201
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Mahboubi A, Niittylä T. Sucrose transport and carbon fluxes during wood formation. PHYSIOLOGIA PLANTARUM 2018; 164:67-81. [PMID: 29572842 DOI: 10.1111/ppl.12729] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 03/05/2018] [Accepted: 03/15/2018] [Indexed: 06/08/2023]
Abstract
Wood biosynthesis defines the chemical and structural properties of wood. The metabolic pathways that produce the precursors of wood cell wall polymers have a central role in defining wood properties. To make rational design of wood properties feasible, we need not only to understand the cell wall biosynthetic machinery, but also how sucrose transport and metabolism in developing wood connect to cell wall biosynthesis and how they respond to genetic and environmental cues. Here, we review the current understanding of the sucrose transport and primary metabolism pathways leading to the precursors of cell wall biosynthesis in woody plant tissues. We present both old, persistent questions and new emerging themes with a focus on wood formation in trees and draw upon evidence from the xylem tissues of herbaceous plants when it is relevant.
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Affiliation(s)
- Amir Mahboubi
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Totte Niittylä
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
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202
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Azoulay‐Shemer T, Schwankl N, Rog I, Moshelion M, Schroeder JI. Starch biosynthesis by
AGP
ase, but not starch degradation by
BAM
1/3 and
SEX
1, is rate‐limiting for
CO
2
‐regulated stomatal movements under short‐day conditions. FEBS Lett 2018; 592:2739-2759. [DOI: 10.1002/1873-3468.13198] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 07/10/2018] [Accepted: 07/11/2018] [Indexed: 01/27/2023]
Affiliation(s)
- Tamar Azoulay‐Shemer
- Division of Biological Sciences, Cell and Developmental Biology Section University of California San Diego La Jolla CA USA
| | - Nikki Schwankl
- Division of Biological Sciences, Cell and Developmental Biology Section University of California San Diego La Jolla CA USA
| | - Ido Rog
- Department of Plant & Environmental Sciences Weizmann Institute of Science Rehovot Israel
| | - Menachem Moshelion
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture The Robert H. Smith Faculty of Agriculture, Food and Environment The Hebrew University of Jerusalem Rehovot Israel
| | - Julian I. Schroeder
- Division of Biological Sciences, Cell and Developmental Biology Section University of California San Diego La Jolla CA USA
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203
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Andrés-Colás N, Carrió-Seguí A, Abdel-Ghany SE, Pilon M, Peñarrubia L. Expression of the Intracellular COPT3-Mediated Cu Transport Is Temporally Regulated by the TCP16 Transcription Factor. FRONTIERS IN PLANT SCIENCE 2018; 9:910. [PMID: 30018625 PMCID: PMC6037871 DOI: 10.3389/fpls.2018.00910] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 06/08/2018] [Indexed: 05/23/2023]
Abstract
Copper is an essential element in plants. When scarce, copper is acquired from extracellular environment or remobilized from intracellular sites, through members of the high affinity copper transporters family COPT located at the plasma membrane and internal membrane, respectively. Here, we show that COPT3 is an intracellular copper transporter, located at a compartment of the secretory pathway, that is mainly expressed in pollen grains and vascular bundles. Contrary to the COPT1 plasma membrane member, the expression of the internal COPT3 membrane transporter was higher at 12 h than at 0 h of a neutral photoperiod day under copper deficiency. The screening of a library of conditionally overexpressed transcription factors implicated members of the TCP family in the COPT3 differential temporal expression pattern. Particularly, in vitro, TCP16 was found to bind to the COPT3 promoter and down-regulated its expression. Accordingly, TCP16 was mainly expressed at 0 h under copper deficiency and induced at 12 h by copper excess. Moreover, TCP16 overexpression resulted in increased sensitivity to copper deficiency, whereas the tcp16 mutant was sensitive to copper excess. Both copper content and the expression of particular copper status markers were altered in plants with modified levels of TCP16. Consistent with TCP16 affecting pollen development, the lack of COPT3 function led to altered pollen morphology. Furthermore, analysis of copt3 and COPT3 overexpressing plants revealed that COPT3 function exerted a negative effect on TCP16 expression. Taken together, these results suggest a differential daily regulation of copper uptake depending on the external and internal copper pools, in which TCP16 inhibits copper remobilization at dawn through repression of intracellular transporters.
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Affiliation(s)
- Nuria Andrés-Colás
- Departament de Bioquímica i Biologia Molecular, Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina, Universitat de València, Valencia, Spain
| | - Angela Carrió-Seguí
- Departament de Bioquímica i Biologia Molecular, Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina, Universitat de València, Valencia, Spain
| | - Salah E. Abdel-Ghany
- Department of Biology, Colorado State University, Fort Collins, CO, United States
| | - Marinus Pilon
- Department of Biology, Colorado State University, Fort Collins, CO, United States
| | - Lola Peñarrubia
- Departament de Bioquímica i Biologia Molecular, Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina, Universitat de València, Valencia, Spain
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204
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Shi Y, Ding Y, Yang S. Molecular Regulation of CBF Signaling in Cold Acclimation. TRENDS IN PLANT SCIENCE 2018; 23:623-637. [PMID: 29735429 DOI: 10.1016/j.tplants.2018.04.002] [Citation(s) in RCA: 349] [Impact Index Per Article: 58.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 03/28/2018] [Accepted: 04/05/2018] [Indexed: 05/19/2023]
Abstract
Cold stress restricts plant growth, development, and distribution. Understanding how plants transduce and respond to cold signals has long been a topic of interest. Traditional genetic and molecular analyses have identified C-repeat/DREB binding factors (CBFs) as key transcription factors that function in cold acclimation. Recent studies revealed the involvement of pivotal protein kinases and transcription factors in CBF-dependent signaling, expanding our knowledge of cold signal transduction from perception to downstream gene expression events. In this review, we summarize recent advances in our understanding of the molecular regulation of these core components of the CBF cold signaling pathway. Knowledge of the mechanism underlying the ability of plants to survive freezing temperatures will facilitate the development of crop plants with increased freezing tolerance.
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Affiliation(s)
- Yiting Shi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China; These authors contributed equally
| | - Yanglin Ding
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China; These authors contributed equally
| | - Shuhua Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
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205
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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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206
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Iuchi H, Sugimoto M, Tomita M. MICOP: Maximal information coefficient-based oscillation prediction to detect biological rhythms in proteomics data. BMC Bioinformatics 2018; 19:249. [PMID: 29954316 PMCID: PMC6025708 DOI: 10.1186/s12859-018-2257-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 06/20/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Circadian rhythms comprise oscillating molecular interactions, the disruption of the homeostasis of which would cause various disorders. To understand this phenomenon systematically, an accurate technique to identify oscillating molecules among omics datasets must be developed; however, this is still impeded by many difficulties, such as experimental noise and attenuated amplitude. RESULTS To address these issues, we developed a new algorithm named Maximal Information Coefficient-based Oscillation Prediction (MICOP), a sine curve-matching method. The performance of MICOP in labeling oscillation or non-oscillation was compared with four reported methods using Mathews correlation coefficient (MCC) values. The numerical experiments were performed with time-series data with (1) mimicking of molecular oscillation decay, (2) high noise and low sampling frequency and (3) one-cycle data. The first experiment revealed that MICOP could accurately identify the rhythmicity of decaying molecular oscillation (MCC > 0.7). The second experiment revealed that MICOP was robust against high-level noise (MCC > 0.8) even upon the use of low-sampling-frequency data. The third experiment revealed that MICOP could accurately identify the rhythmicity of noisy one-cycle data (MCC > 0.8). As an application, we utilized MICOP to analyze time-series proteome data of mouse liver. MICOP identified that novel oscillating candidates numbered 14 and 30 for C57BL/6 and C57BL/6 J, respectively. CONCLUSIONS In this paper, we presented MICOP, which is an MIC-based algorithm, for predicting periodic patterns in large-scale time-resolved protein expression profiles. The performance test using artificially generated simulation data revealed that the performance of MICOP for decaying data was superior to that of the existing widely used methods. It can reveal novel findings from time-series data and may contribute to biologically significant results. This study suggests that MICOP is an ideal approach for detecting and characterizing oscillations in time-resolved omics data sets.
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Affiliation(s)
- Hitoshi Iuchi
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, 252-8520, Japan.,Institute for Advanced Biosciences, Keio University, Tsuruoka, 997-0052, Japan
| | - Masahiro Sugimoto
- Institute for Advanced Biosciences, Keio University, Tsuruoka, 997-0052, Japan. .,Health Promotion and Preemptive Medicine, Research and Development Center for Minimally Invasive Therapies, Tokyo Medical University, Shinjuku, Tokyo, 160-0022, Japan.
| | - Masaru Tomita
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, 252-8520, Japan.,Institute for Advanced Biosciences, Keio University, Tsuruoka, 997-0052, Japan.,Department of Environment and Information Studies, Keio University, Fujisawa, 252-8520, Japan
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207
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Soengas P, Cartea ME, Velasco P, Francisco M. Endogenous Circadian Rhythms in Polyphenolic Composition Induce Changes in Antioxidant Properties in Brassica Cultivars. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:5984-5991. [PMID: 29851489 DOI: 10.1021/acs.jafc.8b01732] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
There is increasing evidence that the circadian clock is a significant driver of plant phytochemicals. However, little is known about the clock effect on antioxidant metabolites in edible crops. Thus, the aim of the present investigation was to study whether the antioxidant potential of Brassica cultivars is under circadian regulation and its relationship with polyphenol content. To accomplish that we entrain plants of four Brassica cultivars to light-dark cycles prior to release into continuous light. The antioxidant activity and phenolic content was monitored at four time points of the day during four consecutive days: 2 days under light-dark conditions followed by 2 days under continuous light. Results showed daily oscillation of antioxidant activity. In addition, those variations were related with endogenous circadian rhythms in polyphenolics and exhibit a species-specific pattern. Considered together, we determined that Brassica cultivars have an optimal time during a single day with increased levels of health phytochemicals.
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Affiliation(s)
- Pilar Soengas
- Group of Genetics, Breeding and Biochemistry of Brassicas , Misión Biológica de Galicia, Spanish Council for Scientific Research (CSIC) , Pontevedra , Spain
| | - M Elena Cartea
- Group of Genetics, Breeding and Biochemistry of Brassicas , Misión Biológica de Galicia, Spanish Council for Scientific Research (CSIC) , Pontevedra , Spain
| | - Pablo Velasco
- Group of Genetics, Breeding and Biochemistry of Brassicas , Misión Biológica de Galicia, Spanish Council for Scientific Research (CSIC) , Pontevedra , Spain
| | - Marta Francisco
- Group of Genetics, Breeding and Biochemistry of Brassicas , Misión Biológica de Galicia, Spanish Council for Scientific Research (CSIC) , Pontevedra , Spain
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208
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Graf A, Coman D, Uhrig RG, Walsh S, Flis A, Stitt M, Gruissem W. Parallel analysis of Arabidopsis circadian clock mutants reveals different scales of transcriptome and proteome regulation. Open Biol 2018; 7:rsob.160333. [PMID: 28250106 PMCID: PMC5376707 DOI: 10.1098/rsob.160333] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 02/06/2017] [Indexed: 12/12/2022] Open
Abstract
The circadian clock regulates physiological processes central to growth and survival. To date, most plant circadian clock studies have relied on diurnal transcriptome changes to elucidate molecular connections between the circadian clock and observable phenotypes in wild-type plants. Here, we have integrated RNA-sequencing and protein mass spectrometry data to comparatively analyse the lhycca1, prr7prr9, gi and toc1 circadian clock mutant rosette at the end of day and end of night. Each mutant affects specific sets of genes and proteins, suggesting that the circadian clock regulation is modular. Furthermore, each circadian clock mutant maintains its own dynamically fluctuating transcriptome and proteome profile specific to subcellular compartments. Most of the measured protein levels do not correlate with changes in their corresponding transcripts. Transcripts and proteins that have coordinated changes in abundance are enriched for carbohydrate- and cold-responsive genes. Transcriptome changes in all four circadian clock mutants also affect genes encoding starch degradation enzymes, transcription factors and protein kinases. The comprehensive transcriptome and proteome datasets demonstrate that future system-driven research of the circadian clock requires multi-level experimental approaches. Our work also shows that further work is needed to elucidate the roles of post-translational modifications and protein degradation in the regulation of clock-related processes.
