1
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Hu ZH, Zhang N, Qin ZY, Li JW, Tao JP, Yang N, Chen Y, Kong JY, Luo W, Chen X, Li XH, Xiong AS, Zhuang J. Circadian rhythm response and its effect on photosynthetic characteristics of the Lhcb family genes in tea plant. BMC PLANT BIOLOGY 2024; 24:333. [PMID: 38664694 PMCID: PMC11044350 DOI: 10.1186/s12870-024-04958-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 03/28/2024] [Indexed: 04/29/2024]
Abstract
BACKGROUND The circadian clock, also known as the circadian rhythm, is responsible for predicting daily and seasonal changes in the environment, and adjusting various physiological and developmental processes to the appropriate times during plant growth and development. The circadian clock controls the expression of the Lhcb gene, which encodes the chlorophyll a/b binding protein. However, the roles of the Lhcb gene in tea plant remain unclear. RESULTS In this study, a total of 16 CsLhcb genes were identified based on the tea plant genome, which were distributed on 8 chromosomes of the tea plant. The promoter regions of CsLhcb genes have a variety of cis-acting elements including hormonal, abiotic stress responses and light response elements. The CsLhcb family genes are involved in the light response process in tea plant. The photosynthetic parameter of tea leaves showed rhythmic changes during the two photoperiod periods (48 h). Stomata are basically open during the day and closed at night. Real-time quantitative PCR results showed that most of the CsLhcb family genes were highly expressed during the day, but were less expressed at night. CONCLUSIONS Results indicated that CsLhcb genes were involved in the circadian clock process of tea plant, it also provided potential references for further understanding of the function of CsLhcb gene family in tea plant.
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Affiliation(s)
- Zhi-Hang Hu
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Nan Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
| | - Zhi-Yuan Qin
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jing-Wen Li
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jian-Ping Tao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
| | - Ni Yang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yi Chen
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jie-Yu Kong
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wei Luo
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xuan Chen
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xing-Hui Li
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ai-Sheng Xiong
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China.
| | - Jing Zhuang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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2
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Dwivedi SL, Quiroz LF, Spillane C, Wu R, Mattoo AK, Ortiz R. Unlocking allelic variation in circadian clock genes to develop environmentally robust and productive crops. PLANTA 2024; 259:72. [PMID: 38386103 PMCID: PMC10884192 DOI: 10.1007/s00425-023-04324-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/24/2023] [Indexed: 02/23/2024]
Abstract
MAIN CONCLUSION Molecular mechanisms of biological rhythms provide opportunities to harness functional allelic diversity in core (and trait- or stress-responsive) oscillator networks to develop more climate-resilient and productive germplasm. The circadian clock senses light and temperature in day-night cycles to drive biological rhythms. The clock integrates endogenous signals and exogenous stimuli to coordinate diverse physiological processes. Advances in high-throughput non-invasive assays, use of forward- and inverse-genetic approaches, and powerful algorithms are allowing quantitation of variation and detection of genes associated with circadian dynamics. Circadian rhythms and phytohormone pathways in response to endogenous and exogenous cues have been well documented the model plant Arabidopsis. Novel allelic variation associated with circadian rhythms facilitates adaptation and range expansion, and may provide additional opportunity to tailor climate-resilient crops. The circadian phase and period can determine adaptation to environments, while the robustness in the circadian amplitude can enhance resilience to environmental changes. Circadian rhythms in plants are tightly controlled by multiple and interlocked transcriptional-translational feedback loops involving morning (CCA1, LHY), mid-day (PRR9, PRR7, PRR5), and evening (TOC1, ELF3, ELF4, LUX) genes that maintain the plant circadian clock ticking. Significant progress has been made to unravel the functions of circadian rhythms and clock genes that regulate traits, via interaction with phytohormones and trait-responsive genes, in diverse crops. Altered circadian rhythms and clock genes may contribute to hybrid vigor as shown in Arabidopsis, maize, and rice. Modifying circadian rhythms via transgenesis or genome-editing may provide additional opportunities to develop crops with better buffering capacity to environmental stresses. Models that involve clock gene‒phytohormone‒trait interactions can provide novel insights to orchestrate circadian rhythms and modulate clock genes to facilitate breeding of all season crops.
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Affiliation(s)
| | - Luis Felipe Quiroz
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, Galway, H91 REW4, Ireland
| | - Charles Spillane
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, Galway, H91 REW4, Ireland.
| | - Rongling Wu
- Beijing Yanqi Lake Institute of Mathematical Sciences and Applications, Beijing, 101408, China
| | - Autar K Mattoo
- USDA-ARS, Sustainable Agricultural Systems Laboratory, Beltsville, MD, 20705-2350, USA
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Sundsvagen, 10, Box 190, SE 23422, Lomma, Sweden.
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3
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Rajput R, Naik J, Stracke R, Pandey A. Interplay between R2R3 MYB-type activators and repressors regulates proanthocyanidin biosynthesis in banana (Musa acuminata). THE NEW PHYTOLOGIST 2022; 236:1108-1127. [PMID: 35842782 DOI: 10.1111/nph.18382] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
Proanthocyanidins are oligomeric flavonoids that promote plant disease resistance and benefit human health. Banana is one of the world's most extensively farmed crops and its fruit pulp contain proanthocyanidins. However, the transcriptional regulatory network that fine tunes proanthocyanidin biosynthesis in banana remains poorly understood. We characterised two proanthocyanidin-specific R2R3 MYB activators (MaMYBPA1-MaMYBPA2) and four repressors (MaMYBPR1-MaMYBPR4) to elucidate the mechanisms underlying the transcriptional regulation of proanthocyanidin biosynthesis in banana. Heterologous expression of MaMYBPA1 and MaMYBPA2 partially complemented the Arabidopsis thaliana proanthocyanidin-deficient transparent testa2 mutant. MaMYBPA1 and MaMYBPA2 interacted physically with MaMYCs to transactivate anthocyanin synthase, leucoanthocyanidin reductase, and anthocyanidin reductase genes in vitro and form functional MYB-bHLH-WD Repeat (MBW) complexes with MaTTG1 to transactivate these promoters in vivo. Overexpression of MaMYBPAs alone or with MaMYC in banana fruits induced proanthocyanidin accumulation and transcription of proanthocyanidin biosynthesis-related genes. MaMYBPR repressors are also shown to interact with MaMYCs forming repressing MBW complexes, and diminished proanthocyanidin accumulation. Interestingly overexpression of MaMYBPA induces the expression of MaMYBPR, indicating an agile regulation of proanthocyanidin biosynthesis through the formation of competitive MBW complexes. Our results reveal regulatory modules of R2R3 MYB- that fine tune proanthocyanidin biosynthesis and offer possible targets for genetic manipulation for nutritional improvement of banana.
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Affiliation(s)
- Ruchika Rajput
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Jogindra Naik
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Ralf Stracke
- Chair of Genetics and Genomics of Plants, Bielefeld University, 33615, Bielefeld, Germany
| | - Ashutosh Pandey
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
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4
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Yeh CW, Zhong HQ, Ho YF, Tian ZH, Yeh KW. The diurnal emission of floral scent in Oncidium hybrid orchid is controlled by CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) through the direct regulation on terpene synthase. BMC PLANT BIOLOGY 2022; 22:472. [PMID: 36195835 PMCID: PMC9531428 DOI: 10.1186/s12870-022-03850-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 09/16/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND To adapt the periodic fluctuation of environmental factors, plants are subtle to monitor the natural variation for the growth and development. The daily activities and physiological functions in coordination with the natural variation are regulated by circadian clock genes. The circadian emission of floral scents is one of the rhythmic physiological activities controlled by circadian clock genes. Here, we study the molecular mechanism of circadian emission pattern of ocimene and linalool compounds in Oncidium Sharry Baby (Onc. SB) orchid. RESULTS GC-Mass analysis revealed that Onc. SB periodically emitted ocimene and linalool during 6 to 14 o'clock daily. Terpene synthase, one of the key gene in the terpenoid biosynthetic pathway is expressed in coordination with scent emission. The promoter structure of terpene synthase revealed a circadian binding sequence (CBS), 5'-AGATTTTT-3' for CIRCADIAN CLOCK ASSOCIATED1 (CCA1) transcription factor. EMSA data confirms the binding affinity of CCA1. Transactivation assay further verified that TPS expression is regulated by CCA1. It suggests that the emission of floral scents is controlled by CCA1. CONCLUSIONS The work validates that the mechanism of circadian emission of floral scents in Onc. Sharry Baby is controlled by the oscillator gene, CCA1(CIRCADIAN CLOCK ASSOCIATED 1) under light condition. CCA1 transcription factor up-regulates terpene synthase (TPS) by binding on CBS motif, 5'-AGATTTTT-3' of promoter region to affect the circadian emission of floral scents in Onc. SB.
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Affiliation(s)
- Chao-Wei Yeh
- Institute of Plant Biology, College of Life Science, National Taiwan University, No 1, Sect. 4, Roosevelt Road, 106, Taipei, Taiwan
| | - Hui-Qin Zhong
- Fujian Engineering Research Center for Characteristic Floriculture, Crop Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian Province, China
| | - Yung-Feng Ho
- Institute of Plant Biology, College of Life Science, National Taiwan University, No 1, Sect. 4, Roosevelt Road, 106, Taipei, Taiwan
| | - Zhi-Hong Tian
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland, College of Life Science, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Kai-Wun Yeh
- Institute of Plant Biology, College of Life Science, National Taiwan University, No 1, Sect. 4, Roosevelt Road, 106, Taipei, Taiwan.
- Center for Weather Climate and Disaster Research, National Taiwan University, Taipei, 106, Taiwan.
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5
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Rajput R, Tyagi S, Naik J, Pucker B, Stracke R, Pandey A. The R2R3-MYB gene family in Cicer arietinum: genome-wide identification and expression analysis leads to functional characterization of proanthocyanidin biosynthesis regulators in the seed coat. PLANTA 2022; 256:67. [PMID: 36038740 DOI: 10.1007/s00425-022-03979-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
We identified 119 typical CaMYB encoding genes and reveal the major components of the proanthocyanidin regulatory network. CaPARs emerged as promising targets for genetic engineering toward improved agronomic traits in C. arietinum. Chickpea (Cicer arietinum) is among the eight oldest crops and has two main types, i.e., desi and kabuli, whose most obvious difference is the color of their seeds. We show that this color difference is due to differences in proanthocyanidin content of seed coats. Using a targeted approach, we performed in silico analysis, metabolite profiling, molecular, genetic, and biochemical studies to decipher the transcriptional regulatory network involved in proanthocyanidin biosynthesis in the seed coat of C. arietinum. Based on the annotated C. arietinum reference genome sequence, we identified 119 typical CaMYB encoding genes, grouped in 32 distinct clades. Two CaR2R3-MYB transcription factors, named CaPAR1 and CaPAR2, clustering with known proanthocyanidin regulators (PARs) were identified and further analyzed. The expression of CaPAR genes correlated well with the expression of the key structural proanthocyanidin biosynthesis genes CaANR and CaLAR and with proanthocyanidin levels. Protein-protein interaction studies suggest the in vivo interaction of CaPAR1 and CaPAR2 with the bHLH-type transcription factor CaTT8. Co-transfection analyses using Arabidopsis thaliana protoplasts showed that the CaPAR proteins form a MBW complex with CaTT8 and CaTTG1, able to activate the promoters of CaANR and CaLAR in planta. Finally, transgenic expression of CaPARs in the proanthocyanidin-deficient A. thaliana mutant tt2-1 leads to complementation of the transparent testa phenotype. Taken together, our results reveal main components of the proanthocyanidin regulatory network in C. arietinum and suggest that CaPARs are relevant targets of genetic engineering toward improved agronomic traits.
