101
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Yang Y, Moore MJ, Brockington SF, Soltis DE, Wong GKS, Carpenter EJ, Zhang Y, Chen L, Yan Z, Xie Y, Sage RF, Covshoff S, Hibberd JM, Nelson MN, Smith SA. Dissecting Molecular Evolution in the Highly Diverse Plant Clade Caryophyllales Using Transcriptome Sequencing. Mol Biol Evol 2015; 32:2001-14. [PMID: 25837578 PMCID: PMC4833068 DOI: 10.1093/molbev/msv081] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Many phylogenomic studies based on transcriptomes have been limited to “single-copy” genes due to methodological challenges in homology and orthology inferences. Only a relatively small number of studies have explored analyses beyond reconstructing species relationships. We sampled 69 transcriptomes in the hyperdiverse plant clade Caryophyllales and 27 outgroups from annotated genomes across eudicots. Using a combined similarity- and phylogenetic tree-based approach, we recovered 10,960 homolog groups, where each was represented by at least eight ingroup taxa. By decomposing these homolog trees, and taking gene duplications into account, we obtained 17,273 ortholog groups, where each was represented by at least ten ingroup taxa. We reconstructed the species phylogeny using a 1,122-gene data set with a gene occupancy of 92.1%. From the homolog trees, we found that both synonymous and nonsynonymous substitution rates in herbaceous lineages are up to three times as fast as in their woody relatives. This is the first time such a pattern has been shown across thousands of nuclear genes with dense taxon sampling. We also pinpointed regions of the Caryophyllales tree that were characterized by relatively high frequencies of gene duplication, including three previously unrecognized whole-genome duplications. By further combining information from homolog tree topology and synonymous distance between paralog pairs, phylogenetic locations for 13 putative genome duplication events were identified. Genes that experienced the greatest gene family expansion were concentrated among those involved in signal transduction and oxidoreduction, including a cytochrome P450 gene that encodes a key enzyme in the betalain synthesis pathway. Our approach demonstrates a new approach for functional phylogenomic analysis in nonmodel species that is based on homolog groups in addition to inferred ortholog groups.
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Affiliation(s)
- Ya Yang
- Department of Ecology & Evolutionary Biology, University of Michigan
| | - Michael J Moore
- Department of Biology, Oberlin College, Science Center K111, Oberlin, OH
| | - Samuel F Brockington
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Douglas E Soltis
- Department of Biology, University of Florida Florida Museum of Natural History, University of Florida Genetics Institute, University of Florida
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada Department of Medicine, University of Alberta, Edmonton, AB, Canada BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, China
| | - Eric J Carpenter
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Yong Zhang
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, China
| | - Li Chen
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, China
| | - Zhixiang Yan
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, China
| | - Yinlong Xie
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, China
| | - Rowan F Sage
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Sarah Covshoff
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Matthew N Nelson
- School of Plant Biology, The University of Western Australia, Crawley, WA, Australia
| | - Stephen A Smith
- Department of Ecology & Evolutionary Biology, University of Michigan
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102
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Wisecaver JH, Rokas A. Fungal metabolic gene clusters-caravans traveling across genomes and environments. Front Microbiol 2015; 6:161. [PMID: 25784900 PMCID: PMC4347624 DOI: 10.3389/fmicb.2015.00161] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 02/11/2015] [Indexed: 11/13/2022] Open
Abstract
Metabolic gene clusters (MGCs), physically co-localized genes participating in the same metabolic pathway, are signature features of fungal genomes. MGCs are most often observed in specialized metabolism, having evolved in individual fungal lineages in response to specific ecological needs, such as the utilization of uncommon nutrients (e.g., galactose and allantoin) or the production of secondary metabolic antimicrobial compounds and virulence factors (e.g., aflatoxin and melanin). A flurry of recent studies has shown that several MGCs, whose functions are often associated with fungal virulence as well as with the evolutionary arms race between fungi and their competitors, have experienced horizontal gene transfer (HGT). In this review, after briefly introducing HGT as a source of gene innovation, we examine the evidence for HGT's involvement on the evolution of MGCs and, more generally of fungal metabolism, enumerate the molecular mechanisms that mediate such transfers and the ecological circumstances that favor them, as well as discuss the types of evidence required for inferring the presence of HGT in MGCs. The currently available examples indicate that transfers of entire MGCs have taken place between closely related fungal species as well as distant ones and that they sometimes involve large chromosomal segments. These results suggest that the HGT-mediated acquisition of novel metabolism is an ongoing and successful ecological strategy for many fungal species.
