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Wang X, Hao Y, Altaf MA, Shu H, Cheng S, Wang Z, Zhu G. Evolution and Dynamic Transcriptome of Key Genes of Photoperiodic Flowering Pathway in Water Spinach ( Ipomoea aquatica). Int J Mol Sci 2024; 25:1420. [PMID: 38338699 PMCID: PMC10855745 DOI: 10.3390/ijms25031420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/09/2024] [Accepted: 01/16/2024] [Indexed: 02/12/2024] Open
Abstract
The photoperiod is a major environmental factor in flowering control. Water spinach flowering under the inductive short-day condition decreases the yield of vegetative tissues and the eating quality. To obtain an insight into the molecular mechanism of the photoperiod-dependent regulation of the flowering time in water spinach, we performed transcriptome sequencing on water spinach under long- and short-day conditions with eight time points. Our results indicated that there were 6615 circadian-rhythm-related genes under the long-day condition and 8691 under the short-day condition. The three key circadian-rhythm genes, IaCCA1, IaLHY, and IaTOC1, still maintained single copies and similar IaCCA1, IaLHY, and IaTOC1 feedback expression patterns, indicating the conservation of reverse feedback. In the photoperiod pathway, highly conserved GI genes were amplified into two copies (IaGI1 and IaGI2) in water spinach. The significant difference in the expression of the two genes indicates functional diversity. Although the photoperiod core gene FT was duplicated to three copies in water spinach, only IaFT1 was highly expressed and strongly responsive to the photoperiod and circadian rhythms, and the almost complete inhibition of IaFT1 in water spinach may be the reason why water spinach does not bloom, no matter how long it lasts under the long-day condition. Differing from other species (I. nil, I. triloba, I. trifida) of the Ipomoea genus that have three CO members, water spinach lacks one of them, and the other two CO genes (IaCO1 and IaCO2) encode only one CCT domain. In addition, through weighted correlation network analysis (WGCNA), some transcription factors closely related to the photoperiod pathway were obtained. This work provides valuable data for further in-depth analyses of the molecular regulation of the flowering time in water spinach and the Ipomoea genus.
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Affiliation(s)
- Xin Wang
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; (X.W.); (Y.H.); (M.A.A.); (H.S.); (S.C.)
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Yuanyuan Hao
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; (X.W.); (Y.H.); (M.A.A.); (H.S.); (S.C.)
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Muhammad Ahsan Altaf
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; (X.W.); (Y.H.); (M.A.A.); (H.S.); (S.C.)
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Huangying Shu
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; (X.W.); (Y.H.); (M.A.A.); (H.S.); (S.C.)
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Shanhan Cheng
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; (X.W.); (Y.H.); (M.A.A.); (H.S.); (S.C.)
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Zhiwei Wang
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; (X.W.); (Y.H.); (M.A.A.); (H.S.); (S.C.)
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Guopeng Zhu
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; (X.W.); (Y.H.); (M.A.A.); (H.S.); (S.C.)
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
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Newman A, Picot E, Davies S, Hilton S, Carré IA, Bending GD. Circadian rhythms in the plant host influence rhythmicity of rhizosphere microbiota. BMC Biol 2022; 20:235. [PMID: 36266698 PMCID: PMC9585842 DOI: 10.1186/s12915-022-01430-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 09/30/2022] [Indexed: 11/18/2022] Open
Abstract
Background Recent studies demonstrated that microbiota inhabiting the plant rhizosphere exhibit diel changes in abundance. To investigate the impact of plant circadian rhythms on bacterial and fungal rhythms in the rhizosphere, we analysed temporal changes in fungal and bacterial communities in the rhizosphere of Arabidopsis plants overexpressing or lacking function of the circadian clock gene LATE ELONGATED HYPOCOTYL (LHY). Results Under diel light–dark cycles, the knock-out mutant lhy-11 and the gain-of-function mutant lhy-ox both exhibited gene expression rhythms with altered timing and amplitude compared to wild-type plants. Distinct sets of bacteria and fungi were found to display rhythmic changes in abundance in the rhizosphere of both of these mutants, suggesting that abnormal patterns of rhythmicity in the plant host caused temporal reprogramming of the rhizosphere microbiome. This was associated with changes in microbial community structure, including changes in the abundance of fungal guilds known to impact on plant health. Under constant environmental conditions, microbial rhythmicity persisted in the rhizosphere of wild-type plants, indicating control by a circadian oscillator. In contrast, loss of rhythmicity in lhy-ox plants was associated with disrupted rhythms for the majority of rhizosphere microbiota. Conclusions These results show that aberrant function of the plant circadian clock is associated with altered rhythmicity of rhizosphere bacteria and fungi. In the long term, this leads to changes in composition of the rhizosphere microbiome, with potential consequences for plant health. Further research will be required to understand the functional implications of these changes and how they impact on plant health and productivity. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01430-z.
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Affiliation(s)
- Amy Newman
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, West Midlands, UK.,Present address: National STEM Learning Centre, University of York, York, YO10 5DD, UK
| | - Emma Picot
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, West Midlands, UK
| | - Sian Davies
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, West Midlands, UK.,Present address: Micropathology Ltd, Venture Centre, Sir William Lyons Road, Coventry, CV4 7EZ, UK
| | - Sally Hilton
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, West Midlands, UK.,Present address: Micropathology Ltd, Venture Centre, Sir William Lyons Road, Coventry, CV4 7EZ, UK
| | - Isabelle A Carré
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, West Midlands, UK.
| | - Gary D Bending
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, West Midlands, UK
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Philippou K, Davis AM, Davis SJ, Sánchez-Villarreal A. Chemical Perturbation of Chloroplast-Related Processes Affects Circadian Rhythms of Gene Expression in Arabidopsis: Salicylic Acid Application Can Entrain the Clock. Front Physiol 2020; 11:429. [PMID: 32625102 PMCID: PMC7314985 DOI: 10.3389/fphys.2020.00429] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 04/08/2020] [Indexed: 11/26/2022] Open
Abstract
The plant circadian system reciprocally interacts with metabolic processes. To investigate entrainment features in metabolic–circadian interactions, we used a chemical approach to perturb metabolism and monitored the pace of nuclear-driven circadian oscillations. We found that chemicals that alter chloroplast-related functions modified the circadian rhythms. Both vitamin C and paraquat altered the circadian period in a light-quality-dependent manner, whereas rifampicin lengthened the circadian period under darkness. Salicylic acid (SA) increased oscillatory robustness and shortened the period. The latter was attenuated by sucrose addition and was also gated, taking place during the first 3 h of the subjective day. Furthermore, the effect of SA on period length was dependent on light quality and genotype. Period lengthening or shortening by these chemicals was correlated to their inferred impact on photosynthetic electron transport activity and the redox state of plastoquinone (PQ). Based on these data and on previous publications on circadian effects that alter the redox state of PQ, we propose that the photosynthetic electron transport and the redox state of PQ participate in circadian periodicity. Moreover, coupling between chloroplast-derived signals and nuclear oscillations, as observed in our chemical and genetic assays, produces traits that are predicted by previous models. SA signaling or a related process forms a rhythmic input loop to drive robust nuclear oscillations in the context predicted by the zeitnehmer model, which was previously developed for Neurospora. We further discuss the possibility that electron transport chains (ETCs) are part of this mechanism.
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Affiliation(s)
- Koumis Philippou
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Amanda M Davis
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany.,Department of Biology, University of York, York, United Kingdom
| | - Seth J Davis
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany.,Department of Biology, University of York, York, United Kingdom.,Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Alfredo Sánchez-Villarreal
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
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Dantas LLDB, Almeida-Jesus FM, de Lima NO, Alves-Lima C, Nishiyama-Jr MY, Carneiro MS, Souza GM, Hotta CT. Rhythms of Transcription in Field-Grown Sugarcane Are Highly Organ Specific. Sci Rep 2020; 10:6565. [PMID: 32300143 PMCID: PMC7162945 DOI: 10.1038/s41598-020-63440-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 03/25/2020] [Indexed: 12/29/2022] Open
Abstract
Circadian clocks improve plant fitness in a rhythmic environment. As each cell has its own circadian clock, we hypothesized that sets of cells with different functions would have distinct rhythmic behaviour. To test this, we investigated whether different organs in field-grown sugarcane follow the same rhythms in transcription. We assayed the transcriptomes of three organs during a day: leaf, a source organ; internodes 1 and 2, sink organs focused on cell division and elongation; and internode 5, a sink organ focused on sucrose storage. The leaf had twice as many rhythmic transcripts (>68%) as internodes, and the rhythmic transcriptomes of the internodes were more like each other than to those of the leaves. Among the transcripts expressed in all organs, only 7.4% showed the same rhythmic pattern. Surprisingly, the central oscillators of these organs - the networks that generate circadian rhythms - had similar dynamics, albeit with different amplitudes. The differences in rhythmic transcriptomes probably arise from amplitude differences in tissue-specific circadian clocks and different sensitivities to environmental cues, highlighted by the sampling under field conditions. The vast differences suggest that we must study tissue-specific circadian clocks in order to understand how the circadian clock increases the fitness of the whole plant.
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Affiliation(s)
- Luíza Lane de Barros Dantas
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, 05508-000, Brazil
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | | | - Natalia Oliveira de Lima
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, 05508-000, Brazil
| | - Cícero Alves-Lima
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, 05508-000, Brazil
| | | | - Monalisa Sampaio Carneiro
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, São Carlos, SP, 13600-970, Brazil
| | - Glaucia Mendes Souza
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, 05508-000, Brazil
| | - Carlos Takeshi Hotta
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, 05508-000, Brazil.
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5
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Zhang M, Suren H, Holliday JA. Phenotypic and Genomic Local Adaptation across Latitude and Altitude in Populus trichocarpa. Genome Biol Evol 2020; 11:2256-2272. [PMID: 31298685 PMCID: PMC6735766 DOI: 10.1093/gbe/evz151] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2019] [Indexed: 12/14/2022] Open
Abstract
Local adaptation to climate allows plants to cope with temporally and spatially heterogeneous environments, and parallel phenotypic clines provide a natural experiment to uncover the genomic architecture of adaptation. Though extensive effort has been made to investigate the genomic basis of local adaptation to climate across the latitudinal range of tree species, less is known for altitudinal clines. We used exome capture to genotype 451 Populus trichocarpa genotypes across altitudinal and latitudinal gradients spanning the natural species range, and phenotyped these trees for a variety of adaptive traits in two common gardens. We observed clinal variation in phenotypic traits across the two transects, which indicates climate-driven selection, and coupled gene-based genotype–phenotype and genotype–environment association scans to identify imprints of climatic adaptation on the genome. Although many of the phenotype- and climate-associated genes were unique to one transect, we found evidence of parallelism between latitude and altitude, as well as significant convergence when we compared our outlier genes with those putatively involved in climatic adaptation in two gymnosperm species. These results suggest that not only genomic constraint during adaptation to similar environmental gradients in poplar but also different environmental contexts, spatial scale, and perhaps redundant function among potentially adaptive genes and polymorphisms lead to divergent adaptive architectures.
