1
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Calbry J, Goudounet G, Charlot F, Guyon-Debast A, Perroud PF, Nogué F. The SpRY Cas9 variant release the PAM sequence constraint for genome editing in the model plant Physcomitrium patens. Transgenic Res 2024; 33:67-74. [PMID: 38573428 PMCID: PMC11021247 DOI: 10.1007/s11248-024-00381-1] [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: 08/25/2023] [Accepted: 03/18/2024] [Indexed: 04/05/2024]
Abstract
Genome editing via CRISPR/Cas has enabled targeted genetic modifications in various species, including plants. The requirement for specific protospacer-adjacent motifs (PAMs) near the target gene, as seen with Cas nucleases like SpCas9, limits its application. PAMless SpCas9 variants, designed with a relaxed PAM requirement, have widened targeting options. However, these so-call PAMless SpCas9 still show variation of editing efficiency depending on the PAM and their efficiency lags behind the native SpCas9. Here we assess the potential of a PAMless SpCas9 variant for genome editing in the model plant Physcomitrium patens. For this purpose, we developed a SpRYCas9i variant, where expression was optimized, and tested its editing efficiency using the APT as a reporter gene. We show that the near PAMless SpRYCas9i effectively recognizes specific PAMs in P. patens that are not or poorly recognized by the native SpCas9. Pattern of mutations found using the SpRYCas9i are similar to the ones found with the SpCas9 and we could not detect off-target activity for the sgRNAs tested in this study. These findings contribute to advancing versatile genome editing techniques in plants.
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Affiliation(s)
- Julie Calbry
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France
| | - Guillaume Goudounet
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France
| | - Florence Charlot
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France
| | - Anouchka Guyon-Debast
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France
| | - Pierre-François Perroud
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France
| | - Fabien Nogué
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France.
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2
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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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3
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Vollmeister E, Phokas A, Meyberg R, Böhm CV, Peter M, Kohnert E, Yuan J, Grosche C, Göttig M, Ullrich KK, Perroud PF, Hiltbrunner A, Kreutz C, Coates JC, Rensing SA. A DELAY OF GERMINATION 1 (DOG1)-like protein regulates spore germination in the moss Physcomitrium patens. Plant J 2024; 117:909-923. [PMID: 37953711 DOI: 10.1111/tpj.16537] [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: 11/12/2022] [Revised: 10/22/2023] [Accepted: 10/26/2023] [Indexed: 11/14/2023]
Abstract
DELAY OF GERMINATION 1 is a key regulator of dormancy in flowering plants before seed germination. Bryophytes develop haploid spores with an analogous function to seeds. Here, we investigate whether DOG1 function during germination is conserved between bryophytes and flowering plants and analyse the underlying mechanism of DOG1 action in the moss Physcomitrium patens. Phylogenetic and in silico expression analyses were performed to identify and characterise DOG1 domain-containing genes in P. patens. Germination assays were performed to characterise a Ppdog1-like1 mutant, and replacement with AtDOG1 was carried out. Yeast two-hybrid assays were used to test the interaction of the PpDOG1-like protein with DELLA proteins from P. patens and A. thaliana. P. patens possesses nine DOG1 domain-containing genes. The DOG1-like protein PpDOG1-L1 (Pp3c3_9650) interacts with PpDELLAa and PpDELLAb and the A. thaliana DELLA protein AtRGA in yeast. Protein truncations revealed the DOG1 domain as necessary and sufficient for interaction with PpDELLA proteins. Spores of Ppdog1-l1 mutant germinate faster than wild type, but replacement with AtDOG1 reverses this effect. Our data demonstrate a role for the PpDOG1-LIKE1 protein in moss spore germination, possibly alongside PpDELLAs. This suggests a conserved DOG1 domain function in germination, albeit with differential adaptation of regulatory networks in seed and spore germination.
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Affiliation(s)
- Evelyn Vollmeister
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | - Alexandros Phokas
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Rabea Meyberg
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | - Clemens V Böhm
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | - Marlies Peter
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | - Eva Kohnert
- Institute of Medical Biometry and Statistics, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, 79104, Germany
| | - Jinhong Yuan
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Christopher Grosche
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | - Marco Göttig
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | - Kristian K Ullrich
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | | | - Andreas Hiltbrunner
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Germany
| | - Clemens Kreutz
- Institute of Medical Biometry and Statistics, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, 79104, Germany
| | - Juliet C Coates
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Stefan A Rensing
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
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4
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Perroud PF, Guyon-Debast A, Casacuberta JM, Paul W, Pichon JP, Comeau D, Nogué F. Improved prime editing allows for routine predictable gene editing in Physcomitrium patens. J Exp Bot 2023; 74:6176-6187. [PMID: 37243510 PMCID: PMC10575697 DOI: 10.1093/jxb/erad189] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 05/17/2023] [Accepted: 05/25/2023] [Indexed: 05/29/2023]
Abstract
Efficient and precise gene editing is the gold standard of any reverse genetic study. The recently developed prime editing approach, a modified CRISPR/Cas9 [clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein] editing method, has reached the precision goal but its editing rate can be improved. We present an improved methodology that allows for routine prime editing in the model plant Physcomitrium patens, whilst exploring potential new prime editing improvements. Using a standardized protoplast transfection procedure, multiple prime editing guide RNA (pegRNA) structural and prime editor variants were evaluated targeting the APT reporter gene through direct plant selection. Together, enhancements of expression of the prime editor, modifications of the 3' extension of the pegRNA, and the addition of synonymous mutation in the reverse transcriptase template sequence of the pegRNA dramatically improve the editing rate without affecting the quality of the edits. Furthermore, we show that prime editing is amenable to edit a gene of interest through indirect selection, as demonstrated by the generation of a Ppdek10 mutant. Additionally, we determine that a plant retrotransposon reverse transcriptase enables prime editing. Finally, we show for the first time the possibility of performing prime editing with two independently coded peptides.
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Affiliation(s)
- Pierre-François Perroud
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Anouchka Guyon-Debast
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Josep M Casacuberta
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Bellaterra, 08193 Barcelona, Spain
| | - Wyatt Paul
- Limagrain Europe, Centre de Recherche de Chappes, 63720 Chappes, France
| | | | - David Comeau
- Limagrain Europe, Centre de Recherche de Chappes, 63720 Chappes, France
| | - Fabien Nogué
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
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5
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Sreedasyam A, Plott C, Hossain MS, Lovell J, Grimwood J, Jenkins J, Daum C, Barry K, Carlson J, Shu S, Phillips J, Amirebrahimi M, Zane M, Wang M, Goodstein D, Haas F, Hiss M, Perroud PF, Jawdy S, Yang Y, Hu R, Johnson J, Kropat J, Gallaher S, Lipzen A, Shakirov E, Weng X, Torres-Jerez I, Weers B, Conde D, Pappas M, Liu L, Muchlinski A, Jiang H, Shyu C, Huang P, Sebastian J, Laiben C, Medlin A, Carey S, Carrell A, Chen JG, Perales M, Swaminathan K, Allona I, Grattapaglia D, Cooper E, Tholl D, Vogel J, Weston DJ, Yang X, Brutnell T, Kellogg E, Baxter I, Udvardi M, Tang Y, Mockler T, Juenger T, Mullet J, Rensing S, Tuskan G, Merchant S, Stacey G, Schmutz J. JGI Plant Gene Atlas: an updateable transcriptome resource to improve functional gene descriptions across the plant kingdom. Nucleic Acids Res 2023; 51:8383-8401. [PMID: 37526283 PMCID: PMC10484672 DOI: 10.1093/nar/gkad616] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 06/21/2023] [Accepted: 07/11/2023] [Indexed: 08/02/2023] Open
Abstract
Gene functional descriptions offer a crucial line of evidence for candidate genes underlying trait variation. Conversely, plant responses to environmental cues represent important resources to decipher gene function and subsequently provide molecular targets for plant improvement through gene editing. However, biological roles of large proportions of genes across the plant phylogeny are poorly annotated. Here we describe the Joint Genome Institute (JGI) Plant Gene Atlas, an updateable data resource consisting of transcript abundance assays spanning 18 diverse species. To integrate across these diverse genotypes, we analyzed expression profiles, built gene clusters that exhibited tissue/condition specific expression, and tested for transcriptional response to environmental queues. We discovered extensive phylogenetically constrained and condition-specific expression profiles for genes without any previously documented functional annotation. Such conserved expression patterns and tightly co-expressed gene clusters let us assign expression derived additional biological information to 64 495 genes with otherwise unknown functions. The ever-expanding Gene Atlas resource is available at JGI Plant Gene Atlas (https://plantgeneatlas.jgi.doe.gov) and Phytozome (https://phytozome.jgi.doe.gov/), providing bulk access to data and user-specified queries of gene sets. Combined, these web interfaces let users access differentially expressed genes, track orthologs across the Gene Atlas plants, graphically represent co-expressed genes, and visualize gene ontology and pathway enrichments.
