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Prasetyaningrum P, Litthauer S, Vegliani F, Battle MW, Wood MW, Liu X, Dickson C, Jones MA. Inhibition of RNA degradation integrates the metabolic signals induced by osmotic stress into the Arabidopsis circadian system. J Exp Bot 2023; 74:5805-5819. [PMID: 37453132 PMCID: PMC10540740 DOI: 10.1093/jxb/erad274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
The circadian clock system acts as an endogenous timing reference that coordinates many metabolic and physiological processes in plants. Previous studies have shown that the application of osmotic stress delays circadian rhythms via 3'-phospho-adenosine 5'-phosphate (PAP), a retrograde signalling metabolite that is produced in response to redox stress within organelles. PAP accumulation leads to the inhibition of exoribonucleases (XRNs), which are responsible for RNA degradation. Interestingly, we are now able to demonstrate that post-transcriptional processing is crucial for the circadian response to osmotic stress. Our data show that osmotic stress increases the stability of specific circadian RNAs, suggesting that RNA metabolism plays a vital role in circadian clock coordination during drought. Inactivation of XRN4 is sufficient to extend circadian rhythms as part of this response, with PRR7 and LWD1 identified as transcripts that are post-transcriptionally regulated to delay circadian progression.
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Affiliation(s)
| | | | - Franco Vegliani
- School of Molecular Biosciences, University of Glasgow, Glasgow G12 8QQ, UK
| | | | | | - Xinmeng Liu
- School of Molecular Biosciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Cathryn Dickson
- School of Molecular Biosciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Matthew Alan Jones
- School of Molecular Biosciences, University of Glasgow, Glasgow G12 8QQ, UK
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2
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Senger E, Osorio S, Olbricht K, Shaw P, Denoyes B, Davik J, Predieri S, Karhu S, Raubach S, Lippi N, Höfer M, Cockerton H, Pradal C, Kafkas E, Litthauer S, Amaya I, Usadel B, Mezzetti B. Towards smart and sustainable development of modern berry cultivars in Europe. Plant J 2022; 111:1238-1251. [PMID: 35751152 DOI: 10.1111/tpj.15876] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/15/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
Fresh berries are a popular and important component of the human diet. The demand for high-quality berries and sustainable production methods is increasing globally, challenging breeders to develop modern berry cultivars that fulfill all desired characteristics. Since 1994, research projects have characterized genetic resources, developed modern tools for high-throughput screening, and published data in publicly available repositories. However, the key findings of different disciplines are rarely linked together, and only a limited range of traits and genotypes has been investigated. The Horizon2020 project BreedingValue will address these challenges by studying a broader panel of strawberry, raspberry and blueberry genotypes in detail, in order to recover the lost genetic diversity that has limited the aroma and flavor intensity of recent cultivars. We will combine metabolic analysis with sensory panel tests and surveys to identify the key components of taste, flavor and aroma in berries across Europe, leading to a high-resolution map of quality requirements for future berry cultivars. Traits linked to berry yields and the effect of environmental stress will be investigated using modern image analysis methods and modeling. We will also use genetic analysis to determine the genetic basis of complex traits for the development and optimization of modern breeding technologies, such as molecular marker arrays, genomic selection and genome-wide association studies. Finally, the results, raw data and metadata will be made publicly available on the open platform Germinate in order to meet FAIR data principles and provide the basis for sustainable research in the future.
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Affiliation(s)
- Elisa Senger
- Institute of Bio- and Geosciences, IBG-4 Bioinformatics, BioSC, CEPLAS, Forschungszentrum Jülich, Jülich, Germany
| | - Sonia Osorio
- Departamento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos, Málaga, Spain
| | | | - Paul Shaw
- Department of Information and Computational Sciences, The James Hutton Institute, Invergowrie, Scotland, UK
| | - Béatrice Denoyes
- Université de Bordeaux, UMR BFP, INRAE, Villenave d'Ornon, France
| | - Jahn Davik
- Department of Molecular Plant Biology, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
| | - Stefano Predieri
- Bio-Agrofood Department, Institute for Bioeconomy, IBE-CNR, Italian National Research Council, Bologna, Italy
| | - Saila Karhu
- Natural Resources Institute Finland (Luke), Turku, Finland
| | - Sebastian Raubach
- Department of Information and Computational Sciences, The James Hutton Institute, Invergowrie, Scotland, UK
| | - Nico Lippi
- Bio-Agrofood Department, Institute for Bioeconomy, IBE-CNR, Italian National Research Council, Bologna, Italy
| | - Monika Höfer
- Institute of Breeding Research on Fruit Crops, Federal Research Centre for Cultivated Plants (JKI), Dresden, Germany
| | - Helen Cockerton
- Genetics, Genomics and Breeding Department, NIAB, East Malling, UK
| | - Christophe Pradal
- CIRAD and UMR AGAP Institute, Montpellier, France
- INRIA and LIRMM, University Montpellier, CNRS, Montpellier, France
| | - Ebru Kafkas
- Department of Horticulture, Faculty of Agriculture, Çukurova University, Balcalı, Adana, Turkey
| | | | - Iraida Amaya
- Unidad Asociada deI + D + i IFAPA-CSIC Biotecnología y Mejora en Fresa, Málaga, Spain
- Laboratorio de Genómica y Biotecnología, Centro IFAPA de Málaga, Instituto Andaluz de Investigación y Formación Agraria y Pesquera, Málaga, Spain
| | - Björn Usadel
- Institute of Bio- and Geosciences, IBG-4 Bioinformatics, BioSC, CEPLAS, Forschungszentrum Jülich, Jülich, Germany
- Institute for Biological Data Science, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Bruno Mezzetti
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy
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Ordidge M, Litthauer S, Venison E, Blouin-Delmas M, Fernandez-Fernandez F, Höfer M, Kägi C, Kellerhals M, Marchese A, Mariette S, Nybom H, Giovannini D. Towards a Joint International Database: Alignment of SSR Marker Data for European Collections of Cherry Germplasm. Plants (Basel) 2021; 10:1243. [PMID: 34207415 PMCID: PMC8235247 DOI: 10.3390/plants10061243] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 11/17/2022]
Abstract
The objective of our study was the alignment of microsatellite or simple sequence repeat (SSR) marker data across germplasm collections of cherry within Europe. Through the European Cooperative program for Plant Genetic Resources ECPGR, a number of European germplasm collections had previously been analysed using standard sets of SSR loci. However, until now these datasets remained unaligned. We used a combination of standard reference genotypes and ad-hoc selections to compile a central dataset representing as many alleles as possible from national datasets produced in France, Great Britain, Germany, Italy, Sweden and Switzerland. Through the comparison of alleles called in data from replicated samples we were able to create a series of alignment factors, supported across 448 different allele calls, that allowed us to align a dataset of 2241 SSR profiles from six countries. The proportion of allele comparisons that were either in agreement with the alignment factor or confounded by null alleles ranged from 67% to 100% and this was further improved by the inclusion of a series of allele-specific adjustments. The aligned dataset allowed us to identify groups of previously unknown matching accessions and to identify and resolve a number of errors in the prior datasets. The combined and aligned dataset represents a significant step forward in the co-ordinated management of field collections of cherry in Europe.
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Affiliation(s)
- Matthew Ordidge
- Department of Crop Science, School of Agriculture, Policy and Development, University of Reading, Reading RG6 6EU, UK;
| | - Suzanne Litthauer
- NIAB EMR, New Road, East Malling, Kent ME19 6BJ, UK; (S.L.); (F.F.-F.)
| | - Edward Venison
- Department of Crop Science, School of Agriculture, Policy and Development, University of Reading, Reading RG6 6EU, UK;
| | - Marine Blouin-Delmas
- INRAE-Unité Expérimentale Arboricole, Domaine de la Tour de Rance, 47320 Bourran, France;
| | | | - Monika Höfer
- Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Julius Kühn Institute, Pillnitzer Platz 3a, 01326 Dresden, Germany;
| | - Christina Kägi
- Federal Office for Agriculture, Genetic Resources and Technologies, Schwarzenburgstrasse 165, 3003 Bern, Switzerland;
| | - Markus Kellerhals
- Agroscope, Strategic Research Division Plant Breeding, Müller-Thurgau-Str. 29, 8820 Wädenswil, Switzerland;
| | - Annalisa Marchese
- Department of Agricultural, Food and Forest Sciences, University of Palermo, Viale delle Scienze-Ed. 4, 90128 Palermo, Italy;
| | - Stephanie Mariette
- BIOGECO, INRAE, University of Bordeaux, Route d’Arcachon 69, 33612 Cestas, France;
| | - Hilde Nybom
- Balsgård-Department of Plant Breeding, Swedish University of Agricultural Sciences, Fjälkestadsvägen 459, 29194 Kristianstad, Sweden;
| | - Daniela Giovannini
- CREA-Research Centre for Olive, Fruit and Citrus Crops, via la Canapona 1 bis, 47121 Forlì, Italy;
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Litthauer S, Jones MA. SAL1-PAP retrograde signalling extends circadian period by reproducing the loss of exoribonuclease (XRN) activity. Plant Signal Behav 2018; 13:e1500066. [PMID: 30081763 PMCID: PMC6149516 DOI: 10.1080/15592324.2018.1500066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 07/04/2018] [Indexed: 05/31/2023]
Abstract
Plants have developed an internal timing mechanism, the circadian system, that serves to synchronise physiological and metabolic functions with daily cues such as dawn and dusk, and provides plants with an advantage in adapting to changing and challenging conditions. We have recently shown that the SAL1-PAP-XRN retrograde signalling pathway, which is proposed to regulate plant responses under stress conditions, also acts within the circadian system. Here we provide further evidence of circadian regulation by SAL1-PAP-XRN signalling, thereby affirming a link between molecular timekeeping and abiotic stress response mechanisms.
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Litthauer S, Chan KX, Jones MA. 3'-Phosphoadenosine 5'-Phosphate Accumulation Delays the Circadian System. Plant Physiol 2018; 176:3120-3135. [PMID: 29487119 PMCID: PMC5884616 DOI: 10.1104/pp.17.01611] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 02/19/2018] [Indexed: 05/07/2023]
Abstract
The circadian system optimizes cellular responses to stress, but the signaling pathways that convey the metabolic consequences of stress into this molecular timekeeping mechanism remain unclear. Redox regulation of the SAL1 phosphatase during abiotic stress initiates a signaling pathway from chloroplast to nucleus by regulating the accumulation of a metabolite, 3'-phosphoadenosine 5'-phosphate (PAP). Consequently, PAP accumulates in response to redox stress and inhibits the activity of exoribonucleases (XRNs) in the nucleus and cytosol. We demonstrated that osmotic stress induces a lengthening of circadian period and that genetically inducing the SAL1-PAP-XRN pathway in plants lacking either SAL1 or XRNs similarly delays the circadian system. Exogenous application of PAP was also sufficient to extend circadian period. Thus, SAL1-PAP-XRN signaling likely regulates circadian rhythms in response to redox stress. Our findings exemplify how two central processes in plants, molecular timekeeping and responses to abiotic stress, can be interlinked to regulate gene expression.
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Affiliation(s)
- Suzanne Litthauer
- School of Biological Sciences, University of Essex, Colchester, Essex CO4 3SQ, United Kingdom
| | - Kai Xun Chan
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Matthew Alan Jones
- School of Biological Sciences, University of Essex, Colchester, Essex CO4 3SQ, United Kingdom
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Litthauer S, Battle MW, Jones MA. Phototropins do not alter accumulation of evening-phased circadian transcripts under blue light. Plant Signal Behav 2016; 11:e1126029. [PMID: 26653107 PMCID: PMC4883876 DOI: 10.1080/15592324.2015.1126029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 11/23/2015] [Accepted: 11/23/2015] [Indexed: 05/18/2023]
Abstract
The circadian system induces rhythmic variation in a suite of biochemical and physiological processes that serve to optimise plant growth in diel cycles. To be of greatest utility, these rhythmic behaviors are coordinated with regular environmental changes such as the rising and setting of the sun. Photoreceptors, along with metabolites produced during photosynthesis, act to synchronise the internal timing mechanism with lighting cues. We have recently shown that phototropins help maintain robust rhythms of photosynthetic operating efficiency (ϕPSII or Fq'/Fm') under blue light, although rhythmic accumulation of morning-phased circadian transcripts in the nucleus was unaffected. Here we report that evening-phased nuclear clock transcripts were also unaffected. We also observe that rhythms of nuclear clock transcript accumulation are maintained in phototropin mutant plants under a fluctuating lighting regime that induced a loss of Fq'/Fm' rhythms.
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Affiliation(s)
- Suzanne Litthauer
- a School of Biological Sciences, University of Essex , Wivenhoe Park, United Kingdom
| | - Martin W Battle
- a School of Biological Sciences, University of Essex , Wivenhoe Park, United Kingdom
| | - Matthew A Jones
- a School of Biological Sciences, University of Essex , Wivenhoe Park, United Kingdom
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Abstract
The circadian system allows plants to coordinate metabolic and physiological functions with predictable environmental variables such as dusk and dawn. This endogenous oscillator is comprised of biochemical and transcriptional rhythms that are synchronized with a plant's surroundings via environmental signals, including light and temperature. We have used chlorophyll fluorescence techniques to describe circadian rhythms of PSII operating efficiency (Fq'/Fm') in the chloroplasts of Arabidopsis thaliana. These Fq'/Fm' oscillations appear to be influenced by transcriptional feedback loops previously described in the nucleus, and are induced by rhythmic changes in photochemical quenching over circadian time. Our work reveals that a family of blue photoreceptors, phototropins, maintain robust rhythms of Fq'/Fm' under constant blue light. As phototropins do not influence circadian gene expression in the nucleus our imaging methodology highlights differences between the modulation of circadian outputs in distinct subcellular compartments.
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Affiliation(s)
- Suzanne Litthauer
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Martin W Battle
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Tracy Lawson
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Matthew A Jones
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
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Jones MA, Hu W, Litthauer S, Lagarias JC, Harmer SL. A Constitutively Active Allele of Phytochrome B Maintains Circadian Robustness in the Absence of Light. Plant Physiol 2015; 169:814-25. [PMID: 26157113 PMCID: PMC4577416 DOI: 10.1104/pp.15.00782] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 07/06/2015] [Indexed: 05/18/2023]
Abstract
The sensitivity of the circadian system to light allows entrainment of the clock, permitting coordination of plant metabolic function and flowering time across seasons. Light affects the circadian system via both photoreceptors, such as phytochromes and cryptochromes, and sugar production by photosynthesis. In the present study, we introduce a constitutively active version of phytochrome B-Y276H (YHB) into both wild-type and phytochrome null backgrounds of Arabidopsis (Arabidopsis thaliana) to distinguish the effects of photoreceptor signaling on clock function from those of photosynthesis. We find that the YHB mutation is sufficient to phenocopy red light input into the circadian mechanism and to sustain robust rhythms in steady-state mRNA levels even in plants grown without light or exogenous sugars. The pace of the clock is insensitive to light intensity in YHB plants, indicating that light input to the clock is constitutively activated by this allele. Mutation of YHB so that it is retained in the cytoplasm abrogates its effects on clock function, indicating that nuclear localization of phytochrome is necessary for its clock regulatory activity. We also demonstrate a role for phytochrome C as part of the red light sensing network that modulates phytochrome B signaling input into the circadian system. Our findings indicate that phytochrome signaling in the nucleus plays a critical role in sustaining robust clock function under red light, even in the absence of photosynthesis or exogenous sources of energy.
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Affiliation(s)
- Matthew Alan Jones
- School of Biological Sciences, University of Essex, Wivenhoe Park, Essex CO4 3SQ, United Kingdom (M.A.J., S.L.); andDepartment of Plant Biology, College of Biological Sciences (M.A.J., S.L.H.) and Department of Molecular and Cellular Biology (W.H., J.C.L.), University of California, Davis, California 95616
| | - Wei Hu
- School of Biological Sciences, University of Essex, Wivenhoe Park, Essex CO4 3SQ, United Kingdom (M.A.J., S.L.); andDepartment of Plant Biology, College of Biological Sciences (M.A.J., S.L.H.) and Department of Molecular and Cellular Biology (W.H., J.C.L.), University of California, Davis, California 95616
| | - Suzanne Litthauer
- School of Biological Sciences, University of Essex, Wivenhoe Park, Essex CO4 3SQ, United Kingdom (M.A.J., S.L.); andDepartment of Plant Biology, College of Biological Sciences (M.A.J., S.L.H.) and Department of Molecular and Cellular Biology (W.H., J.C.L.), University of California, Davis, California 95616
| | - J Clark Lagarias
- School of Biological Sciences, University of Essex, Wivenhoe Park, Essex CO4 3SQ, United Kingdom (M.A.J., S.L.); andDepartment of Plant Biology, College of Biological Sciences (M.A.J., S.L.H.) and Department of Molecular and Cellular Biology (W.H., J.C.L.), University of California, Davis, California 95616
| | - Stacey Lynn Harmer
- School of Biological Sciences, University of Essex, Wivenhoe Park, Essex CO4 3SQ, United Kingdom (M.A.J., S.L.); andDepartment of Plant Biology, College of Biological Sciences (M.A.J., S.L.H.) and Department of Molecular and Cellular Biology (W.H., J.C.L.), University of California, Davis, California 95616
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Litthauer S, Gargiulo S, van Heerden E, Hollmann F, Opperman D. Heterologous expression and characterization of the ene-reductases from Deinococcus radiodurans and Ralstonia metallidurans. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2013.10.020] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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