1
|
Zong W, Guo X, Zhang K, Chen L, Liu YG, Guo J. Photoperiod and temperature synergistically regulate heading date and regional adaptation in rice. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:3762-3777. [PMID: 38779909 DOI: 10.1093/jxb/erae209] [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: 12/26/2023] [Accepted: 05/22/2024] [Indexed: 05/25/2024]
Abstract
Plants must accurately integrate external environmental signals with their own development to initiate flowering at the appropriate time for reproductive success. Photoperiod and temperature are key external signals that determine flowering time; both are cyclical and periodic, and they are closely related. In this review, we describe photoperiod-sensitive genes that simultaneously respond to temperature signals in rice (Oryza sativa). We introduce the mechanisms by which photoperiod and temperature synergistically regulate heading date and regional adaptation in rice. We also discuss the prospects for designing different combinations of heading date genes and other cold tolerance or thermo-tolerance genes to help rice better adapt to changes in light and temperature via molecular breeding to enhance yield in the future.
Collapse
Affiliation(s)
- Wubei Zong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Xiaotong Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Kai Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Letian Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Yao-Guang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Jingxin Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| |
Collapse
|
2
|
June V, Song X, Chen ZJ. Imprinting but not cytonuclear interactions determines seed size heterosis in Arabidopsis hybrids. PLANT PHYSIOLOGY 2024; 195:1214-1228. [PMID: 38319651 PMCID: PMC11142339 DOI: 10.1093/plphys/kiae061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/14/2023] [Accepted: 12/19/2023] [Indexed: 02/07/2024]
Abstract
The parent-of-origin effect on seeds can result from imprinting (unequal expression of paternal and maternal alleles) or combinational effects between cytoplasmic and nuclear genomes, but their relative contributions remain unknown. To discern these confounding factors, we produced cytoplasmic-nuclear substitution (CNS) lines using recurrent backcrossing in Arabidopsis (Arabidopsis thaliana) ecotypes Col-0 and C24. These CNS lines differed only in the nuclear genome (imprinting) or cytoplasm. The CNS reciprocal hybrids with the same cytoplasm displayed ∼20% seed size difference, whereas the seed size was similar between the reciprocal hybrids with fixed imprinting. Transcriptome analyses in the endosperm of CNS hybrids using laser-capture microdissection identified 104 maternally expressed genes (MEGs) and 90 paternally expressed genes (PEGs). These imprinted genes were involved in pectin catabolism and cell wall modification in the endosperm. Homeodomain Glabrous9 (HDG9), an epiallele and one of 11 cross-specific imprinted genes, affected seed size. In the embryo, there were a handful of imprinted genes in the CNS hybrids but only 1 was expressed at higher levels than in the endosperm. AT4G13495 was found to encode a long-noncoding RNA (lncRNA), but no obvious seed phenotype was observed in lncRNA knockout lines. Nuclear RNA Polymerase D1 (NRPD1), encoding the largest subunit of RNA Pol IV, was involved in the biogenesis of small interfering RNAs. Seed size and embryos were larger in the cross using nrpd1 as the maternal parent than in the reciprocal cross, supporting a role of the maternal NRPD1 allele in seed development. Although limited ecotypes were tested, these results suggest that imprinting and the maternal NRPD1-mediated small RNA pathway play roles in seed size heterosis in plant hybrids.
Collapse
Affiliation(s)
- Viviana June
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Xiaoya Song
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| |
Collapse
|
3
|
Guo L, Wang S, Jiao X, Ye X, Deng D, Liu H, Li Y, Van de Peer Y, Wu W. Convergent and/or parallel evolution of RNA-binding proteins in angiosperms after polyploidization. THE NEW PHYTOLOGIST 2024; 242:1377-1393. [PMID: 38436132 DOI: 10.1111/nph.19656] [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: 05/13/2023] [Accepted: 02/20/2024] [Indexed: 03/05/2024]
Abstract
Increasing studies suggest that the biased retention of stress-related transcription factors (TFs) after whole-genome duplications (WGDs) could rewire gene transcriptional networks, facilitating plant adaptation to challenging environments. However, the role of posttranscriptional factors (e.g. RNA-binding proteins, RBPs) following WGDs has been largely ignored. Uncovering thousands of RBPs in 21 representative angiosperm species, we integrate genomic, transcriptomic, regulatomic, and paleotemperature datasets to unravel their evolutionary trajectories and roles in adapting to challenging environments. We reveal functional enrichments of RBP genes in stress responses and identify their convergent retention across diverse angiosperms from independent WGDs, coinciding with global cooling periods. Numerous RBP duplicates derived from WGDs are then identified as cold-induced. A significant overlap of 29 orthogroups between WGD-derived and cold-induced RBP genes across diverse angiosperms highlights a correlation between WGD and cold stress. Notably, we unveil an orthogroup (Glycine-rich RNA-binding Proteins 7/8, GRP7/8) and relevant TF duplicates (CCA1/LHY, RVE4/8, CBF2/4, etc.), co-retained in different angiosperms post-WGDs. Finally, we illustrate their roles in rewiring circadian and cold-regulatory networks at both transcriptional and posttranscriptional levels during global cooling. Altogether, we underline the adaptive evolution of RBPs in angiosperms after WGDs during global cooling, improving our understanding of plants surviving periods of environmental turmoil.
Collapse
Affiliation(s)
- Liangyu Guo
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Shuo Wang
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Xi Jiao
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Xiaoxue Ye
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Deyin Deng
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Hua Liu
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Yan Li
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, VIB - UGent Center for Plant Systems Biology, Ghent University, B-9052, Ghent, Belgium
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0028, South Africa
| | - Wenwu Wu
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| |
Collapse
|
4
|
Cseresnyés I, Takács T, Füzy A. Detection of plant cadmium toxicity by monitoring dielectric response of intact root systems on a fine timescale. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:30555-30568. [PMID: 38607480 PMCID: PMC11096224 DOI: 10.1007/s11356-024-33279-w] [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: 12/07/2023] [Accepted: 04/06/2024] [Indexed: 04/13/2024]
Abstract
The root dielectric response was measured on a minute scale to assess its efficiency for monitoring short-term cadmium (Cd) toxicity non-destructively. Electrical capacitance (CR), dissipation factor (DR) and electrical conductance (GR) were detected during the 24 to 168 h after Cd treatment (0, 20, 50 mg Cd2+ kg-1 substrate) in potted maize, cucumber and pea. Stress was also evaluated by measuring leaf chlorophyll content, Fv/Fm and stomatal conductance (gs) in situ, and shoot and root mass and total root length after harvest. CR showed a clear diurnal pattern, reflecting the water uptake rate, and decreased significantly in response to excessive Cd due to impeded root growth, the reduced tissue permittivity caused by accelerated lignification, and root ageing. Cd exposure markedly increased DR, indicating greater conductive energy loss due to oxidative membrane damage and enhanced electrolyte leakage. GR, which was coupled with root hydraulic conductance and varied diurnally, was increased transiently by Cd toxicity due to enhanced membrane permeability, but declined thereafter owing to stress-induced leaf senescence and transpiration loss. The time series of impedance components indicated the comparatively high Cd tolerance of the applied maize and the sensitivity of pea cultivar, which was confirmed by visible shoot symptoms, repeated physiological investigations and biomass measurements. The results demonstrated the potential of single-frequency dielectric measurements to follow certain aspects of the stress response of different species on a fine timescale without plant injury. The approach can be combined with widely used plant physiological methods and could contribute to breeding crop genotypes with improved stress tolerance.
Collapse
Affiliation(s)
- Imre Cseresnyés
- Institute for Soil Sciences, HUN-REN Centre for Agricultural Research, Herman Ottó Út 15, 1022, Budapest, Hungary.
| | - Tünde Takács
- Institute for Soil Sciences, HUN-REN Centre for Agricultural Research, Herman Ottó Út 15, 1022, Budapest, Hungary
| | - Anna Füzy
- Institute for Soil Sciences, HUN-REN Centre for Agricultural Research, Herman Ottó Út 15, 1022, Budapest, Hungary
| |
Collapse
|
5
|
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.
Collapse
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.
| |
Collapse
|
6
|
Kim D, Guadagno CR, Ewers BE, Mackay DS. Combining PSII photochemistry and hydraulics improves predictions of photosynthesis and water use from mild to lethal drought. PLANT, CELL & ENVIRONMENT 2024; 47:1255-1268. [PMID: 38178610 DOI: 10.1111/pce.14806] [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: 02/04/2023] [Revised: 12/10/2023] [Accepted: 12/20/2023] [Indexed: 01/06/2024]
Abstract
Rising temperatures and increases in drought negatively impact the efficiency and sustainability of both agricultural and forest ecosystems. Although hydraulic limitations on photosynthesis have been extensively studied, a solid understanding of the links between whole plant hydraulics and photosynthetic processes at the cellular level under changing environmental conditions is still missing, hampering our predictive power for plant mortality. Here, we examined plant hydraulic traits and CO2 assimilation rate under progressive water limitation by implementing Photosystem II (PSII) dynamics with a whole plant process model (TREES). The photosynthetic responses to plant water status were parameterized based on measurements of chlorophyll a fluorescence, gas exchange and water potential for Brassica rapa (R500) grown in a greenhouse under fully watered to lethal drought conditions. The updated model significantly improved predictions of photosynthesis, stomatal conductance and leaf water potential. TREES with PSII knowledge predicted a larger hydraulic safety margin and a decrease in percent loss of conductivity. TREES predicted a slower decrease in leaf water potential, which agreed with measurements. Our results highlight the pressing need for incorporating PSII drought photochemistry into current process models to capture cross-scale plant water dynamics from cell to whole plant level.