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Affiliation(s)
| | | | - Md Shakhawat Hossain
- Division of Plant Science and Technology, C.S. Bond Life Science Center, University of Missouri, Columbia, MO, USA
| | - John T Lovell
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jerry W Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Christopher Daum
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kerrie Barry
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Joseph Carlson
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Shengqiang Shu
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jeremy Phillips
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mojgan Amirebrahimi
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Matthew Zane
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mei Wang
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David Goodstein
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Fabian B Haas
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str, Marburg, Germany
| | - Manuel Hiss
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str, Marburg, Germany
| | - Pierre-François Perroud
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str, Marburg, Germany
| | - Sara S Jawdy
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Yongil Yang
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Rongbin Hu
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jenifer Johnson
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Janette Kropat
- Department of Chemistry and Biochemistry and Institute for Genomics and Proteomics, University of California, Los Angeles, CA, USA
| | - Sean D Gallaher
- Department of Chemistry and Biochemistry and Institute for Genomics and Proteomics, University of California, Los Angeles, CA, USA
| | - Anna Lipzen
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Eugene V Shakirov
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Xiaoyu Weng
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | | | - Brock Weers
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Daniel Conde
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Marilia R Pappas
- Laboratório de Genética Vegetal, EMBRAPA Recursos Genéticos e Biotecnologia, EPQB Final W5 Norte, Brasília, Brazil
| | - Lifeng Liu
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Andrew Muchlinski
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Hui Jiang
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Christine Shyu
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Pu Huang
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Jose Sebastian
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Carol Laiben
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Alyssa Medlin
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Sankalpi Carey
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Alyssa A Carrell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Mariano Perales
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | | | - Isabel Allona
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Dario Grattapaglia
- Laboratório de Genética Vegetal, EMBRAPA Recursos Genéticos e Biotecnologia, EPQB Final W5 Norte, Brasília, Brazil
| | | | - Dorothea Tholl
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - John P Vogel
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Xiaohan Yang
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | | | - Ivan Baxter
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | | | | | - Todd C Mockler
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - John Mullet
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str, Marburg, Germany
| | - Gerald A Tuskan
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry and Institute for Genomics and Proteomics, University of California, Los Angeles, CA, USA
| | - Gary Stacey
- Division of Plant Science and Technology, C.S. Bond Life Science Center, University of Missouri, Columbia, MO, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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6
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Perroud PF, Guyon-Debast A, Veillet F, Kermarrec MP, Chauvin L, Chauvin JE, Gallois JL, Nogué F. Prime Editing in the model plant Physcomitrium patens and its potential in the tetraploid potato. Plant Sci 2022; 316:111162. [PMID: 35151447 DOI: 10.1016/j.plantsci.2021.111162] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [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: 10/08/2021] [Revised: 12/03/2021] [Accepted: 12/19/2021] [Indexed: 06/14/2023]
Abstract
Since its discovery and first applications for genome editing in plants, the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 technology has revolutionized plant research and precision crop breeding. Although the classical CRISPR-Cas9 system is a highly efficient tool for disruptive targeted mutagenesis, this system is mostly inefficient for the introduction of precise and predictable nucleotide substitutions. Recently, Prime Editing technology has been developed, allowing the simultaneous generation of nucleotide transitions and transversions but also short defined indels. In this study, we report on the successful use of Prime Editing in two plants of interest: the plant model Physcomitrium patens and the tetraploid and highly heterozygous potato (Solanum tuberosum). In both cases editing rates were lower than with other CRISPR-Cas9 based techniques, but we were able to successfully introduce nucleotide transversions into targeted genes, a unique feature of Prime Editing. Additionally, the analysis of potential off-target mutation sites in P. patens suggested very high targeting fidelity in this organism. The present work paves the way for the use Prime Editing in Physcomitrium patens and potato, however highlighting the limitations that need to be overcome for more efficient precision plant breeding.
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Affiliation(s)
- Pierre-François Perroud
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France.
| | - Anouchka Guyon-Debast
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Florian Veillet
- IGEPP, INRAE, Institut Agro, Univ Rennes, 29260, Ploudaniel, France
| | | | - Laura Chauvin
- IGEPP, INRAE, Institut Agro, Univ Rennes, 29260, Ploudaniel, France
| | | | | | - Fabien Nogué
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
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7
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Abstract
Protoplast production with the moss Physcomitrium (Physcomitrella) patens has a long and successful history. As a tool, it has not only been the base of reverse genetic studies covering research fields as diverse as development, metabolism, or gene network regulation but also allowed its development as a bioengineering platform for protein production. We present here a standardized protocol for protoplast production from Physcomitrium (Physcomitrella) patens protonemata. Additionally, we detail procedures for their transfection, their plating for optimal regeneration, and three alternative selection approaches. To improve the consistency of protoplast regeneration, we describe a new option for protoplast embedding. The use of an alginate matrix to regenerate moss protoplast alleviates the use of warm agarized medium. Thus, it optimizes transformed protoplast survival without any morphological detrimental effect or impact on transfection efficiency.
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Affiliation(s)
- Florence Charlot
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Guillaume Goudounet
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Fabien Nogué
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Pierre-François Perroud
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France.
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8
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Vendrell-Mir P, Perroud PF, Haas FB, Meyberg R, Charlot F, Rensing SA, Nogué F, Casacuberta JM. A vertically transmitted amalgavirus is present in certain accessions of the bryophyte Physcomitrium patens. Plant J 2021; 108:1786-1797. [PMID: 34687260 DOI: 10.1111/tpj.15545] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 08/10/2021] [Accepted: 10/16/2021] [Indexed: 06/13/2023]
Abstract
In the last few years, next-generation sequencing techniques have started to be used to identify new viruses infecting plants. This has allowed to rapidly increase our knowledge on viruses other than those causing symptoms in economically important crops. Here we used this approach to identify a virus infecting Physcomitrium patens that has the typical structure of the double-stranded RNA endogenous viruses of the Amalgaviridae family, which we named Physcomitrium patens amalgavirus 1, or PHPAV1. PHPAV1 is present only in certain accessions of P. patens, where its RNA can be detected throughout the cell cycle of the plant. Our analysis demonstrates that PHPAV1 can be vertically transmitted through both paternal and maternal germlines, in crosses between accessions that contain the virus with accessions that do not contain it. This work suggests that PHPAV1 can replicate in genomic backgrounds different from those that actually contain the virus and opens the door for future studies on virus-host coevolution.
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Affiliation(s)
- Pol Vendrell-Mir
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Bellaterra, Barcelona, 08193, Spain
| | - Pierre-François Perroud
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, 78000, France
| | - Fabian B Haas
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | - Rabea Meyberg
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | - Florence Charlot
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, 78000, France
| | - Stefan A Rensing
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Fabien Nogué
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, 78000, France
| | - Josep M Casacuberta
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Bellaterra, Barcelona, 08193, Spain
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9
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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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10
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Perroud PF, Demko V. Challenges of in vivo protein localization in plants seen through the DEK1 protein lens. Plant Signal Behav 2020; 15:1780404. [PMID: 32567469 PMCID: PMC8570728 DOI: 10.1080/15592324.2020.1780404] [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] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 06/11/2023]
Abstract
During the last 25 y, fluorescent protein tagging has become a tool of choice to investigate protein function in a cellular context. The information gathered with this approach is not only providing insights into protein subcellular localization but also allows contextualizing protein function in multicellular settings. Here we illustrate the power of this method by commenting on the recent successful localization of the large membrane DEK1 protein during three-dimensional body formation in the moss Physcomitrella patens. But as many approaches, protein tagging is not exempt of caveats. The multiple infructuous (failed) attempts to detect DEK1 using a fluorescent protein tag present a good overview of such potential problems. Here we discuss the insertion of different fluorescent proteins at different positions in the PpDEK1 protein and the resulting unintended range of mutant phenotypes. Albeit none of these mutants generated a detectable fluorescent signal they can still provide interesting biological information about DEK1 function.
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Affiliation(s)
| | - Viktor Demko
- Department of Plant Physiology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
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11
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Haas FB, Fernandez-Pozo N, Meyberg R, Perroud PF, Göttig M, Stingl N, Saint-Marcoux D, Langdale JA, Rensing SA. Single Nucleotide Polymorphism Charting of P. patens Reveals Accumulation of Somatic Mutations During in vitro Culture on the Scale of Natural Variation by Selfing. Front Plant Sci 2020; 11:813. [PMID: 32733496 PMCID: PMC7358436 DOI: 10.3389/fpls.2020.00813] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/20/2020] [Indexed: 06/01/2023]
Abstract
Introduction: Physcomitrium patens (Hedw.) Mitten (previously known as Physcomitrella patens) was collected by H.L.K. Whitehouse in Gransden Wood (Huntingdonshire, United Kingdom) in 1962 and distributed across the globe starting in 1974. Hence, the Gransden accession has been cultured in vitro in laboratories for half a century. Today, there are more than 13 different pedigrees derived from the original accession. Additionally, accessions from other sites worldwide were collected during the last decades. Methods and Results: In this study, 250 high throughput RNA sequencing (RNA-seq) samples and 25 gDNA samples were used to detect single nucleotide polymorphisms (SNPs). Analyses were performed using five different P. patens accessions and 13 different Gransden pedigrees. SNPs were overlaid with metadata and known phenotypic variations. Unique SNPs defining Gransden pedigrees and accessions were identified and experimentally confirmed. They can be successfully employed for PCR-based identification. Conclusion: We show independent mutations in different Gransden laboratory pedigrees, demonstrating that somatic mutations occur and accumulate during in vitro culture. The frequency of such mutations is similar to those observed in naturally occurring populations. We present evidence that vegetative propagation leads to accumulation of deleterious mutations, and that sexual reproduction purges those. Unique SNP sets for five different P. patens accessions were isolated and can be used to determine individual accessions as well as Gransden pedigrees. Based on that, laboratory methods to easily determine P. patens accessions and Gransden pedigrees are presented.
