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Woudenberg S, Alvarez MD, Rienstra J, Levitsky V, Mironova V, Scarpella E, Kuhn A, Weijers D. Analysis of auxin responses in the fern Ceratopteris richardii identifies the developmental phase as a major determinant for response properties. Development 2024; 151:dev203026. [PMID: 39324436 DOI: 10.1242/dev.203026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Accepted: 08/16/2024] [Indexed: 09/27/2024]
Abstract
The auxin signaling molecule regulates a range of plant growth and developmental processes. The core transcriptional machinery responsible for auxin-mediated responses is conserved across all land plants. Genetic, physiological and molecular exploration in bryophyte and angiosperm model species have shown both qualitative and quantitative differences in auxin responses. Given the highly divergent ontogeny of the dominant gametophyte (bryophytes) and sporophyte (angiosperms) generations, however, it is unclear whether such differences derive from distinct phylogeny or ontogeny. Here, we address this question by comparing a range of physiological, developmental and molecular responses to auxin in both generations of the model fern Ceratopteris richardii. We find that auxin response in Ceratopteris gametophytes closely resembles that of a thalloid bryophyte, whereas the sporophyte mimics auxin response in flowering plants. This resemblance manifests both at the phenotypic and transcriptional levels. Furthermore, we show that disrupting auxin transport can lead to ectopic sporophyte induction on the gametophyte, suggesting a role for auxin in the alternation of generations. Our study thus identifies developmental phase, rather than phylogeny, as a major determinant of auxin response properties in land plants.
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Affiliation(s)
- Sjoerd Woudenberg
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708WE Wageningen, The Netherlands
| | - Melissa Dipp Alvarez
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708WE Wageningen, The Netherlands
| | - Juriaan Rienstra
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708WE Wageningen, The Netherlands
| | - Victor Levitsky
- Institute of Cytology and Genetics, Lavrentyeva Avenue 10, Novosibirsk 630090, Russian Federation
| | - Victoria Mironova
- Department of Plant Systems Physiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Enrico Scarpella
- Department of Biological Sciences, University of Alberta, CW-405 Biological Sciences Building, Edmonton AB T6G 2E9, Canada
| | - Andre Kuhn
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708WE Wageningen, The Netherlands
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708WE Wageningen, The Netherlands
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2
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Singh VP, Jaiswal S, Wang Y, Feng S, Tripathi DK, Singh S, Gupta R, Xue D, Xu S, Chen ZH. Evolution of reactive oxygen species cellular targets for plant development. TRENDS IN PLANT SCIENCE 2024; 29:865-877. [PMID: 38519324 DOI: 10.1016/j.tplants.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 02/25/2024] [Accepted: 03/06/2024] [Indexed: 03/24/2024]
Abstract
Reactive oxygen species (ROS) are the key players in regulating developmental processes of plants. Plants have evolved a large array of gene families to facilitate the ROS-regulated developmental process in roots and leaves. However, the cellular targets of ROS during plant evolutionary development are still elusive. Here, we found early evolution and large expansions of protein families such as mitogen-activated protein kinases (MAPK) in the evolutionarily important plant lineages. We review the recent advances in interactions among ROS, phytohormones, gasotransmitters, and protein kinases. We propose that these signaling molecules act in concert to maintain cellular ROS homeostasis in developmental processes of root and leaf to ensure the fine-tuning of plant growth for better adaptation to the changing climate.
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Affiliation(s)
- Vijay Pratap Singh
- Plant Physiology Laboratory, Department of Botany, C.M.P. Degree College, A Constituent Post Graduate College of University of Allahabad, Prayagraj-211002, India.
| | - Saumya Jaiswal
- Plant Physiology Laboratory, Department of Botany, C.M.P. Degree College, A Constituent Post Graduate College of University of Allahabad, Prayagraj-211002, India
| | - Yuanyuan Wang
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
| | - Shouli Feng
- Xianghu Laboratory, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Durgesh Kumar Tripathi
- Crop Nanobiology and Molecular Stress Physiology Lab, Amity Institute of Organic Agriculture, Amity University Uttar Pradesh, Sector-125, Noida 201313, India
| | - Samiksha Singh
- Department of Botany, S.N. Sen B.V. Post Graduate College, Chhatrapati Shahu Ji Maharaj University, Kanpur 208001, India
| | - Ravi Gupta
- College of General Education, Kookmin University, Seoul 02707, South Korea
| | - Dawei Xue
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310018, China
| | - Shengchun Xu
- Xianghu Laboratory, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia.
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Hernández-Muñoz A, Agreda-Laguna KA, Ramírez-Bernabé IE, Oltehua-López O, Arteaga-Vázquez MA, Leon P. Marchantia polymorpha GOLDEN2-LIKE transcriptional factor; a central regulator of chloroplast and plant vegetative development. THE NEW PHYTOLOGIST 2024; 243:1406-1423. [PMID: 38922903 DOI: 10.1111/nph.19916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024]
Abstract
The GOLDEN2-LIKE (GLK) transcription factors act as a central regulatory node involved in both developmental processes and environmental responses. Marchantia polymorpha, a basal terrestrial plant with strategic evolutionary position, contains a single GLK representative that possesses an additional domain compared to spermatophytes. We analyzed the role of MpGLK in chloroplast biogenesis and development by altering its levels, preforming transcriptomic profiling and conducting chromatin immunoprecipitation. Decreased MpGLK levels impair chloroplast differentiation and disrupt the expression of photosynthesis-associated nuclear genes, while overexpressing MpGLK leads to ectopic chloroplast biogenesis. This demonstrates the MpGLK functions as a bona fide GLK protein, likely representing an ancestral GLK architecture. Altering MpGLK levels directly regulates the expression of genes involved in Chl synthesis and degradation, similar to processes observed in eudicots, and causes various developmental defects in Marchantia, including the formation of dorsal structures such as air pores and gemma cups. MpGLK, also directly activates MpMAX2 gene expression, regulating the timing of gemma cup development. Our study shows that MpGLK functions as a master regulator, potentially coupling chloroplast development with vegetative reproduction. This illustrates the complex regulatory networks governing chloroplast function and plant development communication and highlight the evolutionary conservation of GLK-mediated regulatory processes across plant species.
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Affiliation(s)
- Arihel Hernández-Muñoz
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, 62210, Mexico
| | - Kenny Alejandra Agreda-Laguna
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, 62210, Mexico
| | - Ignacio E Ramírez-Bernabé
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, 62210, Mexico
| | - Omar Oltehua-López
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, 62210, Mexico
| | - Mario A Arteaga-Vázquez
- Instituto de Biotecnología y Ecología Aplicada, Universidad Veracruzana, Avenida de las Culturas Veracruzanas 101, Col. Emiliano Zapata, Xalapa, Veracruz, 91090, Mexico
| | - Patricia Leon
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, 62210, Mexico
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4
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Sessa G, Carabelli M, Sassi M. The Ins and Outs of Homeodomain-Leucine Zipper/Hormone Networks in the Regulation of Plant Development. Int J Mol Sci 2024; 25:5657. [PMID: 38891845 PMCID: PMC11171833 DOI: 10.3390/ijms25115657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024] Open
Abstract
The generation of complex plant architectures depends on the interactions among different molecular regulatory networks that control the growth of cells within tissues, ultimately shaping the final morphological features of each structure. The regulatory networks underlying tissue growth and overall plant shapes are composed of intricate webs of transcriptional regulators which synergize or compete to regulate the expression of downstream targets. Transcriptional regulation is intimately linked to phytohormone networks as transcription factors (TFs) might act as effectors or regulators of hormone signaling pathways, further enhancing the capacity and flexibility of molecular networks in shaping plant architectures. Here, we focus on homeodomain-leucine zipper (HD-ZIP) proteins, a class of plant-specific transcriptional regulators, and review their molecular connections with hormonal networks in different developmental contexts. We discuss how HD-ZIP proteins emerge as key regulators of hormone action in plants and further highlight the fundamental role that HD-ZIP/hormone networks play in the control of the body plan and plant growth.
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Affiliation(s)
| | | | - Massimiliano Sassi
- Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, 00185 Rome, Italy; (G.S.); (M.C.)
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5
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Zhang X, Bian A, Yang J, Liang Y, Zhang Z, Yan M, Yuan S, Zhang Q. Morphological Innovation Drives Sperm Release in Bryophytes. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306767. [PMID: 38552153 PMCID: PMC11132054 DOI: 10.1002/advs.202306767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 03/17/2024] [Indexed: 05/29/2024]
Abstract
Plant movements for survival are nontrivial. Antheridia in the moss Physcomitrium patens (P. patens) use motion to eject sperm in the presence of water. However, the biological and mechanical mechanisms that actuate the process are unknown. Here, the burst of the antheridium of P. patens, triggered by water, results from elastic instability and is determined by an asymmetric change in cell geometry. The tension generated in jacket cell walls of antheridium arises from turgor pressure, and is further promoted when the inner walls of apex burst in hydration, causing water and cellular contents of apex quickly influx into sperm chamber. The outer walls of the jacket cells are strengthened by NAC transcription factor VNS4 and serve as key morphomechanical innovations to store hydrostatic energy in a confined space in P. patens. However, the antheridium in liverwort Marchantia polymorpha (M. polymorpha) adopts a different strategy for sperm release; like jacket cell outer walls of P. patens, the cells surrounding the antheridium of M. polymorpha appear to play a similar role in the storage of energy. Collectively, the work shows that plants have evolved different ingenious devices for sperm discharge and that morphological innovations can differ.
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Affiliation(s)
- Xinxin Zhang
- Institute of BotanyChinese Academy of SciencesBeijing100093China
| | - Ang Bian
- College of Computer ScienceSichuan UniversityChengdu610065China
| | - Junbo Yang
- Shenzhen BranchGuangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdong518120China
| | - Ye Liang
- Core Facility of the State Key Laboratory of Membrane BiologyPeking UniversityBeijing100871China
| | - Zhe Zhang
- Department of Mechanical and Aerospace EngineeringThe Hong Kong University of Science and TechnologyClear Water BayHong Kong999077China
| | - Meng Yan
- School of Life ScienceHangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhouZhejiang310024China
| | - Siqi Yuan
- College of Life SciencesState Key Laboratory of Crop Genetics & Germplasm Enhancement and UtilizationNanjing Agricultural UniversityNanjing210095China
| | - Qun Zhang
- College of Life SciencesState Key Laboratory of Crop Genetics & Germplasm Enhancement and UtilizationNanjing Agricultural UniversityNanjing210095China
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6
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Zhao M, Lei Y, Wu L, Qi H, Song Z, Xu M. The miR159a-PeMYB33 module regulates poplar adventitious rooting through the abscisic acid signal pathway. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:879-891. [PMID: 38271219 DOI: 10.1111/tpj.16643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/11/2024] [Indexed: 01/27/2024]
Abstract
As sessile organisms, plants experience variable environments and encounter diverse stresses during their growth and development. Adventitious rooting, orchestrated by multiple coordinated signaling pathways, represents an adaptive strategy evolved by plants to adapt to cope with changing environmental conditions. This study uncovered the role of the miR159a-PeMYB33 module in the formation of adventitious roots (ARs) synergistically with abscisic acid (ABA) signaling in poplar. Overexpression of miR159a increased the number of ARs and plant height while reducing sensitivity to ABA in transgenic plants. In contrast, inhibition of miR159a (using Short Tandem Target Mimic) or overexpression of PeMYB33 decreased the number of ARs in transgenic plants. Additionally, miR159a targets and cleaves transcripts of PeMYB33 using degradome analysis, which was further confirmed by a transient expression experiment of poplar protoplast. We show the miR159a-PeMYB33 module controls ARs development in poplar through ABA signaling. In particular, we demonstrated that miR159a promotes the expression of genes in the ABA signaling pathway. The findings from this study shed light on the intricate regulatory mechanisms governing the development of ARs in poplar plants. The miR159a-PeMYB33 module, in conjunction with ABA signaling, plays a crucial role in modulating AR formation and subsequent plant growth.