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Affiliation(s)
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University Nashville, TN, USA
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103
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Brockington SF, Moyroud E, Sayou C, Monniaux M, Nanao MH, Thévenon E, Chahtane H, Warthmann N, Melkonian M, Zhang Y, Wong GKS, Weigel D, Dumas R, Parcy F. Evolution. Response to Comment on "A promiscuous intermediate underlies the evolution of LEAFY DNA binding specificity". Science 2015; 347:621. [PMID: 25657241 DOI: 10.1126/science.1256011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Brunkard et al. propose that the identification of novel LEAFY sequences contradicts our model of evolution through promiscuous intermediates. Based on the debate surrounding land plant phylogeny and on our analysis of these interesting novel sequences, we explain why there is no solid evidence to disprove our model.
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Affiliation(s)
- Samuel F Brockington
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Edwige Moyroud
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Camille Sayou
- Wellcome Trust Center for Cell Biology, Michael Swann Building 5.1, King's Buildings. Edinburgh, EH9 3JR, UK
| | - Marie Monniaux
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, 50829, Köln, Germany
| | - Max H Nanao
- European Molecular Biology Laboratory (EMBL), 6 Rue Jules Horowitz, BP 181, 38042 Grenoble, France. Unit of Virus Host-Cell Interactions, Université Grenoble Alpes (UGA), Centre National de la Recherche Scientifique (CNRS), EMBL, UMI 3265, 6 Rue Jules Horowitz, 38042 Grenoble Cedex 9, France.
| | - Emmanuel Thévenon
- CNRS, Laboratoire de Physiologie Cellulaire et Végétale (LPCV), UMR 5168, 38054 Grenoble, France. UGA, LPCV, F-38054 Grenoble, France. Commissariat à l'énergie atomique et aux énergies alternatives, Direction des Sciences du Vivant, Institut de Recherches en Technologies et Sciences pour le Vivant, LPCV, F-38054 Grenoble, France. Institut National de la Recherche Agronomique, LPCV, F-38054 Grenoble, France
| | - Hicham Chahtane
- CNRS, Laboratoire de Physiologie Cellulaire et Végétale (LPCV), UMR 5168, 38054 Grenoble, France. UGA, LPCV, F-38054 Grenoble, France. Commissariat à l'énergie atomique et aux énergies alternatives, Direction des Sciences du Vivant, Institut de Recherches en Technologies et Sciences pour le Vivant, LPCV, F-38054 Grenoble, France. Institut National de la Recherche Agronomique, LPCV, F-38054 Grenoble, France
| | - Norman Warthmann
- Research School of Biology, The Australian National University, Acton, ACT 0200, Australia
| | - Michael Melkonian
- Botanisches Institut, Lehrstuhl I, Universität zu Köln, Biozentrum Köln, Zülpicher Strasse 47b, 50674 Köln, Germany
| | - Yong Zhang
- Beijing Genomics Institute, Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Gane Ka-Shu Wong
- Beijing Genomics Institute, Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China Department of Biological Sciences, Department of Medicine, University of Alberta, Edmonton AB, T6G 2E9, Canada
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Renaud Dumas
- CNRS, Laboratoire de Physiologie Cellulaire et Végétale (LPCV), UMR 5168, 38054 Grenoble, France. UGA, LPCV, F-38054 Grenoble, France. Commissariat à l'énergie atomique et aux énergies alternatives, Direction des Sciences du Vivant, Institut de Recherches en Technologies et Sciences pour le Vivant, LPCV, F-38054 Grenoble, France. Institut National de la Recherche Agronomique, LPCV, F-38054 Grenoble, France
| | - François Parcy
- CNRS, Laboratoire de Physiologie Cellulaire et Végétale (LPCV), UMR 5168, 38054 Grenoble, France. UGA, LPCV, F-38054 Grenoble, France. Commissariat à l'énergie atomique et aux énergies alternatives, Direction des Sciences du Vivant, Institut de Recherches en Technologies et Sciences pour le Vivant, LPCV, F-38054 Grenoble, France. Institut National de la Recherche Agronomique, LPCV, F-38054 Grenoble, France.