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Affiliation(s)
- Alexander Graf
- Department of Biology, ETH Zurich, 8092 Zurich, Switzerland.,Max Planck Institute of Molecular Plant Physiology, 14476 Postdam-Golm, Germany
| | - Diana Coman
- Department of Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - R Glen Uhrig
- Department of Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Sean Walsh
- Department of Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Anna Flis
- Max Planck Institute of Molecular Plant Physiology, 14476 Postdam-Golm, Germany
| | - Mark Stitt
- Max Planck Institute of Molecular Plant Physiology, 14476 Postdam-Golm, Germany
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209
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Edwards KD, Takata N, Johansson M, Jurca M, Novák O, Hényková E, Liverani S, Kozarewa I, Strnad M, Millar AJ, Ljung K, Eriksson ME. Circadian clock components control daily growth activities by modulating cytokinin levels and cell division-associated gene expression in Populus trees. PLANT, CELL & ENVIRONMENT 2018; 41:1468-1482. [PMID: 29520862 PMCID: PMC6001645 DOI: 10.1111/pce.13185] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 02/28/2018] [Accepted: 02/28/2018] [Indexed: 05/30/2023]
Abstract
Trees are carbon dioxide sinks and major producers of terrestrial biomass with distinct seasonal growth patterns. Circadian clocks enable the coordination of physiological and biochemical temporal activities, optimally regulating multiple traits including growth. To dissect the clock's role in growth, we analysed Populus tremula × P. tremuloides trees with impaired clock function due to down-regulation of central clock components. late elongated hypocotyl (lhy-10) trees, in which expression of LHY1 and LHY2 is reduced by RNAi, have a short free-running period and show disrupted temporal regulation of gene expression and reduced growth, producing 30-40% less biomass than wild-type trees. Genes important in growth regulation were expressed with an earlier phase in lhy-10, and CYCLIN D3 expression was misaligned and arrhythmic. Levels of cytokinins were lower in lhy-10 trees, which also showed a change in the time of peak expression of genes associated with cell division and growth. However, auxin levels were not altered in lhy-10 trees, and the size of the lignification zone in the stem showed a relative increase. The reduced growth rate and anatomical features of lhy-10 trees were mainly caused by misregulation of cell division, which may have resulted from impaired clock function.
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Affiliation(s)
- Kieron D. Edwards
- School of Biological Sciences, C.H. Waddington BuildingUniversity of EdinburghEdinburghEH9 3BFUK
| | - Naoki Takata
- Department of Plant Physiology, Umeå Plant Science CentreUmeå University901 87UmeåSweden
| | - Mikael Johansson
- Department of Plant Physiology, Umeå Plant Science CentreUmeå University901 87UmeåSweden
- RNA Biology and Molecular PhysiologyBielefeld University33615BielefeldGermany
| | - Manuela Jurca
- Department of Plant Physiology, Umeå Plant Science CentreUmeå University901 87UmeåSweden
| | - Ondřej Novák
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental Botany ASCR and Palacký University783 71OlomoucCzech Republic
| | - Eva Hényková
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental Botany ASCR and Palacký University783 71OlomoucCzech Republic
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science CentreSwedish University of Agricultural Sciences901 83UmeåSweden
| | - Silvia Liverani
- Department of StatisticsUniversity of WarwickCoventryCV4 7ALUK
| | - Iwanka Kozarewa
- Department of Plant Physiology, Umeå Plant Science CentreUmeå University901 87UmeåSweden
| | - Miroslav Strnad
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental Botany ASCR and Palacký University783 71OlomoucCzech Republic
| | - Andrew J. Millar
- School of Biological Sciences, C.H. Waddington BuildingUniversity of EdinburghEdinburghEH9 3BFUK
| | - Karin Ljung
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science CentreSwedish University of Agricultural Sciences901 83UmeåSweden
| | - Maria E. Eriksson
- Department of Plant Physiology, Umeå Plant Science CentreUmeå University901 87UmeåSweden
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210
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Hörnlein C, Confurius-Guns V, Stal LJ, Bolhuis H. Daily rhythmicity in coastal microbial mats. NPJ Biofilms Microbiomes 2018; 4:11. [PMID: 29796291 PMCID: PMC5953948 DOI: 10.1038/s41522-018-0054-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 03/26/2018] [Accepted: 04/17/2018] [Indexed: 12/31/2022] Open
Abstract
Cyanobacteria are major primary producers in coastal microbial mats and provide biochemical energy, organic carbon, and bound nitrogen to the mat community through oxygenic photosynthesis and dinitrogen fixation. In order to anticipate the specific requirements to optimize their metabolism and growth during a day-and-night cycle, Cyanobacteria possess a unique molecular timing mechanism known as the circadian clock that is well-studied under laboratory conditions but little is known about its function in a natural complex community. Here, we investigated daily rhythmicity of gene expression in a coastal microbial mat community sampled at 6 time points during a 24-h period. In order to identify diel expressed genes, meta-transcriptome data was fitted to periodic functions. Out of 24,035 conserved gene transcript clusters, approximately 7% revealed a significant rhythmic expression pattern. These rhythmic genes were assigned to phototrophic micro-eukaryotes, Cyanobacteria but also to Proteobacteria and Bacteroidetes. Analysis of MG-RAST annotated genes and mRNA recruitment analysis of two cyanobacterial and three proteobacterial microbial mat members confirmed that homologs of the cyanobacterial circadian clock genes were also found in other bacterial members of the microbial mat community. These results suggest that various microbial mat members other than Cyanobacteria have their own molecular clock, which can be entrained by a cocktail of Zeitgebers such as light, temperature or metabolites from neighboring species. Hence, microbial mats can be compared to a complex organism consisting of multiple sub-systems that have to be entrained in a cooperative way such that the corpus functions optimally.
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Affiliation(s)
- Christine Hörnlein
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, and Utrecht University, Den Hoorn, The Netherlands
| | - Veronique Confurius-Guns
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, and Utrecht University, Den Hoorn, The Netherlands
| | - Lucas J Stal
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, and Utrecht University, Den Hoorn, The Netherlands.,2Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Henk Bolhuis
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, and Utrecht University, Den Hoorn, The Netherlands
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211
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Bloch G, Bar-Shai N, Cytter Y, Green R. Time is honey: circadian clocks of bees and flowers and how their interactions may influence ecological communities. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0256. [PMID: 28993499 DOI: 10.1098/rstb.2016.0256] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/31/2017] [Indexed: 12/28/2022] Open
Abstract
The interactions between flowering plants and insect pollinators shape ecological communities and provide one of the best examples of coevolution. Although these interactions have received much attention in both ecology and evolution, their temporal aspects are little explored. Here we review studies on the circadian organization of pollination-related traits in bees and flowers. Research, mostly with the honeybee, Apis mellifera, has implicated the circadian clock in key aspects of their foraging for flower rewards. These include anticipation, timing of visits to flowers at specified locations and time-compensated sun-compass orientation. Floral rhythms in traits such as petal opening, scent release and reward availability also show robust daily rhythms. However, in only few studies was it possible to adequately determine whether these oscillations are driven by external time givers such as light and temperature cycles, or endogenous circadian clocks. The interplay between the timing of flower and pollinator rhythms may be ecologically significant. Circadian regulation of pollination-related traits in only few species may influence the entire pollination network and thus affect community structure and local biodiversity. We speculate that these intricate chronobiological interactions may be vulnerable to anthropogenic effects such as the introduction of alien invasive species, pesticides or environmental pollutants.This article is part of the themed issue 'Wild clocks: integrating chronobiology and ecology to understand timekeeping in free-living animals'.
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Affiliation(s)
- Guy Bloch
- Department of Ecology, Evolution, and Behavior, The A. Silberman Institute of Life Sciences, Hebrew University, Jerusalem 91904, Israel
| | - Noam Bar-Shai
- Department of Ecology, Evolution, and Behavior, The A. Silberman Institute of Life Sciences, Hebrew University, Jerusalem 91904, Israel.,Jerusalem Botanical Gardens, Hebrew University, Givat-Ram, Jerusalem 91904, Israel
| | - Yotam Cytter
- Department of Plant and Environmental Sciences, The A. Silberman Institute of Life Sciences, Hebrew University, Jerusalem 91904, Israel
| | - Rachel Green
- Department of Plant and Environmental Sciences, The A. Silberman Institute of Life Sciences, Hebrew University, Jerusalem 91904, Israel
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212
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Guo Y, Huang Y, Gao J, Pu Y, Wang N, Shen W, Wen J, Yi B, Ma C, Tu J, Fu T, Zou J, Shen J. CIPK9 is involved in seed oil regulation in Brassica napus L. and Arabidopsis thaliana (L.) Heynh. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:124. [PMID: 29743952 PMCID: PMC5930439 DOI: 10.1186/s13068-018-1122-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 04/19/2018] [Indexed: 05/10/2023]
Abstract
BACKGROUND Accumulation of storage compounds during seed development plays an important role in the life cycle of oilseed plants; these compounds provide carbon and energy resources to support the establishment of seedlings. RESULTS In this study, we show that BnCIPK9 has a broad expression pattern in Brassica napus L. tissues and that wounding stress strongly induces its expression. The overexpression of BnCIPK9 during seed development reduced oil synthesis in transgenic B. napus compared to that observed in wild-type (WT) plants. Functional analysis revealed that seed oil content (OC) of complementation lines was similar to that of WT plants, whereas OC in Arabidopsis thaliana (L.) Heynh. Atcipk9 knockout mutants (cipk9) was higher than that of WT plants. Seedling of cipk9 mutants failed to establish roots on a sugar-free medium, but root establishment could be rescued by supplementation of sucrose or glucose. The phenotype of complementation transgenic lines was similar to that of WT plants when grown on sugar-free medium. Mutants, cipk9, cbl2, and cbl3 presented similar phenotypes, suggesting that CIPK9, CBL2, and CBL3 might work together and play similar roles in root establishment under sugar-free condition. CONCLUSION This study showed that BnCIPK9 and AtCIPK9 encode a protein kinase that is involved in sugar-related response and plays important roles in the regulation of energy reserves. Our results suggest that AtCIPK9 negatively regulates lipid accumulation and has a significant effect on early seedling establishment in A. thaliana. The functional characterization of CIPK9 provides insights into the regulation of OC, and might be used for improving OC in B. napus. We believe that our study makes a significant contribution to the literature because it provides information on how CIPKs coordinate stress regulation and energy signaling.
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Affiliation(s)
- Yanli Guo
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, 430070 China
- Crop Research Institute of TIANJIN Academy of Agricultural Sciences, Tianjin, 300384 China
| | - Yi Huang
- National Research Council Canada, Saskatoon, SK S7N0 W9 Canada
| | - Jie Gao
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yuanyuan Pu
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, 430070 China
| | - Nan Wang
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, 430070 China
| | - Wenyun Shen
- National Research Council Canada, Saskatoon, SK S7N0 W9 Canada
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, 430070 China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, 430070 China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, 430070 China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, 430070 China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, 430070 China
| | - Jitao Zou
- National Research Council Canada, Saskatoon, SK S7N0 W9 Canada
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, 430070 China
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213
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Genome-wide excision repair in Arabidopsis is coupled to transcription and reflects circadian gene expression patterns. Nat Commun 2018; 9:1503. [PMID: 29666379 PMCID: PMC5904149 DOI: 10.1038/s41467-018-03922-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 03/22/2018] [Indexed: 11/25/2022] Open
Abstract
Plants are exposed to numerous DNA-damaging stresses including the exposure to ultraviolet (UV) component of solar radiation. They employ nucleotide excision repair to remove DNA-bulky adducts and to help eliminate UV-induced DNA lesions, so as to maintain their genome integrity and their fitness. Here, we generated genome-wide single-nucleotide resolution excision repair maps of UV-induced DNA damage in Arabidopsis at different circadian time points. Our data show that the repair of UV lesions for a large fraction of the genome is controlled by the joint actions of the circadian clock and transcription by RNA polymerase II. Our findings reveal very strong repair preference for the transcribed strands of active genes in Arabidopsis, and 10–30% of the transcription-coupled repair is circadian time-dependent. This dynamic range in nucleotide excision repair levels throughout the day enables Arabidopsis to cope with the bulky DNA lesion-inducing environmental factors including UV. Plants use nucleotide excision repair to maintain genome integrity in response to damage caused by stresses such as UV radiation. Here Oztas et al. use genome-wide profiling to show that excision repair in Arabidopsis is strongly coupled to transcription and reflects circadian patterns of gene expression.