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Affiliation(s)
- Ruchika Rajput
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Shivi Tyagi
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Jogindra Naik
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Boas Pucker
- Chair of Genetics and Genomics of Plants, Bielefeld University, 33615, Bielefeld, Germany
- Institute of Plant Biology and Braunschweig Integrated Centre of Systems Biology (BRICS), TU Brunswick, Brunswick, Germany
| | - Ralf Stracke
- Chair of Genetics and Genomics of Plants, Bielefeld University, 33615, Bielefeld, Germany
| | - Ashutosh Pandey
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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6
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Lee SJ, Kang K, Lim JH, Paek NC. Natural alleles of CIRCADIAN CLOCK ASSOCIATED1 contribute to rice cultivation by fine-tuning flowering time. PLANT PHYSIOLOGY 2022; 190:640-656. [PMID: 35723564 PMCID: PMC9434239 DOI: 10.1093/plphys/kiac296] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 05/26/2022] [Indexed: 05/11/2023]
Abstract
The timing of flowering is a crucial factor for successful grain production at a wide range of latitudes. Domestication of rice (Oryza sativa) included selection for natural alleles of flowering-time genes that allow rice plants to adapt to broad geographic areas. Here, we describe the role of natural alleles of CIRCADIAN CLOCK ASSOCIATED1 (OsCCA1) in cultivated rice based on analysis of single-nucleotide polymorphisms deposited in the International Rice Genebank Collection Information System database. Rice varieties harboring japonica-type OsCCA1 alleles (OsCCA1a haplotype) flowered earlier than those harboring indica-type OsCCA1 alleles (OsCCA1d haplotype). In the japonica cultivar "Dongjin", a T-DNA insertion in OsCCA1a resulted in late flowering under long-day and short-day conditions, indicating that OsCCA1 is a floral inducer. Reverse transcription quantitative PCR analysis showed that the loss of OsCCA1a function induces the expression of the floral repressors PSEUDO-RESPONSE REGULATOR 37 (OsPRR37) and Days to Heading 8 (DTH8), followed by repression of the Early heading date 1 (Ehd1)-Heading date 3a (Hd3a)-RICE FLOWERING LOCUS T 1 (RFT1) pathway. Binding affinity assays indicated that OsCCA1 binds to the promoter regions of OsPRR37 and DTH8. Naturally occurring OsCCA1 alleles are evolutionarily conserved in cultivated rice (O. sativa). Oryza rufipogon-I (Or-I) and Or-III type accessions, representing the ancestors of O. sativa indica and japonica, harbored indica- and japonica-type OsCCA1 alleles, respectively. Taken together, our results demonstrate that OsCCA1 is a likely domestication locus that has contributed to the geographic adaptation and expansion of cultivated rice.
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Affiliation(s)
| | | | - Jung-Hyun Lim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea
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7
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Tobin E. Adventures in Life and Science, from Light to Rhythms. ANNUAL REVIEW OF PLANT BIOLOGY 2022; 73:1-16. [PMID: 35130444 DOI: 10.1146/annurev-arplant-090921-091346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The author describes her life's pathway from her beginnings at a time when women were not well represented in the sciences. Her grandparents were immigrants to the United States. Although her parents were not able to go to college because of the Great Depression, they supported her education and other adventures. In addition to her interest in science, she describes her interest and involvement in politics. Her education at Oberlin, Stanford, and Harvard prepared her for her independent career at the University of California, Los Angeles, where she was an affirmative action appointment. Her research initially centered on the plant photoreceptor phytochrome, but later in her career she investigated circadian rhythms in plants, discovering and characterizing one of the members of the central oscillator.
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Affiliation(s)
- Elaine Tobin
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, USA;
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8
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Basu R, Dutta S, Pal A, Sengupta M, Chattopadhyay S. Calmodulin7: recent insights into emerging roles in plant development and stress. PLANT MOLECULAR BIOLOGY 2021; 107:1-20. [PMID: 34398355 DOI: 10.1007/s11103-021-01177-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 07/27/2021] [Indexed: 05/25/2023]
Abstract
Analyses of the function of Arabidopsis Calmodulin7 (CAM7) in concert with multiple regulatory proteins involved in various signal transduction processes. Calmodulin (CaM) plays various regulatory roles in multiple signaling pathways in eukaryotes. Arabidopsis CALMODULIN 7 (CAM7) is a unique member of the CAM family that works as a transcription factor in light signaling pathways. CAM7 works in concert with CONSTITUTIVE PHOTOMORPHOGENIC 1 and ELONGATED HYPOCOTYL 5, and plays an important role in seedling development. Further, it is involved in the regulation of the activity of various Ca2+-gated channels such as cyclic nucleotide gated channel 6 (CNGC6), CNGC14 and auto-inhibited Ca2+ ATPase 8. Recent studies further indicate that CAM7 is also an integral part of multiple signaling pathways including hormone, immunity and stress. Here, we review the recent advances in understanding the multifaceted role of CAM7. We highlight the open-ended questions, and also discuss the diverse aspects of CAM7 characterization that need to be addressed for comprehensive understanding of its cellular functions.
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Affiliation(s)
- Riya Basu
- Department of Biotechnology, National Institute of Technology, Mahatma Gandhi Avenue, Durgapur, West Bengal, 713209, India
| | - Siddhartha Dutta
- Department of Biotechnology, National Institute of Technology, Mahatma Gandhi Avenue, Durgapur, West Bengal, 713209, India
- Department of Biotechnology, University of Engineering and Management, University Area, Plot, Street Number 03, Action Area III, B/5, Newtown, Kolkata, West Bengal, 700156, India
| | - Abhideep Pal
- Department of Biotechnology, National Institute of Technology, Mahatma Gandhi Avenue, Durgapur, West Bengal, 713209, India
| | - Mandar Sengupta
- Department of Biotechnology, National Institute of Technology, Mahatma Gandhi Avenue, Durgapur, West Bengal, 713209, India
| | - Sudip Chattopadhyay
- Department of Biotechnology, National Institute of Technology, Mahatma Gandhi Avenue, Durgapur, West Bengal, 713209, India.
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9
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Fitzpatrick TB, Noordally Z. Of clocks and coenzymes in plants: intimately connected cycles guiding central metabolism? THE NEW PHYTOLOGIST 2021; 230:416-432. [PMID: 33264424 DOI: 10.1111/nph.17127] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 11/03/2020] [Indexed: 06/12/2023]
Abstract
Plant fitness is a measure of the capacity of a plant to survive and reproduce in its particular environment. It is inherently dependent on plant health. Molecular timekeepers like the circadian clock enhance fitness due to their ability to coordinate biochemical and physiological processes with the environment on a daily basis. Central metabolism underlies these events and it is well established that diel metabolite adjustments are intimately and reciprocally associated with the genetically encoded clock. Thus, metabolic pathway activities are time-of-day regulated. Metabolite rhythms are driven by enzymes, a major proportion of which rely on organic coenzymes to facilitate catalysis. The B vitamin complex is the key provider of coenzymes in all organisms. Emerging evidence suggests that B vitamin levels themselves undergo daily oscillations in animals but has not been studied in any depth in plants. Moreover, it is rarely considered that daily rhythmicity in coenzyme levels may dictate enzyme activity levels and therefore metabolite levels. Here we put forward the proposal that B-vitamin-derived coenzyme rhythmicity is intertwined with metabolic and clock derived rhythmicity to achieve a tripartite homeostasis integrated into plant fitness.
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Affiliation(s)
- Teresa B Fitzpatrick
- Vitamins and Environmental Stress Responses in Plants, Department of Botany and Plant Biology, University of Geneva, Geneva, 1211, Switzerland
| | - Zeenat Noordally
- Vitamins and Environmental Stress Responses in Plants, Department of Botany and Plant Biology, University of Geneva, Geneva, 1211, Switzerland
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10
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Garmash EV, Belykh ES, Velegzhaninov IO. The gene expression profiles of mitochondrial respiratory components in Arabidopsis plants with differing amounts of ALTERNATIVE OXIDASE1a under high intensity light. PLANT SIGNALING & BEHAVIOR 2021; 16:1864962. [PMID: 33369529 PMCID: PMC7889022 DOI: 10.1080/15592324.2020.1864962] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
We compared the expression of mitochondrial alternative oxidase (AOX) and other non-phosphorylating respiratory components (NPhPs) in wild type and AOX1a transgenic Arabidopsis thaliana following short-term transfer of plants to higher irradiance conditions to gain more insight into the mechanisms of AOX functioning under light. The AOX1a overexpressing line (XX-2) showed the highest amount of AOX1a transcripts and AOX1A synthesis during the entire experiment, and many NPhPs genes were down-regulated after 6-8 h under the higher light conditions. Antisense AS-12 plants displayed a compensatory effect, typically after 8 h of exposure to higher irradiance, by up-regulating their expression of the majority of genes encoding AOX and other respiratory components. In addition, AS-12 plants displayed 'overcompensation effects' prior to their transfer to high light conditions, i.e., they showed a higher expression level of certain genes. As a result, the ROS content in AS-12, as in XX-2, was consistently lower than in the wild type. All NPhPs genes share, in common with AOX1a, light- and stress-related cis-acting regulatory elements (CAREs) in their promoters. However, the expression of respiratory genes does not always depend on the level of AOX1a expression. This suggests the presence of multiple combinations of signaling pathways in gene induction. Based on our results, we outline possible directions for future research.
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Affiliation(s)
- Elena V. Garmash
- Institute of Biology, Komi Scientific Centre, Ural Branch, Russian Academy of Sciences, Syktyvkar, Russia
- CONTACT Elena V. Garmash Institute of Biology, Komi Scientific Centre, Ural Branch, Russian Academy of Sciences, Syktyvkar, Russia
| | - Elena S. Belykh
- Institute of Biology, Komi Scientific Centre, Ural Branch, Russian Academy of Sciences, Syktyvkar, Russia
| | - Ilya O. Velegzhaninov
- Institute of Biology, Komi Scientific Centre, Ural Branch, Russian Academy of Sciences, Syktyvkar, Russia
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11
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Yan J, Kim YJ, Somers DE. Post-Translational Mechanisms of Plant Circadian Regulation. Genes (Basel) 2021; 12:325. [PMID: 33668215 PMCID: PMC7995963 DOI: 10.3390/genes12030325] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/21/2021] [Accepted: 02/22/2021] [Indexed: 12/15/2022] Open
Abstract
The molecular components of the circadian system possess the interesting feature of acting together to create a self-sustaining oscillator, while at the same time acting individually, and in complexes, to confer phase-specific circadian control over a wide range of physiological and developmental outputs. This means that many circadian oscillator proteins are simultaneously also part of the circadian output pathway. Most studies have focused on transcriptional control of circadian rhythms, but work in plants and metazoans has shown the importance of post-transcriptional and post-translational processes within the circadian system. Here we highlight recent work describing post-translational mechanisms that impact both the function of the oscillator and the clock-controlled outputs.
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Affiliation(s)
| | | | - David E. Somers
- Department of Molecular Genetics, The Ohio State University; Columbus, OH 43210, USA; (J.Y.); (Y.J.K.)
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12
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Peng Z, Liu G, Huang K. Cold Adaptation Mechanisms of a Snow Alga Chlamydomonas nivalis During Temperature Fluctuations. Front Microbiol 2021; 11:611080. [PMID: 33584575 PMCID: PMC7874021 DOI: 10.3389/fmicb.2020.611080] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/10/2020] [Indexed: 11/13/2022] Open
Abstract
Cold environments, such as glaciers and alpine regions, constitute unique habitats for organisms living on Earth. In these harsh ecosystems, snow algae survive, florish, and even become primary producers for microbial communities. How the snow algae maintain physiological activity during violent ambient temperature changes remains unsolved. To explore the cold adaptation mechanisms of the unicellular snow alga Chlamydomonas nivalis, we compared its physiological responses to a model organism from the same genus, Chlamydomonas reinhardtii. When both cell types were exposed to a shift from 22°C to 4°C, C. nivalis exhibited an apparent advantage in cold tolerance over C. reinhardtii, as C. nivalis had both a higher growth rate and photosynthetic efficiency. To determine the cold tolerance mechanisms of C. nivalis, RNA sequencing was used to compare transcriptomes of both species after 1 h of cold treatment, mimicking temperature fluctuations in the polar region. Differential expression analysis showed that C. nivalis had fewer transcriptomic changes and was more stable during rapid temperature decrease relative to C. reinhardtii, especially for the expression of photosynthesis related genes. Additionally, we found that transcription in C. nivalis was precisely regulated by the cold response network, consisting of at least 12 transcription factors and 3 RNA-binding proteins. Moreover, genes participating in nitrogen metabolism, the pentose phosphate pathway, and polysaccharide biosynthesis were upregulated, indicating that increasing resource assimilation and remodeling of metabolisms were critical for cold adaptation in C. nivalis. Furthermore, we identified horizontally transferred genes differentially expressed in C. nivalis, which are critical for cold adaptation in other psychrophiles. Our results reveal that C. nivalis adapts rapid temperature decrease by efficiently regulating transcription of specific genes to optimize resource assimilation and metabolic pathways, providing critical insights into how snow algae survive and propagate in cold environments.