Collapse
Affiliation(s)
- Dohyoung Kim
- Department of Geography, State University of New York at Buffalo, Buffalo, New York, USA
| | | | - Brent E Ewers
- Department of Botany, University of Wyoming, Laramie, Wyoming, USA
| | - D Scott Mackay
- Department of Geography, State University of New York at Buffalo, Buffalo, New York, USA
| |
Collapse
|
7
|
Yuan L, Avello P, Zhu Z, Lock SCL, McCarthy K, Redmond EJ, Davis AM, Song Y, Ezer D, Pitchford JW, Quint M, Xie Q, Xu X, Davis SJ, Ronald J. Complex epistatic interactions between ELF3, PRR9, and PRR7 regulate the circadian clock and plant physiology. Genetics 2024; 226:iyad217. [PMID: 38142447 PMCID: PMC10917503 DOI: 10.1093/genetics/iyad217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 08/07/2023] [Accepted: 12/05/2023] [Indexed: 12/26/2023] Open
Abstract
Circadian clocks are endogenous timekeeping mechanisms that coordinate internal physiological responses with the external environment. EARLY FLOWERING3 (ELF3), PSEUDO RESPONSE REGULATOR (PRR9), and PRR7 are essential components of the plant circadian clock and facilitate entrainment of the clock to internal and external stimuli. Previous studies have highlighted a critical role for ELF3 in repressing the expression of PRR9 and PRR7. However, the functional significance of activity in regulating circadian clock dynamics and plant development is unknown. To explore this regulatory dynamic further, we first employed mathematical modeling to simulate the effect of the prr9/prr7 mutation on the elf3 circadian phenotype. These simulations suggested that simultaneous mutations in prr9/prr7 could rescue the elf3 circadian arrhythmia. Following these simulations, we generated all Arabidopsis elf3/prr9/prr7 mutant combinations and investigated their circadian and developmental phenotypes. Although these assays could not replicate the results from the mathematical modeling, our results have revealed a complex epistatic relationship between ELF3 and PRR9/7 in regulating different aspects of plant development. ELF3 was essential for hypocotyl development under ambient and warm temperatures, while PRR9 was critical for root thermomorphogenesis. Finally, mutations in prr9 and prr7 rescued the photoperiod-insensitive flowering phenotype of the elf3 mutant. Together, our results highlight the importance of investigating the genetic relationship among plant circadian genes.
Collapse
Affiliation(s)
- Li Yuan
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Paula Avello
- Department of Mathematics, University of York, York, YO10 5DD, UK
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Zihao Zhu
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle (Saale) 06108, Germany
| | - Sarah C L Lock
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Kayla McCarthy
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Ethan J Redmond
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Amanda M Davis
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Yang Song
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Daphne Ezer
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Jonathan W Pitchford
- Department of Mathematics, University of York, York, YO10 5DD, UK
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Marcel Quint
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle (Saale) 06108, Germany
| | - Qiguang Xie
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Xiaodong Xu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Seth J Davis
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - James Ronald
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bower Building, University Avenue, Glasgow G12 8QQ, UK
| |
Collapse
|
8
|
Yao Q, Feng Y, Wang J, Zhang Y, Yi F, Li Z, Zhang M. Integrated Metabolome and Transcriptome Analysis of Gibberellins Mediated the Circadian Rhythm of Leaf Elongation by Regulating Lignin Synthesis in Maize. Int J Mol Sci 2024; 25:2705. [PMID: 38473951 DOI: 10.3390/ijms25052705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 02/08/2024] [Accepted: 02/24/2024] [Indexed: 03/14/2024] Open
Abstract
Plant growth exhibits rhythmic characteristics, and gibberellins (GAs) are involved in regulating cell growth, but it is still unclear how GAs crosstalk with circadian rhythm to regulate cell elongation. The study analyzed growth characteristics of wild-type (WT), zmga3ox and zmga3ox with GA3 seedlings. We integrated metabolomes and transcriptomes to study the interaction between GAs and circadian rhythm in mediating leaf elongation. The rates of leaf growth were higher in WT than zmga3ox, and zmga3ox cell length was shorter when proliferated in darkness than light, and GA3 restored zmga3ox leaf growth. The differentially expressed genes (DEGs) between WT and zmga3ox were mainly enriched in hormone signaling and cell wall synthesis, while DEGs in zmga3ox were restored to WT by GA3. Moreover, the number of circadian DEGs that reached the peak expression in darkness was more than light, and the upregulated circadian DEGs were mainly enriched in cell wall synthesis. The differentially accumulated metabolites (DAMs) were mainly attributed to flavonoids and phenolic acid. Twenty-two DAMs showed rhythmic accumulation, especially enriched in lignin synthesis. The circadian DEGs ZmMYBr41/87 and ZmHB34/70 were identified as regulators of ZmHCT8 and ZmBM1, which were enzymes in lignin synthesis. Furthermore, GAs regulated ZmMYBr41/87 and ZmHB34/70 to modulate lignin biosynthesis for mediating leaf rhythmic growth.
Collapse
Affiliation(s)
- Qingqing Yao
- State Key Laboratory of Plant Environmental Resilience, Engineering Research Center of Plant Growth Regulator, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, No 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Ying Feng
- State Key Laboratory of Plant Environmental Resilience, Engineering Research Center of Plant Growth Regulator, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, No 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Jiajie Wang
- State Key Laboratory of Plant Environmental Resilience, Engineering Research Center of Plant Growth Regulator, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, No 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Yushi Zhang
- State Key Laboratory of Plant Environmental Resilience, Engineering Research Center of Plant Growth Regulator, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, No 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Fei Yi
- State Key Laboratory of Plant Environmental Resilience, Engineering Research Center of Plant Growth Regulator, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, No 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Zhaohu Li
- State Key Laboratory of Plant Environmental Resilience, Engineering Research Center of Plant Growth Regulator, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, No 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Mingcai Zhang
- State Key Laboratory of Plant Environmental Resilience, Engineering Research Center of Plant Growth Regulator, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, No 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| |
Collapse
|
9
|
Liang T, Yu S, Pan Y, Wang J, Kay SA. The interplay between the circadian clock and abiotic stress responses mediated by ABF3 and CCA1/LHY. Proc Natl Acad Sci U S A 2024; 121:e2316825121. [PMID: 38319968 PMCID: PMC10873597 DOI: 10.1073/pnas.2316825121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 01/09/2024] [Indexed: 02/08/2024] Open
Abstract
Climate change is a global concern for all life on our planet, including humans and plants. Plants' growth and development are significantly affected by abiotic stresses, including adverse temperature, inadequate or excess water availability, nutrient deficiency, and salinity. The circadian clock is a master regulator of numerous developmental and metabolic processes in plants. In an effort to identify new clock-related genes and outputs through bioinformatic analysis, we have revealed that CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY) play a crucial role in regulating a wide range of abiotic stress responses and target ABSCISIC ACID RESPONSIVE ELEMENTS-BINDING FACTOR3 (ABF3), a key transcription factor in the plant hormone Abscisic acid (ABA)-signaling pathway. Specifically, we found that CCA1 and LHY regulate the expression of ABF3 under diel conditions, as well as seed germination under salinity. Conversely, ABF3 controls the expression of core clock genes and orchestrates the circadian period in a stress-responsive manner. ABF3 delivers the stress signal to the central oscillator by binding to the promoter of CCA1 and LHY. Overall, our study uncovers the reciprocal regulation between ABF3 and CCA1/LHY and molecular mechanisms underlying the interaction between the circadian clock and abiotic stress. This finding may aid in developing molecular and genetic solutions for plants to survive and thrive in the face of climate change.
Collapse
Affiliation(s)
- Tong Liang
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA90089
| | - Shi Yu
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA90089
| | - Yuanzhong Pan
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA90089
| | - Jiarui Wang
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA90089
| | - Steve A. Kay
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA90089
| |
Collapse
|
10
|
Jang J, Lee S, Kim JI, Lee S, Kim JA. The Roles of Circadian Clock Genes in Plant Temperature Stress Responses. Int J Mol Sci 2024; 25:918. [PMID: 38255990 PMCID: PMC10815334 DOI: 10.3390/ijms25020918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/17/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
Plants monitor day length and memorize changes in temperature signals throughout the day, creating circadian rhythms that support the timely control of physiological and metabolic processes. The DEHYDRATION-RESPONSE ELEMENT-BINDING PROTEIN 1/C-REPEAT BINDING FACTOR (DREB1/CBF) transcription factors are known as master regulators for the acquisition of cold stress tolerance, whereas PHYTOCHROME INTERACTING FACTOR 4 (PIF4) is involved in plant adaptation to heat stress through thermomorphogenesis. Recent studies have shown that circadian clock genes control plant responses to temperature. Temperature-responsive transcriptomes show a diurnal cycle and peak expression levels at specific times of throughout the day. Circadian clock genes play essential roles in allowing plants to maintain homeostasis by accommodating temperature changes within the normal temperature range or by altering protein properties and morphogenesis at the cellular level for plant survival and growth under temperature stress conditions. Recent studies revealed that the central oscillator genes CIRCADIAN CLOCK ASSOCIATED 1/LATE ELONGATED HYPOCOTYL (CCA1/LHY) and PSEUDO-RESPONSE REGULATOR5/7/9 (PRR5/7/9), as well as the EVENING COMPLEX (EC) genes REVEILLE4/REVEILLE8 (REV4/REV8), were involved in the DREB1 pathway of the cold signaling transcription factor and regulated the thermomorphogenesis gene PIF4. Further studies showed that another central oscillator, TIMING OF CAB EXPRESSION 1 (TOC1), and the regulatory protein ZEITLUPE (ZTL) are also involved. These studies led to attempts to utilize circadian clock genes for the acquisition of temperature-stress resistance in crops. In this review, we highlight circadian rhythm regulation and the clock genes involved in plant responses to temperature changes, as well as strategies for plant survival in a rapidly changing global climate.
Collapse
Affiliation(s)
- Juna Jang
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Jeonju 54874, Republic of Korea; (J.J.); (S.L.); (S.L.)
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea;
| | - Sora Lee
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Jeonju 54874, Republic of Korea; (J.J.); (S.L.); (S.L.)
| | - Jeong-Il Kim
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea;
| | - Sichul Lee
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Jeonju 54874, Republic of Korea; (J.J.); (S.L.); (S.L.)
| | - Jin A. Kim
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Jeonju 54874, Republic of Korea; (J.J.); (S.L.); (S.L.)
| |
Collapse
|
11
|
Cseresnyés I, Füzy A, Kabos S, Kelemen B, Rajkai K, Takács T. Monitoring of plant water uptake by measuring root dielectric properties on a fine timescale: diurnal changes and response to leaf excision. PLANT METHODS 2024; 20:5. [PMID: 38195647 PMCID: PMC10775601 DOI: 10.1186/s13007-023-01133-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 12/28/2023] [Indexed: 01/11/2024]
Abstract
BACKGROUND The measurement of root dielectric response is a useful non-destructive method to evaluate root growth and function. Previous studies tracked root development throughout the plant growing cycle by single-time electrical measurements taken repeatedly. However, it is known that root conductivity and uptake activity can change rapidly, coupled with the day/night cycles of photosynthetic and transpiration rate. Therefore, the low-frequency dielectric monitoring of intact root-substrate systems at minute-scale temporal resolution was tested using a customized impedance measurement system in a laboratory environment. Electrical capacitance (CR) and conductance (GR) and the dissipation factor (DR) were detected for 144 h in potted maize, cucumber and pea grown under various light/dark and temperature conditions, or subjected to progressive leaf excision or decapitation. Photosynthetic parameters and stomatal conductance were also measured to evaluate the stress response. RESULTS The CR and GR data series showed significant 24-h seasonality associated with the light/dark and temperature cycles applied. This was attributed to the diurnal patterns in whole-plant transpiration (detected via stomatal conductance), which is strongly linked to the root water uptake rate. CR and GR decreased during the 6-day dark treatment, and dropped proportionally with increasing defoliation levels, likely due to the loss of canopy transpiration caused by dark-induced senescence or removal of leaves. DR showed a decreasing trend for plants exposed to 6-day darkness, whereas it was increased markedly by decapitation, indicating altered root membrane structure and permeability, and a modified ratio of apoplastic to cell-to-cell water and current pathways. CONCLUSIONS Dynamic, in situ impedance measurement of the intact root system was an efficient way of following integrated root water uptake, including diurnal cycles, and stress-induced changes. It was also demonstrated that the dielectric response mainly originated from root tissue polarization and current conduction, and was influenced by the actual physiological activity of the root system. Dielectric measurement on fine timescale, as a diagnostic tool for monitoring root physiological status and environmental response, deserves future attention.