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214
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Iwayama K, Aisaka Y, Kutsuna N, Nagano AJ. FIT: statistical modeling tool for transcriptome dynamics under fluctuating field conditions. Bioinformatics 2018; 33:1672-1680. [PMID: 28158396 PMCID: PMC5447243 DOI: 10.1093/bioinformatics/btx049] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 01/28/2017] [Indexed: 12/31/2022] Open
Abstract
Motivation Considerable attention has been given to the quantification of environmental effects on organisms. In natural conditions, environmental factors are continuously changing in a complex manner. To reveal the effects of such environmental variations on organisms, transcriptome data in field environments have been collected and analyzed. Nagano et al. proposed a model that describes the relationship between transcriptomic variation and environmental conditions and demonstrated the capability to predict transcriptome variation in rice plants. However, the computational cost of parameter optimization has prevented its wide application. Results We propose a new statistical model and efficient parameter optimization based on the previous study. We developed and released FIT, an R package that offers functions for parameter optimization and transcriptome prediction. The proposed method achieves comparable or better prediction performance within a shorter computational time than the previous method. The package will facilitate the study of the environmental effects on transcriptomic variation in field conditions. Availability and Implementation Freely available from CRAN (https://cran.r-project.org/web/packages/FIT/). Supplementary information Supplementary data are available at Bioinformatics online
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Affiliation(s)
- Koji Iwayama
- Research Institute for Food and Agriculture, Ryukoku University, Otsu, Shiga, Japan
| | | | - Natsumaro Kutsuna
- LPixel Inc, Hongo, Bunkyo-ku, Tokyo, Japan.,Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-shi, Chiba, Japan
| | - Atsushi J Nagano
- Department of Plant Life Science, Faculty of Agriculture, Ryukoku University, Otsu, Shiga, Japan.,Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan.,JST PRESTO, Kawaguchi, Saitama, Japan
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215
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Liu C, Qu X, Zhou Y, Song G, Abiri N, Xiao Y, Liang F, Jiang D, Hu Z, Yang D. OsPRR37 confers an expanded regulation of the diurnal rhythms of the transcriptome and photoperiodic flowering pathways in rice. PLANT, CELL & ENVIRONMENT 2018; 41:630-645. [PMID: 29314052 DOI: 10.1111/pce.13135] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 12/05/2017] [Accepted: 12/16/2017] [Indexed: 05/24/2023]
Abstract
The circadian clock enables organisms to rapidly adapt to the ever-changing environmental conditions that are caused by daily light/dark cycles. Circadian clock genes universally affect key agricultural traits, particularly flowering time. Here, we show that OsPRR37, a circadian clock gene, delays rice flowering time in an expression level-dependent manner. Using high-throughput mRNA sequencing on an OsPRR37 overexpressing transgenic line (OsPRR37-OE5) and the recipient parent Guangluai4 that contains the loss-of-function Osprr37, we identify 14,992 genes that display diurnal rhythms, which account for 52.9% of the transcriptome. Overexpressing OsPRR37 weakens the transcriptomic rhythms and alters the phases of rhythmic genes. In total, 3,210 differentially expressed genes (DEGs) are identified, among which 1,863 rhythmic DEGs show a correlation between the change of absolute amplitudes and the mean expression levels. We further reveal that OsPRR37 functions as a transcriptional repressor to repress the expression levels and amplitudes of day-phased clock genes. More importantly, OsPRR37 confers expanded regulation on the evening-phased rhythmic DEGs by repressing the morning-phased rhythmic DEGs. Further study shows that OsPRR37 expands its regulation on flowering pathways by repressing Ehd1. Thus, our results demonstrate an expanded regulation mechanism of the circadian clock on the diurnal rhythms of the transcriptome.
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Affiliation(s)
- Chuan Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Xuefeng Qu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yanhao Zhou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Gaoyuan Song
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Naghmeh Abiri
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yuhui Xiao
- Nextomics Biosciences Co., Ltd., Wuhan, 430000, China
| | - Fan Liang
- Nextomics Biosciences Co., Ltd., Wuhan, 430000, China
| | - Daiming Jiang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhongli Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Daichang Yang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
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216
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Weiss J, Terry MI, Martos-Fuentes M, Letourneux L, Ruiz-Hernández V, Fernández JA, Egea-Cortines M. Diel pattern of circadian clock and storage protein gene expression in leaves and during seed filling in cowpea (Vigna unguiculata). BMC PLANT BIOLOGY 2018; 18:33. [PMID: 29444635 PMCID: PMC5813328 DOI: 10.1186/s12870-018-1244-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 01/18/2018] [Indexed: 05/15/2023]
Abstract
BACKGROUND Cowpea (Vigna unguiculata) is an important source of protein supply for animal and human nutrition. The major storage globulins VICILIN and LEGUMIN (LEG) are synthesized from several genes including LEGA, LEGB, LEGJ and CVC (CONVICILIN). The current hypothesis is that the plant circadian core clock genes are conserved in a wide array of species and that primary metabolism is to a large extent controlled by the plant circadian clock. Our aim was to investigate a possible link between gene expression of storage proteins and the circadian clock. RESULTS We identified cowpea orthologues of the core clock genes VunLHY, VunTOC1, VunGI and VunELF3, the protein storage genes VunLEG, VunLEGJ, and VunCVC as well as nine candidate reference genes used in RT-PCR. ELONGATION FACTOR 1-A (ELF1A) resulted the most suitable reference gene. The clock genes VunELF3, VunGI, VunTOC1 and VunLHY showed a rhythmic expression profile in leaves with a typical evening/night and morning/midday phased expression. The diel patterns were not completely robust and only VungGI and VungELF3 retained a rhythmic pattern under free running conditions of darkness. Under field conditions, rhythmicity and phasing apparently faded during early pod and seed development and was regained in ripening pods for VunTOC1 and VunLHY. Mature seeds showed a rhythmic expression of VunGI resembling leaf tissue under controlled growth chamber conditions. Comparing time windows during developmental stages we found that VunCVC and VunLEG were significantly down regulated during the night in mature pods as compared to intermediate ripe pods, while changes in seeds were non-significant due to high variance. The rhythmic expression under field conditions was lost under growth chamber conditions. CONCLUSIONS The core clock gene network is conserved in cowpea leaves showing a robust diel expression pattern except VunELF3 under growth chamber conditions. There appears to be a clock transcriptional reprogramming in pods and seeds compared to leaves. Storage protein deposition may be circadian regulated under field conditions but the strong environmental signals are not met under artificial growth conditions. Diel expression pattern in field conditions may result in better usage of energy for protein storage.
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Affiliation(s)
- Julia Weiss
- Genetics, ETSIA, Instituto de Biotecnología Vegetal, Universidad Politécnica de Cartagena, 30202, Cartagena, Spain.
| | - Marta I Terry
- Genetics, ETSIA, Instituto de Biotecnología Vegetal, Universidad Politécnica de Cartagena, 30202, Cartagena, Spain
| | - Marina Martos-Fuentes
- Genetics, ETSIA, Instituto de Biotecnología Vegetal, Universidad Politécnica de Cartagena, 30202, Cartagena, Spain
| | - Lisa Letourneux
- Mapping Consulting, 26 Rue St Antoine du T, 31000, Toulouse, France
| | - Victoria Ruiz-Hernández
- Genetics, ETSIA, Instituto de Biotecnología Vegetal, Universidad Politécnica de Cartagena, 30202, Cartagena, Spain
| | - Juan A Fernández
- Producción Vegetal, ETSIA, Instituto de Biotecnología Vegetal, Universidad Politécnica de Cartagena, 30202, Cartagena, Spain
| | - Marcos Egea-Cortines
- Genetics, ETSIA, Instituto de Biotecnología Vegetal, Universidad Politécnica de Cartagena, 30202, Cartagena, Spain
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217
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Mure LS, Le HD, Benegiamo G, Chang MW, Rios L, Jillani N, Ngotho M, Kariuki T, Dkhissi-Benyahya O, Cooper HM, Panda S. Diurnal transcriptome atlas of a primate across major neural and peripheral tissues. Science 2018; 359:science.aao0318. [PMID: 29439024 DOI: 10.1126/science.aao0318] [Citation(s) in RCA: 450] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 01/24/2018] [Indexed: 12/23/2022]
Abstract
Diurnal gene expression patterns underlie time-of-the-day-specific functional specialization of tissues. However, available circadian gene expression atlases of a few organs are largely from nocturnal vertebrates. We report the diurnal transcriptome of 64 tissues, including 22 brain regions, sampled every 2 hours over 24 hours, from the primate Papio anubis (baboon). Genomic transcription was highly rhythmic, with up to 81.7% of protein-coding genes showing daily rhythms in expression. In addition to tissue-specific gene expression, the rhythmic transcriptome imparts another layer of functional specialization. Most ubiquitously expressed genes that participate in essential cellular functions exhibit rhythmic expression in a tissue-specific manner. The peak phases of rhythmic gene expression clustered around dawn and dusk, with a "quiescent period" during early night. Our findings also unveil a different temporal organization of central and peripheral tissues between diurnal and nocturnal animals.
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Affiliation(s)
- Ludovic S Mure
- Regulatory Biology Laboratory, Salk Institute for Biological Studies, 10010, North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Hiep D Le
- Regulatory Biology Laboratory, Salk Institute for Biological Studies, 10010, North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Giorgia Benegiamo
- Regulatory Biology Laboratory, Salk Institute for Biological Studies, 10010, North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Max W Chang
- Regulatory Biology Laboratory, Salk Institute for Biological Studies, 10010, North Torrey Pines Road, La Jolla, CA 92037, USA.,Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Luis Rios
- Regulatory Biology Laboratory, Salk Institute for Biological Studies, 10010, North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ngalla Jillani
- Institute of Primate Research (IPR), National Museums of Kenya, Nairobi, Kenya
| | - Maina Ngotho
- Institute of Primate Research (IPR), National Museums of Kenya, Nairobi, Kenya
| | - Thomas Kariuki
- Institute of Primate Research (IPR), National Museums of Kenya, Nairobi, Kenya
| | - Ouria Dkhissi-Benyahya
- Université Lyon, Universite Claude Bernard Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500 Bron, France
| | - Howard M Cooper
- Université Lyon, Universite Claude Bernard Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500 Bron, France.
| | - Satchidananda Panda
- Regulatory Biology Laboratory, Salk Institute for Biological Studies, 10010, North Torrey Pines Road, La Jolla, CA 92037, USA.
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218
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Zhou T, Meng L, Ma Y, Liu Q, Zhang Y, Yang Z, Yang D, Bian M. Overexpression of sweet sorghum cryptochrome 1a confers hypersensitivity to blue light, abscisic acid and salinity in Arabidopsis. PLANT CELL REPORTS 2018; 37:251-264. [PMID: 29098377 DOI: 10.1007/s00299-017-2227-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 10/16/2017] [Indexed: 05/14/2023]
Abstract
This work provides the bioinformatics, expression pattern and functional analyses of cryptochrome 1a from sweet sorghum (SbCRY1a), together with an exploration of the signaling mechanism mediated by SbCRY1a. Sweet sorghum [Sorghum bicolor (L.) Moench] is considered to be an ideal candidate for biofuel production due to its high efficiency of photosynthesis and the ability to maintain yield under harsh environmental conditions. Blue light receptor cryptochromes regulate multiple aspects of plant growth and development. Here, we reported the function and signal mechanism of sweet sorghum cryptochrome 1a (SbCRY1a) to explore its potential for genetic improvement of sweet sorghum varieties. SbCRY1a transcripts experienced almost 24 h diurnal cycling; however, its protein abundance showed no oscillation. Overexpression of SbCRY1a in Arabidopsis rescued the phenotype of cry1 mutant in a blue light-specific manner and regulated HY5 accumulation under blue light. SbCRY1a protein was present in both nucleus and cytoplasm. The photoexcited SbCRY1a interacted directly with a putative RING E3 ubiquitin ligase constitutive photomorphogenesis 1 (COP1) from sweet sorghum (SbCOP1) instead of SbSPA1 to suppress SbCOP1-SbHY5 interaction responding to blue light. These observations indicate that the function and signaling mechanism of cryptochromes are basically conservative between monocotyledons and dicotyledons. Moreover, SbCRY1a-overexpressed transgenic Arabidopsis showed oversensitive to abscisic acid (ABA) and salinity. The ABA-responsive gene ABI5 was up-regulated evidently in SbCRY1a transgenic lines, suggesting that SbCRY1a might regulate ABA signaling through the HY5-ABI5 regulon.
