option events across more than 740 eukaryote families, eight of which have not been reported previously. Among these retrotransposon gag gene co-option events, nine, four, and one involve gag genes of Ty3/Gypsy, Ty1/Copia, and Bel-Pao retrotransposons, respectively. Seven, four, and three co-option events occurred in animals, plants, and fungi, respectively. Interestingly, two co-option events took place in the early evolution of angiosperms. Both selective pressure and gene expression analyses further support that these co-opted gag genes might perform diverse cellular functions in their hosts, and several co-opted gag genes might be subject to positive selection. Taken together, our results provide a comprehensive picture of LTR retrotransposon gag gene co-option events that occurred during the deep evolution of eukaryotes, and suggest paucity of LTR retrotransposon gag gene co-option during the deep evolution of eukaryotes.

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Chironomidae: Biology, Ecology and Systematics

10.5772/intechopen.95577 ◽

2021 ◽

Author(s):

Zerguine Karima

Keyword(s):

Life Cycle ◽

Larval Stage ◽

Adult Stage ◽

Aquatic Environments ◽

Biting Midges ◽

Important Family ◽

Theoretical Synthesis ◽

The Family ◽

The World ◽

Holarctic Region

The family of Chironomidae is a group of Diptera insects belonging to the suborder of Nematocera, commonly called “non-biting midges” in the adult stage and “bloodworms” in the larval stage. The Chironomidae are often the most abundant group of macroinvertebrates, in number of species and individuals, encountered in all aquatic environments of freshwater, brackish, terrestrial and even the sea. Likewise, Chironomidae occur in all the continents. The Chironomidae family is divided into 11 sub-families that have diffrent ecological statues. Despite the wealth of data on Chironomidae in the Holarctic region, other parts of the world are poorly studied and few guides to identifying Chironomidae have been produced. This chapter includes a theoretical synthesis on the Chironomidae, it deals with the Biology (life cycle and description of different stages), description of all subfamilies and the ecology of this important family of Diptera.

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Gene Expression Profile of RNA N1-methyladenosine methyltransferases

E3S Web of Conferences ◽

10.1051/e3sconf/202021803052 ◽

2020 ◽

Vol 218 ◽

pp. 03052

Author(s):

Mingzhu Rao

Keyword(s):

Gene Expression ◽

Gene Expression Profile ◽

Expression Profile ◽

Active Sites ◽

Evolutionary Analysis ◽

Base Modification ◽

Binding Domains ◽

Non Coding Rna ◽

Beta Sheet Structure ◽

The Family

N1-methyladenosine (m1A) is a kind of common and abundant methylation modification in eukaryotic mRNA and long-chain non-coding RNA. Nucleoside methyltransferase (MTase) of m1A is a diverse protein family, which is characterized by the presence of methyltransferases like domains and conserved S-adenosylmethionine (SAM) binding domains formed by the central sevenstranded beta-sheet structure. However, comprehensive analysis of the gene expression profile of such enzymes has not been performed to classify them according to evolutionary criteria and to guide the functional prediction. Here, we conducted extensive searches of databases to collect all members of previously identified m1A RNA methyltransferases. And we report bioinformatics studies on gene expression profile based on evolutionary analysis, sequence alignment, expression in tissues and cells within the family of RNA methyltransferases. Our analysis showed that the base modification behavior mediated by m1A RNA methyltransferases evolved from invertebrate, and the active sites of m1A RNA methyltransferases were highly conserved during the evolution from invertebrates to human. And m1A RNA methyltransferases have low tissue and cell specificity.

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GENETIC REPRESENTATION AND GENETIC NEUTRALITY IN GENE EXPRESSION PROGRAMMING

Advances in Complex Systems ◽

10.1142/s0219525902000626 ◽

2002 ◽

Vol 05 (04) ◽

pp. 389-408 ◽

Cited By ~ 33

Author(s):

CÂNDIDA FERREIRA

Keyword(s):

Gene Expression ◽

Molecular Evolution ◽

Gene Expression Programming ◽

Neutral Theory ◽

Artificial System ◽

Evolutionary Systems ◽

Theory Of Evolution ◽

Coding Regions ◽

Neutral Mutations

The neutral theory of molecular evolution states that the accumulation of neutral mutations in the genome is fundamental for evolution to occur. The genetic representation of gene expression programming, an artificial genotype/phenotype system, not only allows the existence of non-coding regions in the genome where neutral mutations can accumulate but also allows the controlled manipulation of both the number and the extent of these non-coding regions. Therefore, gene expression programming is an ideal artificial system where the neutral theory of evolution can be tested in order to gain some insights into the workings of artificial evolutionary systems. The results presented in this work show beyond any doubt that the existence of neutral regions in the genome is fundamental for evolution to occur efficiently.