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104
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Kanegae T. Intramolecular co-action of two independent photosensory modules in the fern phytochrome 3. PLANT SIGNALING & BEHAVIOR 2015; 10:e1086857. [PMID: 26340326 PMCID: PMC4883953 DOI: 10.1080/15592324.2015.1086857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 08/20/2015] [Accepted: 08/20/2015] [Indexed: 06/05/2023]
Abstract
Fern phytochrome3/neochrome1 (phy3/neo1) is a chimeric photoreceptor composed of a phytochrome-chromophore binding domain and an almost full-length phototropin. phy3 thus contains two different light-sensing modules; a red/far-red light receptor phytochrome and a blue light receptor phototropin. phy3 induces both red light- and blue light-dependent phototropism in phototropin-deficient Arabidopsis thaliana (phot1 phot2) seedlings. The red-light response is dependent on the phytochrome module of phy3, and the blue-light response is dependent on the phototropin module. We recently showed that both the phototropin-sensing module and the phytochrome-sensing module mediate the blue light-dependent phototropic response. Particularly under low-light conditions, these two light-sensing modules cooperate to induce the blue light-dependent phototropic response. This intramolecular co-action of two independent light-sensing modules in phy3 enhances light sensitivity, and perhaps allowed ferns to adapt to the low-light canopy conditions present in angiosperm forests.
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Affiliation(s)
- Takeshi Kanegae
- Department of Biological Sciences; Graduate School of Science and Technology; Tokyo Metropolitan University; Tokyo, Japan
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105
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Li FW, Rothfels CJ, Melkonian M, Villarreal JC, Stevenson DW, Graham SW, Wong GKS, Mathews S, Pryer KM. The origin and evolution of phototropins. FRONTIERS IN PLANT SCIENCE 2015; 6:637. [PMID: 26322073 PMCID: PMC4532919 DOI: 10.3389/fpls.2015.00637] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Accepted: 07/31/2015] [Indexed: 05/19/2023]
Abstract
Plant phototropism, the ability to bend toward or away from light, is predominantly controlled by blue-light photoreceptors, the phototropins. Although phototropins have been well-characterized in Arabidopsis thaliana, their evolutionary history is largely unknown. In this study, we complete an in-depth survey of phototropin homologs across land plants and algae using newly available transcriptomic and genomic data. We show that phototropins originated in an ancestor of Viridiplantae (land plants + green algae). Phototropins repeatedly underwent independent duplications in most major land-plant lineages (mosses, lycophytes, ferns, and seed plants), but remained single-copy genes in liverworts and hornworts-an evolutionary pattern shared with another family of photoreceptors, the phytochromes. Following each major duplication event, the phototropins differentiated in parallel, resulting in two specialized, yet partially overlapping, functional forms that primarily mediate either low- or high-light responses. Our detailed phylogeny enables us to not only uncover new phototropin lineages, but also link our understanding of phototropin function in Arabidopsis with what is known in Adiantum and Physcomitrella (the major model organisms outside of flowering plants). We propose that the convergent functional divergences of phototropin paralogs likely contributed to the success of plants through time in adapting to habitats with diverse and heterogeneous light conditions.
