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Li G, Zhao X, Yang J, Hu S, Ponnu J, Kimura S, Hwang I, Torii KU, Hou H. Water wisteria genome reveals environmental adaptation and heterophylly regulation in amphibious plants. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39076061 DOI: 10.1111/pce.15050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 07/03/2024] [Accepted: 07/12/2024] [Indexed: 07/31/2024]
Abstract
Heterophylly is a phenomenon whereby an individual plant dramatically changes leaf shape in response to the surroundings. Hygrophila difformis (Acanthaceae; water wisteria), has recently emerged as a model plant to study heterophylly because of its striking leaf shape variation in response to various environmental factors. When submerged, H. difformis often develops complex leaves, but on land it develops simple leaves. Leaf complexity is also influenced by other factors, such as light density, humidity, and temperature. Here, we sequenced and assembled the H. difformis chromosome-level genome (scaffold N50: 60.43 Mb, genome size: 871.92 Mb), which revealed 36 099 predicted protein-coding genes distributed over 15 pseudochromosomes. H. difformis diverged from its relatives during the Oligocene climate-change period and expanded gene families related to its amphibious habit. Genes related to environmental stimuli, leaf development, and other pathways were differentially expressed in submerged and terrestrial conditions, possibly modulating morphological and physiological acclimation to changing environments. We also found that auxin plays a role in H. difformis heterophylly. Finally, we discovered candidate genes that respond to different environmental conditions and elucidated the role of LATE MERISTEM IDENTITY 1 (LMI1) in heterophylly. We established H. difformis as a model for studying interconnections between environmental adaptation and morphogenesis.
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Affiliation(s)
- Gaojie Li
- The State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xuyao Zhao
- The State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jingjing Yang
- The State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shiqi Hu
- Laboratory of Marine Biological Resources Development and Utilization, Zhejiang Marine Development Research Institute, Zhoushan, Zhejiang, China
| | - Jathish Ponnu
- Joseph Gottlieb Kölreuter Institute for Plant Sciences, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Seisuke Kimura
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
- Center for Plant Sciences, Kyoto Sangyo University, Kyoto, Japan
| | - Inhwan Hwang
- Department of Life Science, Pohang University of Science and Technology, Pohang, South Korea
| | - Keiko U Torii
- Institute of Transformative Biomolecules (WPI-ITbM), Nagoya University, Nagoya, Aichi, Japan
- Howard Hughes Medical Institute, The University of Texas at Austin, Austin, Texas, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Hongwei Hou
- The State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
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Wang Z, Li F, Feng C, Zheng D, Pang Z, Ma Y, Xu Y, Yang C, Li X, Peng S, Liu Z, Mu X. 1-Naphthaleneacetic Acid Improved the In Vitro Cell Culturing by Inhibiting Apoptosis. Adv Biol (Weinh) 2024; 8:e2300593. [PMID: 38221687 DOI: 10.1002/adbi.202300593] [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: 11/04/2023] [Revised: 12/12/2023] [Indexed: 01/16/2024]
Abstract
In vitro cell culturing witnessed its applications in scientific research and industrial activities. Attempts to shorten the doubling time of cultured cells have never ceased. In plants, auxin is applied to promote plant growth, the synthetic derivative 1-Naphthaleneacetic acid (NAA) is a good example. Despite the auxin's naturally occurring receptors are not present in mammalian cells, studies suggested they may affect cell culturing. Yet the effects and mechanisms are still unclear. Here, an up to 2-fold increase in the yield of in vitro cultured human cells is observed. Different types of human cell lines and primary cells are tested and found that NAA is effective in all the cells tested. The PI staining followed by FACS suggested that NAA do not affect the cell cycling. Apoptosis-specific dye staining analysis implicated that NAA rescued cell death. Further bulk RNA sequencing is done and it is identified that the lipid metabolism-engaging and anti-apoptosis gene, ANGPTL4, is enhanced in expression upon NAA treatment. Studies on ANGPTL4 knockout cells indicated that ANGPTL4 is required for NAA-mediated response. Thus, the data identified a beneficial role of NAA in human cell culturing and highlighted its potency in in vitro cell culturing.
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Affiliation(s)
- Zhongyi Wang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
- Tianjin University and Health-Biotech United Group Joint Laboratory of Innovative Drug Development and Translational Medicine, Tianjin University, Tianjin, 300072, China
| | - Fengqi Li
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
- Tianjin University and Health-Biotech United Group Joint Laboratory of Innovative Drug Development and Translational Medicine, Tianjin University, Tianjin, 300072, China
| | - Chunjing Feng
- Tianjin University and Health-Biotech United Group Joint Laboratory of Innovative Drug Development and Translational Medicine, Tianjin University, Tianjin, 300072, China
- Health-Biotech Group Stem Cell Research Institute, Tianjin, 301799, China
| | - Dongpeng Zheng
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
- Tianjin University and Health-Biotech United Group Joint Laboratory of Innovative Drug Development and Translational Medicine, Tianjin University, Tianjin, 300072, China
| | - Zhaojun Pang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
- Tianjin University and Health-Biotech United Group Joint Laboratory of Innovative Drug Development and Translational Medicine, Tianjin University, Tianjin, 300072, China
| | - Yue Ma
- Tianjin University and Health-Biotech United Group Joint Laboratory of Innovative Drug Development and Translational Medicine, Tianjin University, Tianjin, 300072, China
- Health-Biotech Group Stem Cell Research Institute, Tianjin, 301799, China
| | - Ying Xu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
- Tianjin University and Health-Biotech United Group Joint Laboratory of Innovative Drug Development and Translational Medicine, Tianjin University, Tianjin, 300072, China
| | - Ce Yang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
- Tianjin University and Health-Biotech United Group Joint Laboratory of Innovative Drug Development and Translational Medicine, Tianjin University, Tianjin, 300072, China
| | - Xueren Li
- Jinnan Hospital, Tianjin University, (Tianjin Jinnan Hospital), Tianjin, 300350, China
| | - Shouchun Peng
- Jinnan Hospital, Tianjin University, (Tianjin Jinnan Hospital), Tianjin, 300350, China
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, 300072, China
| | - Zichuan Liu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
- Tianjin University and Health-Biotech United Group Joint Laboratory of Innovative Drug Development and Translational Medicine, Tianjin University, Tianjin, 300072, China
| | - Xin Mu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
- Tianjin University and Health-Biotech United Group Joint Laboratory of Innovative Drug Development and Translational Medicine, Tianjin University, Tianjin, 300072, China
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Daroodi Z, Taheri P. The genus Acrophialophora: History, phylogeny, morphology, beneficial effects and pathogenicity. Fungal Genet Biol 2024; 171:103875. [PMID: 38367800 DOI: 10.1016/j.fgb.2024.103875] [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: 11/04/2023] [Revised: 01/21/2024] [Accepted: 02/12/2024] [Indexed: 02/19/2024]
Abstract
The genus Acrophialophora is a thermotolerant fungus, which is widely distributed in temperate and tropical zones. This fungus is classified in Ascomycota and belongs to the Chaetomiaceae family and the genera of Parathielavia, Pseudothielavia and Hyalosphaerella are closely related to Acrophialophora. For this genus have been reported 28 species so far, which two species of Acrophialophora jodhpurensis and Acrophialophora teleoafricana produce only sexual phase and other species produce asexual form. Therefore, producing both sexual and asexual forms were not reported by any species. Many applications were reported by some species in agriculture, pharmacy and industry. Production of enzymes, antimicrobial metabolites and plant growth-promoting factors were reported by some species. The species of A. nainiana is used in the industries of textile, fruit juice, pulp and paper due to extracellular enzyme production. Also, other species produce extracellular enzymes that can be used in various industries. The species Acrophialophora are used in the composting industry due to the production of various enzymes and to be thermotolerant. In addition, some species were isolated from hostile environmental conditions. Therefore has been suggested that it can be used for mycoremediation. Also, antimicrobial metabolites of Acrophialophora have been reported to be effective against human and plant pathogens. In contrast to the beneficial effects described, the Acrophialophora pathogenicity has been rarely reported. Two species A. fusispora and A. levis are opportunistic fungi and have been reported as pathogens in humans, animals and plants. Currently, the development and applications of Acrophialophora species have increased more than past. To our knowledge, there is no report with comprehensive information on the species of Acrophialophora, which include their disadvantage and beneficial effects, particularly in agriculture. Therefore, it seems necessary to pay more in-depth attention to the application of this genus as a beneficial fungus in agriculture, pharmaceutical and industry. This review is focused on the history, phylogeny, morphology, valuable roles of Acrophialophora and pathogenicity.
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Affiliation(s)
- Zoha Daroodi
- Department of Plant Protection, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Parissa Taheri
- Department of Plant Protection, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran.
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Pietrykowska H, Alisha A, Aggarwal B, Watanabe Y, Ohtani M, Jarmolowski A, Sierocka I, Szweykowska-Kulinska Z. Conserved and non-conserved RNA-target modules in plants: lessons for a better understanding of Marchantia development. PLANT MOLECULAR BIOLOGY 2023; 113:121-142. [PMID: 37991688 PMCID: PMC10721683 DOI: 10.1007/s11103-023-01392-y] [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: 06/27/2023] [Accepted: 10/19/2023] [Indexed: 11/23/2023]
Abstract
A wide variety of functional regulatory non-coding RNAs (ncRNAs) have been identified as essential regulators of plant growth and development. Depending on their category, ncRNAs are not only involved in modulating target gene expression at the transcriptional and post-transcriptional levels but also are involved in processes like RNA splicing and RNA-directed DNA methylation. To fulfill their molecular roles properly, ncRNAs must be precisely processed by multiprotein complexes. In the case of small RNAs, DICER-LIKE (DCL) proteins play critical roles in the production of mature molecules. Land plant genomes contain at least four distinct classes of DCL family proteins (DCL1-DCL4), of which DCL1, DCL3 and DCL4 are also present in the genomes of bryophytes, indicating the early divergence of these genes. The liverwort Marchantia polymorpha has become an attractive model species for investigating the evolutionary history of regulatory ncRNAs and proteins that are responsible for ncRNA biogenesis. Recent studies on Marchantia have started to uncover the similarities and differences in ncRNA production and function between the basal lineage of bryophytes and other land plants. In this review, we summarize findings on the essential role of regulatory ncRNAs in Marchantia development. We provide a comprehensive overview of conserved ncRNA-target modules among M. polymorpha, the moss Physcomitrium patens and the dicot Arabidopsis thaliana, as well as Marchantia-specific modules. Based on functional studies and data from the literature, we propose new connections between regulatory pathways involved in Marchantia's vegetative and reproductive development and emphasize the need for further functional studies to understand the molecular mechanisms that control ncRNA-directed developmental processes.
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Affiliation(s)
- Halina Pietrykowska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Alisha Alisha
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Bharti Aggarwal
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Yuichiro Watanabe
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, 153-8902, Japan
| | - Misato Ohtani
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, 630-0192, Nara, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8562, Chiba, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Kanagawa, Japan
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Izabela Sierocka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland.
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland.
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Parra-Aguilar TJ, Sarmiento-López LG, Santana O, Olivares JE, Pascual-Morales E, Jiménez-Jiménez S, Quero-Hostos A, Palacios-Martínez J, Chávez-Martínez AI, Cárdenas L. TETRASPANIN 8-1 from Phaseolus vulgaris plays a key role during mutualistic interactions. FRONTIERS IN PLANT SCIENCE 2023; 14:1152493. [PMID: 37465390 PMCID: PMC10352089 DOI: 10.3389/fpls.2023.1152493] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 06/13/2023] [Indexed: 07/20/2023]
Abstract
Arbuscular mycorrhizal (AM) fungi and rhizobia form two of the most important plant-microbe associations for the assimilation of phosphorus (P) and nitrogen (N). Symbiont-derived signals are able to coordinate the infection process by triggering multiple responses in the plant root, such as calcium influxes and oscillations, increased reactive oxygen species (ROS), cytoskeletal rearrangements and altered gene expression. An examination was made of the role of tetraspanins, which are transmembrane proteins that self-organize into tetraspanin web regions, where they recruit specific proteins into platforms required for signal transduction, membrane fusion, cell trafficking, and ROS generation. In plant cells, tetraspanins are scaffolding proteins associated with root radial patterning, biotic and abiotic stress responses, cell fate determination, plasmodesmata and hormonal regulation. Some plant tetraspanins, such as Arabidopsis thaliana TETRASPANIN 8 and TETRASPANIN 9 (AtTET8 and AtTET9) are associated with exosomes during inter-kingdom communication. In this study, a homolog of AtTET8, PvTET8-1, in common bean (Phaseolus vulgaris L. var. Negro Jamapa) was examined in roots during interactions with Rhizobium tropici and Rhizophagus irregularis. The promoter of PvTET8-1 contained several cis-acting regulatory DNA elements potentially related to mutualistic interactions, and PvTET8-1 was transcriptionally activated during AM fungal and rhizobial associations. Silencing it decreased the size and number of nodules, nitrogen fixation, and mycorrhizal arbuscule formation, whereas overexpressing it increased the size and number of nodules, and mycorrhizal arbuscule formation but decreased nitrogen fixation. PvTET8-1 appears to be an important element in both of these mutualistic interactions, perhaps through its interaction with NADPH oxidase and the generation of ROS during the infection processes.
