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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] [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: 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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Perroud PF, Demko V, Ako AE, Khanal R, Bokor B, Pavlovič A, Jásik J, Johansen W. The nuclear GUCT domain-containing DEAD-box RNA helicases govern gametophytic and sporophytic development in Physcomitrium patens. Plant Mol Biol 2021; 107:307-325. [PMID: 33886069 PMCID: PMC8648619 DOI: 10.1007/s11103-021-01152-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 12/03/2020] [Accepted: 04/06/2021] [Indexed: 05/29/2023]
Abstract
KEY MESSAGE In Physcomitrium patens, PpRH1/PpRH2 are GUCT-domain-containing DEAD-BOX RNA helicases localize to the nucleus. They are implicated in cell and tissue development in all stages of the moss life cycle. ABSTRACT The DEAD-box-containing RNA helicase family encompasses a large and functionally important group of enzymes involved in cellular processes committed to the metabolism of RNA, including its transcription, processing, transport, translation and decay. Studies indicate this protein family has implied roles in plant vegetative and reproductive developmental processes as well as response to environmental stresses such has cold and high salinity. We focus here on a small conserved sub-group of GUCT domain-containing RNA helicase in the moss Physcomitrium patens. Phylogenetic analysis shows that RNA helicases containing the GUCT domain form a distinct conserved clade across the green lineage. In this clade, the P. patens genome possesses two closely related paralogues RNA helicases predicted to be nuclear, PpRH1 and PpRH2. Using in-locus gene fluorescent tagging we show that PpRH1 is localized to the nucleus in protonema. Analysis of PpRH1 and PpRH2 deletions, individually and together, indicates their potential roles in protonema, gametophore and sporophyte cellular and tissue development in P. patens. Additionally, the ultrastructural analysis of phyllid chloroplasts in Δrh2 and Δrh1/2 shows distinct starch granule accumulation under standard growth conditions associated with changes in photosynthetic activity parameters. We could not detect effects of either temperature or stress on protonema growth or PpRH1 and PpRH2 expression. Together, these results suggest that nuclear GUCT-containing RNA helicases play a role primarily in developmental processes directly or indirectly linked to photosynthesis activity in the moss P. patens. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s11103-021-01152-w.
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Affiliation(s)
- Pierre-François Perroud
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch Str. 8, 35043, Marburg, Germany
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Viktor Demko
- Department of Plant Physiology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 84215, Bratislava, Slovakia
- Plant Science and Biodiversity Center, Slovak Academy of Sciences, Dúbravská cesta 9, 84523, Bratislava, Slovakia
| | - 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, NG25 0QF, Nottinghamshire, UK
| | - Rajendra Khanal
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata 31, 2318, Hamar, Norway
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Boris Bokor
- Department of Plant Physiology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 84215, Bratislava, Slovakia
- Comenius University in Bratislava Science Park, Ilkovicova 8, 84215, Bratislava, Slovakia
| | - Andrej Pavlovič
- Department of Biophysics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Ján Jásik
- Plant Science and Biodiversity Center, Slovak Academy of Sciences, Dúbravská cesta 9, 84523, Bratislava, Slovakia
| | - Wenche Johansen
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata 31, 2318, Hamar, Norway.
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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 Physiol 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] [What about the content of this article? (0)] [Affiliation(s)] [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, Perroud PF, Johansen W, Delwiche CF, Cooper ED, Remme P, Ako AE, Kugler KG, Mayer KFX, Quatrano R, Olsen OA. Genetic analysis of DEFECTIVE KERNEL1 loop function in three-dimensional body patterning in Physcomitrella patens. Plant Physiol 2014; 166:903-19. [PMID: 25185121 PMCID: PMC4213117 DOI: 10.1104/pp.114.243758] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 08/31/2014] [Indexed: 05/02/2023]
Abstract
DEFECTIVE KERNEL1 (DEK1) of higher plants plays an essential role in position-dependent signaling and consists of a large transmembrane domain (MEM) linked to a protease catalytic domain and a regulatory domain. Here, we show that the postulated sensory Loop of the MEM domain plays an important role in the developmental regulation of DEK1 activity in the moss Physcomitrella patens. Compared with P. patens lacking DEK1 (∆dek1), the dek1∆loop mutant correctly positions the division plane in the bud apical cell. In contrast with an early developmental arrest of ∆dek1 buds, dek1∆loop develops aberrant gametophores lacking expanded phyllids resulting from misregulation of mitotic activity. In contrast with the highly conserved sequence of the protease catalytic domain, the Loop is highly variable in land plants. Functionally, the sequence from Marchantia polymorpha fully complements the dek1∆loop phenotype, whereas sequences from maize (Zea mays) and Arabidopsis (Arabidopsis thaliana) give phenotypes with retarded growth and affected phyllid development. Bioinformatic analysis identifies MEM as a member of the Major Facilitator Superfamily, membrane transporters reacting to stimuli from the external environment. Transcriptome analysis comparing wild-type and ∆dek1 tissues identifies an effect on two groups of transcripts connected to dek1 mutant phenotypes: transcripts related to cell wall remodeling and regulation of the AINTEGUMENTA, PLETHORA, and BABY BOOM2 (APB2) and APB3 transcription factors known to regulate bud initiation. Finally, sequence data support the hypothesis that the advanced charophyte algae that evolved into ancestral land plants lost cytosolic calpains, retaining DEK1 as the sole calpain in the evolving land plant lineage.