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Affiliation(s)
- Fay-Wei Li
- Department of Biology, Duke UniversityDurham, NC, USA
- *Correspondence: Fay-Wei Li, Department of Biology, Duke University, Biological Sciences Building, 130 Science Drive, Durham, NC 27708, USA,
| | - Carl J. Rothfels
- University Herbarium and Department of Integrative Biology, University of California at BerkeleyBerkeley, CA, USA
| | - Michael Melkonian
- Botany Department, Cologne Biocenter, University of CologneCologne, Germany
| | | | | | - Sean W. Graham
- Department of Botany, University of British ColumbiaVancouver, BC, Canada
| | - Gane K.-S. Wong
- Department of Biological Sciences, University of AlbertaEdmonton, AB, Canada
- Department of Medicine, University of AlbertaEdmonton, AB, Canada
- BGI-ShenzhenShenzhen, China
| | - Sarah Mathews
- CSIRO, Centre for Australian National Biodiversity ResearchCanberra, ACT, Australia
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106
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Bao L, Yamamoto KT, Fujita T. Phototropism in gametophytic shoots of the moss Physcomitrella patens. PLANT SIGNALING & BEHAVIOR 2015; 10:e1010900. [PMID: 25848889 PMCID: PMC4623243 DOI: 10.1080/15592324.2015.1010900] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 01/13/2015] [Accepted: 01/15/2015] [Indexed: 06/04/2023]
Abstract
Shoot phototropism enables plants to position their photosynthetic organs in favorable light conditions and thus benefits growth and metabolism in land plants. To understand the evolution of this response, we established an experimental system to study phototropism in gametophores of the moss Physcomitrella patens. The phototropic response of gametophores occurs slowly; a clear response takes place more than 24 hours after the onset of unilateral light irradiation, likely due to the slow growth rate of gametophores. We also found that red and far-red light can induce phototropism, with blue light being less effective. These results suggest that plants used a broad range of light wavelengths as phototropic signals during the early evolution of land plants.
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Affiliation(s)
- Liang Bao
- Biosystems Science Course; Graduate School of Life Science; Hokkaido University; Sapporo, Japan
| | - Kotaro T Yamamoto
- Department of Biological Sciences; Faculty of Science; Hokkaido University; Sapporo, Japan
| | - Tomomichi Fujita
- Department of Biological Sciences; Faculty of Science; Hokkaido University; Sapporo, Japan
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107
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Aya K, Kobayashi M, Tanaka J, Ohyanagi H, Suzuki T, Yano K, Takano T, Yano K, Matsuoka M. De Novo Transcriptome Assembly of a Fern, Lygodium japonicum, and a Web Resource Database, Ljtrans DB. ACTA ACUST UNITED AC 2014; 56:e5. [DOI: 10.1093/pcp/pcu184] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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108
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Burgie ES, Vierstra RD. Phytochromes: an atomic perspective on photoactivation and signaling. THE PLANT CELL 2014; 26:4568-83. [PMID: 25480369 PMCID: PMC4311201 DOI: 10.1105/tpc.114.131623] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/10/2014] [Accepted: 11/14/2014] [Indexed: 05/19/2023]
Abstract
The superfamily of phytochrome (Phy) photoreceptors regulates a wide array of light responses in plants and microorganisms through their unique ability to reversibly switch between stable dark-adapted and photoactivated end states. Whereas the downstream signaling cascades and biological consequences have been described, the initial events that underpin photochemistry of the coupled bilin chromophore and the ensuing conformational changes needed to propagate the light signal are only now being understood. Especially informative has been the rapidly expanding collection of 3D models developed by x-ray crystallographic, NMR, and single-particle electron microscopic methods from a remarkably diverse array of bacterial Phys. These structures have revealed how the modular architecture of these dimeric photoreceptors engages the buried chromophore through distinctive knot, hairpin, and helical spine features. When collectively viewed, these 3D structures reveal complex structural alterations whereby photoisomerization of the bilin drives nanometer-scale movements within the Phy dimer through bilin sliding, hairpin reconfiguration, and spine deformation that ultimately impinge upon the paired signal output domains. When integrated with the recently described structure of the photosensory module from Arabidopsis thaliana PhyB, new opportunities emerge for the rational redesign of plant Phys with novel photochemistries and signaling properties potentially beneficial to agriculture and their exploitation as optogenetic reagents.
