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Schluttenhofer C. Origin and evolution of jasmonate signaling. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 298:110542. [PMID: 32771155 DOI: 10.1016/j.plantsci.2020.110542] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 05/25/2020] [Accepted: 05/26/2020] [Indexed: 05/15/2023]
Abstract
Jasmonate (JA) signaling is a key mediator of plant development and defense which arose during plants transition from an aqueous to terrestrial environment. Elucidating the evolution of JA signaling is important for understanding plant development, defense, and production of specialized metabolites. The lineage of key protein domains characterizing JA signaling factors was traced to identify the origins of CORONITINE INSENSITIVE 1 (COI1), JASMONATE ZIM-DOMAIN (JAZ), NOVEL INTERACTOR OF JAZ, MYC2, TOPLESS, and MEDIATOR SUBUNIT 25. Charophytes do not possess genes encoding key JA signaling components, including COI1, JAZ, MYC2, and the JAZ-interacting bHLH factors, yet their orthologs are present in bryophytes. TIFY family genes were found in charophyta and chlorophya algae. JAZs evolved from ZIM genes of the TIFY family through changes to several key amino acids. Dating placed the origin of JA signaling 515 to 473 million years ago during the middle Cambrian to early Ordovician periods. This time is known for rapid biodiversification and mass extinction events. An increased predation from the diversifying and changing fauna may have driven evolution of JA signaling and plant defense.
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Affiliation(s)
- Craig Schluttenhofer
- Agriculture Research and Development Program, 1400 Brush Row Road, Wilberforce OH, 45384, USA.
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52
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Chen Z, Wang W, Dong X, Pu X, Gao B, Liu L. Functional redundancy and divergence of β-carbonic anhydrases in Physcomitrella patens. PLANTA 2020; 252:20. [PMID: 32671568 DOI: 10.1007/s00425-020-03429-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/10/2020] [Indexed: 06/11/2023]
Abstract
β-carbonic anhydrases, which function in regulating plant growth, C/N status, and stomata number, showed functional redundancy and divergence in Physcomitrella patens. Carbonic anhydrases (CAs) catalyze the interconversion of CO2 and HCO3-. Plants have three evolutionarily unrelated CA families: α-, β-, and γ-CAs. βCAs are abundant in plants and are involved in CO2 assimilation, stress responses, and stomata formation. Recent studies of βCAs have mainly examined C3 or C4 plants, whereas their functions in non-vascular plants are mostly unknown. In this study, phylogenetic analysis revealed that the evolution of βCAs were conserved between subaerial green algae and bryophytes after terrestrialization event, and βCAs from some cyanobacteria might begin evolving for the adaptation of terrestrial environment/habitat. In addition, we investigated the physiological roles of βCAs in the basal land plant Physcomitrella patens. High PpβCA expression levels in different tissues suggest that PpβCAs play important roles in development in P. patens. Plants treated with 1-10 mM NaHCO3 had higher fresh and dry weight, PpβCA expression, total CA activity, and photosynthetic yield (Fv/Fm) compared with water-treated plants. However, treatment with 10 mM NaHCO3 influenced the C/N status. Further study of six Ppβca single-gene mutants revealed that PpβCAs have functional redundancy and divergence in regulating the C/N ratio of plants and stomatal formation. This study provides new insight into the physiological roles of βCAs in basal land plants.
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Affiliation(s)
- Zexi Chen
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenbo Wang
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiumei Dong
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China
| | - Xiaojun Pu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China
| | - Bei Gao
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, 999077, China
| | - Li Liu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China.
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei University, Wuhan, 430062, China.
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Genome-Wide Identification of the CrRLK1L Subfamily and Comparative Analysis of Its Role in the Legume-Rhizobia Symbiosis. Genes (Basel) 2020; 11:genes11070793. [PMID: 32674446 PMCID: PMC7397338 DOI: 10.3390/genes11070793] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/07/2020] [Accepted: 07/09/2020] [Indexed: 12/12/2022] Open
Abstract
The plant receptor-like-kinase subfamily CrRLK1L has been widely studied, and CrRLK1Ls have been described as crucial regulators in many processes in Arabidopsis thaliana (L.), Heynh. Little is known, however, about the functions of these proteins in other plant species, including potential roles in symbiotic nodulation. We performed a phylogenetic analysis of CrRLK1L subfamily receptors of 57 different plant species and identified 1050 CrRLK1L proteins, clustered into 11 clades. This analysis revealed that the CrRLK1L subfamily probably arose in plants during the transition from chlorophytes to embryophytes and has undergone several duplication events during its evolution. Among the CrRLK1Ls of legumes and A. thaliana, protein structure, gene structure, and expression patterns were highly conserved. Some legume CrRLK1L genes were active in nodules. A detailed analysis of eight nodule-expressed genes in Phaseolus vulgaris L. showed that these genes were differentially expressed in roots at different stages of the symbiotic process. These data suggest that CrRLK1Ls are both conserved and underwent diversification in a wide group of plants, and shed light on the roles of these genes in legume–rhizobia symbiosis.
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54
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Xu T, Yuan J, Hiltbrunner A. PHYTOCHROME INTERACTING FACTORs in the moss Physcomitrella patens regulate light-controlled gene expression. PHYSIOLOGIA PLANTARUM 2020; 169:467-479. [PMID: 32447760 DOI: 10.1111/ppl.13140] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 05/15/2020] [Accepted: 05/19/2020] [Indexed: 06/11/2023]
Abstract
Phytochromes are red and far-red light receptors in plants that control growth and development in response to changes in the environment. Light-activated phytochromes enter the nucleus and act on a set of downstream signalling components to regulate gene expression. PHYTOCHROME INTERACTING FACTORs (PIFs) belong to the basic helix-loop-helix family of transcription factors and directly bind to light-activated phytochromes. Potential homologues of PIFs have been identified in ferns, bryophytes and streptophyte algae, and it has been shown that the potential PIF homologues from Physcomitrella patens, PIF1 to PIF4, have PIF function when expressed in Arabidopsis. However, their function in Physcomitrella is still unknown. Seed plant PIFs bind to G-box-containing promoters and, therefore, we searched the Physcomitrella genome for genes that contain G-boxes in their promoter. Here, we show that Physcomitrella PIFs activate these promoters in a G-box-dependent manner, suggesting that they could be direct PIF targets. Furthermore, we generated Physcomitrella pif1, pif2, pif3 and pif4 knock out mutant lines and quantified the expression of potential PIF direct target genes. The expression of these genes was generally reduced in pif mutants compared to the wildtype, but for several genes, the relative induction upon a short light treatment was higher in pif mutants than the wildtype. In contrast, expression of these genes was strongly repressed in continuous light, and pif mutants showed partial downregulation of these genes in the dark. Thus, the overall function of PIFs in light-regulated gene expression might be an ancient property of PIFs.
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Affiliation(s)
- Tengfei Xu
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, Freiburg, 79104, Germany
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jinhong Yuan
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, Freiburg, 79104, Germany
| | - Andreas Hiltbrunner
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, Freiburg, 79104, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestrasse 18, Freiburg, 79104, Germany
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55
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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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56
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Ruibal C, Castro A, Fleitas AL, Quezada J, Quero G, Vidal S. A Chloroplast COR413 Protein From Physcomitrella patens Is Required for Growth Regulation Under High Light and ABA Responses. FRONTIERS IN PLANT SCIENCE 2020; 11:845. [PMID: 32636864 PMCID: PMC7317016 DOI: 10.3389/fpls.2020.00845] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 05/26/2020] [Indexed: 05/17/2023]
Abstract
COR413 genes belong to a poorly characterized group of plant-specific cold-regulated genes initially identified as part of the transcriptional activation machinery of plants during cold acclimation. They encode multispanning transmembrane proteins predicted to target the plasma membrane or the chloroplast inner membrane. Despite being ubiquitous throughout the plant kingdom, little is known about their biological function. In this study, we used reverse genetics to investigate the relevance of a predicted chloroplast localized COR413 protein (PpCOR413im) from the moss Physcomitrella patens in developmental and abiotic stress responses. Expression of PpCOR413im was strongly induced by abscisic acid (ABA) and by various environmental stimuli, including low temperature, hyperosmosis, salinity and high light. In vivo subcellular localization of PpCOR413im-GFP fusion protein revealed that this protein is localized in chloroplasts, confirming the in silico predictions. Loss-of-function mutants of PpCOR413im exhibited growth and developmental alterations such as growth retardation, reduced caulonema formation and hypersensitivity to ABA. Mutants also displayed altered photochemistry under various abiotic stresses, including dehydration and low temperature, and exhibited a dramatic growth inhibition upon exposure to high light. Disruption of PpCOR413im also caused altered chloroplast ultrastructure, increased ROS accumulation, and enhanced starch and sucrose levels under high light or after ABA treatment. In addition, loss of PpCOR413im affected both nuclear and chloroplast gene expression in response to ABA and high light, suggesting a role for this gene downstream of ABA in the regulation of growth and environmental stress responses. Developmental alterations exhibited by PpCOR413im knockout mutants had remarkable similarities to those exhibited by hxk1, a mutant lacking a major chloroplastic hexokinase, an enzyme involved in energy homeostasis. Based on these findings, we propose that PpCOR413im is involved in coordinating energy metabolism with ABA-mediated growth and developmental responses.
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Affiliation(s)
- Cecilia Ruibal
- Laboratorio de Biología Molecular Vegetal, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Alexandra Castro
- Laboratorio de Biología Molecular Vegetal, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Andrea L. Fleitas
- Laboratorio de Biología Molecular Vegetal, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Jorge Quezada
- Unidad de Biotecnología Vegetal, Instituto de Biología Molecular y Biotecnología, Carrera de Biología – Facultad de Ciencias Puras y Naturales, Universidad Mayor de San Andrés, La Paz, Bolivia
| | - Gastón Quero
- Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay
| | - Sabina Vidal
- Laboratorio de Biología Molecular Vegetal, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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57
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Fernandez-Pozo N, Haas FB, Meyberg R, Ullrich KK, Hiss M, Perroud PF, Hanke S, Kratz V, Powell AF, Vesty EF, Daum CG, Zane M, Lipzen A, Sreedasyam A, Grimwood J, Coates JC, Barry K, Schmutz J, Mueller LA, Rensing SA. PEATmoss (Physcomitrella Expression Atlas Tool): a unified gene expression atlas for the model plant Physcomitrella patens. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:165-177. [PMID: 31714620 DOI: 10.1111/tpj.14607] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 10/14/2019] [Accepted: 10/30/2019] [Indexed: 05/23/2023]
Abstract
Physcomitrella patens is a bryophyte model plant that is often used to study plant evolution and development. Its resources are of great importance for comparative genomics and evo-devo approaches. However, expression data from Physcomitrella patens were so far generated using different gene annotation versions and three different platforms: CombiMatrix and NimbleGen expression microarrays and RNA sequencing. The currently available P. patens expression data are distributed across three tools with different visualization methods to access the data. Here, we introduce an interactive expression atlas, Physcomitrella Expression Atlas Tool (PEATmoss), that unifies publicly available expression data for P. patens and provides multiple visualization methods to query the data in a single web-based tool. Moreover, PEATmoss includes 35 expression experiments not previously available in any other expression atlas. To facilitate gene expression queries across different gene annotation versions, and to access P. patens annotations and related resources, a lookup database and web tool linked to PEATmoss was implemented. PEATmoss can be accessed at https://peatmoss.online.uni-marburg.de.