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Affiliation(s)
- Fabian B. Haas
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | - Noe Fernandez-Pozo
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | - Rabea Meyberg
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | | | - Marco Göttig
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | - Nora Stingl
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | - Denis Saint-Marcoux
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
- Université de Lyon, UJM-Saint-Etienne, CNRS, Laboratoire BVpam - FRE 3727, Saint-Étienne, France
| | - Jane A. Langdale
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Stefan A. Rensing
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
- SYNMIKRO Center for Synthetic Microbiology, University of Marburg, Marburg, Germany
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12
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Meyberg R, Perroud PF, Haas FB, Schneider L, Heimerl T, Renzaglia KS, Rensing SA. Characterisation of evolutionarily conserved key players affecting eukaryotic flagellar motility and fertility using a moss model. New Phytol 2020; 227:440-454. [PMID: 32064607 PMCID: PMC8224819 DOI: 10.1111/nph.16486] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 12/16/2019] [Accepted: 02/07/2020] [Indexed: 05/18/2023]
Abstract
Defects in flagella/cilia are often associated with infertility and disease. Motile male gametes (sperm cells) are an ancestral eukaryotic trait that has been lost in several lineages like flowering plants. Here, we made use of a phenotypic male fertility difference between two moss (Physcomitrella patens) ecotypes to explore spermatozoid function. We compare genetic and epigenetic variation as well as expression profiles between the Gransden and Reute ecotype to identify a set of candidate genes associated with moss male infertility. We generated a loss-of-function mutant of a coiled-coil domain containing 39 (ccdc39) gene that is part of the flagellar hydin network. Defects in mammal and algal homologues of this gene coincide with a loss of fertility, demonstrating the evolutionary conservation of flagellar function related to male fertility across kingdoms. The Ppccdc39 mutant resembles the Gransden phenotype in terms of male fertility. Potentially, several somatic (epi-)mutations occurred during prolonged vegetative propagation of Gransden, causing regulatory differences of for example the homeodomain transcription factor BELL1. Probably these somatic changes are causative for the observed male fertility defect. We propose that moss spermatozoids might be employed as an easily accessible system to study male infertility of humans and animals in terms of flagellar structure and movement.
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Affiliation(s)
- Rabea Meyberg
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch Str. 8, 35043 Marburg, Germany
| | - Pierre-François Perroud
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch Str. 8, 35043 Marburg, Germany
| | - Fabian B. Haas
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch Str. 8, 35043 Marburg, Germany
| | - Lucas Schneider
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch Str. 8, 35043 Marburg, Germany
| | - Thomas Heimerl
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, Karl-von-Frisch Str. 8, 35043 Marburg, Germany
| | - Karen S. Renzaglia
- Department of Plant Biology, Southern Illinois University, Mail Code 6509, 1125 Lincoln Drive, Carbondale, IL 62901, USA
| | - Stefan A. Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch Str. 8, 35043 Marburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestraße 18, 79104 Freiburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, Karl-von-Frisch Str. 8, 35043 Marburg, Germany
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13
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Perroud PF, Meyberg R, Demko V, Quatrano RS, Olsen OA, Rensing SA. DEK1 displays a strong subcellular polarity during Physcomitrella patens 3D growth. New Phytol 2020; 226:1029-1041. [PMID: 31913503 DOI: 10.1111/nph.16417] [Citation(s) in RCA: 16] [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: 11/26/2019] [Accepted: 12/24/2019] [Indexed: 05/18/2023]
Abstract
Defective Kernel 1 (DEK1) is genetically at the nexus of the 3D morphogenesis of land plants. We aimed to localize DEK1 in the moss Physcomitrella patens to decipher its function during this process. To detect DEK1 in vivo, we inserted the tdTomato fluorophore into PpDEK1 gene locus. Confocal microscopy coupled with the use of time-gating allowed the precise DEK1 subcellular localization during 3D morphogenesis. DEK1 localization displays a strong polarized signal, as it is restricted to the plasma membrane domain between recently divided cells during the early steps of 3D growth development as well as during the subsequent vegetative growth. The signal furthermore displays a clear developmental pattern because it is only detectable in recently divided and elongating cells. Additionally, DEK1 localization appears to be independent of its calpain domain proteolytic activity. The DEK1 polar subcellular distribution in 3D tissue developing cells defines a functional cellular framework to explain its role in this developmental phase. Also, the observation of DEK1 during spermatogenesis suggests another biological function for this protein in plants. Finally the DEK1-tagged strain generated here provides a biological platform upon which further investigations into 3D developmental processes can be performed.
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Affiliation(s)
- Pierre-François Perroud
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch Str. 8, Marburg, 35043, Germany
| | - Rabea Meyberg
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch Str. 8, Marburg, 35043, Germany
| | - Viktor Demko
- Department of Plant Physiology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, Bratislava, 84215, Slovakia
| | - Ralph S Quatrano
- Department of Biology, Washington University in St Louis, One Brookings Dr., Campus, Box 1137, St Louis, MO, 63130, USA
| | - Odd-Arne Olsen
- Norwegian University of Life Sciences, PO Box 5003, Aas, NO-1432, Norway
| | - Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch Str. 8, Marburg, 35043, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestraße 18, Freiburg im Breisgau, 79104, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, Hans-Meerwein-Straße 6, Marburg, 35043, Germany
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14
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Fernandez-Pozo N, Haas FB, Meyberg R, Ullrich KK, Hiss M, Perroud PF, Hanke S, Kratz V, Powell AF, Vesty EF, Daum CG, Zane M, Lipzen A, Sreedasyam A, Grimwood J, Coates JC, Barry K, Schmutz J, Mueller LA, Rensing SA. PEATmoss (Physcomitrella Expression Atlas Tool): a unified gene expression atlas for the model plant Physcomitrella patens. Plant J 2020; 102:165-177. [PMID: 31714620 DOI: 10.1111/tpj.14607] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [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: 03/26/2019] [Revised: 10/14/2019] [Accepted: 10/30/2019] [Indexed: 05/23/2023]
Abstract
Physcomitrella patens is a bryophyte model plant that is often used to study plant evolution and development. Its resources are of great importance for comparative genomics and evo-devo approaches. However, expression data from Physcomitrella patens were so far generated using different gene annotation versions and three different platforms: CombiMatrix and NimbleGen expression microarrays and RNA sequencing. The currently available P. patens expression data are distributed across three tools with different visualization methods to access the data. Here, we introduce an interactive expression atlas, Physcomitrella Expression Atlas Tool (PEATmoss), that unifies publicly available expression data for P. patens and provides multiple visualization methods to query the data in a single web-based tool. Moreover, PEATmoss includes 35 expression experiments not previously available in any other expression atlas. To facilitate gene expression queries across different gene annotation versions, and to access P. patens annotations and related resources, a lookup database and web tool linked to PEATmoss was implemented. PEATmoss can be accessed at https://peatmoss.online.uni-marburg.de.
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Affiliation(s)
- Noe Fernandez-Pozo
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Fabian B Haas
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Rabea Meyberg
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Kristian K Ullrich
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Ploen, Germany
| | - Manuel Hiss
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | | | - Sebastian Hanke
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Viktor Kratz
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | | | - Eleanor F Vesty
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Christopher G Daum
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Matthew Zane
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Anna Lipzen
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | | | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Juliet C Coates
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Kerrie Barry
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Jeremy Schmutz
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA, 94598, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | | | - 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
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, Germany
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15
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Le Bail A, Schulmeister S, Perroud PF, Ntefidou M, Rensing SA, Kost B. Analysis of the Localization of Fluorescent PpROP1 and PpROP-GEF4 Fusion Proteins in Moss Protonemata Based on Genomic "Knock-In" and Estradiol-Titratable Expression. Front Plant Sci 2019; 10:456. [PMID: 31031790 PMCID: PMC6473103 DOI: 10.3389/fpls.2019.00456] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 03/26/2019] [Indexed: 05/26/2023]
Abstract
Tip growth of pollen tubes, root hairs, and apical cells of moss protonemata is controlled by ROP (Rho of plants) GTPases, which were shown to accumulate at the apical plasma membrane of these cells. However, most ROP localization patterns reported in the literature are based on fluorescent protein tagging and need to be interpreted with caution, as ROP fusion proteins were generally overexpressed at undefined levels, in many cases without assessing effects on tip growth. ROP-GEFs, important regulators of ROP activity, were also described to accumulate at the apical plasma membrane during tip growth. However, to date only the localization of fluorescent ROP-GEF fusion proteins strongly overexpressed using highly active promoters have been investigated. Here, the intracellular distributions of fluorescent PpROP1 and PpROP-GEF4 fusion proteins expressed at essentially endogenous levels in apical cells of Physcomitrella patens "knock-in" protonemata were analyzed. Whereas PpROP-GEF4 was found to associate with a small apical plasma membrane domain, PpROP1 expression was below the detection limit. Estradiol-titratable expression of a fluorescent PpROP1 fusion protein at the lowest detectable level, at which plant development was only marginally affected, was therefore employed to show that PpROP1 also accumulates at the apical plasma membrane, although within a substantially larger domain. Interestingly, RNA-Seq data indicated that the majority of all genes active in protonemata are expressed at lower levels than PpROP1, suggesting that estradiol-titratable expression may represent an important alternative to "knock-in" based analysis of the intracellular distribution of fluorescent fusion proteins in protonemal cells.