Collapse
Affiliation(s)
- Imre Cseresnyés
- Institute for Soil Sciences, HUN-REN Centre for Agricultural Research, Herman Ottó út 15., 1022, Budapest, Hungary.
| | - Anna Füzy
- Institute for Soil Sciences, HUN-REN Centre for Agricultural Research, Herman Ottó út 15., 1022, Budapest, Hungary
| | - Sándor Kabos
- Department of Statistics, Eötvös Loránd University, Pázmány Péter stny. 1/A., 1117, Budapest, Hungary
| | - Bettina Kelemen
- Institute for Soil Sciences, HUN-REN Centre for Agricultural Research, Herman Ottó út 15., 1022, Budapest, Hungary
| | - Kálmán Rajkai
- Institute for Soil Sciences, HUN-REN Centre for Agricultural Research, Herman Ottó út 15., 1022, Budapest, Hungary
| | - Tünde Takács
- Institute for Soil Sciences, HUN-REN Centre for Agricultural Research, Herman Ottó út 15., 1022, Budapest, Hungary
| |
Collapse
|
12
|
Zhang Y, Ma Y, Zhang H, Xu J, Gao X, Zhang T, Liu X, Guo L, Zhao D. Environmental F actors coordinate circadian clock function and rhythm to regulate plant development. PLANT SIGNALING & BEHAVIOR 2023; 18:2231202. [PMID: 37481743 PMCID: PMC10364662 DOI: 10.1080/15592324.2023.2231202] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 07/25/2023]
Abstract
Changes in the external environment necessitate plant growth plasticity, with environmental signals such as light, temperature, and humidity regulating growth and development. The plant circadian clock is a biological time keeper that can be "reset" to adjust internal time to changes in the external environment. Exploring the regulatory mechanisms behind plant acclimation to environmental factors is important for understanding how plant growth and development are shaped and for boosting agricultural production. In this review, we summarize recent insights into the coordinated regulation of plant growth and development by environmental signals and the circadian clock, further discussing the potential of this knowledge.
Collapse
Affiliation(s)
- Ying Zhang
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
- Institute of Biotechnology and Food Science, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Yuru Ma
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Hao Zhang
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Jiahui Xu
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Xiaokuan Gao
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
| | - Tengteng Zhang
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Xigang Liu
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Lin Guo
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Dan Zhao
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| |
Collapse
|
13
|
Hu F, Zhang Y, Guo J. Effects of drought stress on photosynthetic physiological characteristics, leaf microstructure, and related gene expression of yellow horn. PLANT SIGNALING & BEHAVIOR 2023; 18:2215025. [PMID: 37243677 DOI: 10.1080/15592324.2023.2215025] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/28/2023] [Accepted: 05/01/2023] [Indexed: 05/29/2023]
Abstract
Yellow horn grows in northern China and has a high tolerance to drought and poor soil. Improving photosynthetic efficiency and increasing plant growth and yield under drought conditions have become important research content for researchers worldwide. Our study goal is to provide comprehensive information on photosynthesis and some candidate genes breeding of yellow horn under drought stress. In this study, seedlings' stomatal conductance, chlorophyll content, and fluorescence parameters decreased under drought stress, but non-photochemical quenching increased. The leaf microstructure showed that stomata underwent a process from opening to closing, guard cells from complete to dry, and surrounding leaf cells from smooth to severe shrinkage. The chloroplast ultrastructure showed that the changes of starch granules were different under different drought stress, while plastoglobules increased and expanded continuously. In addition, we found some differentially expressed genes related to photosystem, electron transport component, oxidative phosphate ATPase, stomatal closure, and chloroplast ultrastructure. These results laid a foundation for further genetic improvement and deficit resistance breeding of yellow horn under drought stress.
Collapse
Affiliation(s)
- Fang Hu
- College of Forestry, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Yunxiang Zhang
- College of Forestry, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Jinping Guo
- College of Forestry, Shanxi Agricultural University, Jinzhong, Shanxi, China
| |
Collapse
|
14
|
Xue Z, Gao B, Chen G, Liu J, Ouyang W, Foda MF, Zhang Q, Zhang X, Zhang W, Guo M, Li X, Yi B. Diurnal oscillations of epigenetic modifications are associated with variation in rhythmic expression of homoeologous genes in Brassica napus. BMC Biol 2023; 21:241. [PMID: 37907908 PMCID: PMC10617162 DOI: 10.1186/s12915-023-01735-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 10/12/2023] [Indexed: 11/02/2023] Open
Abstract
BACKGROUND Epigenetic modifications that exhibit circadian oscillations also promote circadian oscillations of gene expression. Brassica napus is a heterozygous polyploid species that has undergone distant hybridization and genome doubling events and has a young and distinct species origin. Studies incorporating circadian rhythm analysis of epigenetic modifications can offer new insights into differences in diurnal oscillation behavior among subgenomes and the regulation of diverse expressions of homologous gene rhythms in biological clocks. RESULTS In this study, we created a high-resolution and multioscillatory gene expression dataset, active histone modification (H3K4me3, H3K9ac), and RNAPII recruitment in Brassica napus. We also conducted the pioneering characterization of the diurnal rhythm of transcription and epigenetic modifications in an allopolyploid species. We compared the evolution of diurnal rhythms between subgenomes and observed that the Cn subgenome had higher diurnal oscillation activity in both transcription and active histone modifications than the An subgenome. Compared to the A subgenome in Brassica rapa, the An subgenome of Brassica napus displayed significant changes in diurnal oscillation characteristics of transcription. Homologous gene pairs exhibited a higher proportion of diurnal oscillation in transcription than subgenome-specific genes, attributed to higher chromatin accessibility and abundance of active epigenetic modification types. We found that the diurnal expression of homologous genes displayed diversity, and the redundancy of the circadian system resulted in extensive changes in the diurnal rhythm characteristics of clock genes after distant hybridization and genome duplication events. Epigenetic modifications influenced the differences in the diurnal rhythm of homologous gene expression, and the diurnal oscillation of homologous gene expression was affected by the combination of multiple histone modifications. CONCLUSIONS Herein, we presented, for the first time, a characterization of the diurnal rhythm characteristics of gene expression and its epigenetic modifications in an allopolyploid species. Our discoveries shed light on the epigenetic factors responsible for the diurnal oscillation activity imbalance between subgenomes and homologous genes' rhythmic expression differences. The comprehensive time-series dataset we generated for gene expression and epigenetic modifications provides a valuable resource for future investigations into the regulatory mechanisms of protein-coding genes in Brassica napus.
Collapse
Affiliation(s)
- Zhifei Xue
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Baibai Gao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Guoting Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Jie Liu
- Lushan Botanical Garden Jiangxi Province and Chinese Academy of Sciences, Jiujiang, 332900, Jiangxi, China
| | - Weizhi Ouyang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Mohamed Frahat Foda
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Department of Biochemistry, Faculty of Agriculture, Benha University, Toukh, 13736, Qalyubiyya, Egypt
| | - Qing Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Xiwen Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Wei Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Mingyue Guo
- College of Informatics, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Xingwang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
- National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
| |
Collapse
|
15
|
Li H, Liu J, Yuan X, Chen X, Cui X. Comparative transcriptome analysis reveals key pathways and regulatory networks in early resistance of Glycine max to soybean mosaic virus. Front Microbiol 2023; 14:1241076. [PMID: 38033585 PMCID: PMC10687721 DOI: 10.3389/fmicb.2023.1241076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 09/22/2023] [Indexed: 12/02/2023] Open
Abstract
As a high-value oilseed crop, soybean [Glycine max (L.) Merr.] is limited by various biotic stresses during its growth and development. Soybean mosaic virus (SMV) is a devastating viral infection of soybean that primarily affects young leaves and causes significant production and economic losses; however, the synergistic molecular mechanisms underlying the soybean response to SMV are largely unknown. Therefore, we performed RNA sequencing on SMV-infected resistant and susceptible soybean lines to determine the molecular mechanism of resistance to SMV. When the clean reads were aligned to the G. max reference genome, a total of 36,260 genes were identified as expressed genes and used for further research. Most of the differentially expressed genes (DEGs) associated with resistance were found to be enriched in plant hormone signal transduction and circadian rhythm according to Kyoto Encyclopedia of Genes and Genomes analysis. In addition to salicylic acid and jasmonic acid, which are well known in plant disease resistance, abscisic acid, indole-3-acetic acid, and cytokinin are also involved in the immune response to SMV in soybean. Most of the Ca2+ signaling related DEGs enriched in plant-pathogen interaction negatively influence SMV resistance. Furthermore, the MAPK cascade was involved in either resistant or susceptible responses to SMV, depending on different downstream proteins. The phytochrome interacting factor-cryptochrome-R protein module and the MEKK3/MKK9/MPK7-WRKY33-CML/CDPK module were found to play essential roles in soybean response to SMV based on protein-protein interaction prediction. Our findings provide general insights into the molecular regulatory networks associated with soybean response to SMV and have the potential to improve legume resistance to viral infection.