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Affiliation(s)
- Meiqi Zhao
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Yijing Lei
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Ling Wu
- Jiangsu Yanjiang Institute of Agricultural Science, Nantong, Jiangsu, 226541, China
| | - Haoran Qi
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Zihe Song
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Meng Xu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
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7
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Li S, Wei L, Gao Q, Xu M, Wang Y, Lin Z, Holford P, Chen ZH, Zhang L. Molecular and phylogenetic evidence of parallel expansion of anion channels in plants. PLANT PHYSIOLOGY 2024; 194:2533-2548. [PMID: 38142233 DOI: 10.1093/plphys/kiad687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/25/2023]
Abstract
Aluminum-activated malate transporters (ALMTs) and slow anion channels (SLACs) are important in various physiological processes in plants, including stomatal regulation, nutrient uptake, and in response to abiotic stress such as aluminum toxicity. To understand their evolutionary history and functional divergence, we conducted phylogenetic and expression analyses of ALMTs and SLACs in green plants. Our findings from phylogenetic studies indicate that ALMTs and SLACs may have originated from green algae and red algae, respectively. The ALMTs of early land plants and charophytes formed a monophyletic clade consisting of three subgroups. A single duplication event of ALMTs was identified in vascular plants and subsequent duplications into six clades occurred in angiosperms, including an identified clade, 1-1. The ALMTs experienced gene number losses in clades 1-1 and 2-1 and expansions in clades 1-2 and 2-2b. Interestingly, the expansion of clade 1-2 was also associated with higher expression levels compared to genes in clades that experienced apparent loss. SLACs first diversified in bryophytes, followed by duplication in vascular plants, giving rise to three distinct clades (I, II, and III), and clade II potentially associated with stomatal control in seed plants. SLACs show losses in clades II and III without substantial expansion in clade I. Additionally, ALMT clade 2-2 and SLAC clade III contain genes specifically expressed in reproductive organs and roots in angiosperms, lycophytes, and mosses, indicating neofunctionalization. In summary, our study demonstrates the evolutionary complexity of ALMTs and SLACs, highlighting their crucial role in the adaptation and diversification of vascular plants.
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Affiliation(s)
- Shanshan Li
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Lanlan Wei
- College of Life Science, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qiang Gao
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Min Xu
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yizhou Wang
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, St.Louis, MO 63104, USA
| | - Paul Holford
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2751, Australia
| | - Liangsheng Zhang
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Hainan Institute of Zhejiang University, Sanya 572025, China
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8
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Gutsche N, Koczula J, Trupp M, Holtmannspötter M, Appelfeller M, Rupp O, Busch A, Zachgo S. MpTGA, together with MpNPR, regulates sexual reproduction and independently affects oil body formation in Marchantia polymorpha. THE NEW PHYTOLOGIST 2024; 241:1559-1573. [PMID: 38095258 DOI: 10.1111/nph.19472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 11/21/2023] [Indexed: 01/26/2024]
Abstract
In angiosperms, basic leucine-zipper (bZIP) TGACG-motif-binding (TGA) transcription factors (TFs) regulate developmental and stress-related processes, the latter often involving NON EXPRESSOR OF PATHOGENESIS-RELATED GENES (NPR) coregulator interactions. To gain insight into their functions in an early diverging land-plant lineage, the single MpTGA and sole MpNPR genes were investigated in the liverwort Marchantia polymorpha. We generated Marchantia MpTGA and MpNPR knockout and overexpression mutants and conducted morphological, transcriptomic and expression studies. Furthermore, we investigated MpTGA interactions with wild-type and mutagenized MpNPR and expanded our analyses including TGA TFs from two streptophyte algae. Mptga mutants fail to induce the switch from vegetative to reproductive development and lack gametangiophore formation. MpTGA and MpNPR proteins interact and Mpnpr mutant analysis reveals a novel coregulatory NPR role in sexual reproduction. Additionally, MpTGA acts independently of MpNPR as a repressor of oil body (OB) formation and can thereby affect herbivory. The single MpTGA TF exerts a dual role in sexual reproduction and OB formation in Marchantia. Common activities of MpTGA/MpNPR in sexual development suggest that coregulatory interactions were established after emergence of land-plant-specific NPR genes and contributed to the diversification of TGA TF functions during land-plant evolution.
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Affiliation(s)
- Nora Gutsche
- Division of Botany, Osnabrück University, 49076, Osnabrück, Germany
| | - Jens Koczula
- Division of Botany, Osnabrück University, 49076, Osnabrück, Germany
| | - Melanie Trupp
- Division of Botany, Osnabrück University, 49076, Osnabrück, Germany
| | - Michael Holtmannspötter
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
| | | | - Oliver Rupp
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, 35392, Giessen, Germany
| | - Andrea Busch
- Division of Botany, Osnabrück University, 49076, Osnabrück, Germany
| | - Sabine Zachgo
- Division of Botany, Osnabrück University, 49076, Osnabrück, Germany
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9
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Turchetto C, Silvério ADC, Waschburger EL, Lacerda MEG, Quintana IV, Turchetto-Zolet AC. Genome-wide identification and evolutionary view of ALOG gene family in Solanaceae. Genet Mol Biol 2023; 46:e20230142. [PMID: 38048778 PMCID: PMC10695626 DOI: 10.1590/1415-4757-gmb-2023-0142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 10/10/2023] [Indexed: 12/06/2023] Open
Abstract
The ALOG gene family, which was named after its earliest identified members ( Arabidopsis LSH1 and Oryza G1), encodes a class of transcription factors (TF) characterized by the presence of a highly conserved ALOG domain. These proteins are found in various plant species playing regulatory roles in plant growth, development, and morphological diversification of inflorescence. The functional characterization of these genes in some plant species has demonstrated their involvement in floral architecture. In this study, we used a genome-wide and phylogenetic approach to gain insights into plants' origin, diversification, and functional aspects of the ALOG gene family. In total, 648 ALOG homologous genes were identified in 77 Viridiplantae species, and their evolutionary relationships were inferred using maximum likelihood phylogenetic analyses. Our results suggested that the ALOG gene family underwent several rounds of gene duplication and diversification during angiosperm evolution. Furthermore, we found three functional orthologous groups in Solanaceae species. The study provides insights into the evolutionary history and functional diversification of the ALOG gene family, which could aid in understanding the mechanisms underlying floral architecture in angiosperms.
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Affiliation(s)
- Caroline Turchetto
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-Graduação em Botânica (PPGBOT), Departamento de Botânica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Departamento de Genética, Porto Alegre, RS, Brazil
| | - Ariadne de Castro Silvério
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-Graduação em Botânica (PPGBOT), Departamento de Botânica, Porto Alegre, RS, Brazil
| | - Edgar Luis Waschburger
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Departamento de Genética, Porto Alegre, RS, Brazil
| | - Maria Eduarda Gonçalves Lacerda
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Departamento de Genética, Porto Alegre, RS, Brazil
| | - Isadora Vieira Quintana
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Departamento de Genética, Porto Alegre, RS, Brazil
| | - Andreia Carina Turchetto-Zolet
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Departamento de Genética, Porto Alegre, RS, Brazil
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10
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Liu W, Cai G, Zhai N, Wang H, Tang T, Zhang Y, Zhang Z, Sun L, Zhang Y, Beeckman T, Xu L. Genome and transcriptome of Selaginella kraussiana reveal evolution of root apical meristems in vascular plants. Curr Biol 2023; 33:4085-4097.e5. [PMID: 37716350 DOI: 10.1016/j.cub.2023.08.061] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/30/2023] [Accepted: 08/22/2023] [Indexed: 09/18/2023]
Abstract
The evolution of roots allowed vascular plants to adapt to land environments. Fossil evidence indicates that roots evolved independently in euphyllophytes (ferns and seed plants) and lycophytes, the two lineages of extant vascular plants. Based on a high-quality genome assembly, mRNA sequencing (mRNA-seq) data, and single-cell RNA-seq data for the lycophyte Selaginella kraussiana, we show that the two root origin events in lycophytes and euphyllophytes adopted partially similar molecular modules in the regulation of root apical meristem (RAM) development. In S. kraussiana, the RAM initiates from the rhizophore primordium guided by auxin and duplicates itself by dichotomous branching. The auxin signaling pathway directly upregulates euAINTEGUMENTAb (SkeuANTb), and then SkeuANTb directly promotes the expression of SkeuANTa and the WUSCHEL-RELATED HOMEOBOX13b (SkWOX13b) for RAM maintenance, partially similar to the molecular pathway involving the euANT-branch PLETHORA (AtPLT) genes and AtWOX5 in root initiation in the seed plant Arabidopsis thaliana. Other molecular modules, e.g., SHORT-ROOT and SCARECROW, also have partially similar expression patterns in the RAMs of S. kraussiana and A. thaliana. Overall, our study not only provides genome and transcriptome tools of S. kraussiana but also indicates the employment of some common molecular modules in RAMs during root origins in lycophytes and euphyllophytes.
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Affiliation(s)
- Wu Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Gui Cai
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Ning Zhai
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Hua Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Tengfei Tang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Yuyun Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Zhiyao Zhang
- School of Life Sciences, Nantong University, Nantong 226019, China
| | - Lijun Sun
- School of Life Sciences, Nantong University, Nantong 226019, China
| | - Yijing Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China; State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.
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11
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Flores-Téllez D, Tankmar MD, von Bülow S, Chen J, Lindorff-Larsen K, Brodersen P, Arribas-Hernández L. Insights into the conservation and diversification of the molecular functions of YTHDF proteins. PLoS Genet 2023; 19:e1010980. [PMID: 37816028 PMCID: PMC10617740 DOI: 10.1371/journal.pgen.1010980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 10/31/2023] [Accepted: 09/17/2023] [Indexed: 10/12/2023] Open
Abstract
YT521-B homology (YTH) domain proteins act as readers of N6-methyladenosine (m6A) in mRNA. Members of the YTHDF clade determine properties of m6A-containing mRNAs in the cytoplasm. Vertebrates encode three YTHDF proteins whose possible functional specialization is debated. In land plants, the YTHDF clade has expanded from one member in basal lineages to eleven so-called EVOLUTIONARILY CONSERVED C-TERMINAL REGION1-11 (ECT1-11) proteins in Arabidopsis thaliana, named after the conserved YTH domain placed behind a long N-terminal intrinsically disordered region (IDR). ECT2, ECT3 and ECT4 show genetic redundancy in stimulation of primed stem cell division, but the origin and implications of YTHDF expansion in higher plants are unknown, as it is unclear whether it involves acquisition of fundamentally different molecular properties, in particular of their divergent IDRs. Here, we use functional complementation of ect2/ect3/ect4 mutants to test whether different YTHDF proteins can perform the same function when similarly expressed in leaf primordia. We show that stimulation of primordial cell division relies on an ancestral molecular function of the m6A-YTHDF axis in land plants that is present in bryophytes and is conserved over YTHDF diversification, as it appears in all major clades of YTHDF proteins in flowering plants. Importantly, although our results indicate that the YTH domains of all arabidopsis ECT proteins have m6A-binding capacity, lineage-specific neo-functionalization of ECT1, ECT9 and ECT11 happened after late duplication events, and involves altered properties of both the YTH domains, and, especially, of the IDRs. We also identify two biophysical properties recurrent in IDRs of YTHDF proteins able to complement ect2 ect3 ect4 mutants, a clear phase separation propensity and a charge distribution that creates electric dipoles. Human and fly YTHDFs do not have IDRs with this combination of properties and cannot replace ECT2/3/4 function in arabidopsis, perhaps suggesting different molecular activities of YTHDF proteins between major taxa.
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Affiliation(s)
- Daniel Flores-Téllez
- University of Copenhagen, Biology Department. Copenhagen, Denmark
- Universidad Francisco de Vitoria, Facultad de Ciencias Experimentales. Pozuelo de Alarcón (Madrid), Spain
| | | | - Sören von Bülow
- University of Copenhagen, Biology Department. Copenhagen, Denmark
| | - Junyu Chen
- University of Copenhagen, Biology Department. Copenhagen, Denmark
| | | | - Peter Brodersen
- University of Copenhagen, Biology Department. Copenhagen, Denmark
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12
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Tsitsekian D, Daras G, Templalexis D, Avgeri F, Lotos L, Orfanidou CG, Ntoukakis V, Maliogka VI, Rigas S. A subset of highly responsive transcription factors upon tomato infection by pepino mosaic virus. PLANT BIOLOGY (STUTTGART, GERMANY) 2023; 25:529-540. [PMID: 36856454 DOI: 10.1111/plb.13515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 02/21/2023] [Indexed: 05/17/2023]
Abstract
Plants have evolved well-tuned surveillance systems, including complex defence mechanisms, to constrain pathogens. TFs are master regulators of host molecular responses against plant pathogens. While PepMV constitutes a major threat to the global tomato production, there is still a lack of information on the key TFs that regulate host responses to this virus. A combinatorial research approach was applied relying on tomato transcriptome analysis, RT-qPCR validation, phylogenetic classification, comparative analysis of structural features, cis-regulatory element mining and in silico co-expression analysis to identify a set of 11 highly responsive TFs involved in the regulation of host responses to PepMV. An endemic PepMV isolate, generating typical mosaic symptoms, modified expression of ca. 3.3% of tomato genes, resulting in 1,120 DEGs. Functional classification of 502 upregulated DEGs revealed that photosynthesis, carbon fixation and gene silencing were widely affected, whereas 618 downregulated genes had an impact mainly on plant defence and carotenoid biosynthesis. Strikingly, all 11 highly responsive TFs carried abiotic stress response cis-regulatory elements, whereas five of them were better aligned with rice than with Arabidopsis gene homologues, suggesting that plant responses against viruses may predate divergence into monocots and dicots. Interestingly, tomato C2H2 family TFs, ZAT1-like and ZF2, may have distinct roles in plant defence due to opposite response patterns, similar to their Arabidopsis ZAT10 and ZAT12 homologues. These highly responsive TFs provide a basis to study in-depth molecular responses of the tomato-PepMV pathosystem, providing a perspective to better comprehend viral infections.
