1
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Jabbur ML, Dani C, Spoelstra K, Dodd AN, Johnson CH. Evaluating the Adaptive Fitness of Circadian Clocks and their Evolution. J Biol Rhythms 2024; 39:115-134. [PMID: 38185853 PMCID: PMC10994774 DOI: 10.1177/07487304231219206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Surely most chronobiologists believe circadian clocks are an adaptation of organisms that enhances fitness, but are we certain that this focus of our research effort really confers a fitness advantage? What is the evidence, and how do we evaluate it? What are the best criteria? These questions are the topic of this review. In addition, we will discuss selective pressures that might have led to the historical evolution of circadian systems while considering the intriguing question of whether the ongoing climate change is modulating these selective pressures so that the clock is still evolving.
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Affiliation(s)
- Maria Luísa Jabbur
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Chitrang Dani
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Kamiel Spoelstra
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Antony N. Dodd
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, UK
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2
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Valim HF, Grande FD, Wong ELY, Schmitt I. Circadian clock- and temperature-associated genes contribute to overall genomic differentiation along elevation in lichenized fungi. Mol Ecol 2024; 33:e17252. [PMID: 38146927 DOI: 10.1111/mec.17252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 11/24/2023] [Accepted: 12/11/2023] [Indexed: 12/27/2023]
Abstract
Circadian regulation is linked to local environmental adaptation, and many species with broad climatic niches display variation in circadian genes. Here, we hypothesize that lichenizing fungi occupying different climate zones tune their metabolism to local environmental conditions with the help of their circadian systems. We study two species of the genus Umbilicaria occupying similar climatic niches (Mediterranean and the cold temperate) in different continents. Using homology to Neurospora crassa genes, we identify gene sets associated with circadian rhythms (11 core, 39 peripheral genes) as well as temperature response (37 genes). Nucleotide diversity of these genes is significantly correlated with mean annual temperature, minimum temperature of the coldest month and mean temperature of the coldest quarter. Furthermore, we identify altitudinal clines in allele frequencies in several non-synonymous substitutions in core clock components, for example, white collar-like, frh-like and various ccg-like genes. A dN/dS approach revealed a few significant peripheral clock- and temperature-associated genes (e.g. ras-1-like, gna-1-like) that may play a role in fine-tuning the circadian clock and temperature-response machinery. An analysis of allele frequency changes demonstrated the strongest evidence for differentiation above the genomic background in the clock-associated genes in U. pustulata. These results highlight the likely relevance of the circadian clock in environmental adaptation, particularly frost tolerance, of lichens. Whether or not the fungal clock modulates the symbiotic interaction within the lichen consortium remains to be investigated. We corroborate the finding of genetic variation in clock components along altitude-not only latitude-as has been reported in other species.
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Affiliation(s)
- Henrique F Valim
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
- Department of Biology, University of Padova, Padua, Italy
| | - Edgar L Y Wong
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany
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3
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Zhang H, Harmer SL. A Luciferase Imaging-Based Assay for Studying Temperature Compensation of the Circadian Clock. Methods Mol Biol 2024; 2795:43-53. [PMID: 38594526 DOI: 10.1007/978-1-0716-3814-9_5] [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] [Indexed: 04/11/2024]
Abstract
The pace of circadian rhythms remains relatively unchanged across a physiologically relevant range of temperatures, a phenomenon known as temperature compensation. Temperature compensation is a defining characteristic of circadian rhythms, ensuring that clock-regulated processes occur at approximately the same time of day across a wide range of conditions. Despite the identification of several genes involved in the regulation of temperature compensation, the molecular mechanisms underlying this process are still not well understood. High-throughput assays of circadian period are essential for the investigation of temperature compensation. In this chapter, we present a luciferase imaging-based method that enables robust and accurate examination of temperature compensation in the plant circadian clock.
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Affiliation(s)
- Hongtao Zhang
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA, USA
| | - Stacey L Harmer
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA, USA.
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4
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Strout RI, Graham CA, Dodd AN, Nagel DH. Investigating Circadian Gating of Temperature Responsive Genes. Methods Mol Biol 2024; 2795:213-225. [PMID: 38594541 DOI: 10.1007/978-1-0716-3814-9_20] [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] [Indexed: 04/11/2024]
Abstract
Understanding gene expression dynamics in the context of the time of day and temperature response is an important part of understanding plant thermotolerance in a changing climate. Performing "gating" experiments under constant conditions and light-dark cycles allows users to identify and dissect the contribution of the time of day and circadian clock to the dynamic nature of stress-responsive genes. Here, we describe the design of specific laboratory experiments in plants (Arabidopsis thaliana and bread wheat, Triticum aestivum) to investigate temporal responses to heat (1 h at 37 °C) or cold (3 h at 4 °C), and we include known marker genes that have circadian-gated responses to temperature changes.
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Affiliation(s)
- Rachel I Strout
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Calum A Graham
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Antony N Dodd
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK.
| | - Dawn H Nagel
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA.
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5
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Michael TP. Time of Day Analysis over a Field Grown Developmental Time Course in Rice. PLANTS (BASEL, SWITZERLAND) 2022; 12:166. [PMID: 36616295 PMCID: PMC9823482 DOI: 10.3390/plants12010166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Plants integrate time of day (TOD) information over an entire season to ensure optimal growth, flowering time, and grain fill. However, most TOD expression studies have focused on a limited number of combinations of daylength and temperature under laboratory conditions. Here, an Oryza sativa (rice) expression study that followed TOD expression in the field over an entire growing season was re-analyzed. Similar to Arabidopsis thaliana, almost all rice genes have a TOD-specific expression over the developmental time course. As has been suggested in other grasses, thermocycles were a stronger cue for TOD expression than the photocycles over the growing season. All the core circadian clock genes display consistent TOD expression over the season with the interesting exception that the two grass paralogs of EARLY FLOWERING 3 (ELF3) display a distinct phasing based on the interaction between thermo- and photo-cycles. The dataset also revealed how specific pathways are modulated to distinct TOD over the season consistent with the changing biology. The data presented here provide a resource for researchers to study how TOD expression changes under natural conditions over a developmental time course, which will guide approaches to engineer more resilient and prolific crops.
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Affiliation(s)
- Todd P Michael
- The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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6
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Oravec MW, Greenham K. The adaptive nature of the plant circadian clock in natural environments. PLANT PHYSIOLOGY 2022; 190:968-980. [PMID: 35894658 PMCID: PMC9516730 DOI: 10.1093/plphys/kiac337] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 06/27/2022] [Indexed: 05/10/2023]
Abstract
The plant circadian clock coordinates developmental, physiological, and metabolic processes with diel changes in light and temperature throughout the year. The balance between the persistence and plasticity of the clock in response to predictable and unpredictable environmental changes may be key to the clock's adaptive nature across temporal and spatial scales. Studies under controlled conditions have uncovered critical signaling pathways involved in light and temperature perception by the clock; however, they don't account for the natural lag of temperature behind photoperiod. Studies in natural environments provide key insights into the clock's adaptive advantage under more complex natural settings. Here, we discuss the role of the circadian clock in light and temperature perception and signaling, how the clock integrates these signals for a coordinated and adaptive response, and the adaptive advantage conferred by the clock across time and space in natural environments.
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Affiliation(s)
- Madeline W Oravec
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108, USA
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7
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Isoda M, Ito S, Oyama T. Interspecific divergence of circadian properties in duckweed plants. PLANT, CELL & ENVIRONMENT 2022; 45:1942-1953. [PMID: 35201626 DOI: 10.1111/pce.14297] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 01/15/2022] [Indexed: 06/14/2023]
Abstract
The circadian clock system is widely conserved in plants; however, divergence in circadian rhythm properties is poorly understood. We conducted a comparative analysis of the circadian properties of closely related duckweed species. Using a particle bombardment method, a circadian bioluminescent reporter was introduced into duckweed plants. We measured bioluminescence circadian rhythms of eight species of the genus Lemna and seven species of the genus Wolffiella at various temperatures (20, 25, and 30°C) and light conditions (constant light or constant dark). Wolffiella species inhabit relatively warm areas and lack some tissues/organs found in Lemna species. Lemna species tended to show robust bioluminescence circadian rhythms under all conditions, while Wolffiella species showed lower rhythm stability, especially at higher temperatures. For Lemna, two species (L. valdiviana and L. minuta) forming a clade showed relatively lower circadian stability. For Wolffiella, two species (W. hyalina and W. repanda) forming a clade showed extremely long period lengths. These analyses reveal that the circadian properties of species primarily reflect their phylogenetic positions. The relationships between geographical and morphological factors and circadian properties are also suggested.
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Affiliation(s)
- Minako Isoda
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Shogo Ito
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Tokitaka Oyama
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
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8
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Xu X, Yuan L, Yang X, Zhang X, Wang L, Xie Q. Circadian clock in plants: Linking timing to fitness. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:792-811. [PMID: 35088570 DOI: 10.1111/jipb.13230] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/25/2022] [Indexed: 05/12/2023]
Abstract
Endogenous circadian clock integrates cyclic signals of environment and daily and seasonal behaviors of organisms to achieve spatiotemporal synchronization, which greatly improves genetic diversity and fitness of species. This review addresses recent studies on the plant circadian system in the field of chronobiology, covering topics on molecular mechanisms, internal and external Zeitgebers, and hierarchical regulation of physiological outputs. The architecture of the circadian clock involves the autoregulatory transcriptional feedback loops, post-translational modifications of core oscillators, and epigenetic modifications of DNA and histones. Here, light, temperature, humidity, and internal elemental nutrients are summarized to illustrate the sensitivity of the circadian clock to timing cues. In addition, the circadian clock runs cell-autonomously, driving independent circadian rhythms in various tissues. The core oscillators responds to each other with biochemical factors including calcium ions, mineral nutrients, photosynthetic products, and hormones. We describe clock components sequentially expressed during a 24-h day that regulate rhythmic growth, aging, immune response, and resistance to biotic and abiotic stresses. Notably, more data have suggested the circadian clock links chrono-culture to key agronomic traits in crops.