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Affiliation(s)
- Thelma J. Parra-Aguilar
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Luis G. Sarmiento-López
- Departamento de Biotecnología Agrícola, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional Unidad Sinaloa-Instituto Politécnico Nacional, Guasave, Sinaloa, Mexico
| | - Olivia Santana
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Juan Elías Olivares
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Edgar Pascual-Morales
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Saul Jiménez-Jiménez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Andrea Quero-Hostos
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Janet Palacios-Martínez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Ana I. Chávez-Martínez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Luis Cárdenas
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
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Ahmad S, Yang K, Chen G, Huang J, Hao Y, Tu S, Zhou Y, Zhao K, Chen J, Shi X, Lan S, Liu Z, Peng D. Transcriptome mining of hormonal and floral integrators in the leafless flowers of three cymbidium orchids. FRONTIERS IN PLANT SCIENCE 2022; 13:1043099. [PMID: 36311107 PMCID: PMC9608508 DOI: 10.3389/fpls.2022.1043099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Flowering is the most studied ornamental trait in orchids where long vegetative phase may span up to three years. Cymbidium orchids produce beautiful flowers with astonishing shapes and pleasant scent. However, an unusually long vegetative phase is a major drawback to their ornamental value. We observed that under certain culture conditions, three cymbidium species (Cymbidium ensifolium, C. goeringii and C. sinense) skipped vegetative growth phase and directly flowered within six months, that could be a breakthrough for future orchids with limited vegetative growth. Hormonal and floral regulators could be the key factors arresting vegetative phase. Therefore, transcriptomic analyses were performed for leafless flowers and normal vegetative leaves to ascertain differentially expressed genes (DEGs) related to hormones (auxin, cytokinin, gibberellin, abscisic acid and ethylene), floral integrators and MADS-box genes. A significant difference of cytokinin and floral regulators was observed among three species as compared to other hormones. The MADS-box genes were significantly expressed in the leafless flowers of C. sinense as compared to other species. Among the key floral regulators, CONSTANS and AGAMOUS-like genes showed the most differential expression in the leafless flowers as compared to leaves where the expression was negligible. However, CONSTANS also showed downregulation. Auxin efflux carriers were mainly downregulated in the leafless flowers of C. ensifolium and C. sinense, while they were upregulated in C. goeringii. Moreover, gibberellin and cytokinin genes were also downregulated in C. ensifolium and C. sinense flowers, while they were upregulated in C. goeringii, suggesting that species may vary in their responses. The data mining thus, outsources the valuable information to direct future research on orchids at industrial levels.
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Affiliation(s)
- Sagheer Ahmad
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kang Yang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Guizhen Chen
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jie Huang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yang Hao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Song Tu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuzhen Zhou
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kai Zhao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Jinliao Chen
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaoling Shi
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Siren Lan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhongjian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Donghui Peng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, China
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Jedličková V, Ebrahimi Naghani S, Robert HS. On the trail of auxin: Reporters and sensors. THE PLANT CELL 2022; 34:3200-3213. [PMID: 35708654 PMCID: PMC9421466 DOI: 10.1093/plcell/koac179] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/07/2022] [Indexed: 05/22/2023]
Abstract
The phytohormone auxin is a master regulator of plant growth and development in response to many endogenous and environmental signals. The underlying coordination of growth is mediated by the formation of auxin maxima and concentration gradients. The visualization of auxin dynamics and distribution can therefore provide essential information to increase our understanding of the mechanisms by which auxin orchestrates these growth and developmental processes. Several auxin reporters have been developed to better perceive the auxin distribution and signaling machinery in vivo. This review focuses on different types of auxin reporters and biosensors used to monitor auxin distribution and its dynamics, as well as auxin signaling, at the cellular and tissue levels in different plant species. We provide a brief history of each reporter and biosensor group and explain their principles and utilities.
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Effects of Naphthaleneacetic Acid, Indole-3-Butyric Acid and Zinc Sulfate on the Rooting and Growth of Mulberry Cuttings. INTERNATIONAL JOURNAL OF PLANT BIOLOGY 2022. [DOI: 10.3390/ijpb13030021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The mulberry tree (Morus alba) is a perennial and fast-growing tree distributed worldwide under different climatic conditions. Most of the world’s silk production (>90%) is facilitated by the feeding of silkworm larvae on the leaves of mulberry (Morus alba L.) varieties. Therefore, exploration of the protocol for improving the propagation efficiency and increasing the reproductive capacity of M. alba varieties could be of great significance. This study aimed to determine the effect of four concentrations (0, 100, 200 and 400 mg L−1) each of naphthaleneacetic acid (NAA), indole-3-butyric acid (IBA), and zinc sulfate (0, 100 and 200 mg L−1), supplied separately or combined, on the rooting and growth of mulberry cuttings. M. alba cuttings were immersed for 5 s in each solution using the quick-dip method and subsequently, the cuttings were dried and planted in plastic pots and maintained in a greenhouse for 60 days. The number of leaves (NL), longest root size (LRS), longest stem size (LSS), number of rooted cuttings (NRC), number of stems per tree (NSP), rooting percentage (RP), wet root weight (WRW), dry root weight (DRW), wet stem weight (WSW), dry stem weight (DSW), wet leaf weight (WLW) and dry leaf weight (DLW) were evaluated. The results obtained showed an increase in all growth parameters of the mulberry cuttings. Treatments of hormones (IBA and NAA) and Zn sulfate were effective on LSS, LRS and WSW. The highest values of LSS were obtained for the treatments T5, T6, T14, T15, T16 and T18. Moreover, T5, T12 and T10 showed the highest values of LRS. The highest value of WSW was observed for T18, T5, T14, T15 and T16. The highest values of WLW and DLW were observed in T20 and T14. Dry stem weight (DSW) was high in T18 and T14. The application of NAA (at 200 mg L−1), IBA (200 and 400 mg L−1) and Zn sulfate (200 and 400 mg L−1), either alone or in double combination, can be a suitable and reliable method for mulberry propagation.
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Understanding the Role of PIN Auxin Carrier Genes under Biotic and Abiotic Stresses in Olea europaea L. BIOLOGY 2022; 11:biology11071040. [PMID: 36101418 PMCID: PMC9312197 DOI: 10.3390/biology11071040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/19/2022] [Accepted: 06/19/2022] [Indexed: 11/16/2022]
Abstract
The PIN-FORMED (PIN) proteins represent the most important polar auxin transporters in plants. Here, we characterized the PIN gene family in two olive genotypes, the Olea europaea subsp. europaea var. sylvestris and the var. europaea (cv. ‘Farga’). Twelve and 17 PIN genes were identified for vars. sylvestris and europaea, respectively, being distributed across 6 subfamilies. Genes encoding canonical OePINs consist of six exons, while genes encoding non-canonical OePINs are composed of five exons, with implications at protein specificities and functionality. A copia-LTR retrotransposon located in intron 4 of OePIN2b of var. europaea and the exaptation of partial sequences of that element as exons of the OePIN2b of var. sylvestris reveals such kind of event as a driving force in the olive PIN evolution. RNA-seq data showed that members from the subfamilies 1, 2, and 3 responded to abiotic and biotic stress factors. Co-expression of OePINs with genes involved in stress signaling and oxidative stress homeostasis were identified. This study highlights the importance of PIN genes on stress responses, contributing for a holistic understanding of the role of auxins in plants.
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10
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Ajayan KV, Saranya K, Harilal CC. Indole-3-butyric acid mediated growth and biochemical enhancement in three Selenastracean green microalgae under limited supply of nitrogen source. J Biotechnol 2022; 351:60-73. [DOI: 10.1016/j.jbiotec.2022.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 04/12/2022] [Accepted: 04/26/2022] [Indexed: 11/29/2022]
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11
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Effect of the PmARF6 Gene from Masson Pine (Pinus massoniana) on the Development of Arabidopsis. Genes (Basel) 2022; 13:genes13030469. [PMID: 35328022 PMCID: PMC8949783 DOI: 10.3390/genes13030469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 11/16/2022] Open
Abstract
Masson pine (Pinus massoniana) is a core industrial tree species that is used for afforestation in southern China. Previous studies have shown that Auxin Response Factors (ARFs) are involved in the growth and development of various species, but the function of ARFs in Masson pine is unclear. In this research, we cloned and identified Masson pine ARF6 cDNA (PmARF6). The results showed that PmARF6 encodes a protein of 681 amino acids that is highly expressed in female flowers. Subcellular analysis showed that the PmARF6 protein occurred predominantly in the nucleus and cytomembrane of Masson pine cells. Compared with wild-type (WT) Arabidopsis, transgenic Arabidopsis plants overexpressing PmARF6 had fewer rosette leaves, and their flower development was slower. These results suggest that overexpression of PmARF6 may inhibit the flower and leaf development of Masson pine and provide new insights into the underlying developmental mechanism.
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12
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Bogaert KA, Blomme J, Beeckman T, De Clerck O. Auxin's origin: do PILS hold the key? TRENDS IN PLANT SCIENCE 2022; 27:227-236. [PMID: 34716098 DOI: 10.1016/j.tplants.2021.09.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 08/23/2021] [Accepted: 09/28/2021] [Indexed: 05/12/2023]
Abstract
Auxin is a key regulator of many developmental processes in land plants and plays a strikingly similar role in the phylogenetically distant brown seaweeds. Emerging evidence shows that the PIN and PIN-like (PILS) auxin transporter families have preceded the evolution of the canonical auxin response pathway. A wide conservation of PILS-mediated auxin transport, together with reports of auxin function in unicellular algae, would suggest that auxin function preceded the advent of multicellularity. We find that PIN and PILS transporters form two eukaryotic subfamilies within a larger bacterial family. We argue that future functional characterisation of algal PIN and PILS transporters can shed light on a common origin of an auxin function followed by independent co-option in a multicellular context.
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Affiliation(s)
- Kenny Arthur Bogaert
- Department of Biology, Ghent University, Krijgslaan 281 S8, B-9000 Ghent, Belgium.
| | - Jonas Blomme
- Department of Biology, Ghent University, Krijgslaan 281 S8, B-9000 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB-UGent, Technologiepark 72, B-9052 Ghent, Belgium
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB-UGent, Technologiepark 72, B-9052 Ghent, Belgium
| | - Olivier De Clerck
- Department of Biology, Ghent University, Krijgslaan 281 S8, B-9000 Ghent, Belgium
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13
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The Genetic and Hormonal Inducers of Continuous Flowering in Orchids: An Emerging View. Cells 2022; 11:cells11040657. [PMID: 35203310 PMCID: PMC8870070 DOI: 10.3390/cells11040657] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/09/2022] [Accepted: 02/11/2022] [Indexed: 02/07/2023] Open
Abstract
Orchids are the flowers of magnetic beauty. Vivid and attractive flowers with magnificent shapes make them the king of the floriculture industry. However, the long-awaited flowering is a drawback to their market success, and therefore, flowering time regulation is the key to studies about orchid flower development. Although there are some rare orchids with a continuous flowering pattern, the molecular regulatory mechanisms are yet to be elucidated to find applicable solutions to other orchid species. Multiple regulatory pathways, such as photoperiod, vernalization, circadian clock, temperature and hormonal pathways are thought to signalize flower timing using a group of floral integrators. This mini review, thus, organizes the current knowledge of floral time regulators to suggest future perspectives on the continuous flowering mechanism that may help to plan functional studies to induce flowering revolution in precious orchid species.
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14
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Ahmad S, Lu C, Gao J, Ren R, Wei Y, Wu J, Jin J, Zheng C, Zhu G, Yang F. Genetic insights into the regulatory pathways for continuous flowering in a unique orchid Arundina graminifolia. BMC PLANT BIOLOGY 2021; 21:587. [PMID: 34893019 PMCID: PMC8662845 DOI: 10.1186/s12870-021-03350-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/17/2021] [Indexed: 05/07/2023]
Abstract
BACKGROUND Manipulation of flowering time and frequency of blooming is key to enhancing the ornamental value of orchids. Arundina graminifolia is a unique orchid that flowers year round, although the molecular basis of this flowering pattern remains poorly understood. RESULTS We compared the A. graminifolia transcriptome across tissue types and floral developmental stages to elucidate important genetic regulators of flowering and hormones. Clustering analyses identified modules specific to floral transition and floral morphogenesis, providing a set of candidate regulators for the floral initiation and timing. Among candidate floral homeotic genes, the expression of two FT genes was positively correlated with flower development. Assessment of the endogenous hormone levels and qRT-PCR analysis of 32 pathway-responsive genes supported a role for the regulatory networks in floral bud control in A. graminifolia. Moreover, WGCNA showed that flowering control can be delineated by modules of coexpressed genes; especially, MEgreen presented group of genes specific to flowering. CONCLUSIONS Candidate gene selection coupled with hormonal regulators brings a robust source to understand the intricate molecular regulation of flowering in precious orchids.