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Affiliation(s)
- D Tsitsekian
- Department of Biotechnology, Molecular Biology Laboratory, Agricultural University of Athens, Athens, Greece
| | - G Daras
- Department of Biotechnology, Molecular Biology Laboratory, Agricultural University of Athens, Athens, Greece
| | - D Templalexis
- Department of Biotechnology, Molecular Biology Laboratory, Agricultural University of Athens, Athens, Greece
| | - F Avgeri
- Department of Biotechnology, Molecular Biology Laboratory, Agricultural University of Athens, Athens, Greece
| | - L Lotos
- School of Agriculture, Plant Pathology Laboratory, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - C G Orfanidou
- School of Agriculture, Plant Pathology Laboratory, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - V Ntoukakis
- School of Life Sciences and Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, UK
| | - V I Maliogka
- School of Agriculture, Plant Pathology Laboratory, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - S Rigas
- Department of Biotechnology, Molecular Biology Laboratory, Agricultural University of Athens, Athens, Greece
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13
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Luan J, Ju J, Li X, Wang X, Tan Y, Xia G. Functional identification of moss PpGATA1 provides insights into the evolution of LLM-domain B-GATA transcription factors in plants. Gene 2023; 855:147103. [PMID: 36513191 DOI: 10.1016/j.gene.2022.147103] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/28/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
B-GATA transcription factors with the LLM domain (LLM-domain B-GATAs) play important roles in developmental processes and environmental responses in flowering plants. Their characterization can therefore provide insights into the structural and functional evolution of functional gene families. Phylogenetic and sequence analysis suggests that LLM-domain B-GATAs evolved from ancestral GATA transcription factors before the divergence of chlorophyte algae and Streptophyta. We compared the function of PpGATA1, a LLM-domain B-GATA gene in moss Physcomitrium patens, with Arabidopsis thaliana counterparts and showed that, in P. patens, PpGATA1 controls growth and greening in haploid gametophytes, while in transgenic Arabidopsis it affects germination, leaf development, flowering time, greening and light responses in diploid sporophytes. These PpGATA1 functions are similar to those of Arabidopsis counterparts, AtGNC, AtGNL and AtGATA17. PpGATA1 was able to complement the role of GNC and GNL in a gnc gnl double mutant, and the LLM domains of PpGATA1 and GNC behaved similarly. The functions of LLM-domain B-GATAs regulating hypocotyl elongation and cotyledon epinasty in flowering plants pre-exist before the divergence of mosses and the lineage leading to flowering plants. This study sheds light on adaption of PpGATA1 and its homologs to new developmental designs during the evolution.
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Affiliation(s)
- Ji Luan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong 266237, China; The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China.
| | - Jianfang Ju
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China
| | - Xiaochen Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong 266237, China
| | - Xiuling Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong 266237, China
| | - Yufei Tan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong 266237, China
| | - Guangmin Xia
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China.
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14
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Bowles AMC, Williamson CJ, Williams TA, Lenton TM, Donoghue PCJ. The origin and early evolution of plants. TRENDS IN PLANT SCIENCE 2023; 28:312-329. [PMID: 36328872 DOI: 10.1016/j.tplants.2022.09.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 09/23/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Plant (archaeplastid) evolution has transformed the biosphere, but we are only now beginning to learn how this took place through comparative genomics, phylogenetics, and the fossil record. This has illuminated the phylogeny of Archaeplastida, Viridiplantae, and Streptophyta, and has resolved the evolution of key characters, genes, and genomes - revealing that many key innovations evolved long before the clades with which they have been casually associated. Molecular clock analyses estimate that Streptophyta and Viridiplantae emerged in the late Mesoproterozoic to late Neoproterozoic, whereas Archaeplastida emerged in the late-mid Palaeoproterozoic. Together, these insights inform on the coevolution of plants and the Earth system that transformed ecology and global biogeochemical cycles, increased weathering, and precipitated snowball Earth events, during which they would have been key to oxygen production and net primary productivity (NPP).
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Affiliation(s)
- Alexander M C Bowles
- School of Geographical Sciences, University of Bristol, University Road, Bristol BS8 1SS, UK; Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK.
| | | | - Tom A Williams
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK
| | - Timothy M Lenton
- Global Systems Institute, University of Exeter, Laver Building, North Park Road, Exeter EX4 4QE, UK
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK.
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15
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Kapoor B, Kumar P, Verma V, Irfan M, Sharma R, Bhargava B. How plants conquered land: evolution of terrestrial adaptation. J Evol Biol 2023; 36:5-14. [PMID: 36083189 DOI: 10.1111/jeb.14062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 01/11/2023]
Abstract
The transition of plants from water to land is considered one of the most significant events in the evolution of life on Earth. The colonization of land by plants, accompanied by their morphological, physiological and developmental changes, resulted in plant biodiversity. Besides significantly influencing oxygen levels in the air and on land, plants manufacture organic matter from CO2 and water with the help of sunlight, paving the way for the diversification of nonplant lineages ranging from microscopic organisms to animals. Land plants regulate the climate by adjusting total biomass and energy flow. At the genetic level, these innovations are achieved through the rearrangement of pre-existing genetic information. Advances in genome sequencing technology are revamping our understanding of plant evolution. This study highlights the morphological and genomic innovations that allow plants to integrate life on Earth.
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Affiliation(s)
- Bhuvnesh Kapoor
- Department of Biotechnology, Dr. Y.S. Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India
| | - Pankaj Kumar
- Department of Biotechnology, Dr. Y.S. Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India
| | - Vipasha Verma
- Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Mohammad Irfan
- Plant Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, New York, USA
| | - Rajnish Sharma
- Department of Biotechnology, Dr. Y.S. Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India
| | - Bhavya Bhargava
- Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
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16
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León-Ruiz JA, Cruz Ramírez A. Predicted landscape of RETINOBLASTOMA-RELATED LxCxE-mediated interactions across the Chloroplastida. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:1507-1524. [PMID: 36305297 DOI: 10.1111/tpj.16012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 09/20/2022] [Accepted: 10/14/2022] [Indexed: 05/16/2023]
Abstract
The colonization of land by a single streptophyte algae lineage some 450 million years ago has been linked to multiple key innovations such as three-dimensional growth, alternation of generations, the presence of stomata, as well as innovations inherent to the birth of major plant lineages, such as the origins of vascular tissues, roots, seeds and flowers. Multicellularity, which evolved multiple times in the Chloroplastida coupled with precise spatiotemporal control of proliferation and differentiation were instrumental for the evolution of these traits. RETINOBLASTOMA-RELATED (RBR), the plant homolog of the metazoan Retinoblastoma protein (pRB), is a highly conserved and multifunctional core cell cycle regulator that has been implicated in the evolution of multicellularity in the green lineage as well as in plant multicellularity-related processes such as proliferation, differentiation, stem cell regulation and asymmetric cell division. RBR fulfills these roles through context-specific protein-protein interactions with proteins containing the Leu-x-Cys-x-Glu (LxCxE) short-linear motif (SLiM); however, how RBR-LxCxE interactions have changed throughout major innovations in the Viridiplantae kingdom is a question that remains unexplored. Here, we employ an in silico evo-devo approach to predict and analyze potential RBR-LxCxE interactions in different representative species of key Chloroplastida lineages, providing a valuable resource for deciphering RBR-LxCxE multiple functions. Furthermore, our analyses suggest that RBR-LxCxE interactions are an important component of RBR functions and that interactions with chromatin modifiers/remodelers, DNA replication and repair machinery are highly conserved throughout the Viridiplantae, while LxCxE interactions with transcriptional regulators likely diversified throughout the water-to-land transition.
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Affiliation(s)
- Jesús A León-Ruiz
- Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera, Irapuato-León, Irapuato, 36821, Guanajuato, Mexico
| | - Alfredo Cruz Ramírez
- Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera, Irapuato-León, Irapuato, 36821, Guanajuato, Mexico
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17
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Harris BJ, Clark JW, Schrempf D, Szöllősi GJ, Donoghue PCJ, Hetherington AM, Williams TA. Divergent evolutionary trajectories of bryophytes and tracheophytes from a complex common ancestor of land plants. Nat Ecol Evol 2022; 6:1634-1643. [PMID: 36175544 PMCID: PMC9630106 DOI: 10.1038/s41559-022-01885-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 08/12/2022] [Indexed: 11/16/2022]
Abstract
The origin of plants and their colonization of land fundamentally transformed the terrestrial environment. Here we elucidate the basis of this formative episode in Earth history through patterns of lineage, gene and genome evolution. We use new fossil calibrations, a relative clade age calibration (informed by horizontal gene transfer) and new phylogenomic methods for mapping gene family origins. Distinct rooting strategies resolve tracheophytes (vascular plants) and bryophytes (non-vascular plants) as monophyletic sister groups that diverged during the Cambrian, 515-494 million years ago. The embryophyte stem is characterized by a burst of gene innovation, while bryophytes subsequently experienced an equally dramatic episode of reductive genome evolution in which they lost genes associated with the elaboration of vasculature and the stomatal complex. Overall, our analyses reveal that extant tracheophytes and bryophytes are both highly derived from a more complex ancestral land plant. Understanding the origin of land plants requires tracing character evolution across a diversity of modern lineages.
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Affiliation(s)
- Brogan J Harris
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - James W Clark
- School of Biological Sciences, University of Bristol, Bristol, UK
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK
| | - Dominik Schrempf
- Department of Biological Physics, Eötvös Loránd University, Budapest, Hungary
| | - Gergely J Szöllősi
- Department of Biological Physics, Eötvös Loránd University, Budapest, Hungary
- MTA-ELTE 'Lendület' Evolutionary Genomics Research Group, Budapest, Hungary
- Institute of Evolution, Centre for Ecological Research, Budapest, Hungary
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK
| | | | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol, UK.
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK.
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18
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Preston JC, Sinha NR, Torii KU, Kellogg EA. Plant structure and function: Evolutionary origins and underlying mechanisms. PLANT PHYSIOLOGY 2022; 190:1-4. [PMID: 35775936 PMCID: PMC9434258 DOI: 10.1093/plphys/kiac320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Affiliation(s)
- Jill C Preston
- Department of Plant Biology, College of Agriculture and Life Sciences, The University of Vermont, Vermont 05405, USA
| | - Neelima R Sinha
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, California 95616, USA
| | - Keiko U Torii
- Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Texas 78712, USA
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19
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Aragón-Raygoza A, Herrera-Estrella L, Cruz-Ramírez A. Transcriptional analysis of Ceratopteris richardii young sporophyte reveals conservation of stem cell factors in the root apical meristem. FRONTIERS IN PLANT SCIENCE 2022; 13:924660. [PMID: 36035690 PMCID: PMC9413220 DOI: 10.3389/fpls.2022.924660] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
Gene expression in roots has been assessed in different plant species in studies ranging from complete organs to specific cell layers, and more recently at the single cell level. While certain genes or functional categories are expressed in the root of all or most plant species, lineage-specific genes have also been discovered. An increasing amount of transcriptomic data is available for angiosperms, while a limited amount of data is available for ferns, and few studies have focused on fern roots. Here, we present a de novo transcriptome assembly from three different parts of the Ceratopteris richardii young sporophyte. Differential gene expression analysis of the root tip transcriptional program showed an enrichment of functional categories related to histogenesis and cell division, indicating an active apical meristem. Analysis of a diverse set of orthologous genes revealed conserved expression in the root meristem, suggesting a preserved role for different developmental roles in this tissue, including stem cell maintenance. The reconstruction of evolutionary trajectories for ground tissue specification genes suggests a high degree of conservation in vascular plants, but not for genes involved in root cap development, showing that certain genes are absent in Ceratopteris or have intricate evolutionary paths difficult to track. Overall, our results suggest different processes of conservation and divergence of genes involved in root development.