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Affiliation(s)
- Xiaodong Xu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Li Yuan
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Xin Yang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Xiao Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Lei Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Qiguang Xie
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
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9
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Fulgione A, Neto C, Elfarargi AF, Tergemina E, Ansari S, Göktay M, Dinis H, Döring N, Flood PJ, Rodriguez-Pacheco S, Walden N, Koch MA, Roux F, Hermisson J, Hancock AM. Parallel reduction in flowering time from de novo mutations enable evolutionary rescue in colonizing lineages. Nat Commun 2022; 13:1461. [PMID: 35304466 PMCID: PMC8933414 DOI: 10.1038/s41467-022-28800-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 02/07/2022] [Indexed: 12/11/2022] Open
Abstract
Understanding how populations adapt to abrupt environmental change is necessary to predict responses to future challenges, but identifying specific adaptive variants, quantifying their responses to selection and reconstructing their detailed histories is challenging in natural populations. Here, we use Arabidopsis from the Cape Verde Islands as a model to investigate the mechanisms of adaptation after a sudden shift to a more arid climate. We find genome-wide evidence of adaptation after a multivariate change in selection pressures. In particular, time to flowering is reduced in parallel across islands, substantially increasing fitness. This change is mediated by convergent de novo loss of function of two core flowering time genes: FRI on one island and FLC on the other. Evolutionary reconstructions reveal a case where expansion of the new populations coincided with the emergence and proliferation of these variants, consistent with models of rapid adaptation and evolutionary rescue. Detailing how populations adapted to environmental change is needed to predict future responses, but identifying adaptive variants and detailing their fitness effects is rare. Here, the authors show that parallel loss of FRI and FLC function reduces time to flowering and drives adaptation in a drought prone environment.
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Affiliation(s)
- Andrea Fulgione
- Max Planck Institute for Plant Breeding Research, Cologne, Germany.,Mathematics and Bioscience, Department of Mathematics and Max F. Perutz Labs, University of Vienna, Vienna, Austria.,Vienna Graduate School for Population Genetics, Vienna, Austria
| | - Célia Neto
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | | | - Shifa Ansari
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Mehmet Göktay
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Herculano Dinis
- Parque Natural do Fogo, Direção Nacional do Ambiente, Praia, Santiago, Cabo Verde.,Associação Projecto Vitó, São Filipe, Fogo, Cabo Verde
| | - Nina Döring
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Pádraic J Flood
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | - Nora Walden
- Centre for Organismal Studies (COS) Heidelberg, Biodiversity and Plant Systematics, Heidelberg University, Heidelberg, Germany.,Biosystematics, Wageningen University, Wageningen, The Netherlands
| | - Marcus A Koch
- Centre for Organismal Studies (COS) Heidelberg, Biodiversity and Plant Systematics, Heidelberg University, Heidelberg, Germany
| | - Fabrice Roux
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Joachim Hermisson
- Mathematics and Bioscience, Department of Mathematics and Max F. Perutz Labs, University of Vienna, Vienna, Austria
| | - Angela M Hancock
- Max Planck Institute for Plant Breeding Research, Cologne, Germany. .,Mathematics and Bioscience, Department of Mathematics and Max F. Perutz Labs, University of Vienna, Vienna, Austria.
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10
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Li X, Liang T, Liu H. How plants coordinate their development in response to light and temperature signals. THE PLANT CELL 2022; 34:955-966. [PMID: 34904672 PMCID: PMC8894937 DOI: 10.1093/plcell/koab302] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/06/2021] [Indexed: 05/12/2023]
Abstract
Light and temperature change constantly under natural conditions and profoundly affect plant growth and development. Light and warmer temperatures promote flowering, higher light intensity inhibits hypocotyl and petiole elongation, and warmer temperatures promote hypocotyl and petiole elongation. Moreover, exogenous light and temperature signals must be integrated with endogenous signals to fine-tune phytohormone metabolism and plant morphology. Plants perceive and respond to light and ambient temperature using common sets of factors, such as photoreceptors and multiple light signal transduction components. These highly structured signaling networks are critical for plant survival and adaptation. This review discusses how plants respond to variable light and temperature conditions using common elements to coordinate their development. Future directions for research on light and temperature signaling pathways are also discussed.
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Affiliation(s)
- Xu Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Tong Liang
- Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
| | - Hongtao Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Author for correspondence:
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11
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Xu X, Yuan L, Xie Q. The circadian clock ticks in plant stress responses. STRESS BIOLOGY 2022; 2:15. [PMID: 37676516 PMCID: PMC10441891 DOI: 10.1007/s44154-022-00040-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/15/2022] [Indexed: 09/08/2023]
Abstract
The circadian clock, a time-keeping mechanism, drives nearly 24-h self-sustaining rhythms at the physiological, cellular, and molecular levels, keeping them synchronized with the cyclic changes of environmental signals. The plant clock is sensitive to external and internal stress signals that act as timing cues to influence the circadian rhythms through input pathways of the circadian clock system. In order to cope with environmental stresses, many core oscillators are involved in defense while maintaining daily growth in various ways. Recent studies have shown that a hierarchical multi-oscillator network orchestrates the defense through rhythmic accumulation of gene transcripts, alternative splicing of mRNA precursors, modification and turnover of proteins, subcellular localization, stimuli-induced phase separation, and long-distance transport of proteins. This review summarizes the essential role of circadian core oscillators in response to stresses in Arabidopsis thaliana and crops, including daily and seasonal abiotic stresses (low or high temperature, drought, high salinity, and nutrition deficiency) and biotic stresses (pathogens and herbivorous insects). By integrating time-keeping mechanisms, circadian rhythms and stress resistance, we provide a temporal perspective for scientists to better understand plant environmental adaptation and breed high-quality crop germplasm for agricultural production.
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Affiliation(s)
- Xiaodong Xu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China.
| | - Li Yuan
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Qiguang Xie
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China.
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12
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Lou P, Greenham K, McClung CR. Rhythmic Leaf and Cotyledon Movement Analysis. Methods Mol Biol 2022; 2494:125-134. [PMID: 35467204 DOI: 10.1007/978-1-0716-2297-1_9] [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] [Indexed: 06/14/2023]
Abstract
The first descriptions of circadian rhythms were of the rhythmic leaf movements of plants. Rhythmic leaf movements offer a sensitive, noninvasive, nondestructive, and non-transgenic assay of plant circadian rhythms that can be readily automated, greatly facilitating genetic studies. Rhythmic leaf movement is particularly useful for the assessment of standing variation in clock function and can be readily applied to a diverse array of dicotyledonous plants, including both wild species and domesticated crops.
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Affiliation(s)
- Ping Lou
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Kathleen Greenham
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
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13
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How to Detect QTLs in the Plant Circadian Clock. Methods Mol Biol 2021. [PMID: 34674170 DOI: 10.1007/978-1-0716-1912-4_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
One of the most powerful methods to identify loci controlling complex quantitative traits has been the quantitative trait locus (QTL) mapping. The QTL mapping approach has proven immensely useful to improve our understanding of key pathways such as flowering time, growth, and disease resistance. Since major circadian clock parameters such as period, phase, and amplitude are quantitative in nature, the QTL mapping approach could also be used to study the complex genetic architecture of the circadian clock. Here, we describe a simple QTL mapping method to identify components controlling clock parameters in natural populations of Arabidopsis thaliana.
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14
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Xu J, Wang JJ, Xue HW, Zhang GH. Leaf direction: Lamina joint development and environmental responses. PLANT, CELL & ENVIRONMENT 2021; 44:2441-2454. [PMID: 33866581 DOI: 10.1111/pce.14065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/07/2021] [Indexed: 06/12/2023]
Abstract
Plant architecture plays a major role in canopy photosynthesis and biomass production, and plants adjust their growth (and thus architecture) in response to changing environments. Leaf angle is one of the most important traits in rice (Oryza sativa L.) plant architecture, because leaf angle strongly affects leaf direction and rice production, with more-erect leaves being advantageous for high-density plantings. The degree of leaf bending depends on the morphology of the lamina joint, which connects the leaf and the sheath. In this review, we discuss cell morphology in different lamina joint tissues and describe the underlying genetic network that governs this morphology and thus regulates leaf direction. Furthermore, we focus on the mechanism by how environmental factors influence rice leaf angle. Our review provides a theoretical framework for the future genetic improvement of rice leaf orientation and plant architecture.
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Affiliation(s)
- Jing Xu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Jia-Jia Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Hong-Wei Xue
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Guang-Heng Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
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15
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Hayes S, Schachtschabel J, Mishkind M, Munnik T, Arisz SA. Hot topic: Thermosensing in plants. PLANT, CELL & ENVIRONMENT 2021; 44:2018-2033. [PMID: 33314270 PMCID: PMC8358962 DOI: 10.1111/pce.13979] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/26/2020] [Accepted: 12/02/2020] [Indexed: 05/13/2023]
Abstract
Plants alter their morphology and cellular homeostasis to promote resilience under a variety of heat regimes. Molecular processes that underlie these responses have been intensively studied and found to encompass diverse mechanisms operating across a broad range of cellular components, timescales and temperatures. This review explores recent progress throughout this landscape with a particular focus on thermosensing in the model plant Arabidopsis. Direct temperature sensors include the photosensors phytochrome B and phototropin, the clock component ELF3 and an RNA switch. In addition, there are heat-regulated processes mediated by ion channels, lipids and lipid-modifying enzymes, taking place at the plasma membrane and the chloroplast. In some cases, the mechanism of temperature perception is well understood but in others, this remains an open question. Potential novel thermosensing mechanisms are based on lipid and liquid-liquid phase separation. Finally, future research directions of high temperature perception and signalling pathways are discussed.
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Affiliation(s)
- Scott Hayes
- Laboratory of Plant PhysiologyWageningen University & ResearchWageningenThe Netherlands
| | - Joëlle Schachtschabel
- Research Cluster Green Life Sciences, Section Plant Cell BiologySwammerdam Institute for Life Sciences, University of AmsterdamAmsterdamThe Netherlands
| | - Michael Mishkind
- Research Cluster Green Life Sciences, Section Plant Cell BiologySwammerdam Institute for Life Sciences, University of AmsterdamAmsterdamThe Netherlands
- IOSNational Science FoundationAlexandriaVirginiaUSA
| | - Teun Munnik
- Research Cluster Green Life Sciences, Section Plant Cell BiologySwammerdam Institute for Life Sciences, University of AmsterdamAmsterdamThe Netherlands
| | - Steven A. Arisz
- Research Cluster Green Life Sciences, Section Plant Cell BiologySwammerdam Institute for Life Sciences, University of AmsterdamAmsterdamThe Netherlands
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16
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Tian W, Wang R, Bo C, Yu Y, Zhang Y, Shin GI, Kim WY, Wang L. SDC mediates DNA methylation-controlled clock pace by interacting with ZTL in Arabidopsis. Nucleic Acids Res 2021; 49:3764-3780. [PMID: 33675668 PMCID: PMC8053106 DOI: 10.1093/nar/gkab128] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 02/13/2021] [Accepted: 02/16/2021] [Indexed: 12/29/2022] Open
Abstract
Molecular bases of eukaryotic circadian clocks mainly rely on transcriptional-translational feedback loops (TTFLs), while epigenetic codes also play critical roles in fine-tuning circadian rhythms. However, unlike histone modification codes that play extensive and well-known roles in the regulation of circadian clocks, whether DNA methylation (5mC) can affect the circadian clock, and the associated underlying molecular mechanisms, remains largely unexplored in many organisms. Here we demonstrate that global genome DNA hypomethylation can significantly lengthen the circadian period of Arabidopsis. Transcriptomic and genetic evidence demonstrate that SUPPRESSOR OF drm1 drm2 cmt3 (SDC), encoding an F-box containing protein, is required for the DNA hypomethylation-tuned circadian clock. Moreover, SDC can physically interact with another F-box containing protein ZEITLUPE (ZTL) to diminish its accumulation. Genetic analysis further revealed that ZTL and its substrate TIMING OF CAB EXPRESSION 1 (TOC1) likely act downstream of DNA methyltransferases to control circadian rhythm. Together, our findings support the notion that DNA methylation is important to maintain proper circadian pace in Arabidopsis, and further established that SDC links DNA hypomethylation with a proteolytic cascade to assist in tuning the circadian clock.
