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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: 1] [Impact Index Per Article: 0.5] [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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2
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Jurca M, Sjölander J, Ibáñez C, Matrosova A, Johansson M, Kozarewa I, Takata N, Bakó L, Webb AAR, Israelsson-Nordström M, Eriksson ME. ZEITLUPE Promotes ABA-Induced Stomatal Closure in Arabidopsis and Populus. FRONTIERS IN PLANT SCIENCE 2022; 13:829121. [PMID: 35310670 PMCID: PMC8924544 DOI: 10.3389/fpls.2022.829121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 01/26/2022] [Indexed: 05/22/2023]
Abstract
Plants balance water availability with gas exchange and photosynthesis by controlling stomatal aperture. This control is regulated in part by the circadian clock, but it remains unclear how signalling pathways of daily rhythms are integrated into stress responses. The serine/threonine protein kinase OPEN STOMATA 1 (OST1) contributes to the regulation of stomatal closure via activation of S-type anion channels. OST1 also mediates gene regulation in response to ABA/drought stress. We show that ZEITLUPE (ZTL), a blue light photoreceptor and clock component, also regulates ABA-induced stomatal closure in Arabidopsis thaliana, establishing a link between clock and ABA-signalling pathways. ZTL sustains expression of OST1 and ABA-signalling genes. Stomatal closure in response to ABA is reduced in ztl mutants, which maintain wider stomatal apertures and show higher rates of gas exchange and water loss than wild-type plants. Detached rosette leaf assays revealed a stronger water loss phenotype in ztl-3, ost1-3 double mutants, indicating that ZTL and OST1 contributed synergistically to the control of stomatal aperture. Experimental studies of Populus sp., revealed that ZTL regulated the circadian clock and stomata, indicating ZTL function was similar in these trees and Arabidopsis. PSEUDO-RESPONSE REGULATOR 5 (PRR5), a known target of ZTL, affects ABA-induced responses, including stomatal regulation. Like ZTL, PRR5 interacted physically with OST1 and contributed to the integration of ABA responses with circadian clock signalling. This suggests a novel mechanism whereby the PRR proteins-which are expressed from dawn to dusk-interact with OST1 to mediate ABA-dependent plant responses to reduce water loss in time of stress.
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Affiliation(s)
- Manuela Jurca
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Johan Sjölander
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Cristian Ibáñez
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
- Departamento de Biología Universidad de La Serena, La Serena, Chile
| | - Anastasia Matrosova
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Mikael Johansson
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
- RNA Biology and Molecular Physiology, Faculty for Biology, Bielefeld University, Bielefeld, Germany
| | - Iwanka Kozarewa
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Naoki Takata
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
- Forest Bio-Research Center, Forestry and Forest Products Research Institute, Hitachi, Japan
| | - Laszlo Bakó
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Alex A. R. Webb
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Maria Israelsson-Nordström
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Maria E. Eriksson
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
- *Correspondence: Maria E. Eriksson,
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3
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Ruocco M, Barrote I, Hofman JD, Pes K, Costa MM, Procaccini G, Silva J, Dattolo E. Daily Regulation of Key Metabolic Pathways in Two Seagrasses Under Natural Light Conditions. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.757187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The circadian clock is an endogenous time-keeping mechanism that enables organisms to adapt to external environmental cycles. It produces rhythms of plant metabolism and physiology, and interacts with signaling pathways controlling daily and seasonal environmental responses through gene expression regulation. Downstream metabolic outputs, such as photosynthesis and sugar metabolism, besides being affected by the clock, can also contribute to the circadian timing itself. In marine plants, studies of circadian rhythms are still way behind in respect to terrestrial species, which strongly limits the understanding of how they coordinate their physiology and energetic metabolism with environmental signals at sea. Here, we provided a first description of daily timing of key core clock components and clock output pathways in two seagrass species, Cymodocea nodosa and Zostera marina (order Alismatales), co-occurring at the same geographic location, thus exposed to identical natural variations in photoperiod. Large differences were observed between species in the daily timing of accumulation of transcripts related to key metabolic pathways, such as photosynthesis and sucrose synthesis/transport, highlighting the importance of intrinsic biological, and likely ecological attributes of the species in determining the periodicity of functions. The two species exhibited a differential sensitivity to light-to-dark and dark-to-light transition times and could adopt different growth timing based on a differential strategy of resource allocation and mobilization throughout the day, possibly coordinated by the circadian clock. This behavior could potentially derive from divergent evolutionary adaptations of the species to their bio-geographical range of distributions.
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4
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Djerrab D, Bertrand B, Breitler JC, Léran S, Dechamp E, Campa C, Barrachina C, Conejero G, Etienne H, Sulpice R. Photoperiod-dependent transcriptional modifications in key metabolic pathways in Coffea arabica. TREE PHYSIOLOGY 2021; 41:302-316. [PMID: 33080620 PMCID: PMC7874067 DOI: 10.1093/treephys/tpaa130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 07/20/2020] [Accepted: 09/30/2020] [Indexed: 06/11/2023]
Abstract
Photoperiod length induces in temperate plants major changes in growth rates, morphology and metabolism with, for example, modifications in the partitioning of photosynthates to avoid starvation at the end of long nights. However, this has never been studied for a tropical perennial species adapted to grow in a natural photoperiod close to 12 h/12 h all year long. We grew Coffea arabica L., an understorey perennial evergreen tropical species in its natural 12 h/12 h and in a short 8 h/16 h photoperiod, and we investigated its responses at the physiological, metabolic and transcriptomic levels. The expression pattern of rhythmic genes, including core clock genes, was affected by changes in photoperiod. Overall, we identified 2859 rhythmic genes, of which 89% were also rhythmic in Arabidopsis thaliana L. Under short-days, plant growth was reduced, and leaves were thinner with lower chlorophyll content. In addition, secondary metabolism was also affected with chlorogenic acid and epicatechin levels decreasing, and in agreement, the genes involved in lignin synthesis were overexpressed and those involved in the flavanol pathway were underexpressed. Our results show that the 8 h/16 h photoperiod induces drastic changes in morphology, metabolites and gene expression, and the responses for gene expression are similar to those observed in the temperate annual A. thaliana species. Short photoperiod induces drastic changes in gene expression, metabolites and leaf structure, some of these responses being similar to those observed in A. thaliana.
