1
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Kumar P, Roy A, Mukul SJ, Singh AK, Singh DK, Nalli A, Banerjee P, Babu KSD, Raman B, Kruparani SP, Siddiqi I, Sankaranarayanan R. A translation proofreader of archaeal origin imparts multi-aldehyde stress tolerance to land plants. eLife 2024; 12:RP92827. [PMID: 38372335 PMCID: PMC10942605 DOI: 10.7554/elife.92827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2024] Open
Abstract
Aldehydes, being an integral part of carbon metabolism, energy generation, and signalling pathways, are ingrained in plant physiology. Land plants have developed intricate metabolic pathways which involve production of reactive aldehydes and its detoxification to survive harsh terrestrial environments. Here, we show that physiologically produced aldehydes, i.e., formaldehyde and methylglyoxal in addition to acetaldehyde, generate adducts with aminoacyl-tRNAs, a substrate for protein synthesis. Plants are unique in possessing two distinct chiral proofreading systems, D-aminoacyl-tRNA deacylase1 (DTD1) and DTD2, of bacterial and archaeal origins, respectively. Extensive biochemical analysis revealed that only archaeal DTD2 can remove the stable D-aminoacyl adducts on tRNA thereby shielding archaea and plants from these system-generated aldehydes. Using Arabidopsis as a model system, we have shown that the loss of DTD2 gene renders plants susceptible to these toxic aldehydes as they generate stable alkyl modification on D-aminoacyl-tRNAs, which are recycled only by DTD2. Bioinformatic analysis identifies the expansion of aldehyde metabolising repertoire in land plant ancestors which strongly correlates with the recruitment of archaeal DTD2. Finally, we demonstrate that the overexpression of DTD2 offers better protection against aldehydes than in wild type Arabidopsis highlighting its role as a multi-aldehyde detoxifier that can be explored as a transgenic crop development strategy.
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Affiliation(s)
- Pradeep Kumar
- CSIR–Centre for Cellular and Molecular BiologyHyderabadIndia
- Academy of Scientific and Innovative Research (AcSIR), CSIR–CCMB CampusHyderabadIndia
- Academy of Scientific and Innovative Research (AcSIR)GhaziabadIndia
| | - Ankit Roy
- CSIR–Centre for Cellular and Molecular BiologyHyderabadIndia
| | - Shivapura Jagadeesha Mukul
- CSIR–Centre for Cellular and Molecular BiologyHyderabadIndia
- Academy of Scientific and Innovative Research (AcSIR), CSIR–CCMB CampusHyderabadIndia
- Academy of Scientific and Innovative Research (AcSIR)GhaziabadIndia
| | | | | | - Aswan Nalli
- CSIR–Centre for Cellular and Molecular BiologyHyderabadIndia
| | | | | | | | | | - Imran Siddiqi
- CSIR–Centre for Cellular and Molecular BiologyHyderabadIndia
- Academy of Scientific and Innovative Research (AcSIR), CSIR–CCMB CampusHyderabadIndia
| | - Rajan Sankaranarayanan
- CSIR–Centre for Cellular and Molecular BiologyHyderabadIndia
- Academy of Scientific and Innovative Research (AcSIR), CSIR–CCMB CampusHyderabadIndia
- Academy of Scientific and Innovative Research (AcSIR)GhaziabadIndia
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2
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Kumar P, Babu K, Singh A, Singh D, Nalli A, Mukul S, Roy A, Mazeed M, Raman B, Kruparani S, Siddiqi I, Sankaranarayanan R. Distinct localization of chiral proofreaders resolves organellar translation conflict in plants. Proc Natl Acad Sci U S A 2023; 120:e2219292120. [PMID: 37276405 PMCID: PMC10268278 DOI: 10.1073/pnas.2219292120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 05/03/2023] [Indexed: 06/07/2023] Open
Abstract
Plants have two endosymbiotic organelles originated from two bacterial ancestors. The transition from an independent bacterium to a successful organelle would have required extensive rewiring of biochemical networks for its integration with archaeal host. Here, using Arabidopsis as a model system, we show that plant D-aminoacyl-tRNA deacylase 1 (DTD1), of bacterial origin, is detrimental to organellar protein synthesis owing to its changed tRNA recognition code. Plants survive this conflict by spatially restricting the conflicted DTD1 to the cytosol. In addition, plants have targeted archaeal DTD2 to both the organelles as it is compatible with their translation machinery due to its strict D-chiral specificity and lack of tRNA determinants. Intriguingly, plants have confined bacterial-derived DTD1 to work in archaeal-derived cytosolic compartment whereas archaeal DTD2 is targeted to bacterial-derived organelles. Overall, the study provides a remarkable example of the criticality of optimization of biochemical networks for survival and evolution of plant mitochondria and chloroplast.
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Affiliation(s)
- Pradeep Kumar
- Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB), Hyderabad500007, India
- Academy of Scientific and Innovative Research, Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB) campus, Hyderabad500007, India
| | - Kandhalu Sagadevan Dinesh Babu
- Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB), Hyderabad500007, India
| | - Avinash Kumar Singh
- Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB), Hyderabad500007, India
| | - Dipesh Kumar Singh
- Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB), Hyderabad500007, India
| | - Aswan Nalli
- Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB), Hyderabad500007, India
| | - Shivapura Jagadeesha Mukul
- Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB), Hyderabad500007, India
- Academy of Scientific and Innovative Research, Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB) campus, Hyderabad500007, India
| | - Ankit Roy
- Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB), Hyderabad500007, India
| | - Mohd Mazeed
- Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB), Hyderabad500007, India
| | - Bakthisaran Raman
- Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB), Hyderabad500007, India
| | - Shobha P. Kruparani
- Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB), Hyderabad500007, India
| | - Imran Siddiqi
- Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB), Hyderabad500007, India
- Academy of Scientific and Innovative Research, Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB) campus, Hyderabad500007, India
| | - Rajan Sankaranarayanan
- Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB), Hyderabad500007, India
- Academy of Scientific and Innovative Research, Council of Scientific and Industrial Research-Centre for Cellular and Molecular Biology (CSIR–CCMB) campus, Hyderabad500007, India
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3
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Moghe G, Kruse LH, Petersen M, Scossa F, Fernie AR, Gaquerel E, D'Auria JC. BAHD Company: The Ever-Expanding Roles of the BAHD Acyltransferase Gene Family in Plants. Annu Rev Plant Biol 2023; 74:165-194. [PMID: 36450296 DOI: 10.1146/annurev-arplant-062922-050122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Plants' ability to chemically modify core structures of specialized metabolites is the main reason why the plant kingdom contains such a wide and rich array of diverse compounds. One of the most important types of chemical modifications of small molecules is the addition of an acyl moiety to produce esters and amides. Large-scale phylogenomics analyses have shown that the enzymes that perform acyl transfer reactions on the myriad small molecules synthesized by plants belong to only a few gene families. This review is focused on describing the biochemistry, evolutionary origins, and chemical ecology implications of one of these families-the BAHD acyltransferases. The growth of advanced metabolomic studies coupled with next-generation sequencing of diverse plant species has confirmed that the BAHD family plays critical roles in modifying nearly all known classes of specialized metabolites. The current and future outlook for research on BAHDs includes expanding their roles in synthetic biology and metabolic engineering.
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Affiliation(s)
- Gaurav Moghe
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, USA;
| | - Lars H Kruse
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada;
| | - Maike Petersen
- Institute for Pharmaceutical Biology and Biotechnology, Philipps-University Marburg, Marburg, Germany;
| | - Federico Scossa
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany; ,
- Council for Agricultural Research and Economics, Research Center for Genomics and Bioinformatics (CREA-GB), Rome, Italy;
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany; ,
| | - Emmanuel Gaquerel
- Institut de Biologie Moléculaire des Plantes du CNRS, Strasbourg University, Strasbourg, France;
| | - John C D'Auria
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Seeland, Germany;
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4
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Waller M, Frangedakis E, Marron AO, Sauret‐Güeto S, Rever J, Sabbagh CRR, Hibberd JM, Haseloff J, Renzaglia KS, Szövényi P. An optimized transformation protocol for Anthoceros agrestis and three more hornwort species. Plant J 2023; 114:699-718. [PMID: 36811359 PMCID: PMC10952725 DOI: 10.1111/tpj.16161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 02/03/2023] [Accepted: 02/17/2023] [Indexed: 05/10/2023]
Abstract
Land plants comprise two large monophyletic lineages, the vascular plants and the bryophytes, which diverged from their most recent common ancestor approximately 480 million years ago. Of the three lineages of bryophytes, only the mosses and the liverworts are systematically investigated, while the hornworts are understudied. Despite their importance for understanding fundamental questions of land plant evolution, they only recently became amenable to experimental investigation, with Anthoceros agrestis being developed as a hornwort model system. Availability of a high-quality genome assembly and a recently developed genetic transformation technique makes A. agrestis an attractive model species for hornworts. Here we describe an updated and optimized transformation protocol for A. agrestis, which can be successfully used to genetically modify one more strain of A. agrestis and three more hornwort species, Anthoceros punctatus, Leiosporoceros dussii, and Phaeoceros carolinianus. The new transformation method is less laborious, faster, and results in the generation of greatly increased numbers of transformants compared with the previous method. We have also developed a new selection marker for transformation. Finally, we report the development of a set of different cellular localization signal peptides for hornworts providing new tools to better understand the hornwort cell biology.