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Affiliation(s)
- Wenwen Tian
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Ruyi Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China
| | - Cunpei Bo
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Yingjun Yu
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Yuanyuan Zhang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China
| | - Gyeong-Im Shin
- Division of Applied Life Science (BK21Plus), Research Institute of Life Sciences (RILS) and Institute of Agricultural and Life Science(IALS), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21Plus), Research Institute of Life Sciences (RILS) and Institute of Agricultural and Life Science(IALS), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Lei Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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17
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McClung CR. Circadian Clock Components Offer Targets for Crop Domestication and Improvement. Genes (Basel) 2021; 12:genes12030374. [PMID: 33800720 PMCID: PMC7999361 DOI: 10.3390/genes12030374] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/01/2021] [Accepted: 03/04/2021] [Indexed: 12/31/2022] Open
Abstract
During plant domestication and improvement, farmers select for alleles present in wild species that improve performance in new selective environments associated with cultivation and use. The selected alleles become enriched and other alleles depleted in elite cultivars. One important aspect of crop improvement is expansion of the geographic area suitable for cultivation; this frequently includes growth at higher or lower latitudes, requiring the plant to adapt to novel photoperiodic environments. Many crops exhibit photoperiodic control of flowering and altered photoperiodic sensitivity is commonly required for optimal performance at novel latitudes. Alleles of a number of circadian clock genes have been selected for their effects on photoperiodic flowering in multiple crops. The circadian clock coordinates many additional aspects of plant growth, metabolism and physiology, including responses to abiotic and biotic stresses. Many of these clock-regulated processes contribute to plant performance. Examples of selection for altered clock function in tomato demonstrate that with domestication, the phasing of the clock is delayed with respect to the light–dark cycle and the period is lengthened; this modified clock is associated with increased chlorophyll content in long days. These and other data suggest the circadian clock is an attractive target during breeding for crop improvement.
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Affiliation(s)
- C Robertson McClung
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
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18
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Rees H, Joynson R, Brown JKM, Hall A. Naturally occurring circadian rhythm variation associated with clock gene loci in Swedish Arabidopsis accessions. PLANT, CELL & ENVIRONMENT 2021; 44:807-820. [PMID: 33179278 PMCID: PMC7986795 DOI: 10.1111/pce.13941] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 11/05/2020] [Accepted: 11/06/2020] [Indexed: 05/25/2023]
Abstract
Circadian clocks have evolved to resonate with external day and night cycles. However, these entrainment signals are not consistent everywhere and vary with latitude, climate and seasonality. This leads to divergent selection for clocks which are locally adapted. To investigate the genetic basis for this circadian variation, we used a delayed fluorescence imaging assay to screen 191 naturally occurring Swedish Arabidopsis accessions for their circadian phenotypes. We demonstrate that the period length co-varies with both geography and population sub-structure. Several candidate loci linked to period, phase and relative amplitude error (RAE) were revealed by genome-wide association mapping and candidate genes were investigated using TDNA mutants. We show that natural variation in a single non-synonymous substitution within COR28 is associated with a long-period and late-flowering phenotype similar to that seen in TDNA knock-out mutants. COR28 is a known coordinator of flowering time, freezing tolerance and the circadian clock; all of which may form selective pressure gradients across Sweden. We demonstrate the effect of the COR28-58S SNP in increasing period length through a co-segregation analysis. Finally, we show that period phenotypic tails remain diverged under lower temperatures and follow a distinctive "arrow-shaped" trend indicative of selection for a cold-biased temperature compensation response.
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Affiliation(s)
- Hannah Rees
- Organisms and EcosystemsEarlham Institute, Norwich Research ParkNorwichUK
- Institute of Integrative Biology, University of LiverpoolLiverpoolUK
| | - Ryan Joynson
- Organisms and EcosystemsEarlham Institute, Norwich Research ParkNorwichUK
| | | | - Anthony Hall
- Organisms and EcosystemsEarlham Institute, Norwich Research ParkNorwichUK
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19
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Leinonen PH, Salmela MJ, Greenham K, McClung CR, Willis JH. Populations Are Differentiated in Biological Rhythms without Explicit Elevational Clines in the Plant Mimulus laciniatus. J Biol Rhythms 2020; 35:452-464. [PMID: 32628567 PMCID: PMC7534027 DOI: 10.1177/0748730420936408] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Environmental variation along an elevational gradient can yield phenotypic differentiation resulting from varying selection pressures on plant traits related to seasonal responses. Thus, genetic clines can evolve in a suite of traits, including the circadian clock, that drives daily cycling in varied traits and that shares its genetic background with adaptation to seasonality. We used populations of annual Mimulus laciniatus from different elevations in the Sierra Nevada in California to explore among-population differentiation in the circadian clock, flowering responses to photoperiod, and phenological traits (days to cotyledon emergence, days to flowering, and days to seed ripening) in controlled common-garden conditions. Further, we examined correlations of these traits with environmental variables related to temperature and precipitation. We observed that the circadian period in leaf movement was differentiated among populations sampled within about 100 km, with population means varying by 1.6 h. Significant local genetic variation occurred within 2 populations in which circadian period among families varied by up to 1.8 h. Replicated treatments with variable ecologically relevant photoperiods revealed marked population differentiation in critical day length for flowering that ranged from 11.0 to 14.1 h, corresponding to the time period between late February and mid-May in the wild. Flowering time varied among populations in a 14-h photoperiod. Regardless of this substantial population-level diversity, obvious linear clinality in trait variability across elevations could not be determined based on our genotypic sample; it is possible that more complex spatial patterns of variation arise in complex terrains such as those in the Sierra Nevada. Moreover, we did not find statistically significant bivariate correlations between population means of different traits. Our research contributes to the understanding of genetic variation in the circadian clock and in seasonal responses in natural populations, highlighting the need for more comprehensive investigations on the association between the clock and other adaptive traits in plants.
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Affiliation(s)
- Päivi H Leinonen
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland.,Department of Biology, Duke University, Durham, North Carolina, USA
| | - Matti J Salmela
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Kathleen Greenham
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA
| | - C Robertson McClung
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA
| | - John H Willis
- Department of Biology, Duke University, Durham, North Carolina, USA
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20
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Li Y, Wang L, Yuan L, Song Y, Sun J, Jia Q, Xie Q, Xu X. Molecular investigation of organ-autonomous expression of Arabidopsis circadian oscillators. PLANT, CELL & ENVIRONMENT 2020; 43:1501-1512. [PMID: 32012302 DOI: 10.1111/pce.13739] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 01/27/2020] [Accepted: 01/28/2020] [Indexed: 06/10/2023]
Abstract
The circadian pacemaker in plants is a hierarchical multioscillator system that directs and maintains a 24-hr oscillation required for organism homeostasis and environmental fitness. Molecular clockwork within individual tissues and organs acts cell autonomously, showing differences in circadian expression of core oscillators and their target genes; there are functional dominance and coupling in the complex regulatory network. However, molecular characteristics of organ-specific clocks are still unknown. Here, we showed the detached shoot and root possess dynamic circadian protein-protein interactions between clock core components, periodicity in organs exhibits a difference. The period length difference between shoot and root was not remarkable in prr7-3 and prr7-3 prr9-1 mutants. In addition, the phase transition curve indicated that shoot and root clock respond differently to the resetting cues of ambient temperature. PRR9 and PRR7 compensate circadian period between 22°C and 28°C in shoot, not in root. The circadian rhythms of PRR9 or PRR7 transcript accumulation showed no difference at 22°C and 28°C in shoot, but differences were observed in root. In summary, our results reveal the specificity of dynamic circadian protein-protein interactions in organ-autonomous clocks and the critical roles of PRR9 and PRR7 in mechanisms regulating temperature compensation in aerial shoot system.
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Affiliation(s)
- Yue Li
- Key Laboratory of Molecular and Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Lingbao Wang
- Key Laboratory of Molecular and Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Li Yuan
- Key Laboratory of Molecular and Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Yang Song
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Junqiu Sun
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Qian Jia
- Key Laboratory of Molecular and Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Qiguang Xie
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Xiaodong Xu
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
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21
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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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22
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Kim TS, Wang L, Kim YJ, Somers DE. Compensatory Mutations in GI and ZTL May Modulate Temperature Compensation in the Circadian Clock. PLANT PHYSIOLOGY 2020; 182:1130-1141. [PMID: 31740505 PMCID: PMC6997678 DOI: 10.1104/pp.19.01120] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 11/02/2019] [Indexed: 05/04/2023]
Abstract
Circadian systems share the three properties of entrainment, free-running period, and temperature compensation (TC). TC ensures nearly the same period over a broad range of physiologically relevant temperatures; however, the mechanisms behind TC remain poorly understood. Here, we identify single point mutations in two key elements of the Arabidopsis circadian clock, GIGANTEA (GI) and ZEITLUPE (ZTL), which likely act as compensatory substitutions to establish a remarkably constant free-running period over a wide range of temperatures. Using near-isogenic lines generated from the introgression of the Cape Verde Islands (Cvi) alleles of GI and ZTL into the Landsberg erecta (Ler) background, we show how longer periods in the Cvi background at higher temperatures correlate with a difference in strength of the GI/ZTL interaction. Pairwise interaction testing of all GI/ZTL allelic combinations shows similar affinities for isogenic alleles at 22°C, but very poor interaction between GI (Cvi) and ZTL (Cvi) at higher temperature. In vivo, this would result in lower ZTL levels at high temperatures leading to longer periods in the Cvi background. Mismatched allelic combinations result in extremely strong or weak GI/ZTL interactions, indicating how the corresponding natural variants likely became fixed through epistatic selection. Additionally, molecular characterization of GI (Cvi) reveals a novel functional motif that can modulate the GI/ZTL interaction as well as nucleocytoplasmic partitioning. Taken together, these results identify a plausible temperature-dependent molecular mechanism, which contributes to the robustness of TC through natural variation in GI and ZTL alleles found on the Cape Verde Islands.
