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Zheng J, Zhang Z, Zhang N, Liang Y, Gong Z, Wang J, Ditta A, Sang Z, Wang J, Li X. Identification and function analysis of GABA branch three gene families in the cotton related to abiotic stresses. BMC PLANT BIOLOGY 2024; 24:57. [PMID: 38238675 PMCID: PMC10797812 DOI: 10.1186/s12870-024-04738-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 01/09/2024] [Indexed: 01/22/2024]
Abstract
γ -aminobutyric acid (GABA) is closely related to the growth, development and stress resistance of plants. Combined with the previous study of GABA to promote the cotton against abiotic stresses, the characteristics and expression patterns of GABA branch gene family laid the foundation for further explaining its role in cotton stress mechanism. Members of GAD, GAB-T and SSADH (three gene families of GABA branch) were identified from the Gossypium hirsutum, Gossypium barbadense, Gossypium arboreum and Gossypium raimondii genome. The GABA branch genes were 10 GAD genes, 4 GABA-T genes and 2 SSADH genes. The promoter sequences of genes mainly contains response-related elements such as light, hormone and environment.Phylogenetic analysis shows that GAD indicating that even in the same species, the homologous sequences in the family. The GABA-T gene of each cotton genus was in sum the family had gene loss in the process of dicotyledon evolution. SSADH families Gossypium hirsutum, Gossypium barbadense, Gossypium arboreum and Gossypium raimondii were closely related to the dicot plants.GABA gene is involved in the regulation of salt stress and high temperature in Gossypium hirsutum.GABA attenuated part of the abiotic stress damage by increasing leaf protective enzyme activity and reducing reactive oxygen species production.This lays the foundation for a thorough analysis of the mechanism of GABA in cotton stress resistance.
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Grants
- 2022YFD1200304-4 National key R&D Program of China
- 2022YFD1200304-4 National key R&D Program of China
- 2022YFD1200304-4 National key R&D Program of China
- 2022YFD1200304-4 National key R&D Program of China
- 2022YFD1200304-4 National key R&D Program of China
- 2022D01E20 Natural Science Foundation for Distinguished Young Scholars of Xinjiang Province, China
- 2022D01E20 Natural Science Foundation for Distinguished Young Scholars of Xinjiang Province, China
- 2022D01E20 Natural Science Foundation for Distinguished Young Scholars of Xinjiang Province, China
- 2022D01E20 Natural Science Foundation for Distinguished Young Scholars of Xinjiang Province, China
- 2022D01E20 Natural Science Foundation for Distinguished Young Scholars of Xinjiang Province, China
- no. U1903204, 31760405 the National Natural Science Foundation of China
- no. U1903204, 31760405 the National Natural Science Foundation of China
- no. U1903204, 31760405 the National Natural Science Foundation of China
- no. U1903204, 31760405 the National Natural Science Foundation of China
- no. U1903204, 31760405 the National Natural Science Foundation of China
- JZRC2019B02 Doctoral Program of Cash Crops Research Institute of Xinjiang Academy of Agricultural Science
- JZRC2019B02 Doctoral Program of Cash Crops Research Institute of Xinjiang Academy of Agricultural Science
- JZRC2019B02 Doctoral Program of Cash Crops Research Institute of Xinjiang Academy of Agricultural Science
- JZRC2019B02 Doctoral Program of Cash Crops Research Institute of Xinjiang Academy of Agricultural Science
- xjnkywdzc-2022001-2 Xinjiang Key Laboratory of Crop Biotechnology
- xjnkywdzc-2022001-2 Xinjiang Key Laboratory of Crop Biotechnology
- xjnkywdzc-2022001-2 Xinjiang Key Laboratory of Crop Biotechnology
- xjnkywdzc-2022001-2 Xinjiang Key Laboratory of Crop Biotechnology
- xjnkywdzc-2022001-2 Xinjiang Key Laboratory of Crop Biotechnology
- National key R&D Program of China
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Affiliation(s)
- Juyun Zheng
- Cash Crops Research Institute of Xinjiang Academy of Agricultural Science ( XAAS ), 830001, Urumqi, Xinjiang, P.R. China
| | - Zeliang Zhang
- Xinjiang Production and Construction Corps, Fifth Division, Eighty-third Regiment, Economic Development Office, 833400, Jinhe, Xinjiang, P.R. China
| | - Nala Zhang
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, 830052, Urumqi, Xinjiang, P.R. China
| | - Yajun Liang
- Cash Crops Research Institute of Xinjiang Academy of Agricultural Science ( XAAS ), 830001, Urumqi, Xinjiang, P.R. China
| | - Zhaolong Gong
- Cash Crops Research Institute of Xinjiang Academy of Agricultural Science ( XAAS ), 830001, Urumqi, Xinjiang, P.R. China
| | - Junhao Wang
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, 830052, Urumqi, Xinjiang, P.R. China
| | - Allah Ditta
- Cotton Group, Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology (NIAB) Faisalabad, NIAB-C Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Zhiwei Sang
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, 830052, Urumqi, Xinjiang, P.R. China
| | - Junduo Wang
- Cash Crops Research Institute of Xinjiang Academy of Agricultural Science ( XAAS ), 830001, Urumqi, Xinjiang, P.R. China.
| | - Xueyuan Li
- Cash Crops Research Institute of Xinjiang Academy of Agricultural Science ( XAAS ), 830001, Urumqi, Xinjiang, P.R. China.