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Affiliation(s)
- Manuel Waller
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZurichSwitzerland
- Zurich‐Basel Plant Science CenterZurichSwitzerland
| | | | - Alan O. Marron
- Department of Plant SciencesUniversity of CambridgeDowning StreetCambridgeCB2 3EAUK
| | - Susanna Sauret‐Güeto
- Department of Plant SciencesUniversity of CambridgeDowning StreetCambridgeCB2 3EAUK
- Present address:
Crop Science CentreUniversity of Cambridge93 Lawrence Weaver RoadCambridgeCB3 0LEUK
| | - Jenna Rever
- Department of Plant SciencesUniversity of CambridgeDowning StreetCambridgeCB2 3EAUK
| | - Cyrus Raja Rubenstein Sabbagh
- Department of Microbiology and Molecular Genetics, College of Biological SciencesUniversity of CaliforniaDavisCalifornia95616USA
| | - Julian M. Hibberd
- Department of Plant SciencesUniversity of CambridgeDowning StreetCambridgeCB2 3EAUK
| | - Jim Haseloff
- Department of Plant SciencesUniversity of CambridgeDowning StreetCambridgeCB2 3EAUK
| | - Karen S. Renzaglia
- Department of Plant BiologySouthern Illinois UniversityCarbondaleIllinois62901USA
| | - Péter Szövényi
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZurichSwitzerland
- Zurich‐Basel Plant Science CenterZurichSwitzerland
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5
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Furumizu C, Aalen RB. Peptide signaling through leucine-rich repeat receptor kinases: insight into land plant evolution. New Phytol 2023; 238:977-982. [PMID: 36811171 DOI: 10.1111/nph.18827] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Multicellular organisms need mechanisms for communication between cells so that they can fulfill their purpose in the organism as a whole. Over the last two decades, several small post-translationally modified peptides (PTMPs) have been identified as components of cell-to-cell signaling modules in flowering plants. Such peptides most often influence growth and development of organs not universally conserved among land plants. PTMPs have been matched to subfamily XI leucine-rich repeat receptor-like kinases with > 20 repeats. Phylogenetic analyses, facilitated by recently published genomic sequences of non-flowering plants, have identified seven clades of such receptors with a history back to the common ancestor of bryophytes and vascular plants. This raises a number of questions: When did peptide signaling arise during land plant evolution? Have orthologous peptide-receptor pairs preserved their biological functions? Has peptide signaling contributed to major innovations, such as stomata, vasculature, roots, seeds, and flowers? Using genomic, genetic, biochemical, and structural data and non-angiosperm model species, it is now possible to address these questions. The vast number of peptides that have not yet found their partners suggests furthermore that we have far more to learn about peptide signaling in the coming decades.
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Affiliation(s)
- Chihiro Furumizu
- Natural Science Center for Basic Research and Development, Hiroshima University, 1-4-2 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8527, Japan
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8530, Japan
| | - Reidunn Birgitta Aalen
- Department of Biosciences, University of Oslo, PO Box 1066, Blindern, Oslo, 0316, Norway
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Ntefidou M, Eklund DM, Le Bail A, Schulmeister S, Scherbel F, Brandl L, Dörfler W, Eichstädt C, Bannmüller A, Ljung K, Kost B. Physcomitrium patens PpRIC, an ancestral CRIB-domain ROP effector, inhibits auxin-induced differentiation of apical initial cells. Cell Rep 2023; 42:112130. [PMID: 36790931 DOI: 10.1016/j.celrep.2023.112130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 12/03/2022] [Accepted: 02/01/2023] [Indexed: 02/16/2023] Open
Abstract
RHO guanosine triphosphatases are important eukaryotic regulators of cell differentiation and behavior. Plant ROP (RHO of plant) family members activate specific, incompletely characterized downstream signaling. The structurally simple land plant Physcomitrium patens is missing homologs of key animal and flowering plant RHO effectors but contains a single CRIB (CDC42/RAC interactive binding)-domain-containing RIC (ROP-interacting CRIB-containing) protein (PpRIC). Protonemal P. patens filaments elongate based on regular division and PpROP-dependent tip growth of apical initial cells, which upon stimulation by the hormone auxin differentiate caulonemal characteristics. PpRIC interacts with active PpROP1, co-localizes with this protein at the plasma membrane at the tip of apical initial cells, and accumulates in the nucleus. Remarkably, PpRIC is not required for tip growth but is targeted to the nucleus to block caulonema differentiation downstream of auxin-controlled gene expression. These observations establish functions of PpRIC in mediating crosstalk between ROP and auxin signaling, which contributes to the maintenance of apical initial cell identity.
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Affiliation(s)
- Maria Ntefidou
- Cell Biology, Department of Biology, University Erlangen-Nuremberg, 91058 Erlangen, Germany
| | - D Magnus Eklund
- Physiology and Environmental Toxicology, Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden
| | - Aude Le Bail
- Cell Biology, Department of Biology, University Erlangen-Nuremberg, 91058 Erlangen, Germany
| | - Sylwia Schulmeister
- Cell Biology, Department of Biology, University Erlangen-Nuremberg, 91058 Erlangen, Germany
| | - Franziska Scherbel
- Cell Biology, Department of Biology, University Erlangen-Nuremberg, 91058 Erlangen, Germany
| | - Lisa Brandl
- Cell Biology, Department of Biology, University Erlangen-Nuremberg, 91058 Erlangen, Germany
| | - Wolfgang Dörfler
- Cell Biology, Department of Biology, University Erlangen-Nuremberg, 91058 Erlangen, Germany
| | - Chantal Eichstädt
- Cell Biology, Department of Biology, University Erlangen-Nuremberg, 91058 Erlangen, Germany
| | - Anna Bannmüller
- Cell Biology, Department of Biology, University Erlangen-Nuremberg, 91058 Erlangen, Germany
| | - Karin Ljung
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden
| | - Benedikt Kost
- Cell Biology, Department of Biology, University Erlangen-Nuremberg, 91058 Erlangen, Germany.
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Ashraf MA. A nuclear Pandora's box: functions of nuclear envelope proteins in cell division. AoB Plants 2023; 15:plac065. [PMID: 36779223 PMCID: PMC9910035 DOI: 10.1093/aobpla/plac065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 12/20/2022] [Indexed: 06/18/2023]
Abstract
The nucleus is characteristic of eukaryotic cells and nuclear envelope proteins are conserved across the kingdoms. Over the years, the function of these proteins was studied in the intact nuclear envelope. Knowledge regarding the localization and function of nuclear envelope proteins during mitosis, after the nuclear envelope breaks down, is limited. Until recently, the localization of nuclear envelope proteins during mitosis has been observed with the mitotic apparatus. In this context, research in plant cell biology is more advanced compared to non-plant model systems. Although current studies shed light on the localization of nuclear envelope proteins, further experiments are required to determine what, if any, functional role different nuclear envelope proteins play during mitosis. This review will highlight our current knowledge about the role of nuclear envelope proteins and point out the unanswered questions as future direction.
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Holzhausen A, Stingl N, Rieth S, Kühn C, Schubert H, Rensing SA. Establishment and optimization of a new model organism to study early land plant evolution: Germination, cultivation and oospore variation of Chara braunii Gmelin, 1826. Front Plant Sci 2022; 13:987741. [PMID: 36438147 PMCID: PMC9691404 DOI: 10.3389/fpls.2022.987741] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
For studying land plant evolution, the establishment and optimization of model organisms representing streptophytic algae, sister to land plants, is essential. Long-term cultivation experiments with Chara braunii S276 were performed over 8 years, since 4 years (Nov. 2018) under constant conditions. Additionally, short-term experiments for optimization of culture conditions were performed with three strains of C. braunii (S276, NIES-1604 and Lausiger Teiche, LaT-2708). Germination success after application of sterilization agents, addition of gibberellic acid and under different incubation conditions with respect to pre-treatment, irradiance regime and substrate was investigated in order to develop protocols for generative cultivation of at least unialgal cultures. The resulting cultivation protocols for C. braunii S276, allowing maintenance of vegetative as well as generative cultures are presented in detail, including protocols for germination induction and growth of sterilized and unsterilized oospores.
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Affiliation(s)
- Anja Holzhausen
- Department of Biology, Plant Cell Biology, University of Marburg, Marburg, Germany
- Institute for Biosciences, Physiology of Plant Metabolism, University of Rostock, Rostock, Germany
| | - Nora Stingl
- Department of Biology, Plant Cell Biology, University of Marburg, Marburg, Germany
| | - Sophie Rieth
- Department of Biology, Plant Cell Biology, University of Marburg, Marburg, Germany
| | - Christine Kühn
- Department of Biology, Plant Cell Biology, University of Marburg, Marburg, Germany
- Institute for Biosciences, Ecology, University of Rostock, Rostock, Germany
| | - Hendrik Schubert
- Institute for Biosciences, Physiology of Plant Metabolism, University of Rostock, Rostock, Germany
| | - Stefan Andreas Rensing
- Department of Biology, Plant Cell Biology, University of Marburg, Marburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
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Li X, Cao X, Li J, Niu Q, Mo Y, Xiao L. Genome-wide characterization of C2H2 zinc-finger gene family provides insight into the mechanisms and evolution of the dehydration-rehydration responses in Physcomitrium and Arabidopsis. Front Plant Sci 2022; 13:953459. [PMID: 36262662 PMCID: PMC9574186 DOI: 10.3389/fpls.2022.953459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/31/2022] [Indexed: 06/16/2023]
Abstract
Dehydration tolerance is a vital factor for land plant evolution and world agricultural production. Numerous studies enlightened that the plant-specific C2H2-type zinc-finger proteins (C2H2-ZFPs) as master regulators played pivotal roles in the abiotic stress responses of plants. However, a comprehensive understanding of the evolution of C2H2-ZFPs in terrestrial plants and its regulatory mechanism in dehydration and rehydration response remains a mystery. In this study, the genome-wide identification of C2H2-ZFP genes revealed 549 homologs in the representatives of terrestrial plant lineages from liverwort to angiosperms. Based on the characteristics of the conserved C2H2-ZF domains, four major C2H2-ZF types (M-, Z-, Q-, and D-type) were identified in the C2H2-ZFPs, with the dominants of M-type in all selected species and followed by Z-type in non-seed plants and Q-type in seed plants, respectively. Phylogenetic analyses of the identified C2H2-ZFPs supported four major groups in the land plant representatives, among which the members from the desiccation-tolerant Physcomitrium patens and the dehydration-sensitive Arabidopsis thaliana displayed different topological relationships in the phylogenies reconstructed for a single species. C2H2-ZFPs clustered in the same subclades shared similar features in their conserved domains and gene structures. Approximately, 81% of the C2H2-ZFP promoters of all 549 identified C2H2-ZFPs harbored the conserved ABA-responsive elements (ABREs) and/or dehydration-responsive elements (DREs). Comparative transcriptomic analyses showed that 50 PpZFPs and 56 AtZFPs significantly changed their transcripts abundance. Interestingly, most of the dehydration- and rehydration-responsive PpZPFs and AtZFPs had been predicted to contain the ABRE and DRE elements in their promoter regions and with over half of which phylogenetically belonging to group III. The differences in the expression patterns of C2H2-ZFPs in responses to dehydration and rehydration between P. patens and A. thaliana reflected their different strategies to adapt to dehydration. The identified candidate PpZFPs were specifically induced by moderate dehydration and reached the peak transcript abundance in severe dehydration. Our study lays the foundations for further functional investigation of C2H2-ZFPs in dehydration responses from an evolutionary perspective in land plants. The findings will provide us with genetic resources and potential targets for drought tolerance breeding in crops and beyond.