Collapse
Affiliation(s)
- Han Li
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Jinyang Liu
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xingxing Yuan
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xin Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xiaoyan Cui
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| |
Collapse
|
16
|
Brooks CJ, Atamian HS, Harmer SL. Multiple light signaling pathways control solar tracking in sunflowers. PLoS Biol 2023; 21:e3002344. [PMID: 37906610 PMCID: PMC10617704 DOI: 10.1371/journal.pbio.3002344] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 09/21/2023] [Indexed: 11/02/2023] Open
Abstract
Sunflowers are famous for their ability to track the sun throughout the day and then reorient at night to face east the following morning. This occurs by differential growth patterns, with the east sides of stems growing more during the day and the west sides of stems growing more at night. This process, termed heliotropism, is generally believed to be a specialized form of phototropism; however, the underlying mechanism is unknown. To better understand heliotropism, we compared gene expression patterns in plants undergoing phototropism in a controlled environment and in plants initiating and maintaining heliotropic growth in the field. We found the expected transcriptome signatures of phototropin-mediated phototropism in sunflower stems bending towards monochromatic blue light. Surprisingly, the expression patterns of these phototropism-regulated genes are quite different in heliotropic plants. Most genes rapidly induced during phototropism display only minor differences in expression across solar tracking stems. However, some genes that are both rapidly induced during phototropism and are implicated in growth responses to foliar shade are rapidly induced on the west sides of stems at the onset of heliotropism, suggesting a possible role for red light photoreceptors in solar tracking. To test the involvement of different photoreceptor signaling pathways in heliotropism, we modulated the light environment of plants initiating solar tracking. We found that depletion of either red and far-red light or blue light did not hinder the initiation or maintenance of heliotropism in the field. Together, our results suggest that the transcriptional regulation of heliotropism is distinct from phototropin-mediated phototropism and likely involves inputs from multiple light signaling pathways.
Collapse
Affiliation(s)
- Christopher J. Brooks
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
| | - Hagop S. Atamian
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
- Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
| | - Stacey L. Harmer
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
| |
Collapse
|
17
|
Prasetyaningrum P, Litthauer S, Vegliani F, Battle MW, Wood MW, Liu X, Dickson C, Jones MA. Inhibition of RNA degradation integrates the metabolic signals induced by osmotic stress into the Arabidopsis circadian system. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5805-5819. [PMID: 37453132 PMCID: PMC10540740 DOI: 10.1093/jxb/erad274] [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: 02/05/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
The circadian clock system acts as an endogenous timing reference that coordinates many metabolic and physiological processes in plants. Previous studies have shown that the application of osmotic stress delays circadian rhythms via 3'-phospho-adenosine 5'-phosphate (PAP), a retrograde signalling metabolite that is produced in response to redox stress within organelles. PAP accumulation leads to the inhibition of exoribonucleases (XRNs), which are responsible for RNA degradation. Interestingly, we are now able to demonstrate that post-transcriptional processing is crucial for the circadian response to osmotic stress. Our data show that osmotic stress increases the stability of specific circadian RNAs, suggesting that RNA metabolism plays a vital role in circadian clock coordination during drought. Inactivation of XRN4 is sufficient to extend circadian rhythms as part of this response, with PRR7 and LWD1 identified as transcripts that are post-transcriptionally regulated to delay circadian progression.
Collapse
Affiliation(s)
| | | | - Franco Vegliani
- School of Molecular Biosciences, University of Glasgow, Glasgow G12 8QQ, UK
| | | | | | - Xinmeng Liu
- School of Molecular Biosciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Cathryn Dickson
- School of Molecular Biosciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Matthew Alan Jones
- School of Molecular Biosciences, University of Glasgow, Glasgow G12 8QQ, UK
| |
Collapse
|
18
|
Zhang Y, Chen G, Deng L, Gao B, Yang J, Ding C, Zhang Q, Ouyang W, Guo M, Wang W, Liu B, Zhang Q, Sung WK, Yan J, Li G, Li X. Integrated 3D genome, epigenome and transcriptome analyses reveal transcriptional coordination of circadian rhythm in rice. Nucleic Acids Res 2023; 51:9001-9018. [PMID: 37572350 PMCID: PMC10516653 DOI: 10.1093/nar/gkad658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 07/11/2023] [Accepted: 08/01/2023] [Indexed: 08/14/2023] Open
Abstract
Photoperiods integrate with the circadian clock to coordinate gene expression rhythms and thus ensure plant fitness to the environment. Genome-wide characterization and comparison of rhythmic genes under different light conditions revealed delayed phase under constant darkness (DD) and reduced amplitude under constant light (LL) in rice. Interestingly, ChIP-seq and RNA-seq profiling of rhythmic genes exhibit synchronous circadian oscillation in H3K9ac modifications at their loci and long non-coding RNAs (lncRNAs) expression at proximal loci. To investigate how gene expression rhythm is regulated in rice, we profiled the open chromatin regions and transcription factor (TF) footprints by time-series ATAC-seq. Although open chromatin regions did not show circadian change, a significant number of TFs were identified to rhythmically associate with chromatin and drive gene expression in a time-dependent manner. Further transcriptional regulatory networks mapping uncovered significant correlation between core clock genes and transcription factors involved in light/temperature signaling. In situ Hi-C of ZT8-specific expressed genes displayed highly connected chromatin association at the same time, whereas this ZT8 chromatin connection network dissociates at ZT20, suggesting the circadian control of gene expression by dynamic spatial chromatin conformation. These findings together implicate the existence of a synchronization mechanism between circadian H3K9ac modifications, chromatin association of TF and gene expression, and provides insights into circadian dynamics of spatial chromatin conformation that associate with gene expression rhythms.
Collapse
Affiliation(s)
- Ying Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Guoting Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Laboratory of Agricultural Bioinformatics, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Li Deng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Baibai Gao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Jing Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Cheng Ding
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Qing Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Weizhi Ouyang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Minrong Guo
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Wenxia Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Beibei Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Qinghua Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Wing-Kin Sung
- Department of Chemical Pathology, Chinese University of Hong Kong, Hong Kong, China
| | - Jiapei Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Laboratory of Agricultural Bioinformatics, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Xingwang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| |
Collapse
|
19
|
Wang X, Hu Y, Wang W. Comparative Analysis of Circadian Transcriptomes Reveals Circadian Characteristics between Arabidopsis and Soybean. PLANTS (BASEL, SWITZERLAND) 2023; 12:3344. [PMID: 37836084 PMCID: PMC10574400 DOI: 10.3390/plants12193344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/11/2023] [Accepted: 09/14/2023] [Indexed: 10/15/2023]
Abstract
The circadian clock, an endogenous timing system, exists in nearly all organisms on Earth. The plant circadian clock has been found to be intricately linked with various essential biological activities. Extensive studies of the plant circadian clock have yielded valuable applications. However, the distinctions of circadian clocks in two important plant species, Arabidopsis thaliana and Glycine max (soybean), remain largely unexplored. This study endeavors to address this gap by conducting a comprehensive comparison of the circadian transcriptome profiles of Arabidopsis and soybean to uncover their distinct circadian characteristics. Utilizing non-linear regression fitting (COS) integrated with weights, we identified circadian rhythmic genes within both organisms. Through an in-depth exploration of circadian parameters, we unveiled notable differences between Arabidopsis and soybean. Furthermore, our analysis of core circadian clock genes shed light on the distinctions in central oscillators between these two species. Additionally, we observed that the homologous genes of Arabidopsis circadian clock genes in soybean exert a significant influence on the regulation of flowering and maturity of soybean. This phenomenon appears to stem from shifts in circadian parameters within soybean genes. These findings highlight contrasting biological activities under circadian regulation in Arabidopsis and soybean. This study not only underscores the distinctive attributes of these species, but also offers valuable insights for further scrutiny into the soybean circadian clock and its potential applications.
Collapse
Affiliation(s)
- Xingwei Wang
- State Key Laboratory for Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; (X.W.); (Y.H.)
- Center for Life Sciences, Beijing 100871, China
| | - Yanfei Hu
- State Key Laboratory for Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; (X.W.); (Y.H.)
- Center for Life Sciences, Beijing 100871, China
| | - Wei Wang
- State Key Laboratory for Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; (X.W.); (Y.H.)
- Center for Life Sciences, Beijing 100871, China
| |
Collapse
|
20
|
June V, Song X, Jeffrey Chen Z. Imprinting but not cytonuclear interactions affects parent-of-origin effect on seed size in Arabidopsis hybrids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.15.557997. [PMID: 37745544 PMCID: PMC10516054 DOI: 10.1101/2023.09.15.557997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The parent-of-origin effect on seed size can result from imprinting or a combinational effect between cytoplasmic and nuclear genomes, but their relative contributions remain unknown. To discern these confounding effects, we generated cytoplasmic-nuclear substitution (CNS) lines using recurrent backcrossing in the Arabidopsis thaliana ecotypes Col-0 and C24. These CNS lines differ only in the nuclear genome (imprinting) or in the cytoplasm. The CNS reciprocal hybrids with the same cytoplasm display a ~20% seed size difference as observed in the conventional hybrids. However, seed size is similar between the reciprocal cybrids with fixed imprinting. Transcriptome analyses in the endosperm of CNS hybrids using laser-capture microdissection have identified 104 maternally expressed genes (MEGs) and 90 paternally-expressed genes (PEGs). These imprinted genes are involved in pectin catabolism and cell wall modification in the endosperm. HDG9, an epiallele and one of 11 cross-specific imprinted genes, controls seed size. In the embryo, a handful of imprinted genes is found in the CNS hybrids but only one is expressed higher in the embryo than endosperm. AT4G13495 encodes a long-noncoding RNA (lncRNA), but no obvious seed phenotype is observed in the lncRNA knockout lines. NRPD1, encoding the largest subunit of RNA Pol IV, is involved in the biogenesis of small interfering RNAs. Seed size and embryo is larger in the cross using nrpd1 as the maternal parent than in the reciprocal cross. In spite of limited ecotypes tested, these results suggest potential roles of imprinting and NRPD1-mediated small RNA pathway in seed size variation in hybrids.
Collapse
Affiliation(s)
- Viviana June
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Xiaoya Song
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Z. Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| |
Collapse
|
21
|
Achary RK, Majee M. CONSTANS, a key-player connecting day length to seed size. TRENDS IN PLANT SCIENCE 2023; 28:975-977. [PMID: 37236861 DOI: 10.1016/j.tplants.2023.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023]
Abstract
Plants sense oscillation in the day length as a reliable seasonal cue to drive optimal vegetative and reproductive growth. A recent study by Yu et al. has revealed how day length regulates seed size through CONSTANS. The CONSTANS-APETALA2 module enables plants to optimize their reproductive growth based on their photoperiod response type.