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Affiliation(s)
- Man Zhang
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, Virginia.,National Engineering Research Center for Floriculture, School of Landscape Architecture, Beijing Forestry University, China
| | - Haktan Suren
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, Virginia
| | - Jason A Holliday
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, Virginia
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6
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Shi Y, Zhao X, Guo S, Dong S, Wen Y, Han Z, Jin W, Chen Y. ZmCCA1a on Chromosome 10 of Maize Delays Flowering of Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2020; 11:78. [PMID: 32153606 PMCID: PMC7044342 DOI: 10.3389/fpls.2020.00078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 01/20/2020] [Indexed: 06/01/2023]
Abstract
Maize (Zea mays) is a major cereal crop that originated at low latitudes, and thus photoperiod sensitivity is an important barrier to the use of tropical/subtropical germplasm in temperate regions. However, studies of the mechanisms underlying circadian regulation in maize are at an early stage. In this study we cloned ZmCCA1a on chromosome 10 of maize by map-based cloning. The gene is homologous to the Myb transcription factor genes AtCCA1/AtLHY in Arabidopsis thaliana; the deduced Myb domain of ZmCCA1a showed high similarity with that of AtCCA1/AtLHY and ZmCCA1b. Transiently or constitutively expressed ZmCCA1a-YFPs were localized to nuclei of Arabidopsis mesophyll protoplasts, agroinfiltrated tobacco leaves, and leaf and root cells of transgenic seedlings of Arabidopsis thaliana. Unlike AtCCA1/AtLHY, ZmCCA1a did not form homodimers nor interact with ZmCCA1b. Transcripts of ZmCCA1a showed circadian rhythm with peak expression around sunrise in maize inbred lines CML288 (photoperiod sensitive) and Huangzao 4 (HZ4; photoperiod insensitive). Under short days, transcription of ZmCCA1a in CML288 and HZ4 was repressed compared with that under long days, whereas the effect of photoperiod on ZmCCA1a expression was moderate in HZ4. In ZmCCA1a-overexpressing A. thaliana (ZmCCA1a-ox) lines, the circadian rhythm was disrupted under constant light and flowering was delayed under long days, but the hypocotyl length was not affected. In addition, expression of endogenous AtCCA1/AtLHY and the downstream genes AtGI, AtCO, and AtFt was repressed in ZmCCA1a-ox seedlings. The present results suggest that the function of ZmCCA1a is similar, at least in part, to that of AtCCA1/AtLHY and ZmCCA1b, implying that ZmCCA1a is likely to be an important component of the circadian clock pathway in maize.
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Affiliation(s)
- Yong Shi
- College of Agronomy/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Xiyong Zhao
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Sha Guo
- College of Agronomy/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Shifeng Dong
- College of Agronomy/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Yanpeng Wen
- College of Agronomy/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Zanping Han
- College of Agronomy, Henan University of Science and Technology, Luoyang, China
| | - Weihuan Jin
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Yanhui Chen
- College of Agronomy/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
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7
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Abstract
The circadian oscillator is a complex network of interconnected feedback loops that regulates a wide range of physiological processes. Indeed, variation in clock genes has been implicated in an array of plant environmental adaptations, including growth regulation, photoperiodic control of flowering, and responses to abiotic and biotic stress. Although the clock is buffered against the environment, maintaining roughly 24-h rhythms across a wide range of conditions, it can also be reset by environmental cues such as acute changes in light or temperature. These competing demands may help explain the complexity of the links between the circadian clock network and environmental response pathways. Here, we discuss our current understanding of the clock and its interactions with light and temperature-signaling pathways. We also describe different clock gene alleles that have been implicated in the domestication of important staple crops.
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Affiliation(s)
- Nicky Creux
- Department of Plant Biology, University of California, Davis, California 95616, USA
| | - Stacey Harmer
- Department of Plant Biology, University of California, Davis, California 95616, USA
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8
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Ramos-Sánchez JM, Triozzi PM, Alique D, Geng F, Gao M, Jaeger KE, Wigge PA, Allona I, Perales M. LHY2 Integrates Night-Length Information to Determine Timing of Poplar Photoperiodic Growth. Curr Biol 2019; 29:2402-2406.e4. [PMID: 31257141 DOI: 10.1016/j.cub.2019.06.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/06/2019] [Accepted: 06/03/2019] [Indexed: 12/18/2022]
Abstract
Day length is a key indicator of seasonal information that determines major patterns of behavior in plants and animals. Photoperiodism has been described in plants for about 100 years, but the underlying molecular mechanisms of day length perception and signal transduction in many systems are not well understood. In trees, photoperiod perception plays a major role in growth cessation during the autumn as well as activating the resumption of shoot growth in the spring, both processes controlled by FLOWERING LOCUS T2 (FT2) expression levels and critical for the survival of perennial plants over winter [1-4]. It has been shown that the conserved role of poplar orthologs to Arabidopsis CONSTANS (CO) directly activates FT2 expression [1, 5]. Overexpression of poplar CO is, however, not sufficient to sustain FT2 expression under short days [5], pointing to the presence of an additional short-day-dependent FT2 repression pathway in poplar. We find that night length information is transmitted via the expression level of a poplar clock gene, LATE ELONGATED HYPOCOTYL 2 (LHY2), which controls FT2 expression. Repression of FT2 is a function of the night extension and LHY2 expression level. We show that LHY2 is necessary and sufficient to activate night length repressive signaling. We propose that the photoperiodic control of shoot growth in poplar involves a balance between FT2 activating and repressing pathways. Our results show that poplar relies on night length measurement to determine photoperiodism through interaction between light signaling pathways and the circadian clock.
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Affiliation(s)
- José M Ramos-Sánchez
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, Pozuelo de Alarcón, Madrid 28223, Spain
| | - Paolo M Triozzi
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, Pozuelo de Alarcón, Madrid 28223, Spain
| | - Daniel Alique
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, Pozuelo de Alarcón, Madrid 28223, Spain
| | - Feng Geng
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, UK
| | - Mingjun Gao
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, UK
| | - Katja E Jaeger
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, UK; Leibniz-Institut für Gemüse- und Zierpflanzenbau, Großbeeren 14979, Germany
| | - Philip A Wigge
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, UK; Leibniz-Institut für Gemüse- und Zierpflanzenbau, Großbeeren 14979, Germany; Institute of Biochemistry and Biology, University of Potsdam, Potsdam 14476, Germany
| | - Isabel Allona
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, Pozuelo de Alarcón, Madrid 28223, Spain; Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid 28040, Spain.
| | - Mariano Perales
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, Pozuelo de Alarcón, Madrid 28223, Spain.
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9
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McClung CR. The Plant Circadian Oscillator. BIOLOGY 2019; 8:E14. [PMID: 30870980 PMCID: PMC6466001 DOI: 10.3390/biology8010014] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/17/2019] [Accepted: 03/09/2019] [Indexed: 12/20/2022]
Abstract
It has been nearly 300 years since the first scientific demonstration of a self-sustaining circadian clock in plants. It has become clear that plants are richly rhythmic, and many aspects of plant biology, including photosynthetic light harvesting and carbon assimilation, resistance to abiotic stresses, pathogens, and pests, photoperiodic flower induction, petal movement, and floral fragrance emission, exhibit circadian rhythmicity in one or more plant species. Much experimental effort, primarily, but not exclusively in Arabidopsis thaliana, has been expended to characterize and understand the plant circadian oscillator, which has been revealed to be a highly complex network of interlocked transcriptional feedback loops. In addition, the plant circadian oscillator has employed a panoply of post-transcriptional regulatory mechanisms, including alternative splicing, adjustable rates of translation, and regulated protein activity and stability. This review focuses on our present understanding of the regulatory network that comprises the plant circadian oscillator. The complexity of this oscillatory network facilitates the maintenance of robust rhythmicity in response to environmental extremes and permits nuanced control of multiple clock outputs. Consistent with this view, the clock is emerging as a target of domestication and presents multiple targets for targeted breeding to improve crop performance.
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Affiliation(s)
- C Robertson McClung
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA.
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10
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van der Horst S, Snel B, Hanson J, Smeekens S. Novel pipeline identifies new upstream ORFs and non-AUG initiating main ORFs with conserved amino acid sequences in the 5' leader of mRNAs in Arabidopsis thaliana. RNA (NEW YORK, N.Y.) 2019; 25:292-304. [PMID: 30567971 PMCID: PMC6380273 DOI: 10.1261/rna.067983.118] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 12/10/2018] [Indexed: 05/10/2023]
Abstract
Eukaryotic mRNAs contain a 5' leader sequence preceding the main open reading frame (mORF) and, depending on the species, 20%-50% of eukaryotic mRNAs harbor an upstream ORF (uORF) in the 5' leader. An unknown fraction of these uORFs encode sequence conserved peptides (conserved peptide uORFs, CPuORFs). Experimentally validated CPuORFs demonstrated to regulate the translation of downstream mORFs often do so in a metabolite concentration-dependent manner. Previous research has shown that most CPuORFs possess a start codon context suboptimal for translation initiation, which turns out to be favorable for translational regulation. The suboptimal initiation context may even include non-AUG start codons, which makes CPuORFs hard to predict. For this reason, we developed a novel pipeline to identify CPuORFs unbiased of start codon using well-annotated sequence data from 31 eudicot plant species and rice. Our new pipeline was able to identify 29 novel Arabidopsis thaliana (Arabidopsis) CPuORFs, conserved across a wide variety of eudicot species of which 15 do not initiate with an AUG start codon. In addition to CPuORFs, the pipeline was able to find 14 conserved coding regions directly upstream and in frame with the mORF, which likely initiate translation on a non-AUG start codon. Altogether, our pipeline identified highly conserved coding regions in the 5' leaders of Arabidopsis transcripts, including in genes with proven functional importance such as LHY, a key regulator of the circadian clock, and the RAPTOR1 subunit of the target of rapamycin (TOR) kinase.
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Affiliation(s)
- Sjors van der Horst
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Berend Snel
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Johannes Hanson
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, 3584 CH, Utrecht, The Netherlands
- Umeå Plant Science Center, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden
| | - Sjef Smeekens
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, 3584 CH, Utrecht, The Netherlands
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11
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Beyond Transcription: Fine-Tuning of Circadian Timekeeping by Post-Transcriptional Regulation. Genes (Basel) 2018; 9:genes9120616. [PMID: 30544736 PMCID: PMC6315869 DOI: 10.3390/genes9120616] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 11/29/2018] [Accepted: 12/03/2018] [Indexed: 12/28/2022] Open
Abstract
The circadian clock is an important endogenous timekeeper, helping plants to prepare for the periodic changes of light and darkness in their environment. The clockwork of this molecular timer is made up of clock proteins that regulate transcription of their own genes with a 24 h rhythm. Furthermore, the rhythmically expressed clock proteins regulate time-of-day dependent transcription of downstream genes, causing messenger RNA (mRNA) oscillations of a large part of the transcriptome. On top of the transcriptional regulation by the clock, circadian rhythms in mRNAs rely in large parts on post-transcriptional regulation, including alternative pre-mRNA splicing, mRNA degradation, and translational control. Here, we present recent insights into the contribution of post-transcriptional regulation to core clock function and to regulation of circadian gene expression in Arabidopsis thaliana.
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12
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Adams S, Grundy J, Veflingstad SR, Dyer NP, Hannah MA, Ott S, Carré IA. Circadian control of abscisic acid biosynthesis and signalling pathways revealed by genome-wide analysis of LHY binding targets. THE NEW PHYTOLOGIST 2018; 220:893-907. [PMID: 30191576 DOI: 10.1111/nph.15415] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 07/23/2018] [Indexed: 05/02/2023]
Abstract
The LATE ELONGATED HYPOCOTYL (LHY) transcription factor functions as part of the oscillatory mechanism of the Arabidopsis circadian clock. This paper reports the genome-wide analysis of its binding targets and reveals a role in the control of abscisic acid (ABA) biosynthesis and downstream responses. LHY directly repressed expression of 9-cis-epoxycarotenoid dioxygenase enzymes, which catalyse the rate-limiting step of ABA biosynthesis. This suggested a mechanism for the circadian control of ABA accumulation in wild-type plants. Consistent with this hypothesis, ABA accumulated rhythmically in wild-type plants, peaking in the evening. LHY-overexpressing plants had reduced levels of ABA under drought stress, whereas loss-of-function mutants exhibited an altered rhythm of ABA accumulation. LHY also bound the promoter of multiple components of ABA signalling pathways, suggesting that it may also act to regulate responses downstream of the hormone. LHY promoted expression of ABA-responsive genes responsible for increased tolerance to drought and osmotic stress but alleviated the inhibitory effect of ABA on seed germination and plant growth. This study reveals a complex interaction between the circadian clock and ABA pathways, which is likely to make an important contribution to plant performance under drought and osmotic stress conditions.
