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Spaninks K, Offringa R. Local phytochrome signalling limits root growth in light by repressing auxin biosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4642-4653. [PMID: 37140032 PMCID: PMC10433924 DOI: 10.1093/jxb/erad163] [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: 02/03/2023] [Accepted: 05/01/2023] [Indexed: 05/05/2023]
Abstract
In nature, plant shoots are exposed to light whereas the roots grow in relative darkness. Surprisingly, many root studies rely on in vitro systems that leave the roots exposed to light whilst ignoring the possible effects of this light on root development. Here, we investigated how direct root illumination affects root growth and development in Arabidopsis and tomato. Our results show that in light-grown Arabidopsis roots, activation of local phytochrome A and B by far-red or red light inhibits respectively PHYTOCHROME INTERACTING FACTORS 1 or 4, resulting in decreased YUCCA4 and YUCCA6 expression. As a result, auxin levels in the root apex become suboptimal, ultimately resulting in reduced growth of light-grown roots. These findings highlight once more the importance of using in vitro systems where roots are grown in darkness for studies that focus on root system architecture. Moreover, we show that the response and components of this mechanism are conserved in tomato roots, thus indicating its importance for horticulture as well. Our findings open up new research possibilities to investigate the importance of light-induced root growth inhibition for plant development, possibly by exploring putative correlations with responses to other abiotic signals, such as temperature, gravity, touch, or salt stress.
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Affiliation(s)
- Kiki Spaninks
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
| | - Remko Offringa
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
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2
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Stafen CF, Kleine-Vehn J, Maraschin FDS. Signaling events for photomorphogenic root development. TRENDS IN PLANT SCIENCE 2022; 27:1266-1282. [PMID: 36057533 DOI: 10.1016/j.tplants.2022.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 07/26/2022] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
A germinating seedling incorporates environmental signals such as light into developmental outputs. Light is not only a source of energy, but also a central coordinative signal in plants. Traditionally, most research focuses on aboveground organs' response to light; therefore, our understanding of photomorphogenesis in roots is relatively scarce. However, root development underground is highly responsive to light signals from the shoot and understanding these signaling mechanisms will give a better insight into early seedling development. Here, we review the central light signaling hubs and their role in root growth promotion of Arabidopsis thaliana seedlings.
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Affiliation(s)
- Cássia Fernanda Stafen
- PPGBM - Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil
| | - Jürgen Kleine-Vehn
- Institute of Biology II, Chair of Molecular Plant Physiology (MoPP), University of Freiburg, Freiburg, Germany; Center for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, 79104 Freiburg, Germany
| | - Felipe Dos Santos Maraschin
- PPGBM - Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil; Departamento de Botânica, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil.
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3
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Cabrera J, Conesa CM, Del Pozo JC. May the dark be with roots: a perspective on how root illumination may bias in vitro research on plant-environment interactions. THE NEW PHYTOLOGIST 2022; 233:1988-1997. [PMID: 34942016 DOI: 10.1111/nph.17936] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
Roots anchor plants to the soil, providing them with nutrients and water while creating a defence network and facilitating beneficial interactions with a multitude of living organisms and climatological conditions. To facilitate morphological and molecular studies, root research has been conducted using in vitro systems. However, under natural conditions, roots grow in the dark, mainly in the absence of illumination, except for the relatively low illumination of the upper soil surface, and this has been largely ignored. Here, we discuss the results found over the last decade on how experimental exposure of roots to light may bias root development and responses through the alteration of hormonal signalling, cytoskeleton organization, reactive oxygen species or the accumulation of flavonoids, among other factors. Illumination alters the uptake of nutrients or water, and also affects the response of the roots to abiotic stresses and root interactions with the microbiota. Furthermore, we review in vitro systems created to maintain roots in darkness, and provide a comparative analysis of root transcriptomes obtained with these devices. Finally, we identify other experimental variables that should be considered to better mimic soil conditions, whose improvement would benefit studies using in vitro cultivation or enclosed ecosystems.
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Affiliation(s)
- Javier Cabrera
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/Consejo Superior de Investigaciones Científicas (UPM-INIA/CSIC), UPM, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Carlos M Conesa
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/Consejo Superior de Investigaciones Científicas (UPM-INIA/CSIC), UPM, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
- Escuela Técnica Superior de Ingeniería Agronómica, Agroambiental y de Biosistemas (ETSIAAB), Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Juan C Del Pozo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/Consejo Superior de Investigaciones Científicas (UPM-INIA/CSIC), UPM, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
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4
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Zhang L, Wu P, Li W, Feng T, Shockey J, Chen L, Zhang L, Lü S. Triacylglycerol biosynthesis in shaded seeds of tung tree (Vernicia fordii) is regulated in part by Homeodomain Leucine Zipper 21. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1735-1753. [PMID: 34643970 DOI: 10.1111/tpj.15540] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 10/07/2021] [Indexed: 06/13/2023]
Abstract
Light quantity and quality affect many aspects of plant growth and development. However, few reports have addressed the molecular connections between seed oil accumulation and light conditions, especially dense shade. Shade-avoiding plants can redirect plant resources into extension growth at the expense of leaf and root expansion in an attempt to reach areas containing richer light. Here, we report that tung tree seed oil accumulation is suppressed by dense shade during the rapid oil accumulation phase. Transcriptome analysis confirmed that oil accumulation suppression due to dense shade was attributed to reduced expression of fatty acid and triacylglycerol biosynthesis-related genes. Through weighted gene co-expression network analysis, we identified 32 core transcription factors (TFs) specifically upregulated in densely shaded seeds during the rapid oil accumulation period. Among these, VfHB21, a class I homeodomain leucine zipper TF, was shown to suppress expression of FAD2 and FADX, two key genes related to α-eleostearic acid, by directly binding to HD-ZIP I/II motifs in their respective promoter regions. VfHB21 also binds to similar motifs in the promoters of VfWRI1 and VfDGAT2, two additional key seed lipid regulatory/biosynthetic genes. Functional conservation of HB21 during plant evolution was demonstrated by the fact that AtWRI1, AtSAD1, and AtFAD2 were downregulated in VfHB21-overexpressor lines of transgenic Arabidopsis, with concomitant seed oil reduction, and the fact that AtHB21 expression also was induced by shade. This study reveals some of the regulatory mechanisms that specifically control tung tree seed oil biosynthesis and more broadly regulate plant storage carbon partitioning in response to dense shade conditions.