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Affiliation(s)
- Noe Fernandez-Pozo
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Fabian B Haas
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Rabea Meyberg
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Kristian K Ullrich
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Ploen, Germany
| | - Manuel Hiss
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | | | - Sebastian Hanke
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Viktor Kratz
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | | | - Eleanor F Vesty
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Christopher G Daum
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Matthew Zane
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Anna Lipzen
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | | | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Juliet C Coates
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Kerrie Barry
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Jeremy Schmutz
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA, 94598, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | | | - Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, Germany
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58
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Lai X, Chahtane H, Martin-Arevalillo R, Zubieta C, Parcy F. Contrasted evolutionary trajectories of plant transcription factors. CURRENT OPINION IN PLANT BIOLOGY 2020; 54:101-107. [PMID: 32417720 DOI: 10.1016/j.pbi.2020.03.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 01/14/2020] [Accepted: 03/04/2020] [Indexed: 05/28/2023]
Abstract
Because of their prominent roles in plant development, transcription factors (TF) play central roles as drivers of innovation in the evolution of the green lineage (viridiplantae). The advent of massive sequencing combined with comparative genetics/genomics allows a rigorous investigation of how TF families have contributed to plant diversification from charophyte algae to bryophytes to angiosperms. Here, we review recent progress on TF family reconstruction and the identification of distantly related TFs present throughout the evolutionary timeline from algae to angiosperms. These data provide examples of contrasting evolutionary trajectories of TF families and illustrate how conserved TFs adopt diverse roles over the course of evolution.
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Affiliation(s)
- Xuelei Lai
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000 Grenoble, France
| | - Hicham Chahtane
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000 Grenoble, France
| | - Raquel Martin-Arevalillo
- Laboratoire de Reproduction et de Développement des Plantes, INRAE, CNRS, ENS de Lyon, UCB Lyon 1, Université de Lyon, France
| | - Chloe Zubieta
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000 Grenoble, France
| | - François Parcy
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000 Grenoble, France.
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59
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Hashida Y, Takechi K, Abiru T, Yabe N, Nagase H, Hattori K, Takio S, Sato Y, Hasebe M, Tsukaya H, Takano H. Two ANGUSTIFOLIA genes regulate gametophore and sporophyte development in Physcomitrella patens. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:1318-1330. [PMID: 31674691 DOI: 10.1111/tpj.14592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 08/06/2019] [Accepted: 10/17/2019] [Indexed: 05/08/2023]
Abstract
In Arabidopsis thaliana the ANGUSTIFOLIA (AN) gene regulates the width of leaves by controlling the diffuse growth of leaf cells in the medio-lateral direction. In the genome of the moss Physcomitrella patens, we found two normal ANs (PpAN1-1 and 1-2). Both PpAN1 genes complemented the A. thaliana an-1 mutant phenotypes. An analysis of spatiotemporal promoter activity of each PpAN1 gene, using transgenic lines that contained each PpAN1-promoter- uidA (GUS) gene, showed that both promoters are mainly active in the stems of haploid gametophores and in the middle to basal region of the young sporophyte that develops into the seta and foot. Analyses of the knockout lines for PpAN1-1 and PpAN1-2 genes suggested that these genes have partially redundant functions and regulate gametophore height by controlling diffuse cell growth in gametophore stems. In addition, the seta and foot were shorter and thicker in diploid sporophytes, suggesting that cell elongation was reduced in the longitudinal direction, whereas no defects were detected in tip-growing protonemata. These results indicate that both PpAN1 genes in P. patens function in diffuse growth of the haploid and diploid generations but not in tip growth. To visualize microtubule distribution in gametophore cells of P. patens, transformed lines expressing P. patens α-tubulin fused to sGFP were generated. Contrary to expectations, the orientation of microtubules in the tips of gametophores in the PpAN1-1/1-2 double-knockout lines was unchanged. The relationships among diffuse cell growth, cortical microtubules and AN proteins are discussed.
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Affiliation(s)
- Yoshikazu Hashida
- Graduate School of Science and Technology, Kumamoto University, Kurokami, Kumamoto, 860-8555, Japan
| | - Katsuaki Takechi
- Faculty of Advanced Science and Technology, Kumamoto University, Kurokami, Kumamoto, 860-8555, Japan
| | - Tomomi Abiru
- Graduate School of Science and Technology, Kumamoto University, Kurokami, Kumamoto, 860-8555, Japan
| | - Noriyuki Yabe
- Graduate School of Science and Technology, Kumamoto University, Kurokami, Kumamoto, 860-8555, Japan
| | - Hiroaki Nagase
- Graduate School of Science and Technology, Kumamoto University, Kurokami, Kumamoto, 860-8555, Japan
| | - Koro Hattori
- Graduate School of Science, University of Tokyo, Tokyo, 113-0033, Japan
| | - Susumu Takio
- Faculty of Advanced Science and Technology, Kumamoto University, Kurokami, Kumamoto, 860-8555, Japan
- Center for Water Cycle, Marine Environment and Disaster Management, Kumamoto University, Kurokami, Kumamoto, 860-8555, Japan
| | - Yoshikatsu Sato
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, 464-8601, Japan
| | - Mitsuyasu Hasebe
- National Institute for Basic Biology and SOKENDAI (Graduate School for Advanced Studies), Okazaki, 444-8585, Japan
| | - Hirokazu Tsukaya
- Graduate School of Science, University of Tokyo, Tokyo, 113-0033, Japan
| | - Hiroyoshi Takano
- Faculty of Advanced Science and Technology, Kumamoto University, Kurokami, Kumamoto, 860-8555, Japan
- Institute of Pulsed Power Science, Kumamoto University, Kumamoto, 860-8555, Japan
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60
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van Gisbergen P, Wu SZ, Cheng X, Pattavina KA, Bezanilla M. In vivo analysis of formin dynamics in the moss P. patens reveals functional class diversification. J Cell Sci 2020; 133:jcs233791. [PMID: 31969472 PMCID: PMC10679510 DOI: 10.1242/jcs.233791] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 01/07/2020] [Indexed: 01/02/2023] Open
Abstract
Formins are actin regulators critical for diverse processes across eukaryotes. With many formins in plants and animals, it has been challenging to determine formin function in vivo We found that the phylogenetically distinct class I integral membrane formins (denoted For1) from the moss P.patens enrich at sites of membrane turnover, with For1D more tightly associated with the plasma membrane than For1A. To probe formin function, we generated formin-null lines with greatly reduced formin complexity. We found that For1A and For1D help to anchor actin near the cell apex, with For1A contributing to formation of cytosolic actin, while For1D contributes to plasma membrane-associated actin. At the cortex, For1A and For1D localized to motile puncta and differentially impacted actin dynamics. We found that class I cortical formin mobility depended on microtubules and only moderately on actin, whereas class II formin (denoted For2) mobility solely depended on actin. Moreover, cortical For2A tightly correlated with the puncta labeled by the endocytic membrane dye FM4-64, and null mutants in class I formins did not affect uptake of a similar dye, FM1-43, suggesting that class I and II formins are involved in distinct membrane trafficking pathways.
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Affiliation(s)
- Peter van Gisbergen
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
| | - Shu-Zon Wu
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Xiaohang Cheng
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Kelli A Pattavina
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
| | - Magdalena Bezanilla
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
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61
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Agudelo-Romero P, Fortes AM, Suárez T, Lascano HR, Saavedra L. Evolutionary insights into FYVE and PHOX effector proteins from the moss Physcomitrella patens. PLANTA 2020; 251:62. [PMID: 32040768 DOI: 10.1007/s00425-020-03354-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 02/01/2020] [Indexed: 06/10/2023]
Abstract
Genome-wide identification, together with gene expression patterns and promoter region analysis of FYVE and PHOX proteins in Physcomitrella patens, emphasized their importance in regulating mainly developmental processes in P. patens. Phosphatidylinositol 3-phosphate (PtdIns3P) is a signaling phospholipid, which regulates several aspects of plant growth and development, as well as responses to biotic and abiotic stresses. The mechanistic insights underlying PtdIns3P mode of action, specifically through effector proteins have been partially explored in plants, with main focus on Arabidopsis thaliana. In this study, we searched for genes coding for PtdIns3P-binding proteins such as FYVE and PHOX domain-containing sequences from different photosynthetic organisms to gather evolutionary insights on these phosphoinositide binding domains, followed by an in silico characterization of the FYVE and PHOX gene families in the moss Physcomitrella patens. Phylogenetic analysis showed that PpFYVE proteins can be grouped in 7 subclasses, with an additional subclass whose FYVE domain was lost during evolution to higher plants. On the other hand, PpPHOX proteins are classified into 5 subclasses. Expression analyses based on RNAseq data together with the analysis of cis-acting regulatory elements and transcription factor (TF) binding sites in promoter regions suggest the importance of these proteins in regulating stress responses but mainly developmental processes in P. patens. The results provide valuable information and robust candidate genes for future functional analysis aiming to further explore the role of this signaling pathway mainly during growth and development of tip growing cells and during the transition from 2 to 3D growth. These studies would identify ancestral regulatory players undertaken during plant evolution.
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Affiliation(s)
- Patricia Agudelo-Romero
- The UWA Institute of Agriculture, The University of Western Australia, M082, Perth, 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, M316 Perth, Perth, 6009, Australia
- Telethon Kids Institute, University of Western Australia, Nedlands, WA, Australia
| | - Ana Margarida Fortes
- Faculdade de Ciências, BioISI-Biosystems and Integrative Sciences Institute, Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
| | - Trinidad Suárez
- Cátedra de Fisiología Vegetal, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
- Facultad de Ciencias Químicas, Centro de Investigaciones en Química Biológica de Córdoba, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Hernán Ramiro Lascano
- Cátedra de Fisiología Vegetal, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
- CONICET-Instituto de Fisiología y Recursos Genéticos Vegetales, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (INTA), Córdoba, Argentina
| | - Laura Saavedra
- Cátedra de Fisiología Vegetal, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina.
- Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), CONICET-Universidad Nacional de Córdoba, Córdoba, Argentina.
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62
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Brodribb TJ, Sussmilch F, McAdam SAM. From reproduction to production, stomata are the master regulators. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:756-767. [PMID: 31596990 DOI: 10.1111/tpj.14561] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 09/14/2019] [Accepted: 10/03/2019] [Indexed: 05/22/2023]
Abstract
The best predictor of leaf level photosynthetic rate is the porosity of the leaf surface, as determined by the number and aperture of stomata on the leaf. This remarkable correlation between stomatal porosity (or diffusive conductance to water vapour gs ) and CO2 assimilation rate (A) applies to all major lineages of vascular plants (Figure 1) and is sufficiently predictable that it provides the basis for the model most widely used to predict water and CO2 fluxes from leaves and canopies. Yet the Ball-Berry formulation is only a phenomenological approximation that captures the emergent character of stomatal behaviour. Progressing to a more mechanistic prediction of plant gas exchange is challenging because of the diversity of biological components regulating stomatal action. These processes are the product of more than 400 million years of co-evolution between stomatal, vascular and photosynthetic tissues. Both molecular and structural components link the abiotic world of the whole plant with the turgor pressure of the epidermis and guard cells, which ultimately determine stomatal pore size and porosity to water and CO2 exchange (New Phytol., 168, 2005, 275). In this review we seek to simplify stomatal behaviour by using an evolutionary perspective to understand the principal selective pressures involved in stomatal evolution, thus identifying the primary regulators of stomatal aperture. We start by considering the adaptive process that has locked together the regulation of water and carbon fluxes in vascular plants, finally examining specific evidence for evolution in the proteins responsible for regulating guard cell turgor.