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Affiliation(s)
- Sally Adams
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Jack Grundy
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- Bayer CropScience NV, Technologiepark 38, 9052, Ghent, Belgium
| | - Siren R Veflingstad
- Systems Biology Centre, University of Warwick, Coventry, CV4 7AL, UK
- Department of Statistics, University of Warwick, Coventry, CV4 7AL, UK
| | - Nigel P Dyer
- Systems Biology Centre, University of Warwick, Coventry, CV4 7AL, UK
| | | | - Sascha Ott
- Systems Biology Centre, University of Warwick, Coventry, CV4 7AL, UK
| | - Isabelle A Carré
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
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13
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Mwimba M, Karapetyan S, Liu L, Marqués J, McGinnis EM, Buchler NE, Dong X. Daily humidity oscillation regulates the circadian clock to influence plant physiology. Nat Commun 2018; 9:4290. [PMID: 30327472 PMCID: PMC6191426 DOI: 10.1038/s41467-018-06692-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 09/20/2018] [Indexed: 01/27/2023] Open
Abstract
Early circadian studies in plants by de Mairan and de Candolle alluded to a regulation of circadian clocks by humidity. However, this regulation has not been described in detail, nor has its influence on physiology been demonstrated. Here we report that, under constant light, circadian humidity oscillation can entrain the plant circadian clock to a period of 24 h probably through the induction of clock genes such as CIRCADIAN CLOCK ASSOCIATED 1. Under simulated natural light and humidity cycles, humidity oscillation increases the amplitude of the circadian clock and further improves plant fitness-related traits. In addition, humidity oscillation enhances effector-triggered immunity at night possibly to counter increased pathogen virulence under high humidity. These results indicate that the humidity oscillation regulates specific circadian outputs besides those co-regulated with the light-dark cycle.
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Affiliation(s)
- Musoki Mwimba
- Howard Hughes Medical Institute, Duke University, Durham, NC, 27708, USA.,Department of Biology, Duke University, PO Box 90338, Durham, NC, 27708, USA
| | - Sargis Karapetyan
- Department of Biology, Duke University, PO Box 90338, Durham, NC, 27708, USA.,Department of Physics, Duke University, Durham, NC, 27708, USA
| | - Lijing Liu
- Howard Hughes Medical Institute, Duke University, Durham, NC, 27708, USA.,Department of Biology, Duke University, PO Box 90338, Durham, NC, 27708, USA
| | - Jorge Marqués
- Howard Hughes Medical Institute, Duke University, Durham, NC, 27708, USA.,Department of Biology, Duke University, PO Box 90338, Durham, NC, 27708, USA
| | - Erin M McGinnis
- Howard Hughes Medical Institute, Duke University, Durham, NC, 27708, USA.,Department of Biology, Duke University, PO Box 90338, Durham, NC, 27708, USA
| | - Nicolas E Buchler
- Department of Biology, Duke University, PO Box 90338, Durham, NC, 27708, USA.,Department of Physics, Duke University, Durham, NC, 27708, USA.,Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, 27606, USA
| | - Xinnian Dong
- Howard Hughes Medical Institute, Duke University, Durham, NC, 27708, USA. .,Department of Biology, Duke University, PO Box 90338, Durham, NC, 27708, USA.
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14
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Mechanism of Overwintering in Trees. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018. [PMID: 30288708 DOI: 10.1007/978-981-13-1244-1_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Boreal trees possess very high freezing resistance, which is induced by short-day length and low temperatures, in order to survive severe subzero temperatures in winter. During autumn, cooperation of photoreceptors and circadian clock system perceiving photoperiod shortening results in growth cessation, dormancy development, and first induction of freezing resistance. The freezing resistance is further enhanced by subsequent low temperature during seasonal cold acclimation with concomitant changes in various morphological and physiological features including accumulation of sugars and late embryogenesis abundant proteins. The mechanism of adaptation to freezing temperatures differs depending on the type of tissue in boreal trees. For example, bark, cambium, and leaf cells tolerate freezing-induced dehydration by extracellular freezing, whereas xylem parenchyma cells avoid intracellular freezing by deep supercooling. In addition, dormant buds in some trees respond by extraorgan freezing. Boreal trees have evolved overwintering mechanisms such as dormancy and high freezing resistance in order to survive freezing temperatures in winter.
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15
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James AB, Calixto CP, Tzioutziou NA, Guo W, Zhang R, Simpson CG, Jiang W, Nimmo GA, Brown JW, Nimmo HG. How does temperature affect splicing events? Isoform switching of splicing factors regulates splicing of LATE ELONGATED HYPOCOTYL (LHY). PLANT, CELL & ENVIRONMENT 2018; 41. [PMID: 29532482 PMCID: PMC6033173 DOI: 10.1111/pce.13193] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
One of the ways in which plants can respond to temperature is via alternative splicing (AS). Previous work showed that temperature changes affected the splicing of several circadian clock gene transcripts. Here, we investigated the role of RNA-binding splicing factors (SFs) in temperature-sensitive AS of the clock gene LATE ELONGATED HYPOCOTYL (LHY). We characterized, in wild type plants, temperature-associated isoform switching and expression patterns for SF transcripts from a high-resolution temperature and time series RNA-seq experiment. In addition, we employed quantitative RT-PCR of SF mutant plants to explore the role of the SFs in cooling-associated AS of LHY. We show that the splicing and expression of several SFs responds sufficiently, rapidly, and sensitively to temperature changes to contribute to the splicing of the 5'UTR of LHY. Moreover, the choice of splice site in LHY was altered in some SF mutants. The splicing of the 5'UTR region of LHY has characteristics of a molecular thermostat, where the ratio of transcript isoforms is sensitive to temperature changes as modest as 2 °C and is scalable over a wide dynamic range of temperature. Our work provides novel insight into SF-mediated coupling of the perception of temperature to post-transcriptional regulation of the clock.
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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 8QQScotlandUK
| | - Cristiane P.G. Calixto
- Plant Sciences Division, College of Life SciencesUniversity of DundeeInvergowrieDundeeDD2 5DAScotlandUK
| | - Nikoleta A. Tzioutziou
- Plant Sciences Division, College of Life SciencesUniversity of DundeeInvergowrieDundeeDD2 5DAScotlandUK
| | - Wenbin Guo
- Informatics and Computational SciencesThe James Hutton InstituteInvergowrieDundeeDD2 5DAScotlandUK
| | - Runxuan Zhang
- Informatics and Computational SciencesThe James Hutton InstituteInvergowrieDundeeDD2 5DAScotlandUK
| | - Craig G. Simpson
- Cell and Molecular SciencesThe James Hutton InstituteInvergowrieDundeeDD2 5DAScotlandUK
| | - Wenying Jiang
- Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary, and Life SciencesUniversity of GlasgowGlasgowG12 8QQScotlandUK
| | - Gillian A. Nimmo
- Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary, and Life SciencesUniversity of GlasgowGlasgowG12 8QQScotlandUK
| | - John W.S. Brown
- Plant Sciences Division, College of Life SciencesUniversity of DundeeInvergowrieDundeeDD2 5DAScotlandUK
- Cell and Molecular SciencesThe James Hutton InstituteInvergowrieDundeeDD2 5DAScotlandUK
| | - Hugh G. Nimmo
- Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary, and Life SciencesUniversity of GlasgowGlasgowG12 8QQScotlandUK
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16
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Multiple feedback loops of the Arabidopsis circadian clock provide rhythmic robustness across environmental conditions. Proc Natl Acad Sci U S A 2018; 115:7147-7152. [PMID: 29915068 DOI: 10.1073/pnas.1805524115] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Although circadian oscillators in diverse eukaryotes all depend on interlinked transcriptional feedback loops, specific components are not conserved across higher taxa. Moreover, the circadian network in the model plant Arabidopsis thaliana is notably more complex than those found in animals and fungi. Here, we combine mathematical modeling and experimental approaches to investigate the functions of two classes of Myb-like transcription factors that antagonistically regulate common target genes. Both CCA1/LHY- and RVE8-clade factors bind directly to the same cis-element, but the former proteins act primarily as repressors, while the latter act primarily as activators of gene expression. We find that simulation of either type of loss-of-function mutant recapitulates clock phenotypes previously reported in mutant plants, while simulated simultaneous loss of both type of factors largely rescues circadian phase at the expense of rhythmic amplitude. In accord with this prediction, we find that plants mutant for both activator- and repressor-type Mybs have near-normal circadian phase and period but reduced rhythmic amplitude. Although these mutants exhibit robust rhythms when grown at mild temperatures, they are largely arrhythmic at physiologically relevant but nonoptimal temperatures. LHY- and RVE8-type Mybs are found in separate clades across the land plant lineage and even in some unicellular green algae, suggesting that they both may have functioned in even the earliest arising plant circadian oscillators. Our data suggest that the complexity of the plant circadian network may have arisen to provide rhythmic robustness across the range of environmental extremes to which plants, as sessile organisms, are regularly subjected.
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17
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Dutta S, Biswas P, Chakraborty S, Mitra D, Pal A, Das M. Identification, characterization and gene expression analyses of important flowering genes related to photoperiodic pathway in bamboo. BMC Genomics 2018. [PMID: 29523071 PMCID: PMC5845326 DOI: 10.1186/s12864-018-4571-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Background Bamboo is an important member of the family Poaceae and has many inflorescence and flowering features rarely observed in other plant groups. It retains an unusual form of perennialism by having a long vegetative phase that can extend up to 120 years, followed by flowering and death of the plants. In contrast to a large number of studies conducted on the annual, reference plants Arabidopsis thaliana and rice, molecular studies to characterize flowering pathways in perennial bamboo are lacking. Since photoperiod plays a crucial role in flower induction in most plants, important genes involved in this pathway have been studied in the field grown Bambusa tulda, which flowers after 40-50 years. Results We identified several genes from B. tulda, including four related to the circadian clock [LATE ELONGATED HYPOCOTYL (LHY), TIMING OF CAB EXPRESSION1 (TOC1), ZEITLUPE (ZTL) and GIGANTEA (GI)], two circadian clock response integrators [CONSTANS A (COA), CONSTANS B (COB)] and four floral pathway integrators [FLOWERING LOCUS T1, 2, 3, 4 (FT1, 2, 3, 4)]. These genes were amplified from either gDNA and/or cDNA using degenerate as well as gene specific primers based on homologous sequences obtained from related monocot species. The sequence identity and phylogenetic comparisons revealed their close relationships to homologs identified in the temperate bamboo Phyllostachys edulis. While the four BtFT homologs were highly similar to each other, BtCOA possessed a full-length B-box domain that was truncated in BtCOB. Analysis of the spatial expression of these genes in selected flowering and non-flowering tissue stages indicated their possible involvement in flowering. The diurnal expression patterns of the clock genes were comparable to their homologs in rice, except for BtZTL. Among multiple BtCO and BtFT homologs, the diurnal pattern of only BtCOA and BtFT3, 4 were synchronized in the flower inductive tissue, but not in the non-flowering tissues. Conclusion This study elucidates the photoperiodic regulation of bamboo homologs of important flowering genes. The finding also identifies copy number expansion and gene expression divergence of CO and FT in bamboo. Further studies are required to understand their functional role in bamboo flowering. Electronic supplementary material The online version of this article (10.1186/s12864-018-4571-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Smritikana Dutta
- Department of Life Sciences, Presidency University, Kolkata, India
| | - Prasun Biswas
- Department of Life Sciences, Presidency University, Kolkata, India
| | | | - Devrani Mitra
- Department of Life Sciences, Presidency University, Kolkata, India
| | - Amita Pal
- Division of Plant Biology, Bose Institute, Kolkata, India
| | - Malay Das
- Department of Life Sciences, Presidency University, Kolkata, India.
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18
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Schepetilnikov M, Ryabova LA. Recent Discoveries on the Role of TOR (Target of Rapamycin) Signaling in Translation in Plants. PLANT PHYSIOLOGY 2018; 176:1095-1105. [PMID: 29122989 PMCID: PMC5813564 DOI: 10.1104/pp.17.01243] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 11/09/2017] [Indexed: 05/18/2023]
Abstract
TOR signaling regulates plant translation via a specific translation initiation mechanism: reinitiation.