Collapse
Affiliation(s)
- Rakesh Kumar Achary
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Manoj Majee
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.
| |
Collapse
|
22
|
Lakin-Thomas P. The Case for the Target of Rapamycin Pathway as a Candidate Circadian Oscillator. Int J Mol Sci 2023; 24:13307. [PMID: 37686112 PMCID: PMC10488232 DOI: 10.3390/ijms241713307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
The molecular mechanisms that drive circadian (24 h) rhythmicity have been investigated for many decades, but we still do not have a complete picture of eukaryotic circadian systems. Although the transcription/translation feedback loop (TTFL) model has been the primary focus of research, there are many examples of circadian rhythms that persist when TTFLs are not functioning, and we lack any good candidates for the non-TTFL oscillators driving these rhythms. In this hypothesis-driven review, the author brings together several lines of evidence pointing towards the Target of Rapamycin (TOR) signalling pathway as a good candidate for a non-TTFL oscillator. TOR is a ubiquitous regulator of metabolism in eukaryotes and recent focus in circadian research on connections between metabolism and rhythms makes TOR an attractive candidate oscillator. In this paper, the evidence for a role for TOR in regulating rhythmicity is reviewed, and the advantages of TOR as a potential oscillator are discussed. Evidence for extensive feedback regulation of TOR provides potential mechanisms for a TOR-driven oscillator. Comparison with ultradian yeast metabolic cycles provides an example of a potential TOR-driven self-sustained oscillation. Unanswered questions and problems to be addressed by future research are discussed.
Collapse
|
23
|
Singh V, Singh V. Characterizing the circadian connectome of Ocimum tenuiflorum using an integrated network theoretic framework. Sci Rep 2023; 13:13108. [PMID: 37567911 PMCID: PMC10421869 DOI: 10.1038/s41598-023-40212-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 08/07/2023] [Indexed: 08/13/2023] Open
Abstract
Across the three domains of life, circadian clock is known to regulate vital physiological processes, like, growth, development, defence etc. by anticipating environmental cues. In this work, we report an integrated network theoretic methodology comprising of random walk with restart and graphlet degree vectors to characterize genome wide core circadian clock and clock associated raw candidate proteins in a plant for which protein interaction information is available. As a case study, we have implemented this framework in Ocimum tenuiflorum (Tulsi); one of the most valuable medicinal plants that has been utilized since ancient times in the management of a large number of diseases. For that, 24 core clock (CC) proteins were mined in 56 template plant genomes to build their hidden Markov models (HMMs). These HMMs were then used to identify 24 core clock proteins in O. tenuiflorum. The local topology of the interologous Tulsi protein interaction network was explored to predict the CC associated raw candidate proteins. Statistical and biological significance of the raw candidates was determined using permutation and enrichment tests. A total of 66 putative CC associated proteins were identified and their functional annotation was performed.
Collapse
Affiliation(s)
- Vikram Singh
- Centre for Computational Biology and Bioinformatics, Central University of Himahcal Pradesh, Dharamshala, Himahcal Pradesh, 176206, India
| | - Vikram Singh
- Centre for Computational Biology and Bioinformatics, Central University of Himahcal Pradesh, Dharamshala, Himahcal Pradesh, 176206, India.
| |
Collapse
|
24
|
Agarwal T, Wang X, Mildenhall F, Ibrahim IM, Puthiyaveetil S, Varala K. Chilling stress drives organ-specific transcriptional cascades and dampens diurnal oscillation in tomato. HORTICULTURE RESEARCH 2023; 10:uhad137. [PMID: 37564269 PMCID: PMC10410299 DOI: 10.1093/hr/uhad137] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 07/02/2023] [Indexed: 08/12/2023]
Abstract
Improving chilling tolerance in cold-sensitive crops, e.g. tomato, requires knowledge of the early molecular response to low temperature in these under-studied species. To elucidate early responding processes and regulators, we captured the transcriptional response at 30 minutes and 3 hours in the shoots and at 3 hours in the roots of tomato post-chilling from 24°C to 4°C. We used a pre-treatment control and a concurrent ambient temperature control to reveal that majority of the differential expression between cold and ambient conditions is due to severely compressed oscillation of a large set of diurnally regulated genes in both the shoots and roots. This compression happens within 30 minutes of chilling, lasts for the duration of cold treatment, and is relieved within 3 hours of return to ambient temperatures. Our study also shows that the canonical ICE1/CAMTA-to-CBF cold response pathway is active in the shoots, but not in the roots. Chilling stress induces synthesis of known cryoprotectants (trehalose and polyamines), in a CBF-independent manner, and induction of multiple genes encoding proteins of photosystems I and II. This study provides nuanced insights into the organ-specific response in a chilling sensitive plant, as well as the genes influenced by an interaction of chilling response and the circadian clock.
Collapse
Affiliation(s)
- Tina Agarwal
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Xiaojin Wang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Frederick Mildenhall
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Iskander M Ibrahim
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Sujith Puthiyaveetil
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Kranthi Varala
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| |
Collapse
|
25
|
Sui Y, Guo X, Zhou R, Fu Z, Chai Y, Xia A, Zhao W. Photoenzymatic Decarboxylation to Produce Hydrocarbon Fuels: A Critical Review. Mol Biotechnol 2023:10.1007/s12033-023-00775-2. [PMID: 37349610 DOI: 10.1007/s12033-023-00775-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 05/19/2023] [Indexed: 06/24/2023]
Abstract
Photoenzymatic decarboxylation shows great promise as a pathway for the generation of hydrocarbon fuels. CvFAP, which is derived from Chlorella variabilis NC64A, is a photodecarboxylase capable of converting fatty acids into hydrocarbons. CvFAP is an example of coupling biocatalysis and photocatalysis to produce alkanes. The catalytic process is mild, and it does not yield toxic substances or excess by-products. However, the activity of CvFAP can be readily inhibited by several factors, and further enhancement is required to improve the enzyme yield and stability. In this article, we will examine the latest advancements in CvFAP research, with a particular focus on the enzyme's structural and catalytic mechanism, summarized some limitations in the application of CvFAP, and laboratory-level methods for enhancing enzyme activity and stability. This review can serve as a reference for future large-scale industrial production of hydrocarbon fuels.
Collapse
Affiliation(s)
- Yaqi Sui
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Xiaobo Guo
- School of Energy and Power Engineering, Chongqing University, Chongqing, 400044, China
| | - Rui Zhou
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Zhisong Fu
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Yingxin Chai
- School of Energy and Power Engineering, Chongqing University, Chongqing, 400044, China
| | - Ao Xia
- School of Energy and Power Engineering, Chongqing University, Chongqing, 400044, China
| | - Wenhui Zhao
- School of Life Sciences, Chongqing University, Chongqing, 401331, China.
| |
Collapse
|
26
|
Heyder K, Neinhuis C, Lautenschläger T. Morphology, anatomy and sleep movements of Ludwigia sedoides. THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 2023; 110:18. [PMID: 37188787 DOI: 10.1007/s00114-023-01848-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 05/01/2023] [Accepted: 05/02/2023] [Indexed: 05/17/2023]
Abstract
The diurnal motion of higher plants, responding to the alternation of day and night, known as nyctinastic movements or "sleep movements", has been discussed frequently. We present the first description of the circadian rhythm of the water plant Ludwigia sedoides (Humb. & Bonpl.) H.Hara of the family Onagraceae, furthermore its morphology and anatomy. Our results indicate that the plant's movements are endogenous, although environmental factors certainly have an influence. The majority of plants with nyctinastic leaf movements have a pulvinus, as the crucial part of the plant enabling this movement. Although the basal section of the L. sedoides petiole is not swollen, the tissue functions similarly to a pulvinus. It consists of a central conducting tissue with thick-walled cells, which is surrounded by thin-walled motor cells that can undergo visible shrinking and swelling. Thus, the tissue functionally corresponds to a pulvinus. Examinations of cellular processes, like measurements of the turgor pressure in the petiole, need to be evaluated in future studies.
Collapse
Affiliation(s)
- Katharina Heyder
- Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | | | | |
Collapse
|
27
|
Xu H, Wang X, Wei J, Zuo Y, Wang L. The Regulatory Networks of the Circadian Clock Involved in Plant Adaptation and Crop Yield. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091897. [PMID: 37176955 PMCID: PMC10181312 DOI: 10.3390/plants12091897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023]
Abstract
Global climatic change increasingly threatens plant adaptation and crop yields. By synchronizing internal biological processes, including photosynthesis, metabolism, and responses to biotic and abiotic stress, with external environmental cures, such as light and temperature, the circadian clock benefits plant adaptation and crop yield. In this review, we focus on the multiple levels of interaction between the plant circadian clock and environmental factors, and we summarize recent progresses on how the circadian clock affects yield. In addition, we propose potential strategies for better utilizing the current knowledge of circadian biology in crop production in the future.
Collapse
Affiliation(s)
- Hang Xu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiling Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Wei
- College of Life Sciences, Changchun Normal University, Changchun 130032, China
| | - Yi Zuo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Lei Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
28
|
Karapetyan S, Mwimba M, Dong X. Circadian redox rhythm gates immune-induced cell death distinctly from the genetic clock. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.21.535069. [PMID: 37131835 PMCID: PMC10153234 DOI: 10.1101/2023.04.21.535069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Organisms use circadian clocks to synchronize physiological processes to anticipate the Earth’s day-night cycles and regulate responses to environmental stresses to gain competitive advantage 1 . While divergent genetic clocks have been studied extensively in bacteria, fungi, plants, and animals, a conserved circadian redox rhythm has only recently been reported and hypothesized to be a more ancient clock 2, 3 . However, it is controversial whether the redox rhythm serves as an independent clock and controls specific biological processes 4 . Here, we uncovered the coexistence of redox and genetic rhythms with distinct period lengths and transcriptional targets through concurrent metabolic and transcriptional time-course measurements in an Arabidopsis long-period clock mutant 5 . Analysis of the target genes indicated regulation of the immune-induced programmed cell death (PCD) by the redox rhythm. Moreover, this time-of-day-sensitive PCD was eliminated by redox perturbation and by blocking the signalling pathway of the plant defence hormones jasmonic acid/ethylene, while remaining intact in a genetic-clock-impaired line. We demonstrate that compared to robust genetic clocks, the more sensitive circadian redox rhythm serves as a signalling hub in regulating incidental energy-intensive processes, such as immune-induced PCD 6 , to provide organisms a flexible strategy to prevent metabolic overload caused by stress, a unique role for the redox oscillator.