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Affiliation(s)
- Alejandro Aragón-Raygoza
- Molecular and Developmental Complexity Group, Unidad De Genómica Avanzada, Laboratorio Nacional De Genómica Para la Biodiversidad, Cinvestav Unidad Irapuato, Irapuato, Guanajuato, Mexico
- Metabolic Engineering Group, Unidad De Genómica Avanzada, Laboratorio Nacional De Genómica Para la Biodiversidad, Cinvestav Unidad Irapuato, Irapuato, Guanajuato, Mexico
| | - Luis Herrera-Estrella
- Metabolic Engineering Group, Unidad De Genómica Avanzada, Laboratorio Nacional De Genómica Para la Biodiversidad, Cinvestav Unidad Irapuato, Irapuato, Guanajuato, Mexico
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX, United States
| | - Alfredo Cruz-Ramírez
- Molecular and Developmental Complexity Group, Unidad De Genómica Avanzada, Laboratorio Nacional De Genómica Para la Biodiversidad, Cinvestav Unidad Irapuato, Irapuato, Guanajuato, Mexico
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20
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Wang QH, Zhang J, Liu Y, Jia Y, Jiao YN, Xu B, Chen ZD. Diversity, phylogeny, and adaptation of bryophytes: insights from genomic and transcriptomic data. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4306-4322. [PMID: 35437589 DOI: 10.1093/jxb/erac127] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 03/24/2022] [Indexed: 06/14/2023]
Abstract
Bryophytes including mosses, liverworts, and hornworts are among the earliest land plants, and occupy a crucial phylogenetic position to aid in the understanding of plant terrestrialization. Despite their small size and simple structure, bryophytes are the second largest group of extant land plants. They live ubiquitously in various habitats and are highly diversified, with adaptive strategies to modern ecosystems on Earth. More and more genomes and transcriptomes have been assembled to address fundamental questions in plant biology. Here, we review recent advances in bryophytes associated with diversity, phylogeny, and ecological adaptation. Phylogenomic studies have provided increasing supports for the monophyly of bryophytes, with hornworts sister to the Setaphyta clade including liverworts and mosses. Further comparative genomic analyses revealed that multiple whole-genome duplications might have contributed to the species richness and morphological diversity in mosses. We highlight that the biological changes through gene gain or neofunctionalization that primarily evolved in bryophytes have facilitated the adaptation to early land environments; among the strategies to adapt to modern ecosystems in bryophytes, desiccation tolerance is the most remarkable. More genomic information for bryophytes would shed light on key mechanisms for the ecological success of these 'dwarfs' in the plant kingdom.
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Affiliation(s)
- Qing-Hua Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jian Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yang Liu
- Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004, China
| | - Yu Jia
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yuan-Nian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Bo Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Zhi-Duan Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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21
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Mizrahi R, Shevtsov-Tal S, Ostersetzer-Biran O. Group II Intron-Encoded Proteins (IEPs/Maturases) as Key Regulators of Nad1 Expression and Complex I Biogenesis in Land Plant Mitochondria. Genes (Basel) 2022; 13:genes13071137. [PMID: 35885919 PMCID: PMC9321910 DOI: 10.3390/genes13071137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 06/15/2022] [Accepted: 06/22/2022] [Indexed: 02/04/2023] Open
Abstract
Mitochondria are semi-autonomous organelles that produce much of the energy required for cellular metabolism. As descendants of a bacterial symbiont, most mitochondria harbor their own genetic system (mtDNA/mitogenome), with intrinsic machineries for transcription and protein translation. A notable feature of plant mitochondria involves the presence of introns (mostly group II-type) that reside in many organellar genes. The splicing of the mtRNAs relies on the activities of various protein cofactors, which may also link organellar functions with cellular or environmental signals. The splicing of canonical group II introns is aided by an ancient class of RT-like enzymes (IEPs/maturases, MATs) that are encoded by the introns themselves and act specifically on their host introns. The plant organellar introns are degenerated in structure and are generally also missing their cognate intron-encoded proteins. The factors required for plant mtRNA processing are mostly nuclearly-encoded, with the exception of a few degenerated MATs. These are in particular pivotal for the maturation of NADH-dehydrogenase transcripts. In the following review we provide an update on the non-canonical MAT factors in angiosperm mitochondria and summarize the current knowledge of their essential roles in regulating Nad1 expression and complex I (CI) biogenesis during embryogenesis and early plant life.
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22
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Nascimento LBDS, Tattini M. Beyond Photoprotection: The Multifarious Roles of Flavonoids in Plant Terrestrialization. Int J Mol Sci 2022; 23:5284. [PMID: 35563675 PMCID: PMC9101737 DOI: 10.3390/ijms23095284] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/29/2022] [Accepted: 05/06/2022] [Indexed: 02/01/2023] Open
Abstract
Plants evolved an impressive arsenal of multifunctional specialized metabolites to cope with the novel environmental pressures imposed by the terrestrial habitat when moving from water. Here we examine the multifarious roles of flavonoids in plant terrestrialization. We reason on the environmental drivers, other than the increase in UV-B radiation, that were mostly responsible for the rise of flavonoid metabolism and how flavonoids helped plants in land conquest. We are reasonably based on a nutrient-deficiency hypothesis for the replacement of mycosporine-like amino acids, typical of streptophytic algae, with the flavonoid metabolism during the water-to-land transition. We suggest that flavonoids modulated auxin transport and signaling and promoted the symbiosis between plants and fungi (e.g., arbuscular mycorrhizal, AM), a central event for the conquest of land by plants. AM improved the ability of early plants to take up nutrients and water from highly impoverished soils. We offer evidence that flavonoids equipped early land plants with highly versatile "defense compounds", essential for the new set of abiotic and biotic stressors imposed by the terrestrial environment. We conclude that flavonoids have been multifunctional since the appearance of plants on land, not only acting as UV filters but especially improving both nutrient acquisition and biotic stress defense.
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Affiliation(s)
| | - Massimiliano Tattini
- Institute for Sustainable Plant Protection (IPSP), National Research Council of Italy, 50019 Sesto Fiorentino, Florence, Italy;
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23
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Sai CB, Chidambaranathan P. In-silico evolutionary analysis of plant-OBERON proteins during compatible MYMV infection in respect of improving host resistance. JOURNAL OF PLANT RESEARCH 2022; 135:405-422. [PMID: 35201523 DOI: 10.1007/s10265-022-01372-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/16/2022] [Indexed: 06/14/2023]
Abstract
Yellow mosaic disease (YMD) of pulses caused by mungbean yellow mosaic virus is a major threat to crop production. An infection that is compatible with regulating and interacting host proteins and the virus causes YMD. Oberon families of proteins OBE1-4 and VIN1-4 are imperative for plants, functions in meristem and vascular development, and were also regulated during compatible disease infection. Furthermore, in-silico expression results suggested the involvement of OBE1 and OBE2 proteins during virus infection of Vigna, Arabidopsis and soybean. Moreover, a common ancestor for the meristem and virus movement related Oberons was inferred through phylogenetic analysis. Protein interaction studies showed three amino acids (Aspartate, glutamate and lysine) in the plant homeodomain (PHD), involved in interaction with the N-terminal region of the virus movement protein and were also conserved in both monocot and dicots. Additionally, major differences in the nuclear localization signal (NLS) showing clade specific conservation and significant variation between dicots and monocots were ascertained in meristem and virus movement related Oberons. Consequently, a combination of PHD, CCD and their interactions with the VPg viral domain increases the susceptibility to YMD. Further, modification in the NLS regions of the viral movement clade Oberons, to knock out allele generation in the OBE1 and OBE2 homologs through genome-editing approaches could be established as alternate strategies for the improvement of host resistance and control yellow mosaic disease in plants, especially in pulse crops.
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Affiliation(s)
- Cayalvizhi B Sai
- ICAR-National Rice Research Institute (ICAR-NRRI), Cuttack, 753006, India.
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24
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Xia Z, Liu L, Wei Z, Wang F, Shen H, Yan Y. Analysis of Comparative Transcriptome and Positively Selected Genes Reveal Adaptive Evolution in Leaf-Less and Root-Less Whisk Ferns. PLANTS 2022; 11:plants11091198. [PMID: 35567199 PMCID: PMC9103481 DOI: 10.3390/plants11091198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/13/2022] [Accepted: 04/25/2022] [Indexed: 12/01/2022]
Abstract
While roots and leaves have evolved independently in lycophytes, ferns and seed plants, there is still confusion regarding the morphological evolution of ferns, especially in whisk ferns, which lack true leaves and roots and instead only exhibit leaf-like appendages and absorptive rhizoids. In this study, analyses of comparative transcriptomics on positively selected genes were performed to provide insights into the adaptive evolution of whisk fern morphologies. Significantly clustered gene families specific to whisk ferns were mainly enriched in Gene Ontology (GO) terms “binding proteins” and “transmembrane transporter activity”, and positive selection was detected in genes involved in transmembrane transporter activities and stress response (e.g., sodium/hydrogen exchanger and heat shock proteins), which could be related to the adaptive evolution of tolerance to epiphytic environments. The analysis of TF/TR gene family sizes indicated that some rapidly evolving gene families (e.g., the GRF and the MADS-MIKC families) related to the development of morphological organs were commonly reduced in whisk ferns and ophioglossoid ferns. Furthermore, the WUS homeobox-containing (WOX) gene family and the knotted1-like homeobox (KNOX) gene family, both associated with root and leaf development, were phylogenetically conserved in whisk ferns and ophioglossoid ferns. In general, our results suggested that adaptive evolution to epiphytic environments might have occurred in whisk ferns. We propose that the simplified and reduced leaf and root system in whisk ferns is the result of reduction from the common ancestor of whisk ferns and ophioglossoid ferns, rather than an independent origin.
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Affiliation(s)
- Zengqiang Xia
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China; (Z.X.); (Z.W.)
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
- CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China;
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Liu
- CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China;
| | - Zuoying Wei
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China; (Z.X.); (Z.W.)
- College of Life and Sciences, Shanghai Normal University, Shanghai 201602, China
| | - Faguo Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China;
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Hui Shen
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
- Correspondence: (H.S.); (Y.Y.)
| | - Yuehong Yan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China; (Z.X.); (Z.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (H.S.); (Y.Y.)
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25
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Elbl PM, de Souza DT, Rosado D, de Oliveira LF, Navarro BV, Matioli SR, Floh EIS. Building an embryo: An auxin gene toolkit for zygotic and somatic embryogenesis in Brazilian pine. Gene 2022; 817:146168. [PMID: 34995731 DOI: 10.1016/j.gene.2021.146168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 12/10/2021] [Accepted: 12/15/2021] [Indexed: 11/04/2022]
Abstract
Many studies in the model species Arabidopsis thaliana characterized genes involved in embryo formation. However, much remains to be learned about the portfolio of genes that are involved in signal transduction and transcriptional regulation during plant embryo development in other species, particularly in an evolutionary context, especially considering that some genes involved in embryo patterning are not exclusive of land plants. This study, used a combination of domain architecture phylostratigraphy and phylogenetic reconstruction to investigate the evolutionary history of embryo patterning and auxin metabolism (EPAM) genes in Viridiplantae. This approach shed light on the co-optation of auxin metabolism and other molecular mechanisms that contributed to the radiation of land plants, and specifically to embryo formation. These results have potential to assist conservation programs, by directing the development of tools for obtaining somatic embryos. In this context, we employed this methodology with critically endangered and non-model species Araucaria angustifolia, the Brazilian pine, which is current focus of conservation efforts using somatic embryogenesis. So far, this approach had little success since somatic embryos fail to completely develop. By profiling the expression of genes that we identified as necessary for the emergence of land-plant embryos, we found striking differences between zygotic and somatic embryos that might explain the developmental arrest and be used to improve A. angustifolia somatic culture.
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Affiliation(s)
- Paula M Elbl
- Laboratory of Plant Cell Biology, Department of Botany, Institute of Biosciences, University of São Paulo, Rua do Matão, 277, São Paulo, SP, Brazil.
| | - Diego T de Souza
- Laboratory of Plant Cell Biology, Department of Botany, Institute of Biosciences, University of São Paulo, Rua do Matão, 277, São Paulo, SP, Brazil; Department of Computer Science, Institute of Mathematics and Statistics, University of São Paulo, São Paulo, SP, Brazil
| | - Daniele Rosado
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, United States
| | - Leandro F de Oliveira
- Laboratory of Plant Cell Biology, Department of Botany, Institute of Biosciences, University of São Paulo, Rua do Matão, 277, São Paulo, SP, Brazil
| | - Bruno V Navarro
- Laboratory of Plant Cell Biology, Department of Botany, Institute of Biosciences, University of São Paulo, Rua do Matão, 277, São Paulo, SP, Brazil; Laboratory of Plant Physiological Ecology, Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Sergio R Matioli
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Eny I S Floh
- Laboratory of Plant Cell Biology, Department of Botany, Institute of Biosciences, University of São Paulo, Rua do Matão, 277, São Paulo, SP, Brazil
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26
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Morón-García O, Garzón-Martínez GA, Martínez-Martín MJP, Brook J, Corke FMK, Doonan JH, Camargo Rodríguez AV. Genetic architecture of variation in Arabidopsis thaliana rosettes. PLoS One 2022; 17:e0263985. [PMID: 35171969 PMCID: PMC8849614 DOI: 10.1371/journal.pone.0263985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 02/01/2022] [Indexed: 12/04/2022] Open
Abstract
Rosette morphology across Arabidopsis accessions exhibits considerable variation. Here we report a high-throughput phenotyping approach based on automatic image analysis to quantify rosette shape and dissect the underlying genetic architecture. Shape measurements of the rosettes in a core set of Recombinant Inbred Lines from an advanced mapping population (Multiparent Advanced Generation Inter-Cross or MAGIC) derived from inter-crossing 19 natural accessions. Image acquisition and analysis was scaled to extract geometric descriptors from time stamped images of growing rosettes. Shape analyses revealed heritable morphological variation at early juvenile stages and QTL mapping resulted in over 116 chromosomal regions associated with trait variation within the population. Many QTL linked to variation in shape were located near genes related to hormonal signalling and signal transduction pathways while others are involved in shade avoidance and transition to flowering. Our results suggest rosette shape arises from modular integration of sub-organ morphologies and can be considered a functional trait subjected to selective pressures of subsequent morphological traits. On an applied aspect, QTLs found will be candidates for further research on plant architecture.