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Affiliation(s)
- Mikhail Schepetilnikov
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, UPR 2357, Université de Strasbourg, 67084 Strasbourg, France
| | - Lyubov A Ryabova
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, UPR 2357, Université de Strasbourg, 67084 Strasbourg, France
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19
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Zhang J, Li D, Shi X, Zhang D, Qiu S, Wei J, Zhang J, Zhou J, Zhu K, Xia Y. Mining and expression analysis of candidate genes involved in regulating the chilling requirement fulfillment of Paeonia lactiflora 'Hang Baishao'. BMC PLANT BIOLOGY 2017; 17:262. [PMID: 29273002 PMCID: PMC5741883 DOI: 10.1186/s12870-017-1205-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 12/06/2017] [Indexed: 05/06/2023]
Abstract
BACKGROUND The artificial enlargement of the planting area and ecological amplitude of ornamentals for horticultural and landscape applications are significant. Herbaceous peony (Paeonia lactiflora Pall.) is a world-famous ornamental with attractive and fragrant flowers and is mainly planted in temperate and cool areas. Comparatively higher winter temperatures in the subtropical and tropical Northern Hemisphere result in a deficit of chilling accumulation for bud dormancy release, which severely hinders "The southward plantation of herbaceous peony". Studies on the dormancy, chilling requirement (CR) and relevant molecular mechanisms of peony are needed to enhance our ability to extend the range of this valuable horticultural species. RESULTS Based on natural and artificial chilling experiments, and chilling hour (CH) and chilling unit (CU) evaluation systems, the lowest CR of 'Hang Baishao' was between 504.00 and 672.00 CHs and the optimal CR was 672.00 CHs and 856.08 CUs for achieving strong sprouting, growth and flowering performance. Transcriptome sequencing and gene identification by RNA-Seq were performed on 'Hang Baishao' buds during the dormancy and sprouting periods. Six gene libraries were constructed, and 66 temperature- and photoperiod-associated unigenes were identified as the potential candidate genes that may regulate or possibly determine CR characteristics. The difference in the expression patterns of SUPPRESSPOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) between the winters of 2012-2013 and 2015-2016, and the difference of CR fulfillment periods also between these two winters represented the interesting congruent relationships. This correlation was also observed for WRKY DNA-BINDING PROTEIN 33 (WRKY 33). CONCLUSIONS Combined with the results acquired from all of experiments, 'Hang Baishao' was confirmed to be a superb peony resource that have significantly low CR characteristics. The two genes of SOC1 and WRKY33 are likely involved in determining the CR amount and fulfillment period of 'Hang Baishao'. HEAT SHOCK PROTEIN, OSMOTIN and TIMING OF CAB EXPRESSION 1 also deserve attention for the CR research. This study could contribute to the knowledge of the deep factors and mechanisms that regulate CR characteristics, and may be beneficial for breeding new germplasms that have low CRs for landscape or horticulture applications in subtropical regions.
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Affiliation(s)
- Jiaping Zhang
- Institute of Landscape Architecture, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Danqing Li
- Institute of Landscape Architecture, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Xiaohua Shi
- Research & Development Centre of Flower, Zhejiang Academy of Agricultural Sciences, Hangzhou, 311202 China
| | - Dong Zhang
- Institute of Landscape Architecture, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Shuai Qiu
- Research & Development Center, Hangzhou Landscaping Incorporated, Hangzhou, 310020 China
| | - Jianfen Wei
- Research & Development Center, Hangzhou Landscaping Incorporated, Hangzhou, 310020 China
| | - Jiao Zhang
- Institute of Landscape Architecture, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Jianghua Zhou
- Research & Development Centre of Flower, Zhejiang Academy of Agricultural Sciences, Hangzhou, 311202 China
| | - Kaiyuan Zhu
- Research & Development Centre of Flower, Zhejiang Academy of Agricultural Sciences, Hangzhou, 311202 China
| | - Yiping Xia
- Institute of Landscape Architecture, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, 310058 China
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Abstract
In most organisms, gene expression over the course of the day is under the control of the circadian clock. The canonical clock operates as a gene expression circuit that is controlled at the level of transcription, and transcriptional control is also a major clock output. However, rhythmic transcription cannot explain all the observed rhythms in protein accumulation. Although it is clear that rhythmic gene expression also involves RNA processing and protein turnover, until two years ago little was known in any eukaryote about diel dynamics of mRNA translation into protein. A recent series of studies in animals and plants demonstrated that diel cycles of translation efficiency are widespread across the tree of life and its transcriptomes. There are surprising parallels between the patterns of diel translation in mammals and plants. For example, ribosomal proteins and mitochondrial proteins are under translational control in mouse liver, human tissue culture, and Arabidopsis seedlings. In contrast, the way in which the circadian clock, light-dark changes, and other environmental factors such as nutritional signals interact to drive the cycles of translation may differ between organisms. Further investigation is needed to identify the signaling pathways, biochemical mechanisms, RNA sequence features, and the physiological implications of diel translation.
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Affiliation(s)
- Sarah Catherine Mills
- a Department of Biochemistry and Cellular & Molecular Biology , The University of Tennessee , Knoxville , TN , USA
| | - Ramya Enganti
- a Department of Biochemistry and Cellular & Molecular Biology , The University of Tennessee , Knoxville , TN , USA
| | - Albrecht G von Arnim
- a Department of Biochemistry and Cellular & Molecular Biology , The University of Tennessee , Knoxville , TN , USA.,b UT-ORNL Graduate School of Genome Science and Technology , The University of Tennessee , Knoxville , TN , USA
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21
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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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Ramos-Sánchez JM, Triozzi PM, Moreno-Cortés A, Conde D, Perales M, Allona I. Real-time monitoring of PtaHMGB activity in poplar transactivation assays. PLANT METHODS 2017; 13:50. [PMID: 28638438 PMCID: PMC5472981 DOI: 10.1186/s13007-017-0199-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 06/08/2017] [Indexed: 05/06/2023]
Abstract
BACKGROUND Precise control of gene expression is essential to synchronize plant development with the environment. In perennial plants, transcriptional regulation remains poorly understood, mainly due to the long time required to perform functional studies. Transcriptional reporters based on luciferase have been useful to study circadian and diurnal regulation of gene expression, both by transcription factors and chromatin remodelers. The high mobility group proteins are considered transcriptional chaperones that also modify the chromatin architecture. They have been found in several species, presenting in some cases a circadian expression of their mRNA or protein. RESULTS Transactivation experiments have been shown as a powerful and fast method to obtain information about the potential role of transcription factors upon a certain reporter. We designed and validated a luciferase transcriptional reporter using the 5' sequence upstream ATG of Populus tremula × alba LHY2 gene. We showed the robustness of this reporter line under long day and continuous light conditions. Moreover, we confirmed that pPtaLHY2::LUC activity reproduces the accumulation of PtaLHY2 mRNA. We performed transactivation studies by transient expression, using the reporter line as a genetic background, unraveling a new function of a high mobility group protein in poplar, which can activate the PtaLHY2 promoter in a gate-dependent manner. We also showed PtaHMGB2/3 needs darkness to produce that activation and exhibits an active degradation after dawn, mediated by the 26S proteasome. CONCLUSIONS We generated a stable luciferase reporter poplar line based on the circadian clock gene PtaLHY2, which can be used to investigate transcriptional regulation and signal transduction pathway. Using this reporter line as a genetic background, we established a methodology to rapidly assess potential regulators of diurnal and circadian rhythms. This tool allowed us to demonstrate that PtaHMGB2/3 promotes the transcriptional activation of our reporter in a gate-dependent manner. Moreover, we added new information about the PtaHMGB2/3 protein regulation along the day. This methodology can be easily adapted to other transcription factors and reporters.
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Affiliation(s)
- José M. Ramos-Sánchez
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Paolo M. Triozzi
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Alicia Moreno-Cortés
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Daniel Conde
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Mariano Perales
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Isabel Allona
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
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23
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Modeling the photoperiodic entrainment of the plant circadian clock. J Theor Biol 2017; 420:220-231. [DOI: 10.1016/j.jtbi.2017.03.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 01/12/2017] [Accepted: 03/07/2017] [Indexed: 11/21/2022]
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24
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Merchante C, Stepanova AN, Alonso JM. Translation regulation in plants: an interesting past, an exciting present and a promising future. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:628-653. [PMID: 28244193 DOI: 10.1111/tpj.13520] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 02/17/2017] [Accepted: 02/21/2017] [Indexed: 05/19/2023]
Abstract
Changes in gene expression are at the core of most biological processes, from cell differentiation to organ development, including the adaptation of the whole organism to the ever-changing environment. Although the central role of transcriptional regulation is solidly established and the general mechanisms involved in this type of regulation are relatively well understood, it is clear that regulation at a translational level also plays an essential role in modulating gene expression. Despite the large number of examples illustrating the critical role played by translational regulation in determining the expression levels of a gene, our understanding of the molecular mechanisms behind such types of regulation has been slow to emerge. With the recent development of high-throughput approaches to map and quantify different critical parameters affecting translation, such as RNA structure, protein-RNA interactions and ribosome occupancy at the genome level, a renewed enthusiasm toward studying translation regulation is warranted. The use of these new powerful technologies in well-established and uncharacterized translation-dependent processes holds the promise to decipher the likely complex and diverse, but also fascinating, mechanisms behind the regulation of translation.
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Affiliation(s)
- Catharina Merchante
- Departamento de Biologia Molecular y Bioquimica, Universidad de Malaga-Instituto de Hortofruticultura Subtropical y Mediterranea, IHSM-UMA-CSIC, Malaga, Andalucía, Spain
| | - Anna N Stepanova
- Department of Plant and Microbial Biology, Genetics Graduate Program, North Carolina State University, Raleigh, NC, 27607, USA
| | - Jose M Alonso
- Department of Plant and Microbial Biology, Genetics Graduate Program, North Carolina State University, Raleigh, NC, 27607, USA
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25
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Flis A, Sulpice R, Seaton DD, Ivakov AA, Liput M, Abel C, Millar AJ, Stitt M. Photoperiod-dependent changes in the phase of core clock transcripts and global transcriptional outputs at dawn and dusk in Arabidopsis. PLANT, CELL & ENVIRONMENT 2016; 39:1955-81. [PMID: 27075884 DOI: 10.1111/pce.12754] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 04/01/2016] [Indexed: 05/06/2023]
Abstract
Plants use the circadian clock to sense photoperiod length. Seasonal responses like flowering are triggered at a critical photoperiod when a light-sensitive clock output coincides with light or darkness. However, many metabolic processes, like starch turnover, and growth respond progressively to photoperiod duration. We first tested the photoperiod response of 10 core clock genes and two output genes. qRT-PCR analyses of transcript abundance under 6, 8, 12 and 18 h photoperiods revealed 1-4 h earlier peak times under short photoperiods and detailed changes like rising PRR7 expression before dawn. Clock models recapitulated most of these changes. We explored the consequences for global gene expression by performing transcript profiling in 4, 6, 8, 12 and 18 h photoperiods. There were major changes in transcript abundance at dawn, which were as large as those between dawn and dusk in a given photoperiod. Contributing factors included altered timing of the clock relative to dawn, light signalling and changes in carbon availability at night as a result of clock-dependent regulation of starch degradation. Their interaction facilitates coordinated transcriptional regulation of key processes like starch turnover, anthocyanin, flavonoid and glucosinolate biosynthesis and protein synthesis and underpins the response of metabolism and growth to photoperiod.