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2
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Kumawat S, Choi JY. No end in sight: Mysteries of the telomeric variation in plants. AMERICAN JOURNAL OF BOTANY 2023; 110:e16244. [PMID: 37733763 PMCID: PMC10873042 DOI: 10.1002/ajb2.16244] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 09/23/2023]
Affiliation(s)
- Surbhi Kumawat
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
| | - Jae Young Choi
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
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3
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Kusová A, Steinbachová L, Přerovská T, Drábková LZ, Paleček J, Khan A, Rigóová G, Gadiou Z, Jourdain C, Stricker T, Schubert D, Honys D, Schrumpfová PP. Completing the TRB family: newly characterized members show ancient evolutionary origins and distinct localization, yet similar interactions. PLANT MOLECULAR BIOLOGY 2023; 112:61-83. [PMID: 37118559 PMCID: PMC10167121 DOI: 10.1007/s11103-023-01348-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/02/2023] [Indexed: 05/09/2023]
Abstract
Telomere repeat binding proteins (TRBs) belong to a family of proteins possessing a Myb-like domain which binds to telomeric repeats. Three members of this family (TRB1, TRB2, TRB3) from Arabidopsis thaliana have already been described as associated with terminal telomeric repeats (telomeres) or short interstitial telomeric repeats in gene promoters (telo-boxes). They are also known to interact with several protein complexes: telomerase, Polycomb repressive complex 2 (PRC2) E(z) subunits and the PEAT complex (PWOs-EPCRs-ARIDs-TRBs). Here we characterize two novel members of the TRB family (TRB4 and TRB5). Our wide phylogenetic analyses have shown that TRB proteins evolved in the plant kingdom after the transition to a terrestrial habitat in Streptophyta, and consequently TRBs diversified in seed plants. TRB4-5 share common TRB motifs while differing in several others and seem to have an earlier phylogenetic origin than TRB1-3. Their common Myb-like domains bind long arrays of telomeric repeats in vitro, and we have determined the minimal recognition motif of all TRBs as one telo-box. Our data indicate that despite the distinct localization patterns of TRB1-3 and TRB4-5 in situ, all members of TRB family mutually interact and also bind to telomerase/PRC2/PEAT complexes. Additionally, we have detected novel interactions between TRB4-5 and EMF2 and VRN2, which are Su(z)12 subunits of PRC2.
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Affiliation(s)
- Alžbeta Kusová
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Lenka Steinbachová
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czech Republic
| | - Tereza Přerovská
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Lenka Záveská Drábková
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jan Paleček
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Ahamed Khan
- Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Gabriela Rigóová
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Zuzana Gadiou
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czech Republic
| | - Claire Jourdain
- Institute of Biology, Freie Universität Berlin, 14195, Berlin, Germany
| | - Tino Stricker
- Institute of Biology, Freie Universität Berlin, 14195, Berlin, Germany
| | - Daniel Schubert
- Institute of Biology, Freie Universität Berlin, 14195, Berlin, Germany
| | - David Honys
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Petra Procházková Schrumpfová
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic.
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
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4
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Borges G, Criqui M, Harrington L. Tieing together loose ends: telomere instability in cancer and aging. Mol Oncol 2022; 16:3380-3396. [PMID: 35920280 PMCID: PMC9490142 DOI: 10.1002/1878-0261.13299] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 07/27/2022] [Accepted: 08/02/2022] [Indexed: 11/29/2022] Open
Abstract
Telomere maintenance is essential for maintaining genome integrity in both normal and cancer cells. Without functional telomeres, chromosomes lose their protective structure and undergo fusion and breakage events that drive further genome instability, including cell arrest or death. One means by which this loss can be overcome in stem cells and cancer cells is via re‐addition of G‐rich telomeric repeats by the telomerase reverse transcriptase (TERT). During aging of somatic tissues, however, insufficient telomerase expression leads to a proliferative arrest called replicative senescence, which is triggered when telomeres reach a critically short threshold that induces a DNA damage response. Cancer cells express telomerase but do not entirely escape telomere instability as they often possess short telomeres; hence there is often selection for genetic alterations in the TERT promoter that result in increased telomerase expression. In this review, we discuss our current understanding of the consequences of telomere instability in cancer and aging, and outline the opportunities and challenges that lie ahead in exploiting the reliance of cells on telomere maintenance for preserving genome stability.
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Affiliation(s)
- Gustavo Borges
- University of Montreal, Molecular Biology Programme, Institute for Research in Immunology and Cancer, 2950 chemin Polytechnique, Montreal, Quebec, Canada H3T 1J4
| | - Mélanie Criqui
- University of Montreal, Molecular Biology Programme, Institute for Research in Immunology and Cancer, 2950 chemin Polytechnique, Montreal, Quebec, Canada H3T 1J4
| | - Lea Harrington
- University of Montreal, Molecular Biology Programme, Institute for Research in Immunology and Cancer, 2950 chemin Polytechnique, Montreal, Quebec, Canada H3T 1J4.,Departments of Medicine and Biochemistry and Molecular Medicine, University of Montreal, Montreal, QC H3T 1J4
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5
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Shakirov EV, Chen JJL, Shippen DE. Plant telomere biology: The green solution to the end-replication problem. THE PLANT CELL 2022; 34:2492-2504. [PMID: 35511166 PMCID: PMC9252485 DOI: 10.1093/plcell/koac122] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/14/2022] [Indexed: 05/04/2023]
Abstract
Telomere maintenance is a fundamental cellular process conserved across all eukaryotic lineages. Although plants and animals diverged over 1.5 billion years ago, lessons learned from plants continue to push the boundaries of science, revealing detailed molecular mechanisms in telomere biology with broad implications for human health, aging biology, and stress responses. Recent studies of plant telomeres have unveiled unexpected divergence in telomere sequence and architecture, and the proteins that engage telomeric DNA and telomerase. The discovery of telomerase RNA components in the plant kingdom and some algae groups revealed new insight into the divergent evolution and the universal core of telomerase across major eukaryotic kingdoms. In addition, resources cataloging the abundant natural variation in Arabidopsis thaliana, maize (Zea mays), and other plants are providing unparalleled opportunities to understand the genetic networks that govern telomere length polymorphism and, as a result, are uncovering unanticipated crosstalk between telomeres, environmental factors, organismal fitness, and plant physiology. Here we recap current advances in plant telomere biology and put this field in perspective relative to telomere and telomerase research in other eukaryotic lineages.
