1
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Collins E, Shou H, Mao C, Whelan J, Jost R. Dynamic interactions between SPX proteins, the ubiquitination machinery, and signalling molecules for stress adaptation at a whole-plant level. Biochem J 2024; 481:363-385. [PMID: 38421035 DOI: 10.1042/bcj20230163] [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: 10/24/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 03/02/2024]
Abstract
The plant macronutrient phosphorus is a scarce resource and plant-available phosphate is limiting in most soil types. Generally, a gene regulatory module called the phosphate starvation response (PSR) enables efficient phosphate acquisition by roots and translocation to other organs. Plants growing on moderate to nutrient-rich soils need to co-ordinate availability of different nutrients and repress the highly efficient PSR to adjust phosphate acquisition to the availability of other macro- and micronutrients, and in particular nitrogen. PSR repression is mediated by a small family of single SYG1/Pho81/XPR1 (SPX) domain proteins. The SPX domain binds higher order inositol pyrophosphates that signal cellular phosphorus status and modulate SPX protein interaction with PHOSPHATE STARVATION RESPONSE1 (PHR1), the central transcriptional regulator of PSR. Sequestration by SPX repressors restricts PHR1 access to PSR gene promoters. Here we focus on SPX4 that primarily acts in shoots and sequesters many transcription factors other than PHR1 in the cytosol to control processes beyond the classical PSR, such as nitrate, auxin, and jasmonic acid signalling. Unlike SPX1 and SPX2, SPX4 is subject to proteasomal degradation not only by singular E3 ligases, but also by SCF-CRL complexes. Emerging models for these different layers of control and their consequences for plant acclimation to the environment will be discussed.
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Affiliation(s)
- Emma Collins
- Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC 3086, Australia
| | - Huixia Shou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China
- Hainan Institute, Zhejiang University, Sanya 572025, China
- The Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, Zhejiang 314400, China
| | - Chuanzao Mao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China
| | - James Whelan
- Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC 3086, Australia
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China
- The Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, Zhejiang 314400, China
| | - Ricarda Jost
- Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC 3086, Australia
- La Trobe Institute for Sustainable Agriculture and Food, La Trobe University, Bundoora, VIC 3086, Australia
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2
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Giese J, Eirich J, Walther D, Zhang Y, Lassowskat I, Fernie AR, Elsässer M, Maurino VG, Schwarzländer M, Finkemeier I. The interplay of post-translational protein modifications in Arabidopsis leaves during photosynthesis induction. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1172-1193. [PMID: 37522418 DOI: 10.1111/tpj.16406] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/10/2023] [Accepted: 07/19/2023] [Indexed: 08/01/2023]
Abstract
Diurnal dark to light transition causes profound physiological changes in plant metabolism. These changes require distinct modes of regulation as a unique feature of photosynthetic lifestyle. The activities of several key metabolic enzymes are regulated by light-dependent post-translational modifications (PTM) and have been studied at depth at the level of individual proteins. In contrast, a global picture of the light-dependent PTMome dynamics is lacking, leaving the response of a large proportion of cellular function undefined. Here, we investigated the light-dependent metabolome and proteome changes in Arabidopsis rosettes in a time resolved manner to dissect their kinetic interplay, focusing on phosphorylation, lysine acetylation, and cysteine-based redox switches. Of over 24 000 PTM sites that were detected, more than 1700 were changed during the transition from dark to light. While the first changes, as measured 5 min after onset of illumination, occurred mainly in the chloroplasts, PTM changes at proteins in other compartments coincided with the full activation of the Calvin-Benson cycle and the synthesis of sugars at later timepoints. Our data reveal connections between metabolism and PTM-based regulation throughout the cell. The comprehensive multiome profiling analysis provides unique insight into the extent by which photosynthesis reprograms global cell function and adds a powerful resource for the dissection of diverse cellular processes in the context of photosynthetic function.
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Affiliation(s)
- Jonas Giese
- Institute of Plant Biology and Biotechnology (IBBP), University of Münster, Schlossplatz 7-8, Münster, D-48149, Germany
| | - Jürgen Eirich
- Institute of Plant Biology and Biotechnology (IBBP), University of Münster, Schlossplatz 7-8, Münster, D-48149, Germany
| | - Dirk Walther
- Max-Planck-Institute of Molecular Plant Physiology (MPIMP), Am Mühlenberg 1, Potsdam, D-14476, Germany
| | - Youjun Zhang
- Max-Planck-Institute of Molecular Plant Physiology (MPIMP), Am Mühlenberg 1, Potsdam, D-14476, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, 4000, Bulgaria
| | - Ines Lassowskat
- Institute of Plant Biology and Biotechnology (IBBP), University of Münster, Schlossplatz 7-8, Münster, D-48149, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology (MPIMP), Am Mühlenberg 1, Potsdam, D-14476, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, 4000, Bulgaria
| | - Marlene Elsässer
- Institute of Plant Biology and Biotechnology (IBBP), University of Münster, Schlossplatz 7-8, Münster, D-48149, Germany
| | - Veronica G Maurino
- Institute of Cellular and Molecular Botany (IZMB), Rheinische Friedrich-Wilhelms-Universität Bonn, Kirschallee 1, Bonn, D-53115, Germany
| | - Markus Schwarzländer
- Institute of Plant Biology and Biotechnology (IBBP), University of Münster, Schlossplatz 7-8, Münster, D-48149, Germany
| | - Iris Finkemeier
- Institute of Plant Biology and Biotechnology (IBBP), University of Münster, Schlossplatz 7-8, Münster, D-48149, Germany
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3
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Hashida Y, Tezuka A, Nomura Y, Kamitani M, Kashima M, Kurita Y, Nagano AJ. Fillable and unfillable gaps in plant transcriptome under field and controlled environments. PLANT, CELL & ENVIRONMENT 2022; 45:2410-2427. [PMID: 35610174 PMCID: PMC9544781 DOI: 10.1111/pce.14367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 03/27/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
The differences between plants grown in field and in controlled environments have long been recognized. However, few studies have addressed the underlying molecular mechanisms. To evaluate plant responses to fluctuating environments using laboratory equipment, we developed SmartGC, a high-performance growth chamber that reproduces the fluctuating irradiance, temperature and humidity of field environments. We analysed massive transcriptome data of rice plants grown under field and SmartGC conditions to clarify the differences in plant responses to field and controlled environments. Rice transcriptome dynamics in SmartGC mimicked those in the field, particularly during the morning and evening but those in conventional growth chamber conditions did not. Further analysis revealed that fluctuation of irradiance affects transcriptome dynamics in the morning and evening, while fluctuation of temperature affects transcriptome dynamics only in the morning. We found upregulation of genes related to biotic and abiotic stress, and their expression was affected by environmental factors that cannot be mimicked by SmartGC. Our results reveal fillable and unfillable gaps in the transcriptomes of rice grown in field and controlled environments and can accelerate the understanding of plant responses to field environments for both basic biology and agricultural applications.