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Affiliation(s)
- Sagheer Ahmad
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
| | - Chuqiao Lu
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
| | - Jie Gao
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
| | - Rui Ren
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
| | - Yonglu Wei
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
| | - Jieqiu Wu
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
| | - Jianpeng Jin
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
| | - Chuanyuan Zheng
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
| | - Genfa Zhu
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
| | - Fengxi Yang
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
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15
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Guillory A, Bonhomme S. Phytohormone biosynthesis and signaling pathways of mosses. PLANT MOLECULAR BIOLOGY 2021; 107:245-277. [PMID: 34245404 DOI: 10.1007/s11103-021-01172-6] [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: 11/28/2020] [Accepted: 06/30/2021] [Indexed: 06/13/2023]
Abstract
Most known phytohormones regulate moss development. We present a comprehensive view of the synthesis and signaling pathways for the most investigated of these compounds in mosses, focusing on the model Physcomitrium patens. The last 50 years of research have shown that most of the known phytohormones are synthesized by the model moss Physcomitrium patens (formerly Physcomitrella patens) and regulate its development, in interaction with responses to biotic and abiotic stresses. Biosynthesis and signaling pathways are best described in P. patens for the three classical hormones auxins, cytokinins and abscisic acid. Furthermore, their roles in almost all steps of development, from early filament growth to gametophore development and sexual reproduction, have been the focus of much research effort over the years. Evidence of hormonal roles exist for ethylene and for CLE signaling peptides, as well as for salicylic acid, although their possible effects on development remain unclear. Production of brassinosteroids by P. patens is still debated, and modes of action for these compounds are even less known. Gibberellin biosynthesis and signaling may have been lost in P. patens, while gibberellin precursors such as ent-kaurene derivatives could be used as signals in a yet to discover pathway. As for jasmonic acid, it is not used per se as a hormone in P. patens, but its precursor OPDA appears to play a corresponding role in defense against abiotic stress. We have tried to gather a comprehensive view of the biosynthesis and signaling pathways for all these compounds in mosses, without forgetting strigolactones, the last class of plant hormones to be reported. Study of the strigolactone response in P. patens points to a novel signaling compound, the KAI2-ligand, which was likely employed as a hormone prior to land plant emergence.
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Affiliation(s)
- Ambre Guillory
- INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, 78000, Versailles, France
| | - Sandrine Bonhomme
- INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, 78000, Versailles, France.
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16
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Yamoune A, Cuyacot AR, Zdarska M, Hejatko J. Hormonal orchestration of root apical meristem formation and maintenance in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6768-6788. [PMID: 34343283 DOI: 10.1093/jxb/erab360] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
Plant hormones are key regulators of a number of developmental and adaptive responses in plants, integrating the control of intrinsic developmental regulatory circuits with environmental inputs. Here we provide an overview of the molecular mechanisms underlying hormonal regulation of root development. We focus on key events during both embryonic and post-embryonic development, including specification of the hypophysis as a future organizer of the root apical meristem (RAM), hypophysis asymmetric division, specification of the quiescent centre (QC) and the stem cell niche (SCN), RAM maturation and maintenance of QC/SCN activity, and RAM size. We address both well-established and newly proposed concepts, highlight potential ambiguities in recent terminology and classification criteria of longitudinal root zonation, and point to contrasting results and alternative scenarios for recent models. In the concluding remarks, we summarize the common principles of hormonal control during root development and the mechanisms potentially explaining often antagonistic outputs of hormone action, and propose possible future research directions on hormones in the root.
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Affiliation(s)
- Amel Yamoune
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Abigail Rubiato Cuyacot
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Marketa Zdarska
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Jan Hejatko
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
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17
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Ahmad S, Lu C, Wei Y, Gao J, Jin J, Zheng C, Zhu G, Yang F. Stage Specificity, the Dynamic Regulators and the Unique Orchid Arundina graminifolia. Int J Mol Sci 2021; 22:ijms222010935. [PMID: 34681593 PMCID: PMC8535972 DOI: 10.3390/ijms222010935] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/06/2021] [Accepted: 10/07/2021] [Indexed: 11/27/2022] Open
Abstract
Orchids take years to reach flowering, but the unique bamboo orchid (Arundina graminifolia) achieves reproductive maturity in six months and then keeps on year round flowering. Therefore, studying different aspects of its growth, development and flowering is key to boost breeding programs for orchids. This study uses transcriptome tools to discuss genetic regulation in five stages of flower development and four tissue types. Stage specificity was focused to distinguish genes specifically expressed in different stages of flower development and tissue types. The top 10 highly expressed genes suggested unique regulatory patterns for each stage or tissue. The A. graminifolia sequences were blasted in Arabidopsis genome to validate stage specific genes and to predict important hormonal and cell regulators. Moreover, weighted gene co-expression network analysis (WGCNA) modules were ascertained to suggest highly influential hubs for early and late stages of flower development, leaf and root. Hormonal regulators were abundant in all data sets, such as auxin (LAX2, GH3.1 and SAUR41), cytokinin (LOG1), gibberellin (GASA3 and YAB4), abscisic acid (DPBF3) and sucrose (SWEET4 and SWEET13). Findings of this study, thus, give a fine sketch of genetic variability in Orchidaceae and broaden our understanding of orchid flower development and the involvement of multiple pathways.
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18
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Sun W, Yu H, Ma Z, Yuan Y, Wang S, Yan J, Xu X, Chen H. Molecular Evolution and Local Root Heterogeneous Expression of the Chenopodium quinoa ARF Genes Provide Insights into the Adaptive Domestication of Crops in Complex Environments. J Mol Evol 2021; 89:287-301. [PMID: 33755734 DOI: 10.1007/s00239-021-10005-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/10/2021] [Indexed: 01/15/2023]
Abstract
Auxin response factors (ARFs) influence plant growth and development via the coupling of basic biological processes. However, the evolution, expansion, and regulatory mechanisms of ARFs in the domesticated crop quinoa after artificial selection remain elusive. In this study, we systematically identified 30 Chenopodium quinoa ARFs (CqARFs). In this typical domesticated crop, ARFs divided into three subfamilies are subjected to strong purification selection and have a highly conserved evolutionary pattern. Polyploidy is the primary reason for the expansion of the ARF family after quinoa domestication. The expression patterns of CqARFs in different tissues have been differentiated, and CqARF2, 5, 9 and 10 from class A have the characteristics of local heterogeneous expression in different regions of roots, which may be the key factors for crops to respond in complex environments. Overall, we examined the evolution and expansion of ARFs in representative domesticated crops using the genome, transcriptome, and molecular biology and discovered a class A ARF-centered heterogeneous expression network that played an important role in auxin signaling and environmental responses. We provide new insights into how ARFs promote domesticated crop adaptation to artificial selection by polyploid expansion.
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Affiliation(s)
- Wenjun Sun
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Haomiao Yu
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Zhaotang Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Key Laboratory of Major Crop Diseases and Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuan Yuan
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Sijiao Wang
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Jun Yan
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture Rural Affairs, School of Pharmacy and Bioengineering, Chengdu University, Chengdu, 610106, China
| | - Xinran Xu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture Rural Affairs, School of Pharmacy and Bioengineering, Chengdu University, Chengdu, 610106, China
| | - Hui Chen
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China.
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19
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Asaoka M, Ooe M, Gunji S, Milani P, Runel G, Horiguchi G, Hamant O, Sawa S, Tsukaya H, Ferjani A. Stem integrity in Arabidopsis thaliana requires a load-bearing epidermis. Development 2021; 148:148/4/dev198028. [PMID: 33637612 DOI: 10.1242/dev.198028] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 01/11/2021] [Indexed: 01/02/2023]
Abstract
Because plant cells are glued to each other via their cell walls, failure to coordinate growth among adjacent cells can create cracks in tissues. Here, we find that the unbalanced growth of inner and outer tissues in the clavata3 de-etiolated3 (clv3 det3) mutant of Arabidopsis thaliana stretched epidermal cells, ultimately generating cracks in stems. Stem growth slowed before cracks appeared along clv3 det3 stems, whereas inner pith cells became drastically distorted and accelerated their growth, yielding to stress, after the appearance of cracks. This is consistent with a key role of the epidermis in restricting growth. Mechanical property measurements recorded using an atomic force microscope revealed that epidermal cell wall stiffness decreased in det3 and clv3 det3 epidermises. Thus, we hypothesized that stem integrity depends on the epidermal resistance to mechanical stress. To formally test this hypothesis, we used the DET3 gene as part of a tissue-specific strategy to complement cell expansion defects. Epidermis-driven DET3 expression restored growth and restored the frequency of stem cracking to 20% of the clv3 det3 mutant, demonstrating the DET3-dependent load-bearing role of the epidermis.
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Affiliation(s)
- Mariko Asaoka
- Department of Biology, Tokyo Gakugei University, 184-8501 Tokyo, Japan.,Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, 69007 Lyon, France
| | - Mao Ooe
- Department of Biology, Tokyo Gakugei University, 184-8501 Tokyo, Japan
| | - Shizuka Gunji
- Department of Biology, Tokyo Gakugei University, 184-8501 Tokyo, Japan.,United Graduated School of Education, Tokyo Gakugei University, 184-8501 Tokyo, Japan
| | - Pascale Milani
- BioMeca company, Ecole Normale Superieure de Lyon, 69007 Lyon, France
| | - Gaël Runel
- BioMeca company, Ecole Normale Superieure de Lyon, 69007 Lyon, France
| | - Gorou Horiguchi
- Department of Life Science, College of Science, Rikkyo University, 171-0021 Tokyo, Japan.,Research Center for Life Science, College of Science, Rikkyo University, 171-0021 Tokyo, Japan
| | - Olivier Hamant
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, 69007 Lyon, France.,The International Research Organization for Advanced Science and Technology, Kumamoto University, 860-8555 Kumamoto, Japan
| | - Shinichiro Sawa
- Graduate School of Science and Technology, Kumamoto University, 860-8555 Kumamoto, Japan
| | - Hirokazu Tsukaya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 113-0033 Tokyo, Japan
| | - Ali Ferjani
- Department of Biology, Tokyo Gakugei University, 184-8501 Tokyo, Japan .,United Graduated School of Education, Tokyo Gakugei University, 184-8501 Tokyo, Japan
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20
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Trinh DC, Alonso-Serra J, Asaoka M, Colin L, Cortes M, Malivert A, Takatani S, Zhao F, Traas J, Trehin C, Hamant O. How Mechanical Forces Shape Plant Organs. Curr Biol 2021; 31:R143-R159. [PMID: 33561417 DOI: 10.1016/j.cub.2020.12.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Plants produce organs of various shapes and sizes. While much has been learned about genetic regulation of organogenesis, the integration of mechanics in the process is also gaining attention. Here, we consider the role of forces as instructive signals in organ morphogenesis. Turgor pressure is the primary cause of mechanical signals in developing organs. Because plant cells are glued to each other, mechanical signals act, in essence, at multiple scales, through cell wall contiguity and water flux. In turn, cells use such signals to resist mechanical stress, for instance, by reinforcing their cell walls. We show that the three elemental shapes behind plant organs - spheres, cylinders and lamina - can be actively maintained by such a mechanical feedback. Combinations of this 3-letter alphabet can generate more complex shapes. Furthermore, mechanical conflicts emerge at the boundary between domains exhibiting different growth rates or directions. These secondary mechanical signals contribute to three other organ shape features - folds, shape reproducibility and growth arrest. The further integration of mechanical signals with the molecular network offers many fruitful prospects for the scientific community, including the role of proprioception in organ shape robustness or the definition of cell and organ identities as a result of an interplay between biochemical and mechanical signals.
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Affiliation(s)
- Duy-Chi Trinh
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCBL, INRAE, CNRS, 46 Allée d'Italie, 69364 Lyon Cedex 07, France; Department of Pharmacological, Medical and Agronomical Biotechnology, University of Science and Technology of Hanoi, Cau Giay District, Hanoi, Vietnam
| | - Juan Alonso-Serra
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCBL, INRAE, CNRS, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
| | - Mariko Asaoka
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCBL, INRAE, CNRS, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
| | - Leia Colin
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCBL, INRAE, CNRS, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
| | - Matthieu Cortes
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCBL, INRAE, CNRS, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
| | - Alice Malivert
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCBL, INRAE, CNRS, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
| | - Shogo Takatani
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCBL, INRAE, CNRS, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
| | - Feng Zhao
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCBL, INRAE, CNRS, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
| | - Jan Traas
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCBL, INRAE, CNRS, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
| | - Christophe Trehin
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCBL, INRAE, CNRS, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
| | - Olivier Hamant
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCBL, INRAE, CNRS, 46 Allée d'Italie, 69364 Lyon Cedex 07, France.