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10
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Briginshaw LN, Flores‐Sandoval E, Dierschke T, Alvarez JP, Bowman JL. KANADI promotes thallus differentiation and FR-induced gametangiophore formation in the liverwort Marchantia. New Phytol 2022; 234:1377-1393. [PMID: 35181887 PMCID: PMC9311212 DOI: 10.1111/nph.18046] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/07/2022] [Indexed: 05/26/2023]
Abstract
In angiosperms, KANADI transcription factors have roles in the sporophyte generation regulating tissue polarity, organogenesis and shade avoidance responses, but are not required during the gametophyte generation. Whether these roles are conserved in the gametophyte-dominant bryophyte lineages is unknown, which we examined by characterising the sole KANADI ortholog, MpKAN, in the liverwort Marchantia polymorpha. In contrast to angiosperm orthologs, MpKAN functions in the gametophyte generation in Marchantia, where it regulates apical branching and tissue differentiation, but does not influence tissue polarity in either generation. MpKAN can partially rescue the sporophyte polarity defects of kanadi mutants in Arabidopsis, indicating that MpKAN has conserved biochemical activity to its angiosperm counterparts. Mpkan loss-of-function plants display defects in far-red (FR) light responses. Mpkan plants have reduced FR-induced growth tropisms, have a delayed transition to sexual reproduction and fail to correctly form gametangiophores. Our results indicate that MpKAN is a modulator of FR responses, which may reflect a conserved role for KANADI across land plants. Under FR, MpKAN negatively regulates MpDELLA expression, suggesting that MpKAN and MpDELLA act in a pathway regulating FR responses, placing MpKAN in a gene regulatory network exhibiting similarities with those of angiosperms.
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Affiliation(s)
- Liam N. Briginshaw
- School of Biological SciencesMonash UniversityWellington RdClayton, MelbourneVic.3800Australia
- ARC Centre of Excellence for Plant Success in Nature and AgricultureMonash UniversityWellington RdMelbourneVic.3800Australia
| | - Eduardo Flores‐Sandoval
- School of Biological SciencesMonash UniversityWellington RdClayton, MelbourneVic.3800Australia
- ARC Centre of Excellence for Plant Success in Nature and AgricultureMonash UniversityWellington RdMelbourneVic.3800Australia
| | - Tom Dierschke
- School of Biological SciencesMonash UniversityWellington RdClayton, MelbourneVic.3800Australia
| | - John P. Alvarez
- School of Biological SciencesMonash UniversityWellington RdClayton, MelbourneVic.3800Australia
- ARC Centre of Excellence for Plant Success in Nature and AgricultureMonash UniversityWellington RdMelbourneVic.3800Australia
| | - John L. Bowman
- School of Biological SciencesMonash UniversityWellington RdClayton, MelbourneVic.3800Australia
- ARC Centre of Excellence for Plant Success in Nature and AgricultureMonash UniversityWellington RdMelbourneVic.3800Australia
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11
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Tomescu AMF. Mysteries of the bryophyte-tracheophyte transition revealed: enter the eophytes. New Phytol 2022; 233:1018-1021. [PMID: 34863044 DOI: 10.1111/nph.17876] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/19/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Alexandru M F Tomescu
- Department of Biological Sciences, Humboldt State University, Arcata, CA, 95521, USA
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Furumizu C, Sawa S. The RGF/GLV/CLEL Family of Short Peptides Evolved Through Lineage-Specific Losses and Diversification and Yet Conserves Its Signaling Role Between Vascular Plants and Bryophytes. Front Plant Sci 2021; 12:703012. [PMID: 34354727 PMCID: PMC8329595 DOI: 10.3389/fpls.2021.703012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/28/2021] [Indexed: 05/12/2023]
Abstract
Short secreted plant peptides act as key signaling molecules and control a plethora of developmental and physiological processes. The ROOT GROWTH FACTOR (RGF)/GOLVEN (GLV)/CLE-Like (CLEL) family of peptides was discovered to be involved in root development in Arabidopsis thaliana. In contrast to active research efforts, which have been revealing receptors and downstream signaling components, little attention has been paid to evolutionary processes that shaped the RGF signaling system as we know it in angiosperms today. As a first step toward understanding how RGF signaling emerged and evolved, this study aimed to elucidate the phylogenetic distribution and functional conservation of RGF-like sequences. Using publicly available, genome and transcriptome data, RGF-like sequences were searched in 27 liverworts, 22 mosses, 8 hornworts, 23 lycophytes, 23 ferns, 38 gymnosperms, and 8 angiosperms. This led to the identification of more than four hundreds of RGF-like sequences in all major extant land plant lineages except for hornworts. Sequence comparisons within and between taxonomic groups identified lineage-specific characters. Notably, one of the two major RGF subgroups, represented by A. thaliana RGF6/GLV1/CLEL6, was found only in vascular plants. This subgroup, therefore, likely emerged in a common ancestor of vascular plants after its divergence from bryophytes. In bryophytes, our results infer independent losses of RGF-like sequences in mosses and hornworts. On the other hand, a single, highly similar RGF-like sequence is conserved in liverworts, including Marchantia polymorpha, a genetically tractable model species. When constitutively expressed, the M. polymorpha RGF-like sequence (MpRGF) affected plant development and growth both in A. thaliana and M. polymorpha. This suggests that MpRGF can exert known RGF-like effects and that MpRGF is under transcriptional control so that its potent activities are precisely controlled. These data suggest that RGFs are conserved as signaling molecules in both vascular plants and bryophytes and that lineage-specific diversification has increased sequence variations of RGFs. All together, our findings form a basis for further studies into RGF peptides and their receptors, which will contribute to our understandings of how peptide signaling pathways evolve.
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Moody LA, Kelly S, Clayton R, Weeks Z, Emms DM, Langdale JA. NO GAMETOPHORES 2 Is a Novel Regulator of the 2D to 3D Growth Transition in the Moss Physcomitrella patens. Curr Biol 2020; 31:555-563.e4. [PMID: 33242390 DOI: 10.1016/j.cub.2020.10.077] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 10/01/2020] [Accepted: 10/26/2020] [Indexed: 12/31/2022]
Abstract
The colonization of land by plants was one of the most transformative events in the history of life on Earth. The transition from water, which coincided with and was likely facilitated by the evolution of three-dimensional (3D) growth, enabled the generation of morphological diversity on land. In many plants, the transition from two-dimensional (2D) to 3D growth occurs during embryo development. However, in the early divergent moss Physcomitrella patens, 3D growth is preceded by an extended filamentous phase that can be maintained indefinitely. Here, we describe the identification of the cytokinin-responsive NO GAMETOPHORES 2 (PpNOG2) gene, which encodes a shikimate o-hydroxycinnamoyltransferase. In mutants lacking PpNOG2 function, transcript levels of CLAVATA and SCARECROW genes are significantly reduced, excessive gametophore initial cells are produced, and buds undergo premature developmental arrest. Mutants also exhibit misregulation of auxin-responsive genes. Our results suggest that PpNOG2 functions in the ascorbic acid pathway leading to cuticle formation and that NOG2-related genes were co-opted into the lignin biosynthesis pathway after the divergence of bryophytes and vascular plants. We present a revised model of 3D growth in which PpNOG2 comprises part of a feedback mechanism that is required for the modulation of gametophore initial cell frequency. We also propose that the 2D to 3D growth transition in P. patens is underpinned by complex auxin-cytokinin crosstalk that is regulated, at least in part, by changes in flavonoid metabolism.
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Affiliation(s)
- Laura A Moody
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
| | - Steven Kelly
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Roxaana Clayton
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Zoe Weeks
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - David M Emms
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Jane A Langdale
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
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14
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Rico-Reséndiz F, Cervantes-Pérez SA, Espinal-Centeno A, Dipp-Álvarez M, Oropeza-Aburto A, Hurtado-Bautista E, Cruz-Hernández A, Bowman JL, Ishizaki K, Arteaga-Vázquez MA, Herrera-Estrella L, Cruz-Ramírez A. Transcriptional and Morpho-Physiological Responses of Marchantia polymorpha upon Phosphate Starvation. Int J Mol Sci 2020; 21:ijms21218354. [PMID: 33171770 PMCID: PMC7672586 DOI: 10.3390/ijms21218354] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 01/22/2023] Open
Abstract
Phosphate (Pi) is a pivotal nutrient that constraints plant development and productivity in natural ecosystems. Land colonization by plants, more than 470 million years ago, evolved adaptive mechanisms to conquer Pi-scarce environments. However, little is known about the molecular basis underlying such adaptations at early branches of plant phylogeny. To shed light on how early divergent plants respond to Pi limitation, we analyzed the morpho-physiological and transcriptional dynamics of Marchantia polymorpha upon Pi starvation. Our phylogenomic analysis highlights some gene networks present since the Chlorophytes and others established in the Streptophytes (e.g., PHR1–SPX1 and STOP1–ALMT1, respectively). At the morpho-physiological level, the response is characterized by the induction of phosphatase activity, media acidification, accumulation of auronidins, reduction of internal Pi concentration, and developmental modifications of rhizoids. The transcriptional response involves the induction of MpPHR1, Pi transporters, lipid turnover enzymes, and MpMYB14, which is an essential transcription factor for auronidins biosynthesis. MpSTOP2 up-regulation correlates with expression changes in genes related to organic acid biosynthesis and transport, suggesting a preference for citrate exudation. An analysis of MpPHR1 binding sequences (P1BS) shows an enrichment of this cis regulatory element in differentially expressed genes. Our study unravels the strategies, at diverse levels of organization, exerted by M. polymorpha to cope with low Pi availability.
