21 results match your criteria sub-functionalization ancestral

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Experimental exchange of paralogous domains in the MLH family provides evidence of sub-functionalization after gene duplication.

G3 (Bethesda) 2021 Apr 19. Epub 2021 Apr 19.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA.

Baker's yeast contains a large number of duplicated genes; some function redundantly, whereas others have more specialized roles. We used the MLH family of DNA mismatch repair proteins as a model to better understand the steps that lead to gene specialization following a gene duplication event. We focused on two highly conserved yeast MLH proteins, Pms1 and Mlh3, with Pms1 having a major role in the repair of misincorporation events during DNA replication and Mlh3 acting to resolve recombination intermediates in meiosis to form crossovers. Read More

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Pervasive duplication, biased molecular evolution and comprehensive functional analysis of the PP2C family in Glycine max.

BMC Genomics 2020 Jul 6;21(1):465. Epub 2020 Jul 6.

Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, P. R. China.

Background: Soybean (Glycine max) is an important oil provider and ecosystem participant. The protein phosphatase 2C (PP2C) plays important roles in key biological processes. Molecular evolution and functional analysis of the PP2C family in soybean are yet to be reported. Read More

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Ancient duplications and grass-specific transposition influenced the evolution of LEAFY transcription factor genes.

Commun Biol 2019 21;2:237. Epub 2019 Jun 21.

2State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China.

The LFY transcription factor gene family are important in the promotion of cell proliferation and floral development. Understanding their evolution offers an insight into floral development in plant evolution. Though a promiscuous transition intermediate and a gene duplication event within the family had been identified previously, the early evolutionary path of this family remained elusive. Read More

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Characterization of paralogous transcription factor encoding genes in zebrafish.

Gene X 2019 Jun;2:100011

Biology and Evolution of Marine Organisms, Zoological Station Anton Dohrn, 80121 Naples, Italy.

The paired-type homeodomain transcription factor Uncx is involved in multiple processes of embryogenesis in vertebrates. Reasoning that zebrafish genes and are orthologs of mouse , we studied their genomic environment and developmental expression. Evolutionary analyses indicate the zebrafish genes as being paralogs deriving from teleost-specific whole-genome duplication. Read More

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Evolutionary significance and regulated expression of Tdrd family genes in gynogenetic Japanese flounder (Paralichthys olivaceus).

Comp Biochem Physiol Part D Genomics Proteomics 2019 09 7;31:100593. Epub 2019 May 7.

Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, Shandong, China. Electronic address:

Tudor domain-containing proteins (TDRDs) are highly conserved among organisms and have a function in gonads to regulate gametogenesis and genome stability through the piwi-interacting RNA (piRNA) pathway. With diverse sexual development patterns in teleost species, the evolution and function of Tdrd genes among teleosts remain unclear. Here, we identified and characterized 12 Tdrd genes (PoTdrds) in Japanese flounder (Paralichthys olivaceus) which represents dramatic sexual dimorphic metrics and sex reversal during sex differentiation. Read More

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September 2019

Evolutionary Conservation and Divergence of Genes Encoding 3-Hydroxy-3-methylglutaryl Coenzyme A Synthase in the Allotetraploid Cotton Species .

Cells 2019 05 3;8(5). Epub 2019 May 3.

Collaborative Innovation Center of Henan Grain Crops/Agronomy College, Henan Agricultural University, Zhengzhou 450002, China.

Polyploidization is important for the speciation and subsequent evolution of many plant species. Analyses of the duplicated genes produced via polyploidization events may clarify the origin and evolution of gene families. During terpene biosynthesis, 3-hydroxy-3-methylglutaryl coenzyme A synthase (HMGS) functions as a key enzyme in the mevalonate pathway. Read More

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Negative regulation of filamentous growth in Candida albicans by Dig1p.

Mol Microbiol 2017 Sep 21;105(5):810-824. Epub 2017 Jul 21.

Department of Biology, Concordia University, Montreal, Quebec, Canada.

Transcriptional regulation involves both positive and negative regulatory elements. The Dig1 negative regulators are part of a fungal-specific module that includes a transcription factor (a Ste12 family member) and a Dig1 family member. In Saccharomyces cerevisiae, the post-genome-duplication Dig1/Dig2 proteins regulate MAP kinase controlled signalling pathways involved in mating and filamentous growth. Read More

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September 2017

The Physcomitrella patens exocyst subunit EXO70.3d has distinct roles in growth and development, and is essential for completion of the moss life cycle.

New Phytol 2017 Oct 11;216(2):438-454. Epub 2017 Apr 11.