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Affiliation(s)
- Timothy J Brodribb
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, 7001, Australia
| | - Frances Sussmilch
- Institute for Molecular Plant Physiology and Biophysics, University of Wurzburg, Wuerzburg, Bavaria, Germany
| | - Scott A M McAdam
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, USA
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63
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van Dop M, Fiedler M, Mutte S, de Keijzer J, Olijslager L, Albrecht C, Liao CY, Janson ME, Bienz M, Weijers D. DIX Domain Polymerization Drives Assembly of Plant Cell Polarity Complexes. Cell 2020; 180:427-439.e12. [PMID: 32004461 PMCID: PMC7042713 DOI: 10.1016/j.cell.2020.01.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 10/18/2019] [Accepted: 01/06/2020] [Indexed: 11/28/2022]
Abstract
Cell polarity is fundamental for tissue morphogenesis in multicellular organisms. Plants and animals evolved multicellularity independently, and it is unknown whether their polarity systems are derived from a single-celled ancestor. Planar polarity in animals is conferred by Wnt signaling, an ancient signaling pathway transduced by Dishevelled, which assembles signalosomes by dynamic head-to-tail DIX domain polymerization. In contrast, polarity-determining pathways in plants are elusive. We recently discovered Arabidopsis SOSEKI proteins, which exhibit polar localization throughout development. Here, we identify SOSEKI as ancient polar proteins across land plants. Concentration-dependent polymerization via a bona fide DIX domain allows these to recruit ANGUSTIFOLIA to polar sites, similar to the polymerization-dependent recruitment of signaling effectors by Dishevelled. Cross-kingdom domain swaps reveal functional equivalence of animal and plant DIX domains. We trace DIX domains to unicellular eukaryotes and thus show that DIX-dependent polymerization is an ancient mechanism conserved between kingdoms and central to polarity proteins. SOSEKI proteins are deeply conserved polar proteins in land plants A DIX domain mediates polymerization and polarization of SOSEKI proteins SOSEKI polymerization allows polar recruitment of an effector protein DIX-dependent polymerization is shared between animal and plant polarity proteins
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Affiliation(s)
- Maritza van Dop
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, Wageningen, the Netherlands
| | - Marc Fiedler
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Sumanth Mutte
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, Wageningen, the Netherlands
| | - Jeroen de Keijzer
- Laboratory of Cell Biology, Wageningen University, Droevendaalsesteeg 1, Wageningen, the Netherlands
| | - Lisa Olijslager
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, Wageningen, the Netherlands
| | - Catherine Albrecht
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, Wageningen, the Netherlands
| | - Che-Yang Liao
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, Wageningen, the Netherlands
| | - Marcel E Janson
- Laboratory of Cell Biology, Wageningen University, Droevendaalsesteeg 1, Wageningen, the Netherlands
| | - Mariann Bienz
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, Wageningen, the Netherlands.
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64
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Rathgeb U, Chen M, Buron F, Feddermann N, Schorderet M, Raisin A, Häberli GY, Marc-Martin S, Keller J, Delaux PM, Schaefer DG, Reinhardt D. VAPYRIN-like is required for development of the moss Physcomitrella patens. Development 2020; 147:dev.184762. [DOI: 10.1242/dev.184762] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 04/19/2020] [Indexed: 12/28/2022]
Abstract
The VAPYRIN (VPY) gene in Medicago truncatula and Petunia hybrida is required for arbuscular mycorrhizal (AM) symbiosis. The moss Physcomitrella patens has a close homologue (VPY-like, VPYL), although it does not form AM. Here, we explore the phylogeny of VPY and VPYL in land plants, and we study the expression and developmental function of VPYL in P. patens. We show that PpVPYL is expressed primarily in the protonema, the early filamentous stage of moss development, and later in rhizoids arising from the leafy gametophores and in adult phyllids. Knockout mutants have specific phenotypes in branching of the protonema and in cell division of the leaves (phyllids) in gametophores. The mutants are responsive to auxin and strigolactone, which are involved in the regulation of protonemal branching, indicating that the mutants are not affected in hormonal signaling. Taken together, these results suggest that PpVPYL exerts negative regulation of protonemal branching and of cell division in phyllids. We discuss VPY and VPYL phylogeny and function in land plants in the context of AM symbiosis in angiosperms, and of development in the moss.
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Affiliation(s)
- Ursina Rathgeb
- Dept. of Biology, University of Fribourg, Fribourg, Switzerland
| | - Min Chen
- Dept. of Biology, University of Fribourg, Fribourg, Switzerland
| | - Flavien Buron
- Dept. of Biology, University of Fribourg, Fribourg, Switzerland
| | | | | | - Axelle Raisin
- Dept. of Biology, University of Fribourg, Fribourg, Switzerland
| | | | | | - Jean Keller
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, Auzeville, Castanet-Tolosan, France
| | - Pierre-Marc Delaux
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, Auzeville, Castanet-Tolosan, France
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65
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Hazra A, Dasgupta N, Sengupta C, Das S. MIPS: Functional dynamics in evolutionary pathways of plant kingdom. Genomics 2019; 111:1929-1945. [DOI: 10.1016/j.ygeno.2019.01.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 11/22/2018] [Accepted: 01/02/2019] [Indexed: 10/27/2022]
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66
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Artz O, Dickopf S, Ranjan A, Kreiss M, Abraham ET, Boll V, Rensing SA, Hoecker U. Characterization of spa mutants in the moss Physcomitrella provides evidence for functional divergence of SPA genes during the evolution of land plants. THE NEW PHYTOLOGIST 2019; 224:1613-1626. [PMID: 31222750 DOI: 10.1111/nph.16004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 06/10/2019] [Indexed: 06/09/2023]
Abstract
The Arabidopsis COP1/SPA complex is a key repressor of photomorphogenesis that suppresses light signaling in the dark. Both COP1 and SPA proteins are essential components of this complex. Although COP1 also exists in humans, SPA genes are specific to the green lineage. To elucidate the evolution of SPA genes we analyzed SPA functions in the moss Physcomitrella patens by characterizing knockout mutants in the two Physcomitrella SPA genes PpSPAa and PpSPAb. Light-grown PpspaAB double mutants exhibit smaller gametophores than the wild-type. In the dark, PpspaAB mutant gametophores show enhanced continuation of growth but etiolate normally. Gravitropism in the dark is reduced in PpspaAB mutant protonemata. The expression of light-regulated genes is mostly not constitutive in PpspaAB mutants. PpSPA and PpCOP1 interact; PpCOP1 also interacts with the transcription factor PpHY5 and, indeed, PpHY5 is destabilized in dark-grown Physcomitrella. Degradation of PpHY5 in darkness, however, does not require PpSPAa and PpSPAb. The data suggest that COP1/SPA-mediated light signaling is only partially conserved between Arabidopsis and Physcomitrella. Whereas COP1/SPA interaction and HY5 degradation in darkness is conserved, the role of SPA proteins appears to have diverged. PpSPA genes, unlike their Arabidopsis counterparts, are only required to suppress a subset of light responses in darkness.
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Affiliation(s)
- Oliver Artz
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Stephen Dickopf
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Aashish Ranjan
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Melanie Kreiss
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Elena Theres Abraham
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Vanessa Boll
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Ute Hoecker
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
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67
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The DEAD-box RNA helicase eIF4A regulates plant development and interacts with the hnRNP LIF2L1 in Physcomitrella patens. Mol Genet Genomics 2019; 295:373-389. [PMID: 31781862 DOI: 10.1007/s00438-019-01628-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 11/20/2019] [Indexed: 12/26/2022]
Abstract
eIF4A is a RNA-stimulated ATPase and helicase. Besides its key role in regulating cap-dependent translation initiation in eukaryotes, it also performs specific functions in regulating cell cycle progression, plant growth and abiotic stress tolerance. Flowering plants encode three eIF4A paralogues, eIF4A1, eIF4A2 and eIF4A3 that share conserved sequence motifs but differ in functions. To date, however, no information is available on eIF4A in basal land plants. In this study we report that genome of the moss Physcomitrella patens encodes multiple eIF4A genes. The encoded proteins possess the highly conserved motifs characteristic of the DEAD box helicases. Spatial expression analysis shows these genes to be ubiquitously expressed in all tissue types with Pp3c6_1080V3.1 showing high expression in filamentous protonemata. Targeted deletion of conserved core motifs in Pp3c6_1080V3.1 slowed protonemata growth and resulted in dwarfing of leafy gametophores suggesting a role for Pp3c6_1080V3.1 in regulating cell division/elongation. Rapid and strong induction of Pp3c6_1080V3.1 under salt stress and slow recovery of knockout plants upon exposure to high salt further suggest Pp3c6_1080V3.1 to be involved in stress management in P. patens. Protein-protein interaction studies that show Pp3c6_1080V3.1 to interact with the Physcomitrella heterogenous ribonucleoprotein, LIF2L1, a transcriptional regulator of stress-responsive genes in Arabidopsis. The results presented in this study provide insight into evolutionary conserved functions of eIF4A and shed light on the novel link between eIF4A activities and stress mitigation pathways/RNA metabolic processes in P. patens.
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68
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Decker EL, Reski R. Mosses in biotechnology. Curr Opin Biotechnol 2019; 61:21-27. [PMID: 31689614 DOI: 10.1016/j.copbio.2019.09.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/12/2019] [Accepted: 09/25/2019] [Indexed: 11/16/2022]
Abstract
Biotechnological exploitation of mosses has several aspects, for example, the use of moss extracts or the whole plant for diverse industrial applications as well as their employment as production platforms for valuable metabolites or pharmaceutical proteins, especially using the genetically and developmentally best-characterised model moss Physcomitrella patens. Whole moss plants, in particular peat mosses (Sphagnum spec.), are useful for environmental approaches, biomonitoring of environmental pollution and CO2-neutral 'farming' on rewetted bogs to combat climate change. In addition, the lifestyle of mosses suggests the evolution of genes necessary to cope with biotic and abiotic stress situations, which could be applied to crop plants, and their structural features bear an inspiring potential for biomimetics approaches.
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Affiliation(s)
- 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; Signalling Research Centres BIOSS and CIBSS, Schaenzlestr. 18, 79104 Freiburg, Germany; Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
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69
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Hata Y, Naramoto S, Kyozuka J. BLADE-ON-PETIOLE genes are not involved in the transition from protonema to gametophore in the moss Physcomitrella patens. JOURNAL OF PLANT RESEARCH 2019; 132:617-627. [PMID: 31432295 DOI: 10.1007/s10265-019-01132-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Accepted: 08/07/2019] [Indexed: 05/05/2023]
Abstract
The timing of the transition between developmental phases is a critical determinant of plant form. In the moss Physcomitrella patens, the transition from protonema to gametophore is a particularly important step as it results in a change from two-dimensional to three-dimensional growth of the plant body. It is well known that this transition is promoted by cytokinin (CK), however, the underlying mechanisms are poorly understood. Previously, it was reported that P. patens orthologs of BLADE-ON-PETIOLE (BOP) genes (PpBOPs) work downstream of CK to promote the transition to gametophore. To further understand the role of PpBOPs in the control of this transition, we performed functional analyses of PpBOP genes. We simultaneously disrupted the function of all three PpBOP genes in P. patens using CRISPR technology, however, no abnormal phenotypes were observed in the triple mutant during either the gametophytic or the sporophytic growth stages. CK treatment did not alter the phase change in the triple mutant. We conclude that PpBOP genes are unnecessary in the control of P. patens development under normal conditions. We propose that BOP genes are not involved in the control of developmental processes in bryophytes and other basal land plants, but may function in physiological processes such as in the defense response.
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Affiliation(s)
- Yuki Hata
- Tohoku University Graduate School of Life Sciences, 2-1-1, Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Satoshi Naramoto
- Tohoku University Graduate School of Life Sciences, 2-1-1, Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Junko Kyozuka
- Tohoku University Graduate School of Life Sciences, 2-1-1, Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan.
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70
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Gene Expression Maps in Plants: Current State and Prospects. PLANTS 2019; 8:plants8090309. [PMID: 31466308 PMCID: PMC6784182 DOI: 10.3390/plants8090309] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 08/26/2019] [Accepted: 08/26/2019] [Indexed: 12/20/2022]
Abstract
For many years, progress in the identification of gene functions has been based on classical genetic approaches. However, considerable recent omics developments have brought to the fore indirect but high-resolution methods of gene function identification such as transcriptomics, proteomics, and metabolomics. A transcriptome map is a powerful source of functional information and the result of the genome-wide expression analysis of a broad sampling of tissues and/or organs from different developmental stages and/or environmental conditions. In plant science, the application of transcriptome maps extends from the inference of gene regulatory networks to evolutionary studies. However, only some of these data have been integrated into databases, thus enabling analyses to be conducted without raw data; without this integration, extensive data preprocessing is required, which limits data usability. In this review, we summarize the state of plant transcriptome maps, analyze the problems associated with the combined analysis of large-scale data from various studies, and outline possible solutions to these problems.