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Affiliation(s)
- Anna Flis
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Golm, Potsdam, Germany
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, GPO Box 475, Canberra, Australian Capital Territory, 2601, Australia
| | - Ronan Sulpice
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Golm, Potsdam, Germany
- Plant Systems Biology Lab, Plant and AgriBiosciences Research Centre, Botany and Plant Science, NUIG, Galway, Ireland
| | - Daniel D Seaton
- SynthSys and School of Biological Sciences, C.H. Waddington Building, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Alexander A Ivakov
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Golm, Potsdam, Germany
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, GPO Box 475, Canberra, Australian Capital Territory, 2601, Australia
| | - Magda Liput
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Golm, Potsdam, Germany
| | - Christin Abel
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Golm, Potsdam, Germany
| | - Andrew J Millar
- SynthSys and School of Biological Sciences, C.H. Waddington Building, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Mark Stitt
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Golm, Potsdam, Germany
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26
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De Caluwé J, Xiao Q, Hermans C, Verbruggen N, Leloup JC, Gonze D. A Compact Model for the Complex Plant Circadian Clock. FRONTIERS IN PLANT SCIENCE 2016; 7:74. [PMID: 26904049 PMCID: PMC4742534 DOI: 10.3389/fpls.2016.00074] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Accepted: 01/16/2016] [Indexed: 05/23/2023]
Abstract
The circadian clock is an endogenous timekeeper that allows organisms to anticipate and adapt to the daily variations of their environment. The plant clock is an intricate network of interlocked feedback loops, in which transcription factors regulate each other to generate oscillations with expression peaks at specific times of the day. Over the last decade, mathematical modeling approaches have been used to understand the inner workings of the clock in the model plant Arabidopsis thaliana. Those efforts have produced a number of models of ever increasing complexity. Here, we present an alternative model that combines a low number of equations and parameters, similar to the very earliest models, with the complex network structure found in more recent ones. This simple model describes the temporal evolution of the abundance of eight clock gene mRNA/protein and captures key features of the clock on a qualitative level, namely the entrained and free-running behaviors of the wild type clock, as well as the defects found in knockout mutants (such as altered free-running periods, lack of entrainment, or changes in the expression of other clock genes). Additionally, our model produces complex responses to various light cues, such as extreme photoperiods and non-24 h environmental cycles, and can describe the control of hypocotyl growth by the clock. Our model constitutes a useful tool to probe dynamical properties of the core clock as well as clock-dependent processes.
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Affiliation(s)
- Joëlle De Caluwé
- Unité de Chronobiologie Théorique, Faculté des Sciences, Université Libre de BruxellesBrussels, Belgium
| | - Qiying Xiao
- Laboratory of Plant Physiology and Molecular Genetics, Faculté des Sciences, Université Libre de BruxellesBrussels, Belgium
| | - Christian Hermans
- Laboratory of Plant Physiology and Molecular Genetics, Faculté des Sciences, Université Libre de BruxellesBrussels, Belgium
| | - Nathalie Verbruggen
- Laboratory of Plant Physiology and Molecular Genetics, Faculté des Sciences, Université Libre de BruxellesBrussels, Belgium
| | - Jean-Christophe Leloup
- Unité de Chronobiologie Théorique, Faculté des Sciences, Université Libre de BruxellesBrussels, Belgium
| | - Didier Gonze
- Unité de Chronobiologie Théorique, Faculté des Sciences, Université Libre de BruxellesBrussels, Belgium
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Xu Z, Ali Z, Xu L, He X, Huang Y, Yi J, Shao H, Ma H, Zhang D. The nuclear protein GmbZIP110 has transcription activation activity and plays important roles in the response to salinity stress in soybean. Sci Rep 2016; 6:20366. [PMID: 26837841 PMCID: PMC4738249 DOI: 10.1038/srep20366] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 12/31/2015] [Indexed: 11/08/2022] Open
Abstract
Plant basic-leucine zipper (bZIP) transcription factors play important roles in many biological processes and are involved in the regulation of salt stress tolerance. Previously, our lab generated digital gene expression profiling (DGEP) data to identify differentially expressed genes in a salt-tolerant genotype of Glycine soja (STGoGS) and a salt-sensitive genotype of Glycine max (SSGoGM). This DGEP data revealed that the expression (log2 ratio) of GmbZIP110 was up-regulated 2.76-fold and 3.38-fold in SSGoGM and STGoGS, respectively. In the present study, the salt inducible gene GmbZIP110 was cloned and characterized through phylogenetic analysis, subcellular localization and in silico transcript abundance analysis in different tissues. The functional role of this gene in salt tolerance was studied through transactivation analysis, DNA binding ability, expression in soybean composite seedlings and transgenic Arabidopsis, and the effect of GmbZIP110 on the expression of stress-related genes in transgenic Arabidopsis was investigated. We found that GmbZIP110 could bind to the ACGT motif, impact the expression of many stress-related genes and the accumulation of proline, Na(+) and K(+), and enhanced the salt tolerance of composite seedlings and transgenic Arabidopsis. Integrating all these results, we propose that GmbZIP110 plays a critical role in the response to salinity stress in soybean and has high potential usefulness in crop improvement.
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Affiliation(s)
- Zhaolong Xu
- Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Zulfiqar Ali
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Punjab, Pakistan
| | - Ling Xu
- Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Xiaolan He
- Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Yihong Huang
- Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Jinxin Yi
- Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Hongbo Shao
- Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Hongxiang Ma
- Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Dayong Zhang
- Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
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Adams S, Manfield I, Stockley P, Carré IA. Revised Morning Loops of the Arabidopsis Circadian Clock Based on Analyses of Direct Regulatory Interactions. PLoS One 2015; 10:e0143943. [PMID: 26625126 PMCID: PMC4666590 DOI: 10.1371/journal.pone.0143943] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 11/11/2015] [Indexed: 11/24/2022] Open
Abstract
The network structure of the plant circadian clock is complex and direct regulatory interactions between individual components have proven particularly difficult to predict from genetic analyses. Here, we systematically investigate in vivo binding interactions between the morning-specific transcription factor, LATE ELONGATED HYPOCOTYL (LHY) and the promoters of other components of the network. We then demonstrate the functionality of these interactions by testing the responsiveness of the target gene to an ethanol-induced change in expression level of the LHY protein. We uncover novel, negative autoregulatory feedback loops from LHY and the closely related CIRCADIAN CLOCK ASSOCIATED-1 (CCA1) onto their own and each other’s expression. Furthermore we show that LHY acts as a repressor of all other clock components, including PSEUDO-RESPONSE REGULATORs (PRRs) 9 and 7, which were previously thought to be positive regulatory targets. These experimental results lead to a substantial revision of the morning loops of the clock.
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Affiliation(s)
- Sally Adams
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Ian Manfield
- Astbury Centre, University of Leeds, Leeds, United Kingdom
| | - Peter Stockley
- Astbury Centre, University of Leeds, Leeds, United Kingdom
| | - Isabelle A. Carré
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- * E-mail:
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29
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Missra A, Ernest B, Lohoff T, Jia Q, Satterlee J, Ke K, von Arnim AG. The Circadian Clock Modulates Global Daily Cycles of mRNA Ribosome Loading. THE PLANT CELL 2015; 27:2582-99. [PMID: 26392078 PMCID: PMC4815098 DOI: 10.1105/tpc.15.00546] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 09/02/2015] [Indexed: 05/03/2023]
Abstract
Circadian control of gene expression is well characterized at the transcriptional level, but little is known about diel or circadian control of translation. Genome-wide translation state profiling of mRNAs in Arabidopsis thaliana seedlings grown in long day was performed to estimate ribosome loading per mRNA. The experiments revealed extensive translational regulation of key biological processes. Notably, translation of mRNAs for ribosomal proteins and mitochondrial respiration peaked at night. Central clock mRNAs are among those subject to fluctuations in ribosome loading. There was no consistent phase relationship between peak translation states and peak transcript levels. The overlay of distinct transcriptional and translational cycles can be expected to alter the waveform of the protein synthesis rate. Plants that constitutively overexpress the clock gene CCA1 showed phase shifts in peak translation, with a 6-h delay from midnight to dawn or from noon to evening being particularly common. Moreover, cycles of ribosome loading that were detected under continuous light in the wild type collapsed in the CCA1 overexpressor. Finally, at the transcript level, the CCA1-ox strain adopted a global pattern of transcript abundance that was broadly correlated with the light-dark environment. Altogether, these data demonstrate that gene-specific diel cycles of ribosome loading are controlled in part by the circadian clock.
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Affiliation(s)
- Anamika Missra
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996-0840
| | - Ben Ernest
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN 37996-0840
| | - Tim Lohoff
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996-0840 Molekulare Zellphysiologie, Fakultät Biologie, Universität Bielefeld, D-33615 Bielefeld, Germany
| | - Qidong Jia
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN 37996-0840
| | - James Satterlee
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996-0840
| | - Kenneth Ke
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996-0840
| | - Albrecht G von Arnim
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996-0840 Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN 37996-0840
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30
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Yeang HY. Cycling of clock genes entrained to the solar rhythm enables plants to tell time: data from Arabidopsis. ANNALS OF BOTANY 2015; 116:15-22. [PMID: 26070640 PMCID: PMC4479757 DOI: 10.1093/aob/mcv070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 03/24/2015] [Accepted: 04/15/2015] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS An endogenous rhythm synchronized to dawn cannot time photosynthesis-linked genes to peak consistently at noon since the interval between sunrise and noon changes seasonally. In this study, a solar clock model that circumvents this limitation is proposed using two daily timing references synchronized to noon and midnight. Other rhythmic genes that are not directly linked to photosynthesis, and which peak at other times, also find an adaptive advantage in entrainment to the solar rhythm. METHODS Fourteen datasets extracted from three published papers were used in a meta-analysis to examine the cyclic behaviour of the Arabidopsis thaliana photosynthesis-related gene CAB2 and the clock oscillator genes TOC1 and LHY in T cycles and N-H cycles. KEY RESULTS Changes in the rhythms of CAB2, TOC1 and LHY in plants subjected to non-24-h light:dark cycles matched the hypothesized changes in their behaviour as predicted by the solar clock model, thus validating it. The analysis further showed that TOC1 expression peaked ∼5·5 h after mid-day, CAB2 peaked close to noon, while LHY peaked ∼7·5 h after midnight, regardless of the cycle period, the photoperiod or the light:dark period ratio. The solar clock model correctly predicted the zeitgeber timing of these genes under 11 different lighting regimes comprising combinations of seven light periods, nine dark periods, four cycle periods and four light:dark period ratios. In short cycles that terminated before LHY could be expressed, the solar clock correctly predicted zeitgeber timing of its expression in the following cycle. CONCLUSIONS Regulation of gene phases by the solar clock enables the plant to tell the time, by which means a large number of genes are regulated. This facilitates the initiation of gene expression even before the arrival of sunrise, sunset or noon, thus allowing the plant to 'anticipate' dawn, dusk or mid-day respectively, independently of the photoperiod.
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31
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Zhang Z, Chen J, Su Y, Liu H, Chen Y, Luo P, Du X, Wang D, Zhang H. TaLHY, a 1R-MYB Transcription Factor, Plays an Important Role in Disease Resistance against Stripe Rust Fungus and Ear Heading in Wheat. PLoS One 2015; 10:e0127723. [PMID: 26010918 PMCID: PMC4444181 DOI: 10.1371/journal.pone.0127723] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 04/20/2015] [Indexed: 01/10/2023] Open
Abstract
LHY (late elongated hypocotyl) is an important gene that regulates and controls biological rhythms in plants. Additionally, LHY is highly expressed in the SSH (suppression subtractive hybridization) cDNA library-induced stripe rust pathogen (CYR32) in our previous research. To identify the function of the LHY gene in disease resistance against stripe rust, we used RACE-PCR technology to clone TaLHY in the wheat variety Chuannong19. The cDNA of TaLHY is 3085 bp long with an open reading frame of 1947 bp. TaLHY is speculated to encode a 70.3 kDa protein of 648 amino acids , which has one typical plant MYB-DNA binding domain; additionally, phylogenetic tree shows that TaLHY has the highest homology with LHY of Brachypodium distachyon(BdLHY-like). Quantitative fluorescence PCR indicates that TaLHY has higher expression in the leaf, ear and stem of wheat but lower expression in the root. Infestation of CYR32 can result in up-regulated expression of TaLHY, peaking at 72 h. Using VIGS (virus-induced gene silencing) technology to disease-resistant wheat in the fourth leaf stage, plants with silenced TaLHY cannot complete their heading stage. Through the compatible interaction with the stripe rust physiological race CYR32, Chuannong 19 loses its immune capability toward the stripe rust pathogen, indicating that TaLHY may regulate and participate in the heading of wheat, as well as the defense responses against stripe rust infection.