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Affiliation(s)
- E Sethe Burgie
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Richard D Vierstra
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706
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109
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Knie N, Polsakiewicz M, Knoop V. Horizontal gene transfer of chlamydial-like tRNA genes into early vascular plant mitochondria. Mol Biol Evol 2014; 32:629-34. [PMID: 25415968 DOI: 10.1093/molbev/msu324] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Mitochondrial genomes of lycophytes are surprisingly diverse, including strikingly different transfer RNA (tRNA) gene complements: No mitochondrial tRNA genes are present in the spikemoss Selaginella moellendorffii, whereas 26 tRNAs are encoded in the chondrome of the clubmoss Huperzia squarrosa. Reinvestigating the latter we found that trnL(gag) and trnS(gga) had never before been identified in any other land plant mitochondrial DNA. Sensitive sequence comparisons showed these two tRNAs as well as trnN(guu) and trnS(gcu) to be very similar to their respective counterparts in chlamydial bacteria. We identified homologs of these chlamydial-type tRNAs also in other lycophyte, fern, and gymnosperm DNAs, suggesting horizontal gene transfer (HGT) into mitochondria in the early vascular plant stem lineages. These findings extend plant mitochondrial HGT to affect individual tRNA genes, to include bacterial donors, and suggest that Chlamydiae on top of their recently proposed key role in primary chloroplast establishment may also have participated in early tracheophyte genome evolution.
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Affiliation(s)
- Nils Knie
- Abteilung Molekulare Evolution, Institut für Zelluläre und Molekulare Botanik, Universität Bonn, Bonn, Germany
| | - Monika Polsakiewicz
- Abteilung Molekulare Evolution, Institut für Zelluläre und Molekulare Botanik, Universität Bonn, Bonn, Germany
| | - Volker Knoop
- Abteilung Molekulare Evolution, Institut für Zelluläre und Molekulare Botanik, Universität Bonn, Bonn, Germany
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110
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Marine algae and land plants share conserved phytochrome signaling systems. Proc Natl Acad Sci U S A 2014; 111:15827-32. [PMID: 25267653 DOI: 10.1073/pnas.1416751111] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Phytochrome photosensors control a vast gene network in streptophyte plants, acting as master regulators of diverse growth and developmental processes throughout the life cycle. In contrast with their absence in known chlorophyte algal genomes and most sequenced prasinophyte algal genomes, a phytochrome is found in Micromonas pusilla, a widely distributed marine picoprasinophyte (<2 µm cell diameter). Together with phytochromes identified from other prasinophyte lineages, we establish that prasinophyte and streptophyte phytochromes share core light-input and signaling-output domain architectures except for the loss of C-terminal response regulator receiver domains in the streptophyte phytochrome lineage. Phylogenetic reconstructions robustly support the presence of phytochrome in the common progenitor of green algae and land plants. These analyses reveal a monophyletic clade containing streptophyte, prasinophyte, cryptophyte, and glaucophyte phytochromes implying an origin in the eukaryotic ancestor of the Archaeplastida. Transcriptomic measurements reveal diurnal regulation of phytochrome and bilin chromophore biosynthetic genes in Micromonas. Expression of these genes precedes both light-mediated phytochrome redistribution from the cytoplasm to the nucleus and increased expression of photosynthesis-associated genes. Prasinophyte phytochromes perceive wavelengths of light transmitted farther through seawater than the red/far-red light sensed by land plant phytochromes. Prasinophyte phytochromes also retain light-regulated histidine kinase activity lost in the streptophyte phytochrome lineage. Our studies demonstrate that light-mediated nuclear translocation of phytochrome predates the emergence of land plants and likely represents a widespread signaling mechanism in unicellular algae.