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Affiliation(s)
- Odín Morón-García
- The National Plant Phenomics Centre, Institute of Biological, Rural and Environmental Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - Gina A. Garzón-Martínez
- The National Plant Phenomics Centre, Institute of Biological, Rural and Environmental Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - M. J. Pilar Martínez-Martín
- The National Plant Phenomics Centre, Institute of Biological, Rural and Environmental Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - Jason Brook
- The National Plant Phenomics Centre, Institute of Biological, Rural and Environmental Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - Fiona M. K. Corke
- The National Plant Phenomics Centre, Institute of Biological, Rural and Environmental Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - John H. Doonan
- The National Plant Phenomics Centre, Institute of Biological, Rural and Environmental Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
- * E-mail: (AVCR); (JHD)
| | - Anyela V. Camargo Rodríguez
- The National Plant Phenomics Centre, Institute of Biological, Rural and Environmental Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
- * E-mail: (AVCR); (JHD)
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27
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Cookson R, Winichayakul S, Xue H, Richardson K, Moraga R, Laugraud A, Biswas A, Bryan G, Roberts N. Evolution and conserved functionality of organ size and shape regulator PEAPOD. PLoS One 2022; 17:e0263928. [PMID: 35148336 PMCID: PMC8836299 DOI: 10.1371/journal.pone.0263928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 01/28/2022] [Indexed: 11/26/2022] Open
Abstract
Transcriptional regulator PEAPOD (PPD) and its binding partners comprise a complex that is conserved throughout many core eudicot plants with regard to protein domain sequence and the function of controlling organ size and shape. Orthologues of PPD also exist in the basal angiosperm Amborella trichopoda, various gymnosperm species, the lycophyte Selaginella moellendorffii and several monocot genera, although until now it was not known if these are functional sequences. Here we report constitutive expression of orthologues from species representing diverse taxa of plant phylogeny in the Arabidopsis Δppd mutant. PPD orthologues from S. moellendorffii, gymnosperm Picea abies, A. trichopoda, monocot Musa acuminata, and dicot Trifolium repens were able to complement the mutant and return it to the wild-type phenotype, demonstrating the conserved functionality of PPD throughout vascular plants. In addition, analysis of bryophyte genomes revealed potential PPD orthologues in model liverwort and moss species, suggesting a more primitive lineage for this conserved regulator. The Poaceae (grasses) lack the genes for the PPD module and the reason for loss of the complex from this economically significant family is unclear, given that grasses were the last of the flowering plants to evolve. Bioinformatic analyses identified putative PPD orthologues in close relatives of the Poaceae, indicating that the explanation for absence of PPD in the grasses may be more complex than previously considered. Understanding the mechanisms which led to loss of PPD from the grasses will provide insight into evolution of the Poaceae.
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Affiliation(s)
- Ruth Cookson
- Plant Biotechnology, Grasslands Research Centre, AgResearch Ltd., Palmerston North, New Zealand
- * E-mail: (RC); (NR)
| | - Somrutai Winichayakul
- Plant Biotechnology, Grasslands Research Centre, AgResearch Ltd., Palmerston North, New Zealand
| | - Hong Xue
- Plant Biotechnology, Grasslands Research Centre, AgResearch Ltd., Palmerston North, New Zealand
| | - Kim Richardson
- Plant Biotechnology, Grasslands Research Centre, AgResearch Ltd., Palmerston North, New Zealand
| | - Roger Moraga
- Bioinformatics and Statistics, Grasslands Research Centre, AgResearch Ltd., Palmerston North, New Zealand
| | - Aurelie Laugraud
- Bioinformatics and Statistics, Grasslands Research Centre, AgResearch Ltd., Palmerston North, New Zealand
| | - Ambarish Biswas
- Bioinformatics and Statistics, Grasslands Research Centre, AgResearch Ltd., Palmerston North, New Zealand
| | - Greg Bryan
- Plant Biotechnology, Grasslands Research Centre, AgResearch Ltd., Palmerston North, New Zealand
| | - Nick Roberts
- Plant Biotechnology, Grasslands Research Centre, AgResearch Ltd., Palmerston North, New Zealand
- * E-mail: (RC); (NR)
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28
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Matilla AJ. The Orthodox Dry Seeds Are Alive: A Clear Example of Desiccation Tolerance. PLANTS (BASEL, SWITZERLAND) 2021; 11:plants11010020. [PMID: 35009023 PMCID: PMC8747232 DOI: 10.3390/plants11010020] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/07/2021] [Accepted: 12/20/2021] [Indexed: 05/17/2023]
Abstract
To survive in the dry state, orthodox seeds acquire desiccation tolerance. As maturation progresses, the seeds gradually acquire longevity, which is the total timespan during which the dry seeds remain viable. The desiccation-tolerance mechanism(s) allow seeds to remain dry without losing their ability to germinate. This adaptive trait has played a key role in the evolution of land plants. Understanding the mechanisms for seed survival after desiccation is one of the central goals still unsolved. That is, the cellular protection during dry state and cell repair during rewatering involves a not entirely known molecular network(s). Although desiccation tolerance is retained in seeds of higher plants, resurrection plants belonging to different plant lineages keep the ability to survive desiccation in vegetative tissue. Abscisic acid (ABA) is involved in desiccation tolerance through tight control of the synthesis of unstructured late embryogenesis abundant (LEA) proteins, heat shock thermostable proteins (sHSPs), and non-reducing oligosaccharides. During seed maturation, the progressive loss of water induces the formation of a so-called cellular "glass state". This glassy matrix consists of soluble sugars, which immobilize macromolecules offering protection to membranes and proteins. In this way, the secondary structure of proteins in dry viable seeds is very stable and remains preserved. ABA insensitive-3 (ABI3), highly conserved from bryophytes to Angiosperms, is essential for seed maturation and is the only transcription factor (TF) required for the acquisition of desiccation tolerance and its re-induction in germinated seeds. It is noteworthy that chlorophyll breakdown during the last step of seed maturation is controlled by ABI3. This update contains some current results directly related to the physiological, genetic, and molecular mechanisms involved in survival to desiccation in orthodox seeds. In other words, the mechanisms that facilitate that an orthodox dry seed is a living entity.
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Affiliation(s)
- Angel J Matilla
- Departamento de Biología Funcional (Área Fisiología Vegetal), Facultad de Farmacia, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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29
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Ponz-Segrelles G, Ribeiro RP, Aguado MT. Monsters reveal patterns: bifurcated annelids and their implications for the study of development and evolution. Biol Rev Camb Philos Soc 2021; 97:896-922. [PMID: 34931440 DOI: 10.1111/brv.12826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 11/30/2022]
Abstract
During recent decades, the study of anatomical anomalies has been of great relevance for research on development and its evolution. Yet most animal groups have never been studied under this perspective. In annelids, one of the most common and remarkable anomalies is anteroposterior axis bifurcation, that is animals that have two or more heads and/or tails. Bifurcated annelids were first described in the 18th century and have been occasionally reported since then. However, these animals have rarely been considered other than curiosities, one-off anomalies, or monsters, and a condensed but comprehensive analysis of this phenomenon is lacking. Such an analysis of the existing knowledge is necessary for addressing the different patterns of annelid bifurcation, as well as to understand possible developmental mechanisms behind them and their evolution. In this review we summarize reports of annelid bifurcation published during the last 275 years and the wide variety of anatomies they present. Our survey reveals bifurcation as a widespread phenomenon found all over the annelid tree. Moreover, it also shows that bifurcations can be classified into different types according to anatomy (lateral versus dorsoventral) or developmental origin (embryonic versus postembryonic, the latter occurring in relation to regeneration, reproduction, or growth). Regarding embryos, three different types of bifurcation can be found: conjoined twins (in clitellates); Janus embryos (two posterior ends with a single head which shows duplicated structures); and duplicitas cruciata embryos (with anterior and posterior bifurcation with a 90° rotation). In adults, we show that while lateral bifurcation can result in well-integrated phenotypes, dorsoventral bifurcation cannot since it requires the discontinuity of at least some internal organs. The relevance of this distinction is highlighted in the case of the Ribbon Clade, a group of syllid annelids in which some species reproduce by collateral and successive gemmiparity (which involves dorsoventral bifurcation), while others grow by branching laterally. Although most known cases of bifurcation came from accidental findings in the wild or were unintentionally produced, experimental studies resulting in the induction of bifurcation of both embryos and adults are also reviewed. In embryos, these experimental studies show how mechanical or chemical disruption of the zygote can result in bifurcation. In adults, the ventral nervous system and the digestive tract seem to play a role in the induction of bifurcation. Based on the reviewed evidence, we argue that the long-forgotten study of annelid developmental anomalies should be incorporated into the growing field of annelid EvoDevo and examined with modern techniques and perspectives.
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Affiliation(s)
- Guillermo Ponz-Segrelles
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin, 2, Madrid, 28049, Spain
| | - Rannyele P Ribeiro
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin, 2, Madrid, 28049, Spain.,Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA, 02543, U.S.A
| | - M Teresa Aguado
- Biodiversitätsmuseum, Animal Evolution & Biodiversity, Georg-August-Universität Göttingen, Untere Karspüle 2, Göttingen, 37073, Germany
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30
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Sharma V, Clark AJ, Kawashima T. Insights into the molecular evolution of fertilization mechanism in land plants. PLANT REPRODUCTION 2021; 34:353-364. [PMID: 34061252 DOI: 10.1007/s00497-021-00414-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/14/2021] [Indexed: 05/27/2023]
Abstract
Comparative genetics and genomics among green plants, including algae, provide deep insights into the evolution of land plant sexual reproduction. Land plants have evolved successive changes during their conquest of the land and innovations in sexual reproduction have played a major role in their terrestrialization. Recent years have seen many revealing dissections of the molecular mechanisms of sexual reproduction and much new genomics data from the land plant lineage, including early diverging land plants, as well as algae. This new knowledge is being integrated to further understand how sexual reproduction in land plants evolved, identifying highly conserved factors and pathways, but also molecular changes that underpinned the emergence of new modes of sexual reproduction. Here, we review recent advances in the knowledge of land plant sexual reproduction from an evolutionary perspective and also revisit the evolution of angiosperm double fertilization.
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Affiliation(s)
- Vijyesh Sharma
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546, USA
| | - Anthony J Clark
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546, USA
| | - Tomokazu Kawashima
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546, USA.
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31
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Del-Saz NF, Douthe C, Carriquí M, Ortíz J, Sanhueza C, Rivas-Medina A, McDonald A, Fernie AR, Ribas-Carbo M, Gago J, Florez-Sarasa I, Flexas J. Different Metabolic Roles for Alternative Oxidase in Leaves of Palustrine and Terrestrial Species. FRONTIERS IN PLANT SCIENCE 2021; 12:752795. [PMID: 34804092 PMCID: PMC8600120 DOI: 10.3389/fpls.2021.752795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/15/2021] [Indexed: 06/13/2023]
Abstract
The alternative oxidase pathway (AOP) is associated with excess energy dissipation in leaves of terrestrial plants. To address whether this association is less important in palustrine plants, we compared the role of AOP in balancing energy and carbon metabolism in palustrine and terrestrial environments by identifying metabolic relationships between primary carbon metabolites and AOP in each habitat. We measured oxygen isotope discrimination during respiration, gas exchange, and metabolite profiles in aerial leaves of ten fern and angiosperm species belonging to five families organized as pairs of palustrine and terrestrial species. We performed a partial least square model combined with variable importance for projection to reveal relationships between the electron partitioning to the AOP (τa) and metabolite levels. Terrestrial plants showed higher values of net photosynthesis (AN) and τa, together with stronger metabolic relationships between τa and sugars, important for water conservation. Palustrine plants showed relationships between τa and metabolites related to the shikimate pathway and the GABA shunt, to be important for heterophylly. Excess energy dissipation via AOX is less crucial in palustrine environments than on land. The basis of this difference resides in the contrasting photosynthetic performance observed in each environment, thus reinforcing the importance of AOP for photosynthesis.