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Affiliation(s)
- Zijin Zhang
- Biophysics and Immune Engineering Lab, Sichuan Agricultural University, Ya’an, Sichuan, People’s Republic of China
| | - Jieming Chen
- Biophysics and Immune Engineering Lab, Sichuan Agricultural University, Ya’an, Sichuan, People’s Republic of China
| | - Yongying Su
- Biophysics and Immune Engineering Lab, Sichuan Agricultural University, Ya’an, Sichuan, People’s Republic of China
| | - Hanmei Liu
- Biophysics and Immune Engineering Lab, Sichuan Agricultural University, Ya’an, Sichuan, People’s Republic of China
| | - Yanger Chen
- Biophysics and Immune Engineering Lab, Sichuan Agricultural University, Ya’an, Sichuan, People’s Republic of China
| | - Peigao Luo
- State Key Laboratory of Plant breeding and Genetics, Sichuan Agricultural University, Chengdu, Sichuan, People’s Republic of China
| | - Xiaogang Du
- Biophysics and Immune Engineering Lab, Sichuan Agricultural University, Ya’an, Sichuan, People’s Republic of China
| | - Dan Wang
- Department of wheat breeding. Puyang Academy of Agricultural Sciences, Puyang, Henan, People’s Republic of China
| | - Huaiyu Zhang
- Biophysics and Immune Engineering Lab, Sichuan Agricultural University, Ya’an, Sichuan, People’s Republic of China
- * E-mail:
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32
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Zhang J, Wu Y, Li D, Wang G, Li X, Xia Y. Transcriptomic analysis of the underground renewal buds during dormancy transition and release in 'Hangbaishao' peony (Paeonia lactiflora). PLoS One 2015; 10:e0119118. [PMID: 25790307 PMCID: PMC4366336 DOI: 10.1371/journal.pone.0119118] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 01/27/2015] [Indexed: 11/18/2022] Open
Abstract
Paeonia lactiflora is one of the most famous species of herbaceous peonies with gorgeous flowers. Bud dormancy is a crucial developmental process that allows P. lactiflora to survive unfavorable environmental conditions. However, little information is available on the molecular mechanism of the bud dormancy in P. lactiflora. We performed de novo transcriptome sequencing using the Illumina RNA sequencing platform for the underground renewal buds of P. lactiflora 'Hangbaishao' to study the molecular mechanism underlying its bud dormancy transition (the period from endodormancy to ecodormancy) and release (the period from ecodormancy to bud elongation and sprouting). Approximately 300 million high-quality clean reads were generated and assembled into 207,827 (mean length = 828 bp) and 51,481 (mean length = 1250 bp) unigenes using two assembly methods named "Trinity" and "Trinity+PRICE", respectively. Based on the data obtained by the latter method, 32,316 unigenes were annotated by BLAST against various databases. Approximately 1,251 putative transcription factors were obtained, of which the largest number of unique transcripts belonged to the basic helix-loop-helix protein (bHLH) transcription factor family, and five of the top ten highly expressed transcripts were annotated as dehydrin (DHN). A total of 17,705 simple sequence repeat (SSR) motifs distributed in 13,797 sequences were obtained. The budbreak morphology, levels of indole-3-acetic acid (IAA) and abscisic acid (ABA), and activities of guaiacol peroxidase (POD) and catalase (CAT) were observed. The expression of 20 interested unigenes, which annotated as DHN, heat shock protein (HSP), histone, late elongated hypocotyl (LHY), and phytochrome (PHY), and so on, were also analyzed. These studies were based on morphological, physiological, biochemical, and molecular levels and provide comprehensive insight into the mechanism of dormancy transition and release in P. lactiflora. Transcriptome dataset can be highly valuable for future investigation on gene expression networks in P. lactiflora as well as research on dormancy in other non-model perennial horticultural crops of commercial significance.
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Affiliation(s)
- Jiaping Zhang
- Institute of Landscape Architecture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, People’s Republic of China
| | - Yun Wu
- Institute of Landscape Architecture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, People’s Republic of China
| | - Danqing Li
- Institute of Landscape Architecture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, People’s Republic of China
| | - Guanqun Wang
- Institute of Landscape Architecture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, People’s Republic of China
| | - Xin Li
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
| | - Yiping Xia
- Institute of Landscape Architecture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, People’s Republic of China
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33
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Romanowski A, Yanovsky MJ. Circadian rhythms and post-transcriptional regulation in higher plants. FRONTIERS IN PLANT SCIENCE 2015; 6:437. [PMID: 26124767 PMCID: PMC4464108 DOI: 10.3389/fpls.2015.00437] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 05/28/2015] [Indexed: 05/06/2023]
Abstract
The circadian clock of plants allows them to cope with daily changes in their environment. This is accomplished by the rhythmic regulation of gene expression, in a process that involves many regulatory steps. One of the key steps involved at the RNA level is post-transcriptional regulation, which ensures a correct control on the different amounts and types of mRNA that will ultimately define the current physiological state of the plant cell. Recent advances in the study of the processes of regulation of pre-mRNA processing, RNA turn-over and surveillance, regulation of translation, function of lncRNAs, biogenesis and function of small RNAs, and the development of bioinformatics tools have helped to vastly expand our understanding of how this regulatory step performs its role. In this work we review the current progress in circadian regulation at the post-transcriptional level research in plants. It is the continuous interaction of all the information flow control post-transcriptional processes that allow a plant to precisely time and predict daily environmental changes.
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Affiliation(s)
| | - Marcelo J. Yanovsky
- *Correspondence: Marcelo J. Yanovsky, Laboratorio de Genómica Comparativa del Desarrollo Vegetal, Fundación Instituto Leloir, IIBBA-CONICET, Avenida Patricias Argentinas 435, Buenos Aires C1405BWE, Argentina,
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34
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Nolte C, Staiger D. RNA around the clock - regulation at the RNA level in biological timing. FRONTIERS IN PLANT SCIENCE 2015; 6:311. [PMID: 25999975 PMCID: PMC4419606 DOI: 10.3389/fpls.2015.00311] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 04/19/2015] [Indexed: 05/21/2023]
Abstract
The circadian timing system in plants synchronizes their physiological functions with the environment. This is achieved by a global control of gene expression programs with a considerable part of the transcriptome undergoing 24-h oscillations in steady-state abundance. These circadian oscillations are driven by a set of core clock proteins that generate their own 24-h rhythm through periodic feedback on their own transcription. Additionally, post-transcriptional events are instrumental for oscillations of core clock genes and genes in clock output. Here we provide an update on molecular events at the RNA level that contribute to the 24-h rhythm of the core clock proteins and shape the circadian transcriptome. We focus on the circadian system of the model plant Arabidopsis thaliana but also discuss selected regulatory principles in other organisms.
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Affiliation(s)
| | - Dorothee Staiger
- *Correspondence: Dorothee Staiger, Molecular Cell Physiology, Faculty of Biology, Bielefeld University, Universitaetsstrasse 25, Bielefeld D-33615, Germany
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Yeom M, Kim H, Lim J, Shin AY, Hong S, Kim JI, Nam HG. How do phytochromes transmit the light quality information to the circadian clock in Arabidopsis? MOLECULAR PLANT 2014; 7:1701-1704. [PMID: 25095795 DOI: 10.1093/mp/ssu086] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Affiliation(s)
- Miji Yeom
- Division of Molecular and Life Sciences, Pohang University of Science and Technology, Hyojadong, Pohang, Gyeongbuk, 790-784, Republic of Korea
| | - Hyunmin Kim
- Division of Molecular and Life Sciences, Pohang University of Science and Technology, Hyojadong, Pohang, Gyeongbuk, 790-784, Republic of Korea
| | - Junhyun Lim
- Integrative Biosciences & Biotechnology in POSTECH, Hyojadong, Pohang, Gyeongbuk 790-784, Republic of Korea
| | - Ah-Young Shin
- Department of Molecular Biotechnology and Kumho Life Science Laboratory, Chonnam National University, Gwangju, 500-757, Republic of Korea
| | - Sunghyun Hong
- Center for Plant Aging Research, Institute for Basic Science, Daegu 711-873, Republic of Korea
| | - Jeong-Il Kim
- Department of Molecular Biotechnology and Kumho Life Science Laboratory, Chonnam National University, Gwangju, 500-757, Republic of Korea
| | - Hong Gil Nam
- Center for Plant Aging Research, Institute for Basic Science, Daegu 711-873, Republic of Korea; Department of New Biology, DGIST, Hyeongpoong-Myun, Dalsung-gun, Daegu 711-873, Republic of Korea.
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Fogelmark K, Troein C. Rethinking transcriptional activation in the Arabidopsis circadian clock. PLoS Comput Biol 2014; 10:e1003705. [PMID: 25033214 PMCID: PMC4102396 DOI: 10.1371/journal.pcbi.1003705] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 05/19/2014] [Indexed: 12/19/2022] Open
Abstract
Circadian clocks are biological timekeepers that allow living cells to time their activity in anticipation of predictable daily changes in light and other environmental factors. The complexity of the circadian clock in higher plants makes it difficult to understand the role of individual genes or molecular interactions, and mathematical modelling has been useful in guiding clock research in model organisms such as Arabidopsis thaliana. We present a model of the circadian clock in Arabidopsis, based on a large corpus of published time course data. It appears from experimental evidence in the literature that most interactions in the clock are repressive. Hence, we remove all transcriptional activation found in previous models of this system, and instead extend the system by including two new components, the morning-expressed activator RVE8 and the nightly repressor/activator NOX. Our modelling results demonstrate that the clock does not need a large number of activators in order to reproduce the observed gene expression patterns. For example, the sequential expression of the PRR genes does not require the genes to be connected as a series of activators. In the presented model, transcriptional activation is exclusively the task of RVE8. Predictions of how strongly RVE8 affects its targets are found to agree with earlier interpretations of the experimental data, but generally we find that the many negative feedbacks in the system should discourage intuitive interpretations of mutant phenotypes. The dynamics of the clock are difficult to predict without mathematical modelling, and the clock is better viewed as a tangled web than as a series of loops. Like most living organisms, plants are dependent on sunlight, and evolution has endowed them with an internal clock by which they can predict sunrise and sunset. The clock consists of many genes that control each other in a complex network, leading to daily oscillations in protein levels. The interactions between genes can be positive or negative, causing target genes to be turned on or off. By constructing mathematical models that incorporate our knowledge of this network, we can interpret experimental data by comparing with results from the models. Any discrepancy between experimental data and model predictions will highlight where we are lacking in understanding. We compiled more than 800 sets of measured data from published articles about the clock in the model organism thale cress (Arabidopsis thaliana). Using these data, we constructed a mathematical model which compares favourably with previous models for simulating the clock. We used our model to investigate the role of positive interactions between genes, whether they are necessary for the function of the clock and if they can be identified in the model.
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Affiliation(s)
- Karl Fogelmark
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Carl Troein
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
- * E-mail:
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Kwon YJ, Park MJ, Kim SG, Baldwin IT, Park CM. Alternative splicing and nonsense-mediated decay of circadian clock genes under environmental stress conditions in Arabidopsis. BMC PLANT BIOLOGY 2014; 14:136. [PMID: 24885185 PMCID: PMC4035800 DOI: 10.1186/1471-2229-14-136] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 05/14/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND The circadian clock enables living organisms to anticipate recurring daily and seasonal fluctuations in their growth habitats and synchronize their biology to the environmental cycle. The plant circadian clock consists of multiple transcription-translation feedback loops that are entrained by environmental signals, such as light and temperature. In recent years, alternative splicing emerges as an important molecular mechanism that modulates the clock function in plants. Several clock genes are known to undergo alternative splicing in response to changes in environmental conditions, suggesting that the clock function is intimately associated with environmental responses via the alternative splicing of the clock genes. However, the alternative splicing events of the clock genes have not been studied at the molecular level. RESULTS We systematically examined whether major clock genes undergo alternative splicing under various environmental conditions in Arabidopsis. We also investigated the fates of the RNA splice variants of the clock genes. It was found that the clock genes, including EARLY FLOWERING 3 (ELF3) and ZEITLUPE (ZTL) that have not been studied in terms of alternative splicing, undergo extensive alternative splicing through diverse modes of splicing events, such as intron retention, exon skipping, and selection of alternative 5' splice site. Their alternative splicing patterns were differentially influenced by changes in photoperiod, temperature extremes, and salt stress. Notably, the RNA splice variants of TIMING OF CAB EXPRESSION 1 (TOC1) and ELF3 were degraded through the nonsense-mediated decay (NMD) pathway, whereas those of other clock genes were insensitive to NMD. CONCLUSION Taken together, our observations demonstrate that the major clock genes examined undergo extensive alternative splicing under various environmental conditions, suggesting that alternative splicing is a molecular scheme that underlies the linkage between the clock and environmental stress adaptation in plants. It is also envisioned that alternative splicing of the clock genes plays more complex roles than previously expected.