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Affiliation(s)
- Félix Rico-Reséndiz
- Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados, Instituto Politécnico Nacional, Irapuato 36824, Guanajuato, Mexico; (F.R.-R.); (A.E.-C.); (M.D.-Á.)
| | - Sergio Alan Cervantes-Pérez
- Plant Physiology and Metabolic Engineering Group, Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados, Instituto Politécnico Nacional, Irapuato 36824, Guanajuato, Mexico; (S.A.C.-P.); (A.O.-A.); (L.H.-E.)
| | - Annie Espinal-Centeno
- Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados, Instituto Politécnico Nacional, Irapuato 36824, Guanajuato, Mexico; (F.R.-R.); (A.E.-C.); (M.D.-Á.)
| | - Melissa Dipp-Álvarez
- Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados, Instituto Politécnico Nacional, Irapuato 36824, Guanajuato, Mexico; (F.R.-R.); (A.E.-C.); (M.D.-Á.)
| | - Araceli Oropeza-Aburto
- Plant Physiology and Metabolic Engineering Group, Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados, Instituto Politécnico Nacional, Irapuato 36824, Guanajuato, Mexico; (S.A.C.-P.); (A.O.-A.); (L.H.-E.)
| | - Enrique Hurtado-Bautista
- Molecular Biology and Microbial Ecology, Unidad Irapuato, Centro de Investigación y Estudios Avanzados, Instituto Politécnico Nacional, Irapuato 36824, Guanajuato, Mexico;
| | - Andrés Cruz-Hernández
- Escuela de Agronomía, Universidad de La Salle Bajío, León 37160, Guanajuato, Mexico;
| | - John L. Bowman
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia;
| | | | - Mario A. Arteaga-Vázquez
- Group of Epigenetics and Developmental Biology, Instituto de Biotecnología y Ecología Aplicada (INBIOTECA), Universidad Veracruzana, Xalapa 91640, Mexico;
| | - Luis Herrera-Estrella
- Plant Physiology and Metabolic Engineering Group, Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados, Instituto Politécnico Nacional, Irapuato 36824, Guanajuato, Mexico; (S.A.C.-P.); (A.O.-A.); (L.H.-E.)
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Alfredo Cruz-Ramírez
- Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados, Instituto Politécnico Nacional, Irapuato 36824, Guanajuato, Mexico; (F.R.-R.); (A.E.-C.); (M.D.-Á.)
- Correspondence: ; Tel.: +52-462-166-3000 (ext. 3005)
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Sun G, Bai S, Guan Y, Wang S, Wang Q, Liu Y, Liu H, Goffinet B, Zhou Y, Paoletti M, Hu X, Haas FB, Fernandez-Pozo N, Czyrt A, Sun H, Rensing SA, Huang J. Are fungi-derived genomic regions related to antagonism towards fungi in mosses? New Phytol 2020; 228:1169-1175. [PMID: 32578878 DOI: 10.1111/nph.16776] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 06/19/2020] [Indexed: 05/16/2023]
Affiliation(s)
- Guiling Sun
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Shenglong Bai
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Yanlong Guan
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Shuanghua Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Qia Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yang Liu
- Fairy Lake Botanical Garden, Chinese Academy of Sciences, Shenzhen, 518004, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Huan Liu
- BGI-Shenzhen, Shenzhen, 518083, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Bernard Goffinet
- Ecology and Evolutionary Biology, University of Connecticut, 75N Eagleville Rd, Storrs, CT, 06269-3043, USA
| | - Yun Zhou
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Mathieu Paoletti
- Laboratoire de Génétique Moléculaire des Champignons, Institut de Biochimie et de Génétique Cellulaires, UMR 5095 CNRS-Université de Bordeaux 2, 1 rue Camille St Saëns, Bordeaux Cedex, 33077, France
| | - Xiangyang Hu
- College of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Fabian B Haas
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, 35043, Germany
| | - Noe Fernandez-Pozo
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, 35043, Germany
| | - Alia Czyrt
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, 35043, Germany
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Stefan A Rensing
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, 35043, Germany
| | - Jinling Huang
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Department of Biology, East Carolina University, Greenville, NC, 28590, USA
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16
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Renzaglia KS, Browning WB, Merced A. With Over 60 Independent Losses, Stomata Are Expendable in Mosses. Front Plant Sci 2020; 11:567. [PMID: 32547571 PMCID: PMC7270291 DOI: 10.3389/fpls.2020.00567] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 04/16/2020] [Indexed: 05/22/2023]
Abstract
Because stomata in bryophytes are uniquely located on sporangia, the physiological and evolutionary constraints placed on bryophyte stomata are fundamentally different from those on leaves of tracheophytes. Although losses of stomata have been documented in mosses, the extent to which this evolutionary process occurred remains relatively unexplored. We initiated this study by plotting the known occurrences of stomata loss and numbers per capsule on the most recent moss phylogeny. From this, we identified 40 families and 74 genera that lack stomata, of which at least 63 are independent losses. No trends in stomata losses or numbers are evident in any direction across moss diversity. Extant taxa in early divergent moss lineages either lack stomata or produce pseudostomata that do not form pores. The earliest land plant macrofossils from 400 ma exhibit similar sporangial morphologies and stomatal distribution to extant mosses, suggesting that the earliest mosses may have possessed and lost stomata as is common in the group. To understand why stomata are expendable in mosses, we conducted comparative anatomical studies on a range of mosses with and without stomata. We compared the anatomy of stomate and astomate taxa and the development of intercellular spaces, including substomatal cavities, across mosses. Two types of intercellular spaces that develop differently are seen in peristomate mosses, those associated with stomata and those that surround the spore sac. Capsule architecture in astomate mosses ranges from solid in the taxa in early divergent lineages to containing an internal space that is directly connected to the conducing tissue and is involved in capsule expansion and the nourishment, hydration and development of spores. This anatomy reveals there are different architectural arrangements of tissues within moss capsules that are equally effective in accomplishing the essential processes of sporogenesis and spore dispersal. Stomata are not foundational to these processes.
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Affiliation(s)
- Karen S. Renzaglia
- Plant Biology Department, Southern Illinois University, Carbondale, IL, United States
- *Correspondence: Karen S. Renzaglia,
| | - William B. Browning
- Plant Biology Department, Southern Illinois University, Carbondale, IL, United States
| | - Amelia Merced
- International Institute of Tropical Forestry, USDA Forest Service, San Juan, PR, United States
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17
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Moody LA, Kelly S, Rabbinowitsch E, Langdale JA. Genetic Regulation of the 2D to 3D Growth Transition in the Moss Physcomitrella patens. Curr Biol 2019; 28:473-478.e5. [PMID: 29395927 PMCID: PMC5807088 DOI: 10.1016/j.cub.2017.12.052] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Revised: 12/20/2017] [Accepted: 12/22/2017] [Indexed: 01/16/2023]
Abstract
One of the most important events in the history of life on earth was the colonization of land by plants; this transition coincided with and was most likely enabled by the evolution of 3-dimensional (3D) growth. Today, the diverse morphologies exhibited across the terrestrial biosphere arise from the differential regulation of 3D growth processes during development. In many plants, 3D growth is initiated during the first few divisions of the zygote, and therefore, the genetic basis cannot be dissected because mutants do not survive. However, in mosses, which are representatives of the earliest land plants, 3D shoot growth is preceded by a 2D filamentous phase that can be maintained indefinitely. Here, we used the moss Physcomitrella patens to identify genetic regulators of the 2D to 3D transition. Mutant screens yielded individuals that could only grow in 2D, and through an innovative strategy that combined somatic hybridization with bulk segregant analysis and genome sequencing, the causative mutation was identified in one of them. The NO GAMETOPHORES 1 (NOG1) gene, which encodes a ubiquitin-associated protein, is present only in land plant genomes. In mutants that lack PpNOG1 function, transcripts encoding 3D-promoting PpAPB transcription factors [1] are significantly reduced, and apical initial cells specified for 3D growth are not formed. PpNOG1 acts at the earliest identified stage of the 2D to 3D transition, possibly through degradation of proteins that suppress 3D growth. The acquisition of NOG1 function in land plants could thus have enabled the evolution and development of 3D morphology. NO GAMETOPHORES 1 (PpNOG1) regulates the 2D to 3D growth transition in P. patens PpNOG1 acts upstream of 3D-promoting PpAPB transcription factors PpNOG1 is required for the formation of apical initial cells specified for 3D growth NOG1 genes are found only in land plants and thus evolved coincident with 3D growth
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Affiliation(s)
- Laura A Moody
- Department of Plant Sciences, University of Oxford, South Parks Rd., Oxford OX1 3RB, UK
| | - Steven Kelly
- Department of Plant Sciences, University of Oxford, South Parks Rd., Oxford OX1 3RB, UK
| | - Ester Rabbinowitsch
- Department of Plant Sciences, University of Oxford, South Parks Rd., Oxford OX1 3RB, UK
| | - Jane A Langdale
- Department of Plant Sciences, University of Oxford, South Parks Rd., Oxford OX1 3RB, UK.