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Affiliation(s)
- Viktor Demko
- Norwegian University of Life Sciences, N-1432 As, Norway (V.D., O.-A.O.);Department of Biology, Washington University, St. Louis, Missouri 63130 (P.-F.P., R.Q.);Department of Natural Science and Technology, Hedmark University College, N-2318 Hamar, Norway (W.J., P.R., A.E.A., O.-A.O.);Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742 (C.F.D., E.D.C.); andMIPS/IBIS, Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany (K.G.K., K.F.X.M.)
| | - Pierre-François Perroud
- Norwegian University of Life Sciences, N-1432 As, Norway (V.D., O.-A.O.);Department of Biology, Washington University, St. Louis, Missouri 63130 (P.-F.P., R.Q.);Department of Natural Science and Technology, Hedmark University College, N-2318 Hamar, Norway (W.J., P.R., A.E.A., O.-A.O.);Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742 (C.F.D., E.D.C.); andMIPS/IBIS, Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany (K.G.K., K.F.X.M.)
| | - Wenche Johansen
- Norwegian University of Life Sciences, N-1432 As, Norway (V.D., O.-A.O.);Department of Biology, Washington University, St. Louis, Missouri 63130 (P.-F.P., R.Q.);Department of Natural Science and Technology, Hedmark University College, N-2318 Hamar, Norway (W.J., P.R., A.E.A., O.-A.O.);Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742 (C.F.D., E.D.C.); andMIPS/IBIS, Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany (K.G.K., K.F.X.M.)
| | - Charles F Delwiche
- Norwegian University of Life Sciences, N-1432 As, Norway (V.D., O.-A.O.);Department of Biology, Washington University, St. Louis, Missouri 63130 (P.-F.P., R.Q.);Department of Natural Science and Technology, Hedmark University College, N-2318 Hamar, Norway (W.J., P.R., A.E.A., O.-A.O.);Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742 (C.F.D., E.D.C.); andMIPS/IBIS, Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany (K.G.K., K.F.X.M.)
| | - Endymion D Cooper
- Norwegian University of Life Sciences, N-1432 As, Norway (V.D., O.-A.O.);Department of Biology, Washington University, St. Louis, Missouri 63130 (P.-F.P., R.Q.);Department of Natural Science and Technology, Hedmark University College, N-2318 Hamar, Norway (W.J., P.R., A.E.A., O.-A.O.);Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742 (C.F.D., E.D.C.); andMIPS/IBIS, Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany (K.G.K., K.F.X.M.)
| | - Pål Remme
- Norwegian University of Life Sciences, N-1432 As, Norway (V.D., O.-A.O.);Department of Biology, Washington University, St. Louis, Missouri 63130 (P.-F.P., R.Q.);Department of Natural Science and Technology, Hedmark University College, N-2318 Hamar, Norway (W.J., P.R., A.E.A., O.-A.O.);Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742 (C.F.D., E.D.C.); andMIPS/IBIS, Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany (K.G.K., K.F.X.M.)
| | - Ako Eugene Ako
- Norwegian University of Life Sciences, N-1432 As, Norway (V.D., O.-A.O.);Department of Biology, Washington University, St. Louis, Missouri 63130 (P.-F.P., R.Q.);Department of Natural Science and Technology, Hedmark University College, N-2318 Hamar, Norway (W.J., P.R., A.E.A., O.-A.O.);Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742 (C.F.D., E.D.C.); andMIPS/IBIS, Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany (K.G.K., K.F.X.M.)
| | - Karl G Kugler
- Norwegian University of Life Sciences, N-1432 As, Norway (V.D., O.-A.O.);Department of Biology, Washington University, St. Louis, Missouri 63130 (P.-F.P., R.Q.);Department of Natural Science and Technology, Hedmark University College, N-2318 Hamar, Norway (W.J., P.R., A.E.A., O.-A.O.);Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742 (C.F.D., E.D.C.); andMIPS/IBIS, Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany (K.G.K., K.F.X.M.)
| | - Klaus F X Mayer
- Norwegian University of Life Sciences, N-1432 As, Norway (V.D., O.-A.O.);Department of Biology, Washington University, St. Louis, Missouri 63130 (P.-F.P., R.Q.);Department of Natural Science and Technology, Hedmark University College, N-2318 Hamar, Norway (W.J., P.R., A.E.A., O.-A.O.);Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742 (C.F.D., E.D.C.); andMIPS/IBIS, Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany (K.G.K., K.F.X.M.)
| | - Ralph Quatrano
- Norwegian University of Life Sciences, N-1432 As, Norway (V.D., O.-A.O.);Department of Biology, Washington University, St. Louis, Missouri 63130 (P.-F.P., R.Q.);Department of Natural Science and Technology, Hedmark University College, N-2318 Hamar, Norway (W.J., P.R., A.E.A., O.-A.O.);Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742 (C.F.D., E.D.C.); andMIPS/IBIS, Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany (K.G.K., K.F.X.M.)
| | - Odd-Arne Olsen
- Norwegian University of Life Sciences, N-1432 As, Norway (V.D., O.-A.O.);Department of Biology, Washington University, St. Louis, Missouri 63130 (P.-F.P., R.Q.);Department of Natural Science and Technology, Hedmark University College, N-2318 Hamar, Norway (W.J., P.R., A.E.A., O.-A.O.);Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742 (C.F.D., E.D.C.); andMIPS/IBIS, Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany (K.G.K., K.F.X.M.)
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