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Affiliation(s)
- Zhao Peng
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Gai Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Kaiyao Huang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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13
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Ahmadizadeh M, Chen JT, Hasanzadeh S, Ahmar S, Heidari P. Insights into the genes involved in the ethylene biosynthesis pathway in Arabidopsis thaliana and Oryza sativa. J Genet Eng Biotechnol 2020; 18:62. [PMID: 33074438 PMCID: PMC7572930 DOI: 10.1186/s43141-020-00083-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 10/02/2020] [Indexed: 12/12/2022]
Abstract
Background Ethylene is a gaseous plant hormone that acts as a requisite role in many aspects of the plant life cycle, and it is also a regulator of plant responses to abiotic and biotic stresses. In this study, we attempt to provide comprehensive information through analyses of existing data using bioinformatics tools to compare the identified ethylene biosynthesis genes between Arabidopsis (as dicotyledonous) and rice (as monocotyledonous). Results The results exposed that the Arabidopsis proteins of the ethylene biosynthesis pathway had more potential glycosylation sites than rice, and 1-aminocyclopropane-1-carboxylate oxidase proteins were less phosphorylated than 1-aminocyclopropane-1-carboxylate synthase and S-adenosylmethionine proteins. According to the gene expression patterns, S-adenosylmethionine genes were more involved in the rice-ripening stage while in Arabidopsis, ACS2, and 1-aminocyclopropane-1-carboxylate oxidase genes were contributed to seed maturity. Furthermore, the result of miRNA targeting the transcript sequences showed that ath-miR843 and osa-miR1858 play a key role to regulate the post-transcription modification of S-adenosylmethionine genes in Arabidopsis and rice, respectively. The discovered cis- motifs in the promoter site of all the ethylene biosynthesis genes of A. thaliana genes were engaged to light-induced response in the cotyledon and root genes, sulfur-responsive element, dehydration, cell cycle phase-independent activation, and salicylic acid. The ACS4 protein prediction demonstrated strong protein-protein interaction in Arabidopsis, as well as, SAM2, Os04T0578000, Os01T0192900, and Os03T0727600 predicted strong protein-protein interactions in rice. Conclusion In the current study, the complex between miRNAs with transcript sequences of ethylene biosynthesis genes in A. thaliana and O. sativa were identified, which could be helpful to understand the gene expression regulation after the transcription process. The binding sites of common transcription factors such as MYB, WRKY, and ABRE that control target genes in abiotic and biotic stresses were generally distributed in promoter sites of ethylene biosynthesis genes of A. thaliana. This was the first time to wide explore the ethylene biosynthesis pathway using bioinformatics tools that markedly showed the capability of the in silico study to integrate existing data and knowledge and furnish novel insights into the understanding of underlying ethylene biosynthesis pathway genes that will be helpful for more dissection.
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Affiliation(s)
| | - Jen-Tsung Chen
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung, 811, Taiwan
| | - Soosan Hasanzadeh
- Department of Horticultural Sciences, Faculty of Agriculture, Shahrood University of Technology, Shahrood, Iran
| | - Sunny Ahmar
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Parviz Heidari
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahrood University of Technology, Shahrood, Iran.
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14
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Lai X, Bendix C, Yan L, Zhang Y, Schnable JC, Harmon FG. Interspecific analysis of diurnal gene regulation in panicoid grasses identifies known and novel regulatory motifs. BMC Genomics 2020; 21:428. [PMID: 32586356 PMCID: PMC7315539 DOI: 10.1186/s12864-020-06824-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/12/2020] [Indexed: 11/17/2022] Open
Abstract
Background The circadian clock drives endogenous 24-h rhythms that allow organisms to adapt and prepare for predictable and repeated changes in their environment throughout the day-night (diurnal) cycle. Many components of the circadian clock in Arabidopsis thaliana have been functionally characterized, but comparatively little is known about circadian clocks in grass species including major crops like maize and sorghum. Results Comparative research based on protein homology and diurnal gene expression patterns suggests the function of some predicted clock components in grasses is conserved with their Arabidopsis counterparts, while others have diverged in function. Our analysis of diurnal gene expression in three panicoid grasses sorghum, maize, and foxtail millet revealed conserved and divergent evolution of expression for core circadian clock genes and for the overall transcriptome. We find that several classes of core circadian clock genes in these grasses differ in copy number compared to Arabidopsis, but mostly exhibit conservation of both protein sequence and diurnal expression pattern with the notable exception of maize paralogous genes. We predict conserved cis-regulatory motifs shared between maize, sorghum, and foxtail millet through identification of diurnal co-expression clusters for a subset of 27,196 orthologous syntenic genes. In this analysis, a Cochran–Mantel–Haenszel based method to control for background variation identified significant enrichment for both expected and novel 6–8 nucleotide motifs in the promoter regions of genes with shared diurnal regulation predicted to function in common physiological activities. Conclusions This study illustrates the divergence and conservation of circadian clocks and diurnal regulatory networks across syntenic orthologous genes in panacoid grass species. Further, conserved local regulatory sequences contribute to the architecture of these diurnal regulatory networks that produce conserved patterns of diurnal gene expression.
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Affiliation(s)
- Xianjun Lai
- Center for Plant Science Innovation & Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, 68588, USA.,College of Agricultural Sciences, Xichang University, Liangshan, Xichang, 615000, China
| | - Claire Bendix
- Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA.,Plant Gene Expression Center, USDA-ARS, Albany, CA, 94710, USA
| | - Lang Yan
- Center for Plant Science Innovation & Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, 68588, USA.,College of Agricultural Sciences, Xichang University, Liangshan, Xichang, 615000, China
| | - Yang Zhang
- Center for Plant Science Innovation & Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, 68588, USA
| | - James C Schnable
- Center for Plant Science Innovation & Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, 68588, USA.
| | - Frank G Harmon
- Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA. .,Plant Gene Expression Center, USDA-ARS, Albany, CA, 94710, USA.
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15
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Lagercrantz U, Billhardt A, Rousku SN, Ljung K, Eklund DM. Nyctinastic thallus movement in the liverwort Marchantia polymorpha is regulated by a circadian clock. Sci Rep 2020; 10:8658. [PMID: 32457350 PMCID: PMC7251115 DOI: 10.1038/s41598-020-65372-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 04/29/2020] [Indexed: 11/24/2022] Open
Abstract
The circadian clock coordinates an organism's growth, development and physiology with environmental factors. One illuminating example is the rhythmic growth of hypocotyls and cotyledons in Arabidopsis thaliana. Such daily oscillations in leaf position are often referred to as sleep movements or nyctinasty. Here, we report that plantlets of the liverwort Marchantia polymorpha show analogous rhythmic movements of thallus lobes, and that the circadian clock controls this rhythm, with auxin a likely output pathway affecting these movements. The mechanisms of this circadian clock are partly conserved as compared to angiosperms, with homologs to the core clock genes PRR, RVE and TOC1 forming a core transcriptional feedback loop also in M. polymorpha.
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Affiliation(s)
- Ulf Lagercrantz
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
- The Linnean Centre for Plant Biology in Uppsala, Uppsala, Sweden
| | - Anja Billhardt
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
- The Linnean Centre for Plant Biology in Uppsala, Uppsala, Sweden
| | - Sabine N Rousku
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
- The Linnean Centre for Plant Biology in Uppsala, Uppsala, Sweden
| | - Karin Ljung
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | - D Magnus Eklund
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden.
- The Linnean Centre for Plant Biology in Uppsala, Uppsala, Sweden.
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16
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Liu Y, Ma M, Li G, Yuan L, Xie Y, Wei H, Ma X, Li Q, Devlin PF, Xu X, Wang H. Transcription Factors FHY3 and FAR1 Regulate Light-Induced CIRCADIAN CLOCK ASSOCIATED1 Gene Expression in Arabidopsis. THE PLANT CELL 2020; 32:1464-1478. [PMID: 32152179 PMCID: PMC7203938 DOI: 10.1105/tpc.19.00981] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/27/2020] [Accepted: 03/08/2020] [Indexed: 05/22/2023]
Abstract
The circadian clock provides a time-keeping mechanism that synchronizes various biological activities with the surrounding environment. Arabidopsis (Arabidopsis thaliana) CIRCADIAN CLOCK ASSOCIATED1 (CCA1), encoding a MYB-related transcription factor, is a key component of the core oscillator of the circadian clock, with peak expression in the morning. The molecular mechanisms regulating the light induction and rhythmic expression of CCA1 remain elusive. In this study, we show that two phytochrome signaling proteins, FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and its paralog FAR-RED IMPAIRED RESPONSE1 (FAR1), are essential for the light-induced expression of CCA1 FHY3 and FAR1 directly bind to the CCA1 promoter and activate its expression, whereas PHYTOCHROME INTERACTING FACTOR5 (PIF5) directly binds to its promoter and represses its expression. Furthermore, PIF5 and TIMING OF CAB EXPRESSION1 physically interact with FHY3 and FAR1 to repress their transcriptional activation activity on CCA1 expression. These findings demonstrate that the photosensory-signaling pathway integrates with circadian oscillators to orchestrate clock gene expression. This mechanism might form the molecular basis of the regulation of the clock system by light in response to daily changes in the light environment, thus increasing plant fitness.
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Affiliation(s)
- Yang Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Mengdi Ma
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Gang Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Li Yuan
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Yurong Xie
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hongbin Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
| | - Xiaojing Ma
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Quanquan Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Paul F Devlin
- School of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, United Kingdom
| | - Xiaodong Xu
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Haiyang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou 510642, China
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17
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Hara T, Shima T, Nagai H, Ohsawa R. Genetic analysis of photoperiod sensitivity associated with difference in ecotype in common buckwheat. BREEDING SCIENCE 2020; 70:101-111. [PMID: 32351309 PMCID: PMC7180152 DOI: 10.1270/jsbbs.19118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 01/16/2020] [Indexed: 06/10/2023]
Abstract
Ecotype breeding is a key technology in common buckwheat (Fagopyrum esculentum Moench) for the breeding of highly adaptive cultivars and their introduction to other cultivation areas. However, the details of the relationship between photoperiod sensitivity and ecotype remain unclear. Here, we evaluated photoperiod sensitivity in 15 landraces from different parts of Japan, and analyzed quantitative trait loci (QTLs) for photoperiod sensitivity using two F2 segregating populations derived from the crosses between self-compatible lines ('Kyukei SC2' or 'Buckwheat Norin PL1', early days-to-flowering) and allogamous plants (intermediate or late days-to-flowering). We clarified that (1) photoperiod sensitivity and differences in ecotype are closely related; (2) photoperiod sensitivity is controlled by several QTLs common among population of different ecotypes; and (3) orthologues of GIGANTEA and EARLY FLOWERING 3 will be useful markers in future detailed elucidation of the photoperiod sensitivity mechanism in common buckwheat. This study provides the basis for genomics-assisted breeding for local adaptation and ecotype breeding in common buckwheat.
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Affiliation(s)
- Takashi Hara
- National Agriculture and Food Research Organization, Hokkaido Agricultural Research Center, Division of Field Crop Research and Development, Shinsei, Memuro, Kasai, Hokkaido 082-0081, Japan
| | - Taeko Shima
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Hiroya Nagai
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Ryo Ohsawa
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
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18
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REVEILLE Transcription Factors Contribute to the Nighttime Accumulation of Anthocyanins in 'Red Zaosu' ( Pyrus bretschneideri Rehd.) Pear Fruit Skin. Int J Mol Sci 2020; 21:ijms21051634. [PMID: 32120999 PMCID: PMC7084243 DOI: 10.3390/ijms21051634] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 02/14/2020] [Accepted: 02/24/2020] [Indexed: 11/17/2022] Open
Abstract
Anthocyanin biosynthesis exhibits a rhythmic oscillation pattern in some plants. To investigate the correlation between the oscillatory regulatory network and anthocyanin biosynthesis in pear, the anthocyanin accumulation and the expression patterns of anthocyanin late biosynthetic genes (ALBGs) were investigated in fruit skin of ‘Red Zaosu’ (Pyrus bretschneideri Rehd.). The anthocyanin accumulated mainly during the night over three continuous days in the fruit skin, and the ALBGs’ expression patterns in ‘Red Zaosu’ fruit skin were oscillatory. However, the expression levels of typical anthocyanin-related transcription factors did not follow this pattern. Here, we found that the expression patterns of four PbREVEILLEs (PbRVEs), members of a class of atypical anthocyanin-regulated MYBs, were consistent with those of ALBGs in ‘Red Zaosu’ fruit skin over three continuous days. Additionally, transient expression assays indicated that the four PbRVEs promoted anthocyanin biosynthesis by regulating the expression of the anthocyanin biosynthetic genes encoding dihydroflavonol-4-reductase (DFR) and anthocyanidin synthase (ANS) in red pear fruit skin, which was verified using a dual-luciferase reporter assay. Moreover, a yeast one-hybrid assay indicated that PbRVE1a, 1b and 7 directly bound to PbDFR and PbANS promoters. Thus, PbRVEs promote anthocyanin accumulation at night by up-regulating the expression levels of PbDFR and PbANS in ‘Red Zaosu’ fruit skin.