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Affiliation(s)
- Lingling Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Pan Wu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Wenying Li
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Tao Feng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Jay Shockey
- United States Department of Agriculture, Agricultural Research Service, Southern Regional Research Center, New Orleans, LA, USA
| | - Liang Chen
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Lin Zhang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Shiyou Lü
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
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5
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Atif MJ, Amin B, Ghani MI, Ali M, Khursheed S, Cheng Z. Transcriptomic analysis of Allium sativum uncovers putative genes involved in photoperiodic pathway and hormone signaling under long day and short day conditions. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 313:111095. [PMID: 34763878 DOI: 10.1016/j.plantsci.2021.111095] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 10/11/2021] [Accepted: 10/16/2021] [Indexed: 05/20/2023]
Abstract
Photoperiod is dominant environmental factor that controls plant growth and development. Even though research on plants response to photoperiod is significant in agriculture, molecular mechanisms of garlic in response to photoperiod remain largely unknown. In the current investigation, 3 months old garlic plants were treated with long day (LD) and short day (SD) for 10 and 20 days after treatment (DAT). Liquid chromatography-mass spectrometry (LC-MS) analysis of phytohormones exhibited that indole-3-acetic acid (IAA), zeatin riboside (ZR) and salicylic acid (SA) were observed maximum under LD at 10 DAT, whereas abscisic acid (ABA), gibberellic acid 3 (GA3), zeatin (ZT) and jasmonic acid (JA) were observed maximum under LD at 20 DAT. Transcriptome sequencing analysis was done to evaluate the transcriptional response to LD and SD. Differentially expressed genes (DEGs) were detected to have pathway enrichment. i.e., DNA binding transcription factor activity, transcription regulator activity, transferase activity, transferring hexosyl groups, and sequence specific-DNA binding activity, plant hormone signal transduction, circadian rhythm-plant, biosynthesis of amino acids, phenylpropanoid biosynthesis, and starch and sucrose metabolism. Furthermore, 28 and 40 DEGs were identified related to photoperiod and hormone signaling, respectively and their interaction in response to LD and SD were discussed in detail. Outcomes of current investigation might be useful to provide novel resources for garlic bulb formation in response to photoperiod.
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Affiliation(s)
- Muhammad Jawaad Atif
- College of Horticulture, Northwest A&F University, Yangling, 712100, China; Horticultural Research Institute, National Agricultural Research Centre, Islamabad, 44000, Pakistan.
| | - Bakht Amin
- College of Horticulture, Northwest A&F University, Yangling, 712100, China
| | - Muhammad Imran Ghani
- College of Horticulture, Northwest A&F University, Yangling, 712100, China; College of Natural Resource and Environment, Northwest A&F University, Yangling, 712100, China
| | - Muhammad Ali
- College of Horticulture, Northwest A&F University, Yangling, 712100, China
| | | | - Zhihui Cheng
- College of Horticulture, Northwest A&F University, Yangling, 712100, China.
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6
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Eggers R, Jammer A, Jha S, Kerschbaumer B, Lahham M, Strandback E, Toplak M, Wallner S, Winkler A, Macheroux P. The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana. PHYTOCHEMISTRY 2021; 189:112822. [PMID: 34118767 DOI: 10.1016/j.phytochem.2021.112822] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 05/23/2021] [Accepted: 05/24/2021] [Indexed: 06/12/2023]
Abstract
Flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) are utilized as coenzymes in many biochemical reduction-oxidation reactions owing to the ability of the tricyclic isoalloxazine ring system to employ the oxidized, radical and reduced state. We have analyzed the genome of Arabidopsis thaliana to establish an inventory of genes encoding flavin-dependent enzymes (flavoenzymes) as a basis to explore the range of flavin-dependent biochemical reactions that occur in this model plant. Expectedly, flavoenzymes catalyze many pivotal reactions in primary catabolism, which are connected to the degradation of basic metabolites, such as fatty and amino acids as well as carbohydrates and purines. On the other hand, flavoenzymes play diverse roles in anabolic reactions most notably the biosynthesis of amino acids as well as the biosynthesis of pyrimidines and sterols. Importantly, the role of flavoenzymes goes much beyond these basic reactions and extends into pathways that are equally crucial for plant life, for example the production of natural products. In this context, we outline the participation of flavoenzymes in the biosynthesis and maintenance of cofactors, coenzymes and accessory plant pigments (e. g. carotenoids) as well as phytohormones. Moreover, several multigene families have emerged as important components of plant immunity, for example the family of berberine bridge enzyme-like enzymes, flavin-dependent monooxygenases and NADPH oxidases. Furthermore, the versatility of flavoenzymes is highlighted by their role in reactions leading to tRNA-modifications, chromatin regulation and cellular redox homeostasis. The favorable photochemical properties of the flavin chromophore are exploited by photoreceptors to govern crucial processes of plant adaptation and development. Finally, a sequence- and structure-based approach was undertaken to gain insight into the catalytic role of uncharacterized flavoenzymes indicating their involvement in unknown biochemical reactions and pathways in A. thaliana.