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Affiliation(s)
- Tingting Zhou
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, 5333 xi'an Road, Changchun, 130062, China
| | - Lingyang Meng
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, 5333 xi'an Road, Changchun, 130062, China
| | - Yue Ma
- Agronomy College of Northeast Agricultural University, 59 Wood Street, Harbin, 150030, China
| | - Qing Liu
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, 5333 xi'an Road, Changchun, 130062, China
| | - Yunyun Zhang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, 5333 xi'an Road, Changchun, 130062, China
| | - Zhenming Yang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, 5333 xi'an Road, Changchun, 130062, China
| | - Deguang Yang
- Agronomy College of Northeast Agricultural University, 59 Wood Street, Harbin, 150030, China
| | - Mingdi Bian
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, 5333 xi'an Road, Changchun, 130062, China.
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219
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Bekiaris PS, Tekath T, Staiger D, Danisman S. Computational exploration of cis-regulatory modules in rhythmic expression data using the "Exploration of Distinctive CREs and CRMs" (EDCC) and "CRM Network Generator" (CNG) programs. PLoS One 2018; 13:e0190421. [PMID: 29298348 PMCID: PMC5752016 DOI: 10.1371/journal.pone.0190421] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 12/14/2017] [Indexed: 11/19/2022] Open
Abstract
Understanding the effect of cis-regulatory elements (CRE) and clusters of CREs, which are called cis-regulatory modules (CRM), in eukaryotic gene expression is a challenge of computational biology. We developed two programs that allow simple, fast and reliable analysis of candidate CREs and CRMs that may affect specific gene expression and that determine positional features between individual CREs within a CRM. The first program, "Exploration of Distinctive CREs and CRMs" (EDCC), correlates candidate CREs and CRMs with specific gene expression patterns. For pairs of CREs, EDCC also determines positional preferences of the single CREs in relation to each other and to the transcriptional start site. The second program, "CRM Network Generator" (CNG), prioritizes these positional preferences using a neural network and thus allows unbiased rating of the positional preferences that were determined by EDCC. We tested these programs with data from a microarray study of circadian gene expression in Arabidopsis thaliana. Analyzing more than 1.5 million pairwise CRE combinations, we found 22 candidate combinations, of which several contained known clock promoter elements together with elements that had not been identified as relevant to circadian gene expression before. CNG analysis further identified positional preferences of these CRE pairs, hinting at positional information that may be relevant for circadian gene expression. Future wet lab experiments will have to determine which of these combinations confer daytime specific circadian gene expression.
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Affiliation(s)
| | - Tobias Tekath
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Dorothee Staiger
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Selahattin Danisman
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
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220
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Nejat N, Ramalingam A, Mantri N. Advances in Transcriptomics of Plants. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2018; 164:161-185. [PMID: 29392354 DOI: 10.1007/10_2017_52] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The current global population of 7.3 billion is estimated to reach 9.7 billion in the year 2050. Rapid population growth is driving up global food demand. Additionally, global climate change, environmental degradation, drought, emerging diseases, and salty soils are the current threats to global food security. In order to mitigate the adverse effects of these diverse agricultural productivity constraints and enhance crop yield and stress-tolerance in plants, we need to go beyond traditional and molecular plant breeding. The powerful new tools for genome editing, Transcription Activator-Like Effector Nucleases (TALENs) and Clustered Regulatory Interspaced Short Palindromic Repeats (CRISPR)/Cas systems (CRISPR-Cas9), have been hailed as a quantum leap forward in the development of stress-resistant plants. Plant breeding techniques, however, have several drawbacks. Hence, identification of transcriptional regulatory elements and deciphering mechanisms underlying transcriptional regulation are crucial to avoiding unintended consequences in modified crop plants, which could ultimately have negative impacts on human health. RNA splicing as an essential regulated post-transcriptional process, alternative polyadenylation as an RNA-processing mechanism, along with non-coding RNAs (microRNAs, small interfering RNAs and long non-coding RNAs) have been identified as major players in gene regulation. In this chapter, we highlight new findings on the essential roles of alternative splicing and alternative polyadenylation in plant development and response to biotic and abiotic stresses. We also discuss biogenesis and the functions of microRNAs (miRNAs) and small interfering RNAs (siRNAs) in plants and recent advances in our knowledge of the roles of miRNAs and siRNAs in plant stress response. Graphical Abstract.
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Affiliation(s)
- Naghmeh Nejat
- The Pangenomics Group, School of Science, RMIT University, Melbourne, VIC, Australia
| | - Abirami Ramalingam
- The Pangenomics Group, School of Science, RMIT University, Melbourne, VIC, Australia
| | - Nitin Mantri
- The Pangenomics Group, School of Science, RMIT University, Melbourne, VIC, Australia.
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221
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Song Y, Jiang Y, Kuai B, Li L. CIRCADIAN CLOCK-ASSOCIATED 1 Inhibits Leaf Senescence in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2018; 9:280. [PMID: 29559987 PMCID: PMC5845730 DOI: 10.3389/fpls.2018.00280] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 02/19/2018] [Indexed: 05/20/2023]
Abstract
Leaf senescence is an integral part of plant development, and the timing and progressing rate of senescence could substantially affect the yield and quality of crops. It has been known that a circadian rhythm synchronized with external environmental cues is critical for the optimal coordination of various physiological and metabolic processes. However, the reciprocal interactions between the circadian clock and leaf senescence in plants remain unknown. Here, through measuring the physiological and molecular senescence related markers of several circadian components mutants, we found that CIRCADIAN CLOCK-ASSOCIATED 1 inhibits leaf senescence. Further molecular and genetic studies revealed that CCA1 directly activates GLK2 and suppresses ORE1 expression to counteract leaf senescence. As plants age, the expression and periodic amplitude of CCA1 declines and thus weakens the inhibition of senescence. Our findings reveal an age-dependent circadian clock component of the process of leaf senescence.
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222
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Maurya JP, Triozzi PM, Bhalerao RP, Perales M. Environmentally Sensitive Molecular Switches Drive Poplar Phenology. FRONTIERS IN PLANT SCIENCE 2018; 9:1873. [PMID: 30619428 PMCID: PMC6304729 DOI: 10.3389/fpls.2018.01873] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 12/04/2018] [Indexed: 05/20/2023]
Abstract
Boreal and temperate woody perennials are highly adapted to their local climate, which delimits the length of the growing period. Moreover, seasonal control of growth-dormancy cycles impacts tree productivity and geographical distribution. Therefore, traits related to phenology are of great interest to tree breeders and particularly relevant in the context of global warming. The recent application of transcriptional profiling and genetic association studies to poplar species has provided a robust molecular framework for investigating molecules with potential links to phenology. The environment dictates phenology by modulating the expression of endogenous molecular switches, the identities of which are currently under investigation. This review outlines the current knowledge of these molecular switches in poplar and covers several perspectives concerning the environmental control of growth-dormancy cycles. In the process, we highlight certain genetic pathways which are affected by short days, low temperatures and cold-induced signaling.
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Affiliation(s)
- Jay P. Maurya
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Paolo M. Triozzi
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | - Rishikesh P. Bhalerao
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
- *Correspondence: Rishikesh P. Bhalerao, Mariano Perales,
| | - Mariano Perales
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
- *Correspondence: Rishikesh P. Bhalerao, Mariano Perales,
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223
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SEKI N, TANIGAKI Y, YOSHIDA A, FUKUDA H. Spatiotemporal Analysis of Localized Circadian Arrhythmias in Plant Roots. ACTA ACUST UNITED AC 2018. [DOI: 10.2525/ecb.56.93] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Naoki SEKI
- Graduate School of Engineering, Osaka Prefecture University
| | | | | | - Hirokazu FUKUDA
- Graduate School of Engineering, Osaka Prefecture University
- Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology
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224
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Inoue K, Araki T, Endo M. Circadian clock during plant development. JOURNAL OF PLANT RESEARCH 2018; 131:59-66. [PMID: 29134443 PMCID: PMC5897470 DOI: 10.1007/s10265-017-0991-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 10/06/2017] [Indexed: 05/14/2023]
Abstract
Plants have endogenous biological clocks that allow organisms to anticipate and prepare for daily and seasonal environmental changes and increase their fitness in changing environments. The circadian clock in plants, as in animals and insects, mainly consists of multiple interlocking transcriptional/translational feedback loops. The circadian clock can be entrained by environmental cues such as light, temperature and nutrient status to synchronize internal biological rhythms with surrounding environments. Output pathways link the circadian oscillator to various physiological, developmental, and reproductive processes for adjusting the timing of these biological processes to an appropriate time of day or a suitable season. Recent genomic studies have demonstrated that polymorphism in circadian clock genes may contribute to local adaptations over a wide range of latitudes in many plant species. In the present review, we summarize the circadian regulation of biological processes throughout the life cycle of plants, and describe the contribution of the circadian clock to local adaptation.
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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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225
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Johnson-Buck A, Shih WM. Single-Molecule Clocks Controlled by Serial Chemical Reactions. NANO LETTERS 2017; 17:7940-7944. [PMID: 29090576 PMCID: PMC6090534 DOI: 10.1021/acs.nanolett.7b04336] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Chemical clocks usually achieve well-defined temporal delays through concentration thresholding coupled to the production, degradation, activation, or inhibition of downstream effectors. In this way, the stochastic dynamics of many individual molecules yield essentially deterministic bulk behavior through ensemble averaging. As a result, their temporal evolution is governed by ensemble dynamics rather than by the behavior of an individual molecule or complex. Here, we present a general approach for the design of single-molecule clocks that permits quasi-deterministic control over the lifetime of single molecular interactions without any external synchronization. By coupling the dissociation of a bimolecular complex to a series of irreversible chemical steps, we interpose a well-defined time delay between binding and dissociation. The number and speed of irreversible steps can be varied to systematically tune both the lifetimes of complexes and the precision of the time delay, raising the prospect of localized timekeeping in nanoscale systems and devices.
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Affiliation(s)
- Alexander Johnson-Buck
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, Massachusetts 02115, United States
- Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Present Address: Department of Internal Medicine, The University of Michigan, Ann Arbor, Michigan, 48109, United States
| | - William M. Shih
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, Massachusetts 02115, United States
- Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
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226
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Cui P, Zhong T, Wang Z, Wang T, Zhao H, Liu C, Lu H. Identification of human circadian genes based on time course gene expression profiles by using a deep learning method. Biochim Biophys Acta Mol Basis Dis 2017; 1864:2274-2283. [PMID: 29241666 DOI: 10.1016/j.bbadis.2017.12.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 11/28/2017] [Accepted: 12/03/2017] [Indexed: 01/11/2023]
Abstract
Circadian genes express periodically in an approximate 24-h period and the identification and study of these genes can provide deep understanding of the circadian control which plays significant roles in human health. Although many circadian gene identification algorithms have been developed, large numbers of false positives and low coverage are still major problems in this field. In this study we constructed a novel computational framework for circadian gene identification using deep neural networks (DNN) - a deep learning algorithm which can represent the raw form of data patterns without imposing assumptions on the expression distribution. Firstly, we transformed time-course gene expression data into categorical-state data to denote the changing trend of gene expression. Two distinct expression patterns emerged after clustering of the state data for circadian genes from our manually created learning dataset. DNN was then applied to discriminate the aperiodic genes and the two subtypes of periodic genes. In order to assess the performance of DNN, four commonly used machine learning methods including k-nearest neighbors, logistic regression, naïve Bayes, and support vector machines were used for comparison. The results show that the DNN model achieves the best balanced precision and recall. Next, we conducted large scale circadian gene detection using the trained DNN model for the remaining transcription profiles. Comparing with JTK_CYCLE and a study performed by Möller-Levet et al. (doi: https://doi.org/10.1073/pnas.1217154110), we identified 1132 novel periodic genes. Through the functional analysis of these novel circadian genes, we found that the GTPase superfamily exhibits distinct circadian expression patterns and may provide a molecular switch of circadian control of the functioning of the immune system in human blood. Our study provides novel insights into both the circadian gene identification field and the study of complex circadian-driven biological control. This article is part of a Special Issue entitled: Accelerating Precision Medicine through Genetic and Genomic Big Data Analysis edited by Yudong Cai & Tao Huang.
