1
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Wegner L, Ehlers K. Plasmodesmata dynamics in bryophyte model organisms: secondary formation and developmental modifications of structure and function. PLANTA 2024; 260:45. [PMID: 38965075 PMCID: PMC11224097 DOI: 10.1007/s00425-024-04476-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 06/25/2024] [Indexed: 07/06/2024]
Abstract
MAIN CONCLUSION Developing bryophytes differentially modify their plasmodesmata structure and function. Secondary plasmodesmata formation via twinning appears to be an ancestral trait. Plasmodesmata networks in hornwort sporophyte meristems resemble those of angiosperms. All land-plant taxa use plasmodesmata (PD) cell connections for symplasmic communication. In angiosperm development, PD networks undergo an extensive remodeling by structural and functional PD modifications, and by postcytokinetic formation of additional secondary PD (secPD). Since comparable information on PD dynamics is scarce for the embryophyte sister groups, we investigated maturating tissues of Anthoceros agrestis (hornwort), Physcomitrium patens (moss), and Marchantia polymorpha (liverwort). As in angiosperms, quantitative electron microscopy revealed secPD formation via twinning in gametophytes of all model bryophytes, which gives rise to laterally adjacent PD pairs or to complex branched PD. This finding suggests that PD twinning is an ancient evolutionary mechanism to adjust PD numbers during wall expansion. Moreover, all bryophyte gametophytes modify their existing PD via taxon-specific strategies resembling those of angiosperms. Development of type II-like PD morphotypes with enlarged diameters or formation of pit pairs might be required to maintain PD transport rates during wall thickening. Similar to angiosperm leaves, fluorescence redistribution after photobleaching revealed a considerable reduction of the PD permeability in maturating P. patens phyllids. In contrast to previous reports on monoplex meristems of bryophyte gametophytes with single initials, we observed targeted secPD formation in the multi-initial basal meristems of A. agrestis sporophytes. Their PD networks share typical features of multi-initial angiosperm meristems, which may hint at a putative homologous origin. We also discuss that monoplex and multi-initial meristems may require distinct types of PD networks, with or without secPD formation, to control maintenance of initial identity and positional signaling.
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Affiliation(s)
- Linus Wegner
- Institute of Botany, Justus-Liebig University, 35392, Giessen, Germany.
| | - Katrin Ehlers
- Institute of Botany, Justus-Liebig University, 35392, Giessen, Germany.
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2
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Haslam TM, Herrfurth C, Feussner I. Diverse INOSITOL PHOSPHORYLCERAMIDE SYNTHASE mutant alleles of Physcomitrium patens offer new insight into complex sphingolipid metabolism. THE NEW PHYTOLOGIST 2024; 242:1189-1205. [PMID: 38523559 DOI: 10.1111/nph.19667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 02/26/2024] [Indexed: 03/26/2024]
Abstract
Sphingolipids are widespread, abundant, and essential lipids in plants and in other eukaryotes. Glycosyl inositol phosphorylceramides (GIPCs) are the most abundant class of plant sphingolipids, and are enriched in the plasma membrane of plant cells. They have been difficult to study due to lethal or pleiotropic mutant phenotypes. To overcome this, we developed a CRISPR/Cas9-based method for generating multiple and varied knockdown and knockout populations of mutants in a given gene of interest in the model moss Physcomitrium patens. This system is uniquely convenient due to the predominantly haploid state of the Physcomitrium life cycle, and totipotency of Physcomitrium protoplasts used for transformation. We used this approach to target the INOSITOL PHOSPHORYLCERAMIDE SYNTHASE (IPCS) gene family, which catalyzes the first, committed step in the synthesis of GIPCs. We isolated knockout single mutants and knockdown higher-order mutants showing a spectrum of deficiencies in GIPC content. Remarkably, we also identified two mutant alleles accumulating inositol phosphorylceramides, the direct products of IPCS activity, and provide our best explanation for this unexpected phenotype. Our approach is broadly applicable for studying essential genes and gene families, and for obtaining unusual lesions within a gene of interest.
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Affiliation(s)
- Tegan M Haslam
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Goettingen, D-37077, Germany
| | - Cornelia Herrfurth
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Goettingen, D-37077, Germany
- Goettingen Center for Molecular Biosciences (GZMB), Service Unit for Metabolomics and Lipidomics, University of Goettingen, Goettingen, D-37077, Germany
| | - Ivo Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Goettingen, D-37077, Germany
- Department of Plant Biochemistry, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goettingen, D-37077, Germany
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3
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Hembach L, Niemeyer PW, Schmitt K, Zegers JMS, Scholz P, Brandt D, Dabisch JJ, Valerius O, Braus GH, Schwarzländer M, de Vries J, Rensing SA, Ischebeck T. Proteome plasticity during Physcomitrium patens spore germination - from the desiccated phase to heterotrophic growth and reconstitution of photoautotrophy. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1466-1486. [PMID: 38059656 DOI: 10.1111/tpj.16574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 11/13/2023] [Accepted: 11/22/2023] [Indexed: 12/08/2023]
Abstract
The establishment of moss spores is considered a milestone in plant evolution. They harbor protein networks underpinning desiccation tolerance and accumulation of storage compounds that can be found already in algae and that are also utilized in seeds and pollen. Furthermore, germinating spores must produce proteins that drive the transition through heterotrophic growth to the autotrophic plant. To get insight into the plasticity of this proteome, we investigated it at five timepoints of moss (Physcomitrium patens) spore germination and in protonemata and gametophores. The comparison to previously published Arabidopsis proteome data of seedling establishment showed that not only the proteomes of spores and seeds are functionally related, but also the proteomes of germinating spores and young seedlings. We observed similarities with regard to desiccation tolerance, lipid droplet proteome composition, control of dormancy, and β-oxidation and the glyoxylate cycle. However, there were also striking differences. For example, spores lacked any obvious storage proteins. Furthermore, we did not detect homologs to the main triacylglycerol lipase in Arabidopsis seeds, SUGAR DEPENDENT1. Instead, we discovered a triacylglycerol lipase of the oil body lipase family and a lipoxygenase as being the overall most abundant proteins in spores. This finding indicates an alternative pathway for triacylglycerol degradation via oxylipin intermediates in the moss. The comparison of spores to Nicotiana tabacum pollen indicated similarities for example in regards to resistance to desiccation and hypoxia, but the overall developmental pattern did not align as in the case of seedling establishment and spore germination.
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Affiliation(s)
- Lea Hembach
- Green Biotechnology, Institute of Plant Biology and Biotechnology (IBBP), University of Münster, 48143, Münster, Germany
| | - Philipp W Niemeyer
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences and Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, 37077, Göttingen, Germany
| | - Kerstin Schmitt
- Department for Molecular Microbiology and Genetics, Genetics and Göttingen Center for Molecular Biosciences (GZMB) and Service Unit LCMS Protein Analytics, Institute for Microbiology, University of Göttingen, 37077, Göttingen, Germany
| | - Jaccoline M S Zegers
- Department of Applied Bioinformatics, Göttingen Center for Molecular Biosciences (GZMB) and Campus Institute Data Science (CIDAS), Institute for Microbiology and Genetics, University of Göttingen, 37077, Göttingen, Germany
| | - Patricia Scholz
- Laboratoire Reproduction et Développement des Plantes (RDP), UCB Lyon 1, CNRS, INRAE, Université de Lyon, ENS de Lyon, Lyon, France
| | - Dennis Brandt
- Plant Energy Biology, Institute of Plant Biology and Biotechnology (IBBP), University of Münster, 48143, Münster, Germany
| | - Janis J Dabisch
- Green Biotechnology, Institute of Plant Biology and Biotechnology (IBBP), University of Münster, 48143, Münster, Germany
| | - Oliver Valerius
- Department for Molecular Microbiology and Genetics, Genetics and Göttingen Center for Molecular Biosciences (GZMB) and Service Unit LCMS Protein Analytics, Institute for Microbiology, University of Göttingen, 37077, Göttingen, Germany
| | - Gerhard H Braus
- Department for Molecular Microbiology and Genetics, Genetics and Göttingen Center for Molecular Biosciences (GZMB) and Service Unit LCMS Protein Analytics, Institute for Microbiology, University of Göttingen, 37077, Göttingen, Germany
| | - Markus Schwarzländer
- Plant Energy Biology, Institute of Plant Biology and Biotechnology (IBBP), University of Münster, 48143, Münster, Germany
| | - Jan de Vries
- Department of Applied Bioinformatics, Göttingen Center for Molecular Biosciences (GZMB) and Campus Institute Data Science (CIDAS), Institute for Microbiology and Genetics, University of Göttingen, 37077, Göttingen, Germany
| | - 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
| | - Till Ischebeck
- Green Biotechnology, Institute of Plant Biology and Biotechnology (IBBP), University of Münster, 48143, Münster, Germany
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences and Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, 37077, Göttingen, Germany
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4
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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. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:909-923. [PMID: 37953711 DOI: 10.1111/tpj.16537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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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5
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Niederau PA, Eglé P, Willig S, Parsons J, Hoernstein SNW, Decker EL, Reski R. Multifactorial analysis of terminator performance on heterologous gene expression in Physcomitrella. PLANT CELL REPORTS 2024; 43:43. [PMID: 38246952 PMCID: PMC10800305 DOI: 10.1007/s00299-023-03088-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 11/02/2023] [Indexed: 01/23/2024]
Abstract
KEY MESSAGE Characterization of Physcomitrella 3'UTRs across different promoters yields endogenous single and double terminators for usage in molecular pharming. The production of recombinant proteins for health applications accounts for a large share of the biopharmaceutical market. While many drugs are produced in microbial and mammalian systems, plants gain more attention as expression hosts to produce eukaryotic proteins. In particular, the good manufacturing practice (GMP)-compliant moss Physcomitrella (Physcomitrium patens) has outstanding features, such as excellent genetic amenability, reproducible bioreactor cultivation, and humanized protein glycosylation patterns. In this study, we selected and characterized novel terminators for their effects on heterologous gene expression. The Physcomitrella genome contains 53,346 unique 3'UTRs (untranslated regions) of which 7964 transcripts contain at least one intron. Over 91% of 3'UTRs exhibit more than one polyadenylation site, indicating the prevalence of alternative polyadenylation in Physcomitrella. Out of all 3'UTRs, 14 terminator candidates were selected and characterized via transient Dual-Luciferase assays, yielding a collection of endogenous terminators performing equally high as established heterologous terminators CaMV35S, AtHSP90, and NOS. High performing candidates were selected for testing as double terminators which impact reporter levels, dependent on terminator identity and positioning. Testing of 3'UTRs among the different promoters NOS, CaMV35S, and PpActin5 showed an increase of more than 1000-fold between promoters PpActin5 and NOS, whereas terminators increased reporter levels by less than tenfold, demonstrating the stronger effect promoters play as compared to terminators. Among selected terminator attributes, the number of polyadenylation sites as well as polyadenylation signals were found to influence terminator performance the most. Our results improve the biotechnology platform Physcomitrella and further our understanding of how terminators influence gene expression in plants in general.