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Affiliation(s)
- Doâa Djerrab
- Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), UMR IPME, F-34398 Montpellier, France
- UMR IPME, Université de Montpellier, CIRAD, IRD, F-34398 Montpellier, France
| | | | - Jean-Christophe Breitler
- Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), UMR IPME, F-34398 Montpellier, France
- UMR IPME, Université de Montpellier, CIRAD, IRD, F-34398 Montpellier, France
| | - Sophie Léran
- Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), UMR IPME, F-34398 Montpellier, France
- UMR IPME, Université de Montpellier, CIRAD, IRD, F-34398 Montpellier, France
| | - Eveline Dechamp
- Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), UMR IPME, F-34398 Montpellier, France
- UMR IPME, Université de Montpellier, CIRAD, IRD, F-34398 Montpellier, France
| | - Claudine Campa
- UMR IPME, Université de Montpellier, CIRAD, IRD, F-34398 Montpellier, France
- IRD, UMR IPME, F-34394 Montpellier, France
| | - Célia Barrachina
- MGX, Biocampus Montpellier, CNRS, INSERM, University of Montpellier, 34000 Montpellier, France
| | - Geneviève Conejero
- BPMP, University of Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier, France
| | - Hervé Etienne
- Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), UMR IPME, F-34398 Montpellier, France
- UMR IPME, Université de Montpellier, CIRAD, IRD, F-34398 Montpellier, France
| | - Ronan Sulpice
- National University of Ireland, Plant Systems Biology Lab, Ryan Institute, School of Natural Sciences, University Road, Galway H91 TK33, Ireland
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5
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Michael TP, Ernst E, Hartwick N, Chu P, Bryant D, Gilbert S, Ortleb S, Baggs EL, Sree KS, Appenroth KJ, Fuchs J, Jupe F, Sandoval JP, Krasileva KV, Borisjuk L, Mockler TC, Ecker JR, Martienssen RA, Lam E. Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control. Genome Res 2021; 31:225-238. [PMID: 33361111 PMCID: PMC7849404 DOI: 10.1101/gr.266429.120] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 12/16/2020] [Indexed: 11/24/2022]
Abstract
Rootless plants in the genus Wolffia are some of the fastest growing known plants on Earth. Wolffia have a reduced body plan, primarily multiplying through a budding type of asexual reproduction. Here, we generated draft reference genomes for Wolffia australiana (Benth.) Hartog & Plas, which has the smallest genome size in the genus at 357 Mb and has a reduced set of predicted protein-coding genes at about 15,000. Comparison between multiple high-quality draft genome sequences from W. australiana clones confirmed loss of several hundred genes that are highly conserved among flowering plants, including genes involved in root developmental and light signaling pathways. Wolffia has also lost most of the conserved nucleotide-binding leucine-rich repeat (NLR) genes that are known to be involved in innate immunity, as well as those involved in terpene biosynthesis, while having a significant overrepresentation of genes in the sphingolipid pathways that may signify an alternative defense system. Diurnal expression analysis revealed that only 13% of Wolffia genes are expressed in a time-of-day (TOD) fashion, which is less than the typical ∼40% found in several model plants under the same condition. In contrast to the model plants Arabidopsis and rice, many of the pathways associated with multicellular and developmental processes are not under TOD control in W. australiana, where genes that cycle the conditions tested predominantly have carbon processing and chloroplast-related functions. The Wolffia genome and TOD expression data set thus provide insight into the interplay between a streamlined plant body plan and optimized growth.
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Affiliation(s)
- Todd P Michael
- Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Evan Ernst
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Nolan Hartwick
- Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Philomena Chu
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, USA
| | - Douglas Bryant
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | - Sarah Gilbert
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, USA
| | - Stefan Ortleb
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben 06466, Germany
| | - Erin L Baggs
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California 94720, USA
| | - K Sowjanya Sree
- Department of Environmental Science, Central University of Kerala, Periye, Kerala 671316, India
| | | | - Joerg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben 06466, Germany
| | - Florian Jupe
- Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Justin P Sandoval
- Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Ksenia V Krasileva
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California 94720, USA
| | - Ljudmylla Borisjuk
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben 06466, Germany
| | - Todd C Mockler
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | - Joseph R Ecker
- Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Robert A Martienssen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Eric Lam
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, USA
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6
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de Leone MJ, Hernando CE, Mora-García S, Yanovsky MJ. It's a matter of time: the role of transcriptional regulation in the circadian clock-pathogen crosstalk in plants. Transcription 2020; 11:100-116. [PMID: 32936724 DOI: 10.1080/21541264.2020.1820300] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Most living organisms possess an internal timekeeping mechanism known as the circadian clock, which enhances fitness by synchronizing the internal timing of biological processes with diurnal and seasonal environmental changes. In plants, the pace of these biological rhythms relies on oscillations in the expression level of hundreds of genes tightly controlled by a group of core clock regulators and co-regulators that engage in transcriptional and translational feedback loops. In the last decade, the role of several core clock genes in the control of defense responses has been addressed, and a growing amount of evidence demonstrates that circadian regulation is relevant for plant immunity. A reciprocal connection between these pathways was also established following the observation that in Arabidopsis thaliana, as well as in crop species like tomato, plant-pathogen interactions trigger a reconfiguration of the circadian transcriptional network. In this review, we summarize the current knowledge regarding the interaction between the circadian clock and biotic stress responses at the transcriptional level, and discuss the relevance of this crosstalk in the plant-pathogen evolutionary arms race. A better understanding of these processes could aid in the development of genetic tools that improve traditional breeding practices, enhancing tolerance to plant diseases that threaten crop yield and food security all around the world.