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Affiliation(s)
- Aude Le Bail
- Cell Biology, Department of Biology, Friedrich–Alexander University Erlangen–Nürnberg, Erlangen, Germany
| | - Sylwia Schulmeister
- Cell Biology, Department of Biology, Friedrich–Alexander University Erlangen–Nürnberg, Erlangen, Germany
| | | | - Maria Ntefidou
- Cell Biology, Department of Biology, Friedrich–Alexander University Erlangen–Nürnberg, Erlangen, Germany
| | - Stefan A. Rensing
- Plant Cell Biology, Faculty of Biology, Philipps University of Marburg, Marburg, Germany
| | - Benedikt Kost
- Cell Biology, Department of Biology, Friedrich–Alexander University Erlangen–Nürnberg, Erlangen, Germany
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16
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Perroud PF, Haas FB, Hiss M, Ullrich KK, Alboresi A, Amirebrahimi M, Barry K, Bassi R, Bonhomme S, Chen H, Coates JC, Fujita T, Guyon-Debast A, Lang D, Lin J, Lipzen A, Nogué F, Oliver MJ, Ponce de León I, Quatrano RS, Rameau C, Reiss B, Reski R, Ricca M, Saidi Y, Sun N, Szövényi P, Sreedasyam A, Grimwood J, Stacey G, Schmutz J, Rensing SA. The Physcomitrella patens gene atlas project: large-scale RNA-seq based expression data. Plant J 2018; 95:168-182. [PMID: 29681058 DOI: 10.1111/tpj.13940] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [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: 11/29/2017] [Revised: 04/02/2018] [Accepted: 04/05/2018] [Indexed: 05/08/2023]
Abstract
High-throughput RNA sequencing (RNA-seq) has recently become the method of choice to define and analyze transcriptomes. For the model moss Physcomitrella patens, although this method has been used to help analyze specific perturbations, no overall reference dataset has yet been established. In the framework of the Gene Atlas project, the Joint Genome Institute selected P. patens as a flagship genome, opening the way to generate the first comprehensive transcriptome dataset for this moss. The first round of sequencing described here is composed of 99 independent libraries spanning 34 different developmental stages and conditions. Upon dataset quality control and processing through read mapping, 28 509 of the 34 361 v3.3 gene models (83%) were detected to be expressed across the samples. Differentially expressed genes (DEGs) were calculated across the dataset to permit perturbation comparisons between conditions. The analysis of the three most distinct and abundant P. patens growth stages - protonema, gametophore and sporophyte - allowed us to define both general transcriptional patterns and stage-specific transcripts. As an example of variation of physico-chemical growth conditions, we detail here the impact of ammonium supplementation under standard growth conditions on the protonemal transcriptome. Finally, the cooperative nature of this project allowed us to analyze inter-laboratory variation, as 13 different laboratories around the world provided samples. We compare differences in the replication of experiments in a single laboratory and between different laboratories.
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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
| | - Fabian B Haas
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Manuel Hiss
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Kristian K Ullrich
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Alessandro Alboresi
- Dipartimento di Biotecnologie, Università di Verona, Cà Vignal 1, Strada Le Grazie 15, 37134, Verona, Italy
| | - Mojgan Amirebrahimi
- US Department of Energy (DOE) Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Kerrie Barry
- US Department of Energy (DOE) Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Roberto Bassi
- Dipartimento di Biotecnologie, Università di Verona, Cà Vignal 1, Strada Le Grazie 15, 37134, Verona, Italy
| | - Sandrine Bonhomme
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Route de St-Cyr RD10, 78026, Versailles Cedex, France
| | - Haodong Chen
- School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Juliet C Coates
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Tomomichi Fujita
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - Anouchka Guyon-Debast
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Route de St-Cyr RD10, 78026, Versailles Cedex, France
| | - Daniel Lang
- Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Junyan Lin
- US Department of Energy (DOE) Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Anna Lipzen
- US Department of Energy (DOE) Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Fabien Nogué
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Route de St-Cyr RD10, 78026, Versailles Cedex, France
| | - Melvin J Oliver
- USDA-ARS-MWA, Plant Genetics Research Unit, University of Missouri, Columbia, MO, 652117, USA
| | - Inés Ponce de León
- Department of Molecular Biology, Clemente Estable Biological Research Institute, Avenida Italia 3318, CP 11600, Montevideo, Uruguay
| | - Ralph S Quatrano
- Department of Biology, Washington University in St Louis, One Brookings Drive, St Louis, MO, 63130, USA
| | - Catherine Rameau
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Route de St-Cyr RD10, 78026, Versailles Cedex, France
| | - Bernd Reiss
- Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829, Köln, Germany
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Mariana Ricca
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstr. 107, 8008 Zürich, Switzerland
| | - Younousse Saidi
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Ning Sun
- School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstr. 107, 8008 Zürich, Switzerland
| | - Avinash Sreedasyam
- HudsonAlpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL, 35806, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL, 35806, USA
| | - Gary Stacey
- Divisions of Plant Science and Biochemistry, National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA
| | - Jeremy Schmutz
- US Department of Energy (DOE) Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
- HudsonAlpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL, 35806, USA
| | - Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
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17
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Lang D, Ullrich KK, Murat F, Fuchs J, Jenkins J, Haas FB, Piednoel M, Gundlach H, Van Bel M, Meyberg R, Vives C, Morata J, Symeonidi A, Hiss M, Muchero W, Kamisugi Y, Saleh O, Blanc G, Decker EL, van Gessel N, Grimwood J, Hayes RD, Graham SW, Gunter LE, McDaniel SF, Hoernstein SNW, Larsson A, Li FW, Perroud PF, Phillips J, Ranjan P, Rokshar DS, Rothfels CJ, Schneider L, Shu S, Stevenson DW, Thümmler F, Tillich M, Villarreal Aguilar JC, Widiez T, Wong GKS, Wymore A, Zhang Y, Zimmer AD, Quatrano RS, Mayer KFX, Goodstein D, Casacuberta JM, Vandepoele K, Reski R, Cuming AC, Tuskan GA, Maumus F, Salse J, Schmutz J, Rensing SA. The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution. Plant J 2018; 93:515-533. [PMID: 29237241 DOI: 10.1111/tpj.13801] [Citation(s) in RCA: 247] [Impact Index Per Article: 41.2] [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: 10/11/2017] [Revised: 11/20/2017] [Accepted: 11/24/2017] [Indexed: 05/18/2023]
Abstract
The draft genome of the moss model, Physcomitrella patens, comprised approximately 2000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome-scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle. Unlike in flowering plant genomes, gene- and TE-rich regions show an overall even distribution along the chromosomes. However, the chromosomes are mono-centric with peaks of a class of Copia elements potentially coinciding with centromeres. Gene body methylation is evident in 5.7% of the protein-coding genes, typically coinciding with low GC and low expression. Some giant virus insertions are transcriptionally active and might protect gametes from viral infection via siRNA mediated silencing. Structure-based detection methods show that the genome evolved via two rounds of whole genome duplications (WGDs), apparently common in mosses but not in liverworts and hornworts. Several hundred genes are present in colinear regions conserved since the last common ancestor of plants. These syntenic regions are enriched for functions related to plant-specific cell growth and tissue organization. The P. patens genome lacks the TE-rich pericentromeric and gene-rich distal regions typical for most flowering plant genomes. More non-seed plant genomes are needed to unravel how plant genomes evolve, and to understand whether the P. patens genome structure is typical for mosses or bryophytes.