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Affiliation(s)
- Tae-Sung Kim
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
| | - Lei Wang
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
| | - Yeon Jeong Kim
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
| | - David E Somers
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
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23
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Panter PE, Muranaka T, Cuitun-Coronado D, Graham CA, Yochikawa A, Kudoh H, Dodd AN. Circadian Regulation of the Plant Transcriptome Under Natural Conditions. Front Genet 2019; 10:1239. [PMID: 31850080 PMCID: PMC6895068 DOI: 10.3389/fgene.2019.01239] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 11/08/2019] [Indexed: 11/16/2022] Open
Abstract
Circadian rhythms produce a biological measure of the time of day. In plants, circadian regulation forms an essential adaptation to the fluctuating environment. Most of our knowledge of the molecular aspects of circadian regulation in plants is derived from laboratory experiments that are performed under controlled conditions. However, it is emerging that the circadian clock has complex roles in the coordination of the transcriptome under natural conditions, in both naturally occurring populations of plants and in crop species. In this review, we consider recent insights into circadian regulation under natural conditions. We examine how circadian regulation is integrated with the acute responses of plants to the daily and seasonally fluctuating environment that also presents environmental stresses, in order to coordinate the transcriptome and dynamically adapt plants to their continuously changing environment.
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Affiliation(s)
- Paige E. Panter
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | | | - David Cuitun-Coronado
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Calum A. Graham
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Aline Yochikawa
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Otsu, Japan
| | - Antony N. Dodd
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
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24
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Bdolach E, Prusty MR, Faigenboim-Doron A, Filichkin T, Helgerson L, Schmid KJ, Greiner S, Fridman E. Thermal plasticity of the circadian clock is under nuclear and cytoplasmic control in wild barley. PLANT, CELL & ENVIRONMENT 2019; 42:3105-3120. [PMID: 31272129 DOI: 10.1111/pce.13606] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 06/27/2019] [Accepted: 06/30/2019] [Indexed: 06/09/2023]
Abstract
Temperature compensation, expressed as the ability to maintain clock characteristics (mainly period) in face of temperature changes, that is, robustness, is considered a key feature of circadian clock systems. In this study, we explore the genetic basis for lack of robustness, that is, plasticity, of circadian clock as reflected by photosynthesis rhythmicity. The clock rhythmicity of a new wild barley reciprocal doubled haploid population was analysed with a high temporal resolution of pulsed amplitude modulation of chlorophyll fluorescence under optimal (22°C) and high (32°C) temperature. This comparison between two environments pointed to the prevalence of clock acceleration under heat. Genotyping by sequencing of doubled haploid lines indicated a rich recombination landscape with minor fixation (less than 8%) for one of the parental alleles. Quantitative genetic analysis included genotype by environment interactions and binary-threshold models. Variation in the circadian rhythm plasticity phenotypes, expressed as change (delta) of period and amplitude under two temperatures, was associated with maternal organelle genome (the plasmotype), as well as with several nuclear loci. This first reported rhythmicity driven by nuclear loci and plasmotype with few identified variants, paves the way for studying impact of cytonuclear variations on clock robustness and on plant adaptation to changing environments.
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Affiliation(s)
- Eyal Bdolach
- Plant Sciences Institute, Volcani Agricultural Research Organization (ARO), Bet Dagan, Israel
- Department of Life Sciences, Ben-Gurion University, Beer-Sheva, Israel
| | - Manas Ranjan Prusty
- Plant Sciences Institute, Volcani Agricultural Research Organization (ARO), Bet Dagan, Israel
| | - Adi Faigenboim-Doron
- Plant Sciences Institute, Volcani Agricultural Research Organization (ARO), Bet Dagan, Israel
| | - Tanya Filichkin
- Crop and Soil Science Department, Oregon State University, Corvallis, Oregon
| | - Laura Helgerson
- Crop and Soil Science Department, Oregon State University, Corvallis, Oregon
| | - Karl J Schmid
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
| | - Stephan Greiner
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Eyal Fridman
- Plant Sciences Institute, Volcani Agricultural Research Organization (ARO), Bet Dagan, Israel
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25
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Salmela MJ, Weinig C. The fitness benefits of genetic variation in circadian clock regulation. CURRENT OPINION IN PLANT BIOLOGY 2019; 49:86-93. [PMID: 31302588 DOI: 10.1016/j.pbi.2019.06.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 05/31/2019] [Accepted: 06/04/2019] [Indexed: 06/10/2023]
Abstract
Functional circadian clocks are essential for fitness in diverse ecosystems, facilitating detection of predictable light-dark and temperature cycles. The molecular basis of endogenous clocks is variable across the tree of life, but it has one omnipresent attribute: natural genetic diversity that manifests as variation for instance in circadian period length around the hypothesised optimum of 24 hours. Latitudinal variation in photoperiod alone is unlikely to account for the vast diversity documented in varied organisms, but we have yet to achieve a solid understanding of the interplay between clock variability and natural selection. Recent circadian studies sampling populations have drawn attention to the hierarchical structure of genetic diversity in the wild, unveiling pronounced genetic variation even on a scale of metres.
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Affiliation(s)
- Matti J Salmela
- Natural Resources Institute Finland, Latokartanonkaari 9, 00790 Helsinki, Finland
| | - Cynthia Weinig
- Department of Botany, 3165, University of Wyoming, 1000 E. University Ave., Laramie, WY 82071, USA; Program in Ecology, University of Wyoming, Laramie, WY 82071, USA; Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA.
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26
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Rees H, Duncan S, Gould P, Wells R, Greenwood M, Brabbs T, Hall A. A high-throughput delayed fluorescence method reveals underlying differences in the control of circadian rhythms in Triticum aestivum and Brassica napus. PLANT METHODS 2019; 15:51. [PMID: 31139241 PMCID: PMC6530173 DOI: 10.1186/s13007-019-0436-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 05/10/2019] [Indexed: 05/25/2023]
Abstract
BACKGROUND A robust circadian clock has been implicated in plant resilience, resource-use efficiency, competitive growth and yield. A huge number of physiological processes are under circadian control in plants including: responses to biotic and abiotic stresses; flowering time; plant metabolism; and mineral uptake. Understanding how the clock functions in crops such as Triticum aestivum (bread wheat) and Brassica napus (oilseed rape) therefore has great agricultural potential. Delayed fluorescence (DF) imaging has been shown to be applicable to a wide range of plant species and requires no genetic transformation. Although DF has been used to measure period length of both mutants and wild ecotypes of Arabidopsis, this assay has never been systematically optimised for crop plants. The physical size of both B. napus and T. aestivum led us to develop a representative sampling strategy which enables high-throughput imaging of these crops. RESULTS In this study, we describe the plant-specific optimisation of DF imaging to obtain reliable circadian phenotypes with the robustness and reproducibility to detect diverging periods between cultivars of the same species. We find that the age of plant material, light regime and temperature conditions all significantly effect DF rhythms and describe the optimal conditions for measuring robust rhythms in each species. We also show that sections of leaf can be used to obtain period estimates with improved throughput for larger sample size experiments. CONCLUSIONS We present an optimized protocol for high-throughput phenotyping of circadian period specific to two economically valuable crop plants. Application of this method revealed significant differences between the periods of several widely grown elite cultivars. This method also identified intriguing differential responses of circadian rhythms in T. aestivum compared to B. napus; specifically the dramatic change to rhythm robustness when plants were imaged under constant light versus constant darkness. This points towards diverging networks underlying circadian control in these two species.
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Affiliation(s)
- Hannah Rees
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UG UK
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB UK
| | - Susan Duncan
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UG UK
| | - Peter Gould
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB UK
| | - Rachel Wells
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Mark Greenwood
- Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR UK
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW UK
| | - Thomas Brabbs
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UG UK
| | - Anthony Hall
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UG UK
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27
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Rubin MJ, Brock MT, Davis SJ, Weinig C. QTL Underlying Circadian Clock Parameters Under Seasonally Variable Field Settings in Arabidopsis thaliana. G3 (BETHESDA, MD.) 2019; 9:1131-1139. [PMID: 30755409 PMCID: PMC6469418 DOI: 10.1534/g3.118.200770] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 02/06/2019] [Indexed: 11/18/2022]
Abstract
The circadian clock facilitates coordination of the internal rhythms of an organism to daily environmental conditions, such as the light-dark cycle of one day. Circadian period length (the duration of one endogenous cycle) and phase (the timing of peak activity) exhibit quantitative variation in natural populations. Here, we measured circadian period and phase in June, July and September in three Arabidopsis thaliana recombinant inbred line populations. Circadian period and phase were estimated from bioluminescence of a genetic construct between a native circadian clock gene (COLD CIRCADIAN RHYTHM RNA BINDING 2) and the reporter gene (LUCIFERASE) after lines were entrained under field settings. Using a Bayesian mapping approach, we estimated the median number and effect size of genomic regions (Quantitative Trait Loci, QTL) underlying circadian parameters and the degree to which these regions overlap across months of the growing season. We also tested for QTL associations between the circadian clock and plant morphology. The genetic architecture of circadian phase was largely independent across months, as evidenced by the fact that QTL determining phase values in one month of the growing season were different from those determining phase in a second month. QTL for circadian parameters were shared with both cauline and rosette branching in at least one mapping population. The results provide insights into the QTL architecture of the clock under field settings, and suggest that the circadian clock is highly responsive to changing environments and that selection can act on clock phase in a nuanced manner.