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Affiliation(s)
- Peng Cui
- School of Life Science and Biotechnology, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, China; SJTU-Yale Joint Center for Biostatistics, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, China
| | - Tingyan Zhong
- School of Life Science and Biotechnology, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, China; SJTU-Yale Joint Center for Biostatistics, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, China
| | - Zhuo Wang
- School of Life Science and Biotechnology, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, China
| | - Tao Wang
- School of Life Science and Biotechnology, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, China; SJTU-Yale Joint Center for Biostatistics, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, China
| | - Hongyu Zhao
- SJTU-Yale Joint Center for Biostatistics, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, China; Department of Biostatistics, Yale University, New Heaven, USA
| | - Chenglin Liu
- School of Life Science and Biotechnology, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, China.
| | - Hui Lu
- School of Life Science and Biotechnology, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, China; SJTU-Yale Joint Center for Biostatistics, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, China.
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227
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Kim JA, Kim HS, Choi SH, Jang JY, Jeong MJ, Lee SI. The Importance of the Circadian Clock in Regulating Plant Metabolism. Int J Mol Sci 2017; 18:E2680. [PMID: 29232921 PMCID: PMC5751282 DOI: 10.3390/ijms18122680] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 12/07/2017] [Accepted: 12/08/2017] [Indexed: 11/16/2022] Open
Abstract
Carbohydrates are the primary energy source for plant development. Plants synthesize sucrose in source organs and transport them to sink organs during plant growth. This metabolism is sensitive to environmental changes in light quantity, quality, and photoperiod. In the daytime, the synthesis of sucrose and starch accumulates, and starch is degraded at nighttime. The circadian clock genes provide plants with information on the daily environmental changes and directly control many developmental processes, which are related to the path of primary metabolites throughout the life cycle. The circadian clock mechanism and processes of metabolism controlled by the circadian rhythm were studied in the model plant Arabidopsis and in the crops potato and rice. However, the translation of molecular mechanisms obtained from studies of model plants to crop plants is still difficult. Crop plants have specific organs such as edible seed and tuber that increase the size or accumulate valuable metabolites by harvestable metabolic components. Human consumers are interested in the regulation and promotion of these agriculturally significant crops. Circadian clock manipulation may suggest various strategies for the increased productivity of food crops through using environmental signal or overcoming environmental stress.
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Affiliation(s)
- Jin A Kim
- National Academy of Agricultural Science, Rural Development Administration, 370, Nongsaengmyeong-ro, Wansan-gu, Jeonju-si, Jeollabuk-do 560-500, Korea.
| | - Hyun-Soon Kim
- Plant System Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea.
| | - Seo-Hwa Choi
- National Academy of Agricultural Science, Rural Development Administration, 370, Nongsaengmyeong-ro, Wansan-gu, Jeonju-si, Jeollabuk-do 560-500, Korea.
| | - Ji-Young Jang
- Plant System Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea.
| | - Mi-Jeong Jeong
- National Academy of Agricultural Science, Rural Development Administration, 370, Nongsaengmyeong-ro, Wansan-gu, Jeonju-si, Jeollabuk-do 560-500, Korea.
| | - Soo In Lee
- National Academy of Agricultural Science, Rural Development Administration, 370, Nongsaengmyeong-ro, Wansan-gu, Jeonju-si, Jeollabuk-do 560-500, Korea.
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228
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Improving Gene Regulatory Network Inference by Incorporating Rates of Transcriptional Changes. Sci Rep 2017; 7:17244. [PMID: 29222512 PMCID: PMC5722905 DOI: 10.1038/s41598-017-17143-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 11/22/2017] [Indexed: 11/18/2022] Open
Abstract
Organisms respond to changes in their environment through transcriptional regulatory networks (TRNs). The regulatory hierarchy of these networks can be inferred from expression data. Computational approaches to identify TRNs can be applied in any species where quality RNA can be acquired, However, ChIP-Seq and similar validation methods are challenging to employ in non-model species. Improving the accuracy of computational inference methods can significantly reduce the cost and time of subsequent validation experiments. We have developed ExRANGES, an approach that improves the ability to computationally infer TRN from time series expression data. ExRANGES utilizes both the rate of change in expression and the absolute expression level to identify TRN connections. We evaluated ExRANGES in five data sets from different model systems. ExRANGES improved the identification of experimentally validated transcription factor targets for all species tested, even in unevenly spaced and sparse data sets. This improved ability to predict known regulator-target relationships enhances the utility of network inference approaches in non-model species where experimental validation is challenging. We integrated ExRANGES with two different network construction approaches and it has been implemented as an R package available here: http://github.com/DohertyLab/ExRANGES. To install the package type: devtools::install_github(“DohertyLab/ExRANGES”).
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229
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Oakenfull RJ, Davis SJ. Shining a light on the Arabidopsis circadian clock. PLANT, CELL & ENVIRONMENT 2017; 40:2571-2585. [PMID: 28732105 DOI: 10.1111/pce.13033] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 07/10/2017] [Accepted: 07/11/2017] [Indexed: 05/23/2023]
Abstract
The circadian clock provides essential timing information to ensure optimal growth to prevailing external environmental conditions. A major time-setting mechanism (zeitgeber) in clock synchronization is light. Differing light wavelengths, intensities, and photoperiodic duration are processed for the clock-setting mechanism. Many studies on light-input pathways to the clock have focused on Arabidopsis thaliana. Photoreceptors are specific chromic proteins that detect light signals and transmit this information to the central circadian oscillator through a number of different signalling mechanisms. The most well-characterized clock-mediating photoreceptors are cryptochromes and phytochromes, detecting blue, red, and far-red wavelengths of light. Ultraviolet and shaded light are also processed signals to the oscillator. Notably, the clock reciprocally generates rhythms of photoreceptor action leading to so-called gating of light responses. Intermediate proteins, such as Phytochrome interacting factors (PIFs), constitutive photomorphogenic 1 (COP1) and EARLY FLOWERING 3 (ELF3), have been established in signalling pathways downstream of photoreceptor activation. However, the precise details for these signalling mechanisms are not fully established. This review highlights both historical and recent efforts made to understand overall light input to the oscillator, first looking at how each wavelength of light is detected, this is then related to known input mechanisms and their interactions.
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Affiliation(s)
| | - Seth J Davis
- Department of Biology, University of York, York, YO10 5DD, UK
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230
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Taybi T, Cushman JC, Borland AM. Leaf carbohydrates influence transcriptional and post-transcriptional regulation of nocturnal carboxylation and starch degradation in the facultative CAM plant, Mesembryanthemum crystallinum. JOURNAL OF PLANT PHYSIOLOGY 2017; 218:144-154. [PMID: 28822907 DOI: 10.1016/j.jplph.2017.07.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 07/19/2017] [Accepted: 07/28/2017] [Indexed: 05/09/2023]
Abstract
Nocturnal degradation of transitory starch is a limiting factor for the optimal function of crassulacean acid metabolism and must be coordinated with phosphoenolypyruvate carboxylase (PEPC)-mediated CO2 uptake to optimise carbon gain over the diel cycle. The aim of this study was to test the hypothesis that nocturnal carboxylation is coordinated with starch degradation in CAM via a mechanism whereby the products of these pathways regulate diel transcript abundance and enzyme activities for both processes. To test this hypothesis, a starch and CAM-deficient mutant of Mesembryanthemum crystallinum was compared with wild type plants under well-watered and saline (CAM-inducing) conditions. Exposure to salinity increased the transcript abundance of genes required for nocturnal carboxylation, starch and sucrose degradation in both wild type and mutant, but the transcript abundance of several of these genes was not sustained over the dark period in the low-carbohydrate, CAM-deficient mutant. The diel pattern of transcript abundance for PEPC mirrored that of PEPC protein, as did the transcripts, protein, and activity of chloroplastic starch phosphorylase in both wild type and mutant, suggesting robust diel coordination of these metabolic processes. Activities of several amylase isoforms were low or lacking in the mutant, whilst the activity of a cytosolic isoform of starch phosphorylase was significantly elevated, indicating contrasting modes of metabolic regulation for the hydrolytic and phosphorylytic routes of starch degradation. Externally supplied sucrose resulted in an increase in nocturnal transcript abundance of genes required for nocturnal carboxylation and starch degradation. These results demonstrate that carbohydrates impact on transcriptional and post-transcriptional regulation of nocturnal carboxylation and starch degradation in CAM.
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Affiliation(s)
- Tahar Taybi
- School of Natural & Environmental Sciences, Ridley Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.
| | - John C Cushman
- Department of Biochemistry and Molecular Biology, MS330, University of Nevada, Reno, NV 89557 USA
| | - Anne M Borland
- School of Natural & Environmental Sciences, Ridley Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
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231
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Jenkins GI. Photomorphogenic responses to ultraviolet-B light. PLANT, CELL & ENVIRONMENT 2017; 40:2544-2557. [PMID: 28183154 DOI: 10.1111/pce.12934] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 02/03/2017] [Accepted: 02/04/2017] [Indexed: 05/18/2023]
Abstract
Exposure to ultraviolet B (UV-B) light regulates numerous aspects of plant metabolism, morphology and physiology through the differential expression of hundreds of genes. Photomorphogenic responses to UV-B are mediated by the photoreceptor UV RESISTANCE LOCUS8 (UVR8). Considerable progress has been made in understanding UVR8 action: the structural basis of photoreceptor function, how interaction with CONSTITUTIVELY PHOTOMORPHOGENIC 1 initiates signaling and how REPRESSOR OF UV-B PHOTOMORPHOGENESIS proteins negatively regulate UVR8 action. In addition, recent research shows that UVR8 mediates several responses through interaction with other signaling pathways, in particular auxin signaling. Nevertheless, many aspects of UVR8 action remain poorly understood. Most research to date has been undertaken with Arabidopsis, and it is important to explore the functions and regulation of UVR8 in diverse plant species. Furthermore, it is essential to understand how UVR8, and UV-B signaling in general, regulates processes under natural growth conditions. Ultraviolet B regulates the expression of many genes through UVR8-independent pathways, but the activity and importance of these pathways in plants growing in sunlight are poorly understood.
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Affiliation(s)
- Gareth I Jenkins
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, Bower Building, University of Glasgow, Glasgow, G12 8QQ, UK
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232
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The plant circadian clock influences rhizosphere community structure and function. ISME JOURNAL 2017; 12:400-410. [PMID: 29053146 PMCID: PMC5776454 DOI: 10.1038/ismej.2017.172] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 08/02/2017] [Accepted: 08/09/2017] [Indexed: 01/22/2023]
Abstract
Plants alter chemical and physical properties of soil, and thereby influence rhizosphere microbial community structure. The structure of microbial communities may in turn affect plant performance. Yet, outside of simple systems with pairwise interacting partners, the plant genetic pathways that influence microbial community structure remain largely unknown, as are the performance feedbacks of microbial communities selected by the host plant genotype. We investigated the role of the plant circadian clock in shaping rhizosphere community structure and function. We performed 16S ribosomal RNA gene sequencing to characterize rhizosphere bacterial communities of Arabidopsis thaliana between day and night time points, and tested for differences in community structure between wild-type (Ws) vs clock mutant (toc1-21, ztl-30) genotypes. We then characterized microbial community function, by growing wild-type plants in soils with an overstory history of Ws, toc1-21 or ztl-30 and measuring plant performance. We observed that rhizosphere community structure varied between day and night time points, and clock misfunction significantly altered rhizosphere communities. Finally, wild-type plants germinated earlier and were larger when inoculated with soils having an overstory history of wild-type in comparison with clock mutant genotypes. Our findings suggest the circadian clock of the plant host influences rhizosphere community structure and function.
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233
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Huang H, Gehan MA, Huss SE, Alvarez S, Lizarraga C, Gruebbling EL, Gierer J, Naldrett MJ, Bindbeutel RK, Evans BS, Mockler TC, Nusinow DA. Cross-species complementation reveals conserved functions for EARLY FLOWERING 3 between monocots and dicots. PLANT DIRECT 2017; 1:e00018. [PMID: 31245666 PMCID: PMC6508535 DOI: 10.1002/pld3.18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/10/2017] [Accepted: 09/13/2017] [Indexed: 05/03/2023]
Abstract
Plant responses to the environment are shaped by external stimuli and internal signaling pathways. In both the model plant Arabidopsis thaliana (Arabidopsis) and crop species, circadian clock factors are critical for growth, flowering, and circadian rhythms. Outside of Arabidopsis, however, little is known about the molecular function of clock gene products. Therefore, we sought to compare the function of Brachypodium distachyon (Brachypodium) and Setaria viridis (Setaria) orthologs of EARLY FLOWERING 3, a key clock gene in Arabidopsis. To identify both cycling genes and putative ELF3 functional orthologs in Setaria, a circadian RNA-seq dataset and online query tool (Diel Explorer) were generated to explore expression profiles of Setaria genes under circadian conditions. The function of ELF3 orthologs from Arabidopsis, Brachypodium, and Setaria was tested for complementation of an elf3 mutation in Arabidopsis. We find that both monocot orthologs were capable of rescuing hypocotyl elongation, flowering time, and arrhythmic clock phenotypes. Using affinity purification and mass spectrometry, our data indicate that BdELF3 and SvELF3 could be integrated into similar complexes in vivo as AtELF3. Thus, we find that, despite 180 million years of separation, BdELF3 and SvELF3 can functionally complement loss of ELF3 at the molecular and physiological level.