Collapse
|
29
|
Sorkin ML, Tzeng SC, King S, Romanowski A, Kahle N, Bindbeutel R, Hiltbrunner A, Yanovsky MJ, Evans BS, Nusinow DA. COLD REGULATED GENE 27 and 28 Antagonize the Transcriptional Activity of the RVE8/LNK1/LNK2 Circadian Complex. PLANT PHYSIOLOGY 2023:kiad210. [PMID: 37017001 DOI: 10.1093/plphys/kiad210] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 03/01/2023] [Accepted: 04/04/2023] [Indexed: 06/19/2023]
Abstract
Many molecular and physiological processes in plants occur at a specific time of day. These daily rhythms are coordinated in part by the circadian clock, a timekeeper that uses daylength and temperature to maintain rhythms of approximately 24 hours in various clock-regulated phenotypes. The circadian MYB-like transcription factor REVEILLE 8 (RVE8) interacts with its transcriptional coactivators NIGHT LIGHT INDUCIBLE AND CLOCK REGULATED 1 (LNK1) and LNK2 to promote the expression of evening-phased clock genes and cold tolerance factors. While genetic approaches have commonly been used to discover connections within the clock and between clock elements and other pathways, here we used affinity purification coupled with mass spectrometry to identify time-of-day-specific protein interactors of the RVE8-LNK1/LNK2 complex in Arabidopsis (Arabidopsis thaliana). Among the interactors of RVE8/LNK1/LNK2 were COLD REGULATED GENE 27 (COR27) and COR28, which coprecipitated in an evening-specific manner. In addition to COR27 and COR28, we found an enrichment of temperature-related interactors that led us to establish a previously uncharacterized role for LNK1 and LNK2 in temperature entrainment of the clock. We established that RVE8, LNK1, and either COR27 or COR28 form a tripartite complex in yeast (Saccharomyces cerevisiae) and that the effect of this interaction in planta serves to antagonize transcriptional activation of RVE8 target genes, potentially through mediating RVE8 protein degradation in the evening. Together, these results illustrate how a proteomic approach can be used to identify time-of-day-specific protein interactions. Discovery of the RVE8-LNK-COR protein complex indicates a previously unknown regulatory mechanism for circadian and temperature signaling pathways.
Collapse
Affiliation(s)
- Maria L Sorkin
- Donald Danforth Plant Science Center, St. Louis, MO, USA
- Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO, USA
| | | | - Stefanie King
- Donald Danforth Plant Science Center, St. Louis, MO, USA
- Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO, USA
| | - Andrés Romanowski
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Nikolai Kahle
- Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | | | - Andreas Hiltbrunner
- Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Marcelo J Yanovsky
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | | | | |
Collapse
|
30
|
Huang P, Ding Z, Duan M, Xiong Y, Li X, Yuan X, Huang J. OsLUX Confers Rice Cold Tolerance as a Positive Regulatory Factor. Int J Mol Sci 2023; 24:ijms24076727. [PMID: 37047700 PMCID: PMC10094877 DOI: 10.3390/ijms24076727] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 03/26/2023] [Accepted: 03/28/2023] [Indexed: 04/07/2023] Open
Abstract
During the early seedling stage, rice (Oryza sativa L.) must overcome low-temperature stress. While a few cold-tolerance genes have been characterized, further excavation of cold-resistance genes is still needed. In this study, we identified a cold-induced transcription factor—LUX ARRHYTHMO (LUX)—in rice. OsLUX was found to be specifically expressed in leaf blades and upregulated by both cold stress and circadian rhythm. The full-length OsLUX showed autoactivation activity, and the OsLUX protein localized throughout the entire onion cell. Overexpressing OsLUX resulted in increased cold tolerance and reduced ion leakage under cold-stress conditions during the seedling stage. In contrast, the knockout of OsLUX decreased seedling cold tolerance and showed higher ion leakage compared to the wild type. Furthermore, overexpressing OsLUX upregulated the expression levels of oxidative stress-responsive genes, which improved reactive oxygen species (ROS) scavenging ability and enhanced tolerance to chilling stress. Promoter analysis showed that the OsLUX promoter contains two dehydration-responsive element binding (DREB) motifs at positions −510/−505 (GTCGGa) and −162/−170 (cCACCGccc), which indicated that OsDREB1s and OsDREB2s probably regulate OsLUX expression by binding to the motif to respond to cold stress. Thus, OsLUX may act as a downstream gene of the DREB pathway. These results demonstrate that OsLUX serves as a positive regulatory factor of cold stress and that overexpressing OsLUX could be used in rice breeding programs to enhance abiotic stress tolerance.
Collapse
Affiliation(s)
- Peng Huang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Zhengquan Ding
- Jiaxing Academy of Agricultural Sciences, Jiaxing 314016, China
| | - Min Duan
- Taizhou Academy Agricultural of Sciences, Taizhou 317000, China
| | - Yi Xiong
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Xinxin Li
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Xi Yuan
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Ji Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| |
Collapse
|
31
|
Chen K, Su X, Yang H, Peng Y, Wu L, Zhao Z, Lin T, Bai L, Wang L. Multi-omics analyses reveal the crosstalk between the circadian clock and the response to herbicide application in Oryza sativa. FRONTIERS IN PLANT SCIENCE 2023; 14:1155258. [PMID: 37035069 PMCID: PMC10080033 DOI: 10.3389/fpls.2023.1155258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/13/2023] [Indexed: 06/19/2023]
Abstract
Plants have evolved circadian clock systems that enable biological processes to occur in tandem with periodic changes in the environment. However, it is largely unknown whether crosstalk occurs between the circadian clock and the response to herbicide in rice. We identified 19 conserved rhythmic metabolites which were response to pesticide application and their metabolic abundance peaked mainly at ZT2 or ZT14-ZT18. We found a series of glyphosate, s-Metolachlor, fenclorim, metcamifen and GA3 response genes were expressed following stable circadian rhythms. In order to determine the patterns of their temporal expression, co-expression network analysis was done on 10,467 genes that were periodically expressed throughout a 24-hour period. Next, we identified 4,031 potential direct target genes of OsCCA1 in using DAP-seq data for OsCCA1. Of these, 339, 22, 53, 53 and 63 genes showed a response to glyphosate, s-Metolachlor, fenclorim, metcamifen and GA3 application, respectively. And they were mainly phased from dusk to midnight. Interestingly, we identified significant OsCCA1 binding peaks in the promoter regions of four herbicide resistance genes, including OsCYP81A12, OsCYP81E22, OsCYP76C2, and OsCYP76C4. Finally, we found that herbicide application could affects the expression of some of the central oscillator genes of the rice circadian clock. Here, we used multi-omics data to reveal the crosstalk between the circadian clock and herbicide response processes at the epigenomics, transcriptome, and metabolome levels in rice. This work will serve as a theoretical guide for identifying rhythmic herbicide targets, leading to the creation of new herbicides or the breeding of crops resistant to herbicides.
Collapse
Affiliation(s)
- Ke Chen
- Longping Branch, College of Biology, Hunan University, Changsha, China
- Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture and Rural Affairs, Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
- Huangpu Research Institute of Longping Agricultural Science and Technology, Guangzhou, China
| | - Xiao Su
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, China
| | - Haona Yang
- Longping Branch, College of Biology, Hunan University, Changsha, China
- Huangpu Research Institute of Longping Agricultural Science and Technology, Guangzhou, China
| | - Yajun Peng
- Longping Branch, College of Biology, Hunan University, Changsha, China
- Huangpu Research Institute of Longping Agricultural Science and Technology, Guangzhou, China
| | - Lamei Wu
- Longping Branch, College of Biology, Hunan University, Changsha, China
- Huangpu Research Institute of Longping Agricultural Science and Technology, Guangzhou, China
| | - Zhenghong Zhao
- Longping Branch, College of Biology, Hunan University, Changsha, China
- Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture and Rural Affairs, Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
- Huangpu Research Institute of Longping Agricultural Science and Technology, Guangzhou, China
| | - Tao Lin
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, China
| | - Lianyang Bai
- Longping Branch, College of Biology, Hunan University, Changsha, China
- Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture and Rural Affairs, Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
- Huangpu Research Institute of Longping Agricultural Science and Technology, Guangzhou, China
| | - Lifeng Wang
- Longping Branch, College of Biology, Hunan University, Changsha, China
- Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture and Rural Affairs, Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
- Huangpu Research Institute of Longping Agricultural Science and Technology, Guangzhou, China
| |
Collapse
|
32
|
Martínez-Vasallo C, Cole B, Gallego-Bartolomé J, Chory J, Kay SA, Nohales MA. Epidermal GIGANTEA adjusts the response to shade at dusk by directly impinging on PHYTOCHROME INTERACTING FACTOR 7 function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.21.533699. [PMID: 36993677 PMCID: PMC10055326 DOI: 10.1101/2023.03.21.533699] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
For plants adapted to bright light, a decrease in the amount of light received can be detrimental to their growth and survival. Consequently, in response to shade from surrounding vegetation, they initiate a suite of molecular and morphological changes known as the shade avoidance response (SAR) through which stems and petioles elongate in search for light. Under sunlight-night cycles, the plant's responsiveness to shade varies across the day, being maximal at dusk time. While a role for the circadian clock in this regulation has long been proposed, mechanistic understanding of how it is achieved is incomplete. Here we show that the clock component GIGANTEA (GI) directly interacts with the transcriptional regulator PHYTOCHROME INTERACTING FACTOR 7 (PIF7), a key player in the response to shade. GI represses PIF7 transcriptional activity and the expression of its target genes in response to shade, thereby fine-tuning the magnitude of the response to limiting light conditions. We find that, under light/dark cycles, this function of GI is required to adequately modulate the gating of the response to shade at dusk. Importantly, we also show that GI expression in epidermal cells is sufficient for proper SAR regulation.