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Affiliation(s)
- Matthew J Rubin
- Department of Botany, University of Wyoming, Laramie, WY 82071
- Program in Ecology, University of Wyoming, Laramie, WY 82071
| | - Marcus T Brock
- Department of Botany, University of Wyoming, Laramie, WY 82071
| | - Seth J Davis
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Cynthia Weinig
- Department of Botany, University of Wyoming, Laramie, WY 82071
- Program in Ecology, University of Wyoming, Laramie, WY 82071
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071
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28
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Xiao D, Shen HR, Zhao JJ, Wei YP, Liu DR, Hou XL, Bonnema G. Genetic dissection of flowering time in Brassica rapa responses to temperature and photoperiod. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 280:110-119. [PMID: 30823988 DOI: 10.1016/j.plantsci.2018.10.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/19/2018] [Accepted: 10/31/2018] [Indexed: 06/09/2023]
Abstract
The Brassica rapa (B. rapa) species displays enormous phenotypic diversity, with leafy vegetables, storage root vegetables and oil crops. These different crops all have different flowering time, which determine their growing season and cultivation area. Little is known about the effects of diverse temperature and day-lengths on flowering time QTL associated with FLC paralogues. We phenotyped the flowering time of a doubled haploid population, established from a cross between Yellow sarson and Pak choi under diverse environmental conditions. We identified flowering-time QTL (fQTL) in different photoperiod and temperature regimes in the greenhouse, and studied their colocation with known flowering time genes. As several fQTL colocalized with FLC paralogues, we studied the expression patterns of four FLC paralogues during the course of vernalization in parental lines. Under all environmental conditions tested the major fQTL that mapped to the BrFLC2_A02 locus was detected, however its effect decreased when plants were grown at low temperatures. Another fQTL that mapped to the FLC paralogue, BrFLC5_A03 was also identified under all tested environments, while no fQTL colocated with BrFLC1_A10 or BrFLC3_A03. Furthermore, the vernalization treatment decreased expression of all BrFLC paralogues in the parental lines, and showed the lowest transcript level after 28 days of vernalization. Transcript abundance stayed low after returning the plants for seven days to normal growth temperature. Interestingly, transcript abundance of BrFLC3_A03 and BrFLC5_A03 was repressed much stronger and already reached lowest levels after 14d in the early-flowering type YS-143. This study improves understanding of the effects of daylength and vernalization on flowering time in B. rapa and the role of the different BrFLC paralogues therein.
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Affiliation(s)
- Dong Xiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China; Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hao-Ran Shen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jian-Jun Zhao
- Horticultural College, Agricultural University of Hebei, Baoding, 071001, China
| | - Yan-Ping Wei
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Dong-Rang Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xi-Lin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Guusje Bonnema
- Plant Breeding, Wageningen University and Research, 6708 PB, Wageningen, the Netherlands.
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Gil KE, Park CM. Thermal adaptation and plasticity of the plant circadian clock. THE NEW PHYTOLOGIST 2019; 221:1215-1229. [PMID: 30289568 DOI: 10.1111/nph.15518] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 09/11/2018] [Indexed: 05/20/2023]
Abstract
Contents Summary 1215 I. Introduction 1215 II. Molecular organization of the plant circadian clock 1216 III. Temperature compensation 1219 IV. Temperature regulation of circadian behaviors 1220 V. Thermal adaptation of the clock: evolutionary considerations 1223 VI. Light and temperature information for the clock function - synergic or individual? 1224 VII. Concluding remarks and future prospects 1225 Acknowledgements 1225 References 1225 SUMMARY: Plant growth and development is widely affected by diverse temperature conditions. Although studies have been focused mainly on the effects of stressful temperature extremes in recent decades, nonstressful ambient temperatures also influence an array of plant growth and morphogenic aspects, a process termed thermomorphogenesis. Notably, accumulating evidence indicates that both stressful and nonstressful temperatures modulate the functional process of the circadian clock, a molecular timer of biological rhythms in higher eukaryotes and photosynthetic prokaryotes. The circadian clock can sustain robust and precise timing over a range of physiological temperatures. Genes and molecular mechanisms governing the temperature compensation process have been explored in different plant species. In addition, a ZEITLUPE/HSP90-mediated protein quality control mechanism helps plants maintain the thermal stability of the clock under heat stress. The thermal adaptation capability and plasticity of the clock are of particular interest in view of the growing concern about global climate changes. Considering these circumstances in the field, we believe that it is timely to provide a provoking discussion on the current knowledge of temperature regulation of the clock function. The review also will discuss stimulating ideas on this topic along with ecosystem management and future agricultural innovation.
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Affiliation(s)
- Kyung-Eun Gil
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
| | - Chung-Mo Park
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Korea
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30
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Soengas P, Cartea ME, Velasco P, Francisco M. Brassica glucosinolate rhythmicity in response to light-dark entrainment cycles is cultivar-dependent. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 275:28-35. [PMID: 30107879 DOI: 10.1016/j.plantsci.2018.07.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 07/16/2018] [Accepted: 07/19/2018] [Indexed: 06/08/2023]
Abstract
Coordination of plant circadian rhythms with the external environment provides growth and reproductive advantages to plants as well as enhanced resistance to insects and pathogens. Since glucosinolates (GLSs) play a major role as plant defensive compounds and could affect the palatability and health value of edible crops, the aim of this study was to investigate the species-specific patterns in circadian rhythmicity of these plant phytochemicals. Five different GLS-containing cultivars, from three Brassica crop species were studied. Plants were entrained to light-dark cycles (LD) for five weeks prior to release them into continuous light (LL). GLSs levels were monitored during five consecutive days (two days at LD conditions and three days at LL). The remaining plants were re-entrained to LD cycles (Re-LD plants) and GLS levels were studied as stated before during two consecutive days. Results showed that the period and amplitude of GLSs circadian outputs were cultivar-dependent. In addition, we assessed that the plant endogenous clock can be re-entrained for GLSs accumulation after a period of free-running conditions. Together, these data suggests that Brassica cultivars keep track the time of the day to coordinate their defenses. The demonstration of the cultivar-specific circadian effect on the GLSs levels in plants of different Brassica cultivars have the potential to identify new targets for improving cultivar phytochemicals using temporally informed approaches. In addition, provides an exceptional model to study the complexity of signal integration in plants.
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Affiliation(s)
- Pilar Soengas
- Group of Genetics, Breeding and Biochemistry of Brassicas, MisiónBiológica de Galicia, Spanish Council for Scientific Research (CSIC), Pontevedra, Spain
| | - M Elena Cartea
- Group of Genetics, Breeding and Biochemistry of Brassicas, MisiónBiológica de Galicia, Spanish Council for Scientific Research (CSIC), Pontevedra, Spain
| | - Pablo Velasco
- Group of Genetics, Breeding and Biochemistry of Brassicas, MisiónBiológica de Galicia, Spanish Council for Scientific Research (CSIC), Pontevedra, Spain
| | - Marta Francisco
- Group of Genetics, Breeding and Biochemistry of Brassicas, MisiónBiológica de Galicia, Spanish Council for Scientific Research (CSIC), Pontevedra, Spain.
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31
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Rubin MJ, Brock MT, Baker RL, Wilcox S, Anderson K, Davis SJ, Weinig C. Circadian rhythms are associated with shoot architecture in natural settings. THE NEW PHYTOLOGIST 2018; 219:246-258. [PMID: 29672861 DOI: 10.1111/nph.15162] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 03/11/2018] [Indexed: 06/08/2023]
Abstract
Circadian rhythms are key regulators of diverse biological processes under controlled settings. Yet, the phenotypic and fitness consequences of quantitative variation in circadian rhythms remain largely unexplored in the field. As with other pathways, phenotypic characterization of circadian outputs in the field may reveal novel clock functions. Across consecutive growing seasons, we test for associations between clock variation and flowering phenology, plant size, shoot architecture, and fruit set in clock mutants and segregating progenies of Arabidopsis thaliana expressing quantitative variation in circadian rhythms. Using structural equation modeling, we find that genotypic variation in circadian rhythms within a growing season is associated directly with branching, which in turn affects fruit production. Consistent with direct associations between the clock and branching in segregating progenies, cauline branch number is lower and rosette branch number higher in a short-period mutant relative to wild-type and long-period genotypes, independent of flowering time. Differences in branching arise from variation in meristem fate as well as leaf production rate before flowering and attendant increases in meristem number. Our results suggest that clock variation directly affects shoot architecture in the field, suggesting a novel clock function and means by which the clock affects performance.
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Affiliation(s)
- Matthew J Rubin
- Department of Botany, University of Wyoming, Laramie, WY, 82071, USA
- Program in Ecology, University of Wyoming, Laramie, WY, 82071, USA
| | - Marcus T Brock
- Department of Botany, University of Wyoming, Laramie, WY, 82071, USA
| | - Robert L Baker
- Biology Department, Miami University, Oxford, OH, 45056, USA
| | - Stephanie Wilcox
- Department of Botany, University of Wyoming, Laramie, WY, 82071, USA
| | - Kyle Anderson
- Department of Botany, University of Wyoming, Laramie, WY, 82071, USA
| | - Seth J Davis
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Cynthia Weinig
- Department of Botany, University of Wyoming, Laramie, WY, 82071, USA
- Program in Ecology, University of Wyoming, Laramie, WY, 82071, USA
- Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA
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32
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James AB, Sullivan S, Nimmo HG. Global spatial analysis of Arabidopsis natural variants implicates 5'UTR splicing of LATE ELONGATED HYPOCOTYL in responses to temperature. PLANT, CELL & ENVIRONMENT 2018; 41. [PMID: 29520807 PMCID: PMC6033021 DOI: 10.1111/pce.13188] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
How plants perceive and respond to temperature remains an important question in the plant sciences. Temperature perception and signal transduction may occur through temperature-sensitive intramolecular folding of primary mRNA transcripts. Recent studies suggested a role for retention of the first intron in the 5'UTR of the clock component LATE ELONGATED HYPOCOTYL (LHY) in response to changes in temperature. Here, we identified a set of haplotypes in the LHY 5'UTR, examined their global spatial distribution, and obtained evidence that haplotype can affect temperature-dependent splicing of LHY transcripts. Correlations of haplotype spatial distributions with global bioclimatic variables and altitude point to associations with annual mean temperature and temperature fluctuation. Relatively rare relict type accessions correlate with lower mean temperature and greater temperature fluctuation and the spatial distribution of other haplotypes may be informative of evolutionary processes driving colonization of ecosystems. We propose that haplotypes may possess distinct 5'UTR pre-mRNA folding thermodynamics and/or specific biological stabilities based around the binding of trans-acting RNA splicing factors, a consequence of which is scalable splicing sensitivity of a central clock component that is likely tuned to specific temperature environments.