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Affiliation(s)
- Reinmar Eggers
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
| | - Alexandra Jammer
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
| | - Shalinee Jha
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
| | - Bianca Kerschbaumer
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
| | - Majd Lahham
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
| | - Emilia Strandback
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
| | - Marina Toplak
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
| | - Silvia Wallner
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
| | - Andreas Winkler
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
| | - Peter Macheroux
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria.
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7
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Rusaczonek A, Czarnocka W, Willems P, Sujkowska-Rybkowska M, Van Breusegem F, Karpiński S. Phototropin 1 and 2 Influence Photosynthesis, UV-C Induced Photooxidative Stress Responses, and Cell Death. Cells 2021; 10:cells10020200. [PMID: 33498294 PMCID: PMC7909289 DOI: 10.3390/cells10020200] [Citation(s) in RCA: 4] [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: 11/30/2020] [Revised: 01/10/2021] [Accepted: 01/16/2021] [Indexed: 12/26/2022] Open
Abstract
Phototropins are plasma membrane-associated photoreceptors of blue light and UV-A/B radiation. The Arabidopsis thaliana genome encodes two phototropins, PHOT1 and PHOT2, that mediate phototropism, chloroplast positioning, and stomatal opening. They are well characterized in terms of photomorphogenetic processes, but so far, little was known about their involvement in photosynthesis, oxidative stress responses, and cell death. By analyzing phot1, phot2 single, and phot1phot2 double mutants, we demonstrated that both phototropins influence the photochemical and non-photochemical reactions, photosynthetic pigments composition, stomata conductance, and water-use efficiency. After oxidative stress caused by UV-C treatment, phot1 and phot2 single and double mutants showed a significantly reduced accumulation of H2O2 and more efficient photosynthetic electron transport compared to the wild type. However, all phot mutants exhibited higher levels of cell death four days after UV-C treatment, as well as deregulated gene expression. Taken together, our results reveal that on the one hand, both phot1 and phot2 contribute to the inhibition of UV-C-induced foliar cell death, but on the other hand, they also contribute to the maintenance of foliar H2O2 levels and optimal intensity of photochemical reactions and non-photochemical quenching after an exposure to UV-C stress. Our data indicate a novel role for phototropins in the condition-dependent optimization of photosynthesis, growth, and water-use efficiency as well as oxidative stress and cell death response after UV-C exposure.
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Affiliation(s)
- Anna Rusaczonek
- Department of Botany, Institute of Biology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland; (W.C.); (M.S.-R.)
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
- Correspondence: (A.R.); (S.K.)
| | - Weronika Czarnocka
- Department of Botany, Institute of Biology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland; (W.C.); (M.S.-R.)
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Patrick Willems
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; (P.W.); (F.V.B.)
- VIB Center of Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Marzena Sujkowska-Rybkowska
- Department of Botany, Institute of Biology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland; (W.C.); (M.S.-R.)
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; (P.W.); (F.V.B.)
- VIB Center of Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Stanisław Karpiński
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
- Correspondence: (A.R.); (S.K.)
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8
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Spaninks K, van Lieshout J, van Ieperen W, Offringa R. Regulation of Early Plant Development by Red and Blue Light: A Comparative Analysis Between Arabidopsis thaliana and Solanum lycopersicum. FRONTIERS IN PLANT SCIENCE 2020; 11:599982. [PMID: 33424896 PMCID: PMC7785528 DOI: 10.3389/fpls.2020.599982] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
In vertical farming, plants are grown in multi-layered growth chambers supplied with energy-efficient LEDs that produce less heat and can thus be placed in close proximity to the plants. The spectral quality control allowed by LED lighting potentially enables steering plant development toward desired phenotypes. However, this requires detailed knowledge on how light quality affects different developmental processes per plant species or even cultivar, and how well information from model plants translates to horticultural crops. Here we have grown the model dicot Arabidopsis thaliana (Arabidopsis) and the crop plant Solanum lycopersicum (tomato) under white or monochromatic red or blue LED conditions. In addition, seedlings were grown in vitro in either light-grown roots (LGR) or dark-grown roots (DGR) LED conditions. Our results present an overview of phenotypic traits that are sensitive to red or blue light, which may be used as a basis for application by tomato nurseries. Our comparative analysis showed that young tomato plants were remarkably indifferent to the LED conditions, with red and blue light effects on primary growth, but not on organ formation or flowering. In contrast, Arabidopsis appeared to be highly sensitive to light quality, as dramatic differences in shoot and root elongation, organ formation, and developmental phase transitions were observed between red, blue, and white LED conditions. Our results highlight once more that growth responses to environmental conditions can differ significantly between model and crop species. Understanding the molecular basis for this difference will be important for designing lighting systems tailored for specific crops.