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19
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Panahi B, Farhadian M, Hejazi MA. Systems biology approach identifies functional modules and regulatory hubs related to secondary metabolites accumulation after transition from autotrophic to heterotrophic growth condition in microalgae. PLoS One 2020; 15:e0225677. [PMID: 32084664 PMCID: PMC7035001 DOI: 10.1371/journal.pone.0225677] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 01/21/2020] [Indexed: 11/22/2022] Open
Abstract
Heterotrophic growth mode is among the most promising strategies put forth to overcome the low biomass and secondary metabolites productivity challenge. To shedding light on the underlying molecular mechanisms, transcriptome meta-analysis was integrated with weighted gene co-expression network analysis (WGCNA), connectivity analysis, functional enrichment, and hubs identification. Meta-analysis and Functional enrichment analysis demonstrated that most of the biological processes are up-regulated at heterotrophic growth condition, which leads to change of genetic architectures and phenotypic outcomes. WGNCA analysis of meta-genes also resulted four significant functional modules across logarithmic (LG), transition (TR), and production peak (PR) phases. The expression pattern and connectivity characteristics of the brown module as a non-preserved module vary across LG, TR, and PR phases. Functional analysis identified Carotenoid biosynthesis, Fatty acid metabolism and Methane metabolism as enriched pathways in the non-preserved module. Our integrated approach was applied here, identified some hubs, such as a serine hydroxymethyltransferase (SHMT1), which is the best candidate for development of metabolites accumulating strains in microalgae. Current study provided a new insight into underlying metabolite accumulation mechanisms and opens new avenue for the future applied studies in the microalgae field.
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Affiliation(s)
- Bahman Panahi
- Department of Genomics, Branch for Northwest & West Region, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Tabriz, Iran
- * E-mail: ,
| | - Mohammad Farhadian
- Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Mohammad Amin Hejazi
- Department of Food Biotechnology, Branch for Northwest & West Region, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Tabriz, Iran
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20
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Peng H, Neff MM. CIRCADIAN CLOCK ASSOCIATED 1 and ATAF2 differentially suppress cytochrome P450-mediated brassinosteroid inactivation. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:970-985. [PMID: 31639820 PMCID: PMC6977193 DOI: 10.1093/jxb/erz468] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 10/15/2019] [Indexed: 05/20/2023]
Abstract
Brassinosteroids (BRs) are a group of steroid hormones regulating plant growth and development. Since BRs do not undergo transport among plant tissues, their metabolism is tightly regulated by transcription factors (TFs) and feedback loops. BAS1 (CYP734A1, formerly CYP72B1) and SOB7 (CYP72C1) are two BR-inactivating cytochrome P450s identified in Arabidopsis thaliana. We previously found that a TF ATAF2 (ANAC081) suppresses BAS1 and SOB7 expression by binding to the Evening Element (EE) and CIRCADIAN CLOCK ASSOCIATED 1 (CCA1)-binding site (CBS) on their promoters. Both the EE and CBS are known binding targets of the circadian regulatory protein CCA1. Here, we confirm that CCA1 binds the EE and CBS motifs on BAS1 and SOB7 promoters, respectively. Elevated accumulations of BAS1 and SOB7 transcripts in the CCA1 null mutant cca1-1 indicate that CCA1 is a repressor of their expression. When compared with either cca1-1 or the ATAF2 null mutant ataf2-2, the cca1-1 ataf2-2 double mutant shows higher SOB7 transcript accumulations and a stronger BR-insensitive phenotype of hypocotyl elongation in white light. CCA1 interacts with ATAF2 at both DNA-protein and protein-protein levels. ATAF2, BAS1, and SOB7 are all circadian regulated with distinct expression patterns. These results demonstrate that CCA1 and ATAF2 differentially suppress BAS1- and SOB7-mediated BR inactivation.
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Affiliation(s)
- Hao Peng
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
| | - Michael M Neff
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
- Correspondence:
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21
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Ke YT, Lin KF, Gu CH, Yeh CH. Molecular Characterization and Expression Profile of PaCOL1, a CONSTANS-like Gene in Phalaenopsis Orchid. PLANTS (BASEL, SWITZERLAND) 2020; 9:plants9010068. [PMID: 31947959 PMCID: PMC7020484 DOI: 10.3390/plants9010068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/30/2019] [Accepted: 01/02/2020] [Indexed: 06/10/2023]
Abstract
CONSTANS (CO) and CONSTANS-like (COL) genes play important roles in coalescing signals from photoperiod and temperature pathways. However, the mechanism of CO and COLs involved in regulating the developmental stage transition and photoperiod/temperature senescing remains unclear. In this study, we identified a COL ortholog gene from the Taiwan native orchid Phalaenopsis aphrodite. The Phalaenopsis aphrodite CONSTANS-like 1 (PaCOL1) belongs to the B-box protein family and functions in the nucleus and cytosol. Expression profile analysis of Phalaenopsis aphrodite revealed that PaCOL1 was significantly expressed in leaves, but its accumulation was repressed during environmental temperature shifts. We found a differential profile for PaCOL1 accumulation, with peak accumulation at late afternoon and at the middle of the night. Arabidopsis with PaCOL1 overexpression showed earlier flowering under short-day (SD) conditions (8 h/23 °C light and 16 h/23 °C dark) but similar flowering time under long-day (LD) conditions (16 h/23 °C light and 8 h/23 °C dark). Transcriptome sequencing revealed several genes upregulated in PaCOL1-overexpressing Arabidopsis plants that were previously involved in flowering regulation of the photoperiod pathway. Yeast two-hybrid (Y2H) analysis and bimolecular fluorescence complementation (BiFC) analysis revealed that PaCOL1 could interact with a crucial clock-associated regulator, AtCCA1, and a flowering repressor, AtFLC. Furthermore, expressing PaCOL1 in cca1.lhy partially reversed the mutant flowering time under photoperiod treatment, which confirms the role of PaCOL1 function in the rhythmic associated factors for modulating flowering.
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22
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Goldman JAL, Schatz MJ, Berthiaume CT, Coesel SN, Orellana MV, Armbrust EV. Fe limitation decreases transcriptional regulation over the diel cycle in the model diatom Thalassiosira pseudonana. PLoS One 2019; 14:e0222325. [PMID: 31509589 PMCID: PMC6738920 DOI: 10.1371/journal.pone.0222325] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 08/27/2019] [Indexed: 01/02/2023] Open
Abstract
Iron (Fe) is an important growth factor for diatoms and its availability is further restricted by changes in the carbonate chemistry of seawater. We investigated the physiological attributes and transcriptional profiles of the diatom Thalassiosira pseudonana grown on a day: night cycle under different CO2/pH and iron concentrations, that in combination generated available iron (Fe') concentrations of 1160, 233, 58 and 12 pM. We found the light-dark conditions to be the main driver of transcriptional patterns, followed by Fe' concentration and CO2 availability, respectively. At the highest Fe' (1160 pM), 55% of the transcribed genes were differentially expressed between day and night, whereas at the lowest Fe' (12 pM), only 28% of the transcribed genes displayed comparable patterns. While Fe limitation disrupts the diel expression patterns for genes in most central metabolism pathways, the diel expression of light- signaling molecules and glycolytic genes was relatively robust in response to reduced Fe'. Moreover, we identified a non-canonical splicing of transcripts encoding triose-phosphate isomerase, a key-enzyme of glycolysis, generating transcript isoforms that would encode proteins with and without an active site. Transcripts that encoded an active enzyme maintained a diel expression at low Fe', while transcripts that encoded the non-active enzyme lost the diel expression. This work illustrates the interplay between nutrient limitation and transcriptional regulation over the diel cycle. Considering that future ocean conditions will reduce the availability of Fe in many parts of the oceans, our work identifies some of the regulatory mechanisms that may shape future ecological communities.
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Affiliation(s)
- Johanna A. L. Goldman
- School of Oceanography, University of Washington, Seattle, Washington, United States of America
| | - Megan J. Schatz
- School of Oceanography, University of Washington, Seattle, Washington, United States of America
| | - Chris T. Berthiaume
- School of Oceanography, University of Washington, Seattle, Washington, United States of America
| | - Sacha N. Coesel
- School of Oceanography, University of Washington, Seattle, Washington, United States of America
| | - Mónica V. Orellana
- Polar Science Center, Applied Physics Laboratory, University of Washington, Seattle, Washington, United States of America
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - E. Virginia Armbrust
- School of Oceanography, University of Washington, Seattle, Washington, United States of America
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Zhou Q, Yang Y, Yang Z. Molecular dissection of cadmium-responsive transcriptome profile in a low-cadmium-accumulating cultivar of Brassica parachinensis. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 176:85-94. [PMID: 30921700 DOI: 10.1016/j.ecoenv.2019.03.077] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 03/17/2019] [Accepted: 03/18/2019] [Indexed: 06/09/2023]
Abstract
Brassica parachinensis L., a daily consumed leaf vegetable, is a high-Cd accumulator that substantially threatens human health. Screening and breeding Cd pollution-safe cultivars (Cd-PSCs) of crops is a low-cost strategy to restrict human Cd intake from contaminated soils via the food chain. However, little is known about the molecular mechanisms underlying the low-Cd-accumulating traits of B. parachinensis Cd-PSCs. In the current study, we analyzed the transcriptomes of the Cd-treated (5 μM) roots and shoots of a low-Cd-accumulating cultivar (SJ19) and a high-Cd-accumulating cultivar (CX4) of B. parachinensis to reveal the molecular mechanisms in response to Cd stress. Compared to CX4, many pathways involved in carbohydrate and amino acid metabolisms were exclusively up-regulated in SJ19 roots upon exposure to low Cd concentrations, which may produce more energy and metabolites for Cd detoxification. Antioxidant enzymes in the peroxisome were up-regulated in both SJ19 and CX4 roots in response to Cd, while glutathione biosynthesis was only activated in SJ19 roots. In SJ19 shoots, pathways of photosynthesis and cell growth were activated to mitigate Cd-induced damages. Furthermore, Cd transport genes, such as MTP1, HMA3 and CAX family genes, were highly induced by Cd stress in SJ19 roots in accordance with the high Cd concentration in roots, while genes involved in root-to-shoot Cd translocation such as FRD3 and CESA3 were suppressed, which may contribute to the low Cd concertation in edible part of SJ19. Our study provides a genetic basis for further Cd-PSCs screening and breeding.
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Affiliation(s)
- Qian Zhou
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China; Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China.
| | - Yuchen Yang
- Department of Genetics, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC, 27599, USA.
| | - Zhongyi Yang
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
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Raimundo J, Sobral R, Laranjeira S, Costa MMR. Successive Domain Rearrangements Underlie the Evolution of a Regulatory Module Controlled by a Small Interfering Peptide. Mol Biol Evol 2019; 35:2873-2885. [PMID: 30203071 PMCID: PMC6278869 DOI: 10.1093/molbev/msy178] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The establishment of new interactions between transcriptional regulators increases the regulatory diversity that drives phenotypic novelty. To understand how such interactions evolve, we have studied a regulatory module (DDR) composed by three MYB-like proteins: DIVARICATA (DIV), RADIALIS (RAD), and DIV-and-RAD-Interacting Factor (DRIF). The DIV and DRIF proteins form a transcriptional complex that is disrupted in the presence of RAD, a small interfering peptide, due to the formation of RAD–DRIF dimers. This dynamic interaction result in a molecular switch mechanism responsible for the control of distinct developmental processes in plants. Here, we have determined how the DDR regulatory module was established by analyzing the origin and evolution of the DIV, DRIF, and RAD protein families and the evolutionary history of their interactions. We show that duplications of a pre-existing MYB domain originated the DIV and DRIF protein families in the ancestral lineage of green algae, and, later, the RAD family in seed plants. Intraspecies interactions between the MYB domains of DIV and DRIF proteins are detected in green algae, whereas the earliest evidence of an interaction between DRIF and RAD proteins occurs in the gymnosperms, coincident with the establishment of the RAD family. Therefore, the DDR module evolved in a stepwise progression with the DIV–DRIF transcription complex evolving prior to the antagonistic RAD–DRIF interaction that established the molecular switch mechanism. Our results suggest that the successive rearrangement and divergence of a single protein domain can be an effective evolutionary mechanism driving new protein interactions and the establishment of novel regulatory modules.