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Affiliation(s)
- Allan B. James
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowG12 8QQUK
| | - Stuart Sullivan
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowG12 8QQUK
| | - Hugh G. Nimmo
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowG12 8QQUK
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33
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Salmela MJ, McMinn RL, Guadagno CR, Ewers BE, Weinig C. Circadian Rhythms and Reproductive Phenology Covary in a Natural Plant Population. J Biol Rhythms 2018; 33:245-254. [DOI: 10.1177/0748730418764525] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
| | - Robby L. McMinn
- Department of Botany, University of Wyoming, Laramie, Wyoming
- Program in Ecology, University of Wyoming, Laramie, Wyoming
| | | | - Brent E. Ewers
- Department of Botany, University of Wyoming, Laramie, Wyoming
- Program in Ecology, University of Wyoming, Laramie, Wyoming
| | - Cynthia Weinig
- Department of Botany, University of Wyoming, Laramie, Wyoming
- Program in Ecology, University of Wyoming, Laramie, Wyoming
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming
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34
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Hansen LL, van den Burg HA, van Ooijen G. Sumoylation Contributes to Timekeeping and Temperature Compensation of the Plant Circadian Clock. J Biol Rhythms 2017; 32:560-569. [PMID: 29172926 DOI: 10.1177/0748730417737633] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The transcriptional circadian clock network is tuned into a 24-h oscillator by numerous posttranslational modifications on the proteins encoded by clock genes, differentially influencing their subcellular localization or activity. Clock proteins in any circadian organism are subject to posttranslational regulation, and many of the key enzymes, notably kinases and phosphatases, are functionally conserved between the clocks of mammals, fungi, and plants. We now establish sumoylation, the posttranslational modification of target proteins by the covalent attachment of the small ubiquitin-like modifier protein SUMO, as a novel mechanism regulating key clock properties in the model plant Arabidopsis. Using 2 different approaches, we show that mutant plant lines with decreased or increased levels of global sumoylation exhibit shortened or lengthened circadian period, respectively. One known functional role of sumoylation is to protect the proteome from temperature stress. The circadian clock is characterized by temperature compensation, meaning that proper timekeeping is ensured over the full range of physiologically relevant temperatures. Interestingly, we observed that the period defects in sumoylation mutant plants are strongly differential across temperature. Increased global sumoylation leads to undercompensation of the clock against temperature and decreased sumoylation to overcompensation, implying that sumoylation buffers the plant clock system against differential ambient temperature.
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Affiliation(s)
- Louise L Hansen
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Harrold A van den Burg
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Gerben van Ooijen
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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35
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Gil KE, Kim WY, Lee HJ, Faisal M, Saquib Q, Alatar AA, Park CM. ZEITLUPE Contributes to a Thermoresponsive Protein Quality Control System in Arabidopsis. THE PLANT CELL 2017; 29:2882-2894. [PMID: 29061867 PMCID: PMC5728135 DOI: 10.1105/tpc.17.00612] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 10/06/2017] [Accepted: 10/20/2017] [Indexed: 05/19/2023]
Abstract
Cellular proteins undergo denaturation and oxidative damage under heat stress, forming insoluble aggregates that are toxic to cells. Plants possess versatile mechanisms to deal with insoluble protein aggregates. Denatured proteins are either renatured to their native conformations or removed from cellular compartments; these processes are often referred to as protein quality control. Heat shock proteins (HSPs) act as molecular chaperones that assist in the renaturation-degradation process. However, how protein aggregates are cleared from cells in plants is largely unknown. Here, we demonstrate that heat-induced protein aggregates are removed by a protein quality control system that includes the ZEITLUPE (ZTL) E3 ubiquitin ligase, a central circadian clock component in Arabidopsis thaliana ZTL mediates the polyubiquitination of aggregated proteins, which leads to proteasomal degradation and enhances the thermotolerance of plants growing at high temperatures. The ZTL-defective ztl-105 mutant exhibited reduced thermotolerance, which was accompanied by a decline in polyubiquitination but an increase in protein aggregate formation. ZTL and its interacting partner HSP90 were cofractionated with insoluble aggregates under heat stress, indicating that ZTL contributes to the thermoresponsive protein quality control machinery. Notably, the circadian clock was hypersensitive to heat in ztl-105 We propose that ZTL-mediated protein quality control contributes to the thermal stability of the circadian clock.
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Affiliation(s)
- Kyung-Eun Gil
- Department of Chemistry, Seoul National University, Seoul 08825, Korea
| | - Woe-Yeon Kim
- Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju 52828, Korea
| | - Hyo-Jun Lee
- Department of Chemistry, Seoul National University, Seoul 08825, Korea
| | - Mohammad Faisal
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Quaiser Saquib
- Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Abdulrahman A Alatar
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Chung-Mo Park
- Department of Chemistry, Seoul National University, Seoul 08825, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea
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36
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Koritala BSC, Lee K. Natural Variation of the Circadian Clock in Neurospora. ADVANCES IN GENETICS 2017; 99:1-37. [PMID: 29050553 DOI: 10.1016/bs.adgen.2017.09.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Most living organisms on earth experience daily and expected changes from the rotation of the earth. For an organism, the ability to predict and prepare for incoming stresses or resources is a very important skill for survival. This cellular process of measuring daily time of the day is collectively called the circadian clock. Because of its fundamental role in survival in nature, there is a great interest in studying the natural variation of the circadian clock. However, characterizing the genetic and molecular mechanisms underlying natural variation of circadian clocks remains a challenging task. In this chapter, we will summarize the progress in studying natural variation of the circadian clock in the successful eukaryotic model Neurospora, which led to discovering many design principles of the molecular mechanisms of the eukaryotic circadian clock. Despite the success of the system in revealing the molecular mechanisms of the circadian clock, Neurospora has not been utilized to extensively study natural variation. We will review the challenges that hindered the natural variation studies in Neurospora, and how they were overcome. We will also review the advantages of Neurospora for natural variation studies. Since Neurospora is the model fungal species for circadian study, it represents over 5 million species of fungi on earth. These fungi play important roles in ecosystems on earth, and as such Neurospora could serve as an important model for understanding the ecological role of natural variation in fungal circadian clocks.
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Affiliation(s)
- Bala S C Koritala
- Department of Biology, Rutgers, The State University of New Jersey, Camden, NJ, United States; Center for Computational and Integrative Biology, Rutgers, The State University of New Jersey, Camden, NJ, United States
| | - Kwangwon Lee
- Department of Biology, Rutgers, The State University of New Jersey, Camden, NJ, United States; Center for Computational and Integrative Biology, Rutgers, The State University of New Jersey, Camden, NJ, United States.
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37
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Rubin MJ, Brock MT, Davis AM, German ZM, Knapp M, Welch SM, Harmer SL, Maloof JN, Davis SJ, Weinig C. Circadian rhythms vary over the growing season and correlate with fitness components. Mol Ecol 2017; 26:5528-5540. [PMID: 28792639 DOI: 10.1111/mec.14287] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 06/15/2017] [Accepted: 06/29/2017] [Indexed: 12/21/2022]
Abstract
Circadian clocks have evolved independently in all three domains of life, suggesting that internal mechanisms of time-keeping are adaptive in contemporary populations. However, the performance consequences of either discrete or quantitative clock variation have rarely been tested in field settings. Clock sensitivity of diverse segregating lines to the environment remains uncharacterized as do the statistical genetic parameters that determine evolutionary potential. In field studies with Arabidopsis thaliana, we found that major perturbations to circadian cycle length (referred to as clock period) via mutation reduce both survival and fecundity. Subtler adjustments via genomic introgression of naturally occurring alleles indicated that clock periods slightly >24 hr were adaptive, consistent with prior models describing how well the timing of biological processes is adjusted within a diurnal cycle (referred to as phase). In segregating recombinant inbred lines (RILs), circadian phase varied up to 2 hr across months of the growing season, and both period and phase expressed significant genetic variances. Performance metrics including developmental rate, size and fruit set were described by principal components (PC) analyses and circadian parameters correlated with the first PC, such that period lengths slightly >24 hr were associated with improved performance in multiple RIL sets. These experiments translate functional analyses of clock behaviour performed in controlled settings to natural ones, demonstrating that quantitative variation in circadian phase is highly responsive to seasonally variable abiotic factors. The results expand upon prior studies in controlled settings, showing that discrete and quantitative variation in clock phenotypes correlates with performance in nature.
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Affiliation(s)
- Matthew J Rubin
- Department of Botany, University of Wyoming, Laramie, WY, USA.,Program in Ecology, University of Wyoming, Laramie, WY, USA
| | - Marcus T Brock
- Department of Botany, University of Wyoming, Laramie, WY, USA
| | - Amanda M Davis
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany.,Department of Biology, University of York, Heslington, York, UK
| | - Zachary M German
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Mary Knapp
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | - Stephen M Welch
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | - Stacey L Harmer
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
| | - Julin N Maloof
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
| | - Seth J Davis
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany.,Department of Biology, University of York, Heslington, York, UK
| | - Cynthia Weinig
- Department of Botany, University of Wyoming, Laramie, WY, USA.,Program in Ecology, University of Wyoming, Laramie, WY, USA.,Department of Molecular Biology, University of Wyoming, Laramie, WY, USA
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38
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Inoue K, Araki T, Endo M. Integration of Input Signals into the Gene Network in the Plant Circadian Clock. PLANT AND CELL PHYSIOLOGY 2017. [PMID: 0 DOI: 10.1093/pcp/pcx066] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Affiliation(s)
- Keisuke Inoue
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502 Japan
| | - Takashi Araki
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502 Japan
| | - Motomu Endo
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502 Japan
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39
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Yuan G, Wan Y, Li X, He B, Zhang Y, Xu B, Wang S, Xie W, Zhou X, Wu Q. Development of Near-Isogenic Lines in a Parthenogenetically Reproduced Thrips Species, Frankliniella occidentalis. Front Physiol 2017; 8:130. [PMID: 28348528 PMCID: PMC5346592 DOI: 10.3389/fphys.2017.00130] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 02/20/2017] [Indexed: 12/14/2022] Open
Abstract
Although near-isogenic lines (NILs) can standardize genetic backgrounds among individuals, it has never been applied in parthenogenetically reproduced animals. Here, through multiple rounds of backcrossing and spinosad screening, we generated spinosad resistant NILs in the western flower thrips, Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae), with a haplo-diploid reproduction system. The resultant F. occidentalis NIL-R strain maintained a resistance ratio over 30,000-fold, which was comparable to its parental resistant strain, Spin-R. More importantly, F. occidentalis NIL-R shared 98.90% genetic similarity with its susceptible parental strain Ivf03. By developing this toolset, we are able to segregate individual resistance and facilitate the mechanistic study of insecticide resistances in phloem-feeding arthropods, a group of devastating pest species reproducing sexually as well as asexually.