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Affiliation(s)
- María José de Leone
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Buenos Aires, Argentina
| | - C Esteban Hernando
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Buenos Aires, Argentina
| | - Santiago Mora-García
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Buenos Aires, Argentina
| | - Marcelo J Yanovsky
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Buenos Aires, Argentina
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7
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MacKinnon KJM, Cole BJ, Yu C, Coomey JH, Hartwick NT, Remigereau MS, Duffy T, Michael TP, Kay SA, Hazen SP. Changes in ambient temperature are the prevailing cue in determining Brachypodium distachyon diurnal gene regulation. THE NEW PHYTOLOGIST 2020; 227:1709-1724. [PMID: 32112414 DOI: 10.1111/nph.16507] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 02/12/2020] [Indexed: 06/10/2023]
Abstract
Plants are continuously exposed to diurnal fluctuations in light and temperature, and spontaneous changes in their physical or biotic environment. The circadian clock coordinates regulation of gene expression with a 24 h period, enabling the anticipation of these events. We used RNA sequencing to characterize the Brachypodium distachyon transcriptome under light and temperature cycles, as well as under constant conditions. Approximately 3% of the transcriptome was regulated by the circadian clock, a smaller proportion than reported in most other species. For most transcripts that were rhythmic under all conditions, including many known clock genes, the period of gene expression lengthened from 24 to 27 h in the absence of external cues. To functionally characterize the cyclic transcriptome in B. distachyon, we used Gene Ontology enrichment analysis, and found several terms significantly associated with peak expression at particular times of the day. Furthermore, we identified sequence motifs enriched in the promoters of similarly phased genes, some potentially associated with transcription factors. When considering the overlap in rhythmic gene expression and specific pathway behavior, thermocycles was the prevailing cue that controlled diurnal gene regulation. Taken together, our characterization of the rhythmic B. distachyon transcriptome represents a foundational resource with implications in other grass species.
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Affiliation(s)
- Kirk J-M MacKinnon
- Biology Department, University of Massachusetts, Amherst, MA, 01003, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA, 01003, USA
| | - Benjamin J Cole
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Chang Yu
- Biology Department, University of Massachusetts, Amherst, MA, 01003, USA
| | - Joshua H Coomey
- Biology Department, University of Massachusetts, Amherst, MA, 01003, USA
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA, 01003, USA
| | | | - Marie-Stanislas Remigereau
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Tomás Duffy
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | | | - Steve A Kay
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Samuel P Hazen
- Biology Department, University of Massachusetts, Amherst, MA, 01003, USA
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8
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Lai X, Bendix C, Yan L, Zhang Y, Schnable JC, Harmon FG. Interspecific analysis of diurnal gene regulation in panicoid grasses identifies known and novel regulatory motifs. BMC Genomics 2020; 21:428. [PMID: 32586356 PMCID: PMC7315539 DOI: 10.1186/s12864-020-06824-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/12/2020] [Indexed: 11/17/2022] Open
Abstract
Background The circadian clock drives endogenous 24-h rhythms that allow organisms to adapt and prepare for predictable and repeated changes in their environment throughout the day-night (diurnal) cycle. Many components of the circadian clock in Arabidopsis thaliana have been functionally characterized, but comparatively little is known about circadian clocks in grass species including major crops like maize and sorghum. Results Comparative research based on protein homology and diurnal gene expression patterns suggests the function of some predicted clock components in grasses is conserved with their Arabidopsis counterparts, while others have diverged in function. Our analysis of diurnal gene expression in three panicoid grasses sorghum, maize, and foxtail millet revealed conserved and divergent evolution of expression for core circadian clock genes and for the overall transcriptome. We find that several classes of core circadian clock genes in these grasses differ in copy number compared to Arabidopsis, but mostly exhibit conservation of both protein sequence and diurnal expression pattern with the notable exception of maize paralogous genes. We predict conserved cis-regulatory motifs shared between maize, sorghum, and foxtail millet through identification of diurnal co-expression clusters for a subset of 27,196 orthologous syntenic genes. In this analysis, a Cochran–Mantel–Haenszel based method to control for background variation identified significant enrichment for both expected and novel 6–8 nucleotide motifs in the promoter regions of genes with shared diurnal regulation predicted to function in common physiological activities. Conclusions This study illustrates the divergence and conservation of circadian clocks and diurnal regulatory networks across syntenic orthologous genes in panacoid grass species. Further, conserved local regulatory sequences contribute to the architecture of these diurnal regulatory networks that produce conserved patterns of diurnal gene expression.
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Affiliation(s)
- Xianjun Lai
- Center for Plant Science Innovation & Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, 68588, USA.,College of Agricultural Sciences, Xichang University, Liangshan, Xichang, 615000, China
| | - Claire Bendix
- Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA.,Plant Gene Expression Center, USDA-ARS, Albany, CA, 94710, USA
| | - Lang Yan
- Center for Plant Science Innovation & Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, 68588, USA.,College of Agricultural Sciences, Xichang University, Liangshan, Xichang, 615000, China
| | - Yang Zhang
- Center for Plant Science Innovation & Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, 68588, USA
| | - James C Schnable
- Center for Plant Science Innovation & Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, 68588, USA.
| | - Frank G Harmon
- Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA. .,Plant Gene Expression Center, USDA-ARS, Albany, CA, 94710, USA.