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Affiliation(s)
- João Raimundo
- Biosystems and Integrative Sciences Institute (BioISI), Plant Functional Biology Center, University of Minho, Braga, Portugal.,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ
| | - Rómulo Sobral
- Biosystems and Integrative Sciences Institute (BioISI), Plant Functional Biology Center, University of Minho, Braga, Portugal
| | - Sara Laranjeira
- Biosystems and Integrative Sciences Institute (BioISI), Plant Functional Biology Center, University of Minho, Braga, Portugal
| | - Maria Manuela R Costa
- Biosystems and Integrative Sciences Institute (BioISI), Plant Functional Biology Center, University of Minho, Braga, Portugal
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25
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SHB1 and CCA1 interaction desensitizes light responses and enhances thermomorphogenesis. Nat Commun 2019; 10:3110. [PMID: 31308379 PMCID: PMC6629618 DOI: 10.1038/s41467-019-11071-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 06/18/2019] [Indexed: 12/13/2022] Open
Abstract
Light and temperature are two important environmental signals to plants. After dawn, photo-activated phytochromes translocate into the nucleus and interact with a family of negative basic helix-loop-helix PIF regulators. Subsequent phosphorylation and degradation of PIFs triggers a series of photomorphogenic responses. However, excess light can damage the photosynthetic apparatus and leads to photoinhibition. Plants acclimate to a balanced state of photomorphogenesis to avoid photodamage. Here, we show that upregulation of PIF4 expression by SHB1 and CCA1 under red light represents a desensitization step. After dawn, the highly expressed circadian clock protein CCA1 brings circadian signals to the regulatory region of the PIF4 signaling hub. Recruitment of SHB1 by CCA1 modulates red light-specific induction of PIF4 expression thus integrating circadian and light signals. As noon approaches and light intensity and ambient temperature tend to increase, the SHB1–CCA1 interaction sustains PIF4 expression to trigger thermomorphogenic responses to changing light and temperature conditions. The PIF4 transcription factor promotes adaptation to elevated temperature but is degraded under red light to trigger photomorphogenesis. Here Sun et al. show that the core circadian component CCA1 recruits SHB1 to sustain PIF4 expression after dawn to balance thermomorphogenesis and light responses.
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26
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Lee HG, Hong C, Seo PJ. The Arabidopsis Sin3-HDAC Complex Facilitates Temporal Histone Deacetylation at the CCA1 and PRR9 Loci for Robust Circadian Oscillation. FRONTIERS IN PLANT SCIENCE 2019; 10:171. [PMID: 30833956 PMCID: PMC6387943 DOI: 10.3389/fpls.2019.00171] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 02/01/2019] [Indexed: 06/09/2023]
Abstract
The circadian clock synchronizes endogenous rhythmic processes with environmental cycles and maximizes plant fitness. Multiple regulatory layers shape circadian oscillation, and chromatin modification is emerging as an important scheme for precise circadian waveforms. Here, we report the role of an evolutionarily conserved Sin3-histone deacetylase complex (HDAC) in circadian oscillation in Arabidopsis. SAP30 FUNCTION-RELATED 1 (AFR1) and AFR2, which are key components of Sin3-HDAC complex, are circadianly-regulated and possibly facilitate the temporal formation of the Arabidopsis Sin3-HDAC complex at dusk. The evening-expressed AFR proteins bind directly to the CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and PSEUDO-RESPONSE REGULATOR 9 (PRR9) promoters and catalyze histone 3 (H3) deacetylation at the cognate regions to repress expression, allowing the declining phase of their expression at dusk. In support, the CCA1 and PRR9 genes were de-repressed around dusk in the afr1-1afr2-1 double mutant. These findings indicate that periodic histone deacetylation at the morning genes by the Sin3-HDAC complex contributes to robust circadian maintenance in higher plants.
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Affiliation(s)
- Hong Gil Lee
- Department of Chemistry, Seoul National University, Seoul, South Korea
| | - Cheljong Hong
- Department of Chemistry, Seoul National University, Seoul, South Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul, South Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
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27
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Ferrari C, Proost S, Janowski M, Becker J, Nikoloski Z, Bhattacharya D, Price D, Tohge T, Bar-Even A, Fernie A, Stitt M, Mutwil M. Kingdom-wide comparison reveals the evolution of diurnal gene expression in Archaeplastida. Nat Commun 2019; 10:737. [PMID: 30760717 PMCID: PMC6374488 DOI: 10.1038/s41467-019-08703-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 01/23/2019] [Indexed: 01/19/2023] Open
Abstract
Plants have adapted to the diurnal light-dark cycle by establishing elaborate transcriptional programs that coordinate many metabolic, physiological, and developmental responses to the external environment. These transcriptional programs have been studied in only a few species, and their function and conservation across algae and plants is currently unknown. We performed a comparative transcriptome analysis of the diurnal cycle of nine members of Archaeplastida, and we observed that, despite large phylogenetic distances and dramatic differences in morphology and lifestyle, diurnal transcriptional programs of these organisms are similar. Expression of genes related to cell division and the majority of biological pathways depends on the time of day in unicellular algae but we did not observe such patterns at the tissue level in multicellular land plants. Hence, our study provides evidence for the universality of diurnal gene expression and elucidates its evolutionary history among different photosynthetic eukaryotes.
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Affiliation(s)
- Camilla Ferrari
- Max-Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Sebastian Proost
- Max-Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Marcin Janowski
- Max-Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Jörg Becker
- Instituto Gulbenkian de Ciência, R. Q.ta Grande 6, 2780-156, Oeiras, Portugal
| | - Zoran Nikoloski
- Max-Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany.,Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Dana Price
- Department of Plant Biology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Takayuki Tohge
- Max-Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany.,Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Arren Bar-Even
- Max-Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Alisdair Fernie
- Max-Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Mark Stitt
- Max-Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Marek Mutwil
- Max-Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany. .,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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28
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Xu G, Jiang Z, Wang H, Lin R. The central circadian clock proteins CCA1 and LHY regulate iron homeostasis in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:168-181. [PMID: 29989313 DOI: 10.1111/jipb.12696] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 07/06/2018] [Indexed: 06/08/2023]
Abstract
Circadian clock is the endogenous time-keeping machinery that synchronizes an organism's metabolism, behavior, and physiology to the daily light-dark circles, thereby contributing to organismal fitness. Iron (Fe) is an essential micronutrient for all organisms and it plays important roles in diverse processes of plant growth and development. Here, we show that, in Arabidopsis thaliana, loss of the central clock genes, CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY), results in both reduced Fe uptake and photosynthetic efficiency, whereas CCA1 overexpression confers the opposite effects. We show that root Fe(III) reduction activity, and expression of FERRIC REDUCTION OXIDASE 2 (FRO2) and IRON-REGULATED TRANSPORTER 1 (IRT1) exhibit circadian oscillations, which are disrupted in the cca1 lhy double mutant. Furthermore, CCA1 directly binds to the specific regulatory regions of multiple Fe homeostasis genes and activates their expression. Thus, this study established that, in plants, CCA1 and LHY function as master regulators that maintain cyclic Fe homeostasis.
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Affiliation(s)
- Gang Xu
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhimin Jiang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haiyang Wang
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Rongcheng Lin
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Beijing 100093, China
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29
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Johansson M, Köster T. On the move through time - a historical review of plant clock research. PLANT BIOLOGY (STUTTGART, GERMANY) 2019; 21 Suppl 1:13-20. [PMID: 29607587 DOI: 10.1111/plb.12729] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 03/27/2018] [Indexed: 06/08/2023]
Abstract
The circadian clock is an important regulator of growth and development that has evolved to help organisms to anticipate the predictably occurring events on the planet, such as light-dark transitions, and adapt growth and development to these. This review looks back in history on how knowledge about the endogenous biological clock has been acquired over the centuries, with a focus on discoveries in plants. Key findings at the physiological, genetic and molecular level are described and the role of the circadian clock in important molecular processes is reviewed.
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Affiliation(s)
- M Johansson
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - T Köster
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
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30
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Jiménez-Guillen D, Pérez-Pascual D, Souza-Perera R, Godoy-Hernández G, Zúñiga-Aguilar JJ. Cloning of the Coffea canephora SERK1 promoter and its molecular analysis during the cell-to-embryo transition. ELECTRON J BIOTECHN 2018. [DOI: 10.1016/j.ejbt.2018.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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31
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Chenge-Espinosa M, Cordoba E, Romero-Guido C, Toledo-Ortiz G, León P. Shedding light on the methylerythritol phosphate (MEP)-pathway: long hypocotyl 5 (HY5)/phytochrome-interacting factors (PIFs) transcription factors modulating key limiting steps. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:828-841. [PMID: 30144333 DOI: 10.1111/tpj.14071] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/14/2018] [Accepted: 08/20/2018] [Indexed: 05/22/2023]
Abstract
The plastidial methylerythritol phosphate (MEP) pathway is an essential route for plants as the source of precursors for all plastidial isoprenoids, many of which are of medical and biotechnological importance. The MEP pathway is highly sensitive to environmental cues as many of these compounds are linked to photosynthesis and growth and light is one of the main regulatory factors. However, the mechanisms coordinating the MEP pathway with light cues are not fully understood. Here we demonstrate that by a differential direct transcriptional modulation, via the key-master integrators of light signal transduction HY5 and PIFs which target the genes that encode the rate-controlling DXS1, DXR and HDR enzymes, light imposes a direct, rapid and potentially multi-faceted response that leads to unique protein dynamics of this pathway, resulting in a significant difference in the protein levels. For DXS1, PIF1/HY5 act as a direct activation/suppression module. In contrast, DXR accumulation in response to light results from HY5 induction with minor contribution of de-repression by PIF1. Finally, HDR transcription increases in the light exclusively by suppression of the PIFs repression. This is an example of how light signaling components can differentially multi-target the initial steps of a pathway whose products branch downstream to all chloroplastic isoprenoids. These findings demonstrate the diversity and flexibility of light signaling components that optimize key biochemical pathways essential for plant growth.
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Affiliation(s)
- Marel Chenge-Espinosa
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad # 2001, Col. Chamilpa, Cuernavaca, Morelos, C.P. 62210, México
| | - Elizabeth Cordoba
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad # 2001, Col. Chamilpa, Cuernavaca, Morelos, C.P. 62210, México
| | - Cynthia Romero-Guido
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad # 2001, Col. Chamilpa, Cuernavaca, Morelos, C.P. 62210, México
| | | | - Patricia León
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad # 2001, Col. Chamilpa, Cuernavaca, Morelos, C.P. 62210, México
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32
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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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33
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Martí Ruiz MC, Hubbard KE, Gardner MJ, Jung HJ, Aubry S, Hotta CT, Mohd-Noh NI, Robertson FC, Hearn TJ, Tsai YC, Dodd AN, Hannah M, Carré IA, Davies JM, Braam J, Webb AAR. Circadian oscillations of cytosolic free calcium regulate the Arabidopsis circadian clock. NATURE PLANTS 2018; 4:690-698. [PMID: 30127410 PMCID: PMC6152895 DOI: 10.1038/s41477-018-0224-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 07/17/2018] [Indexed: 05/04/2023]
Abstract
In the last decade, the view of circadian oscillators has expanded from transcriptional feedback to incorporate post-transcriptional, post-translational, metabolic processes and ionic signalling. In plants and animals, there are circadian oscillations in the concentration of cytosolic free Ca2+ ([Ca2+]cyt), though their purpose has not been fully characterized. We investigated whether circadian oscillations of [Ca2+]cyt regulate the circadian oscillator of Arabidopsis thaliana. We report that in Arabidopsis, [Ca2+]cyt circadian oscillations can regulate circadian clock function through the Ca2+-dependent action of CALMODULIN-LIKE24 (CML24). Genetic analyses demonstrate a linkage between CML24 and the circadian oscillator, through pathways involving the circadian oscillator gene TIMING OF CAB2 EXPRESSION1 (TOC1).