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71
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A KNOX-Cytokinin Regulatory Module Predates the Origin of Indeterminate Vascular Plants. Curr Biol 2019; 29:2743-2750.e5. [DOI: 10.1016/j.cub.2019.06.083] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 06/10/2019] [Accepted: 06/27/2019] [Indexed: 12/29/2022]
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72
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Liu MM, Wang MM, Yang J, Wen J, Guo PC, Wu YW, Ke YZ, Li PF, Li JN, Du H. Evolutionary and Comparative Expression Analyses of TCP Transcription Factor Gene Family in Land Plants. Int J Mol Sci 2019; 20:E3591. [PMID: 31340456 PMCID: PMC6679135 DOI: 10.3390/ijms20143591] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/15/2019] [Accepted: 07/19/2019] [Indexed: 01/01/2023] Open
Abstract
The plant-specific Teosinte-branched 1/Cycloidea/Proliferating (TCP) transcription factor genes are involved in plants' development, hormonal pathways, and stress response but their evolutionary history is uncertain. The genome-wide analysis performed here for 47 plant species revealed 535 TCP candidates in terrestrial plants and none in aquatic plants, and that TCP family genes originated early in the history of land plants. Phylogenetic analysis divided the candidate genes into Classes I and II, and Class II was further divided into CYCLOIDEA (CYC) and CINCINNATA (CIN) clades; CYC is more recent and originated from CIN in angiosperms. Protein architecture, intron pattern, and sequence characteristics were conserved in each class or clade supporting this classification. The two classes significantly expanded through whole-genome duplication during evolution. Expression analysis revealed the conserved expression of TCP genes from lower to higher plants. The expression patterns of Class I and CIN genes in different stages of the same tissue revealed their function in plant development and their opposite effects in the same biological process. Interaction network analysis showed that TCP proteins tend to form protein complexes, and their interaction networks were conserved during evolution. These results contribute to further functional studies on TCP family genes.
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Affiliation(s)
- Ming-Ming Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Mang-Mang Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Jin Yang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Jing Wen
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Peng-Cheng Guo
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Yun-Wen Wu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Yun-Zhuo Ke
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Peng-Feng Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Jia-Na Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Hai Du
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China.
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73
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Physicochemical modeling of the phytochrome-mediated photothermal sensing. Sci Rep 2019; 9:10485. [PMID: 31324849 PMCID: PMC6642129 DOI: 10.1038/s41598-019-47019-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 07/09/2019] [Indexed: 11/08/2022] Open
Abstract
Light and temperature cues share many common signaling events towards plant photothermal morphogenesis. Particularly, the red (R)/far-red (FR)-absorbing phytochrome photoreceptors also function as temperature sensors, suggesting that light and temperature responses are intimately associated with each other. Here, we present data from physicochemical modeling of temperature sensing and thermomorphogenic patterning of hypocotyl growth, which illustrate that the two seemingly distinct stimulating cues are tightly coupled through physicochemical principles and temperature effects can be described as a function of infra-red (IR) thermal radiation. It is possible that the dark reversion from the FR-absorbing Pfr to the R-absorbing Pr phytochromes is essentially an IR-mediated thermal conversion. We propose that the phytochromes modulate photothermal responses by monitoring R:IR ratios, as they sense R:FR ratios during photomorphogenesis.
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74
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Sussmilch FC, Roelfsema MRG, Hedrich R. On the origins of osmotically driven stomatal movements. THE NEW PHYTOLOGIST 2019; 222:84-90. [PMID: 30444541 DOI: 10.1111/nph.15593] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 10/26/2018] [Indexed: 06/09/2023]
Abstract
Contents Summary 84 I. Introduction 84 II. Stomatal form and biomechanics 85 III. Stomatal function 86 IV. Evolution of guard cell ion channels 87 V. Conclusions 88 Acknowledgements 88 Author contributions 88 References 88 SUMMARY: Stomatal pores with apertures that can be adjusted by changes in guard cell turgor have facilitated plant success in dry environments. We explore their evolutionary origins, considering recent findings from bryophytes. Unlike vascular plant stomata, which close to prevent water loss, bryophyte stomata become locked open to promote spore desiccation. We find that the families of ion channels, known to control stomatal movements in angiosperms, are ancient and represented across extant land plants. However, although angiosperm guard cells express specific ion channel genes, none appear specifically expressed in stomata-bearing moss tissues. Given the evolutionary shift in stomatal function from promotion to prevention of water loss, we postulate that ion channels adopted guard cell-specific functions after the divergence of bryophytes.
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Affiliation(s)
- Frances C Sussmilch
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, D-97082, Würzburg, Germany
| | - M Rob G Roelfsema
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, D-97082, Würzburg, Germany
| | - Rainer Hedrich
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, D-97082, Würzburg, Germany
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75
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Sussmilch FC, Schultz J, Hedrich R, Roelfsema MRG. Acquiring Control: The Evolution of Stomatal Signalling Pathways. TRENDS IN PLANT SCIENCE 2019; 24:342-351. [PMID: 30797685 DOI: 10.1016/j.tplants.2019.01.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 01/02/2019] [Accepted: 01/10/2019] [Indexed: 05/24/2023]
Abstract
In vascular plants, stomata balance two opposing functions: they open to facilitate CO2 uptake and close to prevent excessive water loss. Here, we discuss the evolution of three major signalling pathways that are known to control stomatal movements in angiosperms in response to light, CO2, and abscisic acid (ABA). We examine the evolutionary origins of key signalling genes involved in these pathways, and compare their expression patterns between an angiosperm and moss. We propose that variation in stomatal sensitivity to stimuli between plant groups are rooted in differences in: (i) gene presence/absence, (ii) specificity of gene spatial expression pattern, and (iii) protein characteristics and functional interactions.
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Affiliation(s)
- Frances C Sussmilch
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, D-97082 Würzburg, Germany
| | - Jörg Schultz
- Center for Computational and Theoretical Biology, University of Würzburg, D-97218 Würzburg, Germany
| | - Rainer Hedrich
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, D-97082 Würzburg, Germany
| | - M Rob G Roelfsema
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, D-97082 Würzburg, Germany.
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76
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Klepikova AV, Kulakovskiy IV, Kasianov AS, Logacheva MD, Penin AA. An update to database TraVA: organ-specific cold stress response in Arabidopsis thaliana. BMC PLANT BIOLOGY 2019; 19:49. [PMID: 30813912 PMCID: PMC6393959 DOI: 10.1186/s12870-019-1636-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
BACKGROUND Transcriptome map is a powerful tool for a variety of biological studies; transcriptome maps that include different organs, tissues, cells and stages of development are currently available for at least 30 plants. Some of them include samples treated by environmental or biotic stresses. However, most studies explore only limited set of organs and developmental stages (leaves or seedlings). In order to provide broader view of organ-specific strategies of cold stress response we studied expression changes that follow exposure to cold (+ 4 °C) in different aerial parts of plant: cotyledons, hypocotyl, leaves, young flowers, mature flowers and seeds using RNA-seq. RESULTS The results on differential expression in leaves are congruent with current knowledge on stress response pathways, in particular, the role of CBF genes. In other organs, both essence and dynamics of gene expression changes are different. We show the involvement of genes that are confined to narrow expression patterns in non-stress conditions into stress response. In particular, the genes that control cell wall modification in pollen, are activated in leaves. In seeds, predominant pattern is the change of lipid metabolism. CONCLUSIONS Stress response is highly organ-specific; different pathways are involved in this process in each type of organs. The results were integrated with previously published transcriptome map of Arabidopsis thaliana and used for an update of a public database TraVa: http://travadb.org/browse/Species=AthStress .
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Affiliation(s)
- Anna V. Klepikova
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Bolshoy Karetny per. 19, build.1, Moscow, 127051 Russia
| | - Ivan V. Kulakovskiy
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina 3, Moscow, 119991 Russia
- Institute of Mathematical Problems of Biology RAS - the Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Vitkevicha 1, Pushchino, Moscow Region, 142290 Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, 119991 Moscow, Russia
| | - Artem S. Kasianov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina 3, Moscow, 119991 Russia
| | - Maria D. Logacheva
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Bolshoy Karetny per. 19, build.1, Moscow, 127051 Russia
- Moscow State University, Leninskye gory, build 1, Moscow, 119992 Russia
- Skolkovo Institute of Science and Technology, Nobelya Ulitsa 3, Moscow, 121205 Russia
| | - Aleksey A. Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Bolshoy Karetny per. 19, build.1, Moscow, 127051 Russia
- Moscow State University, Leninskye gory, build 1, Moscow, 119992 Russia
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77
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Wang M, Le Moigne MA, Bertheloot J, Crespel L, Perez-Garcia MD, Ogé L, Demotes-Mainard S, Hamama L, Davière JM, Sakr S. BRANCHED1: A Key Hub of Shoot Branching. FRONTIERS IN PLANT SCIENCE 2019; 10:76. [PMID: 30809235 PMCID: PMC6379311 DOI: 10.3389/fpls.2019.00076] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 01/17/2019] [Indexed: 05/20/2023]
Abstract
Shoot branching is a key process for plant growth and fitness. Newly produced axes result from axillary bud outgrowth, which is at least partly mediated through the regulation of BRANCHED1 gene expression (BRC1/TB1/FC1). BRC1 encodes a pivotal bud-outgrowth-inhibiting transcription factor belonging to the TCP family. As the regulation of BRC1 expression is a hub for many shoot-branching-related mechanisms, it is influenced by endogenous (phytohormones and nutrients) and exogenous (light) inputs, which involve so-far only partly identified molecular networks. This review highlights the central role of BRC1 in shoot branching and its responsiveness to different stimuli, and emphasizes the different knowledge gaps that should be addressed in the near future.
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Affiliation(s)
- Ming Wang
- Institut de Recherche en Horticulture et Semences, Agrocampus-Ouest, INRA, SFR 4207 QUASAV, Université d’Angers, Beaucouzé, France
| | - Marie-Anne Le Moigne
- Institut de Recherche en Horticulture et Semences, Agrocampus-Ouest, INRA, SFR 4207 QUASAV, Université d’Angers, Beaucouzé, France
| | - Jessica Bertheloot
- Institut de Recherche en Horticulture et Semences, Agrocampus-Ouest, INRA, SFR 4207 QUASAV, Université d’Angers, Beaucouzé, France
| | - Laurent Crespel
- Institut de Recherche en Horticulture et Semences, Agrocampus-Ouest, INRA, SFR 4207 QUASAV, Université d’Angers, Beaucouzé, France
| | - Maria-Dolores Perez-Garcia
- Institut de Recherche en Horticulture et Semences, Agrocampus-Ouest, INRA, SFR 4207 QUASAV, Université d’Angers, Beaucouzé, France
| | - Laurent Ogé
- Institut de Recherche en Horticulture et Semences, Agrocampus-Ouest, INRA, SFR 4207 QUASAV, Université d’Angers, Beaucouzé, France
| | - Sabine Demotes-Mainard
- Institut de Recherche en Horticulture et Semences, Agrocampus-Ouest, INRA, SFR 4207 QUASAV, Université d’Angers, Beaucouzé, France
| | - Latifa Hamama
- Institut de Recherche en Horticulture et Semences, Agrocampus-Ouest, INRA, SFR 4207 QUASAV, Université d’Angers, Beaucouzé, France
| | - Jean-Michel Davière
- Institut de Biologie Moléculaire des Plantes, UPR2357, Université de Strasbourg, Strasbourg, France
| | - Soulaiman Sakr
- Institut de Recherche en Horticulture et Semences, Agrocampus-Ouest, INRA, SFR 4207 QUASAV, Université d’Angers, Beaucouzé, France
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78
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Tang H, de Keijzer J, Overdijk EJR, Sweep E, Steentjes M, Vermeer JEM, Janson ME, Ketelaar T. Exocyst subunit Sec6 is positioned by microtubule overlaps in the moss phragmoplast prior to cell plate membrane arrival. J Cell Sci 2019; 132:jcs222430. [PMID: 30635445 DOI: 10.1242/jcs.222430] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 01/02/2019] [Indexed: 12/21/2022] Open
Abstract
During plant cytokinesis a radially expanding membrane-enclosed cell plate is formed from fusing vesicles that compartmentalizes the cell in two. How fusion is spatially restricted to the site of cell plate formation is unknown. Aggregation of cell-plate membrane starts near regions of microtubule overlap within the bipolar phragmoplast apparatus of the moss Physcomitrella patens Since vesicle fusion generally requires coordination of vesicle tethering and subsequent fusion activity, we analyzed the subcellular localization of several subunits of the exocyst, a tethering complex active during plant cytokinesis. We found that the exocyst complex subunit Sec6 but not the Sec3 or Sec5 subunits localized to microtubule overlap regions in advance of cell plate construction in moss. Moreover, Sec6 exhibited a conserved physical interaction with an ortholog of the Sec1/Munc18 protein KEULE, an important regulator for cell-plate membrane vesicle fusion in Arabidopsis Recruitment of the P. patens protein KEULE and vesicles to the early cell plate was delayed upon Sec6 gene silencing. Our findings, thus, suggest that vesicle-vesicle fusion is, in part, enabled by a pool of exocyst subunits at microtubule overlaps, which is recruited independently of vesicle delivery.