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Affiliation(s)
- He Huang
- Donald Danforth Plant Science CenterSt. LouisMOUSA
| | | | | | - Sophie Alvarez
- Donald Danforth Plant Science CenterSt. LouisMOUSA
- Present address:
University of Nebraska‐LincolnLincolnNEUSA
| | | | | | - John Gierer
- Donald Danforth Plant Science CenterSt. LouisMOUSA
| | - Michael J. Naldrett
- Donald Danforth Plant Science CenterSt. LouisMOUSA
- Present address:
University of Nebraska‐LincolnLincolnNEUSA
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234
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Linde A, Eklund DM, Kubota A, Pederson ERA, Holm K, Gyllenstrand N, Nishihama R, Cronberg N, Muranaka T, Oyama T, Kohchi T, Lagercrantz U. Early evolution of the land plant circadian clock. THE NEW PHYTOLOGIST 2017; 216:576-590. [PMID: 28244104 PMCID: PMC5638080 DOI: 10.1111/nph.14487] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 01/18/2017] [Indexed: 05/21/2023]
Abstract
While angiosperm clocks can be described as an intricate network of interlocked transcriptional feedback loops, clocks of green algae have been modelled as a loop of only two genes. To investigate the transition from a simple clock in algae to a complex one in angiosperms, we performed an inventory of circadian clock genes in bryophytes and charophytes. Additionally, we performed functional characterization of putative core clock genes in the liverwort Marchantia polymorpha and the hornwort Anthoceros agrestis. Phylogenetic construction was combined with studies of spatiotemporal expression patterns and analysis of M. polymorpha clock gene mutants. Homologues to core clock genes identified in Arabidopsis were found not only in bryophytes but also in charophytes, albeit in fewer copies. Circadian rhythms were detected for most identified genes in M. polymorpha and A. agrestis, and mutant analysis supports a role for putative clock genes in M. polymorpha. Our data are in line with a recent hypothesis that adaptation to terrestrial life occurred earlier than previously expected in the evolutionary history of charophyte algae. Both gene duplication and acquisition of new genes was important in the evolution of the plant circadian clock, but gene loss has also contributed to shaping the clock of bryophytes.
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Affiliation(s)
- Anna‐Malin Linde
- Department of Plant Ecology and EvolutionEvolutionary Biology CentreUppsala UniversityNorbyvägen 18DSE‐75236UppsalaSweden
- The Linnean Centre for Plant Biology in UppsalaUppsalaSweden
| | - D. Magnus Eklund
- Department of Plant Ecology and EvolutionEvolutionary Biology CentreUppsala UniversityNorbyvägen 18DSE‐75236UppsalaSweden
- The Linnean Centre for Plant Biology in UppsalaUppsalaSweden
| | - Akane Kubota
- Graduate School of BiostudiesKyoto UniversityKyoto606‐8502Japan
| | - Eric R. A. Pederson
- Department of Plant Ecology and EvolutionEvolutionary Biology CentreUppsala UniversityNorbyvägen 18DSE‐75236UppsalaSweden
- The Linnean Centre for Plant Biology in UppsalaUppsalaSweden
| | - Karl Holm
- Department of Plant Ecology and EvolutionEvolutionary Biology CentreUppsala UniversityNorbyvägen 18DSE‐75236UppsalaSweden
- The Linnean Centre for Plant Biology in UppsalaUppsalaSweden
| | - Niclas Gyllenstrand
- Department of Plant Ecology and EvolutionEvolutionary Biology CentreUppsala UniversityNorbyvägen 18DSE‐75236UppsalaSweden
- The Linnean Centre for Plant Biology in UppsalaUppsalaSweden
| | | | - Nils Cronberg
- Department of BiologyLund UniversityEcology BuildingSE‐22362LundSweden
| | | | - Tokitaka Oyama
- Graduate School of ScienceKyoto UniversityKyoto606‐8502Japan
| | - Takayuki Kohchi
- Graduate School of BiostudiesKyoto UniversityKyoto606‐8502Japan
| | - Ulf Lagercrantz
- Department of Plant Ecology and EvolutionEvolutionary Biology CentreUppsala UniversityNorbyvägen 18DSE‐75236UppsalaSweden
- The Linnean Centre for Plant Biology in UppsalaUppsalaSweden
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235
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Jończyk M, Sobkowiak A, Trzcinska-Danielewicz J, Skoneczny M, Solecka D, Fronk J, Sowiński P. Global analysis of gene expression in maize leaves treated with low temperature. II. Combined effect of severe cold (8 °C) and circadian rhythm. PLANT MOLECULAR BIOLOGY 2017; 95:279-302. [PMID: 28828699 DOI: 10.1007/s11103-017-0651-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 08/06/2017] [Indexed: 05/27/2023]
Abstract
In maize seedlings, severe cold results in dysregulation of circadian pattern of gene expression causing profound modulation of transcription of genes related to photosynthesis and other key biological processes. Plants live highly cyclic life and their response to environmental stresses must allow for underlying biological rhythms. To study the interplay of a stress and a rhythmic cue we investigated transcriptomic response of maize seedlings to low temperature in the context of diurnal gene expression. Severe cold stress had pronounced effect on the circadian rhythm of a substantial proportion of genes. Their response was strikingly dual, comprising either flattening (partial or complete) of the diel amplitude or delay of expression maximum/minimum by several hours. Genes encoding central oscillator components behaved in the same dual manner, unlike their Arabidopsis counterparts reported earlier to cease cycling altogether upon cold treatment. Also numerous genes lacking circadian rhythm responded to the cold by undergoing up- or down-regulation. Notably, the transcriptome changes preceded major physiological manifestations of cold stress. In silico analysis of metabolic processes likely affected by observed gene expression changes indicated major down-regulation of photosynthesis, profound and multifarious modulation of plant hormone levels, and of chromatin structure, transcription, and translation. A role of trehalose and stachyose in cold stress signaling was also suggested. Meta-analysis of published transcriptomic data allowed discrimination between general stress response of maize and that unique to severe cold. Several cis- and trans-factors likely involved in the latter were predicted, albeit none of them seemed to have a major role. These results underscore a key role of modulation of diel gene expression in maize response to severe cold and the unique character of the cold-response of the maize circadian clock.
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Affiliation(s)
- M Jończyk
- Department of Plant Molecular Ecophysiology, Institute of Plant Experimental Biology and Biotechnology, Faculty of Biology, University of Warsaw, Miecznikowa 1, Warszawa, Poland
| | - A Sobkowiak
- Department of Plant Molecular Ecophysiology, Institute of Plant Experimental Biology and Biotechnology, Faculty of Biology, University of Warsaw, Miecznikowa 1, Warszawa, Poland
| | - J Trzcinska-Danielewicz
- Department of Molecular Biology, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Miecznikowa 1, Warszawa, Poland
| | - M Skoneczny
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, Warszawa, Poland
| | - D Solecka
- Department of Plant Molecular Ecophysiology, Institute of Plant Experimental Biology and Biotechnology, Faculty of Biology, University of Warsaw, Miecznikowa 1, Warszawa, Poland
| | - J Fronk
- Department of Molecular Biology, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Miecznikowa 1, Warszawa, Poland
| | - P Sowiński
- Department of Plant Molecular Ecophysiology, Institute of Plant Experimental Biology and Biotechnology, Faculty of Biology, University of Warsaw, Miecznikowa 1, Warszawa, Poland.
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236
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Agostinelli F, Ceglia N, Shahbaba B, Sassone-Corsi P, Baldi P. What time is it? Deep learning approaches for circadian rhythms. Bioinformatics 2017; 32:i8-i17. [PMID: 27307647 PMCID: PMC4908327 DOI: 10.1093/bioinformatics/btw243] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Motivation: Circadian rhythms date back to the origins of life, are found in virtually every species and every cell, and play fundamental roles in functions ranging from metabolism to cognition. Modern high-throughput technologies allow the measurement of concentrations of transcripts, metabolites and other species along the circadian cycle creating novel computational challenges and opportunities, including the problems of inferring whether a given species oscillate in circadian fashion or not, and inferring the time at which a set of measurements was taken. Results: We first curate several large synthetic and biological time series datasets containing labels for both periodic and aperiodic signals. We then use deep learning methods to develop and train BIO_CYCLE, a system to robustly estimate which signals are periodic in high-throughput circadian experiments, producing estimates of amplitudes, periods, phases, as well as several statistical significance measures. Using the curated data, BIO_CYCLE is compared to other approaches and shown to achieve state-of-the-art performance across multiple metrics. We then use deep learning methods to develop and train BIO_CLOCK to robustly estimate the time at which a particular single-time-point transcriptomic experiment was carried. In most cases, BIO_CLOCK can reliably predict time, within approximately 1 h, using the expression levels of only a small number of core clock genes. BIO_CLOCK is shown to work reasonably well across tissue types, and often with only small degradation across conditions. BIO_CLOCK is used to annotate most mouse experiments found in the GEO database with an inferred time stamp. Availability and Implementation: All data and software are publicly available on the CircadiOmics web portal: circadiomics.igb.uci.edu/. Contacts:fagostin@uci.edu or pfbaldi@uci.edu Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | | | - Paolo Sassone-Corsi
- Department of Biological Chemistry, University of California-Irvine, Irvine, CA 92697, USA
| | - Pierre Baldi
- Department of Computer Science, Department of Biological Chemistry, University of California-Irvine, Irvine, CA 92697, USA
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237
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Greenham K, Guadagno CR, Gehan MA, Mockler TC, Weinig C, Ewers BE, McClung CR. Temporal network analysis identifies early physiological and transcriptomic indicators of mild drought in Brassica rapa. eLife 2017; 6:e29655. [PMID: 28826479 PMCID: PMC5628015 DOI: 10.7554/elife.29655] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 08/11/2017] [Indexed: 11/13/2022] Open
Abstract
The dynamics of local climates make development of agricultural strategies challenging. Yield improvement has progressed slowly, especially in drought-prone regions where annual crop production suffers from episodic aridity. Underlying drought responses are circadian and diel control of gene expression that regulate daily variations in metabolic and physiological pathways. To identify transcriptomic changes that occur in the crop Brassica rapa during initial perception of drought, we applied a co-expression network approach to associate rhythmic gene expression changes with physiological responses. Coupled analysis of transcriptome and physiological parameters over a two-day time course in control and drought-stressed plants provided temporal resolution necessary for correlation of network modules with dynamic changes in stomatal conductance, photosynthetic rate, and photosystem II efficiency. This approach enabled the identification of drought-responsive genes based on their differential rhythmic expression profiles in well-watered versus droughted networks and provided new insights into the dynamic physiological changes that occur during drought.
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Affiliation(s)
- Kathleen Greenham
- Department of Biological SciencesDartmouth CollegeHanoverUnited States
| | | | - Malia A Gehan
- Donald Danforth Plant Science CenterSt. LouisUnited States
| | - Todd C Mockler
- Donald Danforth Plant Science CenterSt. LouisUnited States
| | - Cynthia Weinig
- Department of BotanyUniversity of WyomingLaramieUnited States
- Department of Molecular BiologyUniversity of WyomingLaramieUnited States
- Program in EcologyUniversity of WyomingLaramieUnited States
| | - Brent E Ewers
- Department of BotanyUniversity of WyomingLaramieUnited States
- Program in EcologyUniversity of WyomingLaramieUnited States
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Lu H, McClung CR, Zhang C. Tick Tock: Circadian Regulation of Plant Innate Immunity. ANNUAL REVIEW OF PHYTOPATHOLOGY 2017; 55:287-311. [PMID: 28590878 DOI: 10.1146/annurev-phyto-080516-035451] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Many living organisms on Earth have evolved the ability to integrate environmental and internal signals to determine time and thereafter adjust appropriately their metabolism, physiology, and behavior. The circadian clock is the endogenous timekeeper critical for multiple biological processes in many organisms. A growing body of evidence supports the importance of the circadian clock for plant health. Plants activate timed defense with various strategies to anticipate daily attacks of pathogens and pests and to modulate responses to specific invaders in a time-of-day-dependent manner (gating). Pathogen infection is also known to reciprocally modulate clock activity. Such a cross talk likely reflects the adaptive nature of plants to coordinate limited resources for growth, development, and defense. This review summarizes recent progress in circadian regulation of plant innate immunity with a focus on the molecular events linking the circadian clock and defense. More and better knowledge of clock-defense cross talk could help to improve disease resistance and productivity in economically important crops.