Laboratory of Cell Morphogenesis, Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 128 44, Prague 2, Czech Republic.

The exocyst, an evolutionarily conserved secretory vesicle-tethering complex, spatially controls exocytosis and membrane turnover in fungi, metazoans and plants. The exocyst subunit EXO70 exists in multiple paralogs in land plants, forming three conserved clades with assumed distinct roles. Here we report functional analysis of the first moss exocyst subunit to be studied, Physcomitrella patens PpEXO70. Read More

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October 2017

Extending a Single Residue Switch for Abbreviating Catalysis in Plant -Kaurene Synthases.

Front Plant Sci 2016 22;7:1765. Epub 2016 Nov 22.

Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames IA, USA.

Production of -kaurene as a precursor for important signaling molecules such as the gibberellins seems to have arisen early in plant evolution, with corresponding cyclase(s) present in all land plants (i.e., embryophyta). Read More

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November 2016

Evolutionary Expansion of WRKY Gene Family in Banana and Its Expression Profile during the Infection of Root Lesion Nematode, Pratylenchus coffeae.

PLoS One 2016 7;11(9):e0162013. Epub 2016 Sep 7.

Crop Improvement Division, ICAR-National Research Centre for Banana, Tamil Nadu, Tiruchirapalli, India.

The WRKY family of transcription factors orchestrate the reprogrammed expression of the complex network of defense genes at various biotic and abiotic stresses. Within the last 96 million years, three rounds of Musa polyploidization events had occurred from selective pressure causing duplication of MusaWRKYs with new activities. Here, we identified a total of 153 WRKY transcription factors available from the DH Pahang genome. Read More

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Sub-functionalization to ovule development following duplication of a floral organ identity gene.

Dev Biol 2015 Sep 27;405(1):158-72. Epub 2015 Jun 27.

Department of Biology, University of Washington, Seattle, WA 98195, United States.

Gene duplications result in paralogs that may be maintained due to the gain of novel functions (neo-functionalization) or the partitioning of ancestral function (sub-functionalization). Plant genomes are especially prone to duplication; paralogs are particularly widespread in the floral MADS box transcription factors that control organ identity through the ABC model of flower development. C class genes establish stamen and carpel identity and control floral meristem determinacy, and are largely conserved across the angiosperm phylogeny. Read More

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September 2015

The fate of recent duplicated genes following a fourth-round whole genome duplication in a tetraploid fish, common carp (Cyprinus carpio).

Sci Rep 2015 Feb 3;5:8199. Epub 2015 Feb 3.

CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, 100141, China.

Whole genome duplication (WGD) results in extensive genetic redundancy. In plants and yeast, WGD is followed by rapid gene deletions and intense expression differentiation with slow functional divergence. However, the early evolution of the gene differentiation processes is poorly understood in vertebrates because almost all studied WGDs are extremely ancient, and the genomes have returned to a diploid status. Read More

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February 2015

Arabidopsis replacement histone variant H3.3 occupies promoters of regulated genes.

Genome Biol 2014 Mar 21;15(4):R62. Epub 2014 Mar 21.

Background: Histone variants establish structural and functional diversity of chromatin by affecting nucleosome stability and histone-protein interactions. H3.3 is an H3 histone variant that is incorporated into chromatin outside of S-phase in various eukaryotes. Read More

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Functional Evolution in the Plant SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) Gene Family.

Front Plant Sci 2013 5;4:80. Epub 2013 Apr 5.

Plant Biology, The University of Vermont Burlington, VT, USA.

The SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) family of transcription factors is functionally diverse, controlling a number of fundamental aspects of plant growth and development, including vegetative phase change, flowering time, branching, and leaf initiation rate. In natural plant populations, variation in flowering time and shoot architecture have major consequences for fitness. Likewise, in crop species, variation in branching and developmental rate impact biomass and yield. Read More

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Sub-functionalization of duplicated genes in the evolution of nine-spined stickleback hatching enzyme.

J Exp Zool B Mol Dev Evol 2013 May 1;320(3):140-50. Epub 2013 Apr 1.

Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, Tokyo, Japan.

Gene duplication is the primary source of novel genes, and is followed by non-, sub-, or neo-functionalization. In this study, we compared the egg envelope digestion mechanism of hatching enzymes between three-spined stickleback and nine-spined stickleback species, and found that the function of the hatching enzymes of nine-spined sticklebacks was uniquely derived by gene duplication, followed by sub-functionalization. The hatching enzyme of euteleosts consists of two metalloproteases, high choriolytic enzyme (HCE), and low choriolytic enzyme (LCE). Read More

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Evolution of GOLDEN2-LIKE gene function in C(3) and C (4) plants.