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Affiliation(s)
- Han Tang
- Laboratory of Cell Biology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Jeroen de Keijzer
- Laboratory of Cell Biology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Elysa J R Overdijk
- Laboratory of Cell Biology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Els Sweep
- Laboratory of Cell Biology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Maikel Steentjes
- Laboratory of Cell Biology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Joop E M Vermeer
- Laboratory of Cell Biology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, 8008 Zurich, Switzerland
| | - Marcel E Janson
- Laboratory of Cell Biology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Tijs Ketelaar
- Laboratory of Cell Biology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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80
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Sigel EM, Schuettpelz E, Pryer KM, Der JP. Overlapping Patterns of Gene Expression Between Gametophyte and Sporophyte Phases in the Fern Polypodium amorphum (Polypodiales). FRONTIERS IN PLANT SCIENCE 2018; 9:1450. [PMID: 30356815 PMCID: PMC6190754 DOI: 10.3389/fpls.2018.01450] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 09/12/2018] [Indexed: 05/16/2023]
Abstract
Ferns are unique among land plants in having sporophyte and gametophyte phases that are both free living and fully independent. Here, we examine patterns of sporophytic and gametophytic gene expression in the fern Polypodium amorphum, a member of the homosporous polypod lineage that comprises 80% of extant fern diversity, to assess how expression of a common genome is partitioned between two morphologically, ecologically, and nutritionally independent phases. Using RNA-sequencing, we generated transcriptome profiles for three replicates of paired samples of sporophyte leaf tissue and whole gametophytes to identify genes with significant differences in expression between the two phases. We found a nearly 90% overlap in the identity and expression levels of the genes expressed in both sporophytes and gametophytes, with less than 3% of genes uniquely expressed in either phase. We compare our results to those from similar studies to establish how phase-specific gene expression varies among major land plant lineages. Notably, despite having greater similarity in the identity of gene families shared between P. amorphum and angiosperms, P. amorphum has phase-specific gene expression profiles that are more like bryophytes and lycophytes than seed plants. Our findings suggest that shared patterns of phase-specific gene expression among seed-free plants likely reflect having relatively large, photosynthetic gametophytes (compared to the gametophytes of seed plants that are highly reduced). Phylogenetic analyses were used to further investigate the evolution of phase-specific expression for the phototropin, terpene synthase, and MADS-box gene families.
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Affiliation(s)
- Erin M. Sigel
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA, United States
| | - Eric Schuettpelz
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | | | - Joshua P. Der
- Department of Biological Science, California State University Fullerton, Fullerton, CA, United States
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81
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Reski R, Bae H, Simonsen HT. Physcomitrella patens, a versatile synthetic biology chassis. PLANT CELL REPORTS 2018; 37:1409-1417. [PMID: 29797047 DOI: 10.1007/s00299-018-2293-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 05/11/2018] [Indexed: 05/21/2023]
Abstract
During three decades the moss Physcomitrella patens has been developed to a superb green cell factory with the first commercial products on the market. In the past three decades the moss P. patens has been developed from an obscure bryophyte to a model organism in basic biology, biotechnology, and synthetic biology. Some of the key features of this system include a wide range of Omics technologies, precise genome-engineering via homologous recombination with yeast-like efficiency, a certified good-manufacturing-practice production in bioreactors, successful upscaling to 500 L wave reactors, excellent homogeneity of protein products, superb product stability from batch-to-batch, and a reliable procedure for cryopreservation of cell lines in a master cell bank. About a dozen human proteins are being produced in P. patens as potential biopharmaceuticals, some of them are not only similar to their animal-produced counterparts, but are real biobetters with superior performance. A moss-made pharmaceutical successfully passed phase 1 clinical trials, a fragrant moss, and a cosmetic moss-product is already on the market, highlighting the economic potential of this synthetic biology chassis. Here, we focus on the features of mosses as versatile cell factories for synthetic biology and their impact on metabolic engineering.
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Affiliation(s)
- Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany.
- BIOSS, Centre for Biological Signalling Studies, 79104, Freiburg, Germany.
| | - Hansol Bae
- Mosspiration Biotech IVS, 2970, Hørsholm, Denmark
| | - Henrik Toft Simonsen
- Mosspiration Biotech IVS, 2970, Hørsholm, Denmark
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark
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82
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Wilhelmsson PKI, Mühlich C, Ullrich KK, Rensing SA. Comprehensive Genome-Wide Classification Reveals That Many Plant-Specific Transcription Factors Evolved in Streptophyte Algae. Genome Biol Evol 2018; 9:3384-3397. [PMID: 29216360 PMCID: PMC5737466 DOI: 10.1093/gbe/evx258] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2017] [Indexed: 02/07/2023] Open
Abstract
Plant genomes encode many lineage-specific, unique transcription factors. Expansion of such gene families has been previously found to coincide with the evolution of morphological complexity, although comparative analyses have been hampered by severe sampling bias. Here, we make use of the recently increased availability of plant genomes. We have updated and expanded previous rule sets for domain-based classification of transcription associated proteins (TAPs), comprising transcription factors and transcriptional regulators. The genome-wide annotation of these protein families has been analyzed and made available via the novel TAPscan web interface. We find that many TAP families previously thought to be specific for land plants actually evolved in streptophyte (charophyte) algae; 26 out of 36 TAP family gains are inferred to have occurred in the common ancestor of the Streptophyta (uniting the land plants—Embryophyta—with their closest algal relatives). In contrast, expansions of TAP families were found to occur throughout streptophyte evolution. 17 out of 76 expansion events were found to be common to all land plants and thus probably evolved concomitant with the water-to-land-transition.
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Affiliation(s)
| | - Cornelia Mühlich
- Plant Cell Biology, Faculty of Biology, University of Marburg, Germany
| | | | - Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Germany.,BIOSS Center for Biological Signaling Studies, University of Freiburg, Germany
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83
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Dangwal M, Das S. Identification and Analysis of OVATE Family Members from Genome of the Early Land Plants Provide Insights into Evolutionary History of OFP Family and Function. J Mol Evol 2018; 86:511-530. [PMID: 30206666 DOI: 10.1007/s00239-018-9863-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 09/05/2018] [Indexed: 01/11/2023]
Abstract
Mosses, liverworts, hornworts and lycophytes represent transition stages between the aquatic to terrestrial/land plants. Several morphological and adaptive novelties driven by genomic components including emergence and expansion of new or existing gene families have played a critical role during and after the transition, and contributed towards successful colonization of terrestrial ecosystems. It is crucial to decipher the evolutionary transitions and natural selection on the gene structure and function to understand the emergence of phenotypic and adaptive diversity. Plants at the "transition zone", between aquatic and terrestrial ecosystem, are also the most vulnerable because of climate change and may contain clues for successful mitigation of the challenges of climate change. Identification and comparative analyses of such genetic elements and gene families are few in mosses, liverworts, hornworts and lycophytes. Ovate family proteins (OFPs) are plant-specific transcriptional repressors and are acknowledged for their roles in important growth and developmental processes in land plants, and information about the functional aspects of OFPs in early land plants is fragmentary. As a first step towards addressing this gap, a comprehensive in silico analysis was carried out utilizing publicly available genome sequences of Marchantia polymorpha (Mp), Physcomitrella patens (Pp), Selaginella moellendorffii (Sm) and Sphagnum fallax (Sf). Our analysis led to the identification of 4 MpOFPs, 19 PpOFPs, 6 SmOFPs and 3 SfOFPs. Cross-genera analysis revealed a drastic change in the structure and physiochemical properties in OFPs suggesting functional diversification and genomic plasticity during the evolutionary course. Knowledge gained from this comparative analysis will form the framework towards deciphering and dissection of their developmental and adaptive role/s in early land plants and could provide insights into evolutionary strategies adapted by land plants.
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Affiliation(s)
| | - Sandip Das
- Department of Botany, University of Delhi, Delhi, 110007, India.
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84
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Behar H, Graham SW, Brumer H. Comprehensive cross-genome survey and phylogeny of glycoside hydrolase family 16 members reveals the evolutionary origin of EG16 and XTH proteins in plant lineages. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:1114-1128. [PMID: 29932263 DOI: 10.1111/tpj.14004] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 06/07/2018] [Accepted: 06/12/2018] [Indexed: 05/05/2023]
Abstract
Carbohydrate-active enzymes (CAZymes) are central to the biosynthesis and modification of the plant cell wall. An ancient clade of bifunctional plant endo-glucanases (EG16 members) was recently revealed and proposed to represent a transitional group uniting plant xyloglucan endo-transglycosylase/hydrolase (XTH) gene products and bacterial mixed-linkage endo-glucanases in the phylogeny of glycoside hydrolase family 16 (GH16). To gain broader insights into the distribution and frequency of EG16 and other GH16 members in plants, the PHYTOZOME, PLAZA, NCBI and 1000 PLANTS databases were mined to build a comprehensive census among 1289 species, spanning the broad phylogenetic diversity of multiple algae through recent plant lineages. EG16, newly identified EG16-2 and XTH members appeared first in the green algae. Extant EG16 members represent the early adoption of the β-jellyroll protein scaffold from a bacterial or early-lineage eukaryotic GH16 gene, which is characterized by loop deletion and extension of the N terminus (in EG16-2 members) or C terminus (in XTH members). Maximum-likelihood phylogenetic analysis of EG16 and EG16-2 sequences are directly concordant with contemporary estimates of plant evolution. The lack of expansion of EG16 members into multi-gene families across green plants may point to a core metabolic role under tight control, in contrast to XTH genes that have undergone the extensive duplications typical of cell-wall CAZymes. The present census will underpin future studies to elucidate the physiological role of EG16 members across plant species, and serve as roadmap for delineating the closely related EG16 and XTH gene products in bioinformatic analyses of emerging genomes and transcriptomes.