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Mitigation of Expression of Virulence Genes in Legionella pneumophila Internalized in the Free-Living Amoeba Willaertia magna C2c Maky

Pathogens ◽

10.3390/pathogens9060447 ◽

2020 ◽

Vol 9 (6) ◽

pp. 447 ◽

Cited By ~ 1

Author(s):

Rayane Mouh Mameri ◽

Jacques Bodennec ◽

Laurent Bezin ◽

Sandrine Demanèche

Keyword(s):

Gene Expression ◽

Legionella Pneumophila ◽

Virulence Genes ◽

Natural Habitat ◽

Acanthamoeba Castellanii ◽

Severe Form ◽

Aquatic Environments ◽

Free Living ◽

Intracellular Parasites ◽

Free Living Amoeba

Legionella pneumophila is a human pathogen responsible for a severe form of pneumonia named Legionnaire disease. Its natural habitat is aquatic environments, being in a free state or intracellular parasites of free-living amoebae, such as Acanthamoeba castellanii. This pathogen is able to replicate within some amoebae. Willaertia magna C2c Maky, a non-pathogenic amoeba, was previously demonstrated to resist to L. pneumophila and even to be able to eliminate the L. pneumophila strains Philadelphia, Lens, and Paris. Here, we studied the induction of seven virulence genes of three L. pneumophila strains (Paris, Philadelphia, and Lens) within W. magna C2c Maky in comparison within A. castellanii and with the gene expression level of L. pneumophila strains alone used as controls. We defined a gene expression-based virulence index to compare easily and without bias the transcript levels in different conditions and demonstrated that W. magna C2c Maky did not increase the virulence of L. pneumophila strains in contrast to A. castellanii. These results confirmed the non-permissiveness of W. magna C2c Maky toward L. pneumophila strains.

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Marmoset glutathione peroxidases: cDNA sequences, molecular evolution, and gene expression

Journal of Medical Primatology ◽

10.1111/j.1600-0684.2006.00158.x ◽

2006 ◽

Vol 35 (3) ◽

pp. 155-164 ◽

Cited By ~ 2

Author(s):

Srebrena Atanasova ◽

Nicolas von Ahsen ◽

Christina Schlumbohm ◽

Eberhard Wieland ◽

Michael Oellerich ◽

...

Keyword(s):

Gene Expression ◽

Molecular Evolution ◽

Cdna Sequences ◽

Glutathione Peroxidases

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Concordant changes in gene expression and nucleotides underlie independent adaptation to hydrogen-sulfide-rich environments

Genome Biology and Evolution ◽

10.1093/gbe/evy198 ◽

2018 ◽

Author(s):

Anthony P Brown ◽

Lenin Arias-Rodriguez ◽

Muh-Ching Yee ◽

Michael Tobler ◽

Joanna L Kelley

Keyword(s):

Gene Expression ◽

Hydrogen Sulfide

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Hypoxia regulates gene expression of alveolar epithelial transport proteins

Journal of Applied Physiology ◽

10.1152/jappl.2000.88.5.1890 ◽

2000 ◽

Vol 88 (5) ◽

pp. 1890-1896 ◽

Cited By ~ 72

Author(s):

Christine Clerici ◽

Michael A. Matthay

Keyword(s):

Gene Expression ◽

Epithelial Cells ◽

Alveolar Epithelium ◽

Transport Proteins ◽

Alveolar Epithelial Cells ◽

Type I ◽

Type Ii ◽

Atp Content ◽

Glut 1 ◽

Alveolar Epithelial

Alveolar hypoxia occurs during ascent to high altitude but is also commonly observed in many acute and chronic pulmonary disorders. The alveolar epithelium is directly exposed to decreases in O2tension, but a few studies have evaluated the effects of hypoxia on alveolar cell function. The alveolar epithelium consists of two cell types: large, flat, squamous alveolar type I and cuboidal type II (ATII). ATII cells are more numerous and have a number of critical functions, including transporting ions and substrates required for many physiological processes. ATII cells express 1) membrane proteins used for supplying substrates required for cell metabolism and 2) ion transport proteins such as Na+channels and Na+-K+-ATPase, which are involved in the vectorial transport of Na+from the alveolar to interstitial spaces and therefore drive the resorption of alveolar fluid. This brief review focuses on gene expression regulation of glucose transporters and Na+transport proteins by hypoxia in alveolar epithelial cells. Cells exposed to severe hypoxia (0% or 3% O2) for 24 h upregulate the activity and expression of the glucose transporter GLUT-1, resulting in preservation of ATP content. Hypoxia-induced increases in GLUT-1 mRNA levels are due to O2deprivation and inhibition of oxidative phosphorylation. This regulation occurs at the transcriptional level through activation of a hypoxia-inducible factor. In contrast, hypoxia downregulates expression and activity of Na+channels and Na+-K+-ATPase in cultured alveolar epithelial cells. Hypoxia induces time- and concentration-dependent decreases of α-, β-, and γ-subunits of epithelial Na+channel mRNA and β1- and α1-subunits of Na+-K+-ATPase, effects that are completely reversed after reoxygenation. The mechanisms by which O2deprivation regulates gene expression of Na+transport proteins are not fully elucidated but likely involve the redox status of the cell. Thus hypoxia regulates gene expression of transport proteins in cultured alveolar epithelial type II cells differently, preserving ATP content.

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