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Affiliation(s)
- Daniel Lang
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
- Plant Genome and Systems Biology, Helmholtz Center Munich, 85764, Neuherberg, Germany
| | - Kristian K Ullrich
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Florent Murat
- INRA, UMR 1095 Genetics, Diversity and Ecophysiology of Cereals (GDEC), 5 Chemin de Beaulieu, 63100, Clermont-Ferrand, France
| | - Jörg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, OT Gatersleben, D-06466, Stadt Seeland, Germany
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Fabian B Haas
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Mathieu Piednoel
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829, Cologne, Germany
| | - Heidrun Gundlach
- Plant Genome and Systems Biology, Helmholtz Center Munich, 85764, Neuherberg, Germany
| | - Michiel Van Bel
- VIB Center for Plant Systems Biology, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Rabea Meyberg
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Cristina Vives
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Bellaterra, Cerdanyola del Vallès, 08193, Barcelona, Spain
| | - Jordi Morata
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Bellaterra, Cerdanyola del Vallès, 08193, Barcelona, Spain
| | | | - Manuel Hiss
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Yasuko Kamisugi
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Omar Saleh
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Guillaume Blanc
- Structural and Genomic Information Laboratory (IGS), Aix-Marseille Université, CNRS, UMR 7256 (IMM FR 3479), Marseille, France
| | - Eva L Decker
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Nico van Gessel
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | | | - Sean W Graham
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Lee E Gunter
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Stuart F McDaniel
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Sebastian N W Hoernstein
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Anders Larsson
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | | | | | - Priya Ranjan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Daniel S Rokshar
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
| | - Carl J Rothfels
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, CA, 94720-2465, USA
| | - Lucas Schneider
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Shengqiang Shu
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | | | - Fritz Thümmler
- Vertis Biotechnologie AG, Lise-Meitner-Str. 30, 85354, Freising, Germany
| | - Michael Tillich
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam-Golm, Germany
| | | | - Thomas Widiez
- Department of Plant Biology, University of Geneva, Sciences III, Geneva 4, CH-1211, Switzerland
- Department of Plant Biology & Pathology Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
- Department of Medicine, University of Alberta, Edmonton, AB, T6G 2E1, Canada
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Ann Wymore
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Yong Zhang
- Shenzhen Huahan Gene Life Technology Co. Ltd, Shenzhen, China
| | - Andreas D Zimmer
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Ralph S Quatrano
- Department of Biology, Washington University, St. Louis, MO, USA
| | - Klaus F X Mayer
- Plant Genome and Systems Biology, Helmholtz Center Munich, 85764, Neuherberg, Germany
- WZW, Technical University Munich, Munich, Germany
| | | | - Josep M Casacuberta
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Bellaterra, Cerdanyola del Vallès, 08193, Barcelona, Spain
| | - Klaas Vandepoele
- VIB Center for Plant Systems Biology, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schaenzlestr. 18, 79104, Freiburg, Germany
| | - Andrew C Cuming
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Florian Maumus
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Jérome Salse
- INRA, UMR 1095 Genetics, Diversity and Ecophysiology of Cereals (GDEC), 5 Chemin de Beaulieu, 63100, Clermont-Ferrand, France
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schaenzlestr. 18, 79104, Freiburg, Germany
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18
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Ako AE, Perroud PF, Innocent J, Demko V, Olsen OA, Johansen W. An intragenic mutagenesis strategy in Physcomitrella patens to preserve intron splicing. Sci Rep 2017; 7:5111. [PMID: 28698618 PMCID: PMC5505980 DOI: 10.1038/s41598-017-05309-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 05/26/2017] [Indexed: 12/27/2022] Open
Abstract
Gene targeting is a powerful reverse genetics technique for site-specific genome modification. Intrinsic homologous recombination in the moss Physcomitrella patens permits highly effective gene targeting, a characteristic that makes this organism a valuable model for functional genetics. Functional characterization of domains located within a multi-domain protein depends on the ability to generate mutants harboring genetic modifications at internal gene positions while maintaining the reading-frames of the flanking exons. In this study, we designed and evaluated different gene targeting constructs for targeted gene manipulation of sequences corresponding to internal domains of the DEFECTIVE KERNEL1 protein in Physcomitrella patens. Our results show that gene targeting-associated mutagenesis of introns can have adverse effects on splicing, corrupting the normal reading frame of the transcript. We show that successful genetic modification of internal sequences of multi-exon genes depends on gene-targeting strategies which insert the selection marker cassette into the 5' end of the intron and preserve the nucleotide sequence of the targeted intron.
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Affiliation(s)
- Ako Eugene Ako
- Inland Norway University of Applied Sciences, Holsetgata 31, N-2318, Hamar, Norway
| | - Pierre-François Perroud
- Philipps University Marburg, Plant Cell Biology II, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Joseph Innocent
- Inland Norway University of Applied Sciences, Holsetgata 31, N-2318, Hamar, Norway
| | - Viktor Demko
- Norwegian University of Life Sciences, P.O. Box 5003, N-1432, As, Norway
| | - Odd-Arne Olsen
- Norwegian University of Life Sciences, P.O. Box 5003, N-1432, As, Norway.
| | - Wenche Johansen
- Inland Norway University of Applied Sciences, Holsetgata 31, N-2318, Hamar, Norway.
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19
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Hiss M, Schneider L, Grosche C, Barth MA, Neu C, Symeonidi A, Ullrich KK, Perroud PF, Schallenberg-Rüdinger M, Rensing SA. Combination of the Endogenous lhcsr1 Promoter and Codon Usage Optimization Boosts Protein Expression in the Moss Physcomitrella patens. Front Plant Sci 2017; 8:1842. [PMID: 29163577 PMCID: PMC5671511 DOI: 10.3389/fpls.2017.01842] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Accepted: 10/10/2017] [Indexed: 05/13/2023]
Abstract
The moss Physcomitrella patens is used both as an evo-devo model and biotechnological production system for metabolites and pharmaceuticals. Strong in vivo expression of genes of interest is important for production of recombinant proteins, e.g., selectable markers, fluorescent proteins, or enzymes. In this regard, the choice of the promoter sequence as well as codon usage optimization are two important inside factors to consider in order to obtain optimum protein accumulation level. To reliably quantify fluorescence, we transfected protoplasts with promoter:GFP fusion constructs and measured fluorescence intensity of living protoplasts in a plate reader system. We used the red fluorescent protein mCherry under 2x 35S promoter control as second reporter to normalize for different transfection efficiencies. We derived a novel endogenous promoter and compared deletion variants with exogenous promoters. We used different codon-adapted green fluorescent protein (GFP) genes to evaluate the influence of promoter choice and codon optimization on protein accumulation in P. patens, and show that the promoter of the gene of P. patens chlorophyll a/b binding protein lhcsr1 drives expression of GFP in protoplasts significantly (more than twofold) better than the commonly used 2x 35S promoter or the rice actin1 promoter. We identified a shortened 677 bp version of the lhcsr1 promoter that retains full activity in protoplasts. The codon optimized GFP yields significantly (more than twofold) stronger fluorescence signals and thus demonstrates that adjusting codon usage in P. patens can increase expression strength. In combination, new promotor and codon optimized GFP conveyed sixfold increased fluorescence signal.
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Affiliation(s)
- Manuel Hiss
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Lucas Schneider
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Christopher Grosche
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Melanie A. Barth
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Christina Neu
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | | | - Kristian K. Ullrich
- 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 Signaling Studies, University of Freiburg, Freiburg im Breisgau, Germany
- *Correspondence: Stefan A. Rensing,
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20
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Hackenberg D, Perroud PF, Quatrano R, Pandey S. Sporophyte Formation and Life Cycle Completion in Moss Requires Heterotrimeric G-Proteins. Plant Physiol 2016; 172:1154-1166. [PMID: 27550997 PMCID: PMC5047110 DOI: 10.1104/pp.16.01088] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 08/11/2016] [Indexed: 05/23/2023]
Abstract
In this study, we report the functional characterization of heterotrimeric G-proteins from a nonvascular plant, the moss Physcomitrella patens. In plants, G-proteins have been characterized from only a few angiosperms to date, where their involvement has been shown during regulation of multiple signaling and developmental pathways affecting overall plant fitness. In addition to its unparalleled evolutionary position in the plant lineages, the P. patens genome also codes for a unique assortment of G-protein components, which includes two copies of Gβ and Gγ genes, but no canonical Gα Instead, a single gene encoding an extra-large Gα (XLG) protein exists in the P. patens genome. Here, we demonstrate that in P. patens the canonical Gα is biochemically and functionally replaced by an XLG protein, which works in the same genetic pathway as one of the Gβ proteins to control its development. Furthermore, the specific G-protein subunits in P. patens are essential for its life cycle completion. Deletion of the genomic locus of PpXLG or PpGβ2 results in smaller, slower growing gametophores. Normal reproductive structures develop on these gametophores, but they are unable to form any sporophyte, the only diploid stage in the moss life cycle. Finally, the mutant phenotypes of ΔPpXLG and ΔPpGβ2 can be complemented by the homologous genes from Arabidopsis, AtXLG2 and AtAGB1, respectively, suggesting an overall conservation of their function throughout the plant evolution.
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Affiliation(s)
- Dieter Hackenberg
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, Missouri 63132 (D.H., S.P.); andDepartment of Biology, Washington University, One Brookings Drive, Campus Box 1137, St. Louis, Missouri 63130 (P.-F.P., R.Q.)
| | - Pierre-François Perroud
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, Missouri 63132 (D.H., S.P.); andDepartment of Biology, Washington University, One Brookings Drive, Campus Box 1137, St. Louis, Missouri 63130 (P.-F.P., R.Q.)
| | - Ralph Quatrano
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, Missouri 63132 (D.H., S.P.); andDepartment of Biology, Washington University, One Brookings Drive, Campus Box 1137, St. Louis, Missouri 63130 (P.-F.P., R.Q.)
| | - Sona Pandey
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, Missouri 63132 (D.H., S.P.); andDepartment of Biology, Washington University, One Brookings Drive, Campus Box 1137, St. Louis, Missouri 63130 (P.-F.P., R.Q.)
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21
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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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22
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Plavskin Y, Nagashima A, Perroud PF, Hasebe M, Quatrano RS, Atwal GS, Timmermans MCP. Ancient trans-Acting siRNAs Confer Robustness and Sensitivity onto the Auxin Response. Dev Cell 2016; 36:276-89. [PMID: 26859352 DOI: 10.1016/j.devcel.2016.01.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [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: 08/16/2015] [Revised: 12/03/2015] [Accepted: 01/11/2016] [Indexed: 11/29/2022]
Abstract
Novel developmental programs often evolve via cooption of existing genetic networks. To understand this process, we explored cooption of the TAS3 tasiRNA pathway in the moss Physcomitrella patens. We find an ancestral function for this repeatedly redeployed pathway in the spatial regulation of a conserved set of Auxin Response Factors. In moss, this results in stochastic patterning of the filamentous protonemal tissue. Through modeling and experimentation, we demonstrate that tasiRNA regulation confers sensitivity and robustness onto the auxin response. Increased auxin sensitivity parallels increased developmental sensitivity to nitrogen, a key environmental signal. We propose that the properties lent to the auxin response network, along with the ability to stochastically modulate development in response to environmental cues, have contributed to repeated cooption of the tasiRNA-ARF module during evolution. The signaling properties of a genetic network, and not just its developmental output, are thus critical to understanding evolution of multicellular forms.