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Affiliation(s)
- Eugene V Shakirov
- Department of Biological Sciences, College of Science, Marshall University, Huntington, West Virginia 25701, USA
| | - Julian J -L Chen
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
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6
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Abstract
Repeat-enriched genomic regions evolve rapidly and yet support strictly conserved functions like faithful chromosome transmission and the preservation of genome integrity. The leading resolution to this paradox is that DNA repeat-packaging proteins evolve adaptively to mitigate deleterious changes in DNA repeat copy number, sequence, and organization. Exciting new research has tested this model of coevolution by engineering evolutionary mismatches between adaptively evolving chromatin proteins of one species and the DNA repeats of a close relative. Here, we review these innovative evolution-guided functional analyses. The studies demonstrate that vital, chromatin-mediated cellular processes, including transposon suppression, faithful chromosome transmission, and chromosome retention depend on species-specific versions of chromatin proteins that package species-specific DNA repeats. In many cases, the ever-evolving repeats are selfish genetic elements, raising the possibility that chromatin is a battleground of intragenomic conflict.
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Affiliation(s)
- Cara L Brand
- Department of Biology and Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
| | - Mia T Levine
- Department of Biology and Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
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7
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Genome evolution of the psammophyte Pugionium for desert adaptation and further speciation. Proc Natl Acad Sci U S A 2021; 118:2025711118. [PMID: 34649989 PMCID: PMC8545485 DOI: 10.1073/pnas.2025711118] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2021] [Indexed: 12/01/2022] Open
Abstract
Plants’ adaptations to and divergence in arid deserts have long fascinated scientists and the general public. Here, we present a genomic analysis of two congeneric desert plant species that clarifies their evolutionary history and shows that their common ancestor arose from a hybrid polyploidization, which provided genomic foundations for their survival in deserts. The whole-genome duplication was followed by translocation-based rearrangements of the ancestral chromosomes. Rapid evolution of genes in these reshuffled chromosomes contributed greatly to the divergences of the two species in desert microhabitats during which gene flow was continuous. Our results provide insights into plant adaptation in the arid deserts and highlight the significance of polyploidy-driven chromosomal structural variations in species divergence. Deserts exert strong selection pressures on plants, but the underlying genomic drivers of ecological adaptation and subsequent speciation remain largely unknown. Here, we generated de novo genome assemblies and conducted population genomic analyses of the psammophytic genus Pugionium (Brassicaceae). Our results indicated that this bispecific genus had undergone an allopolyploid event, and the two parental genomes were derived from two ancestral lineages with different chromosome numbers and structures. The postpolyploid expansion of gene families related to abiotic stress responses and lignin biosynthesis facilitated environmental adaptations of the genus to desert habitats. Population genomic analyses of both species further revealed their recent divergence with continuous gene flow, and the most divergent regions were found to be centered on three highly structurally reshuffled chromosomes. Genes under selection in these regions, which were mainly located in one of the two subgenomes, contributed greatly to the interspecific divergence in microhabitat adaptation.
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8
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Distinct functions of POT1 proteins contribute to the regulation of telomerase recruitment to telomeres. Nat Commun 2021; 12:5514. [PMID: 34535663 PMCID: PMC8448735 DOI: 10.1038/s41467-021-25799-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 08/27/2021] [Indexed: 01/07/2023] Open
Abstract
Human shelterin components POT1 and TPP1 form a stable heterodimer that protects telomere ends from ATR-dependent DNA damage responses and regulates telomerase-dependent telomere extension. Mice possess two functionally distinct POT1 proteins. POT1a represses ATR/CHK1 DNA damage responses and the alternative non-homologous end-joining DNA repair pathway while POT1b regulates C-strand resection and recruits the CTC1-STN1-TEN1 (CST) complex to telomeres to mediate C-strand fill-in synthesis. Whether POT1a and POT1b are involved in regulating the length of the telomeric G-strand is unclear. Here we demonstrate that POT1b, independent of its CST function, enhances recruitment of telomerase to telomeres through three amino acids in its TPP1 interacting C-terminus. POT1b thus coordinates the synthesis of both telomeric G- and C-strands. In contrast, POT1a negatively regulates telomere length by inhibiting telomerase recruitment to telomeres. The identification of unique amino acids between POT1a and POT1b helps us understand mechanistically how human POT1 switches between end protective functions and promoting telomerase recruitment.
