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Demko V, Belova T, Messerer M, Hvidsten TR, Perroud PF, Ako AE, Johansen W, Mayer KFX, Olsen OA, Lang D. Regulation of developmental gatekeeping and cell fate transition by the calpain protease DEK1 in Physcomitrium patens. Commun Biol 2024; 7:261. [PMID: 38438476 PMCID: PMC10912778 DOI: 10.1038/s42003-024-05933-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 02/19/2024] [Indexed: 03/06/2024] Open
Abstract
Calpains are cysteine proteases that control cell fate transitions whose loss of function causes severe, pleiotropic phenotypes in eukaryotes. Although mainly considered as modulatory proteases, human calpain targets are directed to the N-end rule degradation pathway. Several such targets are transcription factors, hinting at a gene-regulatory role. Here, we analyze the gene-regulatory networks of the moss Physcomitrium patens and characterize the regulons that are misregulated in mutants of the calpain DEFECTIVE KERNEL1 (DEK1). Predicted cleavage patterns of the regulatory hierarchies in five DEK1-controlled subnetworks are consistent with a pleiotropic and regulatory role during cell fate transitions targeting multiple functions. Network structure suggests DEK1-gated sequential transitions between cell fates in 2D-to-3D development. Our method combines comprehensive phenotyping, transcriptomics and data science to dissect phenotypic traits, and our model explains the protease function as a switch gatekeeping cell fate transitions potentially also beyond plant development.
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Affiliation(s)
- Viktor Demko
- Department of Plant Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
- Department of Plant Physiology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 84104, Bratislava, Slovakia
- Plant Science and Biodiversity Center, Slovak Academy of Sciences, Dubravska cesta 9, 84104, Bratislava, Slovakia
| | - Tatiana Belova
- Department of Plant Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
- Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway
| | - Maxim Messerer
- Plant Genome and Systems Biology, Helmholtz Center Munich-Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Torgeir R Hvidsten
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Pierre-François Perroud
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Ako Eugene Ako
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata 31, 2318, Hamar, Norway
- School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Brackenhurst Campus, Southwell, Nottinghamshire, NG25 0QF, UK
| | - Wenche Johansen
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata 31, 2318, Hamar, Norway
| | - Klaus F X Mayer
- Plant Genome and Systems Biology, Helmholtz Center Munich-Research Center for Environmental Health, 85764, Neuherberg, Germany
- School of Life Sciences, Technical University Munich, 85354, Freising, Germany
| | - Odd-Arne Olsen
- Department of Plant Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
| | - Daniel Lang
- Plant Genome and Systems Biology, Helmholtz Center Munich-Research Center for Environmental Health, 85764, Neuherberg, Germany.
- Bundeswehr Institute of Microbiology, Microbial Genomics and Bioforensics, 80937, Munich, Germany.
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Olsen OA. The Modular Control of Cereal Endosperm Development. TRENDS IN PLANT SCIENCE 2020; 25:279-290. [PMID: 31956036 DOI: 10.1016/j.tplants.2019.12.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 11/20/2019] [Accepted: 12/06/2019] [Indexed: 05/05/2023]
Abstract
Expansion of the human population demands a significant increase in cereal production. The main component of cereal grains is endosperm, a body of starchy endosperm (SE) cells surrounded by aleurone (AL) cells with transfer cells (TC) at the base and embryo surrounding (ESR) cells adjacent to the embryo. The data reviewed here emphasize the modular nature of endosperm by first suggesting that sucrose promotes development of the fertilized triploid endosperm cell. Next, that the basal syncytial endosperm responds to glucose by turning on TC development. The default endosperm cell fate is SE and ESR differentiation is likely activated by signaling from the embryo. Cells on the exterior surface of the endosperm are specified as AL cells.
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Affiliation(s)
- Odd-Arne Olsen
- Department of Plant Science, Norwegian University of Life Sciences, 1434, Ås, Norway.