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18
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Corrigendum. New Phytol 2018; 221:1172. [PMID: 30569608 DOI: 10.1111/nph.15533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
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19
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Plackett AR, Conway SJ, Hewett Hazelton KD, Rabbinowitsch EH, Langdale JA, Di Stilio VS. LEAFY maintains apical stem cell activity during shoot development in the fern Ceratopteris richardii. eLife 2018; 7:39625. [PMID: 30355440 PMCID: PMC6200394 DOI: 10.7554/elife.39625] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 09/22/2018] [Indexed: 12/29/2022] Open
Abstract
During land plant evolution, determinate spore-bearing axes (retained in extant bryophytes such as mosses) were progressively transformed into indeterminate branching shoots with specialized reproductive axes that form flowers. The LEAFY transcription factor, which is required for the first zygotic cell division in mosses and primarily for floral meristem identity in flowering plants, may have facilitated developmental innovations during these transitions. Mapping the LEAFY evolutionary trajectory has been challenging, however, because there is no functional overlap between mosses and flowering plants, and no functional data from intervening lineages. Here, we report a transgenic analysis in the fern Ceratopteris richardii that reveals a role for LEAFY in maintaining cell divisions in the apical stem cells of both haploid and diploid phases of the lifecycle. These results support an evolutionary trajectory in which an ancestral LEAFY module that promotes cell proliferation was progressively co-opted, adapted and specialized as novel shoot developmental contexts emerged. The first plants colonized land around 500 million years ago. These plants had simple shoots with no branches, similar to the mosses that live today. Later on, some plants evolved more complex structures including branched shoots and flowers (collectively known as the “flowering plants”). Ferns are a group of plants that evolved midway between the mosses and flowering plants and have branched shoots but no flowers. The gradual transition from simple to more complex plant structures required changes to the way in which cells divide and grow within plant shoots. Whereas animals produce new cells throughout their body, most plant cells divide in areas known as meristems. All plants grow from embryos, which contain meristems that will form the roots and shoots of the mature plant. A gene called LEAFY is required for cells in moss embryos to divide. However, in flowering plants LEAFY does not carry out this role, instead it is only required to make the meristems that produce flowers. How did LEAFY transition from a general role in embryos to a more specialized role in making flowers? To address this question, Plackett, Conway et al. studied the two LEAFY genes in a fern called Ceratopteris richardii. The experiments showed that at least one of these LEAFY genes was active in the meristems of fern shoots throughout the lifespan of the plant. The shoots of ferns with less active LEAFY genes could not form the leaves seen in normal C. richardii plants. This suggests that as land plants evolved, the role of LEAFY changed from forming embryos to forming complex shoot structures. Most of our major crops are flowering plants. By understanding how the role of LEAFY has changed over the evolution of land plants, it might be possible to manipulate LEAFY genes in crop plants to alter shoot structures to better suit specific environments.
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Affiliation(s)
- Andrew Rg Plackett
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | | | | | | | - Jane A Langdale
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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20
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Whitewoods CD, Cammarata J, Nemec Venza Z, Sang S, Crook AD, Aoyama T, Wang XY, Waller M, Kamisugi Y, Cuming AC, Szövényi P, Nimchuk ZL, Roeder AHK, Scanlon MJ, Harrison CJ. CLAVATA Was a Genetic Novelty for the Morphological Innovation of 3D Growth in Land Plants. Curr Biol 2018; 28:2365-2376.e5. [PMID: 30033333 PMCID: PMC6089843 DOI: 10.1016/j.cub.2018.05.068] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 05/10/2018] [Accepted: 05/23/2018] [Indexed: 11/24/2022]
Abstract
How genes shape diverse plant and animal body forms is a key question in biology. Unlike animal cells, plant cells are confined by rigid cell walls, and cell division plane orientation and growth rather than cell movement determine overall body form. The emergence of plants on land coincided with a new capacity to rotate stem cell divisions through multiple planes, and this enabled three-dimensional (3D) forms to arise from ancestral forms constrained to 2D growth. The genes involved in this evolutionary innovation are largely unknown. The evolution of 3D growth is recapitulated during the development of modern mosses when leafy shoots arise from a filamentous (2D) precursor tissue. Here, we show that a conserved, CLAVATA peptide and receptor-like kinase pathway originated with land plants and orients stem cell division planes during the transition from 2D to 3D growth in a moss, Physcomitrella. We find that this newly identified role for CLAVATA in regulating cell division plane orientation is shared between Physcomitrella and Arabidopsis. We report that roles for CLAVATA in regulating cell proliferation and cell fate are also shared and that CLAVATA-like peptides act via conserved receptor components in Physcomitrella. Our results suggest that CLAVATA was a genetic novelty enabling the morphological innovation of 3D growth in land plants.
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Affiliation(s)
- Chris D Whitewoods
- Plant Sciences Department, Cambridge University, Downing Street, Cambridge CB2 3EA, UK
| | - Joseph Cammarata
- Plant Sciences Department, Cambridge University, Downing Street, Cambridge CB2 3EA, UK; Plant Biology Section, School of Integrative Plant Science, Cornell University, Tower Road, Ithaca, NY 14853, USA; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Zoe Nemec Venza
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Stephanie Sang
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Ashley D Crook
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tsuyoshi Aoyama
- Plant Sciences Department, Cambridge University, Downing Street, Cambridge CB2 3EA, UK; School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Xiao Y Wang
- Plant Sciences Department, Cambridge University, Downing Street, Cambridge CB2 3EA, UK
| | - Manuel Waller
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Yasuko Kamisugi
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Andrew C Cuming
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Zachary L Nimchuk
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Adrienne H K Roeder
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Tower Road, Ithaca, NY 14853, USA; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Michael J Scanlon
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Tower Road, Ithaca, NY 14853, USA
| | - C Jill Harrison
- Plant Sciences Department, Cambridge University, Downing Street, Cambridge CB2 3EA, UK; School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK.
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21
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Flores-Sandoval E, Eklund DM, Hong SF, Alvarez JP, Fisher TJ, Lampugnani ER, Golz JF, Vázquez-Lobo A, Dierschke T, Lin SS, Bowman JL. Class C ARFs evolved before the origin of land plants and antagonize differentiation and developmental transitions in Marchantia polymorpha. New Phytol 2018; 218:1612-1630. [PMID: 29574879 DOI: 10.1111/nph.15090] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 02/05/2018] [Indexed: 05/08/2023]
Abstract
A plethora of developmental and physiological processes in land plants is influenced by auxin, to a large extent via alterations in gene expression by AUXIN RESPONSE FACTORs (ARFs). The canonical auxin transcriptional response system is a land plant innovation, however, charophycean algae possess orthologues of at least some classes of ARF and AUXIN/INDOLE-3-ACETIC ACID (AUX/IAA) genes, suggesting that elements of the canonical land plant system existed in an ancestral alga. We reconstructed the phylogenetic relationships between streptophyte ARF and AUX/IAA genes and functionally characterized the solitary class C ARF, MpARF3, in Marchantia polymorpha. Phylogenetic analyses indicate that multiple ARF classes, including class C ARFs, existed in an ancestral alga. Loss- and gain-of-function MpARF3 alleles result in pleiotropic effects in the gametophyte, with MpARF3 inhibiting differentiation and developmental transitions in multiple stages of the life cycle. Although loss-of-function Mparf3 and Mpmir160 alleles respond to exogenous auxin treatments, strong miR-resistant MpARF3 alleles are auxin-insensitive, suggesting that class C ARFs act in a context-dependent fashion. We conclude that two modules independently evolved to regulate a pre-existing ARF transcriptional network. Whereas the auxin-TIR1-AUX/IAA pathway evolved to repress class A/B ARF activity, miR160 evolved to repress class C ARFs in a dynamic fashion.
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Affiliation(s)
- Eduardo Flores-Sandoval
- School of Biological Sciences, Monash University, Clayton, Melbourne, Victoria, 3800, Australia
| | - D Magnus Eklund
- School of Biological Sciences, Monash University, Clayton, Melbourne, Victoria, 3800, Australia
| | - Syuan-Fei Hong
- Institute of Biotechnology, National Taiwan University, 81, Chang-Xing ST., Taipei, 106, Taiwan
| | - John P Alvarez
- School of Biological Sciences, Monash University, Clayton, Melbourne, Victoria, 3800, Australia
| | - Tom J Fisher
- School of Biological Sciences, Monash University, Clayton, Melbourne, Victoria, 3800, Australia
| | - Edwin R Lampugnani
- School of BioSciences, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - John F Golz
- School of BioSciences, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Alejandra Vázquez-Lobo
- CIByC, Universidad Autónoma del Estado de Morelos, Av. Universidad No. 1001, Colonia Chamilpa, CP 62209, Cuernavaca, Morelos, México
| | - Tom Dierschke
- School of Biological Sciences, Monash University, Clayton, Melbourne, Victoria, 3800, Australia
| | - Shih-Shun Lin
- Institute of Biotechnology, National Taiwan University, 81, Chang-Xing ST., Taipei, 106, Taiwan
| | - John L Bowman
- School of Biological Sciences, Monash University, Clayton, Melbourne, Victoria, 3800, Australia
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22
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Grosche C, Genau AC, Rensing SA. Evolution of the Symbiosis-Specific GRAS Regulatory Network in Bryophytes. Front Plant Sci 2018; 9:1621. [PMID: 30459800 PMCID: PMC6232258 DOI: 10.3389/fpls.2018.01621] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 10/18/2018] [Indexed: 05/08/2023]
Abstract
Arbuscular mycorrhiza is one of the most common plant symbiotic interactions observed today. Due to their nearly ubiquitous occurrence and their beneficial impact on both partners it was suggested that this mutualistic interaction was crucial for plants to colonize the terrestrial habitat approximately 500 Ma ago. On the plant side the association is established via the common symbiotic pathway (CSP). This pathway allows the recognition of the fungal symbiotic partner, subsequent signaling to the nucleus, and initiation of the symbiotic program with respect to specific gene expression and cellular re-organization. The downstream part of the CSP is a regulatory network that coordinates the transcription of genes necessary to establish the symbiosis, comprising multiple GRAS transcription factors (TFs). These regulate their own expression as an intricate transcriptional network. Deduced from non-host genome data the loss of genes encoding CSP components coincides with the loss of the interaction itself. Here, we analyzed bryophyte species with special emphasis on the moss Physcomitrella patens, supposed to be a non-host, for the composition of the GRAS regulatory network components. We show lineage specific losses and expansions of several of these factors in bryophytes, potentially coinciding with the proposed host/non-host status of the lineages. We evaluate losses and expansions and infer clade-specific evolution of GRAS TFs.