Collapse
Affiliation(s)
- Carlos Martínez-Vasallo
- Instituto de Biologίa Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientίficas - Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Benjamin Cole
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Javier Gallego-Bartolomé
- Plant Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Joanne Chory
- Plant Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Steve A. Kay
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Maria A. Nohales
- Instituto de Biologίa Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientίficas - Universidad Politécnica de Valencia, 46022 Valencia, Spain
| |
Collapse
|
33
|
Guo L, Xu Z, Wang S, Nie Y, Ye X, Jin X, Zhu J, Wu W. Integrative multi-omics analysis of three early diverged rosid species reveals an ancient hierarchical cold-responsive regulatory network. PHYSIOLOGIA PLANTARUM 2023; 175:e13892. [PMID: 36929522 DOI: 10.1111/ppl.13892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/06/2023] [Accepted: 03/13/2023] [Indexed: 06/18/2023]
Abstract
Elucidating regulators, including transcription factors (TFs) and RNA-binding proteins (RBPs), underlying gene transcriptional and post-transcriptional co-regulatory network is key to understand plant cold responses. Previous studies were mainly conducted on single species, and whether the regulators are conserved across different species remains elusive. Here, we selected three species that diverged at the early evolution of rosids (~99-113 million years ago), performed cold-responsive phylotranscriptome experiments, and integrated chromatin immunoprecipitation- and DNA affinity purification-sequencing (ChIP/DAP-seq) analysis to explore cold-responsive regulators and their regulatory networks. First, we detected over 10,000 cold-induced differentially expressed genes (DEGs) and alternative splicing genes (DASGs) in each species. Among the DEGs, a set of TFs and RBPs were conserved in rosid cold response. Compared to TFs, RBPs displayed a delayed cold-responsive pattern, implying a hierarchical regulation of DEGs and DASGs. By integrating DEGs and DASGs, we identified 259 overlapping DE-DASG orthogroups (closely-related homologs) that were cold-regulated at both transcriptional and post-transcriptional levels in all three studied species. Notably, pathway analysis on each of the DEGs, DASGs, and DE-DASGs in the three species showed a common enrichment connected to the circadian rhythm. Evidently, 226 cold-responsive genes were directly targeted by at least two circadian rhythm components (CCA1, LHY, RV4, RVE7, and RVE8). Finally, we revealed an ancient hierarchy of cold-responsive regulatory networks at transcriptional and post-transcriptional levels launched by circadian components in rosids. Altogether, this study sheds light on conserved regulators underlying cold-responsive regulatory networks across rosid species, despite a long evolutionary history after their divergence.
Collapse
Affiliation(s)
- Liangyu Guo
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Zhiming Xu
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Shuo Wang
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Yuqi Nie
- Université Paris Saclay, GQE-Le Moulon, Gif-sur-Yvette, 91190, France
| | - Xiaoxue Ye
- Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Yumin Road 7, Sanya, 572025, China
| | - Xuejiao Jin
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Jianhua Zhu
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland, 20742, USA
| | - Wenwu Wu
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| |
Collapse
|
34
|
Liu Z, Liu W, Wang Z, Qi K, Xie Z, Zhang S, Wu J, Wang P. Diurnal transcriptome dynamics reveal the photoperiod response of Pyrus. PHYSIOLOGIA PLANTARUM 2023; 175:e13893. [PMID: 36929905 DOI: 10.1111/ppl.13893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 02/15/2023] [Accepted: 03/14/2023] [Indexed: 06/18/2023]
Abstract
Photoperiod provides a key environmental signal that controls plant growth. Plants have evolved an integrated mechanism for sensing photoperiods with internal clocks to orchestrate physiological events. This mechanism has been identified to enable timely plant growth and improve fitness. Although the components and pathways underlying photoperiod regulation have been described in many species, diurnal patterns of gene expression at the genome-wide level under different photoperiods are rarely reported in perennial fruit trees. To explore the global gene expression in response to photoperiod, pear plants were cultured under long-day (LD) and short-day (SD) conditions. A time-series transcriptomic study was implemented using LD and SD samples collected at 4 h intervals over 2 days. We identified 13,677 rhythmic genes, of which 7639 were identified under LD and 10,557 under SD conditions. Additionally, 4674 genes were differentially expressed in response to photoperiod change. We also characterized the candidate homologs of clock-associated genes in pear. Clock genes were involved in the regulation of many processes throughout the day, including photosynthesis, stress response, hormone dynamics, and secondary metabolism. Strikingly, genes within photosynthesis-related pathways were enriched in both the rhythmic and differential expression analyses. Several key candidate genes were identified to be associated with regulating photosynthesis and improving productivity under different photoperiods. The results suggest that temporal variation in gene expression should not be ignored in pear gene function research. Overall, our work expands the understanding of photoperiod regulation of plant growth, particularly by extending the research to non-model trees.
Collapse
Affiliation(s)
- Zhe Liu
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
- Department of Pharmacy, Changzhi Medical College, Changzhi, 046000, China
| | - Weijuan Liu
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Zhangqing Wang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Kaijie Qi
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Zhihua Xie
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Shaoling Zhang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Juyou Wu
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Peng Wang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
| |
Collapse
|
35
|
Microhabitat-specific diurnal metabolomic responses of the intertidal limpet Cellana toreuma to winter low temperature. iScience 2023; 26:106128. [PMID: 36852273 PMCID: PMC9958412 DOI: 10.1016/j.isci.2023.106128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/02/2022] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
High-throughput determination of circadian rhythms in metabolic response and their divergent patterns in various microhabitats are crucial for understanding how organisms respond to environmental stresses. A mid-intertidal limpet Cellana toreuma was collected at various time points across both daytime and nighttime in winter during low tide for investigating the diurnal metabolomic responses to cold stress and elucidating the divergent metabolic responses to temperature variations across microhabitats. Temperatures of emergent rock microhabitats were lower than the tidal pool and even aggravated at night. A series of metabolomic responses exhibited coordinated diurnal changes in winter. Metabolic responses which were associated with cellular stress responses and energy metabolism of emergent rock microhabitat individuals were highly induced compared to the tidal pool ones. This study shed light on the diurnal patterns of metabolomic responses of intertidal molluscs in the field and emphasized the variations in metabolic responses between microhabitats.
Collapse
|
36
|
Zhao H, Chen Y, Liu J, Wang Z, Li F, Ge X. Recent advances and future perspectives in early-maturing cotton research. THE NEW PHYTOLOGIST 2023; 237:1100-1114. [PMID: 36352520 DOI: 10.1111/nph.18611] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Cotton's fundamental requirements for long periods of growth and specific seasonal temperatures limit the global arable areas that can be utilized to cultivate cotton. This constraint can be alleviated by breeding for early-maturing varieties. By delaying the sowing dates without impacting the boll-opening time, early-maturing varieties not only mitigate the yield losses brought on by unfavorable weathers in early spring and late autumn but also help reducing the competition between cotton and other crops for arable land, thereby optimizing the cropping system. This review presents studies and breeding efforts for early-maturing cotton, which efficiently pyramid early maturity, high-quality, multiresistance traits, and suitable plant architecture by leveraging pleiotropic genes. Attempts are also made to summarize our current understanding of the molecular mechanisms underlying early maturation, which involves many pathways such as epigenetic, circadian clock, and hormone signaling pathways. Moreover, new avenues and effective measures are proposed for fine-scale breeding of early-maturing crops to ensure the healthy development of the agricultural industry.
Collapse
Affiliation(s)
- Hang Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- College of Life Sciences, Qufu Normal University, Qufu, 273165, China
| | - Yanli Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Ji Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Hainan Yazhou Bay Seed Lab, Sanya, 572000, Hainan, China
| | - Zhi Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Sanya Institute, Zhengzhou University, Sanya, 572000, Hainan, China
| | - Fuguang Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Hainan Yazhou Bay Seed Lab, Sanya, 572000, Hainan, China
| | - Xiaoyang Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| |
Collapse
|
37
|
Yu B, He X, Tang Y, Chen Z, Zhou L, Li X, Zhang C, Huang X, Yang Y, Zhang W, Kong F, Miao Y, Hou X, Hu Y. Photoperiod controls plant seed size in a CONSTANS-dependent manner. NATURE PLANTS 2023; 9:343-354. [PMID: 36747051 DOI: 10.1038/s41477-023-01350-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 01/11/2023] [Indexed: 06/18/2023]
Abstract
Photoperiodic plants perceive changes in day length as seasonal cues to orchestrate their vegetative and reproductive growth. Although it is known that the floral transition of photoperiod-sensitive plants is tightly controlled by day length, how photoperiod affects their post-flowering development remains to be clearly defined, as do the underlying mechanisms. Here we demonstrate that photoperiod plays a prominent role in seed development. We found that long-day (LD) and short-day (SD) plants produce larger seeds under LD and SD conditions, respectively; however, seed size remains unchanged when CONSTANS (CO), the central regulatory gene of the photoperiodic response pathway, is mutated in Arabidopsis and soybean. We further found that CO directly represses the transcription of AP2 (a known regulatory gene of seed development) under LD conditions in Arabidopsis and SD conditions in soybean, thereby controlling seed size in a photoperiod-dependent manner, and that these effects are exerted through regulation of the proliferation of seed coat epidermal cells. Collectively, our findings reveal that a crucial regulatory cascade involving CO-AP2 modulates photoperiod-mediated seed development in plants and provide new insights into how plants with different photoperiod response types perceive seasonal changes that enable them to optimize their reproductive growth.
Collapse
Affiliation(s)
- Bin Yu
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Xuemei He
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Yang Tang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Zhonghui Chen
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Limeng Zhou
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Xiaoming Li
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Chunyu Zhang
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Xiang Huang
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Yuhua Yang
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Wenbin Zhang
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Fanjiang Kong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Yansong Miao
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Xingliang Hou
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
- University of the Chinese Academy of Sciences, Beijing, China.
| | - Yilong Hu
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
- University of the Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
38
|
Liu Z, Zhu X, Liu W, Qi K, Xie Z, Zhang S, Wu J, Wang P. Characterization of the REVEILLE family in Rosaceae and role of PbLHY in flowering time regulation. BMC Genomics 2023; 24:49. [PMID: 36707756 PMCID: PMC9883883 DOI: 10.1186/s12864-023-09144-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 01/19/2023] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND The circadian clock integrates endogenous and exogenous signals and regulates various physiological processes in plants. REVEILLE (RVE) proteins play critical roles in circadian clock system, especially CCA1 (CIRCADIAN CLOCK ASSOCIATED 1) and LHY (LATE ELONGATED HYPOCOTYL), which also participate in flowering regulation. However, little is known about the evolution and function of the RVE family in Rosaceae species, especially in Pyrus bretschneideri. RESULTS In this study, we performed a genome-wide analysis and identified 51 RVE genes in seven Rosaceae species. The RVE family members were classified into two groups based on phylogenetic analysis. Dispersed duplication events and purifying selection were the main drivers of evolution in the RVE family. Moreover, the expression patterns of ten PbRVE genes were diverse in P. bretschneideri tissues. All PbRVE genes showed diurnal rhythms under light/dark cycles in P. bretschneideri leaves. Four PbRVE genes also displayed robust rhythms under constant light conditions. PbLHY, the gene with the highest homology to AtCCA1 and AtLHY in P. bretschneideri, is localized in the nucleus. Ectopic overexpression of PbLHY in Arabidopsis delayed flowering time and repressed the expression of flowering time-related genes. CONCLUSION These results contribute to improving the understanding and functional research of RVE genes in P. bretschneideri.