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Affiliation(s)
- Nestor Fernandez Del-Saz
- Laboratorio de Fisiología Vegetal, Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Cyril Douthe
- Research Group on Plant Biology Under Mediterranean Conditions, Departament de Biologia, Institute of Agro-Environmental Research and Water Economy, Universitat de les Illes Balears, Illes Balears, Spain
| | - Marc Carriquí
- Research Group on Plant Biology Under Mediterranean Conditions, Departament de Biologia, Institute of Agro-Environmental Research and Water Economy, Universitat de les Illes Balears, Illes Balears, Spain
| | - Jose Ortíz
- Laboratorio de Fisiología Vegetal, Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Carolina Sanhueza
- Laboratorio de Fisiología Vegetal, Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Alicia Rivas-Medina
- Departamento de Ingeniería Topográfica y Cartografía, Escuela Técnica Superior de Ingenieros en Topografía, Geodesia y Cartografía, Universidad Politécnica de Madrid, Madrid, Spain
| | - Allison McDonald
- Department of Biology, Wilfrid Laurier University, Waterloo, ON, Canada
| | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam, Germany
| | - Miquel Ribas-Carbo
- Research Group on Plant Biology Under Mediterranean Conditions, Departament de Biologia, Institute of Agro-Environmental Research and Water Economy, Universitat de les Illes Balears, Illes Balears, Spain
| | - Jorge Gago
- Research Group on Plant Biology Under Mediterranean Conditions, Departament de Biologia, Institute of Agro-Environmental Research and Water Economy, Universitat de les Illes Balears, Illes Balears, Spain
| | - Igor Florez-Sarasa
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, Spain
- Institut de Recerca i Tecnología Agroalimentàries (IRTA), Edifici CRAG, Barcelona, Spain
| | - Jaume Flexas
- Research Group on Plant Biology Under Mediterranean Conditions, Departament de Biologia, Institute of Agro-Environmental Research and Water Economy, Universitat de les Illes Balears, Illes Balears, Spain
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32
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Pan L, Fonseca De Lima CF, Vu LD, De Smet I. A Comprehensive Phylogenetic Analysis of the MAP4K Family in the Green Lineage. FRONTIERS IN PLANT SCIENCE 2021; 12:650171. [PMID: 34484252 PMCID: PMC8415026 DOI: 10.3389/fpls.2021.650171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 07/22/2021] [Indexed: 06/13/2023]
Abstract
The kinase-mediated phosphorylation impacts every basic cellular process. While mitogen-activated protein kinase technology kinase kinases (MAP4Ks) are evolutionarily conserved, there is no comprehensive overview of the MAP4K family in the green lineage (Viridiplantae). In this study, we identified putative MAP4K members from representative species of the two core groups in the green lineage: Chlorophyta, which is a diverse group of green algae, and Streptophyta, which is mostly freshwater green algae and land plants. From that, we inferred the evolutionary relationships of MAP4K proteins through a phylogenetic reconstruction. Furthermore, we provided a classification of the MAP4Ks in the green lineage into three distinct.
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Affiliation(s)
- Lixia Pan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Cassio Flavio Fonseca De Lima
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Lam Dai Vu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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Bano N, Patel P, Chakrabarty D, Bag SK. Genome-wide identification, phylogeny, and expression analysis of the bHLH gene family in tobacco ( Nicotiana tabacum). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:1747-1764. [PMID: 34539114 PMCID: PMC8405835 DOI: 10.1007/s12298-021-01042-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/24/2021] [Accepted: 07/27/2021] [Indexed: 05/05/2023]
Abstract
UNLABELLED The basic helix-loop-helix (bHLH) is the second-largest TF family in plants that play important roles in plant growth, development, and stress responses. In this study, a total of 100 bHLHs were identified using Hidden Markov Model profiles in the Nicotiana tabacum genome, clustered into 15 major groups (I-XV) based on their conserved domains and phylogenetic relationships. Group VIII genes were found to be the most abundant, with 27 NtbHLH members. The expansion of NtbHLHs in the genome was due to segmental and tandem duplication. The purifying selection was found to have an important role in the evolution of NtHLHs. Subsequent qRT-PCR validation of five selected genes from transcriptome data revealed that NtbHLH3.1, NtbHLH3.2, NtbHLH24, NtbHLH50, and NtbHLH59.2 have higher expressions at 12 and 24 h in comparison to 0 h (control) of chilling stress. The validated results demonstrated that NtbHLH3.2 and NtbHLH24 genes have 3 and fivefold higher expression at 12 h and 2 and threefold higher expression at 24 h than control plant, shows high sensitivity towards chilling stress. Moreover, the co-expression of positively correlated genes of NtbHLH3.2 and NtbHLH24 confirmed their functional significance in chilling stress response. Therefore, suggesting the importance of NtbHLH3.2 and NtbHLH24 genes in exerting control over the chilling stress responses in tobacco. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01042-x.
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Affiliation(s)
- Nasreen Bano
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Preeti Patel
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001 India
| | - Debasis Chakrabarty
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Sumit Kumar Bag
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
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Julca I, Ferrari C, Flores-Tornero M, Proost S, Lindner AC, Hackenberg D, Steinbachová L, Michaelidis C, Gomes Pereira S, Misra CS, Kawashima T, Borg M, Berger F, Goldberg J, Johnson M, Honys D, Twell D, Sprunck S, Dresselhaus T, Becker JD, Mutwil M. Comparative transcriptomic analysis reveals conserved programmes underpinning organogenesis and reproduction in land plants. NATURE PLANTS 2021; 7:1143-1159. [PMID: 34253868 DOI: 10.1101/2020.10.29.361501] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 06/02/2021] [Indexed: 05/19/2023]
Abstract
The appearance of plant organs mediated the explosive radiation of land plants, which shaped the biosphere and allowed the establishment of terrestrial animal life. The evolution of organs and immobile gametes required the coordinated acquisition of novel gene functions, the co-option of existing genes and the development of novel regulatory programmes. However, no large-scale analyses of genomic and transcriptomic data have been performed for land plants. To remedy this, we generated gene expression atlases for various organs and gametes of ten plant species comprising bryophytes, vascular plants, gymnosperms and flowering plants. A comparative analysis of the atlases identified hundreds of organ- and gamete-specific orthogroups and revealed that most of the specific transcriptomes are significantly conserved. Interestingly, our results suggest that co-option of existing genes is the main mechanism for evolving new organs. In contrast to female gametes, male gametes showed a high number and conservation of specific genes, which indicates that male reproduction is highly specialized. The expression atlas capturing pollen development revealed numerous transcription factors and kinases essential for pollen biogenesis and function.
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Affiliation(s)
- Irene Julca
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Camilla Ferrari
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany
| | - María Flores-Tornero
- Cell Biology and Plant Biochemistry, University of Regensburg, Regensburg, Germany
| | - Sebastian Proost
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- VIB, Center for Microbiology, Leuven, Belgium
| | | | - Dieter Hackenberg
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- School of Life Sciences, Gibbet Hill Campus, The University of Warwick, Coventry, UK
| | - Lenka Steinbachová
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czech Republic
| | - Christos Michaelidis
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czech Republic
| | | | - Chandra Shekhar Misra
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Tomokazu Kawashima
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna, BioCenter (VBC), Vienna, Austria
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA
| | - Michael Borg
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna, BioCenter (VBC), Vienna, Austria
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna, BioCenter (VBC), Vienna, Austria
| | - Jacob Goldberg
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA
| | - Mark Johnson
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA
| | - David Honys
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czech Republic
| | - David Twell
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Stefanie Sprunck
- Cell Biology and Plant Biochemistry, University of Regensburg, Regensburg, Germany
| | - Thomas Dresselhaus
- Cell Biology and Plant Biochemistry, University of Regensburg, Regensburg, Germany
| | - Jörg D Becker
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal.
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
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Julca I, Ferrari C, Flores-Tornero M, Proost S, Lindner AC, Hackenberg D, Steinbachová L, Michaelidis C, Gomes Pereira S, Misra CS, Kawashima T, Borg M, Berger F, Goldberg J, Johnson M, Honys D, Twell D, Sprunck S, Dresselhaus T, Becker JD, Mutwil M. Comparative transcriptomic analysis reveals conserved programmes underpinning organogenesis and reproduction in land plants. NATURE PLANTS 2021; 7:1143-1159. [PMID: 34253868 DOI: 10.1038/s41477-021-00958-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 06/02/2021] [Indexed: 05/22/2023]
Abstract
The appearance of plant organs mediated the explosive radiation of land plants, which shaped the biosphere and allowed the establishment of terrestrial animal life. The evolution of organs and immobile gametes required the coordinated acquisition of novel gene functions, the co-option of existing genes and the development of novel regulatory programmes. However, no large-scale analyses of genomic and transcriptomic data have been performed for land plants. To remedy this, we generated gene expression atlases for various organs and gametes of ten plant species comprising bryophytes, vascular plants, gymnosperms and flowering plants. A comparative analysis of the atlases identified hundreds of organ- and gamete-specific orthogroups and revealed that most of the specific transcriptomes are significantly conserved. Interestingly, our results suggest that co-option of existing genes is the main mechanism for evolving new organs. In contrast to female gametes, male gametes showed a high number and conservation of specific genes, which indicates that male reproduction is highly specialized. The expression atlas capturing pollen development revealed numerous transcription factors and kinases essential for pollen biogenesis and function.
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Affiliation(s)
- Irene Julca
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Camilla Ferrari
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany
| | - María Flores-Tornero
- Cell Biology and Plant Biochemistry, University of Regensburg, Regensburg, Germany
| | - Sebastian Proost
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- VIB, Center for Microbiology, Leuven, Belgium
| | | | - Dieter Hackenberg
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- School of Life Sciences, Gibbet Hill Campus, The University of Warwick, Coventry, UK
| | - Lenka Steinbachová
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czech Republic
| | - Christos Michaelidis
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czech Republic
| | | | - Chandra Shekhar Misra
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Tomokazu Kawashima
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna, BioCenter (VBC), Vienna, Austria
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA
| | - Michael Borg
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna, BioCenter (VBC), Vienna, Austria
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna, BioCenter (VBC), Vienna, Austria
| | - Jacob Goldberg
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA
| | - Mark Johnson
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA
| | - David Honys
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czech Republic
| | - David Twell
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Stefanie Sprunck
- Cell Biology and Plant Biochemistry, University of Regensburg, Regensburg, Germany
| | - Thomas Dresselhaus
- Cell Biology and Plant Biochemistry, University of Regensburg, Regensburg, Germany
| | - Jörg D Becker
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal.
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
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Daras G, Templalexis D, Avgeri F, Tsitsekian D, Karamanou K, Rigas S. Updating Insights into the Catalytic Domain Properties of Plant Cellulose synthase ( CesA) and Cellulose synthase-like ( Csl) Proteins. Molecules 2021; 26:molecules26144335. [PMID: 34299608 PMCID: PMC8306620 DOI: 10.3390/molecules26144335] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/15/2021] [Accepted: 07/15/2021] [Indexed: 11/24/2022] Open
Abstract
The wall is the last frontier of a plant cell involved in modulating growth, development and defense against biotic stresses. Cellulose and additional polysaccharides of plant cell walls are the most abundant biopolymers on earth, having increased in economic value and thereby attracted significant interest in biotechnology. Cellulose biosynthesis constitutes a highly complicated process relying on the formation of cellulose synthase complexes. Cellulose synthase (CesA) and Cellulose synthase-like (Csl) genes encode enzymes that synthesize cellulose and most hemicellulosic polysaccharides. Arabidopsis and rice are invaluable genetic models and reliable representatives of land plants to comprehend cell wall synthesis. During the past two decades, enormous research progress has been made to understand the mechanisms of cellulose synthesis and construction of the plant cell wall. A plethora of cesa and csl mutants have been characterized, providing functional insights into individual protein isoforms. Recent structural studies have uncovered the mode of CesA assembly and the dynamics of cellulose production. Genetics and structural biology have generated new knowledge and have accelerated the pace of discovery in this field, ultimately opening perspectives towards cellulose synthesis manipulation. This review provides an overview of the major breakthroughs gathering previous and recent genetic and structural advancements, focusing on the function of CesA and Csl catalytic domain in plants.
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Arabinogalactan-proteins from non-coniferous gymnosperms have unusual structural features. Carbohydr Polym 2021; 261:117831. [PMID: 33766335 DOI: 10.1016/j.carbpol.2021.117831] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/11/2021] [Accepted: 02/12/2021] [Indexed: 11/24/2022]
Abstract
Arabinogalactan-proteins (AGPs), important signalling molecules of the plant cell wall, are structurally extensively investigated in angiosperms, but information on AGPs in gymnosperms is still limited. We characterized AGPs from the gymnosperms Ginkgo biloba, Ephedra distachya, Encephalartos longifolius and Cycas revoluta. The protein contents are comparable to that of angiosperm AGPs. Hydroxyproline is the site of linking the carbohydrate part and was detected in all AGPs with highest concentration in Cycas AGP (1.1 % of the AGP). Interestingly, with the exception of Cycas, all AGPs contained the monosaccharide 3-O-methylrhamnose not present in angiosperm polysaccharides. The carbohydrate moieties of Cycas and Ephredra showed the main components 1,3,6-linked galactose and terminal arabinose typical of angiosperm AGPs, whereas that of Ginkgo AGP was unique with 1,4-linked galactose as dominant structural element. Bioinformatic search for glycosyltransferases in Ginkgo genome also revealed a lower number of galactosyltransferases responsible for biosynthesis of the 1,3-Gal/1,6-Gal AGP backbone.