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9
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Wang X, Cui W, Hu W, Feng C. Abscisic acid-enhanced starch accumulation of bioenergy crop duckweed ( Spirodela polyrrhiza). RSC Adv 2020; 10:10394-10401. [PMID: 35492951 PMCID: PMC9050358 DOI: 10.1039/d0ra00269k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 02/24/2020] [Indexed: 12/03/2022] Open
Abstract
To meet the increasing energy consumption around the world and fight global climate change, there is an urgent need to explore renewable energy crops to replace the traditional energy sources. Duckweed (Spirodela polyrrhiza) is widely distributed in the world and has high starch and low lignin contents, which is perhaps an ideal feedstock for bioenergy production. To investigate the effects of abscisic acid (ABA) on duckweed biomass and starch accumulation, Spirodela polyrrhiza was cultivated at different ABA concentrations. The results showed that the highest starch content in duckweed (21.8% dry weight) was achieved in 1.0 × 10-2 mg L-1 ABA medium, 70.3% higher than that of the control medium without ABA. The number of starch granules in 1.0 × 10-2 mg L-1 ABA medium was far more than that in the control medium. The highest adenosine diphosphate (ADP)-glucose pyrophosphorylase (AGPase) activity was observed in the 1.0 × 10-2 mg L-1 ABA medium, which was caused by the up-regulation expression of ADP-glucose pyrophosphorylase 2 (APL2). Further investigations on cell ultra-structures and stomatal property of the duckweed indicated that ABA increased the number and size of starch granules and stomatal size in duckweed cells. These enhancements lead to a greatly improved energy flow in the aquatic plant from photosynthesis to carbon storage, making duckweed a potential renewable bioenergy crop.
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Affiliation(s)
- Xuezhi Wang
- School of Water Resources and Environment, China University of Geosciences (Beijing) Beijing 100083 China +86 10 82321081 +86 10 82322281
| | - Weihua Cui
- School of Water Resources and Environment, China University of Geosciences (Beijing) Beijing 100083 China +86 10 82321081 +86 10 82322281
- State Key Laboratory of Biogeology and Geology, China University of Geosciences (Beijing) Beijing 100083 China
| | - Weiwu Hu
- School of Water Resources and Environment, China University of Geosciences (Beijing) Beijing 100083 China +86 10 82321081 +86 10 82322281
- The Journal Center, China University of Geosciences (Beijing) Beijing 100083 China
| | - Chuanping Feng
- School of Water Resources and Environment, China University of Geosciences (Beijing) Beijing 100083 China +86 10 82321081 +86 10 82322281
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10
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Valim HF, McGale E, Yon F, Halitschke R, Fragoso V, Schuman MC, Baldwin IT. The Clock Gene TOC1 in Shoots, Not Roots, Determines Fitness of Nicotiana attenuata under Drought. PLANT PHYSIOLOGY 2019; 181:305-318. [PMID: 31182558 PMCID: PMC6716261 DOI: 10.1104/pp.19.00286] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 05/20/2019] [Indexed: 05/05/2023]
Abstract
The highly conserved core circadian clock component TIMING OF CAB EXPRESSION1 (TOC1) contextualizes environmental stress responses in plants, for example by gating abscisic acid signaling and suppressing thermoresponsive growth. Selective interaction of TOC1 with PHYTOCHROME B under far-red-enriched light suggests a connection between circadian gating of light responses and sensitivity to ABA, an important regulator of growth and stress responses, including under drought. However, the fitness consequences of TOC1 function, particularly in the root, are poorly understood. Here, we used the desert annual, Nicotiana attenuata, to investigate the function of TOC1 in shoots and roots for maintaining fitness under drought, in both field and glasshouse experiments. Despite marked decreases in leaf water loss, TOC1-deficient lines failed to maintain fitness in response to drought stress as measured by total seed capsule production. Restoring TOC1 transcript levels in shoots via micrografting was sufficient to restore wild-type drought responses under field conditions. Microarrays identified a coexpression module in leaves strongly linking red and far-red light signaling to drought responses in a TOC1-dependent manner, but experiments with phytochrome-deficient lines revealed that the effects of TOC1 deficiency under drought cannot be attributed to changes in red/far-red light perception alone. Taken together, these results elucidate the sophisticated, tissue-dependent role of the circadian clock in maintaining fitness in the face of long-term abiotic stresses such as drought.
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Affiliation(s)
- Henrique F Valim
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Erica McGale
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Felipe Yon
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
- Centro de Investigación Científico Ecológico Académico, Lima 37, Peru
| | - Rayko Halitschke
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Variluska Fragoso
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
- Research Support Center in Molecular Diversity of Natural Products, Institute of Chemistry, University of São Paulo, São Paulo, SP 05508-000, Brazil
| | - Meredith C Schuman
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
- German Centre for Integrative Biodiversity Research, 04103 Leipzig, Germany
- Department of Geography, University of Zurich, 8057 Zurich, Switzerland
| | - Ian T Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
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Wai CM, Weise SE, Ozersky P, Mockler TC, Michael TP, VanBuren R. Time of day and network reprogramming during drought induced CAM photosynthesis in Sedum album. PLoS Genet 2019; 15:e1008209. [PMID: 31199791 PMCID: PMC6594660 DOI: 10.1371/journal.pgen.1008209] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 06/26/2019] [Accepted: 05/24/2019] [Indexed: 12/22/2022] Open
Abstract
Plants with facultative crassulacean acid metabolism (CAM) maximize performance through utilizing C3 or C4 photosynthesis under ideal conditions while temporally switching to CAM under water stress (drought). While genome-scale analyses of constitutive CAM plants suggest that time of day networks are shifted, or phased to the evening compared to C3, little is known for how the shift from C3 to CAM networks is modulated in drought induced CAM. Here we generate a draft genome for the drought-induced CAM-cycling species Sedum album. Through parallel sampling in well-watered (C3) and drought (CAM) conditions, we uncover a massive rewiring of time of day expression and a CAM and stress-specific network. The core circadian genes are expanded in S. album and under CAM induction, core clock genes either change phase or amplitude. While the core clock cis-elements are conserved in S. album, we uncover a set of novel CAM and stress specific cis-elements consistent with our finding of rewired co-expression networks. We identified shared elements between constitutive CAM and CAM-cycling species and expression patterns unique to CAM-cycling S. album. Together these results demonstrate that drought induced CAM-cycling photosynthesis evolved through the mobilization of a stress-specific, time of day network, and not solely the phasing of existing C3 networks. These results will inform efforts to engineer water use efficiency into crop plants for growth on marginal land.