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Affiliation(s)
- Kiki Spaninks
- Plant Developmental Genetics, Institute for Biology Leiden, Leiden University, Leiden, Netherlands
| | - Jelmer van Lieshout
- Plant Developmental Genetics, Institute for Biology Leiden, Leiden University, Leiden, Netherlands
| | - Wim van Ieperen
- Horticulture and Product Physiology Group, Wageningen University and Research, Wageningen, Netherlands
| | - Remko Offringa
- Plant Developmental Genetics, Institute for Biology Leiden, Leiden University, Leiden, Netherlands
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9
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Waidmann S, Sarkel E, Kleine-Vehn J. Same same, but different: growth responses of primary and lateral roots. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2397-2411. [PMID: 31956903 PMCID: PMC7178446 DOI: 10.1093/jxb/eraa027] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 01/15/2020] [Indexed: 05/20/2023]
Abstract
The root system architecture describes the shape and spatial arrangement of roots within the soil. Its spatial distribution depends on growth and branching rates as well as directional organ growth. The embryonic primary root gives rise to lateral (secondary) roots, and the ratio of both root types changes over the life span of a plant. Most studies have focused on the growth of primary roots and the development of lateral root primordia. Comparably less is known about the growth regulation of secondary root organs. Here, we review similarities and differences between primary and lateral root organ growth, and emphasize particularly how external stimuli and internal signals differentially integrate root system growth.
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Affiliation(s)
- Sascha Waidmann
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Elizabeth Sarkel
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Jürgen Kleine-Vehn
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
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10
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Vandenbrink JP, Herranz R, Poehlman WL, Alex Feltus F, Villacampa A, Ciska M, Javier Medina F, Kiss JZ. RNA-seq analyses of Arabidopsis thaliana seedlings after exposure to blue-light phototropic stimuli in microgravity. AMERICAN JOURNAL OF BOTANY 2019; 106:1466-1476. [PMID: 31709515 DOI: 10.1002/ajb2.1384] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 09/17/2019] [Indexed: 05/04/2023]
Abstract
PREMISE Plants synthesize information from multiple environmental stimuli when determining their direction of growth. Gravity, being ubiquitous on Earth, plays a major role in determining the direction of growth and overall architecture of the plant. Here, we utilized the microgravity environment on board the International Space Station (ISS) to identify genes involved influencing growth and development of phototropically stimulated seedlings of Arabidopsis thaliana. METHODS Seedlings were grown on the ISS, and RNA was extracted from 7 samples (pools of 10-15 plants) grown in microgravity (μg) or Earth gravity conditions (1-g). Transcriptomic analyses via RNA sequencing (RNA-seq) of differential gene expression was performed using the HISAT2-Stringtie-DESeq2 RNASeq pipeline. Differentially expressed genes were further characterized by using Pathway Analysis and enrichment for Gene Ontology classifications. RESULTS For 296 genes that were found significantly differentially expressed between plants in microgravity compared to 1-g controls, Pathway Analysis identified eight molecular pathways that were significantly affected by reduced gravity conditions. Specifically, light-associated pathways (e.g., photosynthesis-antenna proteins, photosynthesis, porphyrin, and chlorophyll metabolism) were significantly downregulated in microgravity. CONCLUSIONS Gene expression in A. thaliana seedlings grown in microgravity was significantly altered compared to that of the 1-g control. Understanding how plants grow in conditions of microgravity not only aids in our understanding of how plants grow and respond to the environment but will also help to efficiently grow plants during long-range space missions.
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Affiliation(s)
- Joshua P Vandenbrink
- School of Biological Sciences, Louisiana Tech University, Ruston, LA, 71272, USA
- Department of Biology, University of North Carolina at Greensboro, Greensboro, NC, 27402, USA
| | - Raul Herranz
- Centro de Investigaciones Biológicas (CSIC), Madrid, E28040, Spain
| | - William L Poehlman
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, 29634, USA
| | - F Alex Feltus
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, 29634, USA
| | | | - Malgorzata Ciska
- Centro de Investigaciones Biológicas (CSIC), Madrid, E28040, Spain
| | - F Javier Medina
- Centro de Investigaciones Biológicas (CSIC), Madrid, E28040, Spain
| | - John Z Kiss
- Department of Biology, University of North Carolina at Greensboro, Greensboro, NC, 27402, USA
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11
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Kutschera U, Briggs WR. Photomorphogenesis of the root system in developing sunflower seedlings: a role for sucrose. PLANT BIOLOGY (STUTTGART, GERMANY) 2019; 21:627-633. [PMID: 30821893 DOI: 10.1111/plb.12981] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 02/28/2019] [Indexed: 06/09/2023]
Abstract
The domestic sunflower (Helianthus annuus L. cv. 'Giganteus') has been used since the 19th century as a model plant for the study of seedling development in darkness and white light (WL) (scoto- versus photomorphogenesis). However, most pertinent studies have focused on the developmental patterns of the hypocotyl and cotyledons, whereas the root system has been largely ignored. In this study, we analysed entire sunflower seedlings (root and shoot) and quantified organ development in the above- and belowground parts of the organism under natural (non-sterile) conditions. We document that seedlings, raised in moist vermiculite, are covered with methylobacteria, microbes that are known to promote root development in Arabidopsis. Quantitative data revealed that during photomorphogenesis in WL, the root system expands by 90%, whereas stem elongation is inhibited, and hook opening/cotyledon expansion occurs. Root morphogenesis may be mediated via imported sucrose provided by the green, photosynthetically active cotyledons. This hypothesis is supported by the documented effect of sucrose on the induction of lateral root initials in sunflower cuttings. Under these experimental conditions, phytohormones (auxin, cytokinin, brassinolide) exerted little effect on root and cotyledon expansion, and no hormone-induced initiation of lateral roots was observed. It is concluded that sucrose not only acts as an energy source to fuel cell metabolism but is also a shoot-derived signalling molecule that triggers root morphogenesis.