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Affiliation(s)
| | - Katharine E Hubbard
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
- School of Biological, Biomedical and Environmental Sciences, University of Hull, Hull, UK
| | - Michael J Gardner
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Hyun Ju Jung
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Sylvain Aubry
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
- Department for Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Carlos T Hotta
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Nur Izzati Mohd-Noh
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
- Department of Bioscience and Health Science, Faculty of Bioscience and Medical Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Fiona C Robertson
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Zimbabwe, Harare, Zimbabwe
| | - Timothy J Hearn
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Yu-Chang Tsai
- Biochemistry and Cell Biology, Rice University, Houston, TX, USA
| | - Antony N Dodd
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
- School of Biological Sciences, Bristol Life Sciences Building, University of Bristol, Bristol, UK
| | - Matthew Hannah
- Bayer CropScience NV Innovation Center, Trait Discovery, Gent, Belgium
| | | | - Julia M Davies
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Janet Braam
- Biochemistry and Cell Biology, Rice University, Houston, TX, USA
| | - Alex A R Webb
- Department of Plant Sciences, University of Cambridge, Cambridge, UK.
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34
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Tang J, Ding Y, Nan J, Yang X, Sun L, Zhao X, Jiang L. Transcriptome sequencing and ITRAQ reveal the detoxification mechanism of Bacillus GJ1, a potential biocontrol agent for Huanglongbing. PLoS One 2018; 13:e0200427. [PMID: 30091977 PMCID: PMC6084860 DOI: 10.1371/journal.pone.0200427] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 06/26/2018] [Indexed: 11/18/2022] Open
Abstract
Huanglongbing (HLB) is the most serious disease affecting citrus production worldwide. No HLB-resistant citrus varieties exist. The HLB pathogen Candidatus Liberibacter asiaticus is nonculturable, increasing the difficulty of preventing and curing the disease. We successfully screened the biocontrol agent Bacillus GJ1 for the control of HLB in nursery-grown citrus plants. RNA sequencing (RNA-seq) of the transcriptome and isobaric tags for relative and absolute quantification of the proteome revealed differences in the detoxification responses of Bacillus GJ1-treated and -untreated Ca. L. asiaticus-infected citrus. Phylogenetic tree alignment showed that GJ1 was classified as B. amyloliquefaciens. The effect of eliminating the HLB pathogen was measured using real-time quantitative polymerase chain reaction (qPCR) and PCR. The results indicate that the rate of detoxification reached 50% after seven irrigations, of plants with an OD600nm≈1 Bacillus GJ1 suspension. Most importantly, photosynthesis-antenna proteins, photosynthesis, plant-pathogen interactions, and protein processing in the endoplasmic reticulum were significantly upregulated (padj < 0.05), as shown by the KEGG enrichment analysis of the transcriptomes; nine of the upregulated genes were validated by qPCR. Transcription factor analysis of the transcriptomes was performed, and 10 TFs were validated by qPCR. Cyanoamino acid metabolism, regulation of autophagy, isoflavonoid biosynthesis, starch and sucrose metabolism, protein export, porphyrin and chlorophyll metabolism, and carotenoid biosynthesis were investigated by KEGG enrichment analysis of the proteome, and significant differences were found in the expression of the genes involved in those pathways. Correlation analysis of the proteome and transcriptome showed common entries for the significantly different expression of proteins and the significantly different expression of genes in the GO and KEGG pathways, respectively. The above results reveal important information about the detoxification pathways.
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Affiliation(s)
- Jizhou Tang
- College of Horticulture and Forestry, Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yuanxi Ding
- College of Horticulture and Forestry, Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jing Nan
- College of Horticulture and Forestry, Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xiangyu Yang
- College of Horticulture and Forestry, Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Liang Sun
- College of Horticulture and Forestry, Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xiuyun Zhao
- College of life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China.,State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Ling Jiang
- College of Horticulture and Forestry, Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei, China.,National Indoor Conservation Center of Virus-free Germplasm of Fruit Crops, Huazhong Agricultural University, Wuhan, Hubei, China
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35
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Edwards KD, Takata N, Johansson M, Jurca M, Novák O, Hényková E, Liverani S, Kozarewa I, Strnad M, Millar AJ, Ljung K, Eriksson ME. Circadian clock components control daily growth activities by modulating cytokinin levels and cell division-associated gene expression in Populus trees. PLANT, CELL & ENVIRONMENT 2018; 41:1468-1482. [PMID: 29520862 PMCID: PMC6001645 DOI: 10.1111/pce.13185] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 02/28/2018] [Accepted: 02/28/2018] [Indexed: 05/30/2023]
Abstract
Trees are carbon dioxide sinks and major producers of terrestrial biomass with distinct seasonal growth patterns. Circadian clocks enable the coordination of physiological and biochemical temporal activities, optimally regulating multiple traits including growth. To dissect the clock's role in growth, we analysed Populus tremula × P. tremuloides trees with impaired clock function due to down-regulation of central clock components. late elongated hypocotyl (lhy-10) trees, in which expression of LHY1 and LHY2 is reduced by RNAi, have a short free-running period and show disrupted temporal regulation of gene expression and reduced growth, producing 30-40% less biomass than wild-type trees. Genes important in growth regulation were expressed with an earlier phase in lhy-10, and CYCLIN D3 expression was misaligned and arrhythmic. Levels of cytokinins were lower in lhy-10 trees, which also showed a change in the time of peak expression of genes associated with cell division and growth. However, auxin levels were not altered in lhy-10 trees, and the size of the lignification zone in the stem showed a relative increase. The reduced growth rate and anatomical features of lhy-10 trees were mainly caused by misregulation of cell division, which may have resulted from impaired clock function.
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Affiliation(s)
- Kieron D. Edwards
- School of Biological Sciences, C.H. Waddington BuildingUniversity of EdinburghEdinburghEH9 3BFUK
| | - Naoki Takata
- Department of Plant Physiology, Umeå Plant Science CentreUmeå University901 87UmeåSweden
| | - Mikael Johansson
- Department of Plant Physiology, Umeå Plant Science CentreUmeå University901 87UmeåSweden
- RNA Biology and Molecular PhysiologyBielefeld University33615BielefeldGermany
| | - Manuela Jurca
- Department of Plant Physiology, Umeå Plant Science CentreUmeå University901 87UmeåSweden
| | - Ondřej Novák
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental Botany ASCR and Palacký University783 71OlomoucCzech Republic
| | - Eva Hényková
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental Botany ASCR and Palacký University783 71OlomoucCzech Republic
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science CentreSwedish University of Agricultural Sciences901 83UmeåSweden
| | - Silvia Liverani
- Department of StatisticsUniversity of WarwickCoventryCV4 7ALUK
| | - Iwanka Kozarewa
- Department of Plant Physiology, Umeå Plant Science CentreUmeå University901 87UmeåSweden
| | - Miroslav Strnad
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental Botany ASCR and Palacký University783 71OlomoucCzech Republic
| | - Andrew J. Millar
- School of Biological Sciences, C.H. Waddington BuildingUniversity of EdinburghEdinburghEH9 3BFUK
| | - Karin Ljung
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science CentreSwedish University of Agricultural Sciences901 83UmeåSweden
| | - Maria E. Eriksson
- Department of Plant Physiology, Umeå Plant Science CentreUmeå University901 87UmeåSweden
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Song Y, Jiang Y, Kuai B, Li L. CIRCADIAN CLOCK-ASSOCIATED 1 Inhibits Leaf Senescence in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2018; 9:280. [PMID: 29559987 PMCID: PMC5845730 DOI: 10.3389/fpls.2018.00280] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 02/19/2018] [Indexed: 05/20/2023]
Abstract
Leaf senescence is an integral part of plant development, and the timing and progressing rate of senescence could substantially affect the yield and quality of crops. It has been known that a circadian rhythm synchronized with external environmental cues is critical for the optimal coordination of various physiological and metabolic processes. However, the reciprocal interactions between the circadian clock and leaf senescence in plants remain unknown. Here, through measuring the physiological and molecular senescence related markers of several circadian components mutants, we found that CIRCADIAN CLOCK-ASSOCIATED 1 inhibits leaf senescence. Further molecular and genetic studies revealed that CCA1 directly activates GLK2 and suppresses ORE1 expression to counteract leaf senescence. As plants age, the expression and periodic amplitude of CCA1 declines and thus weakens the inhibition of senescence. Our findings reveal an age-dependent circadian clock component of the process of leaf senescence.
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Linde A, Eklund DM, Kubota A, Pederson ERA, Holm K, Gyllenstrand N, Nishihama R, Cronberg N, Muranaka T, Oyama T, Kohchi T, Lagercrantz U. Early evolution of the land plant circadian clock. THE NEW PHYTOLOGIST 2017; 216:576-590. [PMID: 28244104 PMCID: PMC5638080 DOI: 10.1111/nph.14487] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 01/18/2017] [Indexed: 05/21/2023]
Abstract
While angiosperm clocks can be described as an intricate network of interlocked transcriptional feedback loops, clocks of green algae have been modelled as a loop of only two genes. To investigate the transition from a simple clock in algae to a complex one in angiosperms, we performed an inventory of circadian clock genes in bryophytes and charophytes. Additionally, we performed functional characterization of putative core clock genes in the liverwort Marchantia polymorpha and the hornwort Anthoceros agrestis. Phylogenetic construction was combined with studies of spatiotemporal expression patterns and analysis of M. polymorpha clock gene mutants. Homologues to core clock genes identified in Arabidopsis were found not only in bryophytes but also in charophytes, albeit in fewer copies. Circadian rhythms were detected for most identified genes in M. polymorpha and A. agrestis, and mutant analysis supports a role for putative clock genes in M. polymorpha. Our data are in line with a recent hypothesis that adaptation to terrestrial life occurred earlier than previously expected in the evolutionary history of charophyte algae. Both gene duplication and acquisition of new genes was important in the evolution of the plant circadian clock, but gene loss has also contributed to shaping the clock of bryophytes.
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Affiliation(s)
- Anna‐Malin Linde
- Department of Plant Ecology and EvolutionEvolutionary Biology CentreUppsala UniversityNorbyvägen 18DSE‐75236UppsalaSweden
- The Linnean Centre for Plant Biology in UppsalaUppsalaSweden
| | - D. Magnus Eklund
- Department of Plant Ecology and EvolutionEvolutionary Biology CentreUppsala UniversityNorbyvägen 18DSE‐75236UppsalaSweden
- The Linnean Centre for Plant Biology in UppsalaUppsalaSweden
| | - Akane Kubota
- Graduate School of BiostudiesKyoto UniversityKyoto606‐8502Japan
| | - Eric R. A. Pederson
- Department of Plant Ecology and EvolutionEvolutionary Biology CentreUppsala UniversityNorbyvägen 18DSE‐75236UppsalaSweden
- The Linnean Centre for Plant Biology in UppsalaUppsalaSweden
| | - Karl Holm
- Department of Plant Ecology and EvolutionEvolutionary Biology CentreUppsala UniversityNorbyvägen 18DSE‐75236UppsalaSweden
- The Linnean Centre for Plant Biology in UppsalaUppsalaSweden
| | - Niclas Gyllenstrand
- Department of Plant Ecology and EvolutionEvolutionary Biology CentreUppsala UniversityNorbyvägen 18DSE‐75236UppsalaSweden
- The Linnean Centre for Plant Biology in UppsalaUppsalaSweden
| | | | - Nils Cronberg
- Department of BiologyLund UniversityEcology BuildingSE‐22362LundSweden
| | | | - Tokitaka Oyama
- Graduate School of ScienceKyoto UniversityKyoto606‐8502Japan
| | - Takayuki Kohchi
- Graduate School of BiostudiesKyoto UniversityKyoto606‐8502Japan
| | - Ulf Lagercrantz
- Department of Plant Ecology and EvolutionEvolutionary Biology CentreUppsala UniversityNorbyvägen 18DSE‐75236UppsalaSweden
- The Linnean Centre for Plant Biology in UppsalaUppsalaSweden
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Sharma A, Wai CM, Ming R, Yu Q. Diurnal Cycling Transcription Factors of Pineapple Revealed by Genome-Wide Annotation and Global Transcriptomic Analysis. Genome Biol Evol 2017; 9:2170-2190. [PMID: 28922793 PMCID: PMC5737478 DOI: 10.1093/gbe/evx161] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2017] [Indexed: 12/22/2022] Open
Abstract
Circadian clock provides fitness advantage by coordinating internal metabolic and physiological processes to external cyclic environments. Core clock components exhibit daily rhythmic changes in gene expression, and the majority of them are transcription factors (TFs) and transcription coregulators (TCs). We annotated 1,398 TFs from 67 TF families and 80 TCs from 20 TC families in pineapple, and analyzed their tissue-specific and diurnal expression patterns. Approximately 42% of TFs and 45% of TCs displayed diel rhythmic expression, including 177 TF/TCs cycling only in the nonphotosynthetic leaf tissue, 247 cycling only in the photosynthetic leaf tissue, and 201 cycling in both. We identified 68 TF/TCs whose cycling expression was tightly coupled between the photosynthetic and nonphotosynthetic leaf tissues. These TF/TCs likely coordinate key biological processes in pineapple as we demonstrated that this group is enriched in homologous genes that form the core circadian clock in Arabidopsis and includes a STOP1 homolog. Two lines of evidence support the important role of the STOP1 homolog in regulating CAM photosynthesis in pineapple. First, STOP1 responds to acidic pH and regulates a malate channel in multiple plant species. Second, the cycling expression pattern of the pineapple STOP1 and the diurnal pattern of malate accumulation in pineapple leaf are correlated. We further examined duplicate-gene retention and loss in major known circadian genes and refined their evolutionary relationships between pineapple and other plants. Significant variations in duplicate-gene retention and loss were observed for most clock genes in both monocots and dicots.