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Affiliation(s)
- Christopher Grosche
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | | | - Stefan A. Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
- *Correspondence: Stefan A. Rensing,
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23
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Bowman JL, Kohchi T, Yamato KT, Jenkins J, Shu S, Ishizaki K, Yamaoka S, Nishihama R, Nakamura Y, Berger F, Adam C, Aki SS, Althoff F, Araki T, Arteaga-Vazquez MA, Balasubrmanian S, Barry K, Bauer D, Boehm CR, Briginshaw L, Caballero-Perez J, Catarino B, Chen F, Chiyoda S, Chovatia M, Davies KM, Delmans M, Demura T, Dierschke T, Dolan L, Dorantes-Acosta AE, Eklund DM, Florent SN, Flores-Sandoval E, Fujiyama A, Fukuzawa H, Galik B, Grimanelli D, Grimwood J, Grossniklaus U, Hamada T, Haseloff J, Hetherington AJ, Higo A, Hirakawa Y, Hundley HN, Ikeda Y, Inoue K, Inoue SI, Ishida S, Jia Q, Kakita M, Kanazawa T, Kawai Y, Kawashima T, Kennedy M, Kinose K, Kinoshita T, Kohara Y, Koide E, Komatsu K, Kopischke S, Kubo M, Kyozuka J, Lagercrantz U, Lin SS, Lindquist E, Lipzen AM, Lu CW, De Luna E, Martienssen RA, Minamino N, Mizutani M, Mizutani M, Mochizuki N, Monte I, Mosher R, Nagasaki H, Nakagami H, Naramoto S, Nishitani K, Ohtani M, Okamoto T, Okumura M, Phillips J, Pollak B, Reinders A, Rövekamp M, Sano R, Sawa S, Schmid MW, Shirakawa M, Solano R, Spunde A, Suetsugu N, Sugano S, Sugiyama A, Sun R, Suzuki Y, Takenaka M, Takezawa D, Tomogane H, Tsuzuki M, Ueda T, Umeda M, Ward JM, Watanabe Y, Yazaki K, Yokoyama R, Yoshitake Y, Yotsui I, Zachgo S, Schmutz J. Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome. Cell 2017; 171:287-304.e15. [PMID: 28985561 DOI: 10.1016/j.cell.2017.09.030] [Citation(s) in RCA: 673] [Impact Index Per Article: 96.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Revised: 04/21/2017] [Accepted: 09/18/2017] [Indexed: 02/01/2023]
Abstract
The evolution of land flora transformed the terrestrial environment. Land plants evolved from an ancestral charophycean alga from which they inherited developmental, biochemical, and cell biological attributes. Additional biochemical and physiological adaptations to land, and a life cycle with an alternation between multicellular haploid and diploid generations that facilitated efficient dispersal of desiccation tolerant spores, evolved in the ancestral land plant. We analyzed the genome of the liverwort Marchantia polymorpha, a member of a basal land plant lineage. Relative to charophycean algae, land plant genomes are characterized by genes encoding novel biochemical pathways, new phytohormone signaling pathways (notably auxin), expanded repertoires of signaling pathways, and increased diversity in some transcription factor families. Compared with other sequenced land plants, M. polymorpha exhibits low genetic redundancy in most regulatory pathways, with this portion of its genome resembling that predicted for the ancestral land plant. PAPERCLIP.
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Affiliation(s)
- John L Bowman
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia.
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan.
| | - Katsuyuki T Yamato
- Faculty of Biology-Oriented Science and Technology, Kindai University, 930 Nishimitani, Kinokawa, Wakayama 649-6493, Japan.
| | - Jerry Jenkins
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA; HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA
| | - Shengqiang Shu
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | | | - Shohei Yamaoka
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Yasukazu Nakamura
- National Institute of Genetics, Research Organization of Information and Systems, Yata, Mishima 411-8540, Japan
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Catherine Adam
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Shiori Sugamata Aki
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara 630-0192, Japan
| | - Felix Althoff
- Botany Department, University of Osnabrück, Barbarastr. 11, D-49076 Osnabrück, Germany
| | - Takashi Araki
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Mario A Arteaga-Vazquez
- Universidad Veracruzana, INBIOTECA - Instituto de Biotecnología y Ecología Aplicada, Av. de las Culturas Veracruzanas No.101, Colonia Emiliano Zapata, 91090, Xalapa, Veracruz, México
| | | | - Kerrie Barry
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Diane Bauer
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Christian R Boehm
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom
| | - Liam Briginshaw
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia
| | - Juan Caballero-Perez
- National Laboratory of Genomics for Biodiversity, CINVESTAV-IPN, Km 9.6 Lib. Norte Carr. Irapuato-León, 36821, Irapuato, Guanajuato, México
| | - Bruno Catarino
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Feng Chen
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | - Shota Chiyoda
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Mansi Chovatia
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Kevin M Davies
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11-600, Palmerston North, New Zealand
| | - Mihails Delmans
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom
| | - Taku Demura
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara 630-0192, Japan
| | - Tom Dierschke
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia; Botany Department, University of Osnabrück, Barbarastr. 11, D-49076 Osnabrück, Germany
| | - Liam Dolan
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Ana E Dorantes-Acosta
- Universidad Veracruzana, INBIOTECA - Instituto de Biotecnología y Ecología Aplicada, Av. de las Culturas Veracruzanas No.101, Colonia Emiliano Zapata, 91090, Xalapa, Veracruz, México
| | - D Magnus Eklund
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia; Department of Plant Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236 Uppsala, Sweden
| | - Stevie N Florent
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia
| | | | - Asao Fujiyama
- National Institute of Genetics, Research Organization of Information and Systems, Yata, Mishima 411-8540, Japan
| | - Hideya Fukuzawa
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Bence Galik
- Bioinformatics & Scientific Computing, Vienna Biocenter Core Facilities (VBCF), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Daniel Grimanelli
- Institut de Recherche pour le Développement (IRD), UMR232, Université de Montpellier, Montpellier 34394, France
| | - Jane Grimwood
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA; HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, 8008 Zürich, Switzerland
| | - Takahiro Hamada
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902 Japan
| | - Jim Haseloff
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom
| | | | - Asuka Higo
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Yuki Hirakawa
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia; Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan; Department of Life Science, Faculty of Science, Gakushuin University, Tokyo 171-8588, Japan
| | - Hope N Hundley
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Yoko Ikeda
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki, Okayama 710-0046, Japan
| | - Keisuke Inoue
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Shin-Ichiro Inoue
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8602, Japan
| | - Sakiko Ishida
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Qidong Jia
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | - Mitsuru Kakita
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8602, Japan
| | - Takehiko Kanazawa
- National Institute for Basic Biology, 38 Nishigounaka, Myodaiji, Okazaki 444-8585, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yosuke Kawai
- Department of Integrative Genomics, Tohoku Medical Bank Organization, Tohoku University, Aoba, Sendai 980-8573, Japan
| | - Tomokazu Kawashima
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria; Department of Plant and Soil Sciences, University of Kentucky, 321 Plant Science Building, 1405 Veterans Dr., Lexington, KY 40546, USA
| | - Megan Kennedy
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Keita Kinose
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Toshinori Kinoshita
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan; Department of Life Science, Faculty of Science, Gakushuin University, Tokyo 171-8588, Japan; Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8602, Japan
| | - Yuji Kohara
- National Institute of Genetics, Research Organization of Information and Systems, Yata, Mishima 411-8540, Japan
| | - Eri Koide
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Kenji Komatsu
- Department of Bioproduction Technology, Junior College of Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Sarah Kopischke
- Botany Department, University of Osnabrück, Barbarastr. 11, D-49076 Osnabrück, Germany
| | - Minoru Kubo
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara 630-0192, Japan
| | - Junko Kyozuka
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Ulf Lagercrantz
- Department of Plant Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236 Uppsala, Sweden
| | - Shih-Shun Lin
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Erika Lindquist
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Anna M Lipzen
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Chia-Wei Lu
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Efraín De Luna
- Instituto de Ecología, AC., Red de Biodiversidad y Sistemática, Xalapa, Veracruz, 91000, México
| | | | - Naoki Minamino
- National Institute for Basic Biology, 38 Nishigounaka, Myodaiji, Okazaki 444-8585, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masaharu Mizutani
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada, Kobe 657-8501, Japan
| | - Miya Mizutani
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | | | - Isabel Monte
- Department Genética Molecular de Plantas, Centro Nacional de Biotecnologia-CSIC, Universidad Autónoma de Madrid 28049 Madrid. Spain
| | - Rebecca Mosher
- The School of Plant Sciences, The University of Arizona, Tuscon, AZ, USA
| | - Hideki Nagasaki
- National Institute of Genetics, Research Organization of Information and Systems, Yata, Mishima 411-8540, Japan; Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Hirofumi Nakagami
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan; Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Satoshi Naramoto
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Kazuhiko Nishitani
- Laboratory of Plant Cell Wall Biology, Graduate School of Life Sciences, Tohoku University, Aoba, Sendai 980-8578, Japan
| | - Misato Ohtani
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara 630-0192, Japan
| | - Takashi Okamoto
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Masaki Okumura
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8602, Japan
| | - Jeremy Phillips
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Bernardo Pollak
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom
| | - Anke Reinders
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
| | - Moritz Rövekamp
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, 8008 Zürich, Switzerland
| | - Ryosuke Sano
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara 630-0192, Japan
| | - Shinichiro Sawa
- Graduate school of Science and Technology, Kumamoto University, Kurokami 2-39-1, Kumamoto 860-8555, Japan
| | - Marc W Schmid
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, 8008 Zürich, Switzerland
| | - Makoto Shirakawa
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Roberto Solano
- Department Genética Molecular de Plantas, Centro Nacional de Biotecnologia-CSIC, Universidad Autónoma de Madrid 28049 Madrid. Spain
| | - Alexander Spunde
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Noriyuki Suetsugu
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Sumio Sugano
- Department of Computational Biology and Medical Sciences, the University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562 Japan
| | - Akifumi Sugiyama
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji 611-0011, Japan
| | - Rui Sun
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, the University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562 Japan
| | | | - Daisuke Takezawa
- Graduate School of Science and Engineering and Institute for Environmental Science and Technology, Saitama University, Saitama 338-8570, Japan
| | - Hirokazu Tomogane
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Masayuki Tsuzuki
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902 Japan
| | - Takashi Ueda
- National Institute for Basic Biology, 38 Nishigounaka, Myodaiji, Okazaki 444-8585, Japan
| | - Masaaki Umeda
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara 630-0192, Japan
| | - John M Ward
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
| | - Yuichiro Watanabe
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902 Japan
| | - Kazufumi Yazaki
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji 611-0011, Japan
| | - Ryusuke Yokoyama
- Laboratory of Plant Cell Wall Biology, Graduate School of Life Sciences, Tohoku University, Aoba, Sendai 980-8578, Japan
| | | | - Izumi Yotsui
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Sabine Zachgo
- Botany Department, University of Osnabrück, Barbarastr. 11, D-49076 Osnabrück, Germany
| | - Jeremy Schmutz
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA; HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA
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24
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Frangedakis E, Saint‐Marcoux D, Moody LA, Rabbinowitsch E, Langdale JA. Nonreciprocal complementation of KNOX gene function in land plants. New Phytol 2017; 216:591-604. [PMID: 27886385 PMCID: PMC5637896 DOI: 10.1111/nph.14318] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 09/30/2016] [Indexed: 05/02/2023]
Abstract
Class I KNOTTED-LIKE HOMEOBOX (KNOX) proteins regulate development of the multicellular diploid sporophyte in both mosses and flowering plants; however, the morphological context in which they function differs. In order to determine how Class I KNOX function was modified as land plants evolved, phylogenetic analyses and cross-species complementation assays were performed. Our data reveal that a duplication within the charophyte sister group to land plants led to distinct Class I and Class II KNOX gene families. Subsequently, Class I sequences diverged substantially in the nonvascular bryophyte groups (liverworts, mosses and hornworts), with moss sequences being most similar to those in vascular plants. Despite this similarity, moss mutants were not complemented by vascular plant KNOX genes. Conversely, the Arabidopsis brevipedicellus (bp-9) mutant was complemented by the PpMKN2 gene from the moss Physcomitrella patens. Lycophyte KNOX genes also complemented bp-9 whereas fern genes only partially complemented the mutant. This lycophyte/fern distinction is mirrored in the phylogeny of KNOX-interacting BELL proteins, in that a gene duplication occurred after divergence of the two groups. Together, our results imply that the moss MKN2 protein can function in a broader developmental context than vascular plant KNOX proteins, the narrower scope having evolved progressively as lycophytes, ferns and flowering plants diverged.