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Affiliation(s)
- U Kutschera
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - W R Briggs
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
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12
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Zhou M, Sng NJ, LeFrois CE, Paul AL, Ferl RJ. Epigenomics in an extraterrestrial environment: organ-specific alteration of DNA methylation and gene expression elicited by spaceflight in Arabidopsis thaliana. BMC Genomics 2019; 20:205. [PMID: 30866818 PMCID: PMC6416986 DOI: 10.1186/s12864-019-5554-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 02/21/2019] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Plants adapted to diverse environments on Earth throughout their evolutionary history, and developed mechanisms to thrive in a variety of terrestrial habitats. When plants are grown in the novel environment of spaceflight aboard the International Space Station (ISS), an environment completely outside their evolutionary history, they respond with unique alterations to their gene expression profile. Identifying the genes important for physiological adaptation to spaceflight and dissecting the biological processes and pathways engaged by plants during spaceflight has helped reveal spaceflight adaptation, and has furthered understanding of terrestrial growth processes. However, the underlying regulatory mechanisms responsible for these changes in gene expression patterns are just beginning to be explored. Epigenetic modifications, such as DNA methylation at position five in cytosine, has been shown to play a role in the physiological adaptation to adverse terrestrial environments, and may play a role in spaceflight as well. RESULTS Whole Genome Bisulfite Sequencing of DNA of Arabidopsis grown on the ISS from seed revealed organ-specific patterns of differential methylation compared to ground controls. The overall levels of methylation in CG, CHG, and CHH contexts were similar between flight and ground DNA, however, thousands of specifically differentially methylated cytosines were discovered, and there were clear organ-specific differences in methylation patterns. Spaceflight leaves had higher methylation levels in CHG and CHH contexts within protein-coding genes in spaceflight; about a fifth of the leaf genes were also differentially regulated in spaceflight, almost half of which were associated with reactive oxygen signaling. CONCLUSIONS The physiological adaptation of plants to spaceflight is likely nuanced by epigenomic modification. This is the first examination of differential genomic methylation from plants grown completely in the spaceflight environment of the ISS in plant growth hardware developed for informing exploration life support strategies. Yet even in this optimized plant habitat, plants respond as if stressed. These data suggest that gene expression associated with physiological adaptation to spaceflight is regulated in part by methylation strategies similar to those engaged with familiar terrestrial stress responses. The differential methylation maps generated here provide a useful reference for elucidating the layers of regulation of spaceflight responses.
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Affiliation(s)
- Mingqi Zhou
- 0000 0004 1936 8091grid.15276.37Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL USA ,0000 0004 1936 8091grid.15276.37Horticultural Sciences Department, University of Florida, Gainesville, FL USA
| | - Natasha J. Sng
- 0000 0004 1936 8091grid.15276.37Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL USA ,0000 0004 1936 8091grid.15276.37Horticultural Sciences Department, University of Florida, Gainesville, FL USA
| | - Collin E. LeFrois
- 0000 0004 1936 8091grid.15276.37Horticultural Sciences Department, University of Florida, Gainesville, FL USA
| | - Anna-Lisa Paul
- 0000 0004 1936 8091grid.15276.37Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL USA ,0000 0004 1936 8091grid.15276.37Horticultural Sciences Department, University of Florida, Gainesville, FL USA
| | - Robert J. Ferl
- 0000 0004 1936 8091grid.15276.37Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL USA ,0000 0004 1936 8091grid.15276.37Horticultural Sciences Department, University of Florida, Gainesville, FL USA ,0000 0004 1936 8091grid.15276.37Interdisciplinary Center for Biotechnology, University of Florida, Gainesville, FL USA
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13
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Kumari S, Panigrahi KCS. Light and auxin signaling cross-talk programme root development in plants. J Biosci 2019. [DOI: 10.1007/s12038-018-9838-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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14
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Baluška F, Mancuso S. Plant Cognition and Behavior: From Environmental Awareness to Synaptic Circuits Navigating Root Apices. MEMORY AND LEARNING IN PLANTS 2018. [DOI: 10.1007/978-3-319-75596-0_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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15
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Qu Y, Liu S, Bao W, Xue X, Ma Z, Yokawa K, Baluška F, Wan Y. Expression of Root Genes in Arabidopsis Seedlings Grown by Standard and Improved Growing Methods. Int J Mol Sci 2017; 18:ijms18050951. [PMID: 28467358 PMCID: PMC5454864 DOI: 10.3390/ijms18050951] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 04/25/2017] [Accepted: 04/27/2017] [Indexed: 12/21/2022] Open
Abstract
Roots of Arabidopsis thaliana seedlings grown in the laboratory using the traditional plant-growing culture system (TPG) were covered to maintain them in darkness. This new method is based on a dark chamber and is named the improved plant-growing method (IPG). We measured the light conditions in dark chambers, and found that the highest light intensity was dramatically reduced deeper in the dark chamber. In the bottom and side parts of dark chambers, roots were almost completely shaded. Using the high-throughput RNA sequencing method on the whole RNA extraction from roots, we compared the global gene expression levels in roots of seedlings from these two conditions and identified 141 differently expressed genes (DEGs) between them. According to the KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment, the flavone and flavonol biosynthesis and flavonoid biosynthesis pathways were most affected among all annotated pathways. Surprisingly, no genes of known plant photoreceptors were identified as DEGs by this method. Considering that the light intensity was decreased in the IPG system, we collected four sections (1.5 cm for each) of Arabidopsis roots grown in TPG and IPG conditions, and the spatial-related differential gene expression levels of plant photoreceptors and polar auxin transporters, including CRY1, CRY2, PHYA, PHYB, PHOT1, PHOT2, and UVR8 were analyzed by qRT-PCR. Using these results, we generated a map of the spatial-related expression patterns of these genes under IPG and TPG conditions. The expression levels of light-related genes in roots is highly sensitive to illumination and it provides a background reference for selecting an improved culture method for laboratory-maintained Arabidopsis seedlings.