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Affiliation(s)
| | - Pauline Eglé
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Sandro Willig
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Juliana Parsons
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | | | - Eva L Decker
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany.
- Signalling Research Centre BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.
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6
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Alisha A, Szweykowska-Kulinska Z, Sierocka I. Comparative analysis of SPL transcription factors from streptophyte algae and embryophytes reveals evolutionary trajectories of SPL family in streptophytes. Sci Rep 2024; 14:1611. [PMID: 38238367 PMCID: PMC10796333 DOI: 10.1038/s41598-024-51626-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 01/08/2024] [Indexed: 01/22/2024] Open
Abstract
SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) genes encode plant-specific transcription factors which are important regulators of diverse plant developmental processes. We took advantage of available genome sequences of streptophyte algae representatives to investigate the relationships of SPL genes between freshwater green algae and land plants. Our analysis showed that streptophyte algae, hornwort and liverwort genomes encode from one to four SPL genes which is the smallest set, in comparison to other land plants studied to date. Based on the phylogenetic analysis, four major SPL phylogenetic groups were distinguished with Group 3 and 4 being sister to Group 1 and 2. Comparative motif analysis revealed conserved protein motifs within each phylogenetic group and unique bryophyte-specific motifs within Group 1 which suggests lineage-specific protein speciation processes. Moreover, the gene structure analysis also indicated the specificity of each by identifying differences in exon-intron structures between the phylogenetic groups, suggesting their evolutionary divergence. Since current understanding of SPL genes mostly arises from seed plants, the presented comparative and phylogenetic analyzes from freshwater green algae and land plants provide new insights on the evolutionary trajectories of the SPL gene family in different classes of streptophytes.
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Affiliation(s)
- Alisha Alisha
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Izabela Sierocka
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland.
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7
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Fernie AR, Yan J, Aharoni A, Ma J. Editorial: The past, present and future of The Plant Journal Resource Articles. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:967-973. [PMID: 37943112 DOI: 10.1111/tpj.16515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Affiliation(s)
- Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Jianbing Yan
- National Key Laboratory of Crop Genetics, Huazhong Agricultural District, Wuhan, China
| | - Asaph Aharoni
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Jianxian Ma
- Purdue University, 915 S. University St, West Lafayette, IN, USA
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8
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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: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [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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9
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Barker EI, Rabbi F, Brisbourne WA, Aparato VPM, Escarrega Valenzuela V, Renzaglia KS, Suh DY. Genome-wide analysis of the GDSL esterase/lipase family genes in Physcomitrium patens and the involvement of GELP31 in spore germination. Mol Genet Genomics 2023; 298:1155-1172. [PMID: 37338594 DOI: 10.1007/s00438-023-02041-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 05/28/2023] [Indexed: 06/21/2023]
Abstract
In plants, the ability to produce hydrophobic substances that would provide protection from dehydration was required for the transition to land. This genome-wide investigation outlines the evolution of GDSL-type esterase/lipase (GELP) proteins in the moss Physcomitrium patens and suggests possible functions of some genes. GELP proteins play roles in the formation of hydrophobic polymers such as cutin and suberin that protect against dehydration and pathogen attack. GELP proteins are also implicated in processes such as pollen development and seed metabolism and germination. The P. patens GELP gene family comprises 48 genes and 14 pseudogenes. Phylogenetic analysis of all P. patens GELP sequences along with vascular plant GELP proteins with reported functions revealed that the P. patens genes clustered within previously identified A, B and C clades. A duplication model predicting the expansion of the GELP gene family within the P. patens lineage was constructed. Expression analysis combined with phylogenetic analysis suggested candidate genes for functions such as defence against pathogens, cutin metabolism, spore development and spore germination. The presence of relatively fewer GELP genes in P. patens may reduce the occurrence of functional redundancy that complicates the characterization of vascular plant GELP genes. Knockout lines of GELP31, which is highly expressed in sporophytes, were constructed. Gelp31 spores contained amorphous oil bodies and germinated late, suggesting (a) role(s) of GELP31 in lipid metabolism in spore development or germination. Future knockout studies of other candidate GELP genes will further elucidate the relationship between expansion of the family and the ability to withstand the harsh land environment.
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Affiliation(s)
- Elizabeth I Barker
- Department of Chemistry and Biochemistry, University of Regina, Regina, SK, Canada.
| | - Fazle Rabbi
- Department of Chemistry and Biochemistry, University of Regina, Regina, SK, Canada
| | - Wyllie A Brisbourne
- Department of Chemistry and Biochemistry, University of Regina, Regina, SK, Canada
| | - Vincent P M Aparato
- Department of Chemistry and Biochemistry, University of Regina, Regina, SK, Canada
| | | | - Karen S Renzaglia
- Department of Plant Biology, Southern Illinois University, Carbondale, IL, USA
| | - Dae-Yeon Suh
- Department of Chemistry and Biochemistry, University of Regina, Regina, SK, Canada.
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10
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Wadhwa N, Singh D, Yadav R, Kapoor S, Kapoor M. Role of TRDMT1/DNMT2 in stress adaptation and its influence on transcriptome and proteome dynamics under osmotic stress in Physcomitrium patens. PHYSIOLOGIA PLANTARUM 2023; 175:e14014. [PMID: 37882266 DOI: 10.1111/ppl.14014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/07/2023] [Accepted: 08/21/2023] [Indexed: 10/27/2023]
Abstract
Early land plants such as the moss Physcomitrium patens lack several morphological traits that offer protection to tracheophytes from environmental stresses. These plants instead have evolved several physiological and biochemical mechanisms that facilitate them to adapt to terrestrial stresses such as drought. We have previously shown that loss-of-function mutants of tRNA (cytosine(38)-C(5))-methyltransferase TRDMT1/DNMT2 in P. patens are highly sensitive to oxidative and osmotic stress. To gain insight into the role of PpTRDMT1/PpDNMT2 in modulating genetic networks under osmotic stress, genome-wide transcriptome and proteome studies were undertaken in wild-type and ppdnmt2 plants. Transcriptome analysis revealed 375 genes to be differentially expressed in the ppdnmt2 under stress compared to the WT. Most of these genes are affiliated with carbohydrate metabolic pathways, photosynthesis, cell wall biogenesis, pathways related to isotropic and polarised cell growth and transcription factors among others. Histochemical staining showed elevated levels of reactive oxygen species in ppdnmt2 while transmission electron microscopy revealed no distinct defects in the ultrastructure of chloroplasts. Immunoprecipitation using PpDNMT2-specific antibody coupled with mass spectrometry revealed core proteins of the glycolytic pathway, antioxidant enzymes, proteins of amino acid biosynthetic pathways and photosynthesis-related proteins among others to co-purify with PpTRDMT1/PpDNMT2 under osmotic stress. Yeast two-hybrid assays, protein deletion and α-galactosidase assays showed the cytosol glycolytic protein glyceraldehyde 3-phosphate dehydrogenase to bind to the catalytic motifs in PpTRDMT1/PpDNMT2. Results presented in this study allow us to better understand genetic networks linking enzymes of energy metabolism, epigenetic processes and RNA pol II-mediated transcription during osmotic stress tolerance in P. patens.
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Affiliation(s)
- Nikita Wadhwa
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka, Delhi, India
| | - Darshika Singh
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka, Delhi, India
| | - Radha Yadav
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka, Delhi, India
| | - Sanjay Kapoor
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, Delhi, India
| | - Meenu Kapoor
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka, Delhi, India
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11
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Wu SZ, Chaves AM, Li R, Roberts AW, Bezanilla M. Cellulose synthase-like D movement in the plasma membrane requires enzymatic activity. J Cell Biol 2023; 222:e202212117. [PMID: 37071416 PMCID: PMC10120407 DOI: 10.1083/jcb.202212117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/28/2023] [Accepted: 03/17/2023] [Indexed: 04/19/2023] Open
Abstract
Cellulose Synthase-Like D (CSLD) proteins, important for tip growth and cell division, are known to generate β-1,4-glucan. However, whether they are propelled in the membrane as the glucan chains they produce assemble into microfibrils is unknown. To address this, we endogenously tagged all eight CSLDs in Physcomitrium patens and discovered that they all localize to the apex of tip-growing cells and to the cell plate during cytokinesis. Actin is required to target CSLD to cell tips concomitant with cell expansion, but not to cell plates, which depend on actin and CSLD for structural support. Like Cellulose Synthase (CESA), CSLD requires catalytic activity to move in the plasma membrane. We discovered that CSLD moves significantly faster, with shorter duration and less linear trajectories than CESA. In contrast to CESA, CSLD movement was insensitive to the cellulose synthesis inhibitor isoxaben, suggesting that CSLD and CESA function within different complexes possibly producing structurally distinct cellulose microfibrils.