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38
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Bauer U, Müller UK, Poppinga S. Complexity and diversity of motion amplification and control strategies in motile carnivorous plant traps. Proc Biol Sci 2021; 288:20210771. [PMID: 34036802 PMCID: PMC8150269 DOI: 10.1098/rspb.2021.0771] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Similar to animals, plants have evolved mechanisms for elastic energy storage and release to power and control rapid motion, yet both groups have been largely studied in isolation. This is exacerbated by the lack of consistent terminology and conceptual frameworks describing elastically powered motion in both groups. Iconic examples of fast movements can be found in carnivorous plants, which have become important models to study biomechanics, developmental processes, evolution and ecology. Trapping structures and processes vary considerably between different carnivorous plant groups. Using snap traps, suction traps and springboard-pitfall traps as examples, we illustrate how traps mix and match various mechanisms to power, trigger and actuate motions that contribute to prey capture, retention and digestion. We highlight a fundamental trade-off between energetic investment and movement control and discuss it in a functional-ecological context.
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Affiliation(s)
- Ulrike Bauer
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Ulrike K Müller
- Department of Biology, California State University Fresno, Fresno, CA, USA
| | - Simon Poppinga
- Plant Biomechanics Group, Botanic Garden, University of Freiburg, Freiburg, Germany.,Cluster of Excellence livMatS @ FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Freiburg, Germany
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39
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Brejšková L, Hála M, Rawat A, Soukupová H, Cvrčková F, Charlot F, Nogué F, Haluška S, Žárský V. SEC6 exocyst subunit contributes to multiple steps of growth and development of Physcomitrella (Physcomitrium patens). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:831-843. [PMID: 33599020 DOI: 10.1111/tpj.15205] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 12/18/2020] [Accepted: 01/08/2021] [Indexed: 06/12/2023]
Abstract
Spatially directed cell division and expansion is important for plant growth and morphogenesis and relies on cooperation between the cytoskeleton and the secretory pathway. The phylogenetically conserved octameric complex exocyst mediates exocytotic vesicle tethering at the plasma membrane. Unlike other exocyst subunits of land plants, the core exocyst subunit SEC6 exists as a single paralog in Physcomitrium patens and Arabidopsis thaliana genomes. Arabidopsis SEC6 (AtSEC6) loss-of-function (LOF) mutation causes male gametophytic lethality. Our attempts to inactivate the P. patens SEC6 gene, PpSEC6, using targeted gene replacement produced two independent partial LOF ('weak allele') mutants via perturbation of the PpSEC6 gene locus. These mutants exhibited the same pleiotropic developmental defects: protonema with dominant chloronema stage; diminished caulonemal filament elongation rate; and failure in post-initiation gametophore development. Mutant gametophore buds, mostly initiated from chloronema cells, exhibited disordered cell file organization and cross-wall perforations, resulting in arrested development at the eight- to 10-cell stage. Complementation of both sec6 moss mutant lines by both PpSEC6 and AtSEC6 cDNA rescued gametophore development, including sexual organ differentiation. However, regular sporophyte formation and viable spore production were recovered only by the expression of PpSEC6, whereas the AtSEC6 complementants were only rarely fertile, indicating moss-specific SEC6 functions.
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Affiliation(s)
- Lucie Brejšková
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Rozvojová 263, Prague 6, 165 02, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 128 44, Prague 2, Czech Republic
| | - Michal Hála
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Rozvojová 263, Prague 6, 165 02, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 128 44, Prague 2, Czech Republic
| | - Anamika Rawat
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Rozvojová 263, Prague 6, 165 02, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 128 44, Prague 2, Czech Republic
| | - Hana Soukupová
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Rozvojová 263, Prague 6, 165 02, Czech Republic
| | - Fatima Cvrčková
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 128 44, Prague 2, Czech Republic
| | - Florence Charlot
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, 78000, France
| | - Fabien Nogué
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, 78000, France
| | - Samuel Haluška
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Rozvojová 263, Prague 6, 165 02, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 128 44, Prague 2, Czech Republic
| | - Viktor Žárský
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Rozvojová 263, Prague 6, 165 02, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 128 44, Prague 2, Czech Republic
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Yu J, Zhang Y, Liu W, Wang H, Wen S, Zhang Y, Xu L. Molecular Evolution of Auxin-Mediated Root Initiation in Plants. Mol Biol Evol 2021; 37:1387-1393. [PMID: 31504735 DOI: 10.1093/molbev/msz202] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The root originated independently in euphyllophytes (ferns and seed plants) and lycophytes; however, the molecular evolutionary route of root initiation remains elusive. By analyses of the fern Ceratopteris richardii and seed plants, here we show that the molecular pathway involving auxin, intermediate-clade WUSCHEL-RELATED HOMEOBOX (IC-WOX) genes, and WUSCHEL-clade WOX (WC-WOX) genes could be conserved in root initiation. We propose that the "auxin>IC-WOX>WC-WOX" module in root initiation might have arisen in the common ancestor of euphyllophytes during the second origin of roots, and that this module has further developed during the evolution of different root types in ferns and seed plants.
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Affiliation(s)
- Jie Yu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yuyun Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wu Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Hua Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Shaoting Wen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,College of Life and Environment Sciences, Shanghai Normal University, Shanghai, China
| | - Yijing Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
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Klápště J, Kremer A, Burg K, Garnier-Géré P, El-Dien OG, Ratcliffe B, El-Kassaby YA, Porth I. Quercus species divergence is driven by natural selection on evolutionarily less integrated traits. Heredity (Edinb) 2021; 126:366-382. [PMID: 33110229 PMCID: PMC8027598 DOI: 10.1038/s41437-020-00378-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 10/07/2020] [Accepted: 10/07/2020] [Indexed: 11/09/2022] Open
Abstract
Functional traits are organismal attributes that can respond to environmental cues, thereby providing important ecological functions. In addition, an organism's potential for adaptation is defined by the patterns of covariation among groups of functionally related traits. Whether an organism is evolutionarily constrained or has the potential for adaptation is based on the phenotypic integration or modularity of these traits. Here, we revisited leaf morphology in two European sympatric white oaks (Quercus petraea (Matt.) Liebl. and Quercus robur L.), sampling 2098 individuals, across much of their geographical distribution ranges. At the phenotypic level, leaf morphology traditionally encompasses discriminant attributes among different oak species. Here, we estimated in situ heritability, genetic correlation, and integration across such attributes. Also, we performed Selection Response Decomposition to test these traits for potential differences in oak species' evolutionary responses. Based on the uncovered functional units of traits (modules) in our study, the morphological module "leaf size gradient" was highlighted among functionally integrated traits. Equally, this module was defined in both oaks as being under "global regulation" in vegetative bud establishment and development. Lamina basal shape and intercalary veins' number were not, or, less integrated within the initially defined leaf functional unit, suggesting more than one module within the leaf traits' ensemble. Since these traits generally show the greatest species discriminatory power, they potentially underwent effective differential response to selection among oaks. Indeed, the selection of these traits could have driven the ecological preferences between the two sympatric oaks growing under different microclimates.
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Affiliation(s)
- Jaroslav Klápště
- Department of Genetics and Physiology of Forest Trees, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences in Prague, Kamýcká 129, 165 21, Prague 6, Czechia.
- Scion (New Zealand Forest Research Institute Ltd.), 49 Sala Street, Whakarewarewa, Rotorua, 3010, New Zealand.
| | - Antoine Kremer
- INRA, UMR Biodiversité Gènes et Communautés, 69 route d'Arcachon, 33612, Cestas Cedex, France
- University of Bordeaux, UMR 1202, Biodiversité Gènes et Communautés, F-33400, Talence, France
| | - Kornel Burg
- Department of Health and Environment (Bioresources), AIT Austrian Institute of Technology, Konrad-Lorenz-Straβe 24, 3430, Tulln, Austria
| | - Pauline Garnier-Géré
- INRA, UMR Biodiversité Gènes et Communautés, 69 route d'Arcachon, 33612, Cestas Cedex, France
- University of Bordeaux, UMR 1202, Biodiversité Gènes et Communautés, F-33400, Talence, France
| | - Omnia Gamal El-Dien
- Pharmacognosy Department, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
| | - Blaise Ratcliffe
- Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Ilga Porth
- Département des sciences du bois et de la forêt, Université Laval, 1030, Avenue de la Médecine, Québec, QC, G1V 0A6, Canada
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Halawa M, Cortleven A, Schmülling T, Heyl A. Characterization of CHARK, an unusual cytokinin receptor of rice. Sci Rep 2021; 11:1722. [PMID: 33462253 PMCID: PMC7814049 DOI: 10.1038/s41598-020-80223-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 10/21/2020] [Indexed: 11/14/2022] Open
Abstract
The signal transduction of the plant hormone cytokinin is mediated by a His-to-Asp phosphorelay. The canonical cytokinin receptor consists of an extra cytoplasmic hormone binding domain named cyclase/histidine kinase associated sensory extracellular (CHASE) and cytoplasmic histidine kinase and receiver domains. In addition to classical cytokinin receptors, a different type receptor—named CHASE domain receptor serine/threonine kinase (CHARK)—is also present in rice. It contains the same ligand binding domain as other cytokinin receptors but has a predicted Ser/Thr—instead of a His-kinase domain. Bioinformatic analysis indicates that CHARK is a retrogene and a product of trans-splicing. Here, we analyzed whether CHARK can function as a bona fide cytokinin receptor. A biochemical assay demonstrated its ability to bind cytokinin. Transient expression of CHARK in protoplasts increased their response to cytokinin. Expression of CHARK in an Arabidopsis receptor double mutant complemented its growth defects and restored the ability to activate cytokinin response genes, clearly demonstrating that CHARK functions as a cytokinin receptor. We propose that the CHARK gene presents an evolutionary novelty in the cytokinin signaling system.
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Affiliation(s)
- Mhyeddeen Halawa
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Science, Freie Universität Berlin, Albrecht-Thaer-Weg 6, 14195, Berlin, Germany
| | - Anne Cortleven
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Science, Freie Universität Berlin, Albrecht-Thaer-Weg 6, 14195, Berlin, Germany
| | - Thomas Schmülling
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Science, Freie Universität Berlin, Albrecht-Thaer-Weg 6, 14195, Berlin, Germany
| | - Alexander Heyl
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Science, Freie Universität Berlin, Albrecht-Thaer-Weg 6, 14195, Berlin, Germany. .,Biology Department, Adelphi University, 1 South Avenue, Garden City, NY, 11530-0701, USA.
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Márquez-Zacarías P, Pineau RM, Gomez M, Veliz-Cuba A, Murrugarra D, Ratcliff WC, Niklas KJ. Evolution of Cellular Differentiation: From Hypotheses to Models. Trends Ecol Evol 2021; 36:49-60. [PMID: 32829916 DOI: 10.1016/j.tree.2020.07.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 07/21/2020] [Accepted: 07/23/2020] [Indexed: 01/28/2023]
Abstract
Cellular differentiation is one of the hallmarks of complex multicellularity, allowing individual organisms to capitalize on among-cell functional diversity. The evolution of multicellularity is a major evolutionary transition that allowed for the increase of organismal complexity in multiple lineages, a process that relies on the functional integration of cell-types within an individual. Multiple hypotheses have been proposed to explain the origins of cellular differentiation, but we lack a general understanding of what makes one cell-type distinct from others, and how such differentiation arises. Here, we describe how the use of Boolean networks (BNs) can aid in placing empirical findings into a coherent conceptual framework, and we emphasize some of the standing problems when interpreting data and model behaviors.
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Affiliation(s)
- Pedro Márquez-Zacarías
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, GA, USA; School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Rozenn M Pineau
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, GA, USA; School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Marcella Gomez
- Department of Applied Mathematics, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Alan Veliz-Cuba
- Department of Mathematics, University of Dayton, Dayton, OH, USA
| | - David Murrugarra
- Department of Mathematics, University of Kentucky, Lexington, KY, USA
| | - William C Ratcliff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Karl J Niklas
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA.
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Serrano-Bueno G, Sánchez de Medina Hernández V, Valverde F. Photoperiodic Signaling and Senescence, an Ancient Solution to a Modern Problem? FRONTIERS IN PLANT SCIENCE 2021; 12:634393. [PMID: 33777070 PMCID: PMC7988197 DOI: 10.3389/fpls.2021.634393] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/12/2021] [Indexed: 05/22/2023]
Abstract
The length of the day (photoperiod) is a robust seasonal signal originated by earth orbital and translational movements, a resilient external cue to the global climate change, and a predictable hint to initiate or complete different developmental programs. In eukaryotic algae, the gene expression network that controls the cellular response to photoperiod also regulates other basic physiological functions such as starch synthesis or redox homeostasis. Land plants, evolving in a novel and demanding environment, imbued these external signals within the regulatory networks controlling organogenesis and developmental programs. Unlike algae that largely have to deal with cellular physical cues, within the course of evolution land plants had to transfer this external information from the receiving organs to the target tissues, and mobile signals such as hormones were recruited and incorporated in the regulomes. Control of senescence by photoperiod, as suggested in this perspective, would be an accurate way to feed seasonal information into a newly developed function (senescence) using an ancient route (photoperiodic signaling). This way, the plant would assure that two coordinated aspects of development such as flowering and organ senescence were sequentially controlled. As in the case of senescence, there is growing evidence to support the idea that harnessing the reliability of photoperiod regulation over other, more labile signaling pathways could be used as a robust breeding tool to enhance plants against the harmful effects of climate change.