Collapse
Affiliation(s)
- Zhe Liu
- grid.254020.10000 0004 1798 4253Department of Pharmacy, Changzhi Medical College, Changzhi, 046000 China ,grid.27871.3b0000 0000 9750 7019Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China ,Shanxi Province Key Laboratory of Functional Food with Homologous of Medicine and Food, Changzhi, China
| | - Xiaoxuan Zhu
- grid.27871.3b0000 0000 9750 7019Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Weijuan Liu
- grid.27871.3b0000 0000 9750 7019Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Kaijie Qi
- grid.27871.3b0000 0000 9750 7019Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Zhihua Xie
- grid.27871.3b0000 0000 9750 7019Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Shaoling Zhang
- grid.27871.3b0000 0000 9750 7019Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Juyou Wu
- grid.27871.3b0000 0000 9750 7019Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China ,Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, China
| | - Peng Wang
- grid.27871.3b0000 0000 9750 7019Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| |
Collapse
|
39
|
Marshall CM, Thompson VL, Creux NM, Harmer SL. The circadian clock controls temporal and spatial patterns of floral development in sunflower. eLife 2023; 12:80984. [PMID: 36637156 PMCID: PMC9977281 DOI: 10.7554/elife.80984] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 01/12/2023] [Indexed: 01/14/2023] Open
Abstract
Biological rhythms are ubiquitous. They can be generated by circadian oscillators, which produce daily rhythms in physiology and behavior, as well as by developmental oscillators such as the segmentation clock, which periodically produces modular developmental units. Here, we show that the circadian clock controls the timing of late-stage floret development, or anthesis, in domesticated sunflowers. In these plants, up to thousands of individual florets are tightly packed onto a capitulum disk. While early floret development occurs continuously across capitula to generate iconic spiral phyllotaxy, during anthesis floret development occurs in discrete ring-like pseudowhorls with up to hundreds of florets undergoing simultaneous maturation. We demonstrate circadian regulation of floral organ growth and show that the effects of light on this process are time-of-day dependent. Delays in the phase of floral anthesis delay morning visits by pollinators, while disruption of circadian rhythms in floral organ development causes loss of pseudowhorl formation and large reductions in pollinator visits. We therefore show that the sunflower circadian clock acts in concert with environmental response pathways to tightly synchronize the anthesis of hundreds of florets each day, generating spatial patterns on the developing capitulum disk. This coordinated mass release of floral rewards at predictable times of day likely promotes pollinator visits and plant reproductive success.
Collapse
Affiliation(s)
- Carine M Marshall
- Department of Plant Biology, University of California, DavisDavisUnited States
| | - Veronica L Thompson
- Department of Plant Biology, University of California, DavisDavisUnited States
| | - Nicky M Creux
- Department of Plant Biology, University of California, DavisDavisUnited States
- Department of Plant and Soil Sciences, FABI, Innovation Africa, University of PretoriaPretoriaSouth Africa
| | - Stacey L Harmer
- Department of Plant Biology, University of California, DavisDavisUnited States
| |
Collapse
|
40
|
Park HJ, Gámez-Arjona FM, Lindahl M, Aman R, Villalta I, Cha JY, Carranco R, Lim CJ, García E, Bressan RA, Lee SY, Valverde F, Sánchez-Rodríguez C, Pardo JM, Kim WY, Quintero FJ, Yun DJ. S-acylated and nucleus-localized SALT OVERLY SENSITIVE3/CALCINEURIN B-LIKE4 stabilizes GIGANTEA to regulate Arabidopsis flowering time under salt stress. THE PLANT CELL 2023; 35:298-317. [PMID: 36135824 PMCID: PMC9806564 DOI: 10.1093/plcell/koac289] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 09/16/2022] [Indexed: 05/15/2023]
Abstract
The precise timing of flowering in adverse environments is critical for plants to secure reproductive success. We report a mechanism in Arabidopsis (Arabidopsis thaliana) controlling the time of flowering by which the S-acylation-dependent nuclear import of the protein SALT OVERLY SENSITIVE3/CALCINEURIN B-LIKE4 (SOS3/CBL4), a Ca2+-signaling intermediary in the plant response to salinity, results in the selective stabilization of the flowering time regulator GIGANTEA inside the nucleus under salt stress, while degradation of GIGANTEA in the cytosol releases the protein kinase SOS2 to achieve salt tolerance. S-acylation of SOS3 was critical for its nuclear localization and the promotion of flowering, but partly dispensable for salt tolerance. SOS3 interacted with the photoperiodic flowering components GIGANTEA and FLAVIN-BINDING, KELCH REPEAT, F-BOX1 and participated in the transcriptional complex that regulates CONSTANS to sustain the transcription of CO and FLOWERING LOCUS T under salinity. Thus, the SOS3 protein acts as a Ca2+- and S-acylation-dependent versatile regulator that fine-tunes flowering time in a saline environment through the shared spatial separation and selective stabilization of GIGANTEA, thereby connecting two signaling networks to co-regulate the stress response and the time of flowering.
Collapse
Affiliation(s)
| | | | - Marika Lindahl
- Institute of Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Cientificas and Universidad de Sevilla, Seville 41092, Spain
| | - Rashid Aman
- Division of Applied Life Science (BK21plus Program), Research Institute of Life Sciences, Plant Molecular Biology and Biotechnology Research Center, Graduate School of Gyeongsang National University, Jinju 52828, South Korea
| | - Irene Villalta
- Institut de Recherche sur la Biologie de l’Insecte, Université de Tours, 37200 Tours, France
| | - Joon-Yung Cha
- Division of Applied Life Science (BK21plus Program), Research Institute of Life Sciences, Plant Molecular Biology and Biotechnology Research Center, Graduate School of Gyeongsang National University, Jinju 52828, South Korea
| | - Raul Carranco
- Institute of Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Cientificas and Universidad de Sevilla, Seville 41092, Spain
| | - Chae Jin Lim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, South Korea
| | - Elena García
- Institute of Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Cientificas and Universidad de Sevilla, Seville 41092, Spain
| | - Ray A Bressan
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907, USA
| | - Sang Yeol Lee
- Division of Applied Life Science (BK21plus Program), Research Institute of Life Sciences, Plant Molecular Biology and Biotechnology Research Center, Graduate School of Gyeongsang National University, Jinju 52828, South Korea
| | - Federico Valverde
- Institute of Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Cientificas and Universidad de Sevilla, Seville 41092, Spain
| | | | - Jose M Pardo
- Institute of Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Cientificas and Universidad de Sevilla, Seville 41092, Spain
| | - Woe-Yeon Kim
- Author for correspondence: (D.-J.Y.); (F.J.Q.); (W.-Y.K.)
| | | | - Dae-Jin Yun
- Author for correspondence: (D.-J.Y.); (F.J.Q.); (W.-Y.K.)
| |
Collapse
|
41
|
Qiu Z, Zhuang K, Liu Y, Ge X, Chen C, Hu S, Han H. Functional characterization of C-TERMINALLY ENCODED PEPTIDE (CEP) family in Brassica rapa L. PLANT SIGNALING & BEHAVIOR 2022; 17:2021365. [PMID: 34968412 PMCID: PMC8920145 DOI: 10.1080/15592324.2021.2021365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/16/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
The small regulatory C-TERMINALLY ENCODED PEPTIDE (CEP) peptide family plays crucial roles in plant growth and stress response. However, little is known about this peptide family in Brassica species. Here, we performed a systematic analysis to identify the putative Brassica rapa L. CEP (BrCEP) gene family. In total, 27 BrCEP genes were identified and they were classified into four subgroups based on the CEP motifs similarity. BrCEP genes displayed distinct expression patterns in response to both developmental and several environmental signals, suggesting their broad roles during Brassica rapa development. Furthuremore, the synthetic BrCEP3 peptide accelerated Brassica rapa primary root growth in a hydrogen peroxide (H2O2) and Ca2+ dependent manner. In summary, our work will provide fundamental insights into the physiological function of CEP peptides during Brassica rapa development.
Collapse
Affiliation(s)
- Ziwen Qiu
- Research Center for Plant Functional Genes and Tissue Culture Technology; College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, China
| | - Keqing Zhuang
- Research Center for Plant Functional Genes and Tissue Culture Technology; College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, China
| | - Yiting Liu
- Research Center for Plant Functional Genes and Tissue Culture Technology; College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, China
| | - Xiaomin Ge
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi’an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, Xi’an City, Shaanxi Province, China
| | - Chen Chen
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi’an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, Xi’an City, Shaanxi Province, China
| | - Songping Hu
- Research Center for Plant Functional Genes and Tissue Culture Technology; College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, China
| | - Huibin Han
- Research Center for Plant Functional Genes and Tissue Culture Technology; College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, China
| |
Collapse
|
42
|
Hussain Q, Zheng M, Hänninen H, Bhalerao RP, Riaz MW, Sajjad M, Zhang R, Wu J. Effect of the photoperiod on bud dormancy in Liriodendron chinense. JOURNAL OF PLANT PHYSIOLOGY 2022; 279:153835. [PMID: 36257086 DOI: 10.1016/j.jplph.2022.153835] [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: 07/10/2022] [Revised: 09/27/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Bud dormancy and its release are complex physiological phenomena in plants. The molecular mechanisms of bud dormancy in Liriodendron chinense are mainly unknown. Here, we studied bud dormancy and the related physiological and molecular phenomena in Liriodendron under long-day (LD) and short-day (SD). Bud burst was released faster under LD than under SD. Abscisic acid (ABA), superoxide dismutase (SOD), catalase (CAT), and glutathione reductase (GR) activities were increased significantly under LD in Liriodendron buds. In contrast, the contents of gibberellic acid (GA3), ascorbic acid (AsA), glutathione (GSH), malondialdehyde (MDA), and ascorbate peroxidase (APX) activity decreased under LD but increased under SD. Differentially expressed genes (DEGs) were up-regulated under LD and down-regulated under SD and these changes correspondingly promoted (LD) or repressed (SD) cell division and the number and/or size of cells in the bud. Transcriptomic analysis of Liriodendron buds under different photoperiods identified 187 DEGs enriched in several pathways such as flavonoid biosynthesis and phenylpropanoid biosynthesis, plant hormone and signal transduction, etc. that are associated with antioxidant enzymes, non-enzymatic antioxidants, and subsequently promote the growth of the buds. Our findings provide novel insights into regulating bud dormancy via flavonoid and phenylpropanoid biosynthesis, plant hormone and signal transduction pathways, and ABA content. These physiological and biochemical traits would help detect bud dormancy in plants.
Collapse
Affiliation(s)
- Quaid Hussain
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Hangzhou, 311300, China; Key Laboratory of Modern Silvicultural Technology of Zhejiang Province, Hangzhou, 311300, China
| | - Manjia Zheng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Hangzhou, 311300, China; Key Laboratory of Modern