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9
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Song J, Castillo-González C, Ma Z, Shippen DE. Arabidopsis retains vertebrate-type telomerase accessory proteins via a plant-specific assembly. Nucleic Acids Res 2021; 49:9496-9507. [PMID: 34403479 PMCID: PMC8450087 DOI: 10.1093/nar/gkab699] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/08/2021] [Accepted: 08/11/2021] [Indexed: 11/17/2022] Open
Abstract
The recent discovery of the bona-fide telomerase RNA (TR) from plants reveals conserved and unique secondary structure elements and the opportunity for new insight into the telomerase RNP. Here we examine how two highly conserved proteins previously implicated in Arabidopsis telomere maintenance, AtPOT1a and AtNAP57 (dyskerin), engage plant telomerase. We report that AtPOT1a associates with Arabidopsis telomerase via interaction with TERT. While loss of AtPOT1a does not impact AtTR stability, the templating domain is more accessible in pot1a mutants, supporting the conclusion that AtPOT1a stimulates telomerase activity but does not facilitate telomerase RNP assembly. We also show, that despite the absence of a canonical H/ACA binding motif within AtTR, dyskerin binds AtTR with high affinity and specificity in vitro via a plant specific three-way junction (TWJ). A core element of the TWJ is the P1a stem, which unites the 5′ and 3′ ends of AtTR. P1a is required for dyskerin-mediated stimulation of telomerase repeat addition processivity in vitro, and for AtTR accumulation and telomerase activity in vivo. The deployment of vertebrate-like accessory proteins and unique RNA structural elements by Arabidopsis telomerase provides a new platform for exploring telomerase biogenesis and evolution.
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Affiliation(s)
- Jiarui Song
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA
| | - Claudia Castillo-González
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA
| | - Zeyang Ma
- National Maize Improvement Center of China, China Agricultural University, 100193 Beijing, China
- College of Agronomy and Biotechnology, China Agricultural University, 100193 Beijing, China
| | - Dorothy E Shippen
- To whom correspondence should be addressed. Tel: +1 979 862 2342; Fax: +1 979 862 7638;
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10
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Single-stranded DNA-binding proteins in plant telomeres. Int J Biol Macromol 2020; 165:1463-1467. [PMID: 32998016 DOI: 10.1016/j.ijbiomac.2020.09.211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 09/13/2020] [Accepted: 09/23/2020] [Indexed: 11/21/2022]
Abstract
Telomere single-stranded DNA-binding proteins bind to the terminal single-stranded DNA of telomeres, maintaining and protecting the chromosomal end in eukaryotes. This paper focuses on the protective mechanism of single-stranded DNA-binding proteins in plant telomeres. This review summarizes the roles of plant single-stranded DNA-binding proteins and their influence on telomere length and telomerase. This review provides insights into the mechanism and development of single-stranded DNA-binding proteins in plants.
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11
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Yang Y, Zhou Z, Li Y, Lv Y, Yang D, Yang S, Wu J, Li X, Gu Z, Sun X, Yang Y. Uncovering the role of a positive selection site of wax ester synthase/diacylglycerol acyltransferase in two closely related Stipa species in wax ester synthesis under drought stress. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4159-4170. [PMID: 32309855 PMCID: PMC7475244 DOI: 10.1093/jxb/eraa194] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 04/17/2020] [Indexed: 06/02/2023]
Abstract
Natural selection drives local adaptations of species to biotic or abiotic environmental stresses. As a result, adaptive phenotypic divergence can evolve among related species living in different habitats. However, the genetic foundation of this divergence process remains largely unknown. Two closely related alpine grass species, Stipa capillacea and Stipa purpurea, are distributed in different rainfall regions of northern Tibet. Here, we analyzed the drought tolerance of these two closely related Stipa species, and found that S. purpurea was more resistance to drought stress than S. capillacea. To further understand the genetic diversity behind their adaptation to drought environments, a comprehensive gene repertoire was generated using PacBio isoform and Illumina RNA sequencing technologies. Bioinformatics analyses revealed that differential transcripts were mainly enriched in the wax synthetic pathway, and a threonine residue at position 239 of WSD1 was identified as having undergone positive selection in S. purpurea. Using heterologous expression in the Saccharomyces cerevisiae mutant H1246, site-directed mutagenesis studies demonstrated that a positive selection site results in changes to the wax esters profile. This difference may play an important role in S. purpurea in response to drought conditions, indicating that S. purpurea has evolved specific strategies involving its wax biosynthetic pathway as part of its long-term adaptation to the Qinghai-Tibet Plateau.
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Affiliation(s)
- Yunqiang Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, China
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Zhili Zhou
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, China
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Yan Li
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, China
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanqiu Lv
- College of Life Sciences, Changchun Normal University, Changchun, China
| | - Danni Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, China
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shihai Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, China
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jianshuang Wu
- Functional Biodiversity, Dahlem Center of Plant Sciences, Free University of Berlin, Berlin, Germany
| | - Xiong Li
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, China
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Zhijia Gu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, China
| | - Xudong Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, China
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Yongping Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, China
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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12
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Gong Y, Stock AJ, Liu Y. The enigma of excessively long telomeres in cancer: lessons learned from rare human POT1 variants. Curr Opin Genet Dev 2020; 60:48-55. [PMID: 32155570 DOI: 10.1016/j.gde.2020.02.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 01/17/2020] [Accepted: 02/02/2020] [Indexed: 01/10/2023]
Abstract
The discovery that rare POT1 variants are associated with extremely long telomeres and increased cancer predisposition has provided a framework to revisit the relationship between telomere length and cancer development. Telomere shortening is linked with increased risk for cancer. However, over the past decade, there is increasing evidence to show that extremely long telomeres caused by mutations in shelterin components (POT1, TPP1, and RAP1) also display an increased risk of cancer. Here, we will review current knowledge on germline mutations of POT1 identified from cancer-prone families. In particular, we will discuss some common features presented by the mutations through structure-function studies. We will further provide an overview of how POT1 mutations affect telomere length regulation and tumorigenesis.