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Affiliation(s)
- Shu-Zon Wu
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Arielle M. Chaves
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
| | - Rongrong Li
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
| | - Alison W. Roberts
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
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12
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Phokas A, Meyberg R, Briones‐Moreno A, Hernandez‐Garcia J, Wadsworth PT, Vesty EF, Blazquez MA, Rensing SA, Coates JC. DELLA proteins regulate spore germination and reproductive development in Physcomitrium patens. THE NEW PHYTOLOGIST 2023; 238:654-672. [PMID: 36683399 PMCID: PMC10952515 DOI: 10.1111/nph.18756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Proteins of the DELLA family integrate environmental signals to regulate growth and development throughout the plant kingdom. Plants expressing non-degradable DELLA proteins underpinned the development of high-yielding 'Green Revolution' dwarf crop varieties in the 1960s. In vascular plants, DELLAs are regulated by gibberellins, diterpenoid plant hormones. How DELLA protein function has changed during land plant evolution is not fully understood. We have examined the function and interactions of DELLA proteins in the moss Physcomitrium (Physcomitrella) patens, in the sister group of vascular plants (Bryophytes). PpDELLAs do not undergo the same regulation as flowering plant DELLAs. PpDELLAs are not degraded by diterpenes, do not interact with GID1 gibberellin receptor proteins and do not participate in responses to abiotic stress. PpDELLAs do share a function with vascular plant DELLAs during reproductive development. PpDELLAs also regulate spore germination. PpDELLAs interact with moss-specific photoreceptors although a function for PpDELLAs in light responses was not detected. PpDELLAs likely act as 'hubs' for transcriptional regulation similarly to their homologues across the plant kingdom. Taken together, these data demonstrate that PpDELLA proteins share some biological functions with DELLAs in flowering plants, but other DELLA functions and regulation evolved independently in both plant lineages.
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Affiliation(s)
- Alexandros Phokas
- School of BiosciencesUniversity of BirminghamEdgbastinBirminghamB15 2TTUK
| | - Rabea Meyberg
- Plant Cell Biology, Faculty of BiologyUniversity of MarburgKarl‐von‐Frisch‐Straße 8Marburg35043Germany
| | - Asier Briones‐Moreno
- Instituto de Biología Molecular y Celular de Plantas (CSIC‐Universitat Politècnica de València)C/Ingeniero Fausto Elio s/nValencia46022Spain
| | - Jorge Hernandez‐Garcia
- Instituto de Biología Molecular y Celular de Plantas (CSIC‐Universitat Politècnica de València)C/Ingeniero Fausto Elio s/nValencia46022Spain
| | | | - Eleanor F. Vesty
- School of BiosciencesUniversity of BirminghamEdgbastinBirminghamB15 2TTUK
| | - Miguel A. Blazquez
- Instituto de Biología Molecular y Celular de Plantas (CSIC‐Universitat Politècnica de València)C/Ingeniero Fausto Elio s/nValencia46022Spain
| | - Stefan A. Rensing
- Faculty of Chemistry and PharmacyUniversity of FreiburgStefan‐Meier‐Straße 19Freiburg79104Germany
| | - Juliet C. Coates
- School of BiosciencesUniversity of BirminghamEdgbastinBirminghamB15 2TTUK
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13
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Kreiss M, Haas FB, Hansen M, Rensing SA, Hoecker U. Co-action of COP1, SPA and cryptochrome in light signal transduction and photomorphogenesis of the moss Physcomitrium patens. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:159-175. [PMID: 36710658 DOI: 10.1111/tpj.16128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
The Arabidopsis COP1/SPA ubiquitin ligase suppresses photomorphogenesis in darkness. In the light, photoreceptors inactivate COP1/SPA to allow a light response. While SPA genes are specific to the green lineage, COP1 also exists in humans. This raises the question of when in evolution plant COP1 acquired the need for SPA accessory proteins. We addressed this question by generating Physcomitrium Ppcop1 mutants and comparing their visible and molecular phenotypes with those of Physcomitrium Ppspa mutants. The phenotype of Ppcop1 nonuple mutants resembles that of Ppspa mutants. Most importantly, both mutants produce green chloroplasts in complete darkness. They also exhibit dwarfed gametophores, disturbed branching of protonemata and absent gravitropism. RNA-sequencing analysis indicates that both mutants undergo weak constitutive light signaling in darkness. PpCOP1 and PpSPA proteins form a complex and they interact via their WD repeat domains with the VP motif of the cryptochrome CCE domain in a blue light-dependent manner. This resembles the interaction of Arabidopsis SPA proteins with Arabidopsis CRY1, and is different from that with Arabidopsis CRY2. Taken together, the data indicate that PpCOP1 and PpSPA act together to regulate growth and development of Physcomitrium. However, in contrast to their Arabidopsis orthologs, PpCOP1 and PpSPA proteins execute only partial suppression of light signaling in darkness. Hence, additional repressors may exist that contribute to the repression of a light response in dark-exposed Physcomitrium.
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Affiliation(s)
- Melanie Kreiss
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Strasse 47b, 50674, Cologne, Germany
| | - Fabian B Haas
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Strasse 8, 35043, Marburg, Germany
| | - Maike Hansen
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Strasse 47b, 50674, Cologne, Germany
| | - Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Strasse 8, 35043, Marburg, Germany
| | - Ute Hoecker
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Strasse 47b, 50674, Cologne, Germany
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14
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Lüth VM, Rempfer C, van Gessel N, Herzog O, Hanser M, Braun M, Decker EL, Reski R. A Physcomitrella PIN protein acts in spermatogenesis and sporophyte retention. THE NEW PHYTOLOGIST 2023; 237:2118-2135. [PMID: 36696950 DOI: 10.1111/nph.18691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
The auxin efflux PIN-FORMED (PIN) proteins are conserved in all land plants and important players in plant development. In the moss Physcomitrella (Physcomitrium patens), three canonical PINs (PpPINA-C) are expressed in the leafy shoot (gametophore). PpPINA and PpPINB show functional activity in vegetative growth and sporophyte development. Here, we examined the role of PpPINC in the life cycle of Physcomitrella. We established reporter and knockout lines for PpPINC and analysed vegetative and reproductive tissues using microscopy and transcriptomic sequencing of moss gametangia. PpPINC is expressed in immature leaves, mature gametangia and during sporophyte development. The sperm cells (spermatozoids) of pinC knockout mutants exhibit increased motility and an altered flagella phenotype. Furthermore, the pinC mutants have a higher portion of differentially expressed genes related to spermatogenesis, increased fertility and an increased abortion rate of premeiotic sporophytes. Here, we show that PpPINC is important for spermatogenesis and sporophyte retention. We propose an evolutionary conserved way of polar growth during early moss embryo development and sporophyte attachment to the gametophore while suggesting the mechanical function in sporophyte retention of a ring structure, the Lorch ring.
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Affiliation(s)
- Volker M Lüth
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Christine Rempfer
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104, Freiburg, Germany
| | - Nico van Gessel
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Oliver Herzog
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Melanie Hanser
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Marion Braun
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Eva L Decker
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104, Freiburg, Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, 79110, Freiburg, Germany
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15
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Ntefidou M, Eklund DM, Le Bail A, Schulmeister S, Scherbel F, Brandl L, Dörfler W, Eichstädt C, Bannmüller A, Ljung K, Kost B. Physcomitrium patens PpRIC, an ancestral CRIB-domain ROP effector, inhibits auxin-induced differentiation of apical initial cells. Cell Rep 2023; 42:112130. [PMID: 36790931 DOI: 10.1016/j.celrep.2023.112130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 12/03/2022] [Accepted: 02/01/2023] [Indexed: 02/16/2023] Open
Abstract
RHO guanosine triphosphatases are important eukaryotic regulators of cell differentiation and behavior. Plant ROP (RHO of plant) family members activate specific, incompletely characterized downstream signaling. The structurally simple land plant Physcomitrium patens is missing homologs of key animal and flowering plant RHO effectors but contains a single CRIB (CDC42/RAC interactive binding)-domain-containing RIC (ROP-interacting CRIB-containing) protein (PpRIC). Protonemal P. patens filaments elongate based on regular division and PpROP-dependent tip growth of apical initial cells, which upon stimulation by the hormone auxin differentiate caulonemal characteristics. PpRIC interacts with active PpROP1, co-localizes with this protein at the plasma membrane at the tip of apical initial cells, and accumulates in the nucleus. Remarkably, PpRIC is not required for tip growth but is targeted to the nucleus to block caulonema differentiation downstream of auxin-controlled gene expression. These observations establish functions of PpRIC in mediating crosstalk between ROP and auxin signaling, which contributes to the maintenance of apical initial cell identity.
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Affiliation(s)
- Maria Ntefidou
- Cell Biology, Department of Biology, University Erlangen-Nuremberg, 91058 Erlangen, Germany
| | - D Magnus Eklund
- Physiology and Environmental Toxicology, Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden
| | - Aude Le Bail
- Cell Biology, Department of Biology, University Erlangen-Nuremberg, 91058 Erlangen, Germany
| | - Sylwia Schulmeister
- Cell Biology, Department of Biology, University Erlangen-Nuremberg, 91058 Erlangen, Germany
| | - Franziska Scherbel
- Cell Biology, Department of Biology, University Erlangen-Nuremberg, 91058 Erlangen, Germany
| | - Lisa Brandl
- Cell Biology, Department of Biology, University Erlangen-Nuremberg, 91058 Erlangen, Germany
| | - Wolfgang Dörfler
- Cell Biology, Department of Biology, University Erlangen-Nuremberg, 91058 Erlangen, Germany
| | - Chantal Eichstädt
- Cell Biology, Department of Biology, University Erlangen-Nuremberg, 91058 Erlangen, Germany
| | - Anna Bannmüller
- Cell Biology, Department of Biology, University Erlangen-Nuremberg, 91058 Erlangen, Germany
| | - Karin Ljung
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden
| | - Benedikt Kost
- Cell Biology, Department of Biology, University Erlangen-Nuremberg, 91058 Erlangen, Germany.