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Affiliation(s)
- Yoichi Hashida
- Faculty of AgricultureTakasaki University of Health and WelfareTakasakiGunmaJapan
| | - Ayumi Tezuka
- Research Institute for Food and AgricultureRyukoku UniversityOtsuShigaJapan
| | - Yasuyuki Nomura
- Research Institute for Food and AgricultureRyukoku UniversityOtsuShigaJapan
| | - Mari Kamitani
- Faculty of AgricultureRyukoku UniversityOtsuShigaJapan
| | - Makoto Kashima
- Research Institute for Food and AgricultureRyukoku UniversityOtsuShigaJapan
- College of Science and EngineeringAoyama Gakuin UniversitySagamiharaKanagawaJapan
| | - Yuko Kurita
- Faculty of AgricultureRyukoku UniversityOtsuShigaJapan
| | - Atsushi J. Nagano
- Faculty of AgricultureRyukoku UniversityOtsuShigaJapan
- Institute for Advanced BiosciencesKeio UniversityTsuruokaYamagataJapan
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4
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Ishihara H, Alseekh S, Feil R, Perera P, George GM, Niedźwiecki P, Arrivault S, Zeeman SC, Fernie AR, Lunn JE, Smith AM, Stitt M. Rising rates of starch degradation during daytime and trehalose 6-phosphate optimize carbon availability. PLANT PHYSIOLOGY 2022; 189:1976-2000. [PMID: 35486376 PMCID: PMC9342969 DOI: 10.1093/plphys/kiac162] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/11/2022] [Indexed: 05/06/2023]
Abstract
Many plants, including Arabidopsis (Arabidopsis thaliana), accumulate starch in the light and remobilize it to support maintenance and growth at night. Starch synthesis and degradation are usually viewed as temporally separate processes. Recently, we reported that starch is also degraded in the light. Degradation rates are generally low early in the day but rise with time. Here, we show that the rate of degradation in the light depends on time relative to dawn rather than dusk. We also show that degradation in the light is inhibited by trehalose 6-phosphate, a signal for sucrose availability. The observed responses of degradation in the light can be simulated by a skeletal model in which the rate of degradation is a function of starch content divided by time remaining until dawn. The fit is improved by extension to include feedback inhibition of starch degradation by trehalose 6-phosphate. We also investigate possible functions of simultaneous starch synthesis and degradation in the light, using empirically parameterized models and experimental approaches. The idea that this cycle buffers growth against falling rates of photosynthesis at twilight is supported by data showing that rates of protein and cell wall synthesis remain high during a simulated dusk twilight. Degradation of starch in the light may also counter over-accumulation of starch in long photoperiods and stabilize signaling around dusk. We conclude that starch degradation in the light is regulated by mechanisms similar to those that operate at night and is important for stabilizing carbon availability and signaling, thus optimizing growth in natural light conditions.
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Affiliation(s)
- Hirofumi Ishihara
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Saleh Alseekh
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
- Center for Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
| | - Regina Feil
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Pumi Perera
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Gavin M George
- Institute of Molecular Plant Biology, ETH Zürich, Zürich, Switzerland
| | - Piotr Niedźwiecki
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Stephanie Arrivault
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Samuel C Zeeman
- Institute of Molecular Plant Biology, ETH Zürich, Zürich, Switzerland
| | - Alisdair R Fernie
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
- Center for Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
| | - John E Lunn
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Alison M Smith
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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5
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Alexandre Moraes T, Mengin V, Peixoto B, Encke B, Krohn N, Höhne M, Krause U, Stitt M. The circadian clock mutant lhy cca1 elf3 paces starch mobilization to dawn despite severely disrupted circadian clock function. PLANT PHYSIOLOGY 2022; 189:2332-2356. [PMID: 35567528 PMCID: PMC9348821 DOI: 10.1093/plphys/kiac226] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/22/2022] [Indexed: 06/15/2023]
Abstract
Many plants, including Arabidopsis (Arabidopsis thaliana), accumulate starch in the daytime and remobilize it to support maintenance and growth at night. Starch accumulation is increased when carbon is in short supply, for example, in short photoperiods. Mobilization is paced to exhaust starch around dawn, as anticipated by the circadian clock. This diel pattern of turnover is largely robust against loss of day, dawn, dusk, or evening clock components. Here, we investigated diel starch turnover in the triple circadian clock mutant lhy cca1 elf3, which lacks the LATE ELONGATED HYPOCOTYL and the CIRCADIAN CLOCK-ASSOCIATED1 (CCA1) dawn components and the EARLY FLOWERING3 (ELF3) evening components of the circadian clock. The diel oscillations of transcripts for the remaining clock components and related genes like REVEILLE and PHYTOCHROME-INTERACING FACTOR family members exhibited attenuated amplitudes and altered peak time, weakened dawn dominance, and decreased robustness against changes in the external light-dark cycle. The triple mutant was unable to increase starch accumulation in short photoperiods. However, it was still able to pace starch mobilization to around dawn in different photoperiods and growth irradiances and to around 24 h after the previous dawn in T17 and T28 cycles. The triple mutant was able to slow down starch mobilization after a sudden low-light day or a sudden early dusk, although in the latter case it did not fully compensate for the lengthened night. Overall, there was a slight trend to less linear mobilization of starch. Thus, starch mobilization can be paced rather robustly to dawn despite a major disruption of the transcriptional clock. It is proposed that temporal information can be delivered from clock components or a semi-autonomous oscillator.
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Affiliation(s)
| | - Virginie Mengin
- School of Life Sciences, University of Essex, Colchester CO4 3SQ, UK
| | - Bruno Peixoto
- Instituto Gulbenkian de Ciência, Oeiras 2780-156,Portugal
- GREEN-IT Bioresources for Sustainability, ITQB NOVA, Oeiras 2780-157,Portugal
| | - Beatrice Encke
- Systematic Botany and Biodiversity, Humboldt University of Berlin, Berlin D-10115, Germany
| | - Nicole Krohn
- Abteilung für Parodontologie und Synoptische Zahnmedizin, Charité Universitätsmedizin, Berlin 14197, Germany
| | - Melanie Höhne
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
| | - Ursula Krause
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
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6
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Characterization of the Heat-Stable Proteome during Seed Germination in Arabidopsis with Special Focus on LEA Proteins. Int J Mol Sci 2021; 22:ijms22158172. [PMID: 34360938 PMCID: PMC8347141 DOI: 10.3390/ijms22158172] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 12/22/2022] Open
Abstract
During seed germination, desiccation tolerance is lost in the radicle with progressing radicle protrusion and seedling establishment. This process is accompanied by comprehensive changes in the metabolome and proteome. Germination of Arabidopsis seeds was investigated over 72 h with special focus on the heat-stable proteome including late embryogenesis abundant (LEA) proteins together with changes in primary metabolites. Six metabolites in dry seeds known to be important for seed longevity decreased during germination and seedling establishment, while all other metabolites increased simultaneously with activation of growth and development. Thermo-stable proteins were associated with a multitude of biological processes. In the heat-stable proteome, a relatively similar proportion of fully ordered and fully intrinsically disordered proteins (IDP) was discovered. Highly disordered proteins were found to be associated with functional categories development, protein, RNA and stress. As expected, the majority of LEA proteins decreased during germination and seedling establishment. However, four germination-specific dehydrins were identified, not present in dry seeds. A network analysis of proteins, metabolites and amino acids generated during the course of germination revealed a highly connected LEA protein network.
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7
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Uhrig RG, Echevarría‐Zomeño S, Schlapfer P, Grossmann J, Roschitzki B, Koerber N, Fiorani F, Gruissem W. Diurnal dynamics of the Arabidopsis rosette proteome and phosphoproteome. PLANT, CELL & ENVIRONMENT 2021; 44:821-841. [PMID: 33278033 PMCID: PMC7986931 DOI: 10.1111/pce.13969] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 11/23/2020] [Accepted: 11/26/2020] [Indexed: 05/11/2023]
Abstract
Plant growth depends on the diurnal regulation of cellular processes, but it is not well understood if and how transcriptional regulation controls diurnal fluctuations at the protein level. Here, we report a high-resolution Arabidopsis thaliana (Arabidopsis) leaf rosette proteome acquired over a 12 hr light:12 hr dark diurnal cycle and the phosphoproteome immediately before and after the light-to-dark and dark-to-light transitions. We quantified nearly 5,000 proteins and 800 phosphoproteins, of which 288 fluctuated in their abundance and 226 fluctuated in their phosphorylation status. Of the phosphoproteins, 60% were quantified for changes in protein abundance. This revealed six proteins involved in nitrogen and hormone metabolism that had concurrent changes in both protein abundance and phosphorylation status. The diurnal proteome and phosphoproteome changes involve proteins in key cellular processes, including protein translation, light perception, photosynthesis, metabolism and transport. The phosphoproteome at the light-dark transitions revealed the dynamics at phosphorylation sites in either anticipation of or response to a change in light regime. Phosphorylation site motif analyses implicate casein kinase II and calcium/calmodulin-dependent kinases among the primary light-dark transition kinases. The comparative analysis of the diurnal proteome and diurnal and circadian transcriptome established how mRNA and protein accumulation intersect in leaves during the diurnal cycle of the plant.
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Affiliation(s)
- R. Glen Uhrig
- Department of BiologyInstitute of Molecular Plant Biology, ETH ZurichZurichSwitzerland
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | | | - Pascal Schlapfer
- Department of BiologyInstitute of Molecular Plant Biology, ETH ZurichZurichSwitzerland
| | - Jonas Grossmann
- Functional Genomics Center ZurichUniversity of ZurichZurichSwitzerland
| | - Bernd Roschitzki
- Functional Genomics Center ZurichUniversity of ZurichZurichSwitzerland
| | - Niklas Koerber
- Institute of Bio‐ and GeosciencesIBG‐2: Plant Sciences, Forschungszentrum Jülich GmbHJülichGermany
| | - Fabio Fiorani
- Institute of Bio‐ and GeosciencesIBG‐2: Plant Sciences, Forschungszentrum Jülich GmbHJülichGermany
| | - Wilhelm Gruissem
- Department of BiologyInstitute of Molecular Plant Biology, ETH ZurichZurichSwitzerland
- Institute of BiotechnologyNational Chung Hsing UniversityTaichungTaiwan
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8
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Fichtner F, Barbier FF, Annunziata MG, Feil R, Olas JJ, Mueller-Roeber B, Stitt M, Beveridge CA, Lunn JE. Regulation of shoot branching in arabidopsis by trehalose 6-phosphate. THE NEW PHYTOLOGIST 2021; 229:2135-2151. [PMID: 33068448 DOI: 10.1111/nph.17006] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 10/05/2020] [Indexed: 05/03/2023]
Abstract
Trehalose 6-phosphate (Tre6P) is a sucrose signalling metabolite that has been implicated in regulation of shoot branching, but its precise role is not understood. We expressed tagged forms of TREHALOSE-6-PHOSPHATE SYNTHASE1 (TPS1) to determine where Tre6P is synthesized in arabidopsis (Arabidopsis thaliana), and investigated the impact of localized changes in Tre6P levels, in axillary buds or vascular tissues, on shoot branching in wild-type and branching mutant backgrounds. TPS1 is expressed in axillary buds and the subtending vasculature, as well as in the leaf and stem vasculature. Expression of a heterologous Tre6P phosphatase (TPP) to lower Tre6P in axillary buds strongly delayed bud outgrowth in long days and inhibited branching in short days. TPP expression in the vasculature also delayed lateral bud outgrowth and decreased branching. Increased Tre6P in the vasculature enhanced branching and was accompanied by higher expression of FLOWERING LOCUS T (FT) and upregulation of sucrose transporters. Increased vascular Tre6P levels enhanced branching in branched1 but not in ft mutant backgrounds. These results provide direct genetic evidence of a local role for Tre6P in regulation of axillary bud outgrowth within the buds themselves, and also connect Tre6P with systemic regulation of shoot branching via FT.
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Affiliation(s)
- Franziska Fichtner
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
- School of Biological Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Francois F Barbier
- School of Biological Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Maria G Annunziata
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Regina Feil
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Justyna J Olas
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, Haus 20, Potsdam, 14476, Germany
| | - Bernd Mueller-Roeber
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, Haus 20, Potsdam, 14476, Germany
| | - Mark Stitt
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Christine A Beveridge
- School of Biological Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - John E Lunn
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
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9
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Chen WW, Takahashi N, Hirata Y, Ronald J, Porco S, Davis SJ, Nusinow DA, Kay SA, Mas P. A mobile ELF4 delivers circadian temperature information from shoots to roots. NATURE PLANTS 2020; 6:416-426. [PMID: 32284549 PMCID: PMC7197390 DOI: 10.1038/s41477-020-0634-2] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 03/11/2020] [Indexed: 05/19/2023]
Abstract
The circadian clock is synchronized by environmental cues, mostly by light and temperature. Explaining how the plant circadian clock responds to temperature oscillations is crucial to understanding plant responsiveness to the environment. Here, we found a prevalent temperature-dependent function of the Arabidopsis clock component EARLY FLOWERING 4 (ELF4) in the root clock. Although the clocks in roots are able to run in the absence of shoots, micrografting assays and mathematical analyses show that ELF4 moves from shoots to regulate rhythms in roots. ELF4 movement does not convey photoperiodic information, but trafficking is essential for controlling the period of the root clock in a temperature-dependent manner. Low temperatures favour ELF4 mobility, resulting in a slow-paced root clock, whereas high temperatures decrease movement, leading to a faster clock. Hence, the mobile ELF4 delivers temperature information and establishes a shoot-to-root dialogue that sets the pace of the clock in roots.
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Affiliation(s)
- Wei Wei Chen
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Nozomu Takahashi
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Yoshito Hirata
- Mathematics and Informatics Center, The University of Tokyo, Tokyo, Japan
- Faculty of Engineering, Information and Systems, University of Tsukuba, Tsukuba, Japan
| | - James Ronald
- Department of Biology, University of York, York, UK
| | - Silvana Porco
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Seth J Davis
- Department of Biology, University of York, York, UK
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | | | - Steve A Kay
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan
| | - Paloma Mas
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain.
- Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain.
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10
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Greenwood M, Locke JC. The circadian clock coordinates plant development through specificity at the tissue and cellular level. CURRENT OPINION IN PLANT BIOLOGY 2020; 53:65-72. [PMID: 31783323 DOI: 10.1016/j.pbi.2019.09.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/20/2019] [Accepted: 09/23/2019] [Indexed: 05/27/2023]
Abstract
The circadian clock is a genetic circuit that allows organisms to anticipate daily events caused by the rotation of the Earth. The plant clock regulates physiology at multiple scales, from cell division to ecosystem-scale interactions. It is becoming clear that rather than being a single perfectly synchronised timer throughout the plant, the clock can be sensitive to different cues, run at different speeds, and drive distinct processes in different cell types and tissues. This flexibility may help the plant clock to regulate such a range of developmental and physiological processes. In this review, using examples from the literature, we describe how the clock regulates development at multiple scales and discuss how the clock might allow local flexibility in regulation whilst remaining coordinated across the plant.
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Affiliation(s)
- Mark Greenwood
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge, UK; Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, UK
| | - James Cw Locke
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge, UK.
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11
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Grzegorczyk M, Aderhold A, Husmeier D. Overview and Evaluation of Recent Methods for Statistical Inference of Gene Regulatory Networks from Time Series Data. Methods Mol Biol 2019; 1883:49-94. [PMID: 30547396 DOI: 10.1007/978-1-4939-8882-2_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
A challenging problem in systems biology is the reconstruction of gene regulatory networks from postgenomic data. A variety of reverse engineering methods from machine learning and computational statistics have been proposed in the literature. However, deciding on the best method to adopt for a particular application or data set might be a confusing task. The present chapter provides a broad overview of state-of-the-art methods with an emphasis on conceptual understanding rather than a deluge of mathematical details, and the pros and cons of the various approaches are discussed. Guidance on practical applications with pointers to publicly available software implementations are included. The chapter concludes with a comprehensive comparative benchmark study on simulated data and a real-work application taken from the current plant systems biology.
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Affiliation(s)
- Marco Grzegorczyk
- Johann Bernoulli Institute, University of Groningen, Groningen, The Netherlands
| | - Andrej Aderhold
- Center for Computer Science, Universidade Federal do Rio Grande, Rio Grande, Brazil
| | - Dirk Husmeier
- School of Mathematics and Statistics, University of Glasgow, Glasgow, UK.
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12
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Millar AJ, Urquiza U, Freeman PL, Hume A, Plotkin GD, Sorokina O, Zardilis A, Zielinski T. Practical steps to digital organism models, from laboratory model species to 'Crops in silico. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2403-2418. [PMID: 30615184 DOI: 10.1093/jxb/ery435] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/28/2018] [Indexed: 05/20/2023]
Abstract
A recent initiative named 'Crops in silico' proposes that multi-scale models 'have the potential to fill in missing mechanistic details and generate new hypotheses to prioritize directed engineering efforts' in plant science, particularly directed to crop species. To that end, the group called for 'a paradigm shift in plant modelling, from largely isolated efforts to a connected community'. 'Wet' (experimental) research has been especially productive in plant science, since the adoption of Arabidopsis thaliana as a laboratory model species allowed the emergence of an Arabidopsis research community. Parts of this community invested in 'dry' (theoretical) research, under the rubric of Systems Biology. Our past research combined concepts from Systems Biology and crop modelling. Here we outline the approaches that seem most relevant to connected, 'digital organism' initiatives. We illustrate the scale of experimental research required, by collecting the kinetic parameter values that are required for a quantitative, dynamic model of a gene regulatory network. By comparison with the Systems Biology Markup Language (SBML) community, we note computational resources and community structures that will help to realize the potential for plant Systems Biology to connect with a broader crop science community.
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Affiliation(s)
- Andrew J Millar
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Uriel Urquiza
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Alastair Hume
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
- EPCC, Bayes Centre, University of Edinburgh, Edinburgh, UK
| | - Gordon D Plotkin
- Laboratory for the Foundations of Computer Science, School of Informatics, University of Edinburgh, Edinburgh, UK
| | - Oxana Sorokina
- Institute for Adaptive and Neural Computation, School of Informatics, University of Edinburgh, Edinburgh, UK
| | - Argyris Zardilis
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Tomasz Zielinski
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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13
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Moraes TA, Mengin V, Annunziata MG, Encke B, Krohn N, Höhne M, Stitt M. Response of the Circadian Clock and Diel Starch Turnover to One Day of Low Light or Low CO 2. PLANT PHYSIOLOGY 2019; 179:1457-1478. [PMID: 30670603 PMCID: PMC6446786 DOI: 10.1104/pp.18.01418] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 01/09/2019] [Indexed: 05/18/2023]
Abstract
Diel starch turnover responds rapidly to changes in the light regime. We investigated if these responses require changes in the temporal dynamics of the circadian clock. Arabidopsis (Arabidopsis thaliana) was grown in a 12-h photoperiod for 19 d, shifted to three different reduced light levels or to low CO2 for one light period, and returned to growth conditions. The treatments produced widespread changes in clock transcript abundance. However, almost all of the changes were restricted to extreme treatments that led to carbon starvation and were small compared to the magnitude of the circadian oscillation. Changes included repression of EARLY FLOWERNG 4, slower decay of dusk components, and a slight phase delay at the next dawn, possibly due to abrogated Evening Complex function and sustained expression of PHYTOCHROME INTERACTING FACTORs and REVEILLEs during the night. Mobilization of starch in the night occurred in a linear manner and was paced to dawn, both in moderate treatments that did not alter clock transcripts and in extreme treatments that led to severe carbon starvation. We conclude that pacing of starch mobilization to dawn does not require retrograde carbon signaling to the transcriptional clock. On the following day, growth decreased, sugars rose, and starch accumulation was stimulated in low-light-treated plants compared to controls. This adaptive response was marked after moderate treatments and occurred independently of changes in the transcriptional clock. It is probably a time-delayed response to low-C signaling in the preceding 24-h cycle, possibly including changes in PHYTOCHROME INTERACTING FACTOR and REVEILLE expression.
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Affiliation(s)
- Thiago Alexandre Moraes
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
| | - Virginie Mengin
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
| | - Maria Grazia Annunziata
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
| | - Beatrice Encke
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
| | - Nicole Krohn
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
| | - Melanie Höhne
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
| | - Mark Stitt
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
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14
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Flis A, Mengin V, Ivakov AA, Mugford ST, Hubberten HM, Encke B, Krohn N, Höhne M, Feil R, Hoefgen R, Lunn JE, Millar AJ, Smith AM, Sulpice R, Stitt M. Multiple circadian clock outputs regulate diel turnover of carbon and nitrogen reserves. PLANT, CELL & ENVIRONMENT 2019; 42:549-573. [PMID: 30184255 DOI: 10.1111/pce.13440] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 08/27/2018] [Accepted: 08/31/2018] [Indexed: 05/09/2023]
Abstract
Plants accumulate reserves in the daytime to support growth at night. Circadian regulation of diel reserve turnover was investigated by profiling starch, sugars, glucose 6-phosphate, organic acids, and amino acids during a light-dark cycle and after transfer to continuous light in Arabidopsis wild types and in mutants lacking dawn (lhy cca1), morning (prr7 prr9), dusk (toc1, gi), or evening (elf3) clock components. The metabolite time series were integrated with published time series for circadian clock transcripts to identify circadian outputs that regulate central metabolism. (a) Starch accumulation was slower in elf3 and prr7 prr9. It is proposed that ELF3 positively regulates starch accumulation. (b) Reducing sugars were high early in the T-cycle in elf3, revealing that ELF3 negatively regulates sucrose recycling. (c) The pattern of starch mobilization was modified in all five mutants. A model is proposed in which dawn and dusk/evening components interact to pace degradation to anticipated dawn. (d) An endogenous oscillation of glucose 6-phosphate revealed that the clock buffers metabolism against the large influx of carbon from photosynthesis. (e) Low levels of organic and amino acids in lhy cca1 and high levels in prr7 prr9 provide evidence that the dawn components positively regulate the accumulation of amino acid reserves.
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Affiliation(s)
- Anna Flis
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Virginie Mengin
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Alexander A Ivakov
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Sam T Mugford
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | - Beatrice Encke
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Nicole Krohn
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Melanie Höhne
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Regina Feil
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Rainer Hoefgen
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - John E Lunn
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Andrew J Millar
- SynthSys and School of Biological Sciences, C.H. Waddington Building, University of Edinburgh, Edinburgh, UK
| | | | - Ronan Sulpice
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Mark Stitt
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
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15
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Krahmer J, Goralogia GS, Kubota A, Zardilis A, Johnson RS, Song YH, MacCoss MJ, Le Bihan T, Halliday KJ, Imaizumi T, Millar AJ. Time-resolved interaction proteomics of the GIGANTEA protein under diurnal cycles in Arabidopsis. FEBS Lett 2019; 593:319-338. [PMID: 30536871 PMCID: PMC6373471 DOI: 10.1002/1873-3468.13311] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/26/2018] [Accepted: 11/29/2018] [Indexed: 12/23/2022]
Abstract
The plant-specific protein GIGANTEA (GI) controls many developmental and physiological processes, mediating rhythmic post-translational regulation. GI physically binds several proteins implicated in the circadian clock, photoperiodic flowering, and abiotic stress responses. To understand GI's multifaceted function, we aimed to comprehensively and quantitatively identify potential interactors of GI in a time-specific manner, using proteomics on Arabidopsis plants expressing epitope-tagged GI. We detected previously identified (in)direct interactors of GI, as well as proteins implicated in protein folding, or degradation, and a previously uncharacterized transcription factor, CYCLING DOF FACTOR6 (CDF6). We verified CDF6's direct interaction with GI, and ZEITLUPE/FLAVIN-BINDING, KELCH REPEAT, F-BOX 1/LIGHT KELCH PROTEIN 2 proteins, and demonstrated its involvement in photoperiodic flowering. Extending interaction proteomics to time series provides a data resource of candidate protein targets for GI's post-translational control.
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Affiliation(s)
- Johanna Krahmer
- SynthSys and School of Biological SciencesUniversity of EdinburghUK
- Institute of Molecular Plant SciencesUniversity of EdinburghUK
| | | | - Akane Kubota
- Department of BiologyUniversity of WashingtonSeattleWAUSA
- Graduate School of Biological SciencesNara Institute of Science and TechnologyIkoma, NaraJapan
| | - Argyris Zardilis
- SynthSys and School of Biological SciencesUniversity of EdinburghUK
| | | | - Young Hun Song
- Department of BiologyUniversity of WashingtonSeattleWAUSA
- Department of Life SciencesAjou UniversitySuwonKorea
| | | | - Thierry Le Bihan
- SynthSys and School of Biological SciencesUniversity of EdinburghUK
| | | | | | - Andrew J. Millar
- SynthSys and School of Biological SciencesUniversity of EdinburghUK
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16
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Kim YJ, Somers DE. Luciferase-Based Screen for Post-translational Control Factors in the Regulation of the Pseudo-Response Regulator PRR7. FRONTIERS IN PLANT SCIENCE 2019; 10:667. [PMID: 31191580 PMCID: PMC6540683 DOI: 10.3389/fpls.2019.00667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 05/02/2019] [Indexed: 05/04/2023]
Abstract
Control of protein turnover is a key post-translational control point in the oscillatory network of the circadian clock. Some elements, such as TOC1 and PRR5 are engaged by a well-described F-box protein, ZEITLUPE, dedicated to their proteolytic turnover to shape their expression profile to a specific time of night. For most other clock components the regulation of their protein abundance is unknown, though turnover is often rapid and often lags the cycling of the respective mRNA. Here we report the design and results of an unbiased genetic screen in Arabidopsis to uncover proteolytic regulatory factors of PSEUDO-RESPONSE REGULATOR 7 (PRR7), a transcriptional repressor that peaks in the late afternoon. We performed EMS mutagenesis on a transgenic line expressing a PRR7::PRR7-luciferase (PRR7-LUC) translational fusion that accurately recapitulates the diurnal and circadian oscillations of the endogenous PRR7 protein. Using continuous luciferase imaging under constant light, we recovered mutants that alter the PRR7-LUC waveform and some that change period. We have identified novel alleles of ELF3 and ELF4, core components of the ELF3-ELF4-LUX Evening Complex (EC), that dampen the oscillation of PRR7-LUC. We report the characterization of two new hypomorphic alleles of ELF3 that help to understand the relationship between molecular potency and phenotype.
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17
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Agliassa C, Maffei ME. Reduction of geomagnetic field (GMF) to near null magnetic field (NNMF) affects some Arabidopsis thaliana clock genes amplitude in a light independent manner. JOURNAL OF PLANT PHYSIOLOGY 2019; 232:23-26. [PMID: 30530200 DOI: 10.1016/j.jplph.2018.11.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 11/02/2018] [Accepted: 11/05/2018] [Indexed: 05/20/2023]
Abstract
Plant endogenous clock consists of self-sustained interlocked transcriptional/translational feedback loops whose oscillation regulates many circadian processes, including gene expression. Its free running rhythm can be entrained by external cues, which can influence all clock parameters. Among external cues, the geomagnetic field (GMF) has been demonstrated to influence plant growth and development. We evaluated the quantitative expression (qRT-PCR) of three clock genes (LHY, GI and PRR7) in time-course experiments under either continuous darkness (CD) or long days (LD) conditions in Arabidopsis thaliana seedlings exposed to GMF (∼40 μT) and Near Null Magnetic Field (NNMF; ∼40 nT) conditions. Under both LD and CD conditions, reduction of GMF to NNMF prompted a significant increase of the gene expression of LHY and PRR7, whereas an opposite trend was found for GI gene expression. Exposure of Arabidopsis to NNMF altered clock gene amplitude, regardless the presence of light, by reinforcing the morning loop. Our data are consistent with the existence of a plant magnetoreceptor that affects the Arabidopsis endogenous clock.
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Affiliation(s)
- Chiara Agliassa
- Plant Physiology Unit, Dept. Life Sciences and Systems Biology, University of Turin, Via Quarello 15/A, 10135 Turin, Italy
| | - Massimo E Maffei
- Plant Physiology Unit, Dept. Life Sciences and Systems Biology, University of Turin, Via Quarello 15/A, 10135 Turin, Italy.
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18
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Tokuda IT, Akman OE, Locke JCW. Reducing the complexity of mathematical models for the plant circadian clock by distributed delays. J Theor Biol 2018; 463:155-166. [PMID: 30550861 DOI: 10.1016/j.jtbi.2018.12.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 12/04/2018] [Accepted: 12/11/2018] [Indexed: 11/29/2022]
Abstract
A major bottleneck in the modelling of biological networks is the parameter explosion problem - the exponential increase in the number of parameters that need to be optimised to data as the size of the model increases. Here, we address this problem in the context of the plant circadian clock by applying the method of distributed delays. We show that using this approach, the system architecture can be simplified efficiently - reducing the number of parameters - whilst still preserving the core mechanistic dynamics of the gene regulatory network. Compared to models with discrete time-delays, which are governed by functional differential equations, the distributed delay models can be converted into sets of equivalent ordinary differential equations, enabling the use of standard methods for numerical integration, and for stability and bifurcation analyses. We demonstrate the efficiency of our modelling approach by applying it to three exemplar mathematical models of the Arabidopsis circadian clock of varying complexity, obtaining significant reductions in complexity in each case. Moreover, we revise one of the most up-to-date Arabidopsis models, updating the regulation of the PRR9 and PRR7 genes by LHY in accordance with recent experimental data. The revised model more accurately reproduces the LHY-induction experiments of core clock genes, compared with the original model. Our work thus shows that the method of distributed delays facilitates the optimisation and reformulation of genetic network models.
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Affiliation(s)
- Isao T Tokuda
- Graduate School of Science and Engineering, Ritsumeikan University, Noji-higashi, Kusatsu, Shiga 525-8577, Japan.
| | - Ozgur E Akman
- College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, EX4 4QD, UK.
| | - James C W Locke
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge, CB2 1LR, UK.
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19
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Waveforms of molecular oscillations reveal circadian timekeeping mechanisms. Commun Biol 2018; 1:207. [PMID: 30511021 PMCID: PMC6255756 DOI: 10.1038/s42003-018-0217-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 11/01/2018] [Indexed: 11/12/2022] Open
Abstract
Circadian clocks play a pivotal role in orchestrating numerous physiological and developmental events. Waveform shapes of the oscillations of protein abundances can be informative about the underlying biochemical processes of circadian clocks. We derive a mathematical framework where waveforms do reveal hidden biochemical mechanisms of circadian timekeeping. We find that the cost of synthesizing proteins with particular waveforms can be substantially reduced by rhythmic protein half-lives over time, as supported by previous plant and mammalian data, as well as our own seedling experiment. We also find that previously enigmatic, cyclic expression of positive arm components within the mammalian and insect clocks allows both a broad range of peak time differences between protein waveforms and the symmetries of the waveforms about the peak times. Such various peak-time differences may facilitate tissue-specific or developmental stage-specific multicellular processes. Our waveform-guided approach can be extended to various biological oscillators, including cell-cycle and synthetic genetic oscillators. Hang-Hyun Jo et al. derive a mathematical framework for analyzing circadian clock waveforms. Using data from plants and animals, they find that waveforms of clock protein profiles provide important information about the biochemical mechanisms of circadian timekeeping.
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20
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Annunziata MG, Apelt F, Carillo P, Krause U, Feil R, Koehl K, Lunn JE, Stitt M. Response of Arabidopsis primary metabolism and circadian clock to low night temperature in a natural light environment. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:4881-4895. [PMID: 30053131 PMCID: PMC6137998 DOI: 10.1093/jxb/ery276] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 07/09/2018] [Indexed: 05/18/2023]
Abstract
Plants are exposed to varying irradiance and temperature within a day and from day to day. We previously investigated metabolism in a temperature-controlled greenhouse at the spring equinox on both a cloudy and a sunny day [daily light integral (DLI) of 7 mol m-2 d-1 and 12 mol m-2 d-1]. Diel metabolite profiles were largely captured in sinusoidal simulations at similar DLIs in controlled-environment chambers, except that amino acids were lower in natural light regimes. We now extend the DLI12 study by investigating metabolism in a natural light regime with variable temperature including cool nights. Starch was not completely turned over, anthocyanins and proline accumulated, and protein content rose. Instead of decreasing, amino acid content rose. Connectivity in central metabolism, which decreased in variable light, was not further weakened by variable temperature. We propose that diel metabolism operates better when light and temperature are co-varying. We also compared transcript abundance of 10 circadian clock genes in this temperature-variable regime with the temperature-controlled natural and sinusoidal light regimes. Despite temperature compensation, peak timing and abundance for dawn- and day-phased genes and GIGANTEA were slightly modified in the variable temperature treatment. This may delay dawn clock activity until the temperature rises enough to support rapid metabolism and photosynthesis.
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Affiliation(s)
| | - Federico Apelt
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg, Potsdam-Golm, Germany
| | - Petronia Carillo
- University of Campania ‘Luigi Vanvitelli’, Via Vivaldi, Caserta, Italy
| | - Ursula Krause
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg, Potsdam-Golm, Germany
| | - Regina Feil
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg, Potsdam-Golm, Germany
| | - Karin Koehl
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg, Potsdam-Golm, Germany
| | - John E Lunn
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg, Potsdam-Golm, Germany
| | - Mark Stitt
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg, Potsdam-Golm, Germany
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21
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dos Anjos L, Pandey PK, Moraes TA, Feil R, Lunn JE, Stitt M. Feedback regulation by trehalose 6-phosphate slows down starch mobilization below the rate that would exhaust starch reserves at dawn in Arabidopsis leaves. PLANT DIRECT 2018; 2:e00078. [PMID: 31245743 PMCID: PMC6508811 DOI: 10.1002/pld3.78] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 06/04/2018] [Accepted: 06/26/2018] [Indexed: 05/02/2023]
Abstract
Trehalose 6-phosphate (Tre6P), a sucrose signaling metabolite, inhibits transitory starch breakdown in Arabidopsis (Arabidopsis thaliana) leaves and potentially links starch turnover to leaf sucrose status and demand from sink organs (Plant Physiology, 163, 2013, 1142). To investigate this relationship further, we compared diel patterns of starch turnover in ethanol-inducible Tre6P synthase (iTPS) lines, which have high Tre6P and low sucrose after induction, with those in sweet11;12 sucrose export mutants, which accumulate sucrose in their leaves and were predicted to have high Tre6P. Short-term changes in irradiance were used to investigate whether the strength of inhibition by Tre6P depends on starch levels. sweet11;12 mutants had twofold higher levels of Tre6P and restricted starch mobilization. The relationship between Tre6P and starch mobilization was recapitulated in iTPS lines, pointing to a dominant role for Tre6P in feedback regulation of starch mobilization. Tre6P restricted mobilization across a wide range of conditions. However, there was no correlation between the level of Tre6P and the absolute rate of starch mobilization. Rather, Tre6P depressed the rate of mobilization below that required to exhaust starch at dawn, leading to incomplete use of starch. It is discussed how Tre6P interacts with the clock to set the rate of starch mobilization.
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Affiliation(s)
- Letícia dos Anjos
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGolmGermany
- Universidade Federal do CearáFortalezaBrazil
| | - Prashant Kumar Pandey
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGolmGermany
- Present address:
National Research Council Canada (NRC‐CNRC)110 Gymnasium PlaceSaskatoonSaskatchewanS7N 0W9Canada
| | | | - Regina Feil
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGolmGermany
| | - John E. Lunn
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGolmGermany
| | - Mark Stitt
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGolmGermany
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22
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Graf A, Coman D, Uhrig RG, Walsh S, Flis A, Stitt M, Gruissem W. Parallel analysis of Arabidopsis circadian clock mutants reveals different scales of transcriptome and proteome regulation. Open Biol 2018; 7:rsob.160333. [PMID: 28250106 PMCID: PMC5376707 DOI: 10.1098/rsob.160333] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 02/06/2017] [Indexed: 12/12/2022] Open
Abstract
The circadian clock regulates physiological processes central to growth and survival. To date, most plant circadian clock studies have relied on diurnal transcriptome changes to elucidate molecular connections between the circadian clock and observable phenotypes in wild-type plants. Here, we have integrated RNA-sequencing and protein mass spectrometry data to comparatively analyse the lhycca1, prr7prr9, gi and toc1 circadian clock mutant rosette at the end of day and end of night. Each mutant affects specific sets of genes and proteins, suggesting that the circadian clock regulation is modular. Furthermore, each circadian clock mutant maintains its own dynamically fluctuating transcriptome and proteome profile specific to subcellular compartments. Most of the measured protein levels do not correlate with changes in their corresponding transcripts. Transcripts and proteins that have coordinated changes in abundance are enriched for carbohydrate- and cold-responsive genes. Transcriptome changes in all four circadian clock mutants also affect genes encoding starch degradation enzymes, transcription factors and protein kinases. The comprehensive transcriptome and proteome datasets demonstrate that future system-driven research of the circadian clock requires multi-level experimental approaches. Our work also shows that further work is needed to elucidate the roles of post-translational modifications and protein degradation in the regulation of clock-related processes.
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Affiliation(s)
- Alexander Graf
- Department of Biology, ETH Zurich, 8092 Zurich, Switzerland.,Max Planck Institute of Molecular Plant Physiology, 14476 Postdam-Golm, Germany
| | - Diana Coman
- Department of Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - R Glen Uhrig
- Department of Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Sean Walsh
- Department of Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Anna Flis
- Max Planck Institute of Molecular Plant Physiology, 14476 Postdam-Golm, Germany
| | - Mark Stitt
- Max Planck Institute of Molecular Plant Physiology, 14476 Postdam-Golm, Germany
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23
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Apelt F, Breuer D, Olas JJ, Annunziata MG, Flis A, Nikoloski Z, Kragler F, Stitt M. Circadian, Carbon, and Light Control of Expansion Growth and Leaf Movement. PLANT PHYSIOLOGY 2017; 174:1949-1968. [PMID: 28559360 PMCID: PMC5490918 DOI: 10.1104/pp.17.00503] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 05/16/2017] [Indexed: 05/18/2023]
Abstract
We used Phytotyping4D to investigate the contribution of clock and light signaling to the diurnal regulation of rosette expansion growth and leaf movement in Arabidopsis (Arabidopsis thaliana). Wild-type plants and clock mutants with a short (lhycca1) and long (prr7prr9) period were analyzed in a T24 cycle and in T-cycles that were closer to the mutants' period. Wild types also were analyzed in various photoperiods and after transfer to free-running light or darkness. Rosette expansion and leaf movement exhibited a circadian oscillation, with superimposed transients after dawn and dusk. Diurnal responses were modified in clock mutants. lhycca1 exhibited an inhibition of growth at the end of night and growth rose earlier after dawn, whereas prr7prr9 showed decreased growth for the first part of the light period. Some features were partly rescued by a matching T-cycle, like the inhibition in lhycca1 at the end of the night, indicating that it is due to premature exhaustion of starch. Other features were not rescued, revealing that the clock also regulates expansion growth more directly. Expansion growth was faster at night than in the daytime, whereas published work has shown that the synthesis of cellular components is faster in the day than at nighttime. This temporal uncoupling became larger in short photoperiods and may reflect the differing dependence of expansion and biosynthesis on energy, carbon, and water. While it has been proposed that leaf expansion and movement are causally linked, we did not observe a consistent temporal relationship between expansion and leaf movement.
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Affiliation(s)
- Federico Apelt
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - David Breuer
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | | | | | - Anna Flis
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Zoran Nikoloski
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Friedrich Kragler
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Mark Stitt
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
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24
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Dobisova T, Hrdinova V, Cuesta C, Michlickova S, Urbankova I, Hejatkova R, Zadnikova P, Pernisova M, Benkova E, Hejatko J. Light Controls Cytokinin Signaling via Transcriptional Regulation of Constitutively Active Sensor Histidine Kinase CKI1. PLANT PHYSIOLOGY 2017; 174:387-404. [PMID: 28292856 PMCID: PMC5411129 DOI: 10.1104/pp.16.01964] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 03/04/2017] [Indexed: 05/07/2023]
Abstract
In plants, the multistep phosphorelay (MSP) pathway mediates a range of regulatory processes, including those activated by cytokinins. The cross talk between cytokinin response and light has been known for a long time. However, the molecular mechanism underlying the interaction between light and cytokinin signaling remains elusive. In the screen for upstream regulators we identified a LONG PALE HYPOCOTYL (LPH) gene whose activity is indispensable for spatiotemporally correct expression of CYTOKININ INDEPENDENT1 (CKI1), encoding the constitutively active sensor His kinase that activates MSP signaling. lph is a new allele of HEME OXYGENASE1 (HY1) that encodes the key protein in the biosynthesis of phytochromobilin, a cofactor of photoconvertible phytochromes. Our analysis confirmed the light-dependent regulation of the CKI1 expression pattern. We show that CKI1 expression is under the control of phytochrome A (phyA), functioning as a dual (both positive and negative) regulator of CKI1 expression, presumably via the phyA-regulated transcription factors (TF) PHYTOCHROME INTERACTING FACTOR3 and CIRCADIAN CLOCK ASSOCIATED1. Changes in CKI1 expression observed in lph/hy1-7 and phy mutants correlate with misregulation of MSP signaling, changed cytokinin sensitivity, and developmental aberrations that were previously shown to be associated with cytokinin and/or CKI1 action. Besides that, we demonstrate a novel role of phyA-dependent CKI1 expression in the hypocotyl elongation and hook development during skotomorphogenesis. Based on these results, we propose that the light-dependent regulation of CKI1 provides a plausible mechanistic link underlying the well-known interaction between light- and cytokinin-controlled plant development.
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Affiliation(s)
- Tereza Dobisova
- CEITEC - Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, CZ-62500, Brno, Czech Republic (T.D., V.H., S.M., I.U., R.H., P.Z., M.P., E.B., J.H.); and Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria (C.C., P.Z., E.B.)
| | - Vendula Hrdinova
- CEITEC - Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, CZ-62500, Brno, Czech Republic (T.D., V.H., S.M., I.U., R.H., P.Z., M.P., E.B., J.H.); and Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria (C.C., P.Z., E.B.)
| | - Candela Cuesta
- CEITEC - Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, CZ-62500, Brno, Czech Republic (T.D., V.H., S.M., I.U., R.H., P.Z., M.P., E.B., J.H.); and Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria (C.C., P.Z., E.B.)
| | - Sarka Michlickova
- CEITEC - Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, CZ-62500, Brno, Czech Republic (T.D., V.H., S.M., I.U., R.H., P.Z., M.P., E.B., J.H.); and Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria (C.C., P.Z., E.B.)
| | - Ivana Urbankova
- CEITEC - Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, CZ-62500, Brno, Czech Republic (T.D., V.H., S.M., I.U., R.H., P.Z., M.P., E.B., J.H.); and Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria (C.C., P.Z., E.B.)
| | - Romana Hejatkova
- CEITEC - Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, CZ-62500, Brno, Czech Republic (T.D., V.H., S.M., I.U., R.H., P.Z., M.P., E.B., J.H.); and Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria (C.C., P.Z., E.B.)
| | - Petra Zadnikova
- CEITEC - Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, CZ-62500, Brno, Czech Republic (T.D., V.H., S.M., I.U., R.H., P.Z., M.P., E.B., J.H.); and Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria (C.C., P.Z., E.B.)
| | - Marketa Pernisova
- CEITEC - Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, CZ-62500, Brno, Czech Republic (T.D., V.H., S.M., I.U., R.H., P.Z., M.P., E.B., J.H.); and Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria (C.C., P.Z., E.B.)
| | - Eva Benkova
- CEITEC - Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, CZ-62500, Brno, Czech Republic (T.D., V.H., S.M., I.U., R.H., P.Z., M.P., E.B., J.H.); and Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria (C.C., P.Z., E.B.)
| | - Jan Hejatko
- CEITEC - Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, CZ-62500, Brno, Czech Republic (T.D., V.H., S.M., I.U., R.H., P.Z., M.P., E.B., J.H.); and Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria (C.C., P.Z., E.B.)
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Flis A, Sulpice R, Seaton DD, Ivakov AA, Liput M, Abel C, Millar AJ, Stitt M. Photoperiod-dependent changes in the phase of core clock transcripts and global transcriptional outputs at dawn and dusk in Arabidopsis. PLANT, CELL & ENVIRONMENT 2016; 39:1955-81. [PMID: 27075884 DOI: 10.1111/pce.12754] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 04/01/2016] [Indexed: 05/06/2023]
Abstract
Plants use the circadian clock to sense photoperiod length. Seasonal responses like flowering are triggered at a critical photoperiod when a light-sensitive clock output coincides with light or darkness. However, many metabolic processes, like starch turnover, and growth respond progressively to photoperiod duration. We first tested the photoperiod response of 10 core clock genes and two output genes. qRT-PCR analyses of transcript abundance under 6, 8, 12 and 18 h photoperiods revealed 1-4 h earlier peak times under short photoperiods and detailed changes like rising PRR7 expression before dawn. Clock models recapitulated most of these changes. We explored the consequences for global gene expression by performing transcript profiling in 4, 6, 8, 12 and 18 h photoperiods. There were major changes in transcript abundance at dawn, which were as large as those between dawn and dusk in a given photoperiod. Contributing factors included altered timing of the clock relative to dawn, light signalling and changes in carbon availability at night as a result of clock-dependent regulation of starch degradation. Their interaction facilitates coordinated transcriptional regulation of key processes like starch turnover, anthocyanin, flavonoid and glucosinolate biosynthesis and protein synthesis and underpins the response of metabolism and growth to photoperiod.
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Affiliation(s)
- Anna Flis
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Golm, Potsdam, Germany
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, GPO Box 475, Canberra, Australian Capital Territory, 2601, Australia
| | - Ronan Sulpice
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Golm, Potsdam, Germany
- Plant Systems Biology Lab, Plant and AgriBiosciences Research Centre, Botany and Plant Science, NUIG, Galway, Ireland
| | - Daniel D Seaton
- SynthSys and School of Biological Sciences, C.H. Waddington Building, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Alexander A Ivakov
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Golm, Potsdam, Germany
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, GPO Box 475, Canberra, Australian Capital Territory, 2601, Australia
| | - Magda Liput
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Golm, Potsdam, Germany
| | - Christin Abel
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Golm, Potsdam, Germany
| | - Andrew J Millar
- SynthSys and School of Biological Sciences, C.H. Waddington Building, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Mark Stitt
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Golm, Potsdam, Germany
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26
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Aderhold A, Husmeier D, Grzegorczyk M. Approximate Bayesian inference in semi-mechanistic models. STATISTICS AND COMPUTING 2016; 27:1003-1040. [PMID: 32226236 PMCID: PMC7089672 DOI: 10.1007/s11222-016-9668-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 05/05/2016] [Indexed: 06/10/2023]
Abstract
Inference of interaction networks represented by systems of differential equations is a challenging problem in many scientific disciplines. In the present article, we follow a semi-mechanistic modelling approach based on gradient matching. We investigate the extent to which key factors, including the kinetic model, statistical formulation and numerical methods, impact upon performance at network reconstruction. We emphasize general lessons for computational statisticians when faced with the challenge of model selection, and we assess the accuracy of various alternative paradigms, including recent widely applicable information criteria and different numerical procedures for approximating Bayes factors. We conduct the comparative evaluation with a novel inferential pipeline that systematically disambiguates confounding factors via an ANOVA scheme.
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Affiliation(s)
- Andrej Aderhold
- School of Mathematics and Statistics, Glasgow University, Glasgow, UK
| | - Dirk Husmeier
- School of Mathematics and Statistics, Glasgow University, Glasgow, UK
| | - Marco Grzegorczyk
- Johann Bernoulli Institute (JBI), Groningen University, Groningen, The Netherlands
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27
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Millar AJ. The Intracellular Dynamics of Circadian Clocks Reach for the Light of Ecology and Evolution. ANNUAL REVIEW OF PLANT BIOLOGY 2016; 67:595-618. [PMID: 26653934 DOI: 10.1146/annurev-arplant-043014-115619] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
A major challenge for biology is to extend our understanding of molecular regulation from the simplified conditions of the laboratory to ecologically relevant environments. Tractable examples are essential to make these connections for complex, pleiotropic regulators and, to go further, to link relevant genome sequences to field traits. Here, I review the case for the biological clock in higher plants. The gene network of the circadian clock drives pervasive, 24-hour rhythms in metabolism, behavior, and physiology across the eukaryotes and in some prokaryotes. In plants, the scope of chronobiology is now extending from the most tractable, intracellular readouts to the clock's many effects at the whole-organism level and across the life cycle, including biomass and flowering. I discuss five research areas where recent progress might be integrated in the future, to understand not only circadian functions in natural conditions but also the evolution of the clock's molecular mechanisms.
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Affiliation(s)
- Andrew J Millar
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, Scotland, United Kingdom;
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