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Affiliation(s)
- Yi Gong
- Biomedical Research Center, National Institute on Aging/National Institutes of Health, 251 Bayview Blvd, Baltimore, MD, USA.
| | - Amanda J Stock
- Biomedical Research Center, National Institute on Aging/National Institutes of Health, 251 Bayview Blvd, Baltimore, MD, USA
| | - Yie Liu
- Biomedical Research Center, National Institute on Aging/National Institutes of Health, 251 Bayview Blvd, Baltimore, MD, USA.
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13
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Saint-Leandre B, Levine MT. The Telomere Paradox: Stable Genome Preservation with Rapidly Evolving Proteins. Trends Genet 2020; 36:232-242. [PMID: 32155445 DOI: 10.1016/j.tig.2020.01.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 01/08/2020] [Accepted: 01/13/2020] [Indexed: 01/08/2023]
Abstract
Telomeres ensure chromosome length homeostasis and protection from catastrophic end-to-end chromosome fusions. All eukaryotes require this essential, strictly conserved telomere-dependent genome preservation. However, recent evolutionary analyses of mammals, plants, and flies report pervasive rapid evolution of telomere proteins. The causes of this paradoxical observation - that unconserved machinery underlies an essential, conserved function - remain enigmatic. Indeed, these fast-evolving telomere proteins bind, extend, and protect telomeric DNA, which itself evolves slowly in most systems. We hypothesize that the universally fast-evolving subtelomere - the telomere-adjacent, repetitive sequence - is a primary driver of the 'telomere paradox'. Under this model, radical sequence changes in the subtelomere perturb subtelomere-dependent, telomere functions. Compromised telomere function then spurs adaptation of telomere proteins to maintain telomere length homeostasis and protection. We propose an experimental framework that leverages both protein divergence and subtelomeric sequence divergence to test the hypothesis that subtelomere sequence evolution shapes recurrent innovation of telomere machinery.
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Affiliation(s)
- Bastien Saint-Leandre
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Mia T Levine
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA.
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14
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Luo M, Teng X, Wang B, Zhang J, Liu Y, Liu D, Li H, Lu H. Protection of telomeres 1 (POT1) of Pinus tabuliformis bound the telomere ssDNA. TREE PHYSIOLOGY 2020; 40:119-127. [PMID: 31860719 DOI: 10.1093/treephys/tpz125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 10/14/2019] [Accepted: 11/15/2019] [Indexed: 06/10/2023]
Abstract
Protection of telomeres 1 (POT1) is a telomeric protein that binds to the telomere single-stranded (ss) region. It plays an essential role in maintaining genomic stability in both plants and animals. In this study, we investigated the properties of POT1 in Pinus tabuliformis Carr. (PtPOT1) through electrophoretic mobility shift assay. PtPOT1 harbored affinity for telomeric ssDNA and could bind plant- and mammalian-type ssDNA sequences. Notably, there were two oligonucleotide/oligosaccharide binding (OB) folds, and OB1 or OB2 alone, or both together, could bind ssDNA, which is significantly different from human POT1. Based on our data, we hypothesized that the two OB folds of PtPOT1 bound the same ssDNA. This model not only provides new insight into the ssDNA binding of PtPOT1 but also sheds light on the functional divergence of POT1 proteins in gymnosperms and humans.
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Affiliation(s)
- Mei Luo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, No.35, Qinghua East road, Haidian District, Beijing 100083, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Xiaotong Teng
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Bing Wang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Jiaxue Zhang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Yadi Liu
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Di Liu
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Hui Li
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Hai Lu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, No.35, Qinghua East road, Haidian District, Beijing 100083, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
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15
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Barbero Barcenilla B, Shippen DE. Back to the future: The intimate and evolving connection between telomere-related factors and genotoxic stress. J Biol Chem 2019; 294:14803-14813. [PMID: 31434740 DOI: 10.1074/jbc.aw119.008145] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The conversion of circular genomes to linear chromosomes during molecular evolution required the invention of telomeres. This entailed the acquisition of factors necessary to fulfill two new requirements: the need to fully replicate terminal DNA sequences and the ability to distinguish chromosome ends from damaged DNA. Here we consider the multifaceted functions of factors recruited to perpetuate and stabilize telomeres. We discuss recent theories for how telomere factors evolved from existing cellular machineries and examine their engagement in nontelomeric functions such as DNA repair, replication, and transcriptional regulation. We highlight the remarkable versatility of protection of telomeres 1 (POT1) proteins that was fueled by gene duplication and divergence events that occurred independently across several eukaryotic lineages. Finally, we consider the relationship between oxidative stress and telomeres and the enigmatic role of telomere-associated proteins in mitochondria. These findings point to an evolving and intimate connection between telomeres and cellular physiology and the strong drive to maintain chromosome integrity.