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Affiliation(s)
- Yevgeniy Plavskin
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Akitomo Nagashima
- National Institute for Basic Biology, Okazaki 444-8585, Japan; Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Okazaki 444-8585, Japan
| | | | - Mitsuyasu Hasebe
- National Institute for Basic Biology, Okazaki 444-8585, Japan; Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Okazaki 444-8585, Japan
| | - Ralph S Quatrano
- Department of Biology, Washington University, St. Louis, MO 63130, USA
| | - Gurinder S Atwal
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Marja C P Timmermans
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Center for Plant Molecular Biology, University of Tübingen, 72076 Tübingen, Germany.
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23
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Xia J, Wang X, Perroud PF, He Y, Quatrano R, Zhang W. Endogenous Small-Noncoding RNAs and Potential Functions in Desiccation Tolerance in Physcomitrella Patens. Sci Rep 2016; 6:30118. [PMID: 27443635 PMCID: PMC4957126 DOI: 10.1038/srep30118] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 06/29/2016] [Indexed: 02/07/2023] Open
Abstract
Early land plants like moss Physcomitrella patens have developed remarkable drought tolerance. Phytohormone abscisic acid (ABA) protects seeds during water stress by activating genes through transcription factors such as ABSCISIC ACID INSENSITIVE (ABI3). Small noncoding RNA (sncRNA), including microRNAs (miRNAs) and endogenous small-interfering RNAs (endo-siRNAs), are key gene regulators in eukaryotes, playing critical roles in stress tolerance in plants. Combining next-generation sequencing and computational analysis, we profiled and characterized sncRNA species from two ABI3 deletion mutants and the wild type P. patens that were subject to ABA treatment in dehydration and rehydration stages. Small RNA profiling using deep sequencing helped identify 22 novel miRNAs and 6 genomic loci producing trans-acting siRNAs (ta-siRNAs) including TAS3a to TAS3e and TAS6. Data from degradome profiling showed that ABI3 genes (ABI3a/b/c) are potentially regulated by the plant-specific miR536 and that other ABA-relevant genes are regulated by miRNAs and ta-siRNAs. We also observed broad variations of miRNAs and ta-siRNAs expression across different stages, suggesting that they could potentially influence desiccation tolerance. This study provided evidence on the potential roles of sncRNA in mediating desiccation-responsive pathways in early land plants.
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Affiliation(s)
- Jing Xia
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, China.,Department of Computer Science and Engineering, Washington University, St. Louis, MO 63130, USA
| | - Xiaoqin Wang
- College of Life Sciences, Capital Normal University, Beijing 100048, China.,Department of Biology, Washington University, St. Louis, MO 63130, USA
| | | | - Yikun He
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Ralph Quatrano
- Department of Biology, Washington University, St. Louis, MO 63130, USA
| | - Weixiong Zhang
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, China.,Department of Computer Science and Engineering, Washington University, St. Louis, MO 63130, USA.,Department of Genetics, Washington University, St. Louis, MO 63130, USA
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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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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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Perroud PF, Demko V, Johansen W, Wilson RC, Olsen OA, Quatrano RS. Defective Kernel 1 (DEK1) is required for three-dimensional growth in Physcomitrella patens. New Phytol 2014; 203:794-804. [PMID: 24844771 PMCID: PMC4285852 DOI: 10.1111/nph.12844] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [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: 02/14/2014] [Accepted: 04/04/2014] [Indexed: 05/18/2023]
Abstract
Orientation of cell division is critical for plant morphogenesis. This is evident in the formation and function of meristems and for morphogenetic transitions. Mosses undergo such transitions: from two-dimensional tip-growing filaments (protonema) to the generation of three-dimensional leaf-like structures (gametophores). The Defective Kernel 1 (DEK1) protein plays a key role in the perception of and/or response to positional cues that specify the formation and function of the epidermal layer in developing seeds of flowering plants. The moss Physcomitrella patens contains the highly conserved DEK1 gene. Using efficient gene targeting, we generated a precise PpDEK1 deletion (∆dek1), which resulted in normal filamentous growth of protonema. Two distinct mutant phenotypes were observed: an excess of buds on the protonema, and abnormal cell divisions in the emerging buds resulting in developmental arrest and the absence of three-dimensional growth. Overexpression of a complete PpDEK1 cDNA, or the calpain domain of PpDEK1 alone, successfully complements both phenotypes. These results in P. patens demonstrate the morphogenetic importance of the DEK1 protein in the control of oriented cell divisions. As it is not for protonema, it will allow dissection of the structure/function relationships of the different domains of DEK1 using gene targeting in null mutant background.
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Affiliation(s)
- Pierre-François Perroud
- Department of Biology, Washington University in St Louis, Campus Box 1137, St Louis, MO, 63130-4899, USA
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Szövényi P, Perroud PF, Symeonidi A, Stevenson S, Quatrano RS, Rensing SA, Cuming AC, McDaniel SF. De novoassembly and comparative analysis of theCeratodon purpureustranscriptome. Mol Ecol Resour 2014; 15:203-15. [DOI: 10.1111/1755-0998.12284] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Revised: 05/12/2014] [Accepted: 05/21/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Péter Szövényi
- Institute of Evolutionary Biology and Environmental Studies; University of Zurich; Winterthurerstr. 190 CH-8057 Zurich Switzerland
- Institute of Systematic Botany; University of Zurich; Zollikerstr. 107 CH-8008 Zurich Switzerland
- Quartier Sorge-Batiment Genopode; Swiss Institute of Bioinformatics; 1015 Lausanne Switzerland
- MTA-ELTE-MTM Ecology Research Group; ELTE; Biological Institute; H-1117, Pázmány P. sétány 1/C Budpaest Hungary
| | - Pierre-François Perroud
- Biology Department; Washington University in St Louis CB #1137; One Brookings Drive St Louis MO 63130 USA
| | - Aikaterini Symeonidi
- Faculty of Biology; University of Marburg; Karl-von-Frisch-Str. 8 D-35043 Marburg Germany
| | - Sean Stevenson
- Centre for Plant Sciences; Faculty of Biological Sciences; University of Leeds; Leeds LS2 9JT UK
| | - Ralph S. Quatrano
- Biology Department; Washington University in St Louis CB #1137; One Brookings Drive St Louis MO 63130 USA
| | - Stefan A. Rensing
- Faculty of Biology; University of Marburg; Karl-von-Frisch-Str. 8 D-35043 Marburg Germany
| | - Andrew C. Cuming
- Centre for Plant Sciences; Faculty of Biological Sciences; University of Leeds; Leeds LS2 9JT UK
| | - Stuart F. McDaniel
- Department of Biology; University of Florida; PO Box 118525 Gainesville FL 32611 USA
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Liang Z, Demko V, Wilson RC, Johnson KA, Ahmad R, Perroud PF, Quatrano R, Zhao S, Shalchian-Tabrizi K, Otegui MS, Olsen OA, Johansen W. The catalytic domain CysPc of the DEK1 calpain is functionally conserved in land plants. Plant J 2013; 75:742-54. [PMID: 23663131 DOI: 10.1111/tpj.12235] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [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: 01/11/2013] [Revised: 03/26/2013] [Accepted: 05/08/2013] [Indexed: 05/09/2023]
Abstract
DEK1, the single calpain of land plants, is a member of the ancient membrane bound TML-CysPc-C2L calpain family that dates back 1.5 billion years. Here we show that the CysPc-C2L domains of land plant calpains form a separate sub-clade in the DEK1 clade of the phylogenetic tree of plants. The charophycean alga Mesostigma viride DEK1-like gene is clearly divergent from those in land plants, suggesting that a major evolutionary shift in DEK1 occurred during the transition to land plants. Based on genetic complementation of the Arabidopsis thaliana dek1-3 mutant using CysPc-C2L domains of various origins, we show that these two domains have been functionally conserved within land plants for at least 450 million years. This conclusion is based on the observation that the CysPc-C2L domains of DEK1 from the moss Physcomitrella patens complements the A. thaliana dek1-3 mutant phenotype. In contrast, neither the CysPc-C2L domains from M. viride nor chimeric animal-plant calpains complement this mutant. Co-evolution analysis identified differences in the interactions between the CysPc-C2L residues of DEK1 and classical calpains, supporting the view that the two enzymes are regulated by fundamentally different mechanisms. Using the A. thaliana dek1-3 complementation assay, we show that four conserved amino acid residues of two Ca²⁺-binding sites in the CysPc domain of classical calpains are conserved in land plants and functionally essential in A. thaliana DEK1.
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Affiliation(s)
- Zhe Liang
- Norwegian University of Life Sciences, Ås, N-1432, Norway
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Perroud PF, Cove DJ, Quatrano RS, McDaniel SF. An experimental method to facilitate the identification of hybrid sporophytes in the moss Physcomitrella patens using fluorescent tagged lines. New Phytol 2011; 191:301-306. [PMID: 21366596 PMCID: PMC3445409 DOI: 10.1111/j.1469-8137.2011.03668.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [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] [Indexed: 05/18/2023]
Abstract
• The sequencing of the Physcomitrella patens genome, combined with the high frequency of gene targeting in this species, makes it ideal for reverse genetic studies. For forward genetic studies, experimental crosses and genetic analysis of progeny are essential. • Since P. patens is monoicous, producing both male and female gametes on the same gametophore, and undergoing self-fertilization at a high frequency, the identification of crossed sporophytes is difficult. Usually spores from many sporophytes from a mixed culture must be tested for the production of recombinant progeny. • Here, we describe the use of transgenic lines that express a fluorescent transgene constitutively, to provide a direct visual screen for hybrid sporophytes. • We show that segregations in crosses obtained with this technique are as expected, and demonstrate its utility for the study of the rate of outcrossing between three isolates of P. patens.