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21
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Geisler MM. A Retro-Perspective on Auxin Transport. FRONTIERS IN PLANT SCIENCE 2021; 12:756968. [PMID: 34675956 PMCID: PMC8524130 DOI: 10.3389/fpls.2021.756968] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 09/08/2021] [Indexed: 05/13/2023]
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22
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Landberg K, Šimura J, Ljung K, Sundberg E, Thelander M. Studies of moss reproductive development indicate that auxin biosynthesis in apical stem cells may constitute an ancestral function for focal growth control. THE NEW PHYTOLOGIST 2021; 229:845-860. [PMID: 32901452 PMCID: PMC7821132 DOI: 10.1111/nph.16914] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 08/23/2020] [Indexed: 05/28/2023]
Abstract
The plant hormone auxin is a key factor for regulation of plant development, and this function was probably reinforced during the evolution of early land plants. We have extended the available toolbox to allow detailed studies of how auxin biosynthesis and responses are regulated in moss reproductive organs, their stem cells and gametes to better elucidate the function of auxin in the morphogenesis of early land plants. We measured auxin metabolites and identified IPyA (indole-3-pyruvic acid) as the main biosynthesis pathway in Physcomitrium (Physcomitrella) patens and established knock-out, overexpressor and reporter lines for biosynthesis genes which were analyzed alongside previously reported auxin-sensing and transport reporters. Vegetative and reproductive apical stem cells synthesize auxin. Sustained stem cell activity depends on an inability to sense the auxin produced while progeny of the stem cells respond to the auxin, aiding in the control of cell division, expansion and differentiation. Gamete precursors are dependent on a certain degree of auxin sensing, while the final differentiation is a low auxin-sensing process. Tha data presented indicate that low auxin activity may represent a conserved hallmark of land plant gametes, and that local auxin biosynthesis in apical stem cells may be part of an ancestral mechanism to control focal growth.
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Affiliation(s)
- Katarina Landberg
- Department of Plant BiologyThe Linnean Centre for Plant Biology in UppsalaSwedish University of Agricultural SciencesUppsalaSE‐750 07Sweden
| | - Jan Šimura
- Department of Forest Genetics and Plant PhysiologyUmeå Plant Science CentreSwedish University of Agricultural Sciences (SLU)UmeåSE‐901 83Sweden
| | - Karin Ljung
- Department of Forest Genetics and Plant PhysiologyUmeå Plant Science CentreSwedish University of Agricultural Sciences (SLU)UmeåSE‐901 83Sweden
| | - Eva Sundberg
- Department of Plant BiologyThe Linnean Centre for Plant Biology in UppsalaSwedish University of Agricultural SciencesUppsalaSE‐750 07Sweden
| | - Mattias Thelander
- Department of Plant BiologyThe Linnean Centre for Plant Biology in UppsalaSwedish University of Agricultural SciencesUppsalaSE‐750 07Sweden
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Marquès-Bueno MM, Armengot L, Noack LC, Bareille J, Rodriguez L, Platre MP, Bayle V, Liu M, Opdenacker D, Vanneste S, Möller BK, Nimchuk ZL, Beeckman T, Caño-Delgado AI, Friml J, Jaillais Y. Auxin-Regulated Reversible Inhibition of TMK1 Signaling by MAKR2 Modulates the Dynamics of Root Gravitropism. Curr Biol 2020; 31:228-237.e10. [PMID: 33157019 PMCID: PMC7809621 DOI: 10.1016/j.cub.2020.10.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 09/04/2020] [Accepted: 10/07/2020] [Indexed: 12/14/2022]
Abstract
Plants are able to orient their growth according to gravity, which ultimately controls both shoot and root architecture.1 Gravitropism is a dynamic process whereby gravistimulation induces the asymmetric distribution of the plant hormone auxin, leading to asymmetric growth, organ bending, and subsequent reset of auxin distribution back to the original pre-gravistimulation situation.1, 2, 3 Differential auxin accumulation during the gravitropic response depends on the activity of polarly localized PIN-FORMED (PIN) auxin-efflux carriers.1, 2, 3, 4 In particular, the timing of this dynamic response is regulated by PIN2,5,6 but the underlying molecular mechanisms are poorly understood. Here, we show that MEMBRANE ASSOCIATED KINASE REGULATOR2 (MAKR2) controls the pace of the root gravitropic response. We found that MAKR2 is required for the PIN2 asymmetry during gravitropism by acting as a negative regulator of the cell-surface signaling mediated by the receptor-like kinase TRANSMEMBRANE KINASE1 (TMK1).2,7, 8, 9, 10 Furthermore, we show that the MAKR2 inhibitory effect on TMK1 signaling is antagonized by auxin itself, which triggers rapid MAKR2 membrane dissociation in a TMK1-dependent manner. Our findings suggest that the timing of the root gravitropic response is orchestrated by the reversible inhibition of the TMK1 signaling pathway at the cell surface. MAKR2 is co-expressed with PIN2 and regulates the pace of root gravitropism MAKR2 controls PIN2 asymmetric accumulation at the root level during gravitropism MAKR2 binds to and is a negative regulator of the TMK1 receptor kinase Auxin antagonizes the MAKR2 inhibition of TMK1 by delocalizing MAKR2 in the cytosol
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Affiliation(s)
- Maria Mar Marquès-Bueno
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, 69342 Lyon, France; Department of Molecular Genetics, Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain
| | - Laia Armengot
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, 69342 Lyon, France
| | - Lise C Noack
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, 69342 Lyon, France
| | - Joseph Bareille
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, 69342 Lyon, France
| | - Lesia Rodriguez
- Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Matthieu Pierre Platre
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, 69342 Lyon, France
| | - Vincent Bayle
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, 69342 Lyon, France
| | - Mengying Liu
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, 69342 Lyon, France
| | - Davy Opdenacker
- Center for Plant Systems Biology, VIB, Technologiepark 71, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
| | - Steffen Vanneste
- Center for Plant Systems Biology, VIB, Technologiepark 71, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; Lab of Plant Growth Analysis, Ghent University Global Campus, Songdomunhwa-Ro, 119, Yeonsu-gu, Incheon 21985, Republic of Korea
| | - Barbara K Möller
- Center for Plant Systems Biology, VIB, Technologiepark 71, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
| | - Zachary L Nimchuk
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tom Beeckman
- Center for Plant Systems Biology, VIB, Technologiepark 71, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
| | - Ana I Caño-Delgado
- Department of Molecular Genetics, Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain
| | - Jiří Friml
- Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Yvon Jaillais
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, 69342 Lyon, France.
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Narchonai G, Arutselvan C, LewisOscar F, Thajuddin N. Enhancing starch accumulation/production in Chlorococcum humicola through sulphur limitation and 2,4- D treatment for butanol production. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2020; 28:e00528. [PMID: 32995316 PMCID: PMC7508686 DOI: 10.1016/j.btre.2020.e00528] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/15/2020] [Accepted: 09/07/2020] [Indexed: 01/18/2023]
Abstract
Depleting fuel resources is a global concern worldwide due to the unstable and cost of fuel resources. Increased transportation has gradually depleted the fossil-based fuel resources leading to find a cost-effective, readily available, and renewable source. Considering these issues, various private and government organizations have focussed on producing bio-based fuels from natural sources. In this scenario, algae are a potential emerging source of feedstock or biomass for biobutanol production, which can effectively replace fossil fuels and their environmental drawbacks. The present study focussed on evaluating the potential of freshwater microalga Chlorococcum humicola isolated from temple pond as feedstock for biobutanol production using Clostridium acetobutylicum. The results indicated that C. humicola produced 846.33 μgmg-1of starch under full strength Chu10 medium. While under sulphur and phosphorus limitation, the accumulation of starch was 947.33 μg mg-1 and 766.67 μgmg-1, respectively. Also, C. humicola was exposed to different concentrations of 2,4-Dichlorophenoxyacetic acid (2,4-D). At 10μgml-1 of 2,4-D, the highest starch concentration of 989μgmg-1was achieved in C. humicola. Finally, starch in C. humicola were hydrolysed and ABE fermentation was performed using C. acetobutylicum under anaerobic condition in a 5 L automated fermenter. After 72 h of fermentation, the fermented broth is analyed in Gas Chromatography showing the fermented product containing Acetone: Butanol: Ethanol. The present study is the first report on the production of biobutanol from C. humicola isolated from Temple pond. This study emphasizes the importance of local isolates of microalgae as a third-generation substrate to produce butanol to replace fossil-based fuels.
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Affiliation(s)
- Ganesan Narchonai
- Division of Microalgal Biodiversity and Bioenergy, National Repository for Microalgae and Cyanobacteria - Freshwater, Department of Microbiology, Bharathidasan University, Tiruchirappalli, 620 024 Tamil Nadu, India
| | - Chitirai Arutselvan
- Division of Microalgal Biodiversity and Bioenergy, National Repository for Microalgae and Cyanobacteria - Freshwater, Department of Microbiology, Bharathidasan University, Tiruchirappalli, 620 024 Tamil Nadu, India.,Department of Microbiology, Bharathidasan University, Tiruchirappalli, 620 024 Tamil Nadu, India
| | - Felix LewisOscar
- Division of Microalgal Biodiversity and Bioenergy, National Repository for Microalgae and Cyanobacteria - Freshwater, Department of Microbiology, Bharathidasan University, Tiruchirappalli, 620 024 Tamil Nadu, India.,Department of Microbiology, Bharathidasan University, Tiruchirappalli, 620 024 Tamil Nadu, India
| | - Nooruddin Thajuddin
- Division of Microalgal Biodiversity and Bioenergy, National Repository for Microalgae and Cyanobacteria - Freshwater, Department of Microbiology, Bharathidasan University, Tiruchirappalli, 620 024 Tamil Nadu, India.,Department of Microbiology, Bharathidasan University, Tiruchirappalli, 620 024 Tamil Nadu, India
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Huang X, Bai X, Guo T, Xie Z, Laimer M, Du D, Gbokie T, Zhang Z, He C, Lu Y, Wu W, Yi K. Genome-Wide Analysis of the PIN Auxin Efflux Carrier Gene Family in Coffee. PLANTS 2020; 9:plants9091061. [PMID: 32825074 PMCID: PMC7570243 DOI: 10.3390/plants9091061] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/18/2020] [Accepted: 08/18/2020] [Indexed: 11/23/2022]
Abstract
Coffee is one of the most popular beverages around the world, which is mainly produced from the allopolyploid Coffea arabica. The genomes of C. arabica and its two ancestors C. canephora and C. eugenioides have been released due to the development of next generation sequencing. However, few studies on C. arabica are related to the PIN-FORMED (PIN) auxin efflux transporter despite its importance in auxin-mediated plant growth and development. In the present study, we conducted a genome-wide analysis of the PIN gene family in the three coffee species. Totals of 17, 9 and 10 of the PIN members were characterized in C. Arabica, C. canephora and C. eugenioides, respectively. Phylogenetic analysis revealed gene loss of PIN1 and PIN2 homologs in C. arabica, as well as gene duplication of PIN5 homologs during the fractionation process after tetraploidy. Furthermore, we conducted expression analysis of PIN genes in C. arabica by in silico and qRT-PCR. The results revealed the existence of gene expression dominance in allopolyploid coffee and illustrated several PIN candidates in regulating auxin transport and homeostasis under leaf rust fungus inoculation and the tissue-specific expression pattern of C. arabica. Together, this study provides the basis and guideline for future functional characterization of the PIN gene family.
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Affiliation(s)
- Xing Huang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (X.H.); (C.H.); (Y.L.); (K.Y.)
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou 571101, China
- Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou 571101, China
| | - Xuehui Bai
- Dehong Tropical Agriculture Research Institute of Yunnan, Ruili 678600, China; (X.B.); (T.G.)
| | - Tieying Guo
- Dehong Tropical Agriculture Research Institute of Yunnan, Ruili 678600, China; (X.B.); (T.G.)
| | - Zhouli Xie
- School of Life Sciences, Peking University, Beijing 100871, China;
| | - Margit Laimer
- Plant Biotechnology Unit, Department of Biotechnology, BOKU-VIBT, University of Natural Resources and Life Sciences, Vienna 1190, Austria
- Correspondence: (M.L.); (W.W.)
| | - Dengxiang Du
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China;
| | - Thomas Gbokie
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China;
| | - Zhirun Zhang
- Coffee Engineering Research Center of China, Mangshi 678400, China;
| | - Chunping He
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (X.H.); (C.H.); (Y.L.); (K.Y.)
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou 571101, China
- Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou 571101, China
| | - Ying Lu
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (X.H.); (C.H.); (Y.L.); (K.Y.)
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou 571101, China
- Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou 571101, China
| | - Weihuai Wu
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (X.H.); (C.H.); (Y.L.); (K.Y.)
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou 571101, China
- Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou 571101, China
- Correspondence: (M.L.); (W.W.)
| | - Kexian Yi
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (X.H.); (C.H.); (Y.L.); (K.Y.)