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Affiliation(s)
- Hila Behar
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, V6T 1Z4, BC, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Life Sciences Centre, 2350 Health Sciences Mall, Vancouver, V6T 1Z3, BC, Canada
| | - Sean W Graham
- Department of Botany, University of British Columbia, 3200-6270 University Blvd, Vancouver, V6H 1Z4, BC, Canada
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, V6T 1Z4, BC, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Life Sciences Centre, 2350 Health Sciences Mall, Vancouver, V6T 1Z3, BC, Canada
- Department of Botany, University of British Columbia, 3200-6270 University Blvd, Vancouver, V6H 1Z4, BC, Canada
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, V6T 1Z4, BC, Canada
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85
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Whitewoods CD, Cammarata J, Nemec Venza Z, Sang S, Crook AD, Aoyama T, Wang XY, Waller M, Kamisugi Y, Cuming AC, Szövényi P, Nimchuk ZL, Roeder AHK, Scanlon MJ, Harrison CJ. CLAVATA Was a Genetic Novelty for the Morphological Innovation of 3D Growth in Land Plants. Curr Biol 2018; 28:2365-2376.e5. [PMID: 30033333 PMCID: PMC6089843 DOI: 10.1016/j.cub.2018.05.068] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 05/10/2018] [Accepted: 05/23/2018] [Indexed: 11/24/2022]
Abstract
How genes shape diverse plant and animal body forms is a key question in biology. Unlike animal cells, plant cells are confined by rigid cell walls, and cell division plane orientation and growth rather than cell movement determine overall body form. The emergence of plants on land coincided with a new capacity to rotate stem cell divisions through multiple planes, and this enabled three-dimensional (3D) forms to arise from ancestral forms constrained to 2D growth. The genes involved in this evolutionary innovation are largely unknown. The evolution of 3D growth is recapitulated during the development of modern mosses when leafy shoots arise from a filamentous (2D) precursor tissue. Here, we show that a conserved, CLAVATA peptide and receptor-like kinase pathway originated with land plants and orients stem cell division planes during the transition from 2D to 3D growth in a moss, Physcomitrella. We find that this newly identified role for CLAVATA in regulating cell division plane orientation is shared between Physcomitrella and Arabidopsis. We report that roles for CLAVATA in regulating cell proliferation and cell fate are also shared and that CLAVATA-like peptides act via conserved receptor components in Physcomitrella. Our results suggest that CLAVATA was a genetic novelty enabling the morphological innovation of 3D growth in land plants.
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Affiliation(s)
- Chris D Whitewoods
- Plant Sciences Department, Cambridge University, Downing Street, Cambridge CB2 3EA, UK
| | - Joseph Cammarata
- Plant Sciences Department, Cambridge University, Downing Street, Cambridge CB2 3EA, UK; Plant Biology Section, School of Integrative Plant Science, Cornell University, Tower Road, Ithaca, NY 14853, USA; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Zoe Nemec Venza
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Stephanie Sang
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Ashley D Crook
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tsuyoshi Aoyama
- Plant Sciences Department, Cambridge University, Downing Street, Cambridge CB2 3EA, UK; School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Xiao Y Wang
- Plant Sciences Department, Cambridge University, Downing Street, Cambridge CB2 3EA, UK
| | - Manuel Waller
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Yasuko Kamisugi
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Andrew C Cuming
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Zachary L Nimchuk
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Adrienne H K Roeder
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Tower Road, Ithaca, NY 14853, USA; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Michael J Scanlon
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Tower Road, Ithaca, NY 14853, USA
| | - C Jill Harrison
- Plant Sciences Department, Cambridge University, Downing Street, Cambridge CB2 3EA, UK; School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK.
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Furumizu C, Hirakawa Y, Bowman JL, Sawa S. 3D Body Evolution: Adding a New Dimension to Colonize the Land. Curr Biol 2018; 28:R838-R840. [DOI: 10.1016/j.cub.2018.06.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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87
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Özdemir B, Asgharzadeh P, Birkhold AI, Mueller SJ, Röhrle O, Reski R. Cytological analysis and structural quantification of FtsZ1-2 and FtsZ2-1 network characteristics in Physcomitrella patens. Sci Rep 2018; 8:11165. [PMID: 30042487 PMCID: PMC6057934 DOI: 10.1038/s41598-018-29284-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 07/05/2018] [Indexed: 11/24/2022] Open
Abstract
Although the concept of the cytoskeleton as a cell-shape-determining scaffold is well established, it remains enigmatic how eukaryotic organelles adopt and maintain a specific morphology. The Filamentous Temperature Sensitive Z (FtsZ) protein family, an ancient tubulin, generates complex polymer networks, with striking similarity to the cytoskeleton, in the chloroplasts of the moss Physcomitrella patens. Certain members of this protein family are essential for structural integrity and shaping of chloroplasts, while others are not, illustrating the functional diversity within the FtsZ protein family. Here, we apply a combination of confocal laser scanning microscopy and a self-developed semi-automatic computational image analysis method for the quantitative characterisation and comparison of network morphologies and connectivity features for two selected, functionally dissimilar FtsZ isoforms, FtsZ1-2 and FtsZ2-1. We show that FtsZ1-2 and FtsZ2-1 networks are significantly different for 8 out of 25 structural descriptors. Therefore, our results demonstrate that different FtsZ isoforms are capable of generating polymer networks with distinctive morphological and connectivity features which might be linked to the functional differences between the two isoforms. To our knowledge, this is the first study to employ computational algorithms in the quantitative comparison of different classes of protein networks in living cells.
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Affiliation(s)
- Bugra Özdemir
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Pouyan Asgharzadeh
- Institute of Applied Mechanics, University of Stuttgart, Pfaffenwaldring 7, 70569, Stuttgart, Germany
- Stuttgart Center for Simulation Science (SimTech), University of Stuttgart, Pfaffenwaldring 5a, 70569, Stuttgart, Germany
| | - Annette I Birkhold
- Institute of Applied Mechanics, University of Stuttgart, Pfaffenwaldring 7, 70569, Stuttgart, Germany
| | - Stefanie J Mueller
- INRES - Chemical Signalling, University of Bonn, Friedrich-Ebert-Allee 144, 53113, Bonn, Germany
| | - Oliver Röhrle
- Institute of Applied Mechanics, University of Stuttgart, Pfaffenwaldring 7, 70569, Stuttgart, Germany.
- Stuttgart Center for Simulation Science (SimTech), University of Stuttgart, Pfaffenwaldring 5a, 70569, Stuttgart, Germany.
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany.
- BIOSS - Centre for Biological Signalling Research, University of Freiburg, Schaenzlestr. 18, 79104, Freiburg, Germany.
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, 79110, Freiburg, Germany.
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88
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Lopez-Obando M, de Villiers R, Hoffmann B, Ma L, de Saint Germain A, Kossmann J, Coudert Y, Harrison CJ, Rameau C, Hills P, Bonhomme S. Physcomitrella patens MAX2 characterization suggests an ancient role for this F-box protein in photomorphogenesis rather than strigolactone signalling. THE NEW PHYTOLOGIST 2018; 219:743-756. [PMID: 29781136 DOI: 10.1111/nph.15214] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 04/07/2018] [Indexed: 05/15/2023]
Abstract
Strigolactones (SLs) are key hormonal regulators of flowering plant development and are widely distributed amongst streptophytes. In Arabidopsis, SLs signal via the F-box protein MORE AXILLARY GROWTH2 (MAX2), affecting multiple aspects of development including shoot branching, root architecture and drought tolerance. Previous characterization of a Physcomitrella patens moss mutant with defective SL synthesis supports an ancient role for SLs in land plants, but the origin and evolution of signalling pathway components are unknown. Here we investigate the function of a moss homologue of MAX2, PpMAX2, and characterize its role in SL signalling pathway evolution by genetic analysis. We report that the moss Ppmax2 mutant shows very distinct phenotypes from the moss SL-deficient mutant. In addition, the Ppmax2 mutant remains sensitive to SLs, showing a clear transcriptional SL response in dark conditions, and the response to red light is also altered. These data suggest divergent evolutionary trajectories for SL signalling pathway evolution in mosses and vascular plants. In P. patens, the primary roles for MAX2 are in photomorphogenesis and moss early development rather than in SL response, which may require other, as yet unidentified, factors.
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Affiliation(s)
- Mauricio Lopez-Obando
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France
| | - Ruan de Villiers
- Institute for Plant Biotechnology, Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Beate Hoffmann
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France
| | - Linnan Ma
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France
| | - Alexandre de Saint Germain
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France
| | - Jens Kossmann
- Institute for Plant Biotechnology, Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Yoan Coudert
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS, INRA, Lyon, 69364, France
| | - C Jill Harrison
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Catherine Rameau
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France
| | - Paul Hills
- Institute for Plant Biotechnology, Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Sandrine Bonhomme
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France
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89
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Perroud PF, Haas FB, Hiss M, Ullrich KK, Alboresi A, Amirebrahimi M, Barry K, Bassi R, Bonhomme S, Chen H, Coates JC, Fujita T, Guyon-Debast A, Lang D, Lin J, Lipzen A, Nogué F, Oliver MJ, Ponce de León I, Quatrano RS, Rameau C, Reiss B, Reski R, Ricca M, Saidi Y, Sun N, Szövényi P, Sreedasyam A, Grimwood J, Stacey G, Schmutz J, Rensing SA. The Physcomitrella patens gene atlas project: large-scale RNA-seq based expression data. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:168-182. [PMID: 29681058 DOI: 10.1111/tpj.13940] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 04/02/2018] [Accepted: 04/05/2018] [Indexed: 05/08/2023]
Abstract
High-throughput RNA sequencing (RNA-seq) has recently become the method of choice to define and analyze transcriptomes. For the model moss Physcomitrella patens, although this method has been used to help analyze specific perturbations, no overall reference dataset has yet been established. In the framework of the Gene Atlas project, the Joint Genome Institute selected P. patens as a flagship genome, opening the way to generate the first comprehensive transcriptome dataset for this moss. The first round of sequencing described here is composed of 99 independent libraries spanning 34 different developmental stages and conditions. Upon dataset quality control and processing through read mapping, 28 509 of the 34 361 v3.3 gene models (83%) were detected to be expressed across the samples. Differentially expressed genes (DEGs) were calculated across the dataset to permit perturbation comparisons between conditions. The analysis of the three most distinct and abundant P. patens growth stages - protonema, gametophore and sporophyte - allowed us to define both general transcriptional patterns and stage-specific transcripts. As an example of variation of physico-chemical growth conditions, we detail here the impact of ammonium supplementation under standard growth conditions on the protonemal transcriptome. Finally, the cooperative nature of this project allowed us to analyze inter-laboratory variation, as 13 different laboratories around the world provided samples. We compare differences in the replication of experiments in a single laboratory and between different laboratories.
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Affiliation(s)
- Pierre-François Perroud
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Fabian B Haas
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Manuel Hiss
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Kristian K Ullrich
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Alessandro Alboresi
- Dipartimento di Biotecnologie, Università di Verona, Cà Vignal 1, Strada Le Grazie 15, 37134, Verona, Italy
| | - Mojgan Amirebrahimi
- US Department of Energy (DOE) Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Kerrie Barry
- US Department of Energy (DOE) Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Roberto Bassi
- Dipartimento di Biotecnologie, Università di Verona, Cà Vignal 1, Strada Le Grazie 15, 37134, Verona, Italy
| | - Sandrine Bonhomme
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Route de St-Cyr RD10, 78026, Versailles Cedex, France
| | - Haodong Chen
- School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Juliet C Coates
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Tomomichi Fujita
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - Anouchka Guyon-Debast
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Route de St-Cyr RD10, 78026, Versailles Cedex, France
| | - Daniel Lang
- Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Junyan Lin
- US Department of Energy (DOE) Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Anna Lipzen
- US Department of Energy (DOE) Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Fabien Nogué
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Route de St-Cyr RD10, 78026, Versailles Cedex, France
| | - Melvin J Oliver
- USDA-ARS-MWA, Plant Genetics Research Unit, University of Missouri, Columbia, MO, 652117, USA
| | - Inés Ponce de León
- Department of Molecular Biology, Clemente Estable Biological Research Institute, Avenida Italia 3318, CP 11600, Montevideo, Uruguay
| | - Ralph S Quatrano
- Department of Biology, Washington University in St Louis, One Brookings Drive, St Louis, MO, 63130, USA
| | - Catherine Rameau
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Route de St-Cyr RD10, 78026, Versailles Cedex, France
| | - Bernd Reiss
- Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829, Köln, Germany
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Mariana Ricca
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstr. 107, 8008 Zürich, Switzerland
| | - Younousse Saidi
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Ning Sun
- School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstr. 107, 8008 Zürich, Switzerland
| | - Avinash Sreedasyam
- HudsonAlpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL, 35806, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL, 35806, USA
| | - Gary Stacey
- Divisions of Plant Science and Biochemistry, National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA
| | - Jeremy Schmutz
- US Department of Energy (DOE) Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
- HudsonAlpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL, 35806, USA
| | - Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
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90
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Song CB, Shan W, Yang YY, Tan XL, Fan ZQ, Chen JY, Lu WJ, Kuang JF. Heterodimerization of MaTCP proteins modulates the transcription of MaXTH10/11 genes during banana fruit ripening. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2018; 1861:613-622. [PMID: 29935343 DOI: 10.1016/j.bbagrm.2018.06.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 06/10/2018] [Accepted: 06/11/2018] [Indexed: 12/14/2022]
Abstract
The biological processes involved in banana fruit ripening are extremely complex and modulated by a number of genes such as transcription factors (TFs). Although TFs like MADS, ERF and NAC are implicated in controlling banana ripening, little is known about other TFs such as TCP in this process. In this work, 25 MaTCPs named MaTCP1 to MaTCP25 were characterized from our previously reported transcriptomes related to banana ripening. Expression analysis revealed that these MaTCPs displayed differential expression patterns during the progression of banana ripening. Particularly, MaTCP5, MaTCP19 and MaTCP20 were ethylene-inducible and nuclear-localized, with MaTCP5 and MaTCP20 acting as transcriptional activators while MaTCP19 being a transcriptional inhibitor. Moreover, MaTCP5 and MaTCP20 promoted the transcription of MaXTH10/11 that may play a role in fruit softening during banana ripening, whereas MaTCP19 repressed their transcription, by directly binding to their promoters. Importantly, protein-protein interaction assays demonstrated that MaTCP20 physically interacts with MaTCP5 and MaTCP19 to form heterodimers in vitro and in vivo, and these protein complexes affects their transcriptional activities in regulating the target genes. Taken together, our results provide an overview of the interactions between MaTCPs in controlling the ripening-associated genes and lay a foundation for further investigation of MaTCP gene family in regulating banana fruit ripening.