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Affiliation(s)
- Anupma Sharma
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas
| | - Ching Man Wai
- Department of Plant Biology, University of Illinois at Urbana-Champaign
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China
| | - Qingyi Yu
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China
- Department of Plant Pathology and Microbiology, Texas A&M University
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Wang WJ, Zheng KL, Gong XD, Xu JL, Huang JR, Lin DZ, Dong YJ. The rice TCD11 encoding plastid ribosomal protein S6 is essential for chloroplast development at low temperature. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 259:1-11. [PMID: 28483049 DOI: 10.1016/j.plantsci.2017.02.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 02/18/2017] [Accepted: 02/20/2017] [Indexed: 05/20/2023]
Abstract
Plastid ribosome proteins (PRPs) are important components for chloroplast biogenesis and early chloroplast development. Although it has been known that chloroplast ribosomes are similar to bacterial ones, the precise molecular function of ribosomal proteins remains to be elucidated in rice. Here, we identified a novel rice mutant, designated tcd11 (thermo-sensitive chlorophyll-deficient mutant 11), characterized by the albino phenotype until it died at 20°C, while displaying normal phenotype at 32°C. The alteration of leaf color in tcd11 mutants was aligned with chlorophyll (Chl) content and chloroplast development. The map-based cloning and molecular complementation showed that TCD11 encodes the ribosomal small subunit protein S6 in chloroplasts (RPS6). TCD11 was abundantly expressed in leaves, suggesting its different expressions in tissues. In addition, the disruption of TCD11 greatly reduced the transcript levels of certain chloroplasts-associated genes and prevented the assembly of ribosome in chloroplasts at low temperature (20°C), whereas they recovered to nearly normal levels at high temperature (32°C). Thus, our data indicate that TCD11 plays an important role in chloroplast development at low temperature. Upon our knowledge, the observations from this study provide a first glimpse into the importance of RPS6 function in rice chloroplast development.
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Affiliation(s)
- Wen-Juan Wang
- Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Kai-Lun Zheng
- Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Xiao-Di Gong
- Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China; Institute of Genetics and Developmental Biology Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing, 10010, China
| | - Jian-Long Xu
- The Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan Cun Street, Beijing 100081, China; Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Ji-Rong Huang
- Institute of Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Dong-Zhi Lin
- Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China.
| | - Yan-Jun Dong
- Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China.
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RNA-Seq analysis of gene expression for floral development in crested wheatgrass (Agropyron cristatum L.). PLoS One 2017; 12:e0177417. [PMID: 28531235 PMCID: PMC5439701 DOI: 10.1371/journal.pone.0177417] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Accepted: 04/26/2017] [Indexed: 01/18/2023] Open
Abstract
Crested wheatgrass [Agropyron cristatum L. (Gaertn.)] is widely used for early spring grazing in western Canada and the development of late maturing cultivars which maintain forage quality for a longer period is desired. However, it is difficult to manipulate the timing of floral transition, as little is known about molecular mechanism of plant maturity in this species. In this study, RNA-Seq and differential gene expression analysis were performed to investigate gene expression for floral initiation and development in crested wheatgrass. Three cDNA libraries were generated and sequenced to represent three successive growth stages by sampling leaves at the stem elongation stage, spikes at boot and anthesis stages. The sequencing generated 25,568,846; 25,144,688 and 25,714,194 qualified Illumina reads for the three successive stages, respectively. De novo assembly of all the reads generated 311,671 transcripts with a mean length of 487 bp, and 152,849 genes with an average sequence length of 669 bp. A total of 48,574 (31.8%) and 105,222 (68.8%) genes were annotated in the Swiss-Prot and NCBI non-redundant (nr) protein databases, respectively. Based on the Kyoto Encyclopedia of Genes and Genome (KEGG) pathway database, 9,723 annotated sequences were mapped onto 298 pathways, including plant circadian clock pathway. Specifically, 113 flowering time-associated genes, 123 MADS-box genes and 22 CONSTANS-LIKE (COL) genes were identified. A COL homolog DN52048-c0-g4 which was clustered with the flowering time genes AtCO and OsHd1 in Arabidopsis (Arabidopsis thaliana L.) and rice (Oryza sativa L.), respectively, showed specific expression in leaves and could be a CONSTANS (CO) candidate gene. Taken together, this study has generated a new set of genomic resources for identifying and characterizing genes and pathways involved in floral transition and development in crested wheatgrass. These findings are significant for further understanding of the molecular basis for late maturity in this grass species.
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Dobisova T, Hrdinova V, Cuesta C, Michlickova S, Urbankova I, Hejatkova R, Zadnikova P, Pernisova M, Benkova E, Hejatko J. Light Controls Cytokinin Signaling via Transcriptional Regulation of Constitutively Active Sensor Histidine Kinase CKI1. PLANT PHYSIOLOGY 2017; 174:387-404. [PMID: 28292856 PMCID: PMC5411129 DOI: 10.1104/pp.16.01964] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 03/04/2017] [Indexed: 05/07/2023]
Abstract
In plants, the multistep phosphorelay (MSP) pathway mediates a range of regulatory processes, including those activated by cytokinins. The cross talk between cytokinin response and light has been known for a long time. However, the molecular mechanism underlying the interaction between light and cytokinin signaling remains elusive. In the screen for upstream regulators we identified a LONG PALE HYPOCOTYL (LPH) gene whose activity is indispensable for spatiotemporally correct expression of CYTOKININ INDEPENDENT1 (CKI1), encoding the constitutively active sensor His kinase that activates MSP signaling. lph is a new allele of HEME OXYGENASE1 (HY1) that encodes the key protein in the biosynthesis of phytochromobilin, a cofactor of photoconvertible phytochromes. Our analysis confirmed the light-dependent regulation of the CKI1 expression pattern. We show that CKI1 expression is under the control of phytochrome A (phyA), functioning as a dual (both positive and negative) regulator of CKI1 expression, presumably via the phyA-regulated transcription factors (TF) PHYTOCHROME INTERACTING FACTOR3 and CIRCADIAN CLOCK ASSOCIATED1. Changes in CKI1 expression observed in lph/hy1-7 and phy mutants correlate with misregulation of MSP signaling, changed cytokinin sensitivity, and developmental aberrations that were previously shown to be associated with cytokinin and/or CKI1 action. Besides that, we demonstrate a novel role of phyA-dependent CKI1 expression in the hypocotyl elongation and hook development during skotomorphogenesis. Based on these results, we propose that the light-dependent regulation of CKI1 provides a plausible mechanistic link underlying the well-known interaction between light- and cytokinin-controlled plant development.
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Affiliation(s)
- Tereza Dobisova
- CEITEC - Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, CZ-62500, Brno, Czech Republic (T.D., V.H., S.M., I.U., R.H., P.Z., M.P., E.B., J.H.); and Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria (C.C., P.Z., E.B.)
| | - Vendula Hrdinova
- CEITEC - Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, CZ-62500, Brno, Czech Republic (T.D., V.H., S.M., I.U., R.H., P.Z., M.P., E.B., J.H.); and Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria (C.C., P.Z., E.B.)
| | - Candela Cuesta
- CEITEC - Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, CZ-62500, Brno, Czech Republic (T.D., V.H., S.M., I.U., R.H., P.Z., M.P., E.B., J.H.); and Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria (C.C., P.Z., E.B.)
| | - Sarka Michlickova
- CEITEC - Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, CZ-62500, Brno, Czech Republic (T.D., V.H., S.M., I.U., R.H., P.Z., M.P., E.B., J.H.); and Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria (C.C., P.Z., E.B.)
| | - Ivana Urbankova
- CEITEC - Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, CZ-62500, Brno, Czech Republic (T.D., V.H., S.M., I.U., R.H., P.Z., M.P., E.B., J.H.); and Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria (C.C., P.Z., E.B.)
| | - Romana Hejatkova
- CEITEC - Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, CZ-62500, Brno, Czech Republic (T.D., V.H., S.M., I.U., R.H., P.Z., M.P., E.B., J.H.); and Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria (C.C., P.Z., E.B.)
| | - Petra Zadnikova
- CEITEC - Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, CZ-62500, Brno, Czech Republic (T.D., V.H., S.M., I.U., R.H., P.Z., M.P., E.B., J.H.); and Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria (C.C., P.Z., E.B.)
| | - Marketa Pernisova
- CEITEC - Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, CZ-62500, Brno, Czech Republic (T.D., V.H., S.M., I.U., R.H., P.Z., M.P., E.B., J.H.); and Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria (C.C., P.Z., E.B.)
| | - Eva Benkova
- CEITEC - Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, CZ-62500, Brno, Czech Republic (T.D., V.H., S.M., I.U., R.H., P.Z., M.P., E.B., J.H.); and Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria (C.C., P.Z., E.B.)
| | - Jan Hejatko
- CEITEC - Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, CZ-62500, Brno, Czech Republic (T.D., V.H., S.M., I.U., R.H., P.Z., M.P., E.B., J.H.); and Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria (C.C., P.Z., E.B.)
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Wagner L, Schmal C, Staiger D, Danisman S. The plant leaf movement analyzer (PALMA): a simple tool for the analysis of periodic cotyledon and leaf movement in Arabidopsis thaliana. PLANT METHODS 2017; 13:2. [PMID: 28053647 PMCID: PMC5209843 DOI: 10.1186/s13007-016-0153-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 12/01/2016] [Indexed: 05/25/2023]
Abstract
BACKGROUND The analysis of circadian leaf movement rhythms is a simple yet effective method to study effects of treatments or gene mutations on the circadian clock of plants. Currently, leaf movements are analysed using time lapse photography and subsequent bioinformatics analyses of leaf movements. Programs that are used for this purpose either are able to perform one function (i.e. leaf tip detection or rhythm analysis) or their function is limited to specific computational environments. We developed a leaf movement analysis tool-PALMA-that works in command line and combines image extraction with rhythm analysis using Fast Fourier transformation and non-linear least squares fitting. RESULTS We validated PALMA in both simulated time series and in experiments using the known short period mutant sensitivity to red light reduced 1 (srr1-1). We compared PALMA with two established leaf movement analysis tools and found it to perform equally well. Finally, we tested the effect of reduced iron conditions on the leaf movement rhythms of wild type plants. Here, we found that PALMA successfully detected period lengthening under reduced iron conditions. CONCLUSIONS PALMA correctly estimated the period of both simulated and real-life leaf movement experiments. As a platform-independent console-program that unites both functions needed for the analysis of circadian leaf movements it is a valid alternative to existing leaf movement analysis tools.
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Affiliation(s)
- Lucas Wagner
- Molecular Cell Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Christoph Schmal
- Molecular Cell Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Institute for Theoretical Biology, Charité Universitätsmedizin, Berlin, Germany
| | - Dorothee Staiger
- Molecular Cell Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Selahattin Danisman
- Molecular Cell Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
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Yi H, Li X, Lee SH, Nou IS, Lim YP, Hur Y. Natural variation in CIRCADIAN CLOCK ASSOCIATED 1 is associated with flowering time in Brassica rapa. Genome 2016; 60:402-413. [PMID: 28177832 DOI: 10.1139/gen-2016-0052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Flowering time is a very important agronomic trait and the development of molecular markers associated with this trait can facilitate crop breeding. CIRCADIAN CLOCK ASSOCIATED 1 (CCA1), a core oscillator component of circadian rhythms that affect metabolic pathways in plants, has been implicated in flowering time control in species of Brassica. CCA1 gene sequences from three Brassica rapa inbred lines, showing either early flowering or late flowering phenotypes, were analyzed and a high level of sequence variation was identified, especially within the fourth intron. Using this information, three PCR primer sets were designed and tested using various inbred lines of B. rapa. The usage of InDel markers was further validated by evaluation of flowering time and high resolution melting (HRM) analysis. Both methods, PCR and HRM, validated the use of newly developed markers. Additional sequence analyses of Brassica plants with diploid (AA, BB, or CC) and allotetraploid genomes further confirmed a large number of sequence polymorphisms in the CCA1 gene, including insertions/deletions in the fourth intron. Our results demonstrated that sequence variations in CCA1 can be used to develop valuable trait-related molecular markers for Brassica crop breeding.