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Affiliation(s)
- Young-Ju Kwon
- Department of Chemistry, Seoul National University, Seoul 151-742, Korea
| | - Mi-Jeong Park
- Department of Chemistry, Seoul National University, Seoul 151-742, Korea
| | - Sang-Gyu Kim
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Ian T Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Chung-Mo Park
- Department of Chemistry, Seoul National University, Seoul 151-742, Korea
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MacGregor DR, Gould P, Foreman J, Griffiths J, Bird S, Page R, Stewart K, Steel G, Young J, Paszkiewicz K, Millar AJ, Halliday KJ, Hall AJ, Penfield S. HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES1 is required for circadian periodicity through the promotion of nucleo-cytoplasmic mRNA export in Arabidopsis. THE PLANT CELL 2013; 25:4391-404. [PMID: 24254125 PMCID: PMC3875725 DOI: 10.1105/tpc.113.114959] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 10/10/2013] [Accepted: 10/25/2013] [Indexed: 05/18/2023]
Abstract
Cold acclimation has been shown to be attenuated by the degradation of the INDUCER OF CBF EXPRESSION1 protein by the E3 ubiquitin ligase HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES1 (HOS1). However, recent work has suggested that HOS1 may have a wider range of roles in plants than previously appreciated. Here, we show that hos1 mutants are affected in circadian clock function, exhibiting a long-period phenotype in a wide range of temperature and light environments. We demonstrate that hos1 mutants accumulate polyadenylated mRNA in the nucleus and that the circadian defect in hos1 is shared by multiple mutants with aberrant mRNA export, but not in a mutant attenuated in nucleo-cytoplasmic transport of microRNAs. As revealed by RNA sequencing, hos1 exhibits gross changes to the transcriptome with genes in multiple functional categories being affected. In addition, we show that hos1 and other previously described mutants with altered mRNA export affect cold signaling in a similar manner. Our data support a model in which altered mRNA export is important for the manifestation of hos1 circadian clock defects and suggest that HOS1 may indirectly affect cold signaling through disruption of the circadian clock.
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Affiliation(s)
- Dana R. MacGregor
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Peter Gould
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Julia Foreman
- Centre for Synthetic and Systems Biology (SynthSys), School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JD, United Kingdom
| | - Jayne Griffiths
- Centre for Synthetic and Systems Biology (SynthSys), School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JD, United Kingdom
| | - Susannah Bird
- Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Rhiannon Page
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Kelly Stewart
- Centre for Synthetic and Systems Biology (SynthSys), School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JD, United Kingdom
| | - Gavin Steel
- Centre for Synthetic and Systems Biology (SynthSys), School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JD, United Kingdom
| | - Jack Young
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Konrad Paszkiewicz
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Andrew J. Millar
- Centre for Synthetic and Systems Biology (SynthSys), School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JD, United Kingdom
| | - Karen J. Halliday
- Centre for Synthetic and Systems Biology (SynthSys), School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JD, United Kingdom
| | - Anthony J. Hall
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Steven Penfield
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom
- Address correspondence to
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Zhang C, Xie Q, Anderson RG, Ng G, Seitz NC, Peterson T, McClung CR, McDowell JM, Kong D, Kwak JM, Lu H. Crosstalk between the circadian clock and innate immunity in Arabidopsis. PLoS Pathog 2013; 9:e1003370. [PMID: 23754942 PMCID: PMC3675028 DOI: 10.1371/journal.ppat.1003370] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2012] [Accepted: 04/04/2013] [Indexed: 12/17/2022] Open
Abstract
The circadian clock integrates temporal information with environmental cues in regulating plant development and physiology. Recently, the circadian clock has been shown to affect plant responses to biotic cues. To further examine this role of the circadian clock, we tested disease resistance in mutants disrupted in CCA1 and LHY, which act synergistically to regulate clock activity. We found that cca1 and lhy mutants also synergistically affect basal and resistance gene-mediated defense against Pseudomonas syringae and Hyaloperonospora arabidopsidis. Disrupting the circadian clock caused by overexpression of CCA1 or LHY also resulted in severe susceptibility to P. syringae. We identified a downstream target of CCA1 and LHY, GRP7, a key constituent of a slave oscillator regulated by the circadian clock and previously shown to influence plant defense and stomatal activity. We show that the defense role of CCA1 and LHY against P. syringae is at least partially through circadian control of stomatal aperture but is independent of defense mediated by salicylic acid. Furthermore, we found defense activation by P. syringae infection and treatment with the elicitor flg22 can feedback-regulate clock activity. Together this data strongly supports a direct role of the circadian clock in defense control and reveal for the first time crosstalk between the circadian clock and plant innate immunity.
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Affiliation(s)
- Chong Zhang
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, United States of America
| | - Qiguang Xie
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Ryan G. Anderson
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Gina Ng
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, United States of America
| | - Nicholas C. Seitz
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, United States of America
| | - Thomas Peterson
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, United States of America
| | - C. Robertson McClung
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, United States of America
| | - John M. McDowell
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Dongdong Kong
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
| | - June M. Kwak
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
- Department of Cell Biology and Molecular Genetics, Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland, United States of America
- Department of Plant Molecular Systems Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, Republic of Korea
| | - Hua Lu
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, United States of America
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Hsu PY, Devisetty UK, Harmer SL. Accurate timekeeping is controlled by a cycling activator in Arabidopsis. eLife 2013. [PMID: 23638299 DOI: 10.7554/elife.00473.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
Transcriptional feedback loops are key to circadian clock function in many organisms. Current models of the Arabidopsis circadian network consist of several coupled feedback loops composed almost exclusively of transcriptional repressors. Indeed, a central regulatory mechanism is the repression of evening-phased clock genes via the binding of morning-phased Myb-like repressors to evening element (EE) promoter motifs. We now demonstrate that a related Myb-like protein, REVEILLE8 (RVE8), is a direct transcriptional activator of EE-containing clock and output genes. Loss of RVE8 and its close homologs causes a delay and reduction in levels of evening-phased clock gene transcripts and significant lengthening of clock pace. Our data suggest a substantially revised model of the circadian oscillator, with a clock-regulated activator essential both for clock progression and control of clock outputs. Further, our work suggests that the plant clock consists of a highly interconnected, complex regulatory network rather than of coupled morning and evening feedback loops. DOI:http://dx.doi.org/10.7554/eLife.00473.001.
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Affiliation(s)
- Polly Yingshan Hsu
- Department of Plant Biology , University of California, Davis , Davis , United States
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41
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Hsu PY, Devisetty UK, Harmer SL. Accurate timekeeping is controlled by a cycling activator in Arabidopsis. eLife 2013; 2:e00473. [PMID: 23638299 PMCID: PMC3639509 DOI: 10.7554/elife.00473] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 03/24/2013] [Indexed: 12/19/2022] Open
Abstract
Transcriptional feedback loops are key to circadian clock function in many organisms. Current models of the Arabidopsis circadian network consist of several coupled feedback loops composed almost exclusively of transcriptional repressors. Indeed, a central regulatory mechanism is the repression of evening-phased clock genes via the binding of morning-phased Myb-like repressors to evening element (EE) promoter motifs. We now demonstrate that a related Myb-like protein, REVEILLE8 (RVE8), is a direct transcriptional activator of EE-containing clock and output genes. Loss of RVE8 and its close homologs causes a delay and reduction in levels of evening-phased clock gene transcripts and significant lengthening of clock pace. Our data suggest a substantially revised model of the circadian oscillator, with a clock-regulated activator essential both for clock progression and control of clock outputs. Further, our work suggests that the plant clock consists of a highly interconnected, complex regulatory network rather than of coupled morning and evening feedback loops. DOI:http://dx.doi.org/10.7554/eLife.00473.001 We live in a world with a 24-hr cycle in which day follows night follows day with complete predictability. Life on earth has evolved to take advantage of this predictability by using circadian clocks to prepare for the coming of night (or day), and plants are no exception. Even in constant darkness, characteristics such as leaf movements show a constant cycle of around 24 hr. Most circadian clocks rely on negative feedback loops involving various genes and proteins to keep track of time. In one of these feedback loops, certain genes—called morning-phased genes—are expressed as proteins during the day, and these proteins prevent other genes—called evening-phased genes—from producing proteins. As night approaches, however, a second feedback loop acts to stop the morning-phased genes being expressed, thus allowing the evening-phased genes to produce proteins. And as day approaches, expression of these genes is stopped and the whole cycle starts again. Many of the genes and proteins involved in the circadian system of Arabidopsis thaliana, a small flowering plant that is widely used as a model organism, have been identified, and its circadian clock was thought to rely almost entirely on proteins called repressors that block the transcription of genes. Now, Hsu et al. have shown that the Arabidopsis clock also involves proteins that increase the expression of certain genes at specific times of the day. Hsu et al. focused on the promoter regions of evening-phased genes: these regions are stretches of DNA that proteins called transcription factors bind to and either encourage the expression of a gene (if the protein is a transcriptional activator) or block its expression (as a transcriptional repressor). In particular, they focused on a protein called RVE8 that is most strongly expressed in the afternoon and, based on previous research, is thought to activate the transcription of genes. Using genetically modified plants in which the gene for RVE8 can be turned on and off, they found that this protein led to increases in the expression of some genes, and reductions in the expression of others. Further analysis showed that RVE8 was able to activate the expression of evening-phased genes directly, without requiring that new proteins be made first. By contrast, morning-expressed genes were likely to be suppressed by RVE8 via an indirect mechanism that involved other proteins that had previously been activated by RVE8. The expression of RVE8 itself is regulated by other clock genes and also by an undefined post-transcriptional process. Therefore rather than consisting of a morning feedback loop coupled to an evening feedback loop, with both loops being based on repressors, the plant clock is instead better viewed as a highly connected network of activators and repressors. Further research is clearly necessary to understand this unexpected complexity in the circadian clock of Arabidopsis. DOI:http://dx.doi.org/10.7554/eLife.00473.002
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Affiliation(s)
- Polly Yingshan Hsu
- Department of Plant Biology , University of California, Davis , Davis , United States
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Schmal C, Reimann P, Staiger D. A circadian clock-regulated toggle switch explains AtGRP7 and AtGRP8 oscillations in Arabidopsis thaliana. PLoS Comput Biol 2013; 9:e1002986. [PMID: 23555221 PMCID: PMC3610657 DOI: 10.1371/journal.pcbi.1002986] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2012] [Accepted: 01/29/2013] [Indexed: 12/25/2022] Open
Abstract
The circadian clock controls many physiological processes in higher plants and causes a large fraction of the genome to be expressed with a 24h rhythm. The transcripts encoding the RNA-binding proteins AtGRP7 (Arabidopsis thaliana Glycine Rich Protein 7) and AtGRP8 oscillate with evening peaks. The circadian clock components CCA1 and LHY negatively affect AtGRP7 expression at the level of transcription. AtGRP7 and AtGRP8, in turn, negatively auto-regulate and reciprocally cross-regulate post-transcriptionally: high protein levels promote the generation of an alternative splice form that is rapidly degraded. This clock-regulated feedback loop has been proposed to act as a molecular slave oscillator in clock output. While mathematical models describing the circadian core oscillator in Arabidopsis thaliana were introduced recently, we propose here the first model of a circadian slave oscillator. We define the slave oscillator in terms of ordinary differential equations and identify the model's parameters by an optimization procedure based on experimental results. The model successfully reproduces the pertinent experimental findings such as waveforms, phases, and half-lives of the time-dependent concentrations. Furthermore, we obtain insights into possible mechanisms underlying the observed experimental dynamics: the negative auto-regulation and reciprocal cross-regulation via alternative splicing could be responsible for the sharply peaking waveforms of the AtGRP7 and AtGRP8 mRNA. Moreover, our results suggest that the AtGRP8 transcript oscillations are subordinated to those of AtGRP7 due to a higher impact of AtGRP7 protein on alternative splicing of its own and of the AtGRP8 pre-mRNA compared to the impact of AtGRP8 protein. Importantly, a bifurcation analysis provides theoretical evidence that the slave oscillator could be a toggle switch, arising from the reciprocal cross-regulation at the post-transcriptional level. In view of this, transcriptional repression of AtGRP7 and AtGRP8 by LHY and CCA1 induces oscillations of the toggle switch, leading to the observed high-amplitude oscillations of AtGRP7 mRNA. The circadian clock organizes the day in the life of a plant by causing 24h rhythms in gene expression. For example, the core clockwork of the model plant Arabidopsis thaliana causes the transcripts encoding the RNA-binding proteins AtGRP7 and AtGRP8 to undergo high amplitude oscillations with a peak at the end of the day. AtGRP7 and AtGRP8, in turn, negatively auto-regulate and reciprocally cross-regulate their own expression by causing alternative splicing of their pre-mRNAs, followed by rapid degradation of the alternatively spliced transcripts. This has led to the suggestion that they represent molecular slave oscillators downstream of the core clock. Using a mathematical model we obtain insights into possible mechanisms underlying the experimentally observed dynamics, e.g. a higher impact of AtGRP7 protein compared to the impact of AtGRP8 protein on the alternative splicing explains the experimentally observed phases of their transcript. Previously, components that reciprocally repress their own transcription (double negative loops) have been shown to potentially act as a toggle switch between two states. We provide theoretical evidence that the slave oscillator could be a bistable toggle switch as well, operating at the post-transcriptional level.