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Affiliation(s)
- Chun-Bo Song
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, PR China
| | - Wei Shan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, PR China
| | - Ying-Ying Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, PR China
| | - Xiao-Li Tan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, PR China
| | - Zhong-Qi Fan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, PR China
| | - Jian-Ye Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, PR China
| | - Wang-Jin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, PR China
| | - Jian-Fei Kuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, PR China.
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91
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Feng ZJ, Xu SC, Liu N, Zhang GW, Hu QZ, Gong YM. Soybean TCP transcription factors: Evolution, classification, protein interaction and stress and hormone responsiveness. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 127:129-142. [PMID: 29579640 DOI: 10.1016/j.plaphy.2018.03.020] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 03/06/2018] [Accepted: 03/19/2018] [Indexed: 05/01/2023]
Abstract
TEOSINTE-BRANCHED1/CYCLOIDEA/PCF (TCP) transcription factors, a family of plant-specific proteins, play crucial roles in plant growth and development and stress response. However, systematical information is unknown regarding the TCP gene family in soybean. In the present study, a total of 54 GmTCPs were identified in soybean, which were grouped into 11 groups with the typical TCP conserved domains. Phylogenetic relationship, protein motif and gene structure analyses distinguished the GmTCPs into two homology classes: Class I and Class II. Class II was then differentiated into two subclasses: CIN and CYC/TB1. Unique cis-element number and composition existed in the promoter regions which might be involved in the gene transcriptional regulation of different GmTCPs. Tissue expression analysis demonstrated the diverse spatiotemporal expression profiles of GmTCPs. Furthermore, the interaction protein of one previously functionally unknown TCP protein-GmTCP8 was investigated. Yeast two-hybrid assay showed the interaction between GmTCP8 and an abscisic acid receptor (GmPYL10). QRT-PCR assays indicated the distinct expression profiles of GmTCPs in response to abiotic stresses (heat, drought and salt) and stress-related signals (abscisic acid, brassinolide, salicylicacid and methyl jasmonate). These results will facilitate to uncover the possible roles of GmTCPs under abiotic stress and hormone signal responses in soybean.
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Affiliation(s)
- Zhi-Juan Feng
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310000, China.
| | - Sheng-Chun Xu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310000, China.
| | - Na Liu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310000, China.
| | - Gu-Wen Zhang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310000, China.
| | - Qi-Zan Hu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310000, China.
| | - Ya-Ming Gong
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310000, China.
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92
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Ding X, Pervere LM, Bascom C, Bibeau JP, Khurana S, Butt AM, Orr RG, Flaherty PJ, Bezanilla M, Vidali L. Conditional genetic screen in Physcomitrella patens reveals a novel microtubule depolymerizing-end-tracking protein. PLoS Genet 2018; 14:e1007221. [PMID: 29746462 PMCID: PMC5944918 DOI: 10.1371/journal.pgen.1007221] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 01/24/2018] [Indexed: 11/19/2022] Open
Abstract
Our ability to identify genes that participate in cell growth and division is limited because their loss often leads to lethality. A solution to this is to isolate conditional mutants where the phenotype is visible under restrictive conditions. Here, we capitalize on the haploid growth-phase of the moss Physcomitrella patens to identify conditional loss-of-growth (CLoG) mutants with impaired growth at high temperature. We used whole-genome sequencing of pooled segregants to pinpoint the lesion of one of these mutants (clog1) and validated the identified mutation by rescuing the conditional phenotype by homologous recombination. We found that CLoG1 is a novel and ancient gene conserved in plants. At the restrictive temperature, clog1 plants have smaller cells but can complete cell division, indicating an important role of CLoG1 in cell growth, but not an essential role in cell division. Fluorescent protein fusions of CLoG1 indicate it is localized to microtubules with a bias towards depolymerizing microtubule ends. Silencing CLoG1 decreases microtubule dynamics, suggesting that CLoG1 plays a critical role in regulating microtubule dynamics. By discovering a novel gene critical for plant growth, our work demonstrates that P. patens is an excellent genetic system to study genes with a fundamental role in plant cell growth.
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Affiliation(s)
- Xinxin Ding
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA
| | - Leah M. Pervere
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA
| | - Carl Bascom
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA
- Department of Biological Sciences, Dartmouth College, Hanover, NH
| | - Jeffrey P. Bibeau
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA
| | - Sakshi Khurana
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA
| | - Allison M. Butt
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA
| | - Robert G. Orr
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA
| | - Patrick J. Flaherty
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA
- Department of Mathematics and Statistics, University of Massachusetts, Amherst, MA
- Department of Biomedical Engineering, Worcester Polytechnic Institute, Worcester, MA
| | | | - Luis Vidali
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA
- * E-mail:
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93
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Toplak M, Wiedemann G, Ulićević J, Daniel B, Hoernstein SNW, Kothe J, Niederhauser J, Reski R, Winkler A, Macheroux P. The single berberine bridge enzyme homolog of Physcomitrella patens is a cellobiose oxidase. FEBS J 2018; 285:1923-1943. [PMID: 29633551 PMCID: PMC6001459 DOI: 10.1111/febs.14458] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 03/17/2018] [Accepted: 03/29/2018] [Indexed: 11/28/2022]
Abstract
The berberine bridge enzyme from the California poppy Eschscholzia californica (EcBBE) catalyzes the oxidative cyclization of (S)‐reticuline to (S)‐scoulerine, that is, the formation of the berberine bridge in the biosynthesis of benzylisoquinoline alkaloids. Interestingly, a large number of BBE‐like genes have been identified in plants that lack alkaloid biosynthesis. This finding raised the question of the primordial role of BBE in the plant kingdom, which prompted us to investigate the closest relative of EcBBE in Physcomitrella patens (PpBBE1), the most basal plant harboring a BBE‐like gene. Here, we report the biochemical, structural, and in vivo characterization of PpBBE1. Our studies revealed that PpBBE1 is structurally and biochemically very similar to EcBBE. In contrast to EcBBE, we found that PpBBE1 catalyzes the oxidation of the disaccharide cellobiose to the corresponding lactone, that is, PpBBE1 is a cellobiose oxidase. The enzymatic reaction mechanism was characterized by a structure‐guided mutagenesis approach that enabled us to assign a catalytic role to amino acid residues in the active site of PpBBE1. In vivo experiments revealed the highest level of PpBBE1 expression in chloronema, the earliest stage of the plant's life cycle, where carbon metabolism is strongly upregulated. It was also shown that the enzyme is secreted to the extracellular space, where it may be involved in later steps of cellulose degradation, thereby allowing the moss to make use of cellulose for energy production. Overall, our results suggest that the primordial role of BBE‐like enzymes in plants revolved around primary metabolic reactions in carbohydrate utilization. Database Structural data are available in the PDB under the accession numbers 6EO4 and 6EO5.
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Affiliation(s)
- Marina Toplak
- Institute of Biochemistry, Graz University of Technology, Austria
| | - Gertrud Wiedemann
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Germany
| | - Jelena Ulićević
- Institute of Biochemistry, Graz University of Technology, Austria
| | - Bastian Daniel
- Institute of Biochemistry, Graz University of Technology, Austria
| | | | - Jennifer Kothe
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Germany
| | | | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany
| | - Andreas Winkler
- Institute of Biochemistry, Graz University of Technology, Austria
| | - Peter Macheroux
- Institute of Biochemistry, Graz University of Technology, Austria
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94
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Guan Y, Liu L, Wang Q, Zhao J, Li P, Hu J, Yang Z, Running MP, Sun H, Huang J. Gene refashioning through innovative shifting of reading frames in mosses. Nat Commun 2018; 9:1555. [PMID: 29674719 PMCID: PMC5908804 DOI: 10.1038/s41467-018-04025-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 03/28/2018] [Indexed: 12/20/2022] Open
Abstract
Early-diverging land plants such as mosses are known for their outstanding abilities to grow in various terrestrial habitats, incorporating tremendous structural and physiological innovations, as well as many lineage-specific genes. How these genes and functional innovations evolved remains unclear. In this study, we show that a dual-coding gene YAN/AltYAN in the moss Physcomitrella patens evolved from a pre-existing hemerythrin gene. Experimental evidence indicates that YAN/AltYAN is involved in fatty acid and lipid metabolism, as well as oil body and wax formation. Strikingly, both the recently evolved dual-coding YAN/AltYAN and the pre-existing hemerythrin gene might have similar physiological effects on oil body biogenesis and dehydration resistance. These findings bear important implications in understanding the mechanisms of gene origination and the strategies of plants to fine-tune their adaptation to various habitats. Extant representatives of the earliest land plant lineages adapt to various terrestrial habitats with structural and physiological innovations. Here the authors show a dual-coding gene in the moss Physcomitrella patens evolved from a hemerythrin gene, with effects on oil body biogenesis and dehydration resistance.
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Affiliation(s)
- Yanlong Guan
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, China
| | - Li Liu
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, China
| | - Qia Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, China
| | - Jinjie Zhao
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, China
| | - Ping Li
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Jinyong Hu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, China
| | - Zefeng Yang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, 225009, Yangzhou, China
| | - Mark P Running
- Department of Biology, University of Louisville, Louisville, KY, 40292, USA
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, China
| | - Jinling Huang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, China. .,Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, 475001, Kaifeng, China. .,Department of Biology, East Carolina University, Greenville, NC, 27858, USA.
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95
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Simultaneous imaging and functional studies reveal a tight correlation between calcium and actin networks. Proc Natl Acad Sci U S A 2018; 115:E2869-E2878. [PMID: 29507239 DOI: 10.1073/pnas.1711037115] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Tip-growing cells elongate in a highly polarized manner via focused secretion of flexible cell-wall material. Calcium has been implicated as a vital factor in regulating the deposition of cell-wall material. However, deciphering the molecular and mechanistic calcium targets in vivo has remained challenging. Here, we investigated intracellular calcium dynamics in the moss Physcomitrella patens, which provides a system with an abundant source of genetically identical tip-growing cells, excellent cytology, and a large molecular genetic tool kit. To visualize calcium we used a genetically encoded cytosolic FRET probe, revealing a fluctuating tipward gradient with a complex oscillatory profile. Wavelet analysis coupled with a signal-sifting algorithm enabled the quantitative comparison of the calcium behavior in cells where growth was inhibited mechanically, pharmacologically, or genetically. We found that cells with suppressed growth have calcium oscillatory profiles with longer frequencies, suggesting that there is a feedback between the calcium gradient and growth. To investigate the mechanistic basis for this feedback we simultaneously imaged cytosolic calcium and actin, which has been shown to be essential for tip growth. We found that high cytosolic calcium promotes disassembly of a tip-focused actin spot, while low calcium promotes assembly. In support of this, abolishing the calcium gradient resulted in dramatic actin accumulation at the tip. Together these data demonstrate that tipward calcium is quantitatively linked to actin accumulation in vivo and that the moss P. patens provides a powerful system to uncover mechanistic links between calcium, actin, and growth.