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A KNOX-Cytokinin Regulatory Module Predates the Origin of Indeterminate Vascular Plants. Curr Biol 2019; 29:2743-2750.e5. [DOI: 10.1016/j.cub.2019.06.083] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 06/10/2019] [Accepted: 06/27/2019] [Indexed: 12/29/2022]
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Harrison CJ, Morris JL. The origin and early evolution of vascular plant shoots and leaves. Philos Trans R Soc Lond B Biol Sci 2018; 373:20160496. [PMID: 29254961 PMCID: PMC5745332 DOI: 10.1098/rstb.2016.0496] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/11/2017] [Indexed: 12/22/2022] Open
Abstract
The morphology of plant fossils from the Rhynie chert has generated longstanding questions about vascular plant shoot and leaf evolution, for instance, which morphologies were ancestral within land plants, when did vascular plants first arise and did leaves have multiple evolutionary origins? Recent advances combining insights from molecular phylogeny, palaeobotany and evo-devo research address these questions and suggest the sequence of morphological innovation during vascular plant shoot and leaf evolution. The evidence pinpoints testable developmental and genetic hypotheses relating to the origin of branching and indeterminate shoot architectures prior to the evolution of leaves, and demonstrates underestimation of polyphyly in the evolution of leaves from branching forms in 'telome theory' hypotheses of leaf evolution. This review discusses fossil, developmental and genetic evidence relating to the evolution of vascular plant shoots and leaves in a phylogenetic framework.This article is part of a discussion meeting issue 'The Rhynie cherts: our earliest terrestrial ecosystem revisited'.
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Affiliation(s)
- C Jill Harrison
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Jennifer L Morris
- School of Earth Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
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Harrison CJ. Auxin transport in the evolution of branching forms. THE NEW PHYTOLOGIST 2017; 215:545-551. [PMID: 27883193 DOI: 10.1111/nph.14333] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 09/29/2016] [Indexed: 06/06/2023]
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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Jill Harrison C. Development and genetics in the evolution of land plant body plans. Philos Trans R Soc Lond B Biol Sci 2017; 372:20150490. [PMID: 27994131 PMCID: PMC5182422 DOI: 10.1098/rstb.2015.0490] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2016] [Indexed: 12/22/2022] Open
Abstract
The colonization of land by plants shaped the terrestrial biosphere, the geosphere and global climates. The nature of morphological and molecular innovation driving land plant evolution has been an enigma for over 200 years. Recent phylogenetic and palaeobotanical advances jointly demonstrate that land plants evolved from freshwater algae and pinpoint key morphological innovations in plant evolution. In the haploid gametophyte phase of the plant life cycle, these include the innovation of mulitcellular forms with apical growth and multiple growth axes. In the diploid phase of the life cycle, multicellular axial sporophytes were an early innovation priming subsequent diversification of indeterminate branched forms with leaves and roots. Reverse and forward genetic approaches in newly emerging model systems are starting to identify the genetic basis of such innovations. The data place plant evo-devo research at the cusp of discovering the developmental and genetic changes driving the radiation of land plant body plans.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.
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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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Johansen W, Ako AE, Demko V, Perroud PF, Rensing SA, Mekhlif AK, Olsen OA. The DEK1 Calpain Linker Functions in Three-Dimensional Body Patterning in Physcomitrella patens. PLANT PHYSIOLOGY 2016; 172:1089-1104. [PMID: 27506240 PMCID: PMC5047102 DOI: 10.1104/pp.16.00925] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 08/04/2016] [Indexed: 05/02/2023]
Abstract
The DEFECTIVE KERNEL1 (DEK1) calpain is a conserved 240-kD key regulator of three-dimensional body patterning in land plants acting via mitotic cell plane positioning. The activity of the cytosolic C-terminal calpain protease is regulated by the membrane-anchored DEK1 MEM, which is connected to the calpain via the 600-amino acid residue Linker. Similar to the calpain and MEM domains, the Linker is highly conserved in the land plant lineage, the similarity dropping sharply compared with orthologous charophyte sequences. Using site-directed mutagenesis, we studied the effect on Physcomitrella patens development by deleting the Linker and two conserved Linker motifs. The results show that removal of the Linker has nearly the same effect as removal of the entire DEK1 gene. In contrast, deletion of the conserved Laminin_G3 (LG3) domain had a milder effect, perturbing leafy gametophore patterning and archegonia development. The LG3 domain from Marchantia polymorpha is fully functional in P. patens, whereas angiosperm sequences are not functional. Deletion of a C-terminal Linker subsegment containing a potential calpain autolytic site severely disturbs gametophore development. Finally, changing one of the three calpain active-site amino acid residues results in the same phenotype as deleting the entire DEK1 gene. Based on the conserved nature of animal and DEK1 calpains, we propose that the DEK1 MEM-Linker complex inactivates the calpain by forcing apart the two calpain subunits carrying the three amino acids of the active site.