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Affiliation(s)
- Christoph Schmal
- Condensed Matter Theory, Faculty of Physics, Bielefeld University, Bielefeld, Germany.
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43
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Kangisser S, Yakir E, Green RM. Proteasomal regulation of CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) stability is part of the complex control of CCA1. PLANT SIGNALING & BEHAVIOR 2013; 8:e23206. [PMID: 23299326 PMCID: PMC3676491 DOI: 10.4161/psb.23206] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The circadian (~24 h) clock has an enormous influence on the biology of plants and controls a plethora of processes including growth, photosynthesis, photoperiodic flowering and transcription of more than 30% of the genome. The oscillator mechanism that generates these circadian rhythms consists of interlocking feedback loops. CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) is a single MYB-transcription factor with a key role in the main feedback loop. CCA1 regulation is important for correct oscillator function and may be an important integration point for environmental signals such as temperature and light that entrain the oscillator. Here we show that CCA1 protein stability is controlled by the proteasome and discuss our findings in the context of the different levels of CCA1 regulation.
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44
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Chow BY, Kay SA. Global approaches for telling time: omics and the Arabidopsis circadian clock. Semin Cell Dev Biol 2013; 24:383-92. [PMID: 23435351 DOI: 10.1016/j.semcdb.2013.02.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 02/08/2013] [Accepted: 02/12/2013] [Indexed: 12/31/2022]
Abstract
The circadian clock is an endogenous timer that anticipates and synchronizes biological processes to the environment. Traditional genetic approaches identified the underlying principles and genetic components, but new discoveries have been greatly impeded by the embedded redundancies that confer necessary robustness to the clock architecture. To overcome this, global (omic) techniques have provided a new depth of information about the Arabidopsis clock. Our understanding of the factors, regulation, and mechanistic connectivity between clock genes and with output processes has substantially broadened through genomic (cDNA libraries, yeast one-hybrid, protein binding microarrays, and ChIP-seq), transcriptomic (microarrays, RNA-seq), proteomic (mass spectrometry and chemical libraries), and metabolomic (mass spectrometry) approaches. This evolution in research will undoubtedly enhance our understanding of how the circadian clock optimizes growth and fitness.
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Affiliation(s)
- Brenda Y Chow
- Section of Cell and Developmental Biology and Center for Chronobiology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, United States.
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Unanticipated regulatory roles for Arabidopsis phytochromes revealed by null mutant analysis. Proc Natl Acad Sci U S A 2013; 110:1542-7. [PMID: 23302690 DOI: 10.1073/pnas.1221738110] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In view of the extensive literature on phytochrome mutants in the Ler accession of Arabidopsis, we sought to secure a phytochrome-null line in the same genetic background for comparative studies. Here we report the isolation and phenotypic characterization of phyABCDE quintuple and phyABDE quadruple mutants in the Ler background. Unlike earlier studies, these lines possess a functional allele of FT permitting measurements of photoperiod-dependent flowering behavior. Comparative studies of both classes of mutants establish that phytochromes are dispensable for completion of the Arabidopsis life cycle under red light, despite the lack of a transcriptomic response, and also indicate that phyC is nonfunctional in the absence of other phytochromes. Phytochrome-less plants can produce chlorophyll for photosynthesis under continuous red light, yet require elevated fluence rates for survival. Unexpectedly, our analyses reveal both light-dependent and -independent roles for phytochromes to regulate the Arabidopsis circadian clock. The rapid transition of these mutants from vegetative to reproductive growth, as well as their insensitivity to photoperiod, establish a dual role for phytochromes to arrest and to promote progression of plant development in response to the prevailing light environment.
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Shaw LM, Turner AS, Laurie DA. The impact of photoperiod insensitive Ppd-1a mutations on the photoperiod pathway across the three genomes of hexaploid wheat (Triticum aestivum). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 71:71-84. [PMID: 22372488 DOI: 10.1111/j.1365-313x.2012.04971.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Flowering time is a trait that has been extensively altered during wheat domestication, enabling it to be highly productive in diverse environments and providing a rich source of variation for studying adaptation mechanisms. Hexaploid wheat is ancestrally a long-day plant, but many environments require varieties with photoperiod insensitivity (PI) that can flower in short days. PI results from mutations in the Ppd-1 gene on the A, B or D genomes, with individual mutations conferring different degrees of earliness. The basis of this is poorly understood. Using a common genetic background, the effects of A, B and D genome PI mutations on genes of the circadian clock and photoperiod pathway were studied using genome-specific expression assays. Ppd-1 PI mutations did not affect the clock or immediate clock outputs, but affected TaCO1 and TaFT1, with a reduction in TaCO1 expression as TaFT1 expression increased. Therefore, although Ppd-1 is related to PRR genes of the Arabidopsis circadian clock, Ppd-1 affects flowering by an alternative route, most likely by upregulating TaFT1 with a feedback effect that reduces TaCO1 expression. Individual genes in the circadian clock and photoperiod pathway were predominantly expressed from one genome, and there was no genome specificity in Ppd-1 action. Lines combining PI mutations on two or three genomes had enhanced earliness with higher levels, but not earlier induction, of TaFT1, showing that there is a direct quantitative relationship between Ppd-1 mutations, TaFT1 expression and flowering.
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Affiliation(s)
- Lindsay M Shaw
- Crop Genetics Department, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
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Interaction between the Late Elongated hypocotyl (LHY) and Early flowering 3 (ELF3) genes in the Arabidopsis circadian clock. Genes Genomics 2012. [DOI: 10.1007/s13258-012-0011-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Guerriero ML, Pokhilko A, Fernández AP, Halliday KJ, Millar AJ, Hillston J. Stochastic properties of the plant circadian clock. J R Soc Interface 2012; 9:744-56. [PMID: 21880617 PMCID: PMC3284129 DOI: 10.1098/rsif.2011.0378] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Accepted: 08/08/2011] [Indexed: 11/12/2022] Open
Abstract
Circadian clocks are gene regulatory networks whose role is to help the organisms to cope with variations in environmental conditions such as the day/night cycle. In this work, we explored the effects of molecular noise in single cells on the behaviour of the circadian clock in the plant model species Arabidopsis thaliana. The computational modelling language Bio-PEPA enabled us to give a stochastic interpretation of an existing deterministic model of the clock, and to easily compare the results obtained via stochastic simulation and via numerical solution of the deterministic model. First, the introduction of stochasticity in the model allowed us to estimate the unknown size of the system. Moreover, stochasticity improved the description of the available experimental data in several light conditions: noise-induced fluctuations yield a faster entrainment of the plant clock under certain photoperiods and are able to explain the experimentally observed dampening of the oscillations in plants under constant light conditions. The model predicts that the desynchronization between noisy oscillations in single cells contributes to the observed damped oscillations at the level of the cell population. Analysis of the phase, period and amplitude distributions under various light conditions demonstrated robust entrainment of the plant clock to light/dark cycles which closely matched the available experimental data.
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Affiliation(s)
- Maria Luisa Guerriero
- Centre for Systems Biology at Edinburgh, University of Edinburgh, C. H. Waddington Building, King's Buildings Campus, Mayfield Road, Edinburgh EH9 3JD, UK.
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Pokhilko A, Fernández AP, Edwards KD, Southern MM, Halliday KJ, Millar AJ. The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops. Mol Syst Biol 2012; 8:574. [PMID: 22395476 PMCID: PMC3321525 DOI: 10.1038/msb.2012.6] [Citation(s) in RCA: 280] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Accepted: 02/13/2012] [Indexed: 12/17/2022] Open
Abstract
Circadian clocks synchronise biological processes with the day/night cycle, using molecular mechanisms that include interlocked, transcriptional feedback loops. Recent experiments identified the evening complex (EC) as a repressor that can be essential for gene expression rhythms in plants. Integrating the EC components in this role significantly alters our mechanistic, mathematical model of the clock gene circuit. Negative autoregulation of the EC genes constitutes the clock's evening loop, replacing the hypothetical component Y. The EC explains our earlier conjecture that the morning gene Pseudo-Response Regulator 9 was repressed by an evening gene, previously identified with Timing Of CAB Expression1 (TOC1). Our computational analysis suggests that TOC1 is a repressor of the morning genes Late Elongated Hypocotyl and Circadian Clock Associated1 rather than an activator as first conceived. This removes the necessity for the unknown component X (or TOC1mod) from previous clock models. As well as matching timeseries and phase-response data, the model provides a new conceptual framework for the plant clock that includes a three-component repressilator circuit in its complex structure.
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50
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James AB, Syed NH, Bordage S, Marshall J, Nimmo GA, Jenkins GI, Herzyk P, Brown JW, Nimmo HG. Alternative splicing mediates responses of the Arabidopsis circadian clock to temperature changes. THE PLANT CELL 2012; 24:961-81. [PMID: 22408072 PMCID: PMC3336117 DOI: 10.1105/tpc.111.093948] [Citation(s) in RCA: 159] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 01/25/2012] [Accepted: 02/17/2012] [Indexed: 05/18/2023]
Abstract
Alternative splicing plays crucial roles by influencing the diversity of the transcriptome and proteome and regulating protein structure/function and gene expression. It is widespread in plants, and alteration of the levels of splicing factors leads to a wide variety of growth and developmental phenotypes. The circadian clock is a complex piece of cellular machinery that can regulate physiology and behavior to anticipate predictable environmental changes on a revolving planet. We have performed a system-wide analysis of alternative splicing in clock components in Arabidopsis thaliana plants acclimated to different steady state temperatures or undergoing temperature transitions. This revealed extensive alternative splicing in clock genes and dynamic changes in alternatively spliced transcripts. Several of these changes, notably those affecting the circadian clock genes late elongated hypocotyl (LHY) and pseudo response regulator7, are temperature-dependent and contribute markedly to functionally important changes in clock gene expression in temperature transitions by producing nonfunctional transcripts and/or inducing nonsense-mediated decay. Temperature effects on alternative splicing contribute to a decline in LHY transcript abundance on cooling, but LHY promoter strength is not affected. We propose that temperature-associated alternative splicing is an additional mechanism involved in the operation and regulation of the plant circadian clock.
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Affiliation(s)
- Allan B. James
- Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland
| | - Naeem Hasan Syed
- Division of Plant Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland
| | - Simon Bordage
- Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland
| | - Jacqueline Marshall
- Division of Plant Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland
| | - Gillian A. Nimmo
- Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland
| | - Gareth I. Jenkins
- Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland
| | - Pawel Herzyk
- Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland
| | - John W.S. Brown
- Division of Plant Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland
| | - Hugh G. Nimmo
- Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland
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