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16
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A deeply conserved protease, acylamino acid-releasing enzyme (AARE), acts in ageing in Physcomitrella and Arabidopsis. Commun Biol 2023; 6:61. [PMID: 36650210 PMCID: PMC9845386 DOI: 10.1038/s42003-023-04428-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 01/05/2023] [Indexed: 01/18/2023] Open
Abstract
Reactive oxygen species (ROS) are constant by-products of aerobic life. In excess, ROS lead to cytotoxic protein aggregates, which are a hallmark of ageing in animals and linked to age-related pathologies in humans. Acylamino acid-releasing enzymes (AARE) are bifunctional serine proteases, acting on oxidized proteins. AARE are found in all domains of life, albeit under different names, such as acylpeptide hydrolase (APEH/ACPH), acylaminoacyl peptidase (AAP), or oxidized protein hydrolase (OPH). In humans, AARE malfunction is associated with age-related pathologies, while their function in plants is less clear. Here, we provide a detailed analysis of AARE genes in the plant lineage and an in-depth analysis of AARE localization and function in the moss Physcomitrella and the angiosperm Arabidopsis. AARE loss-of-function mutants have not been described for any organism so far. We generated and analysed such mutants and describe a connection between AARE function, aggregation of oxidized proteins and plant ageing, including accelerated developmental progression and reduced life span. Our findings complement similar findings in animals and humans, and suggest a unified concept of ageing may exist in different life forms.
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17
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Fernandez-Pozo N. PEATmoss: A Gene Expression Atlas for Bryophytes. Methods Mol Biol 2023; 2703:91-107. [PMID: 37646940 DOI: 10.1007/978-1-0716-3389-2_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
PEATmoss is an interactive gene expression atlas for bryophytes, which originally unified Physcomitrium patens RNA-seq and microarray expression data from multiple gene annotation versions. This atlas includes more than 100 experiments of P. patens, is expanding to host Anthoceros agrestis and Marchantia polymorpha, and aims to host data from more species in the future. PEATmoss has multiple visualization methods and tools for data downloading and is connected to the Physcomitrium patens Gene Model Lookup DB (PpGML DB), which links P. patens genes to annotations and resources from several databases and contains tools for gene version lookup and sequence and annotation extraction. Among the new features available in PEATmoss are dataset privacy control, multispecies menu, interactive color scale, co-expression network visualization, and replicate data downloading.
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Affiliation(s)
- Noe Fernandez-Pozo
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany.
- Institute for Mediterranean and Subtropical Horticulture (IHSM-CSIC-UMA), Algarrobo-Costa, Málaga, Spain.
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18
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Tu M, Zeng J, Zhang J, Fan G, Song G. Unleashing the power within short-read RNA-seq for plant research: Beyond differential expression analysis and toward regulomics. FRONTIERS IN PLANT SCIENCE 2022; 13:1038109. [PMID: 36570898 PMCID: PMC9773216 DOI: 10.3389/fpls.2022.1038109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
RNA-seq has become a state-of-the-art technique for transcriptomic studies. Advances in both RNA-seq techniques and the corresponding analysis tools and pipelines have unprecedently shaped our understanding in almost every aspects of plant sciences. Notably, the integration of huge amount of RNA-seq with other omic data sets in the model plants and major crop species have facilitated plant regulomics, while the RNA-seq analysis has still been primarily used for differential expression analysis in many less-studied plant species. To unleash the analytical power of RNA-seq in plant species, especially less-studied species and biomass crops, we summarize recent achievements of RNA-seq analysis in the major plant species and representative tools in the four types of application: (1) transcriptome assembly, (2) construction of expression atlas, (3) network analysis, and (4) structural alteration. We emphasize the importance of expression atlas, coexpression networks and predictions of gene regulatory relationships in moving plant transcriptomes toward regulomics, an omic view of genome-wide transcription regulation. We highlight what can be achieved in plant research with RNA-seq by introducing a list of representative RNA-seq analysis tools and resources that are developed for certain minor species or suitable for the analysis without species limitation. In summary, we provide an updated digest on RNA-seq tools, resources and the diverse applications for plant research, and our perspective on the power and challenges of short-read RNA-seq analysis from a regulomic point view. A full utilization of these fruitful RNA-seq resources will promote plant omic research to a higher level, especially in those less studied species.
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Affiliation(s)
- Min Tu
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Jian Zeng
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan, Guangdong, China
| | - Juntao Zhang
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Guozhi Fan
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Guangsen Song
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, China
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19
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Graf L, Shin Y, Yang JH, Hwang IK, Yoon HS. Transcriptome analysis reveals the spatial and temporal differentiation of gene expression in the sporophyte of Undaria pinnatifida. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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20
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Niemeyer PW, Irisarri I, Scholz P, Schmitt K, Valerius O, Braus GH, Herrfurth C, Feussner I, Sharma S, Carlsson AS, de Vries J, Hofvander P, Ischebeck T. A seed-like proteome in oil-rich tubers. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:518-534. [PMID: 36050843 DOI: 10.1111/tpj.15964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 08/09/2022] [Accepted: 08/26/2022] [Indexed: 06/15/2023]
Abstract
There are numerous examples of plant organs or developmental stages that are desiccation-tolerant and can withstand extended periods of severe water loss. One prime example are seeds and pollen of many spermatophytes. However, in some plants, also vegetative organs can be desiccation-tolerant. One example are the tubers of yellow nutsedge (Cyperus esculentus), which also store large amounts of lipids similar to seeds. Interestingly, the closest known relative, purple nutsedge (Cyperus rotundus), generates tubers that do not accumulate oil and are not desiccation-tolerant. We generated nanoLC-MS/MS-based proteomes of yellow nutsedge in five replicates of four stages of tuber development and compared them to the proteomes of roots and leaves, yielding 2257 distinct protein groups. Our data reveal a striking upregulation of hallmark proteins of seeds in the tubers. A deeper comparison to the tuber proteome of the close relative purple nutsedge (C. rotundus) and a previously published proteome of Arabidopsis seeds and seedlings indicates that indeed a seed-like proteome was found in yellow but not purple nutsedge. This was further supported by an analysis of the proteome of a lipid droplet-enriched fraction of yellow nutsedge, which also displayed seed-like characteristics. One reason for the differences between the two nutsedge species might be the expression of certain transcription factors homologous to ABSCISIC ACID INSENSITIVE3, WRINKLED1, and LEAFY COTYLEDON1 that drive gene expression in Arabidopsis seed embryos.
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Affiliation(s)
- Philipp William Niemeyer
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences and Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, 37077, Göttingen, Germany
| | - Iker Irisarri
- Department of Applied Bioinformatics, Göttingen Center for Molecular Biosciences (GZMB) and Campus Institute Data Science (CIDAS), Institute for Microbiology and Genetics, University of Göttingen, 37077, Göttingen, Germany
| | - Patricia Scholz
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences and Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, 37077, Göttingen, Germany
| | - Kerstin Schmitt
- Department for Molecular Microbiology and Genetics, Genetics and Göttingen Center for Molecular Biosciences (GZMB) and Service Unit LCMS Protein Analytics, Institute for Microbiology, University of Göttingen, 37077, Göttingen, Germany
| | - Oliver Valerius
- Department for Molecular Microbiology and Genetics, Genetics and Göttingen Center for Molecular Biosciences (GZMB) and Service Unit LCMS Protein Analytics, Institute for Microbiology, University of Göttingen, 37077, Göttingen, Germany
| | - Gerhard H Braus
- Department for Molecular Microbiology and Genetics, Genetics and Göttingen Center for Molecular Biosciences (GZMB) and Service Unit LCMS Protein Analytics, Institute for Microbiology, University of Göttingen, 37077, Göttingen, Germany
| | - Cornelia Herrfurth
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences and Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, 37077, Göttingen, Germany
- Department of Plant Biochemistry, Service Unit for Metabolomics and Lipidomics, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, 37077, Göttingen, Germany
| | - Ivo Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences and Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, 37077, Göttingen, Germany
- Department of Plant Biochemistry, Service Unit for Metabolomics and Lipidomics, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, 37077, Göttingen, Germany
| | - Shrikant Sharma
- Department of Plant Breeding, SLU Alnarp, Swedish University of Agricultural Sciences, Box 190, SE-234 22, Lomma, Sweden
| | - Anders S Carlsson
- Department of Plant Breeding, SLU Alnarp, Swedish University of Agricultural Sciences, Box 190, SE-234 22, Lomma, Sweden
| | - Jan de Vries
- Department of Applied Bioinformatics, Göttingen Center for Molecular Biosciences (GZMB) and Campus Institute Data Science (CIDAS), Institute for Microbiology and Genetics, University of Göttingen, 37077, Göttingen, Germany
| | - Per Hofvander
- Department of Plant Breeding, SLU Alnarp, Swedish University of Agricultural Sciences, Box 190, SE-234 22, Lomma, Sweden
| | - Till Ischebeck
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences and Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, 37077, Göttingen, Germany
- Green Biotechnology, Institute of Plant Biology and Biotechnology (IBBP), University of Münster, 48143, Münster, Germany
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21
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Fernandez-Pozo N, Haas FB, Gould SB, Rensing SA. An overview of bioinformatics, genomics, and transcriptomics resources for bryophytes. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4291-4305. [PMID: 35148385 DOI: 10.1093/jxb/erac052] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/22/2022] [Indexed: 06/14/2023]
Abstract
Bryophytes are useful models for the study of plant evolution, development, plant-fungal symbiosis, stress responses, and gametogenesis. Additionally, their dominant haploid gametophytic phase makes them great models for functional genomics research, allowing straightforward genome editing and gene knockout via CRISPR or homologous recombination. Until 2016, however, the only bryophyte genome sequence published was that of Physcomitrium patens. Throughout recent years, several other bryophyte genomes and transcriptome datasets became available, enabling better comparative genomics in evolutionary studies. The increase in the number of bryophyte genome and transcriptome resources available has yielded a plethora of annotations, databases, and bioinformatics tools to access the new data, which covers the large diversity of this clade and whose biology comprises features such as association with arbuscular mycorrhiza fungi, sex chromosomes, low gene redundancy, or loss of RNA editing genes for organellar transcripts. Here we provide a guide to resources available for bryophytes with regards to genome and transcriptome databases and bioinformatics tools.