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou 571101, China
- Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou 571101, China
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Park SY, Choi JH, Oh DH, Johnson JC, Dassanayake M, Jeong DH, Oh MH. Genome-wide analysis of brassinosteroid responsive small RNAs in Arabidopsis thaliana. Genes Genomics 2020; 42:957-969. [PMID: 32648234 DOI: 10.1007/s13258-020-00964-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 06/29/2020] [Indexed: 12/28/2022]
Abstract
BACKGROUND Brassinosteroids (BRs) are a class of phytohormones with important roles in regulating physiological and developmental processes. Small RNAs, including small interfering RNAs and microRNAs (miRNAs), are non-protein coding RNAs that regulate gene expression at the transcriptional and post-transcriptional levels. However, the roles of small RNAs in BR response have not been studied well. OBJECTIVE In this study, we aimed to identify BR-responsive small RNA clusters and miRNAs in Arabidopsis. In addition, the effect of BR-responsive small RNAs on their transcripts and target genes were examined. METHODS Small RNA libraries were constructed from control and epibrassinolide-treated seedlings expressing wild-type BRI1-Flag protein under its native promoter in the bri1-5 mutant. After sequencing the small RNA libraries, differentially expressed small RNA clusters were identified by examining the expression levels of small RNAs in 100-nt bins of the Arabidopsis genome. To identify the BR-responsive miRNAs, the expression levels of all the annotated mature miRNAs, registered in miRBase, were analyzed. Previously published RNA-seq data were utilized to monitor the BR-responsive expression patterns of differentially expressed small RNA clusters and miRNA target genes. RESULTS In results, 38 BR-responsive small RNA clusters, including 30 down-regulated and eight up-regulated clusters, were identified. These differentially expressed small RNA clusters were from miRNA loci, transposons, protein-coding genes, pseudogenes and others. Of these, a transgene, BRI1, accumulates small RNAs, which are not found in the wild type. Small RNAs in this transgene are up-regulated by BRs while BRI1 mRNA is down-regulated by BRs. By analyzing the expression patterns of mature miRNAs, we have identified BR-repressed miR398a-5p and BR-induced miR156g. Although miR398a-5p is down-regulated by BRs, its predicted targets were not responsive to BRs. However, SPL3, a target of BR-inducible miR156g, is down-regulated by BRs. CONCLUSION BR-responsive small RNAs and miRNAs identified in this study will provide an insight into the role of small RNAs in BR responses in plants. Especially, we suggest that miR156g/SPL3 module might play a role in BR-mediated growth and development in Arabidopsis.
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Affiliation(s)
- So Young Park
- Department of Life Science and Multidisciplinary Genome Institute, Hallym University, Chuncheon, 24252, Republic of Korea
| | - Jae-Han Choi
- Department of Biological Sciences, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon, 34134, Korea
| | - Dong-Ha Oh
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - John C Johnson
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Maheshi Dassanayake
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Dong-Hoon Jeong
- Department of Life Science and Multidisciplinary Genome Institute, Hallym University, Chuncheon, 24252, Republic of Korea.
| | - Man-Ho Oh
- Department of Biological Sciences, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon, 34134, Korea.
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Gao B, Wang L, Oliver M, Chen M, Zhang J. Phylogenomic synteny network analyses reveal ancestral transpositions of auxin response factor genes in plants. PLANT METHODS 2020; 16:70. [PMID: 32467718 PMCID: PMC7226935 DOI: 10.1186/s13007-020-00609-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 04/30/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Auxin response factors (ARFs) have long been a research focus and represent a class of key regulators of plant growth and development. Integrated phylogenomic synteny network analyses were able to provide novel insights into the evolution of the ARF gene family. RESULTS Here, more than 3500 ARFs collected from plant genomes and transcriptomes covering major streptophyte lineages were used to reconstruct the broad-scale family phylogeny, where the early origin and diversification of ARF in charophytes was delineated. Based on the family phylogeny, we proposed a unified six-group classification system for angiosperm ARFs. Phylogenomic synteny network analyses revealed the deeply conserved genomic syntenies within each of the six ARF groups and the interlocking syntenic relationships connecting distinct groups. Recurrent duplication events, such as those that occurred in seed plants, angiosperms, core eudicots and grasses contributed to the expansion of ARF genes which facilitated functional diversification. Ancestral transposition activities in important plant families, including crucifers, legumes and grasses, were unveiled by synteny network analyses. Ancestral gene duplications along with transpositions have profound evolutionary significance which may have accelerated the functional diversification process of paralogues. CONCLUSIONS The broad-scale family phylogeny in combination with the state-of-art phylogenomic synteny network analyses not only allowed us to infer the evolutionary trajectory of ARF genes across distinct plant lineages, but also facilitated to generate a more robust classification regime for this transcription factor family. Our study provides insights into the evolution of ARFs which will enhance our current understanding of this important transcription factor family.
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Affiliation(s)
- Bei Gao
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Liuqiang Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 China
| | - Melvin Oliver
- USDA-ARS, Plant Genetics Research Unit, University of Missouri, Columbia, MO 65211 USA
| | - Moxian Chen
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
| | - Jianhua Zhang
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
- Department of Biology, Faculty of Science, Hong Kong Baptist University, Hong Kong, China
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28
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Sumalan RL, Croitor L, Petric M, Radulov I, Bourosh P, Sumalan RM, Crisan M. p-Aminobenzoate Organic Salts as Potential Plant Growth Regulators for Tomatoes. Molecules 2020; 25:molecules25071635. [PMID: 32252303 PMCID: PMC7180871 DOI: 10.3390/molecules25071635] [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: 03/14/2020] [Revised: 03/26/2020] [Accepted: 03/31/2020] [Indexed: 11/22/2022] Open
Abstract
The discovery of environmentally friendly and inexpensive plant growth regulators (PGRs) for agronomically important crops is a necessity and must be considered a priority worldwide. This study provides the synthesis, structure determination and the biological evaluation of two binary organic salts as potential PGRs. New compounds have dual biological activity and are based on natural metabolite p-aminobenzoic acid (pABAH) and different alkanolamines. Studied compounds exhibit hydrogen-bonded 3D supramolecular architectures with different crystal packing due to the formation of one homosynthon and various heterosynthons. The biological profile of new compounds was investigated in laboratory and greenhouse on Solanum lycopersicum L., revealing the efficiency in promoting plant rooting and plant productivity. The results may have a positive impact on agricultural economics, developing new sustainable PGRs for tomatoes.
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Affiliation(s)
- Radu-Liviu Sumalan
- Faculty of Horticulture and Forestry, Banat′s University of Agriculture Science and Veterinary Medicine “King Michael Ist of Romania” from Timisoara, Calea Aradului nr 119, 300645, Timisoara, Romania; (R.-L.S.); (I.R.); (R.-M.S.)
| | - Lilia Croitor
- “Coriolan Dragulescu” Institute of Chemistry, 24 Mihai Viteazul Blvd., 300223, Timisoara, Romania; (L.C.); (M.P.)
- Institute of Applied Physics, Academiei Street 5, MD2028, Chisinau, Moldova;
| | - Mihaela Petric
- “Coriolan Dragulescu” Institute of Chemistry, 24 Mihai Viteazul Blvd., 300223, Timisoara, Romania; (L.C.); (M.P.)
| | - Isidora Radulov
- Faculty of Horticulture and Forestry, Banat′s University of Agriculture Science and Veterinary Medicine “King Michael Ist of Romania” from Timisoara, Calea Aradului nr 119, 300645, Timisoara, Romania; (R.-L.S.); (I.R.); (R.-M.S.)
| | - Paulina Bourosh
- Institute of Applied Physics, Academiei Street 5, MD2028, Chisinau, Moldova;
| | - Renata-Maria Sumalan
- Faculty of Horticulture and Forestry, Banat′s University of Agriculture Science and Veterinary Medicine “King Michael Ist of Romania” from Timisoara, Calea Aradului nr 119, 300645, Timisoara, Romania; (R.-L.S.); (I.R.); (R.-M.S.)
| | - Manuela Crisan
- “Coriolan Dragulescu” Institute of Chemistry, 24 Mihai Viteazul Blvd., 300223, Timisoara, Romania; (L.C.); (M.P.)
- Correspondence: ; Tel.: +40-256-491818
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Abstract
The coordination of cell fate decisions within complex multicellular structures rests on intercellular communication. To generate ordered patterns, cells need to know their relative positions within the growing structure. This is commonly achieved via the production and perception of mobile signaling molecules. In animal systems, such positional signals often act as morphogens and subdivide a field of cells into domains of discrete cell identities using a threshold-based readout of their mobility gradient. Reflecting the independent origin of multicellularity, plants evolved distinct signaling mechanisms to drive cell fate decisions. Many of the basic principles underlying developmental patterning are, however, shared between animals and plants, including the use of signaling gradients to provide positional information. In plant development, small RNAs can act as mobile instructive signals, and similar to classical morphogens in animals, employ a threshold-based readout of their mobility gradient to generate precisely defined cell fate boundaries. Given the distinctive nature of peptide morphogens and small RNAs, how might mechanisms underlying the function of traditionally morphogens be adapted to create morphogen-like behavior using small RNAs? In this review, we highlight the contributions of mobile small RNAs to pattern formation in plants and summarize recent studies that have advanced our understanding regarding the formation, stability, and interpretation of small RNA gradients.
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Affiliation(s)
- Simon Klesen
- Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
| | - Kristine Hill
- Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
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30
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Mohan A, Dhaliwal AK, Nagarajan R, Gill KS. Molecular Characterization of Auxin Efflux Carrier- ABCB1 in hexaploid wheat. Sci Rep 2019; 9:17327. [PMID: 31757978 PMCID: PMC6874703 DOI: 10.1038/s41598-019-51482-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 09/29/2019] [Indexed: 11/09/2022] Open
Abstract
Auxin is an important phytohormone that regulates response, differentiation, and development of plant cell, tissue, and organs. Along with its local production, long-distance transport coordinated by the efflux/influx membrane transporters is instrumental in plant development and architecture. In the present study, we cloned and characterized a wheat (Triticum aestivum) auxin efflux carrier ABCB1. The TaABCB1 was physically localized to the proximal 15% of the short arm of wheat homoeologous group 7 chromosomes. Size of the Chinese spring (CS) homoeologs genomic copies ranged from 5.3–6.2 kb with the 7A copy being the largest due to novel insertions in its third intron. The three homoeologous copies share 95–97% sequence similarity at the nucleotide, 98–99% amino acid, and overall Q-score of 0.98 at 3-D structure level. Though detected in all analyzed tissues, TaABCB1 predominantly expressed in the meristematic tissues likely due to the presence of meristem-specific activation regulatory element identified in the promoter region. RNAi plants of TaABCB1 gene resulted in reduced plant height and increased seed width. Promoter analysis revealed several responsive elements detected in the promoter region including that for different hormones as auxin, gibberellic acid, jasmonic acid and abscisic acid, light, and circadian regulated elements.
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Affiliation(s)
- Amita Mohan
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Amandeep K Dhaliwal
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Ragupathi Nagarajan
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Kulvinder S Gill
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA.
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31
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Thelander M, Landberg K, Sundberg E. Minimal auxin sensing levels in vegetative moss stem cells revealed by a ratiometric reporter. THE NEW PHYTOLOGIST 2019; 224:775-788. [PMID: 31318450 DOI: 10.1111/nph.16068] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/10/2019] [Indexed: 05/18/2023]
Abstract
Efforts to reveal ancestral functions of auxin, a key regulator of plant growth and development, and its importance for evolution have been hampered by a fragmented picture of auxin response domains in early-diverging land plants. We report the mapping of auxin sensing and responses during vegetative moss development using novel reporters. We established a moss-specific ratiometric reporter (PpR2D2) for Auxin Response Element- and AUXIN RESPONSE FACTOR-independent auxin sensing in Physcomitrella patens, and its readout during vegetative development was compared with new promoter-based GmGH3::GFPGUS and DR5revV2::GFPGUS auxin response reporters. The ratiometric reporter responds rapidly to auxin in a time-, dose- and TRANSPORT INHIBITOR RESISTANT1/AUXIN F-BOX-dependent manner and marks known, anticipated and novel auxin sensing domains. It reveals proximal auxin sensing maxima in filamentous tissues and sensing minima in all five vegetative gametophytic stem cell types as well as dividing cells. PpR2D2 readout is compliant with an ancestral function of auxin as a positive regulator of differentiation vs proliferation in stem cell regions. The PpR2D2 reporter is a sensitive tool for high-resolution mapping of auxin sensing, which can increase our knowledge of auxin function in early-diverging land plants substantially, thereby advancing our understanding of its importance for plant evolution.