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Affiliation(s)
| | - Denis Saint‐Marcoux
- Department of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - Laura A. Moody
- Department of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - Ester Rabbinowitsch
- Department of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - Jane A. Langdale
- Department of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
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25
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Abstract
Contents 545 I. 545 II. 546 III. 546 IV. 548 V. 548 VI. 549 VII. 549 Acknowledgements 549 References 549 SUMMARY: Branching is one of the most striking aspects of land plant architecture, affecting resource acquisition and yield. Polar auxin transport by PIN proteins is a primary determinant of flowering plant branching patterns regulating both branch initiation and branch outgrowth. Several lines of experimental evidence suggest that PIN-mediated polar auxin transport is a conserved regulator of branching in vascular plant sporophytes. However, the mechanisms of branching and auxin transport and relationships between the two are not well known outside the flowering plants, and the paradigm for PIN-regulated branching in flowering plants does not fit bryophyte gametophytes. The evidence reviewed here suggests that divergent auxin transport routes contributed to the diversification of branching forms in distinct land plant lineages.
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Affiliation(s)
- C Jill Harrison
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
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26
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Abstract
The life cycles of eukaryotes alternate between haploid and diploid phases, which are initiated by meiosis and gamete fusion, respectively. In both ascomycete and basidiomycete fungi and chlorophyte algae, the haploid-to-diploid transition is regulated by a pair of paralogous homeodomain protein encoding genes. That a common genetic program controls the haploid-to-diploid transition in phylogenetically disparate eukaryotic lineages suggests this may be the ancestral function for homeodomain proteins. Multicellularity has evolved independently in many eukaryotic lineages in either one or both phases of the life cycle. Organisms, such as land plants, exhibiting a life cycle whereby multicellular bodies develop in both the haploid and diploid phases are often referred to as possessing an alternation of generations. We review recent progress on understanding the genetic basis for the land plant alternation of generations and highlight the roles that homeodomain-encoding genes may have played in the evolution of complex multicellularity in this lineage.
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Affiliation(s)
- John L Bowman
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia;
- Department of Plant Biology, University of California, Davis, California 95616
| | - Keiko Sakakibara
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia;
- Department of Life Science, College of Science, Rikkyo University, Tokyo 171-8501, Japan
| | - Chihiro Furumizu
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia;
| | - Tom Dierschke
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia;
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Quirk J, Leake JR, Johnson DA, Taylor LL, Saccone L, Beerling DJ. Constraining the role of early land plants in Palaeozoic weathering and global cooling. Proc Biol Sci 2016; 282:20151115. [PMID: 26246550 PMCID: PMC4632622 DOI: 10.1098/rspb.2015.1115] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
How the colonization of terrestrial environments by early land plants over 400 Ma influenced rock weathering, the biogeochemical cycling of carbon and phosphorus, and climate in the Palaeozoic is uncertain. Here we show experimentally that mineral weathering by liverworts—an extant lineage of early land plants—partnering arbuscular mycorrhizal (AM) fungi, like those in 410 Ma-old early land plant fossils, amplified calcium weathering from basalt grains threefold to sevenfold, relative to plant-free controls. Phosphate weathering by mycorrhizal liverworts was amplified 9–13-fold over plant-free controls, compared with fivefold to sevenfold amplification by liverworts lacking fungal symbionts. Etching and trenching of phyllosilicate minerals increased with AM fungal network size and atmospheric CO2 concentration. Integration of grain-scale weathering rates over the depths of liverwort rhizoids and mycelia (0.1 m), or tree roots and mycelia (0.75 m), indicate early land plants with shallow anchorage systems were probably at least 10-fold less effective at enhancing the total weathering flux than later-evolving trees. This work challenges the suggestion that early land plants significantly enhanced total weathering and land-to-ocean fluxes of calcium and phosphorus, which have been proposed as a trigger for transient dramatic atmospheric CO2 sequestration and glaciations in the Ordovician.
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Affiliation(s)
- Joe Quirk
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Jonathan R Leake
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - David A Johnson
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Lyla L Taylor
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Loredana Saccone
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - David J Beerling
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
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Ortiz-Ramírez C, Hernandez-Coronado M, Thamm A, Catarino B, Wang M, Dolan L, Feijó JA, Becker JD. A Transcriptome Atlas of Physcomitrella patens Provides Insights into the Evolution and Development of Land Plants. Mol Plant 2016; 9:205-220. [PMID: 26687813 DOI: 10.1016/j.molp.2015.12.002] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 10/28/2015] [Accepted: 12/01/2015] [Indexed: 05/08/2023]
Abstract
Identifying the genetic mechanisms that underpin the evolution of new organ and tissue systems is an aim of evolutionary developmental biology. Comparative functional genetic studies between angiosperms and bryophytes can define those genetic changes that were responsible for developmental innovations. Here, we report the generation of a transcriptome atlas covering most phases in the life cycle of the model bryophyte Physcomitrella patens, including detailed sporophyte developmental progression. We identified a comprehensive set of sporophyte-specific transcription factors, and found that many of these genes have homologs in angiosperms that function in developmental processes such as flowering and shoot branching. Deletion of the PpTCP5 transcription factor results in development of supernumerary sporangia attached to a single seta, suggesting that it negatively regulates branching in the moss sporophyte. Given that TCP genes repress branching in angiosperms, we suggest that this activity is ancient. Finally, comparison of P. patens and Arabidopsis thaliana transcriptomes led us to the identification of a conserved core of transcription factors expressed in tip-growing cells. We identified modifications in the expression patterns of these genes that could account for developmental differences between P. patens tip-growing cells and A. thaliana pollen tubes and root hairs.
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Affiliation(s)
- Carlos Ortiz-Ramírez
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
| | | | - Anna Thamm
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
| | - Bruno Catarino
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Mingyi Wang
- Division of Plant Biology, The Samuel Roberts Noble Foundation, Ardmore, OK 73401, USA
| | - Liam Dolan
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - José A Feijó
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal; Department of Cell Biology and Molecular Genetics, University of Maryland, 0118 BioScience Research Building, College Park, MD 20742-5815, USA
| | - Jörg D Becker
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal.
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Nakano Y, Yamaguchi M, Endo H, Rejab NA, Ohtani M. NAC-MYB-based transcriptional regulation of secondary cell wall biosynthesis in land plants. Front Plant Sci 2015; 6:288. [PMID: 25999964 PMCID: PMC4419676 DOI: 10.3389/fpls.2015.00288] [Citation(s) in RCA: 269] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Accepted: 04/09/2015] [Indexed: 05/08/2023]
Abstract
Plant cells biosynthesize primary cell walls (PCW) in all cells and produce secondary cell walls (SCWs) in specific cell types that conduct water and/or provide mechanical support, such as xylem vessels and fibers. The characteristic mechanical stiffness, chemical recalcitrance, and hydrophobic nature of SCWs result from the organization of SCW-specific biopolymers, i.e., highly ordered cellulose, hemicellulose, and lignin. Synthesis of these SCW-specific biopolymers requires SCW-specific enzymes that are regulated by SCW-specific transcription factors. In this review, we summarize our current knowledge of the transcriptional regulation of SCW formation in plant cells. Advances in research on SCW biosynthesis during the past decade have expanded our understanding of the transcriptional regulation of SCW formation, particularly the functions of the NAC and MYB transcription factors. Focusing on the NAC-MYB-based transcriptional network, we discuss the regulatory systems that evolved in land plants to modify the cell wall to serve as a key component of structures that conduct water and provide mechanical support.