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Affiliation(s)
- Yanli Qu
- College of Biological Sciences and Biotechnology, Beijing Forestry University, 35 Qinghua East Road, Haidian District, Beijing 100083, China.
| | - Shuai Liu
- College of Biological Sciences and Biotechnology, Beijing Forestry University, 35 Qinghua East Road, Haidian District, Beijing 100083, China.
| | - Wenlong Bao
- College of Biological Sciences and Biotechnology, Beijing Forestry University, 35 Qinghua East Road, Haidian District, Beijing 100083, China.
| | - Xian Xue
- College of Biological Sciences and Biotechnology, Beijing Forestry University, 35 Qinghua East Road, Haidian District, Beijing 100083, China.
- College of Agriculture, Henan University of Science and Technology, Luoyang 471003, China.
| | - Zhengwen Ma
- College of Biological Sciences and Biotechnology, Beijing Forestry University, 35 Qinghua East Road, Haidian District, Beijing 100083, China.
| | - Ken Yokawa
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo 192-0397, Japan.
| | - František Baluška
- Institute of Cellular and Molecular Botany, University of Bonn, D-53115 Bonn, Germany.
| | - Yinglang Wan
- College of Biological Sciences and Biotechnology, Beijing Forestry University, 35 Qinghua East Road, Haidian District, Beijing 100083, China.
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16
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Vandenbrink JP, Herranz R, Medina FJ, Edelmann RE, Kiss JZ. A novel blue-light phototropic response is revealed in roots of Arabidopsis thaliana in microgravity. PLANTA 2016; 244:1201-1215. [PMID: 27507239 PMCID: PMC5748516 DOI: 10.1007/s00425-016-2581-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 08/02/2016] [Indexed: 05/21/2023]
Abstract
Blue-light positive phototropism in roots is masked by gravity and revealed in conditions of microgravity. In addition, the magnitude of red-light positive phototropic curvature is correlated to the magnitude of gravity. Due to their sessile nature, plants utilize environmental cues to grow and respond to their surroundings. Two of these cues, light and gravity, play a substantial role in plant orientation and directed growth movements (tropisms). However, very little is currently known about the interaction between light- (phototropic) and gravity (gravitropic)-mediated growth responses. Utilizing the European Modular Cultivation System on board the International Space Station, we investigated the interaction between phototropic and gravitropic responses in three Arabidopsis thaliana genotypes, Landsberg wild type, as well as mutants of phytochrome A and phytochrome B. Onboard centrifuges were used to create a fractional gravity gradient ranging from reduced gravity up to 1g. A novel positive blue-light phototropic response of roots was observed during conditions of microgravity, and this response was attenuated at 0.1g. In addition, a red-light pretreatment of plants enhanced the magnitude of positive phototropic curvature of roots in response to blue illumination. In addition, a positive phototropic response of roots was observed when exposed to red light, and a decrease in response was gradual and correlated with the increase in gravity. The positive red-light phototropic curvature of hypocotyls when exposed to red light was also confirmed. Both red-light and blue-light phototropic responses were also shown to be affected by directional light intensity. To our knowledge, this is the first characterization of a positive blue-light phototropic response in Arabidopsis roots, as well as the first description of the relationship between these phototropic responses in fractional or reduced gravities.
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Affiliation(s)
- Joshua P Vandenbrink
- Department of Biology, University of Mississippi, University, Oxford, MS, 38677, USA
| | - Raul Herranz
- Centro de Investigaciones Biológicas (CSIC), Madrid, Spain
| | | | | | - John Z Kiss
- Department of Biology, University of Mississippi, University, Oxford, MS, 38677, USA.
- Department of Biology, University of North Carolina at Greensboro, Greensboro, NC, 27402, USA.
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17
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Takemiya A, Shimazaki KI. Arabidopsis phot1 and phot2 phosphorylate BLUS1 kinase with different efficiencies in stomatal opening. JOURNAL OF PLANT RESEARCH 2016; 129:167-74. [PMID: 26780063 DOI: 10.1007/s10265-015-0780-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 11/24/2015] [Indexed: 05/20/2023]
Abstract
In Arabidopsis thaliana, phototropins (phot1 and phot2), light-activated receptor kinases, redundantly regulate various photoresponses such as phototropism, chloroplast photorelocation movement, stomatal opening, and leaf flattening. However, it is still unclear how phot1 and phot2 signals are integrated into a common target and regulate physiological responses. In the present study, we provide evidence that phot1 and phot2 phosphorylate BLUE LIGHT SIGNALING1 (BLUS1) kinase as a common substrate in stomatal opening. Biochemical analysis revealed that the recombinant phot2 protein directly phosphorylated BLUS1 in vitro in a blue light-dependent manner, as reported for phot1. BLUS1 phosphorylation was observed in both phot1 and phot2 mutants, and phot2 mutant exhibited higher phosphorylation of BLUS1 than did phot1 mutant. Transgenic plants expressing phot1-GFP (P1G) and phot2-GFP (P2G) at a similar level under the PHOT2 promoter demonstrated that P1G initiated higher phosphorylation of BLUS1 than P2G, suggesting that phot1 phosphorylates BLUS1 more efficiently. Similarly, P1G mediated a higher activation of the plasma membrane H(+)-ATPase and stomatal opening than P2G, indicating that the phosphorylation status of BLUS1 is a key determinant of physiological response. Together, these findings provide insights into the signal integration and different properties of phot1 and phot2 signaling.