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Affiliation(s)
- Guangdi Yuan
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences Beijing, China
| | - Yanran Wan
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences Beijing, China
| | - Xiaoyu Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences Beijing, China
| | - Bingqing He
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences Beijing, China
| | - Youjun Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences Beijing, China
| | - Baoyun Xu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences Beijing, China
| | - Shaoli Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences Beijing, China
| | - Wen Xie
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences Beijing, China
| | - Xuguo Zhou
- Department of Entomology, University of Kentucky Lexington, KY, USA
| | - Qingjun Wu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences Beijing, China
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40
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Dakhiya Y, Hussien D, Fridman E, Kiflawi M, Green R. Correlations between Circadian Rhythms and Growth in Challenging Environments. PLANT PHYSIOLOGY 2017; 173:1724-1734. [PMID: 28153924 PMCID: PMC5338651 DOI: 10.1104/pp.17.00057] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 01/25/2017] [Indexed: 05/25/2023]
Abstract
In plants, the circadian system controls a plethora of processes, many with agronomic importance, such as photosynthesis, photoprotection, stomatal opening, and photoperiodic development, as well as molecular processes, such as gene expression. It has been suggested that modifying circadian rhythms may be a means to manipulate crops to develop improved plants for agriculture. However, there is very little information on how the clock influences the performance of crop plants. We used a noninvasive, high-throughput technique, based on prompt chlorophyll fluorescence, to measure circadian rhythms and demonstrated that the technique works in a range of plants. Using fluorescence, we analyzed circadian rhythms in populations of wild barley (Hordeum vulgare ssp. spontaneum) from widely different ecogeographical locations in the Southern Levant part of the Fertile Crescent, an area with a high proportion of the total genetic variation of wild barley. Our results show that there is variability for circadian traits in the wild barley lines. We observed that circadian period lengths were correlated with temperature and aspect at the sites of origin of the plants, while the amplitudes of the rhythms were correlated with soil composition. Thus, different environmental parameters may exert selection on circadian rhythms.
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Affiliation(s)
- Yuri Dakhiya
- Department of Plant and Environmental Sciences, Silberman Institute for Life Sciences, Hebrew University, Givat Ram, Jerusalem 91904, Israel (D.H., Y.D., R.G.)
- Plant Sciences Institute, Agricultural Research Organization, Volcani Center, Bet Dagan 50250, Israel (E.F.); and
- Department of Life Sciences, Ben Gurion University, Beer Sheva, Interuniversity Institute for Marine Sciences, Eilat 8810, Israel (M.K.)
| | - Duaa Hussien
- Department of Plant and Environmental Sciences, Silberman Institute for Life Sciences, Hebrew University, Givat Ram, Jerusalem 91904, Israel (D.H., Y.D., R.G.)
- Plant Sciences Institute, Agricultural Research Organization, Volcani Center, Bet Dagan 50250, Israel (E.F.); and
- Department of Life Sciences, Ben Gurion University, Beer Sheva, Interuniversity Institute for Marine Sciences, Eilat 8810, Israel (M.K.)
| | - Eyal Fridman
- Department of Plant and Environmental Sciences, Silberman Institute for Life Sciences, Hebrew University, Givat Ram, Jerusalem 91904, Israel (D.H., Y.D., R.G.)
- Plant Sciences Institute, Agricultural Research Organization, Volcani Center, Bet Dagan 50250, Israel (E.F.); and
- Department of Life Sciences, Ben Gurion University, Beer Sheva, Interuniversity Institute for Marine Sciences, Eilat 8810, Israel (M.K.)
| | - Moshe Kiflawi
- Department of Plant and Environmental Sciences, Silberman Institute for Life Sciences, Hebrew University, Givat Ram, Jerusalem 91904, Israel (D.H., Y.D., R.G.)
- Plant Sciences Institute, Agricultural Research Organization, Volcani Center, Bet Dagan 50250, Israel (E.F.); and
- Department of Life Sciences, Ben Gurion University, Beer Sheva, Interuniversity Institute for Marine Sciences, Eilat 8810, Israel (M.K.)
| | - Rachel Green
- Department of Plant and Environmental Sciences, Silberman Institute for Life Sciences, Hebrew University, Givat Ram, Jerusalem 91904, Israel (D.H., Y.D., R.G.);
- Plant Sciences Institute, Agricultural Research Organization, Volcani Center, Bet Dagan 50250, Israel (E.F.); and
- Department of Life Sciences, Ben Gurion University, Beer Sheva, Interuniversity Institute for Marine Sciences, Eilat 8810, Israel (M.K.)
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41
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Greenham K, Lou P, Puzey JR, Kumar G, Arnevik C, Farid H, Willis JH, McClung CR. Geographic Variation of Plant Circadian Clock Function in Natural and Agricultural Settings. J Biol Rhythms 2017; 32:26-34. [PMID: 27920227 DOI: 10.1177/0748730416679307] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
The increasing demand for improved agricultural production will require more efficient breeding for traits that maintain yield under heterogeneous environments. The internal circadian oscillator is essential for perceiving and coordinating environmental cues such as day length, temperature, and abiotic stress responses within physiological processes. To investigate the contribution of the circadian clock to local adaptability, we have analyzed circadian period by leaf movement in natural populations of Mimulus guttatus and domesticated cultivars of Glycine max. We detected consistent variation in circadian period along a latitudinal gradient in annual populations of the wild plant and the selectively bred crop, and this provides novel evidence of natural and artificial selection for circadian performance. These findings provide new support that the circadian clock acts as a central regulator of plant adaptability and further highlight the potential of applying circadian clock gene variation to marker-assisted breeding programs in crops.
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Affiliation(s)
- Kathleen Greenham
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire
| | - Ping Lou
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire
| | - Joshua R Puzey
- Biology Department, College of William and Mary, Williamsburg, Virginia
| | | | | | - Hany Farid
- Department of Computer Science, Dartmouth College, Hanover, New Hampshire
| | - John H Willis
- Biology Department, Duke University, Durham, North Carolina
| | - C Robertson McClung
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire
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42
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Kissen R, Eberl F, Winge P, Uleberg E, Martinussen I, Bones AM. Effect of growth temperature on glucosinolate profiles in Arabidopsis thaliana accessions. PHYTOCHEMISTRY 2016; 130:106-118. [PMID: 27319377 DOI: 10.1016/j.phytochem.2016.06.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 05/23/2016] [Accepted: 06/05/2016] [Indexed: 06/06/2023]
Abstract
Glucosinolates are plant secondary metabolites with important roles in plant defence against pathogens and pests and are also known for their health benefits. Understanding how environmental factors affect the level and composition of glucosinolates is therefore of importance in the perspective of climate change. In this study we analysed glucosinolates in Arabidopsis thaliana accessions when grown at constant standard (21 °C), moderate (15 °C) and low (9 °C) temperatures during three generations. In most of the tested accessions moderate and pronounced chilling temperatures led to higher levels of glucosinolates, especially aliphatic glucosinolates. Which temperature yielded the highest glucosinolate levels was accession-dependent. Transcriptional profiling revealed also accession-specific gene responses, but only a limited correlation between changes in glucosinolate-related gene expression and glucosinolate levels. Different growth temperatures in one generation did not consistently affect glucosinolate composition in subsequent generations, hence a clear transgenerational effect of temperature on glucosinolates was not observed.
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Affiliation(s)
- Ralph Kissen
- Department of Biology, Norwegian University of Science and Technology, Høgskoleringen 5, NO-7491, Trondheim, Norway
| | - Franziska Eberl
- Department of Biology, Norwegian University of Science and Technology, Høgskoleringen 5, NO-7491, Trondheim, Norway
| | - Per Winge
- Department of Biology, Norwegian University of Science and Technology, Høgskoleringen 5, NO-7491, Trondheim, Norway
| | - Eivind Uleberg
- NIBIO, Norwegian Institute of Bioeconomy Research, Box 115, NO-1431, Ås, Norway
| | - Inger Martinussen
- NIBIO, Norwegian Institute of Bioeconomy Research, Box 115, NO-1431, Ås, Norway
| | - Atle M Bones
- Department of Biology, Norwegian University of Science and Technology, Høgskoleringen 5, NO-7491, Trondheim, Norway.
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43
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Ford B, Deng W, Clausen J, Oliver S, Boden S, Hemming M, Trevaskis B. Barley (Hordeum vulgare) circadian clock genes can respond rapidly to temperature in an EARLY FLOWERING 3-dependent manner. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:5517-5528. [PMID: 27580625 PMCID: PMC5049398 DOI: 10.1093/jxb/erw317] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
An increase in global temperatures will impact future crop yields. In the cereal crops wheat and barley, high temperatures accelerate reproductive development, reducing the number of grains per plant and final grain yield. Despite this relationship between temperature and cereal yield, it is not clear what genes and molecular pathways mediate the developmental response to increased temperatures. The plant circadian clock can respond to changes in temperature and is important for photoperiod-dependent flowering, and so is a potential mechanism controlling temperature responses in cereal crops. This study examines the relationship between temperature, the circadian clock, and the expression of flowering-time genes in barley (Hordeum vulgare), a crop model for temperate cereals. Transcript levels of barley core circadian clock genes were assayed over a range of temperatures. Transcript levels of core clock genes CCA1, GI, PRR59, PRR73, PRR95, and LUX are increased at higher temperatures. CCA1 and PRR73 respond rapidly to a decrease in temperature whereas GI and PRR59 respond rapidly to an increase in temperature. The response of GI and the PRR genes to changes in temperature is lost in the elf3 mutant indicating that their response to temperature may be dependent on a functional ELF3 gene.
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Affiliation(s)
- Brett Ford
- CSIRO Agriculture, GPO Box 1600, Canberra, ACT 2601, Australia
| | - Weiwei Deng
- CSIRO Agriculture, GPO Box 1600, Canberra, ACT 2601, Australia
| | - Jenni Clausen
- CSIRO Agriculture, GPO Box 1600, Canberra, ACT 2601, Australia
| | - Sandra Oliver
- CSIRO Agriculture, GPO Box 1600, Canberra, ACT 2601, Australia
| | - Scott Boden
- CSIRO Agriculture, GPO Box 1600, Canberra, ACT 2601, Australia
| | - Megan Hemming
- CSIRO Agriculture, GPO Box 1600, Canberra, ACT 2601, Australia
| | - Ben Trevaskis
- CSIRO Agriculture, GPO Box 1600, Canberra, ACT 2601, Australia
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44
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Marshall CM, Tartaglio V, Duarte M, Harmon FG. The Arabidopsis sickle Mutant Exhibits Altered Circadian Clock Responses to Cool Temperatures and Temperature-Dependent Alternative Splicing. THE PLANT CELL 2016; 28:2560-2575. [PMID: 27624757 PMCID: PMC5134976 DOI: 10.1105/tpc.16.00223] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 08/29/2016] [Accepted: 09/08/2016] [Indexed: 05/20/2023]
Abstract
The circadian clock allows plants to anticipate and respond to daily changes in ambient temperature. Mechanisms establishing the timing of circadian rhythms in Arabidopsis thaliana through temperature entrainment remain unclear. Also incompletely understood is the temperature compensation mechanism that maintains consistent period length within a range of ambient temperatures. A genetic screen for Arabidopsis mutants affecting temperature regulation of the PSEUDO-RESPONSE REGULATOR7 promoter yielded a novel allele of the SICKLE (SIC) gene. This mutant, sic-3, and the existing sic-1 mutant both exhibit low-amplitude or arrhythmic expression of core circadian clock genes under cool ambient temperature cycles, but not under light-dark entrainment. sic mutants also lengthen free running period in a manner consistent with impaired temperature compensation. sic mutant alleles accumulate LATE ELONGATED HYPOCOTYL (LHY) and CIRCADIAN CLOCK ASSOCIATED1 (CCA1) splice variants, among other alternatively spliced transcripts, which is exacerbated by cool temperatures. The cca1-1 lhy-20 double mutant is epistatic to sic-3, indicating the LHY and CCA1 splice variants are needed for sic-3 circadian clock phenotypes. It is not expected that SIC is directly involved in the circadian clock mechanism; instead, SIC likely contributes to pre-mRNA metabolism, and the splice variants that accumulate in sic mutants likely affect the circadian clock response to cool ambient temperature.