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Affiliation(s)
- Hankuil Yi
- a Department of Biological Science, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 305-764, Republic of Korea
| | - Xiaonan Li
- b Department of Horticulture, Chungnam National University, Gung-Dong, Yuseong-Gu, Daejeon 305-764, Republic of Korea.,d Department of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Seong Ho Lee
- b Department of Horticulture, Chungnam National University, Gung-Dong, Yuseong-Gu, Daejeon 305-764, Republic of Korea
| | - Ill-Sup Nou
- c Department of Horticulture, Sunchon National University, Suncheon, Jeonnam, Republic of Korea
| | - Yong Pyo Lim
- b Department of Horticulture, Chungnam National University, Gung-Dong, Yuseong-Gu, Daejeon 305-764, Republic of Korea
| | - Yoonkang Hur
- a Department of Biological Science, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 305-764, Republic of Korea
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Nguyen TD, Moon S, Oo MM, Tayade R, Soh MS, Song JT, Oh SA, Jung KH, Park SK. Application of rice microspore-preferred promoters to manipulate early pollen development in Arabidopsis: a heterologous system. PLANT REPRODUCTION 2016; 29:291-300. [PMID: 27796586 DOI: 10.1007/s00497-016-0293-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 10/23/2016] [Indexed: 06/06/2023]
Abstract
Rice microspore-promoters. Based on microarray data analyzed for developing anthers and pollen grains, we identified nine rice microspore-preferred (RMP) genes, designated RMP1 through RMP9. To extend their biotechnological applicability, we then investigated the activity of RMP promoters originating from monocotyledonous rice in a heterologous system of dicotyledonous Arabidopsis. Expression of GUS was significantly induced in transgenic plants from the microspore to the mature pollen stages and was driven by the RMP1, RMP3, RMP4, RMP5, and RMP9 promoters. We found it interesting that, whereas RMP2 and RMP6 directed GUS expression in microspore at the early unicellular and bicellular stages, RMP7 and RMP8 seemed to be expressed at the late tricellular and mature pollen stages. Moreover, GUS was expressed in seven promoters, RMP3 through RMP9, during the seedling stage, in immature leaves, cotyledons, and roots. To confirm microspore-specific expression, we used complementation analysis with an Arabidopsis male-specific gametophytic mutant, sidecar pollen-2 (scp-2), to verify the activity of three promoters. That mutant shows defects in microspore development prior to pollen mitosis I. These results provide strong evidence that the SIDECAR POLLEN gene, driven by RMP promoters, successfully complements the scp-2 mutation, and they strongly suggest that these promoters can potentially be applied for manipulating the expression of target genes at the microspore stage in various species.
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Affiliation(s)
- Tien Dung Nguyen
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Korea
| | - Sunok Moon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Moe Moe Oo
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Korea
| | - Rupesh Tayade
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Korea
| | - Moon-Soo Soh
- Department of Molecular Biology, Sejong University, Seoul, 143-747, Korea
| | - Jong Tae Song
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Korea
| | - Sung Aeong Oh
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Korea
| | - Ki Hong Jung
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea.
| | - Soon Ki Park
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Korea.
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Delis C, Krokida A, Tomatsidou A, Tsikou D, Beta RAA, Tsioumpekou M, Moustaka J, Stravodimos G, Leonidas DD, Balatsos NAA, Papadopoulou KK. AtHESPERIN: a novel regulator of circadian rhythms with poly(A)-degrading activity in plants. RNA Biol 2016; 13:68-82. [PMID: 26619288 DOI: 10.1080/15476286.2015.1119363] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
We report the identification and characterization of a novel gene, AtHesperin (AtHESP) that codes for a deadenylase in Arabidopsis thaliana. The gene is under circadian clock-gene regulation and has similarity to the mammalian Nocturnin. AtHESP can efficiently degrade poly(A) substrates exhibiting allosteric kinetics. Size exclusion chromatography and native electrophoresis coupled with kinetic analysis support that the native enzyme is oligomeric with at least 3 binding sites. Knockdown and overexpression of AtHESP in plant lines affects the expression and rhythmicity of the clock core oscillator genes TOC1 and CCA1. This study demonstrates an evolutionary conserved poly(A)-degrading activity in plants and suggests deadenylation as a mechanism involved in the regulation of the circadian clock. A role of AtHESP in stress response in plants is also depicted.
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Affiliation(s)
- Costas Delis
- a Department of Biochemistry and Biotechnology , University of Thessaly , Larissa , 412 21 , Greece
| | - Afrodite Krokida
- a Department of Biochemistry and Biotechnology , University of Thessaly , Larissa , 412 21 , Greece
| | - Anastasia Tomatsidou
- a Department of Biochemistry and Biotechnology , University of Thessaly , Larissa , 412 21 , Greece
| | - Daniela Tsikou
- a Department of Biochemistry and Biotechnology , University of Thessaly , Larissa , 412 21 , Greece
| | - Rafailia A A Beta
- a Department of Biochemistry and Biotechnology , University of Thessaly , Larissa , 412 21 , Greece
| | - Maria Tsioumpekou
- a Department of Biochemistry and Biotechnology , University of Thessaly , Larissa , 412 21 , Greece
| | - Julietta Moustaka
- a Department of Biochemistry and Biotechnology , University of Thessaly , Larissa , 412 21 , Greece
| | - Georgios Stravodimos
- a Department of Biochemistry and Biotechnology , University of Thessaly , Larissa , 412 21 , Greece
| | - Demetres D Leonidas
- a Department of Biochemistry and Biotechnology , University of Thessaly , Larissa , 412 21 , Greece
| | - Nikolaos A A Balatsos
- a Department of Biochemistry and Biotechnology , University of Thessaly , Larissa , 412 21 , Greece
| | - Kalliope K Papadopoulou
- a Department of Biochemistry and Biotechnology , University of Thessaly , Larissa , 412 21 , Greece
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46
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Huang H, Nusinow DA. Into the Evening: Complex Interactions in the Arabidopsis Circadian Clock. Trends Genet 2016; 32:674-686. [PMID: 27594171 DOI: 10.1101/068460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 08/02/2016] [Accepted: 08/03/2016] [Indexed: 05/23/2023]
Abstract
In Arabidopsis thaliana an assembly of proteins named the evening complex (EC) has been established as an essential component of the circadian clock with conserved functions in regulating plant growth and development. Recent studies identifying EC-regulated genes and EC-interacting proteins have expanded our understanding of EC function. In this review we focus on new progress uncovering how the EC contributes to the circadian network through the integration of environmental inputs and the direct regulation of key clock genes. We also summarize new findings of how the EC directly regulates clock outputs, such as photoperiodic and thermoresponsive growth, and provide new perspectives on future experiments to address unsolved questions related to the EC.
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Affiliation(s)
- He Huang
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
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47
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Tardu M, Dikbas UM, Baris I, Kavakli IH. RNA-seq analysis of the transcriptional response to blue and red light in the extremophilic red alga, Cyanidioschyzon merolae. Funct Integr Genomics 2016; 16:657-669. [DOI: 10.1007/s10142-016-0521-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Revised: 08/22/2016] [Accepted: 08/30/2016] [Indexed: 10/21/2022]
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48
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Huang H, Nusinow DA. Into the Evening: Complex Interactions in the Arabidopsis Circadian Clock. Trends Genet 2016; 32:674-686. [PMID: 27594171 DOI: 10.1016/j.tig.2016.08.002] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 08/02/2016] [Accepted: 08/03/2016] [Indexed: 12/20/2022]
Abstract
In Arabidopsis thaliana an assembly of proteins named the evening complex (EC) has been established as an essential component of the circadian clock with conserved functions in regulating plant growth and development. Recent studies identifying EC-regulated genes and EC-interacting proteins have expanded our understanding of EC function. In this review we focus on new progress uncovering how the EC contributes to the circadian network through the integration of environmental inputs and the direct regulation of key clock genes. We also summarize new findings of how the EC directly regulates clock outputs, such as photoperiodic and thermoresponsive growth, and provide new perspectives on future experiments to address unsolved questions related to the EC.
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Affiliation(s)
- He Huang
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
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49
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Park HJ, Kim WY, Yun DJ. A New Insight of Salt Stress Signaling in Plant. Mol Cells 2016; 39:447-59. [PMID: 27239814 PMCID: PMC4916396 DOI: 10.14348/molcells.2016.0083] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/06/2016] [Accepted: 05/16/2016] [Indexed: 12/12/2022] Open
Abstract
Many studies have been conducted to understand plant stress responses to salinity because irrigation-dependent salt accumulation compromises crop productivity and also to understand the mechanism through which some plants thrive under saline conditions. As mechanistic understanding has increased during the last decades, discovery-oriented approaches have begun to identify genetic determinants of salt tolerance. In addition to osmolytes, osmoprotectants, radical detoxification, ion transport systems, and changes in hormone levels and hormone-guided communications, the Salt Overly Sensitive (SOS) pathway has emerged to be a major defense mechanism. However, the mechanism by which the components of the SOS pathway are integrated to ultimately orchestrate plant-wide tolerance to salinity stress remains unclear. A higher-level control mechanism has recently emerged as a result of recognizing the involvement of GIGANTEA (GI), a protein involved in maintaining the plant circadian clock and control switch in flowering. The loss of GI function confers high tolerance to salt stress via its interaction with the components of the SOS pathway. The mechanism underlying this observation indicates the association between GI and the SOS pathway and thus, given the key influence of the circadian clock and the pathway on photoperiodic flowering, the association between GI and SOS can regulate growth and stress tolerance. In this review, we will analyze the components of the SOS pathways, with emphasis on the integration of components recognized as hallmarks of a halophytic lifestyle.
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Affiliation(s)
- Hee Jin Park
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Jinju 52828,
Korea
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Jinju 52828,
Korea
- Institute of Agriculture & Life Sciences, Graduate School of Gyeongsang National University, Jinju 52828,
Korea
| | - Dae-Jin Yun
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Jinju 52828,
Korea
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50
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Zhou C, Li C. A Novel R2R3-MYB Transcription Factor BpMYB106 of Birch (Betula platyphylla) Confers Increased Photosynthesis and Growth Rate through Up-regulating Photosynthetic Gene Expression. FRONTIERS IN PLANT SCIENCE 2016; 7:315. [PMID: 27047502 PMCID: PMC4801893 DOI: 10.3389/fpls.2016.00315] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 02/29/2016] [Indexed: 06/01/2023]
Abstract
We isolated a R2R3-MYB transcription factor BpMYB106, which regulates photosynthesis in birch (Betula platyphylla Suk.). BpMYB106 mainly expresses in the leaf and shoot tip of birch, and its protein is localized in the nucleus. We further fused isolated a 1588 bp promoter of BpMYB106 and analyzed it by PLACE, which showed some cis-acting elements related to photosynthesis. BpMYB106 promoter β-glucuronidase (GUS) reporter fusion studies gene, the result, showed the GUS reporter gene in transgenic birch with BpMYB106 promoter showed strong activities in shoot tip, cotyledon margins, and mature leaf trichomes. The overexpression of BpMYB106 in birch resulted in significantly increased trichome density, net photosynthetic rate, and growth rate as compared with the wild-type birch. RNA-Seq profiling revealed the upregulation of several photosynthesis-related genes in the photosynthesis and oxidative phosphorylation pathways in the leaves of transgenic plants. Yeast one-hybrid analysis, coupled with transient assay in tobacco, revealed that BpMYB106 binds a MYB binding site MYB2 in differentially expressed gene promoters. Thus, BpMYB106 may directly activate the expression of a range of photosynthesis related genes through interacting with the MYB2 element in their promoters. Our study demonstrating the overexpression of BpMYB106-a R2R3-MYB transcription factor-upregulates the genes of the photosynthesis and oxidative phosphorylation pathways to improve photosynthesis.
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