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Aragón-Raygoza A, Vasco A, Blilou I, Herrera-Estrella L, Cruz-Ramírez A. Development and Cell Cycle Activity of the Root Apical Meristem in the Fern Ceratopteris richardii. Genes (Basel) 2020; 11:E1455. [PMID: 33291610 PMCID: PMC7761924 DOI: 10.3390/genes11121455] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/23/2020] [Accepted: 11/26/2020] [Indexed: 12/11/2022] Open
Abstract
Ferns are a representative clade in plant evolution although underestimated in the genomic era. Ceratopteris richardii is an emergent model for developmental processes in ferns, yet a complete scheme of the different growth stages is necessary. Here, we present a developmental analysis, at the tissue and cellular levels, of the first shoot-borne root of Ceratopteris. We followed early stages and emergence of the root meristem in sporelings. While assessing root growth, the first shoot-borne root ceases its elongation between the emergence of the fifth and sixth roots, suggesting Ceratopteris roots follow a determinate developmental program. We report cell division frequencies in the stem cell niche after detecting labeled nuclei in the root apical cell (RAC) and derivatives after 8 h of exposure. These results demonstrate the RAC has a continuous mitotic activity during root development. Detection of cell cycle activity in the RAC at early times suggests this cell acts as a non-quiescent organizing center. Overall, our results provide a framework to study root function and development in ferns and to better understand the evolutionary history of this organ.
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Affiliation(s)
- Alejandro Aragón-Raygoza
- Molecular and Developmental Complexity Group at Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera, Irapuato-León, Irapuato 36821, Guanajuato, Mexico;
- Metabolic Engineering Group, Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera, Irapuato-León, Irapuato 36821, Guanajuato, Mexico;
| | - Alejandra Vasco
- Botanical Research Institute of Texas (BRIT), Fort Worth, TX 76107-3400, USA;
| | - Ikram Blilou
- Laboratory of Plant Cell and Developmental Biology, Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia;
| | - Luis Herrera-Estrella
- Metabolic Engineering Group, Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera, Irapuato-León, Irapuato 36821, Guanajuato, Mexico;
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409, USA
| | - Alfredo Cruz-Ramírez
- Molecular and Developmental Complexity Group at Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera, Irapuato-León, Irapuato 36821, Guanajuato, Mexico;
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Rymen B, Ferrafiat L, Blevins T. Non-coding RNA polymerases that silence transposable elements and reprogram gene expression in plants. Transcription 2020; 11:172-191. [PMID: 33180661 PMCID: PMC7714444 DOI: 10.1080/21541264.2020.1825906] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Multisubunit RNA polymerase (Pol) complexes are the core machinery for gene expression in eukaryotes. The enzymes Pol I, Pol II and Pol III transcribe distinct subsets of nuclear genes. This family of nuclear RNA polymerases expanded in terrestrial plants by the duplication of Pol II subunit genes. Two Pol II-related enzymes, Pol IV and Pol V, are highly specialized in the production of regulatory, non-coding RNAs. Pol IV and Pol V are the central players of RNA-directed DNA methylation (RdDM), an RNA interference pathway that represses transposable elements (TEs) and selected genes. Genetic and biochemical analyses of Pol IV/V subunits are now revealing how these enzymes evolved from ancestral Pol II to sustain non-coding RNA biogenesis in silent chromatin. Intriguingly, Pol IV-RdDM regulates genes that influence flowering time, reproductive development, stress responses and plant–pathogen interactions. Pol IV target genes vary among closely related taxa, indicating that these regulatory circuits are often species-specific. Data from crops like maize, rice, tomato and Brassicarapa suggest that dynamic repositioning of TEs, accompanied by Pol IV targeting to TE-proximal genes, leads to the reprogramming of plant gene expression over short evolutionary timescales.
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Affiliation(s)
- Bart Rymen
- Institut de biologie moléculaire des plantes, Université de Strasbourg , Strasbourg, France
| | - Laura Ferrafiat
- Institut de biologie moléculaire des plantes, Université de Strasbourg , Strasbourg, France
| | - Todd Blevins
- Institut de biologie moléculaire des plantes, Université de Strasbourg , Strasbourg, France
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Rico-Reséndiz F, Cervantes-Pérez SA, Espinal-Centeno A, Dipp-Álvarez M, Oropeza-Aburto A, Hurtado-Bautista E, Cruz-Hernández A, Bowman JL, Ishizaki K, Arteaga-Vázquez MA, Herrera-Estrella L, Cruz-Ramírez A. Transcriptional and Morpho-Physiological Responses of Marchantia polymorpha upon Phosphate Starvation. Int J Mol Sci 2020; 21:ijms21218354. [PMID: 33171770 PMCID: PMC7672586 DOI: 10.3390/ijms21218354] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 01/22/2023] Open
Abstract
Phosphate (Pi) is a pivotal nutrient that constraints plant development and productivity in natural ecosystems. Land colonization by plants, more than 470 million years ago, evolved adaptive mechanisms to conquer Pi-scarce environments. However, little is known about the molecular basis underlying such adaptations at early branches of plant phylogeny. To shed light on how early divergent plants respond to Pi limitation, we analyzed the morpho-physiological and transcriptional dynamics of Marchantia polymorpha upon Pi starvation. Our phylogenomic analysis highlights some gene networks present since the Chlorophytes and others established in the Streptophytes (e.g., PHR1–SPX1 and STOP1–ALMT1, respectively). At the morpho-physiological level, the response is characterized by the induction of phosphatase activity, media acidification, accumulation of auronidins, reduction of internal Pi concentration, and developmental modifications of rhizoids. The transcriptional response involves the induction of MpPHR1, Pi transporters, lipid turnover enzymes, and MpMYB14, which is an essential transcription factor for auronidins biosynthesis. MpSTOP2 up-regulation correlates with expression changes in genes related to organic acid biosynthesis and transport, suggesting a preference for citrate exudation. An analysis of MpPHR1 binding sequences (P1BS) shows an enrichment of this cis regulatory element in differentially expressed genes. Our study unravels the strategies, at diverse levels of organization, exerted by M. polymorpha to cope with low Pi availability.
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Affiliation(s)
- Félix Rico-Reséndiz
- Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados, Instituto Politécnico Nacional, Irapuato 36824, Guanajuato, Mexico; (F.R.-R.); (A.E.-C.); (M.D.-Á.)
| | - Sergio Alan Cervantes-Pérez
- Plant Physiology and Metabolic Engineering Group, Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados, Instituto Politécnico Nacional, Irapuato 36824, Guanajuato, Mexico; (S.A.C.-P.); (A.O.-A.); (L.H.-E.)
| | - Annie Espinal-Centeno
- Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados, Instituto Politécnico Nacional, Irapuato 36824, Guanajuato, Mexico; (F.R.-R.); (A.E.-C.); (M.D.-Á.)
| | - Melissa Dipp-Álvarez
- Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados, Instituto Politécnico Nacional, Irapuato 36824, Guanajuato, Mexico; (F.R.-R.); (A.E.-C.); (M.D.-Á.)
| | - Araceli Oropeza-Aburto
- Plant Physiology and Metabolic Engineering Group, Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados, Instituto Politécnico Nacional, Irapuato 36824, Guanajuato, Mexico; (S.A.C.-P.); (A.O.-A.); (L.H.-E.)
| | - Enrique Hurtado-Bautista
- Molecular Biology and Microbial Ecology, Unidad Irapuato, Centro de Investigación y Estudios Avanzados, Instituto Politécnico Nacional, Irapuato 36824, Guanajuato, Mexico;
| | - Andrés Cruz-Hernández
- Escuela de Agronomía, Universidad de La Salle Bajío, León 37160, Guanajuato, Mexico;
| | - John L. Bowman
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia;
| | | | - Mario A. Arteaga-Vázquez
- Group of Epigenetics and Developmental Biology, Instituto de Biotecnología y Ecología Aplicada (INBIOTECA), Universidad Veracruzana, Xalapa 91640, Mexico;
| | - Luis Herrera-Estrella
- Plant Physiology and Metabolic Engineering Group, Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados, Instituto Politécnico Nacional, Irapuato 36824, Guanajuato, Mexico; (S.A.C.-P.); (A.O.-A.); (L.H.-E.)
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Alfredo Cruz-Ramírez
- Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados, Instituto Politécnico Nacional, Irapuato 36824, Guanajuato, Mexico; (F.R.-R.); (A.E.-C.); (M.D.-Á.)
- Correspondence: ; Tel.: +52-462-166-3000 (ext. 3005)
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Functional Principles of Morphological and Anatomical Structures in Pinecones. PLANTS 2020; 9:plants9101343. [PMID: 33053691 PMCID: PMC7599471 DOI: 10.3390/plants9101343] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/06/2020] [Accepted: 10/09/2020] [Indexed: 11/16/2022]
Abstract
In order to better understand the functions of plants, it is important to analyze the internal structure of plants with a complex structure, as well as to efficiently monitor the morphology of plants altered by their external environment. This anatomical study investigated structural characteristics of pinecones to provide detailed descriptions of morphological specifications of complex cone scales. We analyzed cross-sectional image data and internal movement patterns in the opening and closing motions of pinecones, which change according to the moisture content of its external environment. It is possible to propose a scientific system for the deformation of complex pinecone for the variable structures due to changes in relative humidity, as well as the application of technology. This study provided a functional principle for a multidisciplinary approach by exploring the morphological properties and anatomical structures of pinecones. Therefore, the results suggest a potential application for use in energy-efficient materials by incorporating hygroscopic principles into engineering technology and also providing basic data for biomimicry research.
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Mhimdi M, Pérez-Pérez JM. Understanding of Adventitious Root Formation: What Can We Learn From Comparative Genetics? FRONTIERS IN PLANT SCIENCE 2020; 11:582020. [PMID: 33123185 PMCID: PMC7573222 DOI: 10.3389/fpls.2020.582020] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 09/18/2020] [Indexed: 05/23/2023]
Abstract
Adventitious root (AR) formation is a complex developmental process controlled by a plethora of endogenous and environmental factors. Based on fossil evidence and genomic phylogeny, AR formation might be considered the default state of plant roots, which likely evolved independently several times. The application of next-generation sequencing techniques and bioinformatics analyses to non-model plants provide novel approaches to identify genes putatively involved in AR formation in multiple species. Recent results uncovered that the regulation of shoot-borne AR formation in monocots is an adaptive response to nutrient and water deficiency that enhances topsoil foraging and improves plant performance. A hierarchy of transcription factors required for AR initiation has been identified from genetic studies, and recent results highlighted the key involvement of additional regulation through microRNAs. Here, we discuss our current understanding of AR formation in response to specific environmental stresses, such as nutrient deficiency, drought or waterlogging, aimed at providing evidence for the integration of the hormone crosstalk required for the activation of root competent cells within adult tissues from which the ARs develop.
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50
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Althoff F, Zachgo S. Transformation of Riccia fluitans, an Amphibious Liverwort Dynamically Responding to Environmental Changes. Int J Mol Sci 2020; 21:E5410. [PMID: 32751392 PMCID: PMC7432341 DOI: 10.3390/ijms21155410] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 07/24/2020] [Accepted: 07/27/2020] [Indexed: 01/21/2023] Open
Abstract
The colonization of land by streptophyte algae, ancestors of embryophyte plants, was a fundamental event in the history of life on earth. Bryophytes are early diversifying land plants that mark the transition from freshwater to terrestrial ecosystems. The amphibious liverwort Riccia fluitans can thrive in aquatic and terrestrial environments and thus represents an ideal organism to investigate this major transition. Therefore, we aimed to establish a transformation protocol for R. fluitans to make it amenable for genetic analyses. An Agrobacterium transformation procedure using R. fluitans callus tissue allows to generate stably transformed plants within 10 weeks. Furthermore, for comprehensive studies spanning all life stages, we demonstrate that the switch from vegetative to reproductive development can be induced by both flooding and poor nutrient availability. Interestingly, a single R. fluitans plant can consecutively adapt to different growth environments and forms distinctive and reversible features of the thallus, photosynthetically active tissue that is thus functionally similar to leaves of vascular plants. The morphological plasticity affecting vegetative growth, air pore formation, and rhizoid development realized by one genotype in response to two different environments makes R. fluitans ideal to study the adaptive molecular mechanisms enabling the colonialization of land by aquatic plants.
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Affiliation(s)
- Felix Althoff
- Botany Department, School of Biology and Chemistry, Osnabrück University, 49076 Osnabrück, Germany
| | - Sabine Zachgo
- Botany Department, School of Biology and Chemistry, Osnabrück University, 49076 Osnabrück, Germany
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