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Affiliation(s)
- Wenche Johansen
- Hedmark University of Applied Sciences, N-2418 Elverum, Norway (W.J., A.E.A., A.K.M.);Norwegian University of Life Sciences, N-1432 Aas, Norway (V.D., O.-A.O.); andPhilipps University Marburg, Plant Cell Biology, 35043 Marburg, Germany (P.-F.P., S.A.R.)
| | - Ako Eugene Ako
- Hedmark University of Applied Sciences, N-2418 Elverum, Norway (W.J., A.E.A., A.K.M.);Norwegian University of Life Sciences, N-1432 Aas, Norway (V.D., O.-A.O.); andPhilipps University Marburg, Plant Cell Biology, 35043 Marburg, Germany (P.-F.P., S.A.R.)
| | - Viktor Demko
- Hedmark University of Applied Sciences, N-2418 Elverum, Norway (W.J., A.E.A., A.K.M.);Norwegian University of Life Sciences, N-1432 Aas, Norway (V.D., O.-A.O.); andPhilipps University Marburg, Plant Cell Biology, 35043 Marburg, Germany (P.-F.P., S.A.R.)
| | - Pierre-François Perroud
- Hedmark University of Applied Sciences, N-2418 Elverum, Norway (W.J., A.E.A., A.K.M.);Norwegian University of Life Sciences, N-1432 Aas, Norway (V.D., O.-A.O.); andPhilipps University Marburg, Plant Cell Biology, 35043 Marburg, Germany (P.-F.P., S.A.R.)
| | - Stephan A Rensing
- Hedmark University of Applied Sciences, N-2418 Elverum, Norway (W.J., A.E.A., A.K.M.);Norwegian University of Life Sciences, N-1432 Aas, Norway (V.D., O.-A.O.); andPhilipps University Marburg, Plant Cell Biology, 35043 Marburg, Germany (P.-F.P., S.A.R.)
| | - Ahmed Khaleel Mekhlif
- Hedmark University of Applied Sciences, N-2418 Elverum, Norway (W.J., A.E.A., A.K.M.);Norwegian University of Life Sciences, N-1432 Aas, Norway (V.D., O.-A.O.); andPhilipps University Marburg, Plant Cell Biology, 35043 Marburg, Germany (P.-F.P., S.A.R.)
| | - Odd-Arne Olsen
- Hedmark University of Applied Sciences, N-2418 Elverum, Norway (W.J., A.E.A., A.K.M.);Norwegian University of Life Sciences, N-1432 Aas, Norway (V.D., O.-A.O.); andPhilipps University Marburg, Plant Cell Biology, 35043 Marburg, Germany (P.-F.P., S.A.R.)