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Affiliation(s)
- Atsushi Takemiya
- Department of Biology, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan.
| | - Ken-ichiro Shimazaki
- Department of Biology, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
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18
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Sullivan S, Petersen J, Blackwood L, Papanatsiou M, Christie JM. Functional characterization of Ostreococcus tauri phototropin. THE NEW PHYTOLOGIST 2016; 209:612-23. [PMID: 26414490 DOI: 10.1111/nph.13640] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 08/09/2015] [Indexed: 05/05/2023]
Abstract
Phototropins (phots) regulate a range of adaptive processes in plants that serve to optimize photosynthetic efficiency and promote growth. Light sensing by Arabidopsis thaliana phots is predominantly mediated by the Light, Oxygen and Voltage sensing 2 (LOV2) flavin-binding motif located within the N-terminus of the photoreceptor. Here we characterize the photochemical and biochemical properties of phot from the marine picoalga Ostreococcus tauri phototropin (Otphot) and examine its ability to replace phot-mediated function in Arabidopsis. Photochemical properties of Otphot rely on both LOV1 and LOV2. Yet, biochemical analysis indicates that light-dependent receptor autophosphorylation is primarily dependent on LOV2. As found for Arabidopsis phots, Otphot associates with the plasma membrane and partially internalizes, albeit to a limited extent, in response to blue-light irradiation. Otphot is able to elicit a number of phot-regulated processes in Arabidopsis, including petiole positioning, leaf expansion, stomatal opening and chloroplast accumulation movement. However, Otphot is unable to restore phototropism and chloroplast avoidance movement. Consistent with its lack of phototropic function in Arabidopsis, Otphot does not associate with or trigger dephosphorylation of the phototropic signalling component Non-Phototropic Hypocotyl 3 (NPH3). Taken together, these findings indicate that the mechanism of action of plant and evolutionarily distant algal phots is less well conserved than previously thought.
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Affiliation(s)
- Stuart Sullivan
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bower Building, Glasgow, G12 8QQ, UK
| | - Jan Petersen
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bower Building, Glasgow, G12 8QQ, UK
| | - Lisa Blackwood
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bower Building, Glasgow, G12 8QQ, UK
| | - Maria Papanatsiou
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bower Building, Glasgow, G12 8QQ, UK
| | - John M Christie
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bower Building, Glasgow, G12 8QQ, UK
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19
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Silva-Navas J, Moreno-Risueno MA, Manzano C, Pallero-Baena M, Navarro-Neila S, Téllez-Robledo B, Garcia-Mina JM, Baigorri R, Gallego FJ, del Pozo JC. D-Root: a system for cultivating plants with the roots in darkness or under different light conditions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:244-55. [PMID: 26312572 DOI: 10.1111/tpj.12998] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 07/24/2015] [Accepted: 08/18/2015] [Indexed: 05/09/2023]
Abstract
In nature roots grow in the dark and away from light (negative phototropism). However, most current research in root biology has been carried out with the root system grown in the presence of light. Here, we have engineered a device, called Dark-Root (D-Root), to grow plants in vitro with the aerial part exposed to the normal light/dark photoperiod while the roots are in the dark or exposed to specific wavelengths or light intensities. D-Root provides an efficient system for cultivating a large number of seedlings and easily characterizing root architecture in the dark. At the morphological level, root illumination shortens root length and promotes early emergence of lateral roots, therefore inducing expansion of the root system. Surprisingly, root illumination also affects shoot development, including flowering time. Our analyses also show that root illumination alters the proper response to hormones or abiotic stress (e.g. salt or osmotic stress) and nutrient starvation, enhancing inhibition of root growth. In conclusion, D-Root provides a growing system closer to the natural one for assaying Arabidopsis plants, and therefore its use will contribute to a better understanding of the mechanisms involved in root development, hormonal signaling and stress responses.
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Affiliation(s)
- Javier Silva-Navas
- Centro de Biotecnología y Genómica de Plantas (CBGP) INIA-UPM, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, Madrid, 28223, Spain
- Dpto. de Genética, Facultad de Biología, Universidad Complutense de Madrid, Madrid, 28040, Spain
| | - Miguel A Moreno-Risueno
- Centro de Biotecnología y Genómica de Plantas (CBGP) INIA-UPM, Universidad Politecnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, Madrid, 28223, Spain
| | - Concepción Manzano
- Centro de Biotecnología y Genómica de Plantas (CBGP) INIA-UPM, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, Madrid, 28223, Spain
| | - Mercedes Pallero-Baena
- Centro de Biotecnología y Genómica de Plantas (CBGP) INIA-UPM, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, Madrid, 28223, Spain
- Facultad de Ciencias, Universidad de Extremadura, Badajoz, 06006, Spain
| | - Sara Navarro-Neila
- Centro de Biotecnología y Genómica de Plantas (CBGP) INIA-UPM, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, Madrid, 28223, Spain
| | - Bárbara Téllez-Robledo
- Centro de Biotecnología y Genómica de Plantas (CBGP) INIA-UPM, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, Madrid, 28223, Spain
| | - Jose M Garcia-Mina
- CIPAV (Centro de Investigación en Producción Animal y Vegetal), Timac Agro Int-Roullier Group, Polígono Arazuri-Orcoyen, C/C n 32, Orcoyen, 31160, Spain
| | - Roberto Baigorri
- CIPAV (Centro de Investigación en Producción Animal y Vegetal), Timac Agro Int-Roullier Group, Polígono Arazuri-Orcoyen, C/C n 32, Orcoyen, 31160, Spain
| | - Francisco Javier Gallego
- Dpto. de Genética, Facultad de Biología, Universidad Complutense de Madrid, Madrid, 28040, Spain
| | - Juan C del Pozo
- Centro de Biotecnología y Genómica de Plantas (CBGP) INIA-UPM, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, Madrid, 28223, Spain
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20
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Rellán-Álvarez R, Lobet G, Lindner H, Pradier PL, Sebastian J, Yee MC, Geng Y, Trontin C, LaRue T, Schrager-Lavelle A, Haney CH, Nieu R, Maloof J, Vogel JP, Dinneny JR. GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown root systems. eLife 2015; 4:e07597. [PMID: 26287479 PMCID: PMC4589753 DOI: 10.7554/elife.07597] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 08/18/2015] [Indexed: 12/16/2022] Open
Abstract
Root systems develop different root types that individually sense cues from their local environment and integrate this information with systemic signals. This complex multi-dimensional amalgam of inputs enables continuous adjustment of root growth rates, direction, and metabolic activity that define a dynamic physical network. Current methods for analyzing root biology balance physiological relevance with imaging capability. To bridge this divide, we developed an integrated-imaging system called Growth and Luminescence Observatory for Roots (GLO-Roots) that uses luminescence-based reporters to enable studies of root architecture and gene expression patterns in soil-grown, light-shielded roots. We have developed image analysis algorithms that allow the spatial integration of soil properties, gene expression, and root system architecture traits. We propose GLO-Roots as a system that has great utility in presenting environmental stimuli to roots in ways that evoke natural adaptive responses and in providing tools for studying the multi-dimensional nature of such processes.