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Affiliation(s)
- Pierre-François Perroud
- Department of Biology, Campus Box 1137, Washington University in St Louis, St Louis, MO 63130, USA
| | - David J. Cove
- Department of Biology, Campus Box 1137, Washington University in St Louis, St Louis, MO 63130, USA
- Centre for Plant Sciences, Leeds University, Leeds, LS2 9JT, UK
| | - Ralph S. Quatrano
- Department of Biology, Campus Box 1137, Washington University in St Louis, St Louis, MO 63130, USA
| | - Stuart F. McDaniel
- Department of Biology, Box 118525, University of Florida, Gainesville, FL 32611, USA
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Cove DJ, Perroud PF, Charron AJ, McDaniel SF, Khandelwal A, Quatrano RS. Isolation and regeneration of protoplasts of the moss Physcomitrella patens. Cold Spring Harb Protoc 2010; 2009:pdb.prot5140. [PMID: 20147070 DOI: 10.1101/pdb.prot5140] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- David J Cove
- Department of Biology, Washington University, St. Louis, MO 63130, USA
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Cove DJ, Perroud PF, Charron AJ, McDaniel SF, Khandelwal A, Quatrano RS. Culturing the moss Physcomitrella patens. Cold Spring Harb Protoc 2010; 2009:pdb.prot5136. [PMID: 20147066 DOI: 10.1101/pdb.prot5136] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- David J Cove
- Department of Biology, Washington University, St. Louis, MO 63130, USA
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Cove DJ, Perroud PF, Charron AJ, McDaniel SF, Khandelwal A, Quatrano RS. The moss Physcomitrella patens: a novel model system for plant development and genomic studies. Cold Spring Harb Protoc 2010; 2009:pdb.emo115. [PMID: 20147063 DOI: 10.1101/pdb.emo115] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- David J Cove
- Department of Biology, Washington University, St. Louis, MO 63130, USA
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Shakirov EV, Perroud PF, Nelson AD, Cannell ME, Quatrano RS, Shippen DE. Protection of Telomeres 1 is required for telomere integrity in the moss Physcomitrella patens. Plant Cell 2010; 22:1838-48. [PMID: 20515974 PMCID: PMC2910979 DOI: 10.1105/tpc.110.075846] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
In vertebrates, the single-stranded telomeric DNA binding protein Protection of Telomeres 1 (POT1) shields chromosome ends and prevents them from eliciting a DNA damage response. By contrast, Arabidopsis thaliana encodes two divergent full-length POT1 paralogs that do not exhibit telomeric DNA binding in vitro and have evolved to mediate telomerase regulation instead of chromosome end protection. To further investigate the role of POT1 in plants, we established the moss Physcomitrella patens as a new model for telomere biology and a counterpoint to Arabidopsis. The sequence and architecture of the telomere tract is similar in P. patens and Arabidopsis, but P. patens harbors only a single-copy POT1 gene. Unlike At POT1 proteins, Pp POT1 efficiently bound single-stranded telomeric DNA in vitro. Deletion of the P. patens POT1 gene resulted in the rapid onset of severe developmental defects and sterility. Although telomerase activity levels were unperturbed, telomeres were substantially shortened, harbored extended G-overhangs, and engaged in end-to-end fusions. We conclude that the telomere capping function of POT1 is conserved in early diverging land plants but is subsequently lost in Arabidopsis.
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Affiliation(s)
- Eugene V. Shakirov
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128
| | | | - Andrew D. Nelson
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128
| | - Maren E. Cannell
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128
| | - Ralph S. Quatrano
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Dorothy E. Shippen
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128
- Address correspondence to
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Cove DJ, Perroud PF, Charron AJ, McDaniel SF, Khandelwal A, Quatrano RS. Transformation of the moss Physcomitrella patens using T-DNA mutagenesis. Cold Spring Harb Protoc 2010; 2009:pdb.prot5144. [PMID: 20147074 DOI: 10.1101/pdb.prot5144] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
INTRODUCTIONIn this protocol, the transformation of moss (Physcomitrella patens) protoplasts is performed via Agrobacterium-mediated transfer of T-DNA. Protoplasts are incubated with Agrobacterium and acetoseringone in regeneration medium. They are then washed and plated on antibiotic-containing medium to select for T-DNA insertion in stable transformants. The transformation rate for this protocol is typically 10−4 (expressed as the frequency of stable transformants among regenerants surviving the transformation procedure).
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Affiliation(s)
- David J Cove
- Department of Biology, Washington University, St. Louis, MO 63130, USA
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Cove DJ, Perroud PF, Charron AJ, McDaniel SF, Khandelwal A, Quatrano RS. Transformation of moss Physcomitrella patens gametophytes using a biolistic projectile delivery system. Cold Spring Harb Protoc 2010; 2009:pdb.prot5145. [PMID: 20147075 DOI: 10.1101/pdb.prot5145] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
INTRODUCTIONThis method makes use of biolistic bombardment to propel gold particles coated with DNA into protonemal tissue of the moss Physcomitrella patens. It is especially suitable for transient gene expression studies, but it can be used to obtain stable transformants.
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Affiliation(s)
- David J Cove
- Department of Biology, Washington University, St. Louis, MO 63130, USA
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Cove DJ, Perroud PF, Charron AJ, McDaniel SF, Khandelwal A, Quatrano RS. Chemical and UV mutagenesis of spores and protonemal tissue from the moss Physcomitrella patens. Cold Spring Harb Protoc 2010; 2009:pdb.prot5142. [PMID: 20147072 DOI: 10.1101/pdb.prot5142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
INTRODUCTIONThis protocol describes how to mutagenize spores and protonemal tissue from moss (Physcomitrella patens) using chemicals or ultraviolet (UV) light. Spores are mutagenized using the alkylating agents N-methyl-N′-nitro-N-nitrosoguanidine (NTG) and ethyl methanesulfonate (EMS), and protonemal tissue is mutagenized with NTG and UV light. Compared to alkylating agents, UV is less effective as a mutagen, but it may be advantageous because it is less hazardous and may not lead to clustered lesions.
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Affiliation(s)
- David J Cove
- Department of Biology, Washington University, St. Louis, MO 63130, USA
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Cove DJ, Perroud PF, Charron AJ, McDaniel SF, Khandelwal A, Quatrano RS. Transformation of the moss Physcomitrella patens using direct DNA uptake by protoplasts. Cold Spring Harb Protoc 2009; 2009:pdb.prot5143. [PMID: 20147073 DOI: 10.1101/pdb.prot5143] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
INTRODUCTIONThis protocol describes how to transform moss (Physcomitrella patens) protoplasts using polyethylene glycol (PEG)-mediated DNA uptake. The transformation rates for direct uptake by protoplasts of DNA with and without genomic sequence (a targeting construct) are typically 10−5 and 10−3, respectively. (These are the frequencies of stable transformants among regenerants surviving the transformation procedure.)
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Affiliation(s)
- David J Cove
- Department of Biology, Washington University, St. Louis, MO 63130, USA
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Cove DJ, Perroud PF, Charron AJ, McDaniel SF, Khandelwal A, Quatrano RS. Somatic hybridization in the moss Physcomitrella patens using PEG-induced protoplast fusion. Cold Spring Harb Protoc 2009; 2009:pdb.prot5141. [PMID: 20147071 DOI: 10.1101/pdb.prot5141] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
INTRODUCTIONAs an alternative to sexual crossing, protoplasts from two strains of moss (Physcomitrella patens) can be hybridized using polyethylene glycol (PEG). Although the efficiency is low, it requires no sophisticated apparatus. Hybrids are readily obtained using complementary auxotrophic mutants or strains with transgenic antibiotic resistance markers. It is now routine to obtain hybrids using transgenic strains that are hygromycin- or G418-resistant by selecting hybrids on medium containing both antibiotics.
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Affiliation(s)
- David J Cove
- Department of Biology, Washington University, St. Louis, MO 63130, USA
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Perroud PF, Quatrano RS. BRICK1 is required for apical cell growth in filaments of the moss Physcomitrella patens but not for gametophore morphology. Plant Cell 2008; 20:411-22. [PMID: 18263777 PMCID: PMC2276446 DOI: 10.1105/tpc.107.053256] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2007] [Revised: 01/11/2008] [Accepted: 01/25/2008] [Indexed: 05/19/2023]
Abstract
When BRK1, a member of the Wave/SCAR complex, is deleted in Physcomitrella patens (Deltabrk1), we report a striking reduction of filament growth resulting in smaller and fewer cells with misplaced cross walls compared with the normal protonemal cells. Using an inducible green fluorescent protein-talin to detect actin in living tissue, a characteristic broad accumulation of actin is observed at the tip of wild-type apical cells, whereas in Deltabrk1, smaller, more distinct foci of actin are present. Insertion of brk1-yfp into Deltabrk1 rescues the mutant phenotype and results in BRK1 being localized only in the tip of apical cells, the exclusive site of cell extension and division in the filament. Like BRK1, ARPC4 and At RABA4d are normally localized at the tip of apical cells and their localization is correlated with rapid tip growth in filaments. However, neither marker accumulates in apical cells of Deltabrk1 filaments. Although the Deltabrk1 phenotypes in protonema are severe, the leafy shoots or gametophores are normally shaped but stunted. These and other results suggest that BRK1 functions directly or indirectly in the selective accumulation/stabilization of actin and other proteins required for polar cell growth of filaments but not for the basic structure of the gametophore.