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Affiliation(s)
- Ching Man Wai
- Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
| | - Sean E. Weise
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Philip Ozersky
- Donald Danforth Plant Science Center, St. Louis MO, United States of America
| | - Todd C. Mockler
- Donald Danforth Plant Science Center, St. Louis MO, United States of America
| | - Todd P. Michael
- J. Craig Venter Institute, La Jolla, CA, United States of America
| | - Robert VanBuren
- Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
- Plant Resilience Institute, Michigan State University, East Lansing, MI, United States of America
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12
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de Leone MJ, Hernando CE, Romanowski A, García-Hourquet M, Careno D, Casal J, Rugnone M, Mora-García S, Yanovsky MJ. The LNK Gene Family: At the Crossroad between Light Signaling and the Circadian Clock. Genes (Basel) 2018; 10:genes10010002. [PMID: 30577529 PMCID: PMC6356500 DOI: 10.3390/genes10010002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 12/13/2018] [Accepted: 12/17/2018] [Indexed: 12/30/2022] Open
Abstract
Light signaling pathways interact with the circadian clock to help organisms synchronize physiological and developmental processes to periodic environmental cycles. The plant photoreceptors responsible for clock resetting have been characterized, but signaling components that link the photoreceptors to the clock remain to be identified. Members of the family of NIGHT LIGHT–INDUCIBLE AND CLOCK-REGULATED (LNK) genes play key roles linking light regulation of gene expression to the control of daily and seasonal rhythms in Arabidopsis thaliana. Particularly, LNK1 and LNK2 were shown to control circadian rhythms, photomorphogenic responses, and photoperiod-dependent flowering time. Here we analyze the role of the four members of the LNK family in Arabidopsis in these processes. We found that depletion of the closely related LNK3 and LNK4 in a lnk1;lnk2 mutant background affects circadian rhythms, but not other clock-regulated processes such as flowering time and seedling photomorphogenesis. Nevertheless, plants defective in all LNK genes (lnkQ quadruple mutants) display developmental alterations that lead to increased rosette size, biomass, and enhanced phototropic responses. Our work indicates that members of the LNK family have both distinctive and partially overlapping functions, and are an essential link to orchestrate light-regulated developmental processes.
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Affiliation(s)
- María José de Leone
- Leloir Institute, Biochemical Research Institute of Buenos Aires (IIBBA)⁻ National Scientific and Technical Research Council (CONICET), Av. Patricias Argentinas 435, Ciudad de Buenos Aires C1405BWE, Argentina.
| | - Carlos Esteban Hernando
- Leloir Institute, Biochemical Research Institute of Buenos Aires (IIBBA)⁻ National Scientific and Technical Research Council (CONICET), Av. Patricias Argentinas 435, Ciudad de Buenos Aires C1405BWE, Argentina.
| | - Andrés Romanowski
- Leloir Institute, Biochemical Research Institute of Buenos Aires (IIBBA)⁻ National Scientific and Technical Research Council (CONICET), Av. Patricias Argentinas 435, Ciudad de Buenos Aires C1405BWE, Argentina.
| | - Mariano García-Hourquet
- Leloir Institute, Biochemical Research Institute of Buenos Aires (IIBBA)⁻ National Scientific and Technical Research Council (CONICET), Av. Patricias Argentinas 435, Ciudad de Buenos Aires C1405BWE, Argentina.
| | - Daniel Careno
- Leloir Institute, Biochemical Research Institute of Buenos Aires (IIBBA)⁻ National Scientific and Technical Research Council (CONICET), Av. Patricias Argentinas 435, Ciudad de Buenos Aires C1405BWE, Argentina.
| | - Joaquín Casal
- Leloir Institute, Biochemical Research Institute of Buenos Aires (IIBBA)⁻ National Scientific and Technical Research Council (CONICET), Av. Patricias Argentinas 435, Ciudad de Buenos Aires C1405BWE, Argentina.
| | - Matías Rugnone
- The Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
| | - Santiago Mora-García
- Leloir Institute, Biochemical Research Institute of Buenos Aires (IIBBA)⁻ National Scientific and Technical Research Council (CONICET), Av. Patricias Argentinas 435, Ciudad de Buenos Aires C1405BWE, Argentina.
| | - Marcelo Javier Yanovsky
- Leloir Institute, Biochemical Research Institute of Buenos Aires (IIBBA)⁻ National Scientific and Technical Research Council (CONICET), Av. Patricias Argentinas 435, Ciudad de Buenos Aires C1405BWE, Argentina.
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13
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Liu TL, Newton L, Liu MJ, Shiu SH, Farré EM. A G-Box-Like Motif Is Necessary for Transcriptional Regulation by Circadian Pseudo-Response Regulators in Arabidopsis. PLANT PHYSIOLOGY 2016; 170:528-39. [PMID: 26586835 PMCID: PMC4704597 DOI: 10.1104/pp.15.01562] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 11/17/2015] [Indexed: 05/18/2023]
Abstract
PSEUDO-RESPONSE REGULATORs (PRRs) play overlapping and distinct roles in maintaining circadian rhythms and regulating diverse biological processes, including the photoperiodic control of flowering, growth, and abiotic stress responses. PRRs act as transcriptional repressors and associate with chromatin via their conserved C-terminal CCT (CONSTANS, CONSTANS-like, and TIMING OF CAB EXPRESSION 1 [TOC1/PRR1]) domains by a still-poorly understood mechanism. Here, we identified genome-wide targets of PRR9 using chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) and compared them with PRR7, PRR5, and TOC1/PRR1 ChIP-seq data. We found that PRR binding sites are located within genomic regions of low nucleosome occupancy and high DNase I hypersensitivity. Moreover, conserved noncoding regions among Brassicaceae species are enriched around PRR binding sites, indicating that PRRs associate with functionally relevant cis-regulatory regions. The PRRs shared a significant number of binding regions, and our results indicate that they coordinately restrict the expression of target genes to around dawn. A G-box-like motif was overrepresented at PRR binding regions, and we showed that this motif is necessary for mediating transcriptional regulation of CIRCADIAN CLOCK ASSOCIATED 1 and PRR9 by the PRRs. Our results further our understanding of how PRRs target specific promoters and provide an extensive resource for studying circadian regulatory networks in plants.
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Affiliation(s)
- Tiffany L Liu
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Linsey Newton
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Ming-Jung Liu
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Shin-Han Shiu
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Eva M Farré
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
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14
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15
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Bendix C, Marshall CM, Harmon FG. Circadian Clock Genes Universally Control Key Agricultural Traits. MOLECULAR PLANT 2015; 8:1135-52. [PMID: 25772379 DOI: 10.1016/j.molp.2015.03.003] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 02/26/2015] [Accepted: 03/04/2015] [Indexed: 05/17/2023]
Abstract
Circadian clocks are endogenous timers that enable plants to synchronize biological processes with daily and seasonal environmental conditions in order to allocate resources during the most beneficial times of day and year. The circadian clock regulates a number of central plant activities, including growth, development, and reproduction, primarily through controlling a substantial proportion of transcriptional activity and protein function. This review examines the roles that alleles of circadian clock genes have played in domestication and improvement of crop plants. The focus here is on three groups of circadian clock genes essential to clock function in Arabidopsis thaliana: PSEUDO-RESPONSE REGULATORs, GIGANTEA, and the evening complex genes early flowering 3, early flowering 4, and lux arrhythmo. homologous genes from each group underlie quantitative trait loci that have beneficial influences on key agricultural traits, especially flowering time but also yield, biomass, and biennial growth habit. Emerging insights into circadian clock regulation of other fundamental plant processes, including responses to abiotic and biotic stresses, are discussed to highlight promising avenues for further crop improvement.
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Affiliation(s)
- Claire Bendix
- Plant Gene Expression Center, USDA-ARS, Albany, CA 94710, USA; Department of Plant & Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Carine M Marshall
- Plant Gene Expression Center, USDA-ARS, Albany, CA 94710, USA; Department of Plant & Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Frank G Harmon
- Plant Gene Expression Center, USDA-ARS, Albany, CA 94710, USA; Department of Plant & Microbial Biology, University of California, Berkeley, CA 94720, USA.
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16
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Johansson M, Ibáñez C, Takata N, Eriksson ME. The perennial clock is an essential timer for seasonal growth events and cold hardiness. Methods Mol Biol 2014; 1158:297-311. [PMID: 24792060 DOI: 10.1007/978-1-4939-0700-7_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Over the last several decades, changes in global temperatures have led to changes in local environments affecting the growth conditions for many species. This is a trend that makes it even more important to understand how plants respond to local variations and seasonal changes in climate. To detect daily and seasonal changes as well as acute stress factors such as cold and drought, plants rely on a circadian clock. This chapter introduces the current knowledge and literature about the setup and function of the circadian clock in various tree and perennial species, with a focus on the Populus genus.
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Affiliation(s)
- Mikael Johansson
- Molecular Cell Physiology, Bielefeld University, 100131, 33615, Bielefeld, Germany,
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17
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Zhang T, Zhao X, Wang W, Huang L, Liu X, Zong Y, Zhu L, Yang D, Fu B, Li Z. Deep transcriptome sequencing of rhizome and aerial-shoot in Sorghum propinquum. PLANT MOLECULAR BIOLOGY 2014; 84:315-27. [PMID: 24104862 DOI: 10.1007/s11103-013-0135-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 09/23/2013] [Indexed: 05/25/2023]
Abstract
Transcriptomic data for Sorghum propinquum, the wild-type sorghum, are limited in public databases. S. propinquum has a subterranean rhizome and transcriptome data will help in understanding the molecular mechanisms underlying rhizome formation. We sequenced the transcriptome of S. propinquum aerial-shoot and rhizome using an Illumina platform. More than 70 % of the genes in the S. propinquum genome were expressed in aerial-shoot and rhizome. The expression patterns of 1963 and 599 genes, including transcription factors, were specific or enriched in aerial-shoot and rhizome respectively, indicating their possible roles in physiological processes in these tissues. Comparative analysis revealed several cis-elements, ACGT box, GCCAC, GATC and TGACG box, which showed significantly higher abundance in aerial-shoot-specific genes. In rhizome-specific genes MYB and ROOTMOTIFTAPOX1 motifs, and 10 promoter and cytokinin-responsive elements were highly enriched. Of the S. propinquum genes, 27.9 % were identified as alternatively spliced and about 60 % of the alternative splicing (AS) events were tissue-specific, suggesting that AS played a crucial role in determining tissue-specific cellular function. The transcriptome data, especially the co-localized rhizome-enriched expressed transcripts that mapped to the publicly available rhizome-related quantitative trait loci, will contribute to gene discovery in S. propinquum and to functional studies of the sorghum genome. Deep transcriptome sequencing revealed a clear difference in the expression patterns of genes between aerial-shoot and rhizome in S. propinquum. This data set provides essential information for future studies into the molecular genetic mechanisms involved in rhizome formation.
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Affiliation(s)
- Ting Zhang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun St., Beijing, 100081, China
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18
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Farré EM, Liu T. The PRR family of transcriptional regulators reflects the complexity and evolution of plant circadian clocks. CURRENT OPINION IN PLANT BIOLOGY 2013; 16:621-9. [PMID: 23856081 DOI: 10.1016/j.pbi.2013.06.015] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 06/20/2013] [Accepted: 06/21/2013] [Indexed: 05/20/2023]
Abstract
Circadian clocks are internal time-keeping mechanisms that provide an adaptive advantage by enabling organisms to anticipate daily changes and orchestrate biological processes accordingly. Circadian regulated pseudo-response regulators are key components of transcription/translation circadian networks in green alga and plants. Recent studies in Arabidopsis thaliana have shown that most of them act as transcriptional repressors and directly regulate output pathways suggesting a close relationship between the central oscillator and circadian regulated processes. Moreover, phylogenetic studies on this small gene family have shed light on the evolution of circadian clocks in the green lineage.
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Affiliation(s)
- Eva M Farré
- Michigan State University, Department of Plant Biology, East Lansing, MI, USA.
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19
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McClung CR. Beyond Arabidopsis: the circadian clock in non-model plant species. Semin Cell Dev Biol 2013; 24:430-6. [PMID: 23466287 DOI: 10.1016/j.semcdb.2013.02.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2012] [Revised: 02/13/2013] [Accepted: 02/15/2013] [Indexed: 01/26/2023]
Abstract
Circadian clocks allow plants to temporally coordinate many aspects of their biology with the diurnal cycle derived from the rotation of Earth on its axis. Although there is a rich history of the study of clocks in many plant species, in recent years much progress in elucidating the architecture and function of the plant clock has emerged from studies of the model plant, Arabidopsis thaliana. There is considerable interest in extending this knowledge of the circadian clock into diverse plant species in order to address its role in topics as varied as agricultural productivity and the responses of individual species and plant communities to global climate change and environmental degradation. The analysis of circadian clocks in the green lineage provides insight into evolutionary processes in plants and throughout the eukaryotes.
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Affiliation(s)
- C Robertson McClung
- Department of Biological Sciences, Dartmouth College, Class of 1978 Life Sciences Center, Hanover, NH 03755, USA.
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Wang W, Messing J. Analysis of ADP-glucose pyrophosphorylase expression during turion formation induced by abscisic acid in Spirodela polyrhiza (greater duckweed). BMC PLANT BIOLOGY 2012; 12:5. [PMID: 22235974 PMCID: PMC3268088 DOI: 10.1186/1471-2229-12-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Accepted: 01/11/2012] [Indexed: 05/10/2023]
Abstract
BACKGROUND Aquatic plants differ in their development from terrestrial plants in their morphology and physiology, but little is known about the molecular basis of the major phases of their life cycle. Interestingly, in place of seeds of terrestrial plants their dormant phase is represented by turions, which circumvents sexual reproduction. However, like seeds turions provide energy storage for starting the next growing season. RESULTS To begin a characterization of the transition from the growth to the dormant phase we used abscisic acid (ABA), a plant hormone, to induce controlled turion formation in Spirodela polyrhiza and investigated their differentiation from fronds, representing their growth phase, into turions with respect to morphological, ultra-structural characteristics, and starch content. Turions were rich in anthocyanin pigmentation and had a density that submerged them to the bottom of liquid medium. Transmission electron microscopy (TEM) of turions showed in comparison to fronds shrunken vacuoles, smaller intercellular space, and abundant starch granules surrounded by thylakoid membranes. Turions accumulated more than 60% starch in dry mass after two weeks of ABA treatment. To further understand the mechanism of the developmental switch from fronds to turions, we cloned and sequenced the genes of three large-subunit ADP-glucose pyrophosphorylases (APLs). All three putative protein and exon sequences were conserved, but the corresponding genomic sequences were extremely variable mainly due to the invasion of miniature inverted-repeat transposable elements (MITEs) into introns. A molecular three-dimensional model of the SpAPLs was consistent with their regulatory mechanism in the interaction with the substrate (ATP) and allosteric activator (3-PGA) to permit conformational changes of its structure. Gene expression analysis revealed that each gene was associated with distinct temporal expression during turion formation. APL2 and APL3 were highly expressed in earlier stages of turion development, while APL1 expression was reduced throughout turion development. CONCLUSIONS These results suggest that the differential expression of APLs could be used to enhance energy flow from photosynthesis to storage of carbon in aquatic plants, making duckweeds a useful alternative biofuel feedstock.
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Affiliation(s)
- Wenqin Wang
- Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, NJ 08854, USA
- Department of Plant Biology and Pathology, Rutgers University, 59 Dudley Road, New Brunswick, NJ 08901, USA
| | - Joachim Messing
- Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, NJ 08854, USA
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Filichkin SA, Breton G, Priest HD, Dharmawardhana P, Jaiswal P, Fox SE, Michael TP, Chory J, Kay SA, Mockler TC. Global profiling of rice and poplar transcriptomes highlights key conserved circadian-controlled pathways and cis-regulatory modules. PLoS One 2011; 6:e16907. [PMID: 21694767 PMCID: PMC3111414 DOI: 10.1371/journal.pone.0016907] [Citation(s) in RCA: 133] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Accepted: 01/15/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Circadian clocks provide an adaptive advantage through anticipation of daily and seasonal environmental changes. In plants, the central clock oscillator is regulated by several interlocking feedback loops. It was shown that a substantial proportion of the Arabidopsis genome cycles with phases of peak expression covering the entire day. Synchronized transcriptome cycling is driven through an extensive network of diurnal and clock-regulated transcription factors and their target cis-regulatory elements. Study of the cycling transcriptome in other plant species could thus help elucidate the similarities and differences and identify hubs of regulation common to monocot and dicot plants. METHODOLOGY/PRINCIPAL FINDINGS Using a combination of oligonucleotide microarrays and data mining pipelines, we examined daily rhythms in gene expression in one monocotyledonous and one dicotyledonous plant, rice and poplar, respectively. Cycling transcriptomes were interrogated under different diurnal (driven) and circadian (free running) light and temperature conditions. Collectively, photocycles and thermocycles regulated about 60% of the expressed nuclear genes in rice and poplar. Depending on the condition tested, up to one third of oscillating Arabidopsis-poplar-rice orthologs were phased within three hours of each other suggesting a high degree of conservation in terms of rhythmic gene expression. We identified clusters of rhythmically co-expressed genes and searched their promoter sequences to identify phase-specific cis-elements, including elements that were conserved in the promoters of Arabidopsis, poplar, and rice. CONCLUSIONS/SIGNIFICANCE Our results show that the cycling patterns of many circadian clock genes are highly conserved across poplar, rice, and Arabidopsis. The expression of many orthologous genes in key metabolic and regulatory pathways is diurnal and/or circadian regulated and phased to similar times of day. Our results confirm previous findings in Arabidopsis of three major classes of cis-regulatory modules within the plant circadian network: the morning (ME, GBOX), evening (EE, GATA), and midnight (PBX/TBX/SBX) modules. Identification of identical overrepresented motifs in the promoters of cycling genes from different species suggests that the core diurnal/circadian cis-regulatory network is deeply conserved between mono- and dicotyledonous species.
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Affiliation(s)
- Sergei A. Filichkin
- Department of Botany and Plant Pathology, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Ghislain Breton
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
| | - Henry D. Priest
- Department of Botany and Plant Pathology, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Palitha Dharmawardhana
- Department of Botany and Plant Pathology, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Samuel E. Fox
- Department of Botany and Plant Pathology, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Todd P. Michael
- The Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
| | - Joanne Chory
- Plant Biology Laboratory, The Salk Institute for Biological Studies and Howard Hughes Medical Institute, La Jolla, California, United States of America
| | - Steve A. Kay
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
| | - Todd C. Mockler
- Department of Botany and Plant Pathology, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
- * E-mail:
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Network news: prime time for systems biology of the plant circadian clock. Curr Opin Genet Dev 2011; 20:588-98. [PMID: 20889330 DOI: 10.1016/j.gde.2010.08.010] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Revised: 08/12/2010] [Accepted: 08/31/2010] [Indexed: 11/24/2022]
Abstract
Whole-transcriptome analyses have established that the plant circadian clock regulates virtually every plant biological process and most prominently hormonal and stress response pathways. Systems biology efforts have successfully modeled the plant central clock machinery and an iterative process of model refinement and experimental validation has contributed significantly to the current view of the central clock machinery. The challenge now is to connect this central clock to the output pathways for understanding how the plant circadian clock contributes to plant growth and fitness in a changing environment. Undoubtedly, systems approaches will be needed to integrate and model the vastly increased volume of experimental data in order to extract meaningful biological information. Thus, we have entered an era of systems modeling, experimental testing, and refinement. This approach, coupled with advances from the genetic and biochemical analyses of clock function, is accelerating our progress towards a comprehensive understanding of the plant circadian clock network.
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Abstract
The rotation of the earth on its axis confers the property of dramatic, recurrent, rhythmic environmental change. The rhythmicity of this change from day to night and again to day imparts predictability. As a consequence, most organisms have acquired the capacity to measure time to use this time information to temporally regulate their biology to coordinate with their environment in anticipation of coming change. Circadian rhythms, endogenous rhythms with periods of ∼24h, are driven by an internal circadian clock. This clock integrates temporal information and coordinates of many aspects of biology, including basic metabolism, hormone signaling and responses, and responses to biotic and abiotic stress, making clocks central to "systems biology." This review will first address the extent to which the clock regulates many biological processes. The architecture and mechanisms of the plant circadian oscillator, emphasizing what has been learned from intensive study of the circadian clock in the model plant, Arabidopsis thaliana, will be considered. The conservation of clock components in other species will address the extent to which the Arabidopsis model will inform our consideration of plants in general. Finally, studies addressing the role of clocks in fitness will be discussed. Accumulating evidence indicates that the consonance of the endogenous circadian clock with environmental cycles enhances fitness, including both biomass accumulation and reproductive performance. Thus, increased understanding of plant responses to environmental input and to endogenous temporal cues has ecological and agricultural importance.
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Affiliation(s)
- C Robertson McClung
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA
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Kim WY, Salomé PA, Fujiwara S, Somers DE, McClung CR. Characterization of pseudo-response regulators in plants. Methods Enzymol 2010; 471:357-78. [PMID: 20946857 DOI: 10.1016/s0076-6879(10)71019-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A small family of clock-regulated pseudo-response regulators (PRRs) plays a number of critical roles in the function of the plant circadian clock. The regulation of the PRRs is complex and entails both transcriptional and posttranslational regulation. PRR proteins engage in a number of important protein-protein interactions, some of which are modulated by modifications including phosphorylation. PRR stability is also tightly controlled. This chapter provides methods for studying both the PRR genes and their encoded proteins.
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Affiliation(s)
- Woe-Yeon Kim
- Department of Plant Cellular and Molecular Biology, Ohio State University, Columbus, Ohio, USA
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Priest HD, Filichkin SA, Mockler TC. Cis-regulatory elements in plant cell signaling. CURRENT OPINION IN PLANT BIOLOGY 2009; 12:643-649. [PMID: 19717332 DOI: 10.1016/j.pbi.2009.07.016] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Revised: 06/30/2009] [Accepted: 07/21/2009] [Indexed: 05/26/2023]
Abstract
Plant cell signaling pathways are in part dependent on transcriptional regulatory networks comprising circuits of transcription factors (TFs) and regulatory DNA elements that control the expression of target genes. Here, we describe experimental and bioinformatic approaches for identifying potential cis-regulatory elements. We also discuss recent integrative genomics studies aimed at elucidating the functions of cis-regulatory elements in aspects of plant biology, including the circadian clock, interactions with the environment, stress responses, and regulation of growth and development by phytohormones. Finally, we discuss emerging technologies and approaches that offer great potential for accelerating the discovery and functional characterization of cis-elements and interacting TFs--which will help realize the promise of systems biology.
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Affiliation(s)
- Henry D Priest
- Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA
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