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Affiliation(s)
- Mattias Thelander
- Department of Plant Biology, Swedish University of Agricultural Sciences, The Linnean Centre for Plant Biology in Uppsala, SE-750 07, Uppsala, Sweden
| | - Katarina Landberg
- Department of Plant Biology, Swedish University of Agricultural Sciences, The Linnean Centre for Plant Biology in Uppsala, SE-750 07, Uppsala, Sweden
| | - Eva Sundberg
- Department of Plant Biology, Swedish University of Agricultural Sciences, The Linnean Centre for Plant Biology in Uppsala, SE-750 07, Uppsala, Sweden
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Jimenez-Jimenez S, Santana O, Lara-Rojas F, Arthikala MK, Armada E, Hashimoto K, Kuchitsu K, Salgado S, Aguirre J, Quinto C, Cárdenas L. Differential tetraspanin genes expression and subcellular localization during mutualistic interactions in Phaseolus vulgaris. PLoS One 2019; 14:e0219765. [PMID: 31437164 PMCID: PMC6705802 DOI: 10.1371/journal.pone.0219765] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 07/01/2019] [Indexed: 12/19/2022] Open
Abstract
Arbuscular mycorrhizal fungi and rhizobia association with plants are two of the most successful plant-microbe associations that allow the assimilation of P and N by plants, respectively. These mutualistic interactions require a molecular dialogue, i.e., legume roots exude flavonoids or strigolactones which induce the Nod factors or Myc factors synthesis and secretion from the rhizobia or fungi, respectively. These Nod or Myc factors trigger several responses in the plant root, including calcium oscillations, and reactive oxygen species (ROS). Furthermore, superoxide and H2O2 have emerged as key components that regulate the transitions from proliferation to differentiation in the plant meristems. Similar to the root meristem, the nodule meristem accumulates superoxide and H2O2. Tetraspanins are transmembrane proteins that organize into tetraspanin web regions, where they recruit specific proteins into platforms required for signal transduction, membrane fusion, cell trafficking and ROS generation. Plant tetraspanins are scaffolding proteins associated with root radial patterning, biotic and abiotic stress responses, cell fate determination, and hormonal regulation and recently have been reported as a specific marker of exosomes in animal and plant cells and key players at the site of plant fungal infection. In this study, we conducted transcriptional profiling of the tetraspanin family in common bean (Phaseolus vulgaris L. var. Negro Jamapa) to determine the specific expression patterns and subcellular localization of tetraspanins during nodulation or under mycorrhizal association. Our results demonstrate that the tetraspanins are transcriptionally modulated during the mycorrhizal association, but are also expressed in the infection thread and nodule meristem development. Subcellular localization indicates that tetraspanins have a key role in vesicular trafficking, cell division, and root hair polar growth.
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Affiliation(s)
- Saul Jimenez-Jimenez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Olivia Santana
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Fernando Lara-Rojas
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Manoj-Kumar Arthikala
- Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores Unidad León-Universidad Nacional Autónoma de México, León, Guanajuato, México
| | - Elisabeth Armada
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Kenji Hashimoto
- Department of Applied Biological Science, Tokyo University of Science, Yamazaki, Noda, Chiba, Japan
| | - Kazuyuki Kuchitsu
- Department of Applied Biological Science, Tokyo University of Science, Yamazaki, Noda, Chiba, Japan
| | - Sandra Salgado
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Jesús Aguirre
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Carmen Quinto
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Luis Cárdenas
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
- * E-mail:
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Clark NM, Shen Z, Briggs SP, Walley JW, Kelley DR. Auxin Induces Widespread Proteome Remodeling in Arabidopsis Seedlings. Proteomics 2019; 19:e1900199. [DOI: 10.1002/pmic.201900199] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/25/2019] [Indexed: 01/24/2023]
Affiliation(s)
- Natalie M. Clark
- Department of Plant Pathology and MicrobiologyIowa State University Ames IA 92093 USA
| | - Zhouxin Shen
- Section of Cell and Developmental BiologyUniversity of CaliforniaSan Diego La Jolla CA 92093 USA
| | - Steven P. Briggs
- Section of Cell and Developmental BiologyUniversity of CaliforniaSan Diego La Jolla CA 92093 USA
| | - Justin W. Walley
- Department of Plant Pathology and MicrobiologyIowa State University Ames IA 92093 USA
| | - Dior R. Kelley
- Department of Genetics, Development and Cell BiologyIowa State University Ames IA 50011 USA
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Chen W, Hsu W, Hsu H, Yang C. A tetraspanin gene regulating auxin response and affecting orchid perianth size and various plant developmental processes. PLANT DIRECT 2019; 3:e00157. [PMID: 31406958 PMCID: PMC6680136 DOI: 10.1002/pld3.157] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/18/2019] [Accepted: 07/18/2019] [Indexed: 05/25/2023]
Abstract
The competition between L (lip) and SP (sepal/petal) complexes in P-code model determines the identity of complex perianth patterns in orchids. Orchid tetraspanin gene Auxin Activation Factor (AAF) orthologs, whose expression strongly correlated with the expansion and size of the perianth after P code established, were identified. Virus-induced gene silencing (VIGS) of OAGL6-2 in L complex resulted in smaller lips and the down-regulation of Oncidium OnAAF. VIGS of PeMADS9 in L complex resulted in the enlarged lips and up-regulation of Phalaenopsis PaAAF. Furthermore, the larger size of Phalaenopsis variety flowers was associated with higher PaAAF expression, larger and more cells in the perianth. Thus, a rule is established that whenever bigger perianth organs are made in orchids, higher OnAAF/PaAAF expression is observed after their identities are determined by P-code complexes. Ectopic expression Arabidopsis AtAAF significantly increased the size of flower organs by promoting cell expansion in transgenic Arabidopsis due to the enhancement of the efficiency of the auxin response and the subsequent suppression of the jasmonic acid (JA) biosynthesis genes (DAD1/OPR3) and BIGPETAL gene during late flower development. In addition, auxin-controlled phenotypes, such as indehiscent anthers, enhanced drought tolerance, and increased lateral root formation, were also observed in 35S::AtAAF plants. Furthermore, 35S::AtAAF root tips maintained gravitropism during auxin treatment. In contrast, the opposite phenotype was observed in palmitoylation-deficient AtAAF mutants. Our data demonstrate an interaction between the tetraspanin AAF and auxin/JA that regulates the size of flower organs and impacts various developmental processes.
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Affiliation(s)
- Wei‐Hao Chen
- Institute of BiotechnologyNational Chung Hsing UniversityTaichungTaiwan, ROC
| | - Wei‐Han Hsu
- Institute of BiotechnologyNational Chung Hsing UniversityTaichungTaiwan, ROC
| | - Hsing‐Fun Hsu
- Institute of BiotechnologyNational Chung Hsing UniversityTaichungTaiwan, ROC
| | - Chang‐Hsien Yang
- Institute of BiotechnologyNational Chung Hsing UniversityTaichungTaiwan, ROC
- Advanced Plant Biotechnology CenterNational Chung Hsing UniversityTaichungTaiwan, ROC
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New-Generation Chemical Tools for the Manipulation of Auxin Biosynthesis, Action, and Transport. Methods Mol Biol 2019. [PMID: 30694472 DOI: 10.1007/978-1-4939-9015-3_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Auxin is the master regulator for almost every aspect of plant growth and development. Small molecule inhibitors, fluorescently labeled molecule, and hormone analogs on auxin biosynthesis, transport, and signaling, so-called auxin chemical tools, have been widely utilized to dissect physiological functions of gene families in auxin biosynthesis, transport, and signaling. Auxin chemical tools can manipulate specific auxin-regulated events at any developmental stage. Chemical tools can modulate the function of orthologs of target proteins and also can overcome the redundant function of large family gene controlling auxin-regulated response. On the other hand, chemical tool might induce the off-target effects at high concentration, if the chemical tool shows insufficient specificity on target proteins. This chapter describes a brief overview and practical application of the auxin chemical tools.
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Pu Y, Walley JW, Shen Z, Lang MG, Briggs SP, Estelle M, Kelley DR. Quantitative Early Auxin Root Proteomics Identifies GAUT10, a Galacturonosyltransferase, as a Novel Regulator of Root Meristem Maintenance. Mol Cell Proteomics 2019; 18:1157-1170. [PMID: 30918009 PMCID: PMC6553934 DOI: 10.1074/mcp.ra119.001378] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Indexed: 11/25/2022] Open
Abstract
Auxin induces rapid gene expression changes throughout root development. How auxin-induced transcriptional responses relate to changes in protein abundance is not well characterized. This report identifies early auxin responsive proteins in roots at 30 min and 2 h after hormone treatment using a quantitative proteomics approach in which 3,514 proteins were reliably quantified. A comparison of the >100 differentially expressed proteins at each the time point showed limited overlap, suggesting a dynamic and transient response to exogenous auxin. Several proteins with established roles in auxin-mediated root development exhibited altered abundance, providing support for this approach. While novel targeted proteomics assays demonstrate that all six auxin receptors remain stable in response to hormone. Additionally, 15 of the top responsive proteins display root and/or auxin response phenotypes, demonstrating the validity of these differentially expressed proteins. Auxin signaling in roots dictates proteome reprogramming of proteins enriched for several gene ontology terms, including transcription, translation, protein localization, thigmatropism, and cell wall modification. In addition, we identified auxin-regulated proteins that had not previously been implicated in auxin response. For example, genetic studies of the auxin responsive protein galacturonosyltransferase 10 demonstrate that this enzyme plays a key role in root development. Altogether these data complement and extend our understanding of auxin response beyond that provided by transcriptome studies and can be used to uncover novel proteins that may mediate root developmental programs.
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Affiliation(s)
- Yunting Pu
- From the Departments of ‡Genetics, Development and Cell Biology
| | - Justin W Walley
- ¶Plant Pathology and Microbiology, Iowa State University, Ames, IA
| | - Zhouxin Shen
- §Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA
| | - Michelle G Lang
- From the Departments of ‡Genetics, Development and Cell Biology
| | - Steven P Briggs
- §Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA
| | - Mark Estelle
- §Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA
| | - Dior R Kelley
- From the Departments of ‡Genetics, Development and Cell Biology,
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Matthes MS, Best NB, Robil JM, Malcomber S, Gallavotti A, McSteen P. Auxin EvoDevo: Conservation and Diversification of Genes Regulating Auxin Biosynthesis, Transport, and Signaling. MOLECULAR PLANT 2019; 12:298-320. [PMID: 30590136 DOI: 10.1016/j.molp.2018.12.012] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 12/02/2018] [Accepted: 12/16/2018] [Indexed: 05/08/2023]
Abstract
The phytohormone auxin has been shown to be of pivotal importance in growth and development of land plants. The underlying molecular players involved in auxin biosynthesis, transport, and signaling are quite well understood in Arabidopsis. However, functional characterizations of auxin-related genes in economically important crops, specifically maize and rice, are still limited. In this article, we comprehensively review recent functional studies on auxin-related genes in both maize and rice, compared with what is known in Arabidopsis, and highlight conservation and diversification of their functions. Our analysis is illustrated by phylogenetic analysis and publicly available gene expression data for each gene family, which will aid in the identification of auxin-related genes for future research. Current challenges and future directions for auxin research in maize and rice are discussed. Developments in gene editing techniques provide powerful tools for overcoming the issue of redundancy in these gene families and will undoubtedly advance auxin research in crops.
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Affiliation(s)
- Michaela Sylvia Matthes
- Division of Biological Sciences, Interdisciplinary Plant Group and Missouri Maize Center, University of Missouri-Columbia, 301 Christopher Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Norman Bradley Best
- Division of Biological Sciences, Interdisciplinary Plant Group and Missouri Maize Center, University of Missouri-Columbia, 301 Christopher Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Janlo M Robil
- Division of Biological Sciences, Interdisciplinary Plant Group and Missouri Maize Center, University of Missouri-Columbia, 301 Christopher Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Simon Malcomber
- Department of Biological Sciences, California State University, Long Beach, CA 90840, USA
| | - Andrea Gallavotti
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854-8020, USA; Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Paula McSteen
- Division of Biological Sciences, Interdisciplinary Plant Group and Missouri Maize Center, University of Missouri-Columbia, 301 Christopher Bond Life Sciences Center, Columbia, MO 65211, USA.
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38
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Shirley NJ, Aubert MK, Wilkinson LG, Bird DC, Lora J, Yang X, Tucker MR. Translating auxin responses into ovules, seeds and yield: Insight from Arabidopsis and the cereals. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:310-336. [PMID: 30474296 DOI: 10.1111/jipb.12747] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 11/16/2018] [Indexed: 05/27/2023]
Abstract
Grain production in cereal crops depends on the stable formation of male and female gametes in the flower. In most angiosperms, the female gamete is produced from a germline located deep within the ovary, protected by several layers of maternal tissue, including the ovary wall, ovule integuments and nucellus. In the field, germline formation and floret fertility are major determinants of yield potential, contributing to traits such as seed number, weight and size. As such, stimuli affecting the timing and duration of reproductive phases, as well as the viability, size and number of cells within reproductive organs can significantly impact yield. One key stimulant is the phytohormone auxin, which influences growth and morphogenesis of female tissues during gynoecium development, gametophyte formation, and endosperm cellularization. In this review we consider the role of the auxin signaling pathway during ovule and seed development, first in the context of Arabidopsis and then in the cereals. We summarize the gene families involved and highlight distinct expression patterns that suggest a range of roles in reproductive cell specification and fate. This is discussed in terms of seed production and how targeted modification of different tissues might facilitate improvements.