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Affiliation(s)
- Hua Lu
- Department of Biological Sciences, University of Maryland-Baltimore County, Baltimore, Maryland 21052;
| | - C Robertson McClung
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755
| | - Chong Zhang
- Department of Biological Sciences, University of Maryland-Baltimore County, Baltimore, Maryland 21052;
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239
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Joo Y, Fragoso V, Yon F, Baldwin IT, Kim SG. Circadian clock component, LHY, tells a plant when to respond photosynthetically to light in nature. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2017; 59:572-587. [PMID: 28429400 DOI: 10.1111/jipb.12547] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 04/18/2017] [Indexed: 05/14/2023]
Abstract
The circadian clock is known to increase plant growth and fitness, and is thought to prepare plants for photosynthesis at dawn and dusk; whether this happens in nature was unknown. We transformed the native tobacco, Nicotiana attenuata to silence two core clock components, NaLHY (irLHY) and NaTOC1 (irTOC1). We characterized growth and light- and dark-adapted photosynthetic rates (Ac ) throughout a 24 h day in empty vector-transformed (EV), irLHY, and irTOC1 plants in the field, and in NaPhyA- and NaPhyB1-silenced plants in the glasshouse. The growth rates of irLHY plants were lower than those of EV plants in the field. While irLHY plants reduced Ac earlier at dusk, no differences between irLHY and EV plants were observed at dawn in the field. irLHY, but not EV plants, responded to light in the night by rapidly increasing Ac . Under controlled conditions, EV plants rapidly increased Ac in the day compared to dark-adapted plants at night; irLHY plants lost these time-dependent responses. The role of NaLHY in gating photosynthesis is independent of the light-dependent reactions and red light perceived by NaPhyA, but not NaPhyB1. In summary, the circadian clock allows plants not to respond photosynthetically to light at night by anticipating and gating red light-mediated in native tobacco.
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Affiliation(s)
- Youngsung Joo
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Variluska Fragoso
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Felipe Yon
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Ian T Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Sang-Gyu Kim
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
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240
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Burow M, Halkier BA. How does a plant orchestrate defense in time and space? Using glucosinolates in Arabidopsis as case study. CURRENT OPINION IN PLANT BIOLOGY 2017; 38:142-147. [PMID: 28575680 DOI: 10.1016/j.pbi.2017.04.009] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 04/06/2017] [Accepted: 04/10/2017] [Indexed: 05/20/2023]
Abstract
The sessile nature of plants has caused plants to develop means to defend themselves against attacking organisms. Multiple strategies range from physical barriers to chemical warfare including pre-formed anticipins as well as phytoalexins produced only upon attack. While phytoalexins require rapid induction, constitutive defenses can impose ecological costs if they deter pollinators or attract specialized herbivores. In the model Arabidopsis thaliana, the well-characterized glucosinolate anticipins are categorized into different classes, aliphatic and indole glucosinolates, depending on their amino acid precursor. Using glucosinolates in Arabidopsis as case study, we will discuss how plants orchestrate synthesis, storage and activation of pre-formed defense compounds spatially and temporally.
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Affiliation(s)
- Meike Burow
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Barbara Ann Halkier
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark.
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241
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Feng D, Wang Y, Lu T, Zhang Z, Han X. Proteomics analysis reveals a dynamic diurnal pattern of photosynthesis-related pathways in maize leaves. PLoS One 2017; 12:e0180670. [PMID: 28732011 PMCID: PMC5521766 DOI: 10.1371/journal.pone.0180670] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 06/19/2017] [Indexed: 11/18/2022] Open
Abstract
Plant leaves exhibit differentiated patterns of photosynthesis rates under diurnal light regulation. Maize leaves show a single-peak pattern without photoinhibition at midday when the light intensity is maximized. This mechanism contributes to highly efficient photosynthesis in maize leaves. To understand the molecular basis of this process, an isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomics analysis was performed to reveal the dynamic pattern of proteins related to photosynthetic reactions. Steady, single-peak and double-peak protein expression patterns were discovered in maize leaves, and antenna proteins in these leaves displayed a steady pattern. In contrast, the photosystem, carbon fixation and citrate pathways were highly controlled by diurnal light intensity. Most enzymes in the limiting steps of these pathways were major sites of regulation. Thus, maize leaves optimize photosynthesis and carbon fixation outside of light harvesting to adapt to the changes in diurnal light intensity at the protein level.
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Affiliation(s)
- Dan Feng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Yanwei Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Tiegang Lu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Zhiguo Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
- * E-mail: (ZZ); (XH)
| | - Xiao Han
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
- * E-mail: (ZZ); (XH)
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242
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Schmelling NM, Lehmann R, Chaudhury P, Beck C, Albers SV, Axmann IM, Wiegard A. Minimal tool set for a prokaryotic circadian clock. BMC Evol Biol 2017; 17:169. [PMID: 28732467 PMCID: PMC5520375 DOI: 10.1186/s12862-017-0999-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 06/15/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Circadian clocks are found in organisms of almost all domains including photosynthetic Cyanobacteria, whereby large diversity exists within the protein components involved. In the model cyanobacterium Synechococcus elongatus PCC 7942 circadian rhythms are driven by a unique KaiABC protein clock, which is embedded in a network of input and output factors. Homologous proteins to the KaiABC clock have been observed in Bacteria and Archaea, where evidence for circadian behavior in these domains is accumulating. However, interaction and function of non-cyanobacterial Kai-proteins as well as homologous input and output components remain mainly unclear. RESULTS Using a universal BLAST analyses, we identified putative KaiC-based timing systems in organisms outside as well as variations within Cyanobacteria. A systematic analyses of publicly available microarray data elucidated interesting variations in circadian gene expression between different cyanobacterial strains, which might be correlated to the diversity of genome encoded clock components. Based on statistical analyses of co-occurrences of the clock components homologous to Synechococcus elongatus PCC 7942, we propose putative networks of reduced and fully functional clock systems. Further, we studied KaiC sequence conservation to determine functionally important regions of diverged KaiC homologs. Biochemical characterization of exemplary cyanobacterial KaiC proteins as well as homologs from two thermophilic Archaea demonstrated that kinase activity is always present. However, a KaiA-mediated phosphorylation is only detectable in KaiC1 orthologs. CONCLUSION Our analysis of 11,264 genomes clearly demonstrates that components of the Synechococcus elongatus PCC 7942 circadian clock are present in Bacteria and Archaea. However, all components are less abundant in other organisms than Cyanobacteria and KaiA, Pex, LdpA, and CdpA are only present in the latter. Thus, only reduced KaiBC-based or even simpler, solely KaiC-based timing systems might exist outside of the cyanobacterial phylum, which might be capable of driving diurnal oscillations.
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Affiliation(s)
- Nicolas M. Schmelling
- Institute for Synthetic Microbiology, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, Duesseldorf, 40225 Germany
| | - Robert Lehmann
- Institute for Theoretical Biology, Humboldt University Berlin, Invalidenstrasse 43, Berlin, 10115 Germany
| | - Paushali Chaudhury
- Molecular Biology of Archaea, Albert-Ludwigs-University Freiburg, Institute of Biology II, Schaenzlestrasse 1, Freiburg, 79104 Germany
| | - Christian Beck
- Institute for Theoretical Biology, Humboldt University Berlin, Invalidenstrasse 43, Berlin, 10115 Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Albert-Ludwigs-University Freiburg, Institute of Biology II, Schaenzlestrasse 1, Freiburg, 79104 Germany
| | - Ilka M. Axmann
- Institute for Synthetic Microbiology, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, Duesseldorf, 40225 Germany
| | - Anika Wiegard
- Institute for Synthetic Microbiology, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, Duesseldorf, 40225 Germany
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Comparative transcriptome analysis of the floral transition in Rosa chinensis 'Old Blush' and R. odorata var. gigantea. Sci Rep 2017; 7:6068. [PMID: 28729527 PMCID: PMC5519770 DOI: 10.1038/s41598-017-05850-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 06/05/2017] [Indexed: 11/17/2022] Open
Abstract
The floral transition is a crucial developmental event, but little is known about the underlying regulatory networks in seasonally and continuously flowering roses. In this study, we compared the genetic basis of flowering in two rose species, Rosa chinensis ‘Old Blush’, which flowers continuously, and R. odorata var. gigantea, which blooms in early spring. Gene ontology (GO) terms related to methylation, light reaction, and starch metabolism were enriched in R. odorata var. gigantea and terms associated with sugar metabolism were enriched in R. chinensis ‘Old Blush’ during the floral transition. A MapMan analysis revealed that genes involved in hormone signaling mediate the floral transition in both taxa. Furthermore, differentially expressed genes (DEGs) involved in vernalization, photoperiod, gibberellin (GA), and starch metabolism pathways converged on integrators, e.g., LFY, AGL24, SOC1, CAL, and COLs, to regulate the floral transition in R. odorata var. gigantea, while DEGs related to photoperiod, sugar metabolism, and GA pathways, including COL16, LFY, AGL11, 6PGDH, GASA4, and BAM, modulated the floral transition in R. chinensis ‘Old Blush.’ Our analysis of the genes underlying the floral transition in roses with different patterns of flowering provides a basis for further functional studies.
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244
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García-Plazaola JI, Fernández-Marín B, Ferrio JP, Alday JG, Hoch G, Landais D, Milcu A, Tissue DT, Voltas J, Gessler A, Roy J, Resco de Dios V. Endogenous circadian rhythms in pigment composition induce changes in photochemical efficiency in plant canopies. PLANT, CELL & ENVIRONMENT 2017; 40:1153-1162. [PMID: 28098350 DOI: 10.1111/pce.12909] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 01/03/2017] [Accepted: 01/04/2017] [Indexed: 05/16/2023]
Abstract
There is increasing evidence that the circadian clock is a significant driver of photosynthesis that becomes apparent when environmental cues are experimentally held constant. We studied whether the composition of photosynthetic pigments is under circadian regulation, and whether pigment oscillations lead to rhythmic changes in photochemical efficiency. To address these questions, we maintained canopies of bean and cotton, after an entrainment phase, under constant (light or darkness) conditions for 30-48 h. Photosynthesis and quantum yield peaked at subjective noon, and non-photochemical quenching peaked at night. These oscillations were not associated with parallel changes in carbohydrate content or xanthophyll cycle activity. We observed robust oscillations of Chl a/b during constant light in both species, and also under constant darkness in bean, peaking when it would have been night during the entrainment (subjective nights). These oscillations could be attributed to the synthesis and/or degradation of trimeric light-harvesting complex II (reflected by the rhythmic changes in Chl a/b), with the antenna size minimal at night and maximal around subjective noon. Considering together the oscillations of pigments and photochemistry, the observed pattern of changes is counterintuitive if we assume that the plant strategy is to avoid photodamage, but consistent with a strategy where non-stressed plants maximize photosynthesis.