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Quatrano RS, McDaniel SF, Khandelwal A, Perroud PF, Cove DJ. Physcomitrella patens: mosses enter the genomic age. Curr Opin Plant Biol 2007; 10:182-9. [PMID: 17291824 DOI: 10.1016/j.pbi.2007.01.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2006] [Accepted: 01/29/2007] [Indexed: 05/13/2023]
Abstract
The sequenced genome of the moss Physcomitrella patens provides a powerful tool for comparative analyses of land plant genomes. In parallel, several tools for studying gene function have been developed in P. patens, including RNA interference, inducible promoters and gene targeting, a unique attribute of this plant system. The results of these initiatives are now being realized. For example, transcriptomic analyses illustrate commonalities among plant lineages in gene content, structure, and regulation. Transgenic studies show that the regulatory factors ABSCISIC ACID INSENSITIVE3 (ABI3) and LEAFY (LFY) have molecular functions that are conserved between moss and angiosperms, in spite of the fact that they function in non-homologous tissues. Future work in P. patens will contribute to our understanding of the molecular basis of plant development and evolution.
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Affiliation(s)
- Ralph S Quatrano
- Department of Biology, Washington University, One Brookings Drive, CB 1137, St. Louis, Missouri 63130, USA.
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Kaewsuwan S, Cahoon EB, Perroud PF, Wiwat C, Panvisavas N, Quatrano RS, Cove DJ, Bunyapraphatsara N. Identification and functional characterization of the moss Physcomitrella patens delta5-desaturase gene involved in arachidonic and eicosapentaenoic acid biosynthesis. J Biol Chem 2006; 281:21988-21997. [PMID: 16728405 DOI: 10.1074/jbc.m603022200] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The moss Physcomitrella patens contains high levels of arachidonic acid and lesser amounts of eicosapentaenoic acid. Here we report the identification and characterization of a delta5-desaturase from P. patens that is associated with the synthesis of these fatty acids. A full-length cDNA for this desaturase was identified by data base searches based on homology to sequences of known delta5-desaturase cDNAs from fungal and algal species. The resulting P. patens cDNA encodes a 480-amino acid polypeptide that contains a predicted N-terminal cytochrome b5-like domain as well as three histidine-rich domains. Expression of the enzyme in Saccharomyces cerevisiae resulted in the production of the delta5-containing fatty acid arachidonic acid in cells that were provided di-homo-gamma-linolenic acid. In addition, the expressed enzyme generated delta5-desaturation products with the C20 substrates omega-6 eicosadienoic and omega-3 eicosatrienoic acids, but no products were detected with the C18 fatty acid linoleic and alpha-linolenic acids or with the C22 fatty acid adrenic and docosapentaenoic acids. When the corresponding P. patens genomic sequence was disrupted by replacement through homologous recombination, a dramatic alteration in the fatty acid composition was observed, i.e. an increase in di-homo-gamma-linolenic and eicosatetraenoic acids accompanied by a concomitant disappearance of the delta5-fatty acid arachidonic and eicosapentaenoic acids. In addition, overexpression of the P. patens cDNA in protoplasts isolated from a disrupted line resulted in the restoration of arachidonic acid synthesis.
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Affiliation(s)
- Songsri Kaewsuwan
- Department of Pharmacognosy, Mahidol University, 447 Sri-Ayudhya Road, Ratchathewi, Bangkok 10400, Thailand
| | - Edgar B Cahoon
- United States Department of Agriculture Agricultural Research Service, Plant Genetics Research Unit, Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| | | | - Chanpen Wiwat
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, 447 Sri-Ayudhya Road, Ratchathewi, Bangkok 10400, Thailand
| | - Nathinee Panvisavas
- Department of Plant Sciences, Faculty of Sciences, Mahidol University, Rama VI Road, Bangkok 10400, Thailand
| | - Ralph S Quatrano
- Department of Biology, Washington University in St. Louis, S Louis, Missouri 63130-4899.
| | - David J Cove
- Department of Biology, Washington University in St. Louis, S Louis, Missouri 63130-4899
| | - Nuntavan Bunyapraphatsara
- Department of Pharmacognosy, Mahidol University, 447 Sri-Ayudhya Road, Ratchathewi, Bangkok 10400, Thailand.
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Abstract
When the actin related protein 2/3 (Arp2/3) complex member arpc4 was deleted in Physcomitrella patens (moss), the resulting null mutant (Deltaarpc4) was viable and revealed no gross changes during morphogenesis of filaments into gametophores. However, we observed a striking reduction of filamentous tip growth, resulting in smaller, denser colonies. Although polar responses of Deltaarpc4 filaments to unilateral white light were unaffected, these mutant filaments were defective in their response to polarized white light. These observations strongly suggest a specific role of the Arp2/3 complex as a downstream target for signals regulating oriented tip growth. Insertion of YFP-ARPC4 into Deltaarpc4 rescued the mutant phenotypes and localized ARPC4 exclusively to the tip cell of filaments, the site of actin dynamics and polarized growth. The ability of Deltaarpc4 to perform some but not all cellular responses will allow the study of its function in orientation of tip growth in response to directional cues (e.g. light) in a viable but mutated background.
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Affiliation(s)
- Pierre-François Perroud
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130-4899, USA
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Perroud PF, Diogon T, Crèvecoeur M, Greppin H. Molecular cloning, spatial and temporal characterization of spinach SOGA1 cDNA, encoding an alpha subunit of G protein. Gene 2000; 248:191-201. [PMID: 10806364 DOI: 10.1016/s0378-1119(00)00120-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Heterotrimeric G proteins are an important component of signal transduction pathway in animals. Although these proteins have been described in plants, their exact function and action mode are not clearly defined. In order to analyze the relationship between these proteins and the transduction of light signals in spinach, we have isolated by 5' and 3' RACE-PCR a 1660bp cDNA clone called SOGA1. This codes for a 383aa protein, which reveals a very strong homology with other plant Galpha subunit sequences. Genomic analysis suggested that SOGA1 belonged to a small multiple gene family. Northern blots and in-situ hybridization analyses showed that SOGA1 transcripts accumulate in all organs tested with a specific high level associated with the apex, roots and hypocotyls. Finally, a time-course analysis performed on the green tissues showed that accumulation of SOGA1 transcripts follows a circadian rhythm. However, in-situ hybridization analysis of the apex suggested the opposite behavior, while no variation was observed in the hypocotyl.
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MESH Headings
- Amino Acid Sequence
- Base Sequence
- Blotting, Northern
- Blotting, Southern
- Circadian Rhythm
- Cloning, Molecular
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- DNA, Complementary/isolation & purification
- DNA, Plant/genetics
- Gene Expression Regulation, Developmental
- Gene Expression Regulation, Plant
- Heterotrimeric GTP-Binding Proteins/genetics
- In Situ Hybridization
- Light
- Molecular Sequence Data
- Photoperiod
- Phylogeny
- Plants/genetics
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA, Plant/radiation effects
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Spinacia oleracea/genetics
- Spinacia oleracea/growth & development
- Tissue Distribution
- Transcription, Genetic/radiation effects
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Affiliation(s)
- P F Perroud
- Laboratoire de Biochimie et Physiologie Végétales, Université de Genève, place de l'Université 3, CH-1211, Geneva, Switzerland
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Crespi P, Perroud PF, Greppin H. Guanosine triphosphate-binding proteins on the plasmalemma of spinach leaf cells. Planta 1996; 198:557-562. [PMID: 28321666 DOI: 10.1007/bf00262642] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/1995] [Accepted: 08/21/1995] [Indexed: 06/06/2023]
Abstract
The molecular mechanism of light perception through phytochrome is not well understood. This red-light photosensor has been implicated in various physiological processes, including the photoinduction of flowering. A few recent studies have shown that phytochrome initiates signal transduction chains via guanosine triphosphate (GTP)-binding proteins (G-proteins). We show here by different approaches that G-proteins exist in spinach (Spinacia oleracea L. cv. Nobel). Binding of GTP on the plasmalemma has been partially characterized and its possible regulation by red light examined by in-vitro assays. These experiments indicate a clear regulation of GTP binding by red light and also by Mastoparan. At least three G-proteins or protein subunits were found to be associated with the plasmalemma of leaf cells. The use of an antibody raised against an animal Gβ subunit confirmed the presence of heterotrimeric G-proteins. Separation of a crude membrane extract by free-flow electrophoresis also showed that some G-proteins could exist on the tonoplast.
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Affiliation(s)
- Pierre Crespi
- Laboratoire de Biochimie et Physiologie Végétales, Université de Genève, Place de l'Université 3, CH-1211, Genève 4, Switzerland
| | - Pierre-François Perroud
- Laboratoire de Biochimie et Physiologie Végétales, Université de Genève, Place de l'Université 3, CH-1211, Genève 4, Switzerland
| | - Hubert Greppin
- Laboratoire de Biochimie et Physiologie Végétales, Université de Genève, Place de l'Université 3, CH-1211, Genève 4, Switzerland
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