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Affiliation(s)
- Neil J Shirley
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA, Australia
| | - Matthew K Aubert
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA, Australia
| | - Laura G Wilkinson
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA, Australia
| | - Dayton C Bird
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA, Australia
| | - Jorge Lora
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA, Australia
| | - Xiujuan Yang
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA, Australia
| | - Matthew R Tucker
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA, Australia
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39
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Histology versus phylogeny: Viewing plant embryogenesis from an evo-devo perspective. Curr Top Dev Biol 2019; 131:545-564. [DOI: 10.1016/bs.ctdb.2018.11.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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40
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Busi R, Goggin DE, Heap IM, Horak MJ, Jugulam M, Masters RA, Napier RM, Riar DS, Satchivi NM, Torra J, Westra P, Wright TR. Weed resistance to synthetic auxin herbicides. PEST MANAGEMENT SCIENCE 2018; 74:2265-2276. [PMID: 29235732 PMCID: PMC6175398 DOI: 10.1002/ps.4823] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 12/05/2017] [Accepted: 12/07/2017] [Indexed: 05/03/2023]
Abstract
Herbicides classified as synthetic auxins have been most commonly used to control broadleaf weeds in a variety of crops and in non-cropland areas since the first synthetic auxin herbicide (SAH), 2,4-D, was introduced to the market in the mid-1940s. The incidence of weed species resistant to SAHs is relatively low considering their long-term global application with 30 broadleaf, 5 grass, and 1 grass-like weed species confirmed resistant to date. An understanding of the context and mechanisms of SAH resistance evolution can inform management practices to sustain the longevity and utility of this important class of herbicides. A symposium was convened during the 2nd Global Herbicide Resistance Challenge (May 2017; Denver, CO, USA) to provide an overview of the current state of knowledge of SAH resistance mechanisms including case studies of weed species resistant to SAHs and perspectives on mitigating resistance development in SAH-tolerant crops. © 2017 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Roberto Busi
- Australian Herbicide Resistance Initiative, School of Agriculture and EnvironmentUniversity of Western AustraliaPerthAustralia
| | - Danica E Goggin
- Australian Herbicide Resistance Initiative, School of Agriculture and EnvironmentUniversity of Western AustraliaPerthAustralia
| | - Ian M Heap
- International Survey of Herbicide‐Resistant WeedsCorvallisORUSA
| | | | | | | | | | | | | | - Joel Torra
- Department of Horticulture, Botany and GardeningUniversity of LleidaLleidaSpain
| | - Phillip Westra
- Department of Bioagricultural Sciences and Pest ManagementColorado State UniversityFort CollinsCOUSA
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Ditengou FA, Gomes D, Nziengui H, Kochersperger P, Lasok H, Medeiros V, Paponov IA, Nagy SK, Nádai TV, Mészáros T, Barnabás B, Ditengou BI, Rapp K, Qi L, Li X, Becker C, Li C, Dóczi R, Palme K. Characterization of auxin transporter PIN6 plasma membrane targeting reveals a function for PIN6 in plant bolting. THE NEW PHYTOLOGIST 2018; 217:1610-1624. [PMID: 29218850 DOI: 10.1111/nph.14923] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 10/23/2017] [Indexed: 05/25/2023]
Abstract
Auxin gradients are sustained by series of influx and efflux carriers whose subcellular localization is sensitive to both exogenous and endogenous factors. Recently the localization of the Arabidopsis thaliana auxin efflux carrier PIN-FORMED (PIN) 6 was reported to be tissue-specific and regulated through unknown mechanisms. Here, we used genetic, molecular and pharmacological approaches to characterize the molecular mechanism(s) controlling the subcellular localization of PIN6. PIN6 localizes to endomembrane domains in tissues with low PIN6 expression levels such as roots, but localizes at the plasma membrane (PM) in tissues with increased PIN6 expression such as the inflorescence stem and nectary glands. We provide evidence that this dual localization is controlled by PIN6 phosphorylation and demonstrate that PIN6 is phosphorylated by mitogen-activated protein kinases (MAPKs) MPK4 and MPK6. The analysis of transgenic plants expressing PIN6 at PM or in endomembrane domains reveals that PIN6 subcellular localization is critical for Arabidopsis inflorescence stem elongation post-flowering (bolting). In line with a role for PIN6 in plant bolting, inflorescence stems elongate faster in pin6 mutant plants than in wild-type plants. We propose that PIN6 subcellular localization is under the control of developmental signals acting on tissue-specific determinants controlling PIN6-expression levels and PIN6 phosphorylation.
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Affiliation(s)
- Franck Anicet Ditengou
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, D-79104, Freiburg, Germany
| | - Dulceneia Gomes
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, D-79104, Freiburg, Germany
| | - Hugues Nziengui
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, D-79104, Freiburg, Germany
| | - Philip Kochersperger
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, D-79104, Freiburg, Germany
| | - Hanna Lasok
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, D-79104, Freiburg, Germany
| | - Violante Medeiros
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, D-79104, Freiburg, Germany
| | - Ivan A Paponov
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, D-79104, Freiburg, Germany
- NIBIO, Norwegian Institute for Bioeconomy Research, Postvegen 213, 4353, Klepp Stasjon, Norway
| | - Szilvia Krisztina Nagy
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Tűzoltó u. 37-47, H-1094, Budapest, Hungary
| | - Tímea Virág Nádai
- Department of Plant Cell Biology, Centre for Agricultural Research of the Hungarian Academy of Sciences, Brunszvik u. 2, H-2462, Martonvásár, Hungary
| | - Tamás Mészáros
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Tűzoltó u. 37-47, H-1094, Budapest, Hungary
- Research Group for Technical Analytical Chemistry, Hungarian Academy of Sciences, Budapest University of Technology and Economics, Szt. Gellért tér 4, H-1111, Budapest, Hungary
| | - Beáta Barnabás
- Department of Plant Cell Biology, Centre for Agricultural Research of the Hungarian Academy of Sciences, Brunszvik u. 2, H-2462, Martonvásár, Hungary
| | - Beata Izabela Ditengou
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, D-79104, Freiburg, Germany
| | - Katja Rapp
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, D-79104, Freiburg, Germany
| | - Linlin Qi
- VIB-UGent, Center for Plant Systems Biology, Gent, Belgium
| | - Xugang Li
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, D-79104, Freiburg, Germany
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street 61, Tai'an, 271018, China
| | - Claude Becker
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, D-79104, Freiburg, Germany
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030, Vienna, Austria
| | - Chuanyou Li
- VIB-UGent, Center for Plant Systems Biology, Gent, Belgium
| | - Róbert Dóczi
- Department of Plant Cell Biology, Centre for Agricultural Research of the Hungarian Academy of Sciences, Brunszvik u. 2, H-2462, Martonvásár, Hungary
| | - Klaus Palme
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, D-79104, Freiburg, Germany
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030, Vienna, Austria
- Centre for Biological Systems Analysis, Albert-Ludwigs-University of Freiburg, Habsburgerstrasse 49, 79104, Freiburg, Germany
- Freiburg Institute for Advanced Sciences (FRIAS), Albert-Ludwigs-University of Freiburg, Albertstrasse 19, 79104, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University of Freiburg, Schänzlestrasse 18, 79104, Freiburg, Germany
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42
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Thelander M, Landberg K, Sundberg E. Auxin-mediated developmental control in the moss Physcomitrella patens. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:277-290. [PMID: 28992074 DOI: 10.1093/jxb/erx255] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 06/27/2017] [Indexed: 05/08/2023]
Abstract
The signalling molecule auxin regulates many fundamental aspects of growth and development in plants. We review and discuss what is known about auxin-regulated development in mosses, with special emphasis on the model species Physcomitrella patens. It is well established that mosses and other early diverging plants produce and respond to auxin. By sequencing the P. patens genome, it became clear that it encodes many core proteins important for auxin homeostasis, perception, and signalling, which have also been identified in flowering plants. This suggests that the auxin molecular network was present in the last common ancestor of flowering plants and mosses. Despite fundamental differences in their life cycles, key processes such as organ initiation and outgrowth, branching, tropic responses, as well as cell differentiation, division, and expansion appear to be regulated by auxin in the two lineages. This knowledge paves the way for studies aimed at a better understanding of the origin and evolution of auxin function and how auxin may have contributed to the evolution of land plants.
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Affiliation(s)
- Mattias Thelander
- Department of Plant Biology, Swedish University of Agricultural Sciences, The Linnean Centre for Plant Biology in Uppsala, Sweden
| | - Katarina Landberg
- Department of Plant Biology, Swedish University of Agricultural Sciences, The Linnean Centre for Plant Biology in Uppsala, Sweden
| | - Eva Sundberg
- Department of Plant Biology, Swedish University of Agricultural Sciences, The Linnean Centre for Plant Biology in Uppsala, Sweden
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43
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Dao GH, Wu GX, Wang XX, Zhuang LL, Zhang TY, Hu HY. Enhanced growth and fatty acid accumulation of microalgae Scenedesmus sp. LX1 by two types of auxin. BIORESOURCE TECHNOLOGY 2018; 247:561-567. [PMID: 28982085 DOI: 10.1016/j.biortech.2017.09.079] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 09/09/2017] [Accepted: 09/11/2017] [Indexed: 05/03/2023]
Abstract
Microalgae are potential candidates for the production of valuable products, such as renewable biodiesel, health products and pigments. However, low biomass productivity has restricted their large-scale applications. In this study, the effects of two auxins (one natural type of indole-3-acetic acid (IAA) and the other synthetic type of 2,4-dichlorophenoxyacetic acid (2,4-D)) on the growth and fatty acid methyl esters (FAMEs) production of a freshwater microalgae Scenedesmus sp. LX1 were investigated. Both auxins showed a "low dosage-promotion and high dosage-inhibition" effect on the growth and FAMEs accumulation. The optimum dosage of IAA and 2,4-D were 1mgL-1 and 0.1mgL-1, respectively. Moreover, the IAA could increase the monounsaturated fatty acid content. The auxins may promote the growth by enhancing the photosynthetic activity through increasing chlorophyll contents. Therefore, auxin significantly enhanced microalgal growth and FAMEs accumulation, and has a potential for application in developing efficient microalgal cultivation.
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Affiliation(s)
- Guo-Hua Dao
- Environmental Simulation and Pollution Control State Key Joint Laboratory, State Environmental Protection Key Laboratory of Microorganism Application and Risk Control (SMARC), School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Guang-Xue Wu
- Key Laboratory of Microorganism Application and Risk Control (MARC) of Shenzhen, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, Guangdong, PR China
| | - Xiao-Xiong Wang
- Environmental Simulation and Pollution Control State Key Joint Laboratory, State Environmental Protection Key Laboratory of Microorganism Application and Risk Control (SMARC), School of Environment, Tsinghua University, Beijing 100084, PR China; Shenzhen Environmental Science and New Energy Technology Engineering Laboratory, Tsinghua-Berkeley Shenzhen Institute, Shenzhen 518055, PR China
| | - Lin-Lan Zhuang
- Environmental Simulation and Pollution Control State Key Joint Laboratory, State Environmental Protection Key Laboratory of Microorganism Application and Risk Control (SMARC), School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Tian-Yuan Zhang
- Environmental Simulation and Pollution Control State Key Joint Laboratory, State Environmental Protection Key Laboratory of Microorganism Application and Risk Control (SMARC), School of Environment, Tsinghua University, Beijing 100084, PR China; Shenzhen Environmental Science and New Energy Technology Engineering Laboratory, Tsinghua-Berkeley Shenzhen Institute, Shenzhen 518055, PR China
| | - Hong-Ying Hu
- Environmental Simulation and Pollution Control State Key Joint Laboratory, State Environmental Protection Key Laboratory of Microorganism Application and Risk Control (SMARC), School of Environment, Tsinghua University, Beijing 100084, PR China; Shenzhen Environmental Science and New Energy Technology Engineering Laboratory, Tsinghua-Berkeley Shenzhen Institute, Shenzhen 518055, PR China.
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Wu W, Liu Y, Wang Y, Li H, Liu J, Tan J, He J, Bai J, Ma H. Evolution Analysis of the Aux/IAA Gene Family in Plants Shows Dual Origins and Variable Nuclear Localization Signals. Int J Mol Sci 2017; 18:E2107. [PMID: 28991190 PMCID: PMC5666789 DOI: 10.3390/ijms18102107] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 09/27/2017] [Accepted: 10/01/2017] [Indexed: 11/28/2022] Open
Abstract
The plant hormone auxin plays pivotal roles in many aspects of plant growth and development. The auxin/indole-3-acetic acid (Aux/IAA) gene family encodes short-lived nuclear proteins acting on auxin perception and signaling, but the evolutionary history of this gene family remains to be elucidated. In this study, the Aux/IAA gene family in 17 plant species covering all major lineages of plants is identified and analyzed by using multiple bioinformatics methods. A total of 434 Aux/IAA genes was found among these plant species, and the gene copy number ranges from three (Physcomitrella patens) to 63 (Glycine max). The phylogenetic analysis shows that the canonical Aux/IAA proteins can be generally divided into five major clades, and the origin of Aux/IAA proteins could be traced back to the common ancestor of land plants and green algae. Many truncated Aux/IAA proteins were found, and some of these truncated Aux/IAA proteins may be generated from the C-terminal truncation of auxin response factor (ARF) proteins. Our results indicate that tandem and segmental duplications play dominant roles for the expansion of the Aux/IAA gene family mainly under purifying selection. The putative nuclear localization signals (NLSs) in Aux/IAA proteins are conservative, and two kinds of new primordial bipartite NLSs in P. patens and Selaginella moellendorffii were discovered. Our findings not only give insights into the origin and expansion of the Aux/IAA gene family, but also provide a basis for understanding their functions during the course of evolution.
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Affiliation(s)
- Wentao Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, China.
- Innovation Experimental College, Northwest A&F University, Xianyang 712100, China.
| | - Yaxue Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, China.
- Innovation Experimental College, Northwest A&F University, Xianyang 712100, China.
| | - Yuqian Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, China.