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Affiliation(s)
| | - Beatriz Fernández-Marín
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), 48080, Bilbao, Spain
- Institute of Botany, University of Innsbruck, A6020, Innsbruck, Austria
| | - Juan Pedro Ferrio
- Department of Crop and Forest Sciences-AGROTECNIO Center, Universitat de Lleida, 25198, Lleida, Spain
- Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Casilla 160-C, Concepción, Chile
| | - Josu G Alday
- Department of Crop and Forest Sciences-AGROTECNIO Center, Universitat de Lleida, 25198, Lleida, Spain
| | - Günter Hoch
- Department of Environmental Sciences - Botany, University of Basel, Schönbeinstrasse 6, 4056, Basel, Switzerland
| | - Damien Landais
- Ecotron Européen de Montpellier, CNRS, UPS-3248, Montferrier-sur-Lez, France
| | - Alexandru Milcu
- Ecotron Européen de Montpellier, CNRS, UPS-3248, Montferrier-sur-Lez, France
- Centre d'Ecologie Fonctionnelle et Evolutive, CEFE-CNRS, UMR-5175, Université de Montpellier - Université Paul Valéry - EPHE, 1919 route de Mende, F-34293, Montpellier Cedex 5, France
| | - David T Tissue
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, 2753, New South Wales, Australia
| | - Jordi Voltas
- Department of Crop and Forest Sciences-AGROTECNIO Center, Universitat de Lleida, 25198, Lleida, Spain
| | - Arthur Gessler
- Swiss Federal Institute for Forest, Snow and Landscape Research, 8903, Birmensdorf, Switzerland
- Institute for Landscape Biogeochemistry, Leibniz-Centre for Agricultural Landscape Research (ZALF), 15374, Müncheberg, Germany
| | - Jacques Roy
- Ecotron Européen de Montpellier, CNRS, UPS-3248, Montferrier-sur-Lez, France
| | - Víctor Resco de Dios
- Department of Crop and Forest Sciences-AGROTECNIO Center, Universitat de Lleida, 25198, Lleida, Spain
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, 2753, New South Wales, Australia
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245
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Matsoukas IG. Crosstalk between Photoreceptor and Sugar Signaling Modulates Floral Signal Transduction. Front Physiol 2017; 8:382. [PMID: 28659814 PMCID: PMC5466967 DOI: 10.3389/fphys.2017.00382] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 05/22/2017] [Indexed: 11/13/2022] Open
Abstract
Over the past decade, integrated genetic, cellular, proteomic and genomic approaches have begun to unravel the surprisingly crosstalk between photoreceptors and sugar signaling in regulation of floral signal transduction. Although a number of physiological factors in the pathway have been identified, the molecular genetic interactions of some components are less well understood. The further elucidation of the crosstalk mechanisms between photoreceptors and sugar signaling will certainly contribute to our better understanding of the developmental circuitry that controls floral signal transduction. This article summarizes our current knowledge of this crosstalk, which has not received much attention, and suggests possible directions for future research.
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Affiliation(s)
- Ianis G Matsoukas
- School of Life Sciences, University of WarwickCoventry, United Kingdom
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246
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Bhadra U, Thakkar N, Das P, Pal Bhadra M. Evolution of circadian rhythms: from bacteria to human. Sleep Med 2017; 35:49-61. [DOI: 10.1016/j.sleep.2017.04.008] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 04/07/2017] [Accepted: 04/18/2017] [Indexed: 12/20/2022]
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247
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Ezer D, Jung JH, Lan H, Biswas S, Gregoire L, Box MS, Charoensawan V, Cortijo S, Lai X, Stöckle D, Zubieta C, Jaeger KE, Wigge PA. The evening complex coordinates environmental and endogenous signals in Arabidopsis. NATURE PLANTS 2017; 3:17087. [PMID: 28650433 PMCID: PMC5495178 DOI: 10.1038/nplants.2017.87] [Citation(s) in RCA: 172] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 05/12/2017] [Indexed: 05/18/2023]
Abstract
Plants maximize their fitness by adjusting their growth and development in response to signals such as light and temperature. The circadian clock provides a mechanism for plants to anticipate events such as sunrise and adjust their transcriptional programmes. However, the underlying mechanisms by which plants coordinate environmental signals with endogenous pathways are not fully understood. Using RNA-sequencing and chromatin immunoprecipitation sequencing experiments, we show that the evening complex (EC) of the circadian clock plays a major role in directly coordinating the expression of hundreds of key regulators of photosynthesis, the circadian clock, phytohormone signalling, growth and response to the environment. We find that the ability of the EC to bind targets genome-wide depends on temperature. In addition, co-occurrence of phytochrome B (phyB) at multiple sites where the EC is bound provides a mechanism for integrating environmental information. Hence, our results show that the EC plays a central role in coordinating endogenous and environmental signals in Arabidopsis.
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Affiliation(s)
- Daphne Ezer
- Sainsbury Laboratory, University of Cambridge, 47 Bateman St., Cambridge CB2 1LR, UK
| | - Jae-Hoon Jung
- Sainsbury Laboratory, University of Cambridge, 47 Bateman St., Cambridge CB2 1LR, UK
| | - Hui Lan
- Sainsbury Laboratory, University of Cambridge, 47 Bateman St., Cambridge CB2 1LR, UK
| | - Surojit Biswas
- Sainsbury Laboratory, University of Cambridge, 47 Bateman St., Cambridge CB2 1LR, UK
| | - Laura Gregoire
- LPCV, CNRS, CEA, INRA, Univ. Grenoble Alpes, BIG, 38000, Grenoble, France
| | - Mathew S. Box
- Sainsbury Laboratory, University of Cambridge, 47 Bateman St., Cambridge CB2 1LR, UK
| | - Varodom Charoensawan
- Sainsbury Laboratory, University of Cambridge, 47 Bateman St., Cambridge CB2 1LR, UK
- Department of Biochemistry, Faculty of Science, and Integrative Computational BioScience (ICBS) center, Mahidol University, Bangkok 10400, Thailand
| | - Sandra Cortijo
- Sainsbury Laboratory, University of Cambridge, 47 Bateman St., Cambridge CB2 1LR, UK
| | - Xuelei Lai
- Sainsbury Laboratory, University of Cambridge, 47 Bateman St., Cambridge CB2 1LR, UK
- LPCV, CNRS, CEA, INRA, Univ. Grenoble Alpes, BIG, 38000, Grenoble, France
| | - Dorothee Stöckle
- Sainsbury Laboratory, University of Cambridge, 47 Bateman St., Cambridge CB2 1LR, UK
| | - Chloe Zubieta
- LPCV, CNRS, CEA, INRA, Univ. Grenoble Alpes, BIG, 38000, Grenoble, France
| | - Katja E. Jaeger
- Sainsbury Laboratory, University of Cambridge, 47 Bateman St., Cambridge CB2 1LR, UK
| | - Philip A. Wigge
- Sainsbury Laboratory, University of Cambridge, 47 Bateman St., Cambridge CB2 1LR, UK
- Correspondence to:
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248
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Staley C, Ferrieri AP, Tfaily MM, Cui Y, Chu RK, Wang P, Shaw JB, Ansong CK, Brewer H, Norbeck AD, Markillie M, do Amaral F, Tuleski T, Pellizzaro T, Agtuca B, Ferrieri R, Tringe SG, Paša-Tolić L, Stacey G, Sadowsky MJ. Diurnal cycling of rhizosphere bacterial communities is associated with shifts in carbon metabolism. MICROBIOME 2017; 5:65. [PMID: 28646918 PMCID: PMC5483260 DOI: 10.1186/s40168-017-0287-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 06/07/2017] [Indexed: 05/22/2023]
Abstract
BACKGROUND The circadian clock regulates plant metabolic functions and is an important component in plant health and productivity. Rhizosphere bacteria play critical roles in plant growth, health, and development and are shaped primarily by soil communities. Using Illumina next-generation sequencing and high-resolution mass spectrometry, we characterized bacterial communities of wild-type (Col-0) Arabidopsis thaliana and an acyclic line (OX34) ectopically expressing the circadian clock-associated cca1 transcription factor, relative to a soil control, to determine how cycling dynamics affected the microbial community. Microbial communities associated with Brachypodium distachyon (BD21) were also evaluated. RESULTS Significantly different bacterial community structures (P = 0.031) were observed in the rhizosphere of wild-type plants between light and dark cycle samples. Furthermore, 13% of the community showed cycling, with abundances of several families, including Burkholderiaceae, Rhodospirillaceae, Planctomycetaceae, and Gaiellaceae, exhibiting fluctuation in abundances relative to the light cycle. However, limited-to-no cycling was observed in the acyclic CCAox34 line or in soil controls. Significant cycling was also observed, to a lesser extent, in Brachypodium. Functional gene inference revealed that genes involved in carbohydrate metabolism were likely more abundant in near-dawn, dark samples. Additionally, the composition of organic matter in the rhizosphere showed a significant variation between dark and light cycles. CONCLUSIONS The results of this study suggest that the rhizosphere bacterial community is regulated, to some extent, by the circadian clock and is likely influenced by, and exerts influences, on plant metabolism and productivity. The timing of bacterial cycling in relation to that of Arabidopsis further suggests that diurnal dynamics influence plant-microbe carbon metabolism and exchange. Equally important, our results suggest that previous studies done without relevance to time of day may need to be reevaluated with regard to the impact of diurnal cycles on the rhizosphere microbial community.
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Affiliation(s)
- Christopher Staley
- BioTechnology Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Ave, Saint Paul, MN, 55108, USA
| | - Abigail P Ferrieri
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Malak M Tfaily
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Yaya Cui
- Division of Plant Science and Biochemistry, C.S. Bond Life Science Center, University of Missouri, Columbia, MO, 65211, USA
| | - Rosalie K Chu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Ping Wang
- BioTechnology Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Ave, Saint Paul, MN, 55108, USA
| | - Jared B Shaw
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Charles K Ansong
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Heather Brewer
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Angela D Norbeck
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Meng Markillie
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Fernanda do Amaral
- Division of Plant Science and Biochemistry, C.S. Bond Life Science Center, University of Missouri, Columbia, MO, 65211, USA
| | - Thalita Tuleski
- Division of Plant Science and Biochemistry, C.S. Bond Life Science Center, University of Missouri, Columbia, MO, 65211, USA
| | - Tomás Pellizzaro
- Division of Plant Science and Biochemistry, C.S. Bond Life Science Center, University of Missouri, Columbia, MO, 65211, USA
| | - Beverly Agtuca
- Division of Plant Science and Biochemistry, C.S. Bond Life Science Center, University of Missouri, Columbia, MO, 65211, USA
| | - Richard Ferrieri
- Department of Chemistry, University of Missouri Research Reactor, Columbia, MO, 65211, USA
| | - Susannah G Tringe
- Microbial Systems Group, Metagenome Program, DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA.
| | - Gary Stacey
- Division of Plant Science and Biochemistry, C.S. Bond Life Science Center, University of Missouri, Columbia, MO, 65211, USA
| | - Michael J Sadowsky
- BioTechnology Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Ave, Saint Paul, MN, 55108, USA.
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Abstract
Circadian clocks are molecular timekeepers that synchronise internal physiological processes with the external environment by integrating light and temperature stimuli. As in other eukaryotic organisms, circadian rhythms in plants are largely generated by an array of nuclear transcriptional regulators and associated co-regulators that are arranged into a series of interconnected molecular loops. These transcriptional regulators recruit chromatin-modifying enzymes that adjust the structure of the nucleosome to promote or inhibit DNA accessibility and thus guide transcription rates. In this review, we discuss the recent advances made in understanding the architecture of the
Arabidopsis oscillator and the chromatin dynamics that regulate the generation of rhythmic patterns of gene expression within the circadian clock.
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Affiliation(s)
- James Ronald
- Department of Biology, University of York, York, YO10 5DD, UK
| | - Seth J Davis
- Department of Biology, University of York, York, YO10 5DD, UK
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Groszmann M, Osborn HL, Evans JR. Carbon dioxide and water transport through plant aquaporins. PLANT, CELL & ENVIRONMENT 2017; 40:938-961. [PMID: 27739588 DOI: 10.1111/pce.12844] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 09/01/2016] [Accepted: 09/22/2016] [Indexed: 05/25/2023]
Abstract
Aquaporins are channel proteins that function to increase the permeability of biological membranes. In plants, aquaporins are encoded by multigene families that have undergone substantial diversification in land plants. The plasma membrane intrinsic proteins (PIPs) subfamily of aquaporins is of particular interest given their potential to improve plant water relations and photosynthesis. Flowering plants have between 7 and 28 PIP genes. Their expression varies with tissue and cell type, through development and in response to a variety of factors, contributing to the dynamic and tissue specific control of permeability. There are a growing number of PIPs shown to act as water channels, but those altering membrane permeability to CO2 are more limited. The structural basis for selective substrate specificities has not yet been resolved, although a few key amino acid positions have been identified. Several regions important for dimerization, gating and trafficking are also known. PIP aquaporins assemble as tetramers and their properties depend on the monomeric composition. PIPs control water flux into and out of veins and stomatal guard cells and also increase membrane permeability to CO2 in mesophyll and stomatal guard cells. The latter increases the effectiveness of Rubisco and can potentially influence transpiration efficiency.
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Affiliation(s)
- Michael Groszmann
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Sciences, Research School of Biology, The Australian National University, Acton, ACT, 2601, Australia
| | - Hannah L Osborn
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Sciences, Research School of Biology, The Australian National University, Acton, ACT, 2601, Australia
| | - John R Evans
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Sciences, Research School of Biology, The Australian National University, Acton, ACT, 2601, Australia
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