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Affiliation(s)
- Borja Barbero Barcenilla
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128
| | - Dorothy E Shippen
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128
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16
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Kobayashi CR, Castillo-González C, Survotseva Y, Canal E, Nelson ADL, Shippen DE. Recent emergence and extinction of the protection of telomeres 1c gene in Arabidopsis thaliana. PLANT CELL REPORTS 2019; 38:1081-1097. [PMID: 31134349 PMCID: PMC6708462 DOI: 10.1007/s00299-019-02427-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/27/2019] [Indexed: 05/20/2023]
Abstract
Duplicate POT1 genes must rapidly diverge or be inactivated. Protection of telomeres 1 (POT1) encodes a conserved telomere binding protein implicated in both chromosome end protection and telomere length maintenance. Most organisms harbor a single POT1 gene, but in the few lineages where the POT1 family has expanded, the duplicate genes have diversified. Arabidopsis thaliana bears three POT1-like loci, POT1a, POT1b and POT1c. POT1a retains the ancestral function of telomerase regulation, while POT1b is implicated in chromosome end protection. Here we examine the function and evolution of the third POT1 paralog, POT1c. POT1c is a new gene, unique to A. thaliana, and was derived from a duplication event involving the POT1a locus and a neighboring gene encoding ribosomal protein S17. The duplicate S17 locus (dS17) is highly conserved across A. thaliana accessions, while POT1c is highly divergent, harboring multiple deletions within the gene body and two transposable elements within the promoter. The POT1c locus is transcribed at very low to non-detectable levels under standard growth conditions. In addition, no discernable molecular or developmental defects are associated with plants bearing a CRISPR mutation in the POT1c locus. However, forced expression of POT1c leads to decreased telomerase enzyme activity and shortened telomeres. Evolutionary reconstruction indicates that transposons invaded the POT1c promoter soon after the locus was formed, permanently silencing the gene. Altogether, these findings argue that POT1 dosage is critically important for viability and duplicate gene copies are retained only upon functional divergence.
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Affiliation(s)
- Callie R Kobayashi
- Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | | | - Yulia Survotseva
- Yale Center for Molecular Discovery, Yale University, New Haven, Connecticut, USA
| | - Elijah Canal
- Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Andrew D L Nelson
- The School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Dorothy E Shippen
- Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA.
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17
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Trujillo JT, Seetharam AS, Hufford MB, Beilstein MA, Mosher RA. Evidence for a Unique DNA-Dependent RNA Polymerase in Cereal Crops. Mol Biol Evol 2018; 35:2454-2462. [PMID: 30053133 PMCID: PMC6188566 DOI: 10.1093/molbev/msy146] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Gene duplication is an important driver for the evolution of new genes and protein functions. Duplication of DNA-dependent RNA polymerase (Pol) II subunits within plants led to the emergence of RNA Pol IV and V complexes, each of which possess unique functions necessary for RNA-directed DNA Methylation. Comprehensive identification of Pol V subunit orthologs across the monocot radiation revealed a duplication of the largest two subunits within the grasses (Poaceae), including critical cereal crops. These paralogous Pol subunits display sequence conservation within catalytic domains, but their carboxy terminal domains differ in length and character of the Ago-binding platform, suggesting unique functional interactions. Phylogenetic analysis of the catalytic region indicates positive selection on one paralog following duplication, consistent with retention via neofunctionalization. Positive selection on residue pairs that are predicted to interact between subunits suggests that paralogous subunits have evolved specific assembly partners. Additional Pol subunits as well as Pol-interacting proteins also possess grass-specific paralogs, supporting the hypothesis that a novel Pol complex with distinct function has evolved in the grass family, Poaceae.
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Affiliation(s)
- Joshua T Trujillo
- Department of Molecular & Cellular Biology, The University of Arizona, Tucson, AZ
| | | | - Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA
| | - Mark A Beilstein
- Department of Molecular & Cellular Biology, The University of Arizona, Tucson, AZ
- The School of Plant Sciences, The University of Arizona, Tucson, AZ
| | - Rebecca A Mosher
- Department of Molecular & Cellular Biology, The University of Arizona, Tucson, AZ
- The School of Plant Sciences, The University of Arizona, Tucson, AZ
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18
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Qiu Y, Liu SL, Adams KL. Concerted Divergence after Gene Duplication in Polycomb Repressive Complexes. PLANT PHYSIOLOGY 2017; 174:1192-1204. [PMID: 28455403 PMCID: PMC5462007 DOI: 10.1104/pp.16.01983] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 04/24/2017] [Indexed: 05/29/2023]
Abstract
Duplicated genes are a major contributor to genome evolution and phenotypic novelty. There are multiple possible evolutionary fates of duplicated genes. Here, we provide an example of concerted divergence of simultaneously duplicated genes whose products function in the same complex. We studied POLYCOMB REPRESSIVE COMPLEX2 (PRC2) in Brassicaceae. The VERNALIZATION (VRN)-PRC2 complex contains VRN2 and SWINGER (SWN), and both genes were duplicated during a whole-genome duplication to generate FERTILIZATION INDEPENDENT SEED2 (FIS2) and MEDEA (MEA), which function in the Brassicaceae-specific FIS-PRC2 complex that regulates seed development. We examined the expression of FIS2, MEA, and their paralogs, compared their cytosine and histone methylation patterns, and analyzed the sequence evolution of the genes. We found that FIS2 and MEA have reproductive-specific expression patterns that are correlated and derived from the broadly expressed VRN2 and SWN in outgroup species. In vegetative tissues of Arabidopsis (Arabidopsis thaliana), repressive methylation marks are enriched in FIS2 and MEA, whereas active marks are associated with their paralogs. We detected comparable accelerated amino acid substitution rates in FIS2 and MEA but not in their paralogs. We also show divergence patterns of the PRC2-associated VERNALIZATION5/VIN3-LIKE2 that are similar to FIS2 and MEA These lines of evidence indicate that FIS2 and MEA have diverged in concert, resulting in functional divergence of the PRC2 complexes in Brassicaceae. This type of concerted divergence is a previously unreported fate of duplicated genes. In addition, the Brassicaceae-specific FIS-PRC2 complex modified the regulatory pathways in female gametophyte and seed development.