- Innovation Experimental College, Northwest A&F University, Xianyang 712100, China.
| | - Huimin Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, China.
- Innovation Experimental College, Northwest A&F University, Xianyang 712100, China.
| | - Jiaxi Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, China.
- Innovation Experimental College, Northwest A&F University, Xianyang 712100, China.
| | - Jiaxin Tan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, China.
- Innovation Experimental College, Northwest A&F University, Xianyang 712100, China.
| | - Jiadai He
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, China.
- Innovation Experimental College, Northwest A&F University, Xianyang 712100, China.
| | - Jingwen Bai
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, China.
- Innovation Experimental College, Northwest A&F University, Xianyang 712100, China.
| | - Haoli Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, China.
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45
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Zhang N, Huang X, Bao Y, Wang B, Zeng H, Cheng W, Tang M, Li Y, Ren J, Sun Y. Genome-wide identification of SAUR genes in watermelon ( Citrullus lanatus). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2017; 23:619-628. [PMID: 28878500 PMCID: PMC5567703 DOI: 10.1007/s12298-017-0442-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 04/07/2017] [Accepted: 04/17/2017] [Indexed: 05/22/2023]
Abstract
The early auxin responsive SAUR family is an important gene family in auxin signal transduction. We here present the first report of a genome-wide identification of SAUR genes in watermelon genome. We successfully identified 65 ClaSAURs and provide a genomic framework for future study on these genes. Phylogenetic result revealed a Cucurbitaceae-specific SAUR subfamily and contribute to understanding of the evolutionary pattern of SAUR genes in plants. Quantitative RT-PCR analysis demonstrates the existed expression of 11 randomly selected SAUR genes in watermelon tissues. ClaSAUR36 was highly expressed in fruit, for which further study might bring a new prospective for watermelon fruit development. Moreover, correlation analysis revealed the similar expression profiles of SAUR genes between watermelon and Arabidopsis during shoot organogenesis. This work gives us a new support for the conserved auxin machinery in plants.
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Affiliation(s)
- Na Zhang
- Institute of Crop Science, Wuhan Academy of Agricultural Science and Technology, Huangpi District, Wuhan, 430345 Hubei Province China
| | - Xing Huang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, #4 Xueyuan Road, Longhua District, Haikou, 571101 China
| | - Yaning Bao
- College of Plant Science and Technology, Huazhong Agricultural University, #1 Shizishan Street, Hongshan District, Wuhan, 430070 Hubei Province China
| | - Bo Wang
- College of Plant Science and Technology, Huazhong Agricultural University, #1 Shizishan Street, Hongshan District, Wuhan, 430070 Hubei Province China
| | - Hongxia Zeng
- Institute of Crop Science, Wuhan Academy of Agricultural Science and Technology, Huangpi District, Wuhan, 430345 Hubei Province China
| | - Weishun Cheng
- Institute of Crop Science, Wuhan Academy of Agricultural Science and Technology, Huangpi District, Wuhan, 430345 Hubei Province China
| | - Mi Tang
- Institute of Crop Science, Wuhan Academy of Agricultural Science and Technology, Huangpi District, Wuhan, 430345 Hubei Province China
| | - Yuhua Li
- Institute of Crop Science, Wuhan Academy of Agricultural Science and Technology, Huangpi District, Wuhan, 430345 Hubei Province China
| | - Jian Ren
- Institute of Crop Science, Wuhan Academy of Agricultural Science and Technology, Huangpi District, Wuhan, 430345 Hubei Province China
| | - Yuhong Sun
- Institute of Crop Science, Wuhan Academy of Agricultural Science and Technology, Huangpi District, Wuhan, 430345 Hubei Province China
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46
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Santin F, Bhogale S, Fantino E, Grandellis C, Banerjee AK, Ulloa RM. Solanum tuberosum StCDPK1 is regulated by miR390 at the posttranscriptional level and phosphorylates the auxin efflux carrier StPIN4 in vitro, a potential downstream target in potato development. PHYSIOLOGIA PLANTARUM 2017; 159:244-261. [PMID: 27716933 DOI: 10.1111/ppl.12517] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 09/23/2016] [Accepted: 09/26/2016] [Indexed: 06/06/2023]
Abstract
Among many factors that regulate potato tuberization, calcium and calcium-dependent protein kinases (CDPKs) play an important role. CDPK activity increases at the onset of tuber formation with StCDPK1 expression being strongly induced in swollen stolons. However, not much is known about the transcriptional and posttranscriptional regulation of StCDPK1 or its downstream targets in potato development. To elucidate further, we analyzed its expression in different tissues and stages of the life cycle. Histochemical analysis of StCDPK1::GUS (β-glucuronidase) plants demonstrated that StCDPK1 is strongly associated with the vascular system in stems, roots, during stolon to tuber transition, and in tuber sprouts. In agreement with the observed GUS profile, we found specific cis-acting elements in StCDPK1 promoter. In silico analysis predicted miR390 to be a putative posttranscriptional regulator of StCDPK1. Quantitative real time-polymerase chain reaction (qRT-PCR) analysis showed ubiquitous expression of StCDPK1 in different tissues which correlated well with Western blot data except in leaves. On the contrary, miR390 expression exhibited an inverse pattern in leaves and tuber eyes suggesting a possible regulation of StCDPK1 by miR390. This was further confirmed by Agrobacterium co-infiltration assays. In addition, in vitro assays showed that recombinant StCDPK1-6xHis was able to phosphorylate the hydrophilic loop of the auxin efflux carrier StPIN4. Altogether, these results indicate that StCDPK1 expression is varied in a tissue-specific manner having significant expression in vasculature and in tuber eyes; is regulated by miR390 at posttranscriptional level and suggest that StPIN4 could be one of its downstream targets revealing the overall role of this kinase in potato development.
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Affiliation(s)
- Franco Santin
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), CONICET and Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Vuelta de Obligado 2490 2do piso, 1428 Buenos Aires, Argentina
| | - Sneha Bhogale
- Biology Division, Indian Institute of Science Education and Research (IISER), Dr Homi Bhabha Road, Pune, Maharashtra 411008, India
| | - Elisa Fantino
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), CONICET and Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Vuelta de Obligado 2490 2do piso, 1428 Buenos Aires, Argentina
| | - Carolina Grandellis
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), CONICET and Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Vuelta de Obligado 2490 2do piso, 1428 Buenos Aires, Argentina
| | - Anjan K Banerjee
- Biology Division, Indian Institute of Science Education and Research (IISER), Dr Homi Bhabha Road, Pune, Maharashtra 411008, India
| | - Rita M Ulloa
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), CONICET and Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Vuelta de Obligado 2490 2do piso, 1428 Buenos Aires, Argentina
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47
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Ishizaki K. Evolution of land plants: insights from molecular studies on basal lineages. Biosci Biotechnol Biochem 2017; 81:73-80. [DOI: 10.1080/09168451.2016.1224641] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Abstract
The invasion of the land by plants, or terrestrialization, was one of the most critical events in the history of the Earth. The evolution of land plants included significant transformations in body plans: the emergence of a multicellular diploid sporophyte, transition from gametophyte-dominant to sporophyte-dominant life histories, and development of many specialized tissues and organs, such as stomata, vascular tissues, roots, leaves, seeds, and flowers. Recent advances in molecular genetics in two model basal plants, bryophytes Physcomitrella patens and Marchantia polymorpha, have begun to provide answers to several key questions regarding land plant evolution. This paper discusses the evolution of the genes and regulatory mechanisms that helped drive such significant morphological innovations among land-based plants.
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Affiliation(s)
- Kimitsune Ishizaki
- Department of Biology, Graduate School of Science, Kobe University, Kobe, Japan
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48
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Herrbach V, Chirinos X, Rengel D, Agbevenou K, Vincent R, Pateyron S, Huguet S, Balzergue S, Pasha A, Provart N, Gough C, Bensmihen S. Nod factors potentiate auxin signaling for transcriptional regulation and lateral root formation in Medicago truncatula. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:569-583. [PMID: 28073951 PMCID: PMC6055581 DOI: 10.1093/jxb/erw474] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 11/24/2016] [Indexed: 05/29/2023]
Abstract
Nodulation (Nod) factors (NFs) are symbiotic molecules produced by rhizobia that are essential for establishment of the rhizobium-legume endosymbiosis. Purified NFs can stimulate lateral root formation (LRF) in Medicago truncatula, but little is known about the molecular mechanisms involved. Using a combination of reporter constructs, pharmacological and genetic approaches, we show that NFs act on early steps of LRF in M. truncatula, independently of the ethylene signaling pathway and of the cytokinin receptor MtCRE1, but in interaction with auxin. We conducted a whole-genome transcriptomic study upon NF and/or auxin treatments, using a lateral root inducible system adapted for M. truncatula. This revealed a large overlap between NF and auxin signaling and, more interestingly, synergistic interactions between these molecules. Three groups showing interaction effects were defined: group 1 contained more than 1500 genes responding specifically to the combinatorial treatment of NFs and auxin; group 2 comprised auxin-regulated genes whose expression was enhanced or antagonized by NFs; and in group 3 the expression of NF regulated genes was antagonized by auxin. Groups 1 and 2 were enriched in signaling and metabolic functions, which highlights important crosstalk between NF and auxin signaling for both developmental and symbiotic processes.
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Affiliation(s)
| | - Ximena Chirinos
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - David Rengel
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | | | - Rémy Vincent
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Stéphanie Pateyron
- POPS (transcriptOmic Platform of IPS2) Platform, Institute of Plant Sciences Paris Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Orsay, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Orsay, France
| | - Stéphanie Huguet
- POPS (transcriptOmic Platform of IPS2) Platform, Institute of Plant Sciences Paris Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Orsay, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Orsay, France
| | - Sandrine Balzergue
- POPS (transcriptOmic Platform of IPS2) Platform, Institute of Plant Sciences Paris Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Orsay, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Orsay, France
| | - Asher Pasha
- Department of Cell & Systems Biology/ Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada
| | - Nicholas Provart
- Department of Cell & Systems Biology/ Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada
| | - Clare Gough
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Sandra Bensmihen
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
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49
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Palovaara J, de Zeeuw T, Weijers D. Tissue and Organ Initiation in the Plant Embryo: A First Time for Everything. Annu Rev Cell Dev Biol 2016; 32:47-75. [PMID: 27576120 DOI: 10.1146/annurev-cellbio-111315-124929] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Land plants can grow to tremendous body sizes, yet even the most complex architectures are the result of iterations of the same developmental processes: organ initiation, growth, and pattern formation. A central question in plant biology is how these processes are regulated and coordinated to allow for the formation of ordered, 3D structures. All these elementary processes first occur in early embryogenesis, during which, from a fertilized egg cell, precursors for all major tissues and stem cells are initiated, followed by tissue growth and patterning. Here we discuss recent progress in our understanding of this phase of plant life. We consider the cellular basis for multicellular development in 3D and focus on the genetic regulatory mechanisms that direct specific steps during early embryogenesis.
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Affiliation(s)
- Joakim Palovaara
- Laboratory of Biochemistry, Wageningen University, 6703 HA Wageningen, The Netherlands;
| | - Thijs de Zeeuw
- Laboratory of Biochemistry, Wageningen University, 6703 HA Wageningen, The Netherlands;
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, 6703 HA Wageningen, The Netherlands;
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50
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Plavskin Y, Nagashima A, Perroud PF, Hasebe M, Quatrano RS, Atwal GS, Timmermans MCP. Ancient trans-Acting siRNAs Confer Robustness and Sensitivity onto the Auxin Response. Dev Cell 2016; 36:276-89. [PMID: 26859352 DOI: 10.1016/j.devcel.2016.01.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Revised: 12/03/2015] [Accepted: 01/11/2016] [Indexed: 11/29/2022]
Abstract
Novel developmental programs often evolve via cooption of existing genetic networks. To understand this process, we explored cooption of the TAS3 tasiRNA pathway in the moss Physcomitrella patens. We find an ancestral function for this repeatedly redeployed pathway in the spatial regulation of a conserved set of Auxin Response Factors. In moss, this results in stochastic patterning of the filamentous protonemal tissue. Through modeling and experimentation, we demonstrate that tasiRNA regulation confers sensitivity and robustness onto the auxin response. Increased auxin sensitivity parallels increased developmental sensitivity to nitrogen, a key environmental signal. We propose that the properties lent to the auxin response network, along with the ability to stochastically modulate development in response to environmental cues, have contributed to repeated cooption of the tasiRNA-ARF module during evolution. The signaling properties of a genetic network, and not just its developmental output, are thus critical to understanding evolution of multicellular forms.
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Affiliation(s)
- Yevgeniy Plavskin
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Akitomo Nagashima
- National Institute for Basic Biology, Okazaki 444-8585, Japan; Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Okazaki 444-8585, Japan
| | | | - Mitsuyasu Hasebe
- National Institute for Basic Biology, Okazaki 444-8585, Japan; Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Okazaki 444-8585, Japan
| | - Ralph S Quatrano
- Department of Biology, Washington University, St. Louis, MO 63130, USA
| | - Gurinder S Atwal
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Marja C P Timmermans
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Center for Plant Molecular Biology, University of Tübingen, 72076 Tübingen, Germany.
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