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Affiliation(s)
- Yoshimi Nakano
- Graduate School of Biological Sciences, Nara Institute of Science and TechnologyIkoma, Japan
| | - Masatoshi Yamaguchi
- Division of Strategic Research and Development, Graduate School of Science and Engineering, Saitama UniversitySaitama, Japan
- PRESTO (Precursory Research for Embryonic Science and Technology), Japan Science and Technology AgencyKawaguchi, Japan
| | - Hitoshi Endo
- Graduate School of Biological Sciences, Nara Institute of Science and TechnologyIkoma, Japan
| | - Nur Ardiyana Rejab
- Graduate School of Biological Sciences, Nara Institute of Science and TechnologyIkoma, Japan
- Faculty of Science, Institute of Biological Sciences, University of MalayaKuala Lumpur, Malaysia
| | - Misato Ohtani
- Graduate School of Biological Sciences, Nara Institute of Science and TechnologyIkoma, Japan
- Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
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30
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Cuming AC, Stevenson SR. From pond slime to rain forest: the evolution of ABA signalling and the acquisition of dehydration tolerance. New Phytol 2015; 206:5-7. [PMID: 25711244 DOI: 10.1111/nph.13333] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Affiliation(s)
- Andrew C Cuming
- Centre for Plant Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Sean R Stevenson
- Centre for Plant Sciences, University of Leeds, Leeds, LS2 9JT, UK
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Olsen OA, Perroud PF, Johansen W, Demko V. DEK1; missing piece in puzzle of plant development. Trends Plant Sci 2015; 20:70-1. [PMID: 25612461 DOI: 10.1016/j.tplants.2015.01.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 01/06/2015] [Accepted: 01/07/2015] [Indexed: 05/18/2023]
Abstract
Patterning of land plant bodies is determined by positioning of cell walls. A crucial event in land plant evolution was the ability to utilize spatial information to direct cell wall deposition. Recent studies of DEK1 in Physcomitrella patens support a role for DEK1 in position dependent cell wall orientation.
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Affiliation(s)
- Odd-Arne Olsen
- Department of plant science/CIGENE, Norwegian university of life sciences, 1432 Ås, Norway.
| | | | - Wenche Johansen
- Department of Natural Science and Technology, Hedmark University College, Hamar, Norway
| | - Viktor Demko
- Department of plant science/CIGENE, Norwegian university of life sciences, 1432 Ås, Norway
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Qi X, Chanderbali AS, Wong GKS, Soltis DE, Soltis PS. Phylogeny and evolutionary history of glycogen synthase kinase 3/SHAGGY-like kinase genes in land plants. BMC Evol Biol 2013; 13:143. [PMID: 23834366 PMCID: PMC3710211 DOI: 10.1186/1471-2148-13-143] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 07/02/2013] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND GSK3 (glycogen synthase kinase 3) genes encode signal transduction proteins with roles in a variety of biological processes in eukaryotes. In contrast to the low copy numbers observed in animals, GSK3 genes have expanded into a multi-gene family in land plants (embryophytes), and have also evolved functions in diverse plant specific processes, including floral development in angiosperms. However, despite previous efforts, the phylogeny of land plant GSK3 genes is currently unclear. Here, we analyze genes from a representative sample of phylogenetically pivotal taxa, including basal angiosperms, gymnosperms, and monilophytes, to reconstruct the evolutionary history and functional diversification of the GSK3 gene family in land plants. RESULTS Maximum Likelihood phylogenetic analyses resolve a gene tree with four major gene duplication events that coincide with the emergence of novel land plant clades. The single GSK3 gene inherited from the ancestor of land plants was first duplicated along the ancestral branch to extant vascular plants, and three subsequent duplications produced three GSK3 loci in the ancestor of euphyllophytes, four in the ancestor of seed plants, and at least five in the ancestor of angiosperms. A single gene in the Amborella trichopoda genome may be the sole survivor of a sixth GSK3 locus that originated in the ancestor of extant angiosperms. Homologs of two Arabidopsis GSK3 genes with genetically confirmed roles in floral development, AtSK11 and AtSK12, exhibit floral preferential expression in several basal angiosperms, suggesting evolutionary conservation of their floral functions. Members of other gene lineages appear to have independently evolved roles in plant reproductive tissues in individual taxa. CONCLUSIONS Our phylogenetic analyses provide the most detailed reconstruction of GSK3 gene evolution in land plants to date and offer new insights into the origins, relationships, and functions of family members. Notably, the diversity of this "green" branch of the gene family has increased in concert with the increasing morphological and physiological complexity of land plant life forms. Expression data for seed plants indicate that the functions of GSK3 genes have also diversified during evolutionary time.
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Affiliation(s)
- Xinshuai Qi
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou, China
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - André S Chanderbali
- Department of Biology, University of Florida, Gainesville, FL, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - 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, Bei Shan Industrial Zone, Yantian District, Shenzhen, China
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
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Quirk J, Beerling DJ, Banwart SA, Kakonyi G, Romero-Gonzalez ME, Leake JR. Evolution of trees and mycorrhizal fungi intensifies silicate mineral weathering. Biol Lett 2012; 8:1006-11. [PMID: 22859556 PMCID: PMC3497110 DOI: 10.1098/rsbl.2012.0503] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 07/07/2012] [Indexed: 11/16/2022] Open
Abstract
Forested ecosystems diversified more than 350 Ma to become major engines of continental silicate weathering, regulating the Earth's atmospheric carbon dioxide concentration by driving calcium export into ocean carbonates. Our field experiments with mature trees demonstrate intensification of this weathering engine as tree lineages diversified in concert with their symbiotic mycorrhizal fungi. Preferential hyphal colonization of the calcium silicate-bearing rock, basalt, progressively increased with advancement from arbuscular mycorrhizal (AM) to later, independently evolved ectomycorrhizal (EM) fungi, and from gymnosperm to angiosperm hosts with both fungal groups. This led to 'trenching' of silicate mineral surfaces by AM and EM fungi, with EM gymnosperms and angiosperms releasing calcium from basalt at twice the rate of AM gymnosperms. Our findings indicate mycorrhiza-driven weathering may have originated hundreds of millions of years earlier than previously recognized and subsequently intensified with the evolution of trees and mycorrhizas to affect the Earth's long-term CO(2) and climate history.
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Affiliation(s)
- Joe Quirk
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK.
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Engstrom EM. Phylogenetic analysis of GRAS proteins from moss, lycophyte and vascular plant lineages reveals that GRAS genes arose and underwent substantial diversification in the ancestral lineage common to bryophytes and vascular plants. Plant Signal Behav 2011; 6:850-4. [PMID: 21543899 PMCID: PMC3218485 DOI: 10.4161/psb.6.6.15203] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Accepted: 02/16/2011] [Indexed: 05/02/2023]
Abstract
GRAS genes are a large family of streptophyte specific transcription factors that function in a diverse set of physiological and developmental processes. GRAS proteins of the HAIRY MERISTEM (HAM) sub-family are required for maintenance of shoot and root indeterminacy. The transcriptional targets of HAM proteins and the signaling inputs regulating HAM activity are completely unknown. Understanding the relationship of HAM proteins to other members of the GRAS family may inform hypotheses relating to cellular level HAM functions. I here report a phylogenetic analysis of GRAS proteins employing the complete set of known and probable GRAS proteins from the sequenced genomes of the flowering plants Arabidopsis and Rice, the lycophyte Selaginella moellendorffii, and the bryophyte Physcomitrella patens. HAM proteins are most closely related to DELLA proteins, key components of gibberellin perception. However, GRAS proteins diversified into a minimum of twelve discreet monophyletic lineages, including the HAM and DELLA subfamilies, prior to divergence of the moss and flowering plant lineages. Substantial diversification of GRAS proteins at so early a point in land plant evolution suggests that relative relatedness sequence homology among GRAS proteins sub-families may not substantially reflect shared protein function.
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Affiliation(s)
- Eric M Engstrom
- Biology Department, The College of William and Mary, Williamsburg, VA, USA.
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Abstract
Glutaredoxins (GRXs) are ubiquitous glutathione-dependent oxidoreductase enzymes implicated in redox homeostasis, particularly oxidative stress response. Three major classes of GRX genes exist, the CPYC, CGFS classes are present in all pro- and eukaryote species, whereas the CC-type class GRXs are specific to land plants. In the basal land plant Physcomitrella patens, only two CC-type GRXs are present, compared with 21 in Arabidopsis. In contrast, sizes of the CPYC and CGFS classes remained rather similar throughout plant evolution, raising the interesting question as to when the CC-type GRXs first originated and how and why they expanded during land plant evolution. Recent evidence suggests that CC-type GRXs may have been recruited during evolution into diverse plant-specific functions of flower development (ROXY1, ROXY2) and pathogenesis response (ROXY19/GRX480). In the present study, GRX genes from the genomes of a range of green algae and evolutionarily diverse land plant species were identified; Ostreococcus, Micromonas, Volvox, Selaginella, Vitis, Sorghum, and Brachypodium. Previously identified sequences from Chlamydomonas, Physcomitrella, Oryza, Arabidopsis, and Populus were integrated to generate a more comprehensive understanding of the forces behind the evolution of various GRX classes. The analysis indicates that the CC-type GRXs probably arose by diversification from the CPYC class, at a time coinciding with colonization of land by plants. This strong differential expansion of the CC-type class occurred exclusively in the angiosperms, mainly through paleopolyploidy duplication events shortly after the monocot–eudicot split, and more recently through multiple tandem duplications that occurred independently in five investigated angiosperm lineages. The presented data suggest that following duplications, subfunctionalization, and subsequent neofunctionalization likely facilitated the sequestration of land plant-specific CC-type GRXs into novel functions such as development and pathogenesis response.
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Affiliation(s)
- M Ziemann
- Environment and Biotechnology Centre, Faculty of Life and Social SciencesSwinburne University of Technology, Hawthorn, Victoria, Australia
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Abstract
The coupled evolution of land plants, CO2, and climate over the last half billion years has maintained atmospheric CO2 concentrations within finite limits, indicating the involvement of a complex network of geophysiological feedbacks. But insight into this important regulatory network is extremely limited. Here we present a systems analysis of the physiological and geochemical processes involved, identifying new positive and negative feedbacks between plants and CO2 on geological time scales. Positive feedbacks accelerated falling CO2 concentrations during the evolution and diversification of terrestrial ecosystems in the Paleozoic and enhanced rising CO2 concentrations across the Triassic-Jurassic boundary during flood basalt eruptions. The existence of positive feedbacks reveals the unexpected destabilizing influence of the biota in climate regulation that led to environmental modifications accelerating rates of terrestrial plant and animal evolution in the Paleozoic.
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Affiliation(s)
- David J Beerling
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, United Kingdom.
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