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Affiliation(s)
- Carine M Marshall
- Plant Gene Expression Center, U.S. Department of Agriculture-Agricultural Research Service, Albany, California 94710
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - Virginia Tartaglio
- Plant Gene Expression Center, U.S. Department of Agriculture-Agricultural Research Service, Albany, California 94710
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - Maritza Duarte
- Plant Gene Expression Center, U.S. Department of Agriculture-Agricultural Research Service, Albany, California 94710
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - Frank G Harmon
- Plant Gene Expression Center, U.S. Department of Agriculture-Agricultural Research Service, Albany, California 94710
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
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45
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Press MO, Lanctot A, Queitsch C. PIF4 and ELF3 Act Independently in Arabidopsis thaliana Thermoresponsive Flowering. PLoS One 2016; 11:e0161791. [PMID: 27564448 PMCID: PMC5001698 DOI: 10.1371/journal.pone.0161791] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 08/11/2016] [Indexed: 11/19/2022] Open
Abstract
Plants have evolved elaborate mechanisms controlling developmental responses to environmental stimuli. A particularly important stimulus is temperature. Previous work has identified the interplay of PIF4 and ELF3 as a central circuit underlying thermal responses in Arabidopsis thaliana. However, thermal responses vary widely among strains, possibly offering mechanistic insights into the wiring of this circuit. ELF3 contains a polyglutamine (polyQ) tract that is crucial for ELF3 function and varies in length across strains. Here, we use transgenic analysis to test the hypothesis that natural polyQ variation in ELF3 is associated with the observed natural variation in thermomorphogenesis. We found little evidence that the polyQ tract plays a specific role in thermal responses beyond modulating general ELF3 function. Instead, we made the serendipitous discovery that ELF3 plays a crucial, PIF4-independent role in thermoresponsive flowering under conditions more likely to reflect field conditions. We present evidence that ELF3 acts through the photoperiodic pathway, pointing to a previously unknown symmetry between low and high ambient temperature responses. Moreover, in analyzing two strain backgrounds with different thermal responses, we demonstrate that responses may be shifted rather than fundamentally rewired across strains. Our findings tie together disparate observations into a coherent framework in which multiple pathways converge in accelerating flowering in response to temperature, with some such pathways modulated by photoperiod.
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Affiliation(s)
- Maximilian O. Press
- University of Washington Department of Genome Sciences, Seattle, United States of America
| | - Amy Lanctot
- University of Washington Molecular and Cellular Biology Program, University of Washington Department of Biology, Seattle, United States of America
| | - Christine Queitsch
- University of Washington Department of Genome Sciences, Seattle, United States of America
- * E-mail:
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46
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Salmela MJ, Greenham K, Lou P, McClung CR, Ewers BE, Weinig C. Variation in circadian rhythms is maintained among and within populations in Boechera stricta. PLANT, CELL & ENVIRONMENT 2016; 39:1293-303. [PMID: 26514754 DOI: 10.1111/pce.12670] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 10/19/2015] [Accepted: 10/20/2015] [Indexed: 05/13/2023]
Abstract
Circadian clocks have evolved independently in all three domains of life, and fitness benefits of a functional clock have been demonstrated in experimental genotypes in controlled conditions. Still, little is known about genetic variation in the clock and its fitness consequences in natural populations from heterogeneous environments. Using Wyoming populations of the Arabidopsis relative Boechera stricta as our study system, we demonstrate that genetic variation in the clock can occur at multiple levels: means of circadian period among populations sampled at different elevations differed by less than 1 h, but means among families sampled within populations varied by as much as 3.5 h. Growth traits also varied among and within populations. Within the population with the most circadian variation, we observed evidence for a positive correlation between period and growth and a negative correlation between period and root-to-shoot ratio. We then tested whether performance tradeoffs existed among families of this population across simulated seasonal settings. Growth rankings of families were similar across seasonal environments, but for root-to-shoot ratio, genotype × environment interactions contributed significantly to total variation. Therefore, further experiments are needed to identify evolutionary mechanisms that preserve substantial quantitative genetic diversity in the clock in this and other species.
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Affiliation(s)
- Matti J Salmela
- Department of Botany, University of Wyoming, Laramie, WY, 82071, USA
| | - Kathleen Greenham
- Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA
| | - Ping Lou
- Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA
| | - C Robertson McClung
- Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA
| | - Brent E Ewers
- Department of Botany, University of Wyoming, Laramie, WY, 82071, USA
- Program in Ecology, University of Wyoming
| | - Cynthia Weinig
- Department of Botany, University of Wyoming, Laramie, WY, 82071, USA
- Program in Ecology, University of Wyoming
- Department of Molecular Biology, University of Wyoming
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47
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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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48
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Sanchez-Bermejo E, Zhu W, Tasset C, Eimer H, Sureshkumar S, Singh R, Sundaramoorthi V, Colling L, Balasubramanian S. Genetic Architecture of Natural Variation in Thermal Responses of Arabidopsis. PLANT PHYSIOLOGY 2015; 169. [PMID: 26195568 PMCID: PMC4577429 DOI: 10.1104/pp.15.00942] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Wild strains of Arabidopsis (Arabidopsis thaliana) exhibit extensive natural variation in a wide variety of traits, including response to environmental changes. Ambient temperature is one of the major external factors that modulates plant growth and development. Here, we analyze the genetic architecture of natural variation in thermal responses of Arabidopsis. Exploiting wild accessions and recombinant inbred lines, we reveal extensive phenotypic variation in response to ambient temperature in distinct developmental traits such as hypocotyl elongation, root elongation, and flowering time. We show that variation in thermal response differs between traits, suggesting that the individual phenotypes do not capture all the variation associated with thermal response. Genome-wide association studies and quantitative trait locus analyses reveal that multiple rare alleles contribute to the genetic architecture of variation in thermal response. We identify at least 20 genomic regions that are associated with variation in thermal response. Further characterizations of temperature sensitivity quantitative trait loci that are shared between traits reveal a role for the blue-light receptor CRYPTOCHROME2 (CRY2) in thermosensory growth responses. We show the accession Cape Verde Islands is less sensitive to changes in ambient temperature, and through transgenic analysis, we demonstrate that allelic variation at CRY2 underlies this temperature insensitivity across several traits. Transgenic analyses suggest that the allelic effects of CRY2 on thermal response are dependent on genetic background suggestive of the presence of modifiers. In addition, our results indicate that complex light and temperature interactions, in a background-dependent manner, govern growth responses in Arabidopsis.
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Affiliation(s)
| | - Wangsheng Zhu
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Celine Tasset
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Hannes Eimer
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Sridevi Sureshkumar
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Rupali Singh
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | | | - Luana Colling
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
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49
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Gehan MA, Greenham K, Mockler TC, McClung CR. Transcriptional networks-crops, clocks, and abiotic stress. CURRENT OPINION IN PLANT BIOLOGY 2015; 24:39-46. [PMID: 25646668 DOI: 10.1016/j.pbi.2015.01.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 01/07/2015] [Accepted: 01/08/2015] [Indexed: 05/20/2023]
Abstract
Several factors affect the yield potential and geographical range of crops including the circadian clock, water availability, and seasonal temperature changes. In order to sustain and increase plant productivity on marginal land in the face of both biotic and abiotic stresses, we need to more efficiently generate stress-resistant crops through marker-assisted breeding, genetic modification, and new genome-editing technologies. To leverage these strategies for producing the next generation of crops, future transcriptomic data acquisition should be pursued with an appropriate temporal design and analyzed with a network-centric approach. The following review focuses on recent developments in abiotic stress transcriptional networks in economically important crops and will highlight the utility of correlation-based network analysis and applications.
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Affiliation(s)
- Malia A Gehan
- Donald Danforth Plant Science Center, St. Louis, MO 63132, United States
| | - Kathleen Greenham
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, United States
| | - Todd C Mockler
- Donald Danforth Plant Science Center, St. Louis, MO 63132, United States
| | - C Robertson McClung
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, United States.
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50
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Allelic polymorphism of GIGANTEA is responsible for naturally occurring variation in circadian period in Brassica rapa. Proc Natl Acad Sci U S A 2015; 112:3829-34. [PMID: 25775524 DOI: 10.1073/pnas.1421803112] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
GIGANTEA (GI) was originally identified by a late-flowering mutant in Arabidopsis, but subsequently has been shown to act in circadian period determination, light inhibition of hypocotyl elongation, and responses to multiple abiotic stresses, including tolerance to high salt and cold (freezing) temperature. Genetic mapping and analysis of families of heterogeneous inbred lines showed that natural variation in GI is responsible for a major quantitative trait locus in circadian period in Brassica rapa. We confirmed this conclusion by transgenic rescue of an Arabidopsis gi-201 loss of function mutant. The two B. rapa GI alleles each fully rescued the delayed flowering of Arabidopsis gi-201 but showed differential rescue of perturbations in red light inhibition of hypocotyl elongation and altered cold and salt tolerance. The B. rapa R500 GI allele, which failed to rescue the hypocotyl and abiotic stress phenotypes, disrupted circadian period determination in Arabidopsis. Analysis of chimeric B. rapa GI alleles identified the causal nucleotide polymorphism, which results in an amino acid substitution (S264A) between the two GI proteins. This polymorphism underlies variation in circadian period, cold and salt tolerance, and red light inhibition of hypocotyl elongation. Loss-of-function mutations of B. rapa GI confer delayed flowering, perturbed circadian rhythms in leaf movement, and increased freezing and increased salt tolerance, consistent with effects of similar mutations in Arabidopsis. Collectively, these data suggest that allelic variation of GI-and possibly of clock genes in general-offers an attractive target for molecular breeding for enhanced stress tolerance and potentially for improved crop yield.
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