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111
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Villarreal JC, Renner SS. A review of molecular-clock calibrations and substitution rates in liverworts, mosses, and hornworts, and a timeframe for a taxonomically cleaned-up genus Nothoceros. Mol Phylogenet Evol 2014; 78:25-35. [DOI: 10.1016/j.ympev.2014.04.014] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 03/30/2014] [Accepted: 04/15/2014] [Indexed: 11/16/2022]
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112
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Komatsu A, Terai M, Ishizaki K, Suetsugu N, Tsuboi H, Nishihama R, Yamato KT, Wada M, Kohchi T. Phototropin encoded by a single-copy gene mediates chloroplast photorelocation movements in the liverwort Marchantia polymorpha. PLANT PHYSIOLOGY 2014; 166:411-27. [PMID: 25096976 PMCID: PMC4149725 DOI: 10.1104/pp.114.245100] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 08/02/2014] [Indexed: 05/18/2023]
Abstract
Blue-light-induced chloroplast photorelocation movement is observed in most land plants. Chloroplasts move toward weak-light-irradiated areas to efficiently absorb light (the accumulation response) and escape from strong-light-irradiated areas to avoid photodamage (the avoidance response). The plant-specific kinase phototropin (phot) is the blue-light receptor for chloroplast movements. Although the molecular mechanisms for chloroplast photorelocation movement have been analyzed, the overall aspects of signal transduction common to land plants are still unknown. Here, we show that the liverwort Marchantia polymorpha exhibits the accumulation and avoidance responses exclusively induced by blue light as well as specific chloroplast positioning in the dark. Moreover, in silico and Southern-blot analyses revealed that the M. polymorpha genome encodes a single PHOT gene, MpPHOT, and its knockout line displayed none of the chloroplast photorelocation movements, indicating that the sole MpPHOT gene mediates all types of movement. Mpphot was localized on the plasma membrane and exhibited blue-light-dependent autophosphorylation both in vitro and in vivo. Heterologous expression of MpPHOT rescued the defects in chloroplast movement of phot mutants in the fern Adiantum capillus-veneris and the seed plant Arabidopsis (Arabidopsis thaliana). These results indicate that Mpphot possesses evolutionarily conserved regulatory activities for chloroplast photorelocation movement. M. polymorpha offers a simple and versatile platform for analyzing the fundamental processes of phototropin-mediated chloroplast photorelocation movement common to land plants.
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Affiliation(s)
- Aino Komatsu
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan (A.K., M.T., K.I., N.S., R.N., K.T.Y., T.K.); andFaculty of Sciences, Kyushu University, Fukuoka 812-8581, Japan (N.S., H.T., M.W.)
| | - Mika Terai
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan (A.K., M.T., K.I., N.S., R.N., K.T.Y., T.K.); andFaculty of Sciences, Kyushu University, Fukuoka 812-8581, Japan (N.S., H.T., M.W.)
| | - Kimitsune Ishizaki
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan (A.K., M.T., K.I., N.S., R.N., K.T.Y., T.K.); andFaculty of Sciences, Kyushu University, Fukuoka 812-8581, Japan (N.S., H.T., M.W.)
| | - Noriyuki Suetsugu
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan (A.K., M.T., K.I., N.S., R.N., K.T.Y., T.K.); andFaculty of Sciences, Kyushu University, Fukuoka 812-8581, Japan (N.S., H.T., M.W.)
| | - Hidenori Tsuboi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan (A.K., M.T., K.I., N.S., R.N., K.T.Y., T.K.); andFaculty of Sciences, Kyushu University, Fukuoka 812-8581, Japan (N.S., H.T., M.W.)
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan (A.K., M.T., K.I., N.S., R.N., K.T.Y., T.K.); andFaculty of Sciences, Kyushu University, Fukuoka 812-8581, Japan (N.S., H.T., M.W.)
| | - Katsuyuki T Yamato
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan (A.K., M.T., K.I., N.S., R.N., K.T.Y., T.K.); andFaculty of Sciences, Kyushu University, Fukuoka 812-8581, Japan (N.S., H.T., M.W.)
| | - Masamitsu Wada
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan (A.K., M.T., K.I., N.S., R.N., K.T.Y., T.K.); andFaculty of Sciences, Kyushu University, Fukuoka 812-8581, Japan (N.S., H.T., M.W.)
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan (A.K., M.T., K.I., N.S., R.N., K.T.Y., T.K.); andFaculty of Sciences, Kyushu University, Fukuoka 812-8581, Japan (N.S., H.T., M.W.)
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113
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Jones B. Planting genes. Nat Rev Genet 2014; 15:362. [DOI: 10.1038/nrg3739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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