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Affiliation(s)
- Yichun Qiu
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4 (Y.Q., K.L.A.); and
- Department of Life Science, Tunghai University, Taichung, Taiwan 40704 (S.-L.L.)
| | - Shao-Lun Liu
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4 (Y.Q., K.L.A.); and
- Department of Life Science, Tunghai University, Taichung, Taiwan 40704 (S.-L.L.)
| | - Keith L Adams
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4 (Y.Q., K.L.A.); and
- Department of Life Science, Tunghai University, Taichung, Taiwan 40704 (S.-L.L.)
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19
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Arora A, Beilstein MA, Shippen DE. Evolution of Arabidopsis protection of telomeres 1 alters nucleic acid recognition and telomerase regulation. Nucleic Acids Res 2016; 44:9821-9830. [PMID: 27651456 PMCID: PMC5175356 DOI: 10.1093/nar/gkw807] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 09/01/2016] [Accepted: 09/03/2016] [Indexed: 11/14/2022] Open
Abstract
Protection of telomeres (POT1) binds chromosome ends, recognizing single-strand telomeric DNA via two oligonucleotide/oligosaccharide binding folds (OB-folds). The Arabidopsis thaliana POT1a and POT1b paralogs are atypical: they do not exhibit telomeric DNA binding, and they have opposing roles in regulating telomerase activity. AtPOT1a stimulates repeat addition processivity of the canonical telomerase enzyme, while AtPOT1b interacts with a regulatory lncRNA that represses telomerase activity. Here, we show that OB1 of POT1a, but not POT1b, has an intrinsic affinity for telomeric DNA. DNA binding was dependent upon a highly conserved Phe residue (F65) that in human POT1 directly contacts telomeric DNA. F65A mutation of POT1aOB1 abolished DNA binding and diminished telomerase repeat addition processivity. Conversely, AtPOT1b and other POT1b homologs from Brassicaceae and its sister family, Cleomaceae, naturally bear a non-aromatic amino acid at this position. By swapping Val (V63) with Phe, AtPOT1bOB1 gained the capacity to bind telomeric DNA and to stimulate telomerase repeat addition processivity. We conclude that, in the context of DNA binding, variation at a single amino acid position promotes divergence of the AtPOT1b paralog from the ancestral POT1 protein.
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Affiliation(s)
- Amit Arora
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA
| | - Mark A Beilstein
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Dorothy E Shippen
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA
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20
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Liu Z, Tavares R, Forsythe ES, André F, Lugan R, Jonasson G, Boutet-Mercey S, Tohge T, Beilstein MA, Werck-Reichhart D, Renault H. Evolutionary interplay between sister cytochrome P450 genes shapes plasticity in plant metabolism. Nat Commun 2016; 7:13026. [PMID: 27713409 PMCID: PMC5059761 DOI: 10.1038/ncomms13026] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 08/26/2016] [Indexed: 12/19/2022] Open
Abstract
Expansion of the cytochrome P450 gene family is often proposed to have a critical role in the evolution of metabolic complexity, in particular in microorganisms, insects and plants. However, the molecular mechanisms underlying the evolution of this complexity are poorly understood. Here we describe the evolutionary history of a plant P450 retrogene, which emerged and underwent fixation in the common ancestor of Brassicales, before undergoing tandem duplication in the ancestor of Brassicaceae. Duplication leads first to gain of dual functions in one of the copies. Both sister genes are retained through subsequent speciation but eventually return to a single copy in two of three diverging lineages. In the lineage in which both copies are maintained, the ancestral functions are split between paralogs and a novel function arises in the copy under relaxed selection. Our work illustrates how retrotransposition and gene duplication can favour the emergence of novel metabolic functions.
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Affiliation(s)
- Zhenhua Liu
- Institute of Plant Molecular Biology, CNRS, University of Strasbourg, 12 rue du Général Zimmer, Strasbourg 67084 France
| | - Raquel Tavares
- Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Évolutive, 16 rue Raphael Dubois, 69622 Villeurbanne Cedex, France
| | - Evan S Forsythe
- School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
| | - François André
- iBiTec-S/SB2SM, UMR 9198 CNRS, University Paris Sud, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Raphaël Lugan
- Institute of Plant Molecular Biology, CNRS, University of Strasbourg, 12 rue du Général Zimmer, Strasbourg 67084 France
| | - Gabriella Jonasson
- iBiTec-S/SB2SM, UMR 9198 CNRS, University Paris Sud, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Stéphanie Boutet-Mercey
- Institut Jean-Pierre Bourgin, UMR 1318 INRA-AgroParisTech, Saclay Plant Sciences RD10, 78026 Versailles, France
| | - Takayuki Tohge
- Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology, 14476 Potsdam-Golm, Germany
| | - Mark A Beilstein
- School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
| | - Danièle Werck-Reichhart
- Institute of Plant Molecular Biology, CNRS, University of Strasbourg, 12 rue du Général Zimmer, Strasbourg 67084 France.,University of Strasbourg Institute for Advanced Study, 67000 Strasbourg, France.,Freiburg Institute for Advanced Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Hugues Renault
- Institute of Plant Molecular Biology, CNRS, University of Strasbourg, 12 rue du Général Zimmer, Strasbourg 67084 France.,University of Strasbourg Institute for Advanced Study, 67000 Strasbourg, France.,Freiburg Institute for Advanced Studies, University of Freiburg, 79104 Freiburg, Germany
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21
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Franzke A, Koch MA, Mummenhoff K. Turnip Time Travels: Age Estimates in Brassicaceae. TRENDS IN PLANT SCIENCE 2016; 21:554-561. [PMID: 26917156 DOI: 10.1016/j.tplants.2016.01.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 01/19/2016] [Accepted: 01/31/2016] [Indexed: 05/07/2023]
Abstract
Results of research in life sciences acquire a deeper meaning if they can also be discussed in temporal contexts of evolution. Despite the importance of the mustard family (Brassicaceae) as a prominent angiosperm model family, a robust, generally accepted hypothesis for a family-wide temporal framework does not yet exist. The main cause for this situation is a poor fossil record of the family. We suggest that the few known fossils require a critical re-evaluation of phylogenetic and temporal assignments as a prerequisite for appropriate molecular dating analyses within the family. In addition, (palaeo)biogeographical calibrations, not explored so far in the family, should be integrated in a synthesis of various dating approaches, with each contributing their specific possibilities and limitations.