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Demko V, Ako E, Perroud PF, Quatrano R, Olsen OA. The phenotype of the CRINKLY4 deletion mutant of Physcomitrella patens suggests a broad role in developmental regulation in early land plants. PLANTA 2016; 244:275-84. [PMID: 27100110 DOI: 10.1007/s00425-016-2526-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 04/08/2016] [Indexed: 05/05/2023]
Abstract
Deletion of the ancestral gene of the land plant multigene family of receptor like kinase CR4 in Physcomitrella patens demonstrates involvement in developmental control of gametophytic and sporophytic organs. The CRINKLY4 (CR4) family of receptor kinases in angiosperms consists of three clades, one including CR4, the CR4-related CCR1 and CCR2, a second including CCR3 and CCR4 family members, and a third and more distant clade. In addition to crinkly leaves in maize, which gave rise to the mutant gene name, CR4 is implicated in ovule, embryo, flower and root development in Arabidopsis thaliana. In root tips of the same species the module including a CLAVATA3/ESR-related protein, an Arabidopsis CR4, a CLAVATA1 and a WUSCHEL-related homeobox 5 (CLE40-ACR4-CLV1-WOX5) is implicated in meristem cell regulation. In embryos and shoots, CR4 acts together with A. thaliana MERISTEM LAYER 1 and PROTODERMAL FACTOR 2 to promote A. thaliana epidermis differentiation. Phylogenetic analysis has demonstrated that early land plants, e.g. mosses carry a single ancestral CR4 gene, together with genes encoding the other members of the CLE40-ACR4-CLV1-WOX5 signaling module. Here we show that CR4 serves as a broad regulator of morphogenesis both in gametophyte phyllids, archegonia and in sporophyte epidermis of the moss Physcomitrella patens. The phenotype of the CR4 deletion mutant in moss provides insight into the role of the ancestral CR4 gene as a regulator of development in early land plants.
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Affiliation(s)
- Viktor Demko
- Norwegian University of Life Sciences, P.O.Box 5003, 1432, Ås, Norway
- Department of Plant Physiology, Faculty of Natural Sciences, Mlynska Dolina, 84215, Bratislava, Slovakia
| | - Eugene Ako
- Department of Natural Science and Technology, Hedmark University of Applied Sciences, 2318, Hamar, Norway
| | - Pierre-François Perroud
- Department of Biology, Washington University in St Louis, Campus Box 1137, St. Louis, MO, 63130, USA
- Plant Cell Biology, Philipps University Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Ralph Quatrano
- Department of Biology, Washington University in St Louis, Campus Box 1137, St. Louis, MO, 63130, USA
| | - Odd-Arne Olsen
- Norwegian University of Life Sciences, P.O.Box 5003, 1432, Ås, Norway.
- Department of Natural Science and Technology, Hedmark University of Applied Sciences, 2318, Hamar, Norway.
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Plackett ARG, Di Stilio VS, Langdale JA. Ferns: the missing link in shoot evolution and development. FRONTIERS IN PLANT SCIENCE 2015; 6:972. [PMID: 26594222 PMCID: PMC4635223 DOI: 10.3389/fpls.2015.00972] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 10/23/2015] [Indexed: 05/02/2023]
Abstract
Shoot development in land plants is a remarkably complex process that gives rise to an extreme diversity of forms. Our current understanding of shoot developmental mechanisms comes almost entirely from studies of angiosperms (flowering plants), the most recently diverged plant lineage. Shoot development in angiosperms is based around a layered multicellular apical meristem that produces lateral organs and/or secondary meristems from populations of founder cells at its periphery. In contrast, non-seed plant shoots develop from either single apical initials or from a small population of morphologically distinct apical cells. Although developmental and molecular information is becoming available for non-flowering plants, such as the model moss Physcomitrella patens, making valid comparisons between highly divergent lineages is extremely challenging. As sister group to the seed plants, the monilophytes (ferns and relatives) represent an excellent phylogenetic midpoint of comparison for unlocking the evolution of shoot developmental mechanisms, and recent technical advances have finally made transgenic analysis possible in the emerging model fern Ceratopteris richardii. This review compares and contrasts our current understanding of shoot development in different land plant lineages with the aim of highlighting the potential role that the fern C. richardii could play in shedding light on the evolution of underlying genetic regulatory mechanisms.
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Affiliation(s)
- Andrew R. G. Plackett
- Department of Plant Sciences, University of OxfordOxford, UK
- *Correspondence: Andrew R. G. Plackett,
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