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96
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Harrison CJ, Morris JL. The origin and early evolution of vascular plant shoots and leaves. Philos Trans R Soc Lond B Biol Sci 2018; 373:20160496. [PMID: 29254961 PMCID: PMC5745332 DOI: 10.1098/rstb.2016.0496] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/11/2017] [Indexed: 12/22/2022] Open
Abstract
The morphology of plant fossils from the Rhynie chert has generated longstanding questions about vascular plant shoot and leaf evolution, for instance, which morphologies were ancestral within land plants, when did vascular plants first arise and did leaves have multiple evolutionary origins? Recent advances combining insights from molecular phylogeny, palaeobotany and evo-devo research address these questions and suggest the sequence of morphological innovation during vascular plant shoot and leaf evolution. The evidence pinpoints testable developmental and genetic hypotheses relating to the origin of branching and indeterminate shoot architectures prior to the evolution of leaves, and demonstrates underestimation of polyphyly in the evolution of leaves from branching forms in 'telome theory' hypotheses of leaf evolution. This review discusses fossil, developmental and genetic evidence relating to the evolution of vascular plant shoots and leaves in a phylogenetic framework.This article is part of a discussion meeting issue 'The Rhynie cherts: our earliest terrestrial ecosystem revisited'.
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Affiliation(s)
- C Jill Harrison
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Jennifer L Morris
- School of Earth Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
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97
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Lang D, Ullrich KK, Murat F, Fuchs J, Jenkins J, Haas FB, Piednoel M, Gundlach H, Van Bel M, Meyberg R, Vives C, Morata J, Symeonidi A, Hiss M, Muchero W, Kamisugi Y, Saleh O, Blanc G, Decker EL, van Gessel N, Grimwood J, Hayes RD, Graham SW, Gunter LE, McDaniel SF, Hoernstein SNW, Larsson A, Li FW, Perroud PF, Phillips J, Ranjan P, Rokshar DS, Rothfels CJ, Schneider L, Shu S, Stevenson DW, Thümmler F, Tillich M, Villarreal Aguilar JC, Widiez T, Wong GKS, Wymore A, Zhang Y, Zimmer AD, Quatrano RS, Mayer KFX, Goodstein D, Casacuberta JM, Vandepoele K, Reski R, Cuming AC, Tuskan GA, Maumus F, Salse J, Schmutz J, Rensing SA. The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:515-533. [PMID: 29237241 DOI: 10.1111/tpj.13801] [Citation(s) in RCA: 253] [Impact Index Per Article: 42.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 11/20/2017] [Accepted: 11/24/2017] [Indexed: 05/18/2023]
Abstract
The draft genome of the moss model, Physcomitrella patens, comprised approximately 2000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome-scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle. Unlike in flowering plant genomes, gene- and TE-rich regions show an overall even distribution along the chromosomes. However, the chromosomes are mono-centric with peaks of a class of Copia elements potentially coinciding with centromeres. Gene body methylation is evident in 5.7% of the protein-coding genes, typically coinciding with low GC and low expression. Some giant virus insertions are transcriptionally active and might protect gametes from viral infection via siRNA mediated silencing. Structure-based detection methods show that the genome evolved via two rounds of whole genome duplications (WGDs), apparently common in mosses but not in liverworts and hornworts. Several hundred genes are present in colinear regions conserved since the last common ancestor of plants. These syntenic regions are enriched for functions related to plant-specific cell growth and tissue organization. The P. patens genome lacks the TE-rich pericentromeric and gene-rich distal regions typical for most flowering plant genomes. More non-seed plant genomes are needed to unravel how plant genomes evolve, and to understand whether the P. patens genome structure is typical for mosses or bryophytes.
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Affiliation(s)
- Daniel Lang
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
- Plant Genome and Systems Biology, Helmholtz Center Munich, 85764, Neuherberg, Germany
| | - Kristian K Ullrich
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Florent Murat
- INRA, UMR 1095 Genetics, Diversity and Ecophysiology of Cereals (GDEC), 5 Chemin de Beaulieu, 63100, Clermont-Ferrand, France
| | - Jörg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, OT Gatersleben, D-06466, Stadt Seeland, Germany
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Fabian B Haas
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Mathieu Piednoel
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829, Cologne, Germany
| | - Heidrun Gundlach
- Plant Genome and Systems Biology, Helmholtz Center Munich, 85764, Neuherberg, Germany
| | - Michiel Van Bel
- VIB Center for Plant Systems Biology, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Rabea Meyberg
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Cristina Vives
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Bellaterra, Cerdanyola del Vallès, 08193, Barcelona, Spain
| | - Jordi Morata
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Bellaterra, Cerdanyola del Vallès, 08193, Barcelona, Spain
| | | | - Manuel Hiss
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Yasuko Kamisugi
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Omar Saleh
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Guillaume Blanc
- Structural and Genomic Information Laboratory (IGS), Aix-Marseille Université, CNRS, UMR 7256 (IMM FR 3479), Marseille, France
| | - Eva L Decker
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Nico van Gessel
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | | | - Sean W Graham
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Lee E Gunter
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Stuart F McDaniel
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Sebastian N W Hoernstein
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Anders Larsson
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | | | | | - Priya Ranjan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Daniel S Rokshar
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
| | - Carl J Rothfels
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, CA, 94720-2465, USA
| | - Lucas Schneider
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Shengqiang Shu
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | | | - Fritz Thümmler
- Vertis Biotechnologie AG, Lise-Meitner-Str. 30, 85354, Freising, Germany
| | - Michael Tillich
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam-Golm, Germany
| | | | - Thomas Widiez
- Department of Plant Biology, University of Geneva, Sciences III, Geneva 4, CH-1211, Switzerland
- Department of Plant Biology & Pathology Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
- Department of Medicine, University of Alberta, Edmonton, AB, T6G 2E1, Canada
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Ann Wymore
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Yong Zhang
- Shenzhen Huahan Gene Life Technology Co. Ltd, Shenzhen, China
| | - Andreas D Zimmer
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Ralph S Quatrano
- Department of Biology, Washington University, St. Louis, MO, USA
| | - Klaus F X Mayer
- Plant Genome and Systems Biology, Helmholtz Center Munich, 85764, Neuherberg, Germany
- WZW, Technical University Munich, Munich, Germany
| | | | - Josep M Casacuberta
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Bellaterra, Cerdanyola del Vallès, 08193, Barcelona, Spain
| | - Klaas Vandepoele
- VIB Center for Plant Systems Biology, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schaenzlestr. 18, 79104, Freiburg, Germany
| | - Andrew C Cuming
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Florian Maumus
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Jérome Salse
- INRA, UMR 1095 Genetics, Diversity and Ecophysiology of Cereals (GDEC), 5 Chemin de Beaulieu, 63100, Clermont-Ferrand, France
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schaenzlestr. 18, 79104, Freiburg, Germany
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98
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Li L, Aslam M, Rabbi F, Vanderwel MC, Ashton NW, Suh DY. PpORS, an ancient type III polyketide synthase, is required for integrity of leaf cuticle and resistance to dehydration in the moss, Physcomitrella patens. PLANTA 2018; 247:527-541. [PMID: 29119267 DOI: 10.1007/s00425-017-2806-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Accepted: 10/30/2017] [Indexed: 05/06/2023]
Abstract
PpORS knockout mutants produced abnormal leaves with increased dye permeability and were more susceptible to dehydration, consistent with PpORS products being constituents of a cuticular structure in the moss. Type III polyketide synthases (PKSs) have co-evolved with terrestrial plants such that each taxon can generate a characteristic collection of polyketides, fine-tuned to its needs. 2'-Oxoalkylresorcinol synthase from Physcomitrella patens (PpORS) is basal to all plant type III PKSs in phylogenetic trees and may closely resemble their most recent common ancestor. To gain insight into the roles that ancestral plant type III PKSs might have played during early land plant evolution, we constructed and phenotypically characterized targeted knockouts of PpORS. Ors gametophores, unless submerged in water while they were developing, displayed various leaf malformations that included grossly misshapen leaves, missing or abnormal midribs, multicellular protuberances and localized necrosis. Ors leaves, particularly abnormal ones, showed increased permeability to the hydrophilic dye, toluidine blue. Ors gametophores lost water faster and were more susceptible to dehydration than those of the control strain. Our findings are consistent with ors leaves possessing a partially defective cuticle and implicate PpORS in synthesis of the intact cuticle. PpORS orthologs are present in a few moss species but have not been found in other plants. However, conceivably an ancestral ORS in early land plants may have contributed to their protection from dehydration.
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Affiliation(s)
- Li Li
- Department of Chemistry and Biochemistry, University of Regina, Regina, SK, S4S 0A2, Canada
| | - Misbah Aslam
- Department of Chemistry and Biochemistry, University of Regina, Regina, SK, S4S 0A2, Canada
| | - Fazle Rabbi
- Department of Chemistry and Biochemistry, University of Regina, Regina, SK, S4S 0A2, Canada
| | - Mark C Vanderwel
- Department of Biology, University of Regina, Regina, SK, S4S 0A2, Canada
| | - Neil W Ashton
- Department of Biology, University of Regina, Regina, SK, S4S 0A2, Canada
| | - Dae-Yeon Suh
- Department of Chemistry and Biochemistry, University of Regina, Regina, SK, S4S 0A2, Canada.
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99
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Abstract
Bioinformatic tools have become part of the way plant researchers undertake investigations. Large data sets encompassing genomes, transcriptomes, proteomes, epigenomes, and other "-omes" that have been generated in the past decade may be easily accessed with such tools, such that hypotheses may be generated at the click of a mouse. In this chapter, we'll cover the use of bioinformatic tools available at the Bio-Analytic Resource for Plant Biology at http://bar.utoronto.ca for exploring gene expression and coexpression patterns, undertaking promoter analyses, performing functional classification enrichment analyses for sets of genes, and examining protein-protein interactions. We also touch on some newer bioinformatic tools that allow integration of data from several sources for improved hypothesis generation, both for Arabidopsis and translationally. Most of the data sets come from Arabidopsis, but useful BAR tools for other species will be mentioned where appropriate.
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100
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Thelander M, Landberg K, Sundberg E. Auxin-mediated developmental control in the moss Physcomitrella patens. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:277-290. [PMID: 28992074 DOI: 10.1093/jxb/erx255] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 06/27/2017] [Indexed: 05/08/2023]
Abstract
The signalling molecule auxin regulates many fundamental aspects of growth and development in plants. We review and discuss what is known about auxin-regulated development in mosses, with special emphasis on the model species Physcomitrella patens. It is well established that mosses and other early diverging plants produce and respond to auxin. By sequencing the P. patens genome, it became clear that it encodes many core proteins important for auxin homeostasis, perception, and signalling, which have also been identified in flowering plants. This suggests that the auxin molecular network was present in the last common ancestor of flowering plants and mosses. Despite fundamental differences in their life cycles, key processes such as organ initiation and outgrowth, branching, tropic responses, as well as cell differentiation, division, and expansion appear to be regulated by auxin in the two lineages. This knowledge paves the way for studies aimed at a better understanding of the origin and evolution of auxin function and how auxin may have contributed to the evolution of land plants.
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Affiliation(s)
- Mattias Thelander
- Department of Plant Biology, Swedish University of Agricultural Sciences, The Linnean Centre for Plant Biology in Uppsala, Sweden
| | - Katarina Landberg
- Department of Plant Biology, Swedish University of Agricultural Sciences, The Linnean Centre for Plant Biology in Uppsala, Sweden
| | - Eva Sundberg
- Department of Plant Biology, Swedish University of Agricultural Sciences, The Linnean Centre for Plant Biology in Uppsala, Sweden
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