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Affiliation(s)
- Rubén Rellán-Álvarez
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
| | | | - Heike Lindner
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
| | - Pierre-Luc Pradier
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
| | - Jose Sebastian
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
| | - Muh-Ching Yee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
| | - Yu Geng
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
- Department of Energy, Department of Energy Joint Genome Institute, Walnut Creek, United States
| | - Charlotte Trontin
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
| | - Therese LaRue
- Department of Biology, Stanford University, Stanford, United States
| | | | - Cara H Haney
- Department of Genetics, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, United States
| | - Rita Nieu
- Western Regional Research Center, United States Department of Agriculture, Albany, United States
| | - Julin Maloof
- Department of Plant Biology, University of California, Davis, Davis, United States
| | - John P Vogel
- Department of Energy, Department of Energy Joint Genome Institute, Walnut Creek, United States
| | - José R Dinneny
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
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Mo M, Yokawa K, Wan Y, Baluška F. How and why do root apices sense light under the soil surface? FRONTIERS IN PLANT SCIENCE 2015; 6:775. [PMID: 26442084 PMCID: PMC4585147 DOI: 10.3389/fpls.2015.00775] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Accepted: 09/10/2015] [Indexed: 05/18/2023]
Abstract
Light can penetrate several centimeters below the soil surface. Growth, development and behavior of plant roots are markedly affected by light despite their underground lifestyle. Early studies provided contrasting information on the spatial and temporal distribution of light-sensing cells in the apical region of root apex and discussed the physiological roles of plant hormones in root responses to light. Recent biological and microscopic advances have improved our understanding of the processes involved in the sensing and transduction of light signals, resulting in subsequent physiological and behavioral responses in growing root apices. Here, we review current knowledge of cellular distributions of photoreceptors and their signal transduction pathways in diverse root tissues and root apex zones. We are discussing also the roles of auxin transporters in roots exposed to light, as well as interactions of light signal perceptions with sensing of other environmental factors relevant to plant roots.
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Affiliation(s)
- Mei Mo
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Ken Yokawa
- Institute of Cellular and Molecular Botany, University of Bonn, Bonn, Germany
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
| | - Yinglang Wan
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
- *Correspondence: Yinglang Wan, College of Biological Sciences and Biotechnology, Beijing Forestry University, Qinghua East Road No. 35, 100083 Beijing, China, ; František Baluška, Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee 1, D-53115 Bonn, Germany,
| | - František Baluška
- Institute of Cellular and Molecular Botany, University of Bonn, Bonn, Germany
- *Correspondence: Yinglang Wan, College of Biological Sciences and Biotechnology, Beijing Forestry University, Qinghua East Road No. 35, 100083 Beijing, China, ; František Baluška, Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee 1, D-53115 Bonn, Germany,
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22
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Thomas S, Sreelakshmi Y, Sharma R. Light modulates the root tip excision induced lateral root formation in tomato. PLANT SIGNALING & BEHAVIOR 2014; 9:e970098. [PMID: 25482798 PMCID: PMC4623053 DOI: 10.4161/15592316.2014.970098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 07/02/2014] [Accepted: 07/02/2014] [Indexed: 05/07/2023]
Abstract
During plant growth and development, root tip performs multifarious functions integrating diverse external and internal stimuli to regulate root elongation and architecture. It is believed that a signal originating from root tip inhibits lateral root formation (LRF). The excision of root tip induced LRF in tomato seedlings associated with accumulation of auxin in pericycle founder cells. The excision of cotyledons slightly reduced LRF, whereas severing shoot from root completely abolished LRF. Exogenous ethylene application did not alter LRF. The response was modulated by light with higher LRF in seedlings exposed to light. Our results indicate that light plays a role in LRF in seedlings by likely modulating shoot derived auxin.
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Affiliation(s)
- Sherinmol Thomas
- Repository of Tomato Genomics Resources; Department of Plant Sciences; University of Hyderabad; Hyderabad, India
| | - Yellamaraju Sreelakshmi
- Repository of Tomato Genomics Resources; Department of Plant Sciences; University of Hyderabad; Hyderabad, India
| | - Rameshwar Sharma
- Repository of Tomato Genomics Resources; Department of Plant Sciences; University of Hyderabad; Hyderabad, India
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