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Affiliation(s)
- Andreas Franzke
- Heidelberg Botanic Garden, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, D-69120 Heidelberg, Germany.
| | - Marcus A Koch
- Heidelberg Botanic Garden, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, D-69120 Heidelberg, Germany; Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, D-69120 Heidelberg, German
| | - Klaus Mummenhoff
- Biology Department, Botany, Osnabrück University, D-49069 Osnabrück, Germany
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22
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Procházková Schrumpfová P, Schořová Š, Fajkus J. Telomere- and Telomerase-Associated Proteins and Their Functions in the Plant Cell. FRONTIERS IN PLANT SCIENCE 2016; 7:851. [PMID: 27446102 PMCID: PMC4924339 DOI: 10.3389/fpls.2016.00851] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 05/31/2016] [Indexed: 05/20/2023]
Abstract
Telomeres, as physical ends of linear chromosomes, are targets of a number of specific proteins, including primarily telomerase reverse transcriptase. Access of proteins to the telomere may be affected by a number of diverse factors, e.g., protein interaction partners, local DNA or chromatin structures, subcellular localization/trafficking, or simply protein modification. Knowledge of composition of the functional nucleoprotein complex of plant telomeres is only fragmentary. Moreover, the plant telomeric repeat binding proteins that were characterized recently appear to also be involved in non-telomeric processes, e.g., ribosome biogenesis. This interesting finding was not totally unexpected since non-telomeric functions of yeast or animal telomeric proteins, as well as of telomerase subunits, have been reported for almost a decade. Here we summarize known facts about the architecture of plant telomeres and compare them with the well-described composition of telomeres in other organisms.
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Affiliation(s)
- Petra Procházková Schrumpfová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk UniversityBrno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk UniversityBrno, Czech Republic
- *Correspondence: Petra Procházková Schrumpfová,
| | - Šárka Schořová
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk UniversityBrno, Czech Republic
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk UniversityBrno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk UniversityBrno, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i.Brno, Czech Republic
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23
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Huang Y, Kendall T, Forsythe ES, Dorantes-Acosta A, Li S, Caballero-Pérez J, Chen X, Arteaga-Vázquez M, Beilstein MA, Mosher RA. Ancient Origin and Recent Innovations of RNA Polymerase IV and V. Mol Biol Evol 2015; 32:1788-99. [PMID: 25767205 PMCID: PMC4476159 DOI: 10.1093/molbev/msv060] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Small RNA-mediated chromatin modification is a conserved feature of eukaryotes. In flowering plants, the short interfering (si)RNAs that direct transcriptional silencing are abundant and subfunctionalization has led to specialized machinery responsible for synthesis and action of these small RNAs. In particular, plants possess polymerase (Pol) IV and Pol V, multi-subunit homologs of the canonical DNA-dependent RNA Pol II, as well as specialized members of the RNA-dependent RNA Polymerase (RDR), Dicer-like (DCL), and Argonaute (AGO) families. Together these enzymes are required for production and activity of Pol IV-dependent (p4-)siRNAs, which trigger RNA-directed DNA methylation (RdDM) at homologous sequences. p4-siRNAs accumulate highly in developing endosperm, a specialized tissue found only in flowering plants, and are rare in nonflowering plants, suggesting that the evolution of flowers might coincide with the emergence of specialized RdDM machinery. Through comprehensive identification of RdDM genes from species representing the breadth of the land plant phylogeny, we describe the ancient origin of Pol IV and Pol V, suggesting that a nearly complete and functional RdDM pathway could have existed in the earliest land plants. We also uncover innovations in these enzymes that are coincident with the emergence of seed plants and flowering plants, and recent duplications that might indicate additional subfunctionalization. Phylogenetic analysis reveals rapid evolution of Pol IV and Pol V subunits relative to their Pol II counterparts and suggests that duplicates were retained and subfunctionalized through Escape from Adaptive Conflict. Evolution within the carboxy-terminal domain of the Pol V largest subunit is particularly striking, where illegitimate recombination facilitated extreme sequence divergence.
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Affiliation(s)
- Yi Huang
- The School of Plant Sciences, The University of Arizona
| | - Timmy Kendall
- The School of Plant Sciences, The University of Arizona
| | | | - Ana Dorantes-Acosta
- Instituto de Biotecnología y Ecología Aplicada (INBIOTECA), Universidad Veracruzana, Veracruz, México
| | - Shaofang Li
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside
| | | | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside
| | - Mario Arteaga-Vázquez
- Instituto de Biotecnología y Ecología Aplicada (INBIOTECA), Universidad Veracruzana, Veracruz, México
| | | | - Rebecca A Mosher
- The School of Plant Sciences, The University of Arizona The Bio5 Institute, The University of Arizona
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