Planta 2013 Feb 12;237(2):481-95. Epub 2012 Sep 12.

Department of Plant Sciences, University of Oxford, South Parks Rd., Oxford, UK.

A pair of GOLDEN2-LIKE transcription factors is required for normal chloroplast development in land plant species that encompass the range from bryophytes to angiosperms. In the C(4) plant maize, compartmentalized function of the two GLK genes in bundle sheath and mesophyll cells regulates dimorphic chloroplast differentiation, whereas in the C(3) plants Physcomitrella patens and Arabidopsis thaliana the genes act redundantly in all photosynthetic cells. To assess whether the cell-specific function of GLK genes is unique to maize, we analyzed gene expression patterns in the C(4) monocot Sorghum bicolor and C(4) eudicot Cleome gynandra. Read More

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February 2013

Functional analyses of AGAMOUS family members in Nicotiana benthamiana clarify the evolution of early and late roles of C-function genes in eudicots.

Plant J 2012 Sep 25;71(6):990-1001. Epub 2012 Jun 25.

Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas- Universidad Politécnica de Valencia, Avenida de los Naranjos s/n, 46022 Valencia, Spain.

The C-function, according to the ABC model of floral organ identity, is required for stamen and carpel development and to provide floral meristem determinacy. Members of the AG lineage of the large MADS box gene family specify the C-function in a broadly conserved manner in angiosperms. In core eudicots, two sub-lineages co-exist, euAG and PLE, which have been extensively characterized in Antirrhinum majus and Arabidopsis thaliana, where strong sub-functionalization has led to highly divergent contributions of the respective paralogs to the C-function. Read More

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September 2012

Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication.

BMC Evol Biol 2010 Apr 23;10:108. Epub 2010 Apr 23.

National Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.

Background: Various evolutionary models have been proposed to interpret the fate of paralogous duplicates, which provides substrates on which evolution selection could act. In particular, domestication, as a special selection, has played important role in crop cultivation with divergence of many genes controlling important agronomic traits. Recent studies have indicated that a pair of duplicate genes was often sub-functionalized from their ancestral functions held by the parental genes. Read More

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A role for gene duplication and natural variation of gene expression in the evolution of metabolism.

PLoS One 2008 Mar 19;3(3):e1838. Epub 2008 Mar 19.

Department of Plant Sciences, University of California Davis, Davis, California, United States of America.

Background: Most eukaryotic genomes have undergone whole genome duplications during their evolutionary history. Recent studies have shown that the function of these duplicated genes can diverge from the ancestral gene via neo- or sub-functionalization within single genotypes. An additional possibility is that gene duplicates may also undergo partitioning of function among different genotypes of a species leading to genetic differentiation. Read More

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The family of DOF transcription factors: from green unicellular algae to vascular plants.

Mol Genet Genomics 2007 Apr 16;277(4):379-90. Epub 2006 Dec 16.

Laboratorio de Bioquímica y Biología Molecular, Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, E.T.S. Ingenieros Agrónomos, 28040, Madrid, Spain.

This article deals with the origin and evolution of the DOF transcription factor family through a phylogenetic analysis of those DOF sequences identified from a variety of representative organisms from different taxonomic groups: the green unicellular alga Chlamydomonas reinhardtii, the moss Physcomitrella patens, the fern Selaginella moellendorffii, the gymnosperm Pinus taeda, the dicotyledoneous Arabidopsis thaliana and the monocotyledoneous angiosperms Oryza sativa and Hordeum vulgare. In barley, we have identified 26 different DOF genes by sequence analyses of clones isolated from the screening of genomic libraries and of ESTs, whereas a single DOF gene was identified by bioinformatics searches in the Chlamydomonas genome. The phylogenetic analysis groups all these genes into six major clusters of orthologs originated from a primary basal grade. Read More

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Does lack of recombination enhance asymmetric evolution among duplicate genes? Insights from the Drosophila melanogaster genome.

Gene 2006 Dec 17;385:89-95. Epub 2006 Aug 17.

Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS, Univ. Lyon 1, Villeurbanne Cedex, France.

Gene duplication has different outcomes: pseudogenization (death of one of the two copies), gene amplification (both copies remain the same), sub-functionalization (both copies are required to perform the ancestral function) and neo-functionalization (one copy acquires a new function). Asymmetric evolution (one copy evolves faster than the other) is usually seen as a signature of neo-functionalization. However, it has been proposed that sub-functionalization could also generate asymmetric evolution among duplicate genes when they experience different local recombination rates. Read More

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December 2006
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