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Affiliation(s)
- Noe Fernandez-Pozo
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- Department of Subtropical and Mediterranean Fruit Crops, Institute for Mediterranean and Subtropical Horticulture "La Mayora" (IHSM-CSIC-UMA), Málaga, Spain
| | - Fabian B Haas
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | - Sven B Gould
- Evolutionary Cell Biology, Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Stefan A Rensing
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps University of Marburg, Marburg, Germany
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22
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Reboledo G, Agorio A, Ponce De León I. Moss transcription factors regulating development and defense responses to stress. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4546-4561. [PMID: 35167679 DOI: 10.1093/jxb/erac055] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/11/2022] [Indexed: 06/14/2023]
Abstract
Transcription factors control gene expression, leading to regulation of biological processes that determine plant development and adaptation to the environment. Land colonization by plants occurred 450-470 million years ago and was accompanied by an increase in the complexity of transcriptional regulation associated to transcription factor gene expansions. AP2/ERF, bHLH, MYB, NAC, GRAS, and WRKY transcription factor families increased in land plants compared with algae. In angiosperms, they play crucial roles in regulating plant growth and responses to environmental stressors. However, less information is available in bryophytes and only in a few cases is the functional role of moss transcription factors in stress mechanisms known. In this review, we discuss current knowledge of the transcription factor families involved in development and defense responses to stress in mosses and other bryophytes. By exploring and analysing the Physcomitrium patens public database and published transcriptional profiles, we show that a high number of AP2/ERF, bHLH, MYB, NAC, GRAS, and WRKY genes are differentially expressed in response to abiotic stresses and during biotic interactions. Expression profiles together with a comprehensive analysis provide insights into relevant transcription factors involved in moss defenses, and hint at distinct and conserved biological roles between bryophytes and angiosperms.
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Affiliation(s)
- Guillermo Reboledo
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Astrid Agorio
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Inés Ponce De León
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
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23
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Lim PK, Zheng X, Goh JC, Mutwil M. Exploiting plant transcriptomic databases: Resources, tools, and approaches. PLANT COMMUNICATIONS 2022; 3:100323. [PMID: 35605200 PMCID: PMC9284291 DOI: 10.1016/j.xplc.2022.100323] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/03/2022] [Accepted: 04/06/2022] [Indexed: 05/11/2023]
Abstract
There are now more than 300 000 RNA sequencing samples available, stemming from thousands of experiments capturing gene expression in organs, tissues, developmental stages, and experimental treatments for hundreds of plant species. The expression data have great value, as they can be re-analyzed by others to ask and answer questions that go beyond the aims of the study that generated the data. Because gene expression provides essential clues to where and when a gene is active, the data provide powerful tools for predicting gene function, and comparative analyses allow us to study plant evolution from a new perspective. This review describes how we can gain new knowledge from gene expression profiles, expression specificities, co-expression networks, differential gene expression, and experiment correlation. We also introduce and demonstrate databases that provide user-friendly access to these tools.
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Affiliation(s)
- Peng Ken Lim
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Xinghai Zheng
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Jong Ching Goh
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
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24
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Lopez‐Obando M, Landberg K, Sundberg E, Thelander M. Dependence on clade II bHLH transcription factors for nursing of haploid products by tapetal-like cells is conserved between moss sporangia and angiosperm anthers. THE NEW PHYTOLOGIST 2022; 235:718-731. [PMID: 35037245 PMCID: PMC9306660 DOI: 10.1111/nph.17972] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 12/28/2021] [Indexed: 05/16/2023]
Abstract
Clade II basic helix-loop-helix transcription factors (bHLH TFs) are essential for pollen production and tapetal nursing functions in angiosperm anthers. As pollen has been suggested to be related to bryophyte spores by descent, we characterized two Physcomitrium (Physcomitrella) patens clade II bHLH TFs (PpbHLH092 and PpbHLH098), to test if regulation of sporogenous cells and the nursing cells surrounding them is conserved between angiosperm anthers and bryophyte sporangia. We made CRISPR-Cas9 reporter and loss-of-function lines to address the function of PpbHLH092/098. We sectioned and analyzed WT and mutant sporophytes for a comprehensive stage-by-stage comparison of sporangium development. Spore precursors in the P. patens sporangium are surrounded by nursing cells showing striking similarities to tapetal cells in angiosperms. Moss clade II bHLH TFs are essential for the differentiation of these tapetal-like cells and for the production of functional spores. Clade II bHLH TFs provide a conserved role in controlling the sporophytic somatic cells surrounding and nursing the sporogenous cells in both moss sporangia and angiosperm anthers. This supports the hypothesis that such nursing functions in mosses and angiosperms, lineages separated by c. 450 million years, are related by descent.
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Affiliation(s)
- Mauricio Lopez‐Obando
- Department of Plant BiologyThe Linnean Centre of Plant Biology in UppsalaSwedish University of Agricultural SciencesPO Box 7080UppsalaSE‐75007Sweden
- VEDAS Corporación de Investigación e Innovación (VEDASCII)Cl 8 B 65‐261 050024MedellínColombia
| | - Katarina Landberg
- Department of Plant BiologyThe Linnean Centre of Plant Biology in UppsalaSwedish University of Agricultural SciencesPO Box 7080UppsalaSE‐75007Sweden
| | - Eva Sundberg
- Department of Plant BiologyThe Linnean Centre of Plant Biology in UppsalaSwedish University of Agricultural SciencesPO Box 7080UppsalaSE‐75007Sweden
| | - Mattias Thelander
- Department of Plant BiologyThe Linnean Centre of Plant Biology in UppsalaSwedish University of Agricultural SciencesPO Box 7080UppsalaSE‐75007Sweden
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25
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Fernandez-Pozo N, Bombarely A. EasyGDB: a low-maintenance and highly customizable system to develop genomics portals. Bioinformatics 2022; 38:4048-4050. [PMID: 35748710 PMCID: PMC9364376 DOI: 10.1093/bioinformatics/btac412] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/07/2022] [Accepted: 06/21/2022] [Indexed: 12/24/2022] Open
Abstract
SUMMARY EasyGDB is an easy-to-implement low-maintenance tool developed to create genomic data management web platforms. It can be used for any species, group of species, or multiple genome or annotation versions. EasyGDB provides a framework to develop a web portal that includes the general information about species, projects and members, and bioinformatics tools such as file downloads, BLAST, genome browser, annotation search, gene expression visualization, annotation and sequence download, and gene ids and orthologs lookup. The code of EasyGDB facilitates data maintenance and update for non-experienced bioinformaticians, using BLAST databases to store and retrieve sequence data in gene annotation pages and bioinformatics tools, and JSON files to customize metadata. EasyGDB is a highly customizable tool. Any section and tool can be enabled or disabled like a switch through a single configuration file. This tool aims to simplify the development of genomics portals in non-model species, providing a modern web style with embedded interactive bioinformatics tools to cover all the common needs derived from genomics projects. AVAILABILITY AND IMPLEMENTATION The code and manual to use EasyGDB can be found at https://github.com/noefp/easy_gdb.
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Affiliation(s)
| | - Aureliano Bombarely
- Department of Bioscience, Universita degli Studi di Milano, Milan 20133, Italy,Departamento de Biotecnología y Mejora Vegetal de Especies Cultivadas, Biología Molecular y Celular de Plantas (IBMCP), UPV-CSIC, Valencia 46022, Spain
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Lal M, Bhardwaj E, Chahar N, Yadav S, Das S. Comprehensive analysis of 1R- and 2R-MYBs reveals novel genic and protein features, complex organisation, selective expansion and insights into evolutionary tendencies. Funct Integr Genomics 2022; 22:371-405. [PMID: 35260976 DOI: 10.1007/s10142-022-00836-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 02/10/2022] [Accepted: 02/23/2022] [Indexed: 11/28/2022]
Abstract
Myeloblastosis (MYB) family, the largest plant transcription factor family, has been subcategorised based on the number and type of repeats in the MYB domain. In spite of several reports, evolution of MYB genes and repeats remains enigmatic. Brassicaceae members are endowed with complex genomes, including dysploidy because of its unique history with multiple rounds of polyploidisation, genomic fractionations and rearrangements. The present study is an attempt to gain insights into the complexities of MYB family diversity, understand impacts of genome evolution on gene families and develop an evolutionary framework to understand the origin of various subcategories of MYB gene family. We identified and analysed 1129 MYBs that included 1R-, 2R-, 3R- and atypical-MYBs across sixteen species representing protists, fungi, animals and plants and exclude MYB identified from Brassicaceae except Arabidopsis thaliana; in addition, a total of 1137 2R-MYB genes from six Brassicaceae species were also analysed. Comparative analysis revealed predominance of 1R-MYBs in protists, fungi, animals and lower plants. Phylogenetic reconstruction and analysis of selection pressure suggested ancestral nature of R1-type repeat containing 1R-MYBs that might have undergone intragenic duplication to form multi-repeat MYBs. Distinct differences in gene structure between 1R-MYB and 2R-MYBs were observed regarding intron number, the ratio of gene length to coding DNA sequence (CDS) length and the length of exons encoding the MYB domain. Conserved as well as novel and lineage-specific intron phases were identified. Analyses of physicochemical properties revealed drastic differences indicating functional diversification in MYBs. Phylogenetic reconstruction of 1R- and 2R-MYB genes revealed a shared structure-function relationship in clades which was supported when transcriptome data was analysed in silico. Comparative genomics to study distribution pattern and mapping of 2R-MYBs revealed congruency and greater degree of synteny and collinearity among closely related species. Micro-synteny analysis of genomic segments revealed high conservation of genes that are immediately flanking the surrounding tandemly organised 2R-MYBs along with instances of local duplication, reorganisations and genome fractionation. In summary, polyploidy, dysploidy, reshuffling and genome fractionation were found to cause loss or gain of 2R-MYB genes. The findings need to be supported with functional validation to understand gene structure-function relationship along the evolutionary lineage and adaptive strategies based on comparative functional genomics in plants.
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Affiliation(s)
- Mukund Lal
- Department of Botany, University of Delhi, Delhi, 110007, India
| | - Ekta Bhardwaj
- Department of Botany, University of Delhi, Delhi, 110007, India
| | - Nishu Chahar
- Department of Botany, University of Delhi, Delhi, 110007, India
| | - Shobha Yadav
- Department of Botany, University of Delhi, Delhi, 110007, India
| | - Sandip Das
- Department of Botany, University of Delhi, Delhi, 110007, India.
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27
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Spindle motility skews division site determination during asymmetric cell division in Physcomitrella. Nat Commun 2022; 13:2488. [PMID: 35513464 PMCID: PMC9072379 DOI: 10.1038/s41467-022-30239-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 04/21/2022] [Indexed: 01/09/2023] Open
Abstract
Asymmetric cell division (ACD) underlies the development of multicellular organisms. In animal ACD, the cell division site is determined by active spindle-positioning mechanisms. In contrast, it is considered that the division site in plants is determined prior to mitosis by the microtubule-actin belt known as the preprophase band (PPB) and that the localization of the mitotic spindle is typically static and does not govern the division plane. However, in some plant species, ACD occurs in the absence of PPB. Here, we isolate a hypomorphic mutant of the conserved microtubule-associated protein TPX2 in the moss Physcomitrium patens (Physcomitrella) and observe spindle motility during PPB-independent cell division. This defect compromises the position of the division site and produces inverted daughter cell sizes in the first ACD of gametophore (leafy shoot) development. The phenotype is rescued by restoring endogenous TPX2 function and, unexpectedly, by depolymerizing actin filaments. Thus, we identify an active spindle-positioning mechanism that, reminiscent of acentrosomal ACD in animals, involves microtubules and actin filaments, and sets the division site in plants.
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28
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Li X, Chaves AM, Dees DCT, Mansoori N, Yuan K, Speicher TL, Norris JH, Wallace IS, Trindade LM, Roberts AW. Cellulose synthesis complexes are homo-oligomeric and hetero-oligomeric in Physcomitrium patens. PLANT PHYSIOLOGY 2022; 188:2115-2130. [PMID: 35022793 PMCID: PMC8968406 DOI: 10.1093/plphys/kiac003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 12/03/2021] [Indexed: 05/27/2023]
Abstract
The common ancestor of seed plants and mosses contained homo-oligomeric cellulose synthesis complexes (CSCs) composed of identical subunits encoded by a single CELLULOSE SYNTHASE (CESA) gene. Seed plants use different CESA isoforms for primary and secondary cell wall deposition. Both primary and secondary CESAs form hetero-oligomeric CSCs that assemble and function in planta only when all the required isoforms are present. The moss Physcomitrium (Physcomitrella) patens has seven CESA genes that can be grouped into two functionally and phylogenetically distinct classes. Previously, we showed that PpCESA3 and/or PpCESA8 (class A) together with PpCESA6 and/or PpCESA7 (class B) form obligate hetero-oligomeric complexes required for normal secondary cell wall deposition. Here, we show that gametophore morphogenesis requires a member of class A, PpCESA5, and is sustained in the absence of other PpCESA isoforms. PpCESA5 also differs from the other class A PpCESAs as it is able to self-interact and does not co-immunoprecipitate with other PpCESA isoforms. These results are consistent with the hypothesis that homo-oligomeric CSCs containing only PpCESA5 subunits synthesize cellulose required for gametophore morphogenesis. Analysis of mutant phenotypes also revealed that, like secondary cell wall deposition, normal protonemal tip growth requires class B isoforms (PpCESA4 or PpCESA10), along with a class A partner (PpCESA3, PpCESA5, or PpCESA8). Thus, P. patens contains both homo-oligomeric and hetero-oligomeric CSCs.
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Affiliation(s)
| | | | | | | | | | - Tori L Speicher
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Joanna H Norris
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island 02881, USA
| | - Ian S Wallace
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Luisa M Trindade
- Wageningen UR Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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Kleist TJ, Bortolazzo A, Keyser ZP, Perera AM, Irving TB, Venkateshwaran M, Atanjaoui F, Tang RJ, Maeda J, Cartwright HN, Christianson ML, Lemaux PG, Luan S, Ané JM. Stress-associated developmental reprogramming in moss protonemata by synthetic activation of the common symbiosis pathway. iScience 2022; 25:103754. [PMID: 35146383 PMCID: PMC8819110 DOI: 10.1016/j.isci.2022.103754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 12/22/2021] [Accepted: 01/07/2022] [Indexed: 11/19/2022] Open
Abstract
Symbioses between angiosperms and rhizobia or arbuscular mycorrhizal fungi are controlled through a conserved signaling pathway. Microbe-derived, chitin-based elicitors activate plant cell surface receptors and trigger nuclear calcium oscillations, which are decoded by a calcium/calmodulin-dependent protein kinase (CCaMK) and its target transcription factor interacting protein of DMI3 (IPD3). Genes encoding CCaMK and IPD3 have been lost in multiple non-mycorrhizal plant lineages yet retained among non-mycorrhizal mosses. Here, we demonstrated that the moss Physcomitrium is equipped with a bona fide CCaMK that can functionally complement a Medicago loss-of-function mutant. Conservation of regulatory phosphosites allowed us to generate predicted hyperactive forms of Physcomitrium CCaMK and IPD3. Overexpression of synthetically activated CCaMK or IPD3 in Physcomitrium led to abscisic acid (ABA) accumulation and ectopic development of brood cells, which are asexual propagules that facilitate escape from local abiotic stresses. We therefore propose a functional role for Physcomitrium CCaMK-IPD3 in stress-associated developmental reprogramming.
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Affiliation(s)
- Thomas J. Kleist
- Department of Plant & Microbial Biology, University of California-Berkeley, Berkeley, CA 94720, USA
- Department of Plant Biology, Carnegie Institute for Science, Stanford, CA 94305, USA
- Institute for Molecular Physiology, Department of Biology, Heinrich Heine University, Düsseldorf 40225, Germany
- Corresponding author
| | - Anthony Bortolazzo
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Zachary P. Keyser
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Adele M. Perera
- Department of Plant & Microbial Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Thomas B. Irving
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - Fatiha Atanjaoui
- Institute for Molecular Physiology, Department of Biology, Heinrich Heine University, Düsseldorf 40225, Germany
| | - Ren-Jie Tang
- Department of Plant & Microbial Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Junko Maeda
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Heather N. Cartwright
- Department of Plant Biology, Carnegie Institute for Science, Stanford, CA 94305, USA
| | - Michael L. Christianson
- Department of Plant & Microbial Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Peggy G. Lemaux
- Department of Plant & Microbial Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Sheng Luan
- Department of Plant & Microbial Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI 53706, USA
- Corresponding author
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Ruiz-Molina N, Parsons J, Schroeder S, Posten C, Reski R, Decker EL. Process Engineering of Biopharmaceutical Production in Moss Bioreactors via Model-Based Description and Evaluation of Phytohormone Impact. Front Bioeng Biotechnol 2022; 10:837965. [PMID: 35252145 PMCID: PMC8891706 DOI: 10.3389/fbioe.2022.837965] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/24/2022] [Indexed: 12/24/2022] Open
Abstract
The moss Physcomitrella is an interesting production host for recombinant biopharmaceuticals. Here we produced MFHR1, a synthetic complement regulator which has been proposed for the treatment of diseases associated to the complement system as part of human innate immunity. We studied the impact of different operation modes for the production process in 5 L stirred-tank photobioreactors. The total amount of recombinant protein was doubled by using fed-batch or batch compared to semi-continuous operation, although the maximum specific productivity (mg MFHR1/g FW) increased just by 35%. We proposed an unstructured kinetic model which fits accurately with the experimental data in batch and semi-continuous operation under autotrophic conditions with 2% CO2 enrichment. The model is able to predict recombinant protein production, nitrate uptake and biomass growth, which is useful for process control and optimization. We investigated strategies to further increase MFHR1 production. While mixotrophic and heterotrophic conditions decreased the MFHR1-specific productivity compared to autotrophic conditions, addition of the phytohormone auxin (NAA, 10 µM) to the medium enhanced it by 470% in shaken flasks and up to 230% and 260%, in batch and fed-batch bioreactors, respectively. Supporting this finding, the auxin-synthesis inhibitor L-kynurenine (100 µM) decreased MFHR1 production significantly by 110% and 580% at day 7 and 18, respectively. Expression analysis revealed that the MFHR1 transgene, driven by the Physcomitrella actin5 (PpAct5) promoter, was upregulated 16 h after NAA addition and remained enhanced over the whole process, whereas the auxin-responsive gene PpIAA1A was upregulated within the first 2 hours, indicating that the effect of auxin on PpAct5 promoter-driven expression is indirect. Furthermore, the day of NAA supplementation was crucial, leading to an up to 8-fold increase of MFHR1-specific productivity (0.82 mg MFHR1/g fresh weight, 150 mg accumulated over 7 days) compared to the productivity reported previously. Our findings are likely to be applicable to other plant-based expression systems to increase biopharmaceutical production and yields.
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Affiliation(s)
- Natalia Ruiz-Molina
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Juliana Parsons
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Sina Schroeder
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Clemens Posten
- Institute of Process Engineering in Life Sciences III Bioprocess Engineering, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Eva L. Decker
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- *Correspondence: Eva L. Decker,
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Rempfer C, Wiedemann G, Schween G, Kerres KL, Lucht JM, Horres R, Decker EL, Reski R. Autopolyploidization affects transcript patterns and gene targeting frequencies in Physcomitrella. PLANT CELL REPORTS 2022; 41:153-173. [PMID: 34636965 PMCID: PMC8803787 DOI: 10.1007/s00299-021-02794-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/23/2021] [Indexed: 06/13/2023]
Abstract
In Physcomitrella, whole-genome duplications affected the expression of about 3.7% of the protein-encoding genes, some of them relevant for DNA repair, resulting in a massively reduced gene-targeting frequency. Qualitative changes in gene expression after an autopolyploidization event, a pure duplication of the whole genome (WGD), might be relevant for a different regulation of molecular mechanisms between angiosperms growing in a life cycle with a dominant diploid sporophytic stage and the haploid-dominant mosses. Whereas angiosperms repair DNA double-strand breaks (DSB) preferentially via non-homologous end joining (NHEJ), in the moss Physcomitrella homologous recombination (HR) is the main DNA-DSB repair pathway. HR facilitates the precise integration of foreign DNA into the genome via gene targeting (GT). Here, we studied the influence of ploidy on gene expression patterns and GT efficiency in Physcomitrella using haploid plants and autodiploid plants, generated via an artificial WGD. Single cells (protoplasts) were transfected with a GT construct and material from different time-points after transfection was analysed by microarrays and SuperSAGE sequencing. In the SuperSAGE data, we detected 3.7% of the Physcomitrella genes as differentially expressed in response to the WGD event. Among the differentially expressed genes involved in DNA-DSB repair was an upregulated gene encoding the X-ray repair cross-complementing protein 4 (XRCC4), a key player in NHEJ. Analysing the GT efficiency, we observed that autodiploid plants were significantly GT suppressed (p < 0.001) attaining only one third of the expected GT rates. Hence, an alteration of global transcript patterns, including genes related to DNA repair, in autodiploid Physcomitrella plants correlated with a drastic suppression of HR.
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Affiliation(s)
- Christine Rempfer
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104, Freiburg, Germany
| | - Gertrud Wiedemann
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
| | - Gabriele Schween
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
- Corteva Agriscience, Pioneer Hi-Bred Northern Europe, Münstertäler Strasse 26, 79427, Eschbach, Germany
| | - Klaus L Kerres
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Jan M Lucht
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
- Scienceindustries, Nordstrasse 15, 8006, Zurich, Switzerland
| | - Ralf Horres
- GenXPro GmbH, Altenhöferallee 3, 60438, Frankfurt am Main, Germany
| | - Eva L Decker
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany.
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104, Freiburg, Germany.
- Signalling Research Centres BIOSS and CIBSS, Schaenzlestr. 18, 79104, Freiburg, Germany.
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Balparda M, Elsässer M, Badia MB, Giese J, Bovdilova A, Hüdig M, Reinmuth L, Eirich J, Schwarzländer M, Finkemeier I, Schallenberg-Rüdinger M, Maurino VG. Acetylation of conserved lysines fine-tunes mitochondrial malate dehydrogenase activity in land plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:92-111. [PMID: 34713507 DOI: 10.1111/tpj.15556] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 10/21/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
Plants need to rapidly and flexibly adjust their metabolism to changes of their immediate environment. Since this necessity results from the sessile lifestyle of land plants, key mechanisms for orchestrating central metabolic acclimation are likely to have evolved early. Here, we explore the role of lysine acetylation as a post-translational modification to directly modulate metabolic function. We generated a lysine acetylome of the moss Physcomitrium patens and identified 638 lysine acetylation sites, mostly found in mitochondrial and plastidial proteins. A comparison with available angiosperm data pinpointed lysine acetylation as a conserved regulatory strategy in land plants. Focusing on mitochondrial central metabolism, we functionally analyzed acetylation of mitochondrial malate dehydrogenase (mMDH), which acts as a hub of plant metabolic flexibility. In P. patens mMDH1, we detected a single acetylated lysine located next to one of the four acetylation sites detected in Arabidopsis thaliana mMDH1. We assessed the kinetic behavior of recombinant A. thaliana and P. patens mMDH1 with site-specifically incorporated acetyl-lysines. Acetylation of A. thaliana mMDH1 at K169, K170, and K334 decreases its oxaloacetate reduction activity, while acetylation of P. patens mMDH1 at K172 increases this activity. We found modulation of the malate oxidation activity only in A. thaliana mMDH1, where acetylation of K334 strongly activated it. Comparative homology modeling of MDH proteins revealed that evolutionarily conserved lysines serve as hotspots of acetylation. Our combined analyses indicate lysine acetylation as a common strategy to fine-tune the activity of central metabolic enzymes with likely impact on plant acclimation capacity.
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Affiliation(s)
- Manuel Balparda
- Molecular Plant Physiology, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Marlene Elsässer
- Molecular Evolution, Institute for Cellular and Molecular Botany (IZMB), University of Bonn, Kirschallee 1, 53115, Bonn, Germany
- Plant Energy Biology, Institute of Plant Biology and Biotechnology (IBBP), University of Münster, Schlossplatz 8, 48143, Münster, Germany
| | - Mariana B Badia
- Plant Molecular Physiology and Biotechnology, Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University, and Cluster of Excellence on Plant Sciences (CEPLAS), 40225, Düsseldorf, Germany
- Facultad de Quı́mica e Ingenierı́a del Rosario, Pontificia Universidad Católica Argentina, Av. Pellegrini 3314, S2002QEO, Rosario, Argentina
| | - Jonas Giese
- Plant Physiology, Institute of Plant Biology and Biotechnology (IBBP), University of Münster, Schlossplatz 7, 48149, Münster, Germany
| | - Anastasiia Bovdilova
- Plant Molecular Physiology and Biotechnology, Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University, and Cluster of Excellence on Plant Sciences (CEPLAS), 40225, Düsseldorf, Germany
| | - Meike Hüdig
- Molecular Plant Physiology, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
- Plant Molecular Physiology and Biotechnology, Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University, and Cluster of Excellence on Plant Sciences (CEPLAS), 40225, Düsseldorf, Germany
| | - Lisa Reinmuth
- Molecular Evolution, Institute for Cellular and Molecular Botany (IZMB), University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Jürgen Eirich
- Plant Physiology, Institute of Plant Biology and Biotechnology (IBBP), University of Münster, Schlossplatz 7, 48149, Münster, Germany
| | - Markus Schwarzländer
- Plant Energy Biology, Institute of Plant Biology and Biotechnology (IBBP), University of Münster, Schlossplatz 8, 48143, Münster, Germany
| | - Iris Finkemeier
- Plant Physiology, Institute of Plant Biology and Biotechnology (IBBP), University of Münster, Schlossplatz 7, 48149, Münster, Germany
| | - Mareike Schallenberg-Rüdinger
- Molecular Evolution, Institute for Cellular and Molecular Botany (IZMB), University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Veronica G Maurino
- Molecular Plant Physiology, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
- Plant Molecular Physiology and Biotechnology, Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University, and Cluster of Excellence on Plant Sciences (CEPLAS), 40225, Düsseldorf, Germany
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Perroud PF, Demko V, Ako AE, Khanal R, Bokor B, Pavlovič A, Jásik J, Johansen W. The nuclear GUCT domain-containing DEAD-box RNA helicases govern gametophytic and sporophytic development in Physcomitrium patens. PLANT MOLECULAR BIOLOGY 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] [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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Genau AC, Li Z, Renzaglia KS, Fernandez Pozo N, Nogué F, Haas FB, Wilhelmsson PKI, Ullrich KK, Schreiber M, Meyberg R, Grosche C, Rensing SA. HAG1 and SWI3A/B control of male germ line development in P. patens suggests conservation of epigenetic reproductive control across land plants. PLANT REPRODUCTION 2021; 34:149-173. [PMID: 33839924 PMCID: PMC8128824 DOI: 10.1007/s00497-021-00409-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 04/02/2021] [Indexed: 05/27/2023]
Abstract
KEY MESSAGE Bryophytes as models to study the male germ line: loss-of-function mutants of epigenetic regulators HAG1 and SWI3a/b demonstrate conserved function in sexual reproduction. With the water-to-land transition, land plants evolved a peculiar haplodiplontic life cycle in which both the haploid gametophyte and the diploid sporophyte are multicellular. The switch between these phases was coined alternation of generations. Several key regulators that control the bauplan of either generation are already known. Analyses of such regulators in flowering plants are difficult due to the highly reduced gametophytic generation, and the fact that loss of function of such genes often is embryo lethal in homozygous plants. Here we set out to determine gene function and conservation via studies in bryophytes. Bryophytes are sister to vascular plants and hence allow evolutionary inferences. Moreover, embryo lethal mutants can be grown and vegetatively propagated due to the dominance of the bryophyte gametophytic generation. We determined candidates by selecting single copy orthologs that are involved in transcriptional control, and of which flowering plant mutants show defects during sexual reproduction, with a focus on the under-studied male germ line. We selected two orthologs, SWI3a/b and HAG1, and analyzed loss-of-function mutants in the moss P. patens. In both mutants, due to lack of fertile spermatozoids, fertilization and hence the switch to the diploid generation do not occur. Pphag1 additionally shows arrested male and impaired female gametangia development. We analyzed HAG1 in the dioecious liverwort M. polymorpha and found that in Mphag1 the development of gametangiophores is impaired. Taken together, we find that involvement of both regulators in sexual reproduction is conserved since the earliest divergence of land plants.
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Affiliation(s)
- Anne C Genau
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | - Zhanghai Li
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | - Karen S Renzaglia
- Department of Plant Biology, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Noe Fernandez Pozo
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | - Fabien Nogué
- Institut Jean-Pierre Bourgin, INRAE, Université Paris-Saclay, 78000, Versailles, AgroParisTech, France
| | - Fabian B Haas
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | - Per K I Wilhelmsson
- 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
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Mona Schreiber
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | - Rabea Meyberg
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | - Christopher Grosche
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | - Stefan A Rensing
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany.
- BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany.
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps University of Marburg, Marburg, Germany.
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Fernandez‐Pozo N, Metz T, Chandler JO, Gramzow L, Mérai Z, Maumus F, Mittelsten Scheid O, Theißen G, Schranz ME, Leubner‐Metzger G, Rensing SA. Aethionema arabicum genome annotation using PacBio full-length transcripts provides a valuable resource for seed dormancy and Brassicaceae evolution research. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:275-293. [PMID: 33453123 PMCID: PMC8641386 DOI: 10.1111/tpj.15161] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/31/2020] [Accepted: 01/08/2021] [Indexed: 05/06/2023]
Abstract
Aethionema arabicum is an important model plant for Brassicaceae trait evolution, particularly of seed (development, regulation, germination, dormancy) and fruit (development, dehiscence mechanisms) characters. Its genome assembly was recently improved but the gene annotation was not updated. Here, we improved the Ae. arabicum gene annotation using 294 RNA-seq libraries and 136 307 full-length PacBio Iso-seq transcripts, increasing BUSCO completeness by 11.6% and featuring 5606 additional genes. Analysis of orthologs showed a lower number of genes in Ae. arabicum than in other Brassicaceae, which could be partially explained by loss of homeologs derived from the At-α polyploidization event and by a lower occurrence of tandem duplications after divergence of Aethionema from the other Brassicaceae. Benchmarking of MADS-box genes identified orthologs of FUL and AGL79 not found in previous versions. Analysis of full-length transcripts related to ABA-mediated seed dormancy discovered a conserved isoform of PIF6-β and antisense transcripts in ABI3, ABI4 and DOG1, among other cases found of different alternative splicing between Turkey and Cyprus ecotypes. The presented data allow alternative splicing mining and proposition of numerous hypotheses to research evolution and functional genomics. Annotation data and sequences are available at the Ae. arabicum DB (https://plantcode.online.uni-marburg.de/aetar_db).
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Affiliation(s)
- Noe Fernandez‐Pozo
- Plant Cell BiologyDepartment of BiologyUniversity of MarburgMarburgGermany
| | - Timo Metz
- Plant Cell BiologyDepartment of BiologyUniversity of MarburgMarburgGermany
| | - Jake O. Chandler
- School of Biological SciencesRoyal Holloway University of LondonEghamSurreyUK
| | - Lydia Gramzow
- Matthias Schleiden Institute/GeneticsFriedrich Schiller University JenaJenaGermany
| | - Zsuzsanna Mérai
- Gregor Mendel Institute of Molecular Plant BiologyAustrian Academy of SciencesVienna BioCenter (VBC)ViennaAustria
| | | | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute of Molecular Plant BiologyAustrian Academy of SciencesVienna BioCenter (VBC)ViennaAustria
| | - Günter Theißen
- Matthias Schleiden Institute/GeneticsFriedrich Schiller University JenaJenaGermany
| | - M. Eric Schranz
- Biosystematics GroupWageningen UniversityWageningenThe Netherlands
| | - Gerhard Leubner‐Metzger
- School of Biological SciencesRoyal Holloway University of LondonEghamSurreyUK
- Laboratory of Growth RegulatorsCentre of the Region Haná for Biotechnological and Agricultural ResearchPalacký University and Institute of Experimental BotanyAcademy of Sciences of the Czech RepublicOlomoucCzech Republic
| | - Stefan A. Rensing
- Plant Cell BiologyDepartment of BiologyUniversity of MarburgMarburgGermany
- BIOSS Centre for Biological Signaling StudiesUniversity of FreiburgFreiburgGermany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO)University of MarburgMarburgGermany
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de Vries J, Ischebeck T. Ties between Stress and Lipid Droplets Pre-date Seeds. TRENDS IN PLANT SCIENCE 2020; 25:1203-1214. [PMID: 32921563 DOI: 10.1016/j.tplants.2020.07.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/24/2020] [Accepted: 07/30/2020] [Indexed: 05/12/2023]
Abstract
Seeds were a key evolutionary innovation. These durable structures provide a concerted solution to two challenges on land: dispersal and stress. Lipid droplets (LDs) that act as nutrient storage reservoirs are one of the main cell-biological reasons for seed endurance. Although LDs are key structures in spermatophytes and are especially abundant in seeds, they are found across plants and algae, and increase during stress. Further, the proteins that underpin their form and function often have deep homologs. We propose an evolutionary scenario in which (i) the generation of LDs arose as a mechanism to mediate general drought and desiccation resilience, and (ii) the required protein framework was co-opted by spermatophytes for a seed-specific program.
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Affiliation(s)
- Jan de Vries
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstrasse 1, 37077 Goettingen, Germany; University of Goettingen, Goettingen Center for Molecular Biosciences (GZMB), 37077 Goettingen, Germany; University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidtstrasse 1, 37077 Goettingen, Germany.
| | - Till Ischebeck
- University of Goettingen, Goettingen Center for Molecular Biosciences (GZMB), 37077 Goettingen, Germany; University of Goettingen, Albrecht-von-Haller-Institute for Plant Sciences, Department of Plant Biochemistry, Justus-von-Liebig-Weg 11, 37077 Goettingen, Germany.
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37
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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. FRONTIERS IN PLANT SCIENCE 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] [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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38
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Romanowski A, Schlaen RG, Perez-Santangelo S, Mancini E, Yanovsky MJ. Global transcriptome analysis reveals circadian control of splicing events in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:889-902. [PMID: 32314836 DOI: 10.1111/tpj.14776] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/26/2020] [Accepted: 04/01/2020] [Indexed: 05/21/2023]
Abstract
The circadian clock of Arabidopsis thaliana controls many physiological and molecular processes, allowing plants to anticipate daily changes in their environment. However, developing a detailed understanding of how oscillations in mRNA levels are connected to oscillations in co/post-transcriptional processes, such as splicing, has remained a challenge. Here we applied a combined approach using deep transcriptome sequencing and bioinformatics tools to identify novel circadian-regulated genes and splicing events. Using a stringent approach, we identified 300 intron retention, eight exon skipping, 79 alternative 3' splice site usage, 48 alternative 5' splice site usage, and 350 multiple (more than one event type) annotated events under circadian regulation. We also found seven and 721 novel alternative exonic and intronic events. Depletion of the circadian-regulated splicing factor AtSPF30 homologue resulted in the disruption of a subset of clock-controlled splicing events. Altogether, our global circadian RNA-seq coupled with an in silico, event-centred, splicing analysis tool offers a new approach for studying the interplay between the circadian clock and the splicing machinery at a global scale. The identification of many circadian-regulated splicing events broadens our current understanding of the level of control that the circadian clock has over this co/post-transcriptional regulatory layer.
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Affiliation(s)
- Andrés Romanowski
- Comparative Genomics of Plant Development, Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1405BWE, Buenos Aires, Argentina
| | - Rubén G Schlaen
- Comparative Genomics of Plant Development, Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1405BWE, Buenos Aires, Argentina
| | - Soledad Perez-Santangelo
- Comparative Genomics of Plant Development, Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1405BWE, Buenos Aires, Argentina
| | - Estefanía Mancini
- Comparative Genomics of Plant Development, Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1405BWE, Buenos Aires, Argentina
| | - Marcelo J Yanovsky
- Comparative Genomics of Plant Development, Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1405BWE, Buenos Aires, Argentina
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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. THE NEW PHYTOLOGIST 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] [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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Singh D, Yadav R, Kaushik S, Wadhwa N, Kapoor S, Kapoor M. Transcriptome Analysis of ppdnmt2 and Identification of Superoxide Dismutase as a Novel Interactor of DNMT2 in the Moss Physcomitrella patens. FRONTIERS IN PLANT SCIENCE 2020; 11:1185. [PMID: 32849734 PMCID: PMC7419982 DOI: 10.3389/fpls.2020.01185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/21/2020] [Indexed: 05/07/2023]
Abstract
DNMT2 is a DNA/tRNA cytosine methyltransferase that is highly conserved in structure and function in eukaryotes. In plants however, limited information is available on the function of this methyltransferase. We have previously reported that in the moss Physcomitrella patens, DNMT2 plays a crucial role in stress recovery and tRNAAsp transcription/stability under salt stress. To further investigate the role of PpDNMT2 at genome level, in this study we have performed RNA sequencing of ppdnmt2. Transcriptome analysis reveals a number of genes and pathways to function differentially and suggests a close link between PpDNMT2 function and osmotic and ionic stress tolerance. We propose PpDNMT2 to play a pivotal role in regulating salt tolerance by affecting molecular networks involved in stress perception and signal transduction that underlie maintenance of ion homeostasis in cells. We also examined interactome of PpDNMT2 using affinity purification (AP) coupled to mass spectrometry (AP-MS). Quantitative proteomic analysis reveals several chloroplast proteins involved in light reactions and carbon assimilation and proteins involved in stress response and some not implicated in stress to co-immunoprecipitate with PpDNMT2. Comparison between transcriptome and interactome datasets has revealed novel association between PpDNMT2 activity and the antioxidant enzyme Superoxide dismutase (SOD), protein turnover mediated by the Ubiquitin-proteasome system and epigenetic gene regulation. PpDNMT2 possibly exists in complex with CuZn-SODs in vivo and the two proteins also directly interact in the yeast nucleus as observed by yeast two-hybrid assay. Taken together, the work presented in this study sheds light on diverse roles of PpDNMT2 in maintaining molecular and physiological homeostasis in P. patens. This is a first report describing transcriptome and interactome of DNMT2 in any land plant.
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Affiliation(s)
- Darshika Singh
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - Radha Yadav
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - Shubham Kaushik
- Vproteomics, Valerian Chem Private Limited Green Park Mains, New Delhi, India
| | - Nikita Wadhwa
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - Sanjay Kapoor
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Meenu Kapoor
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
- *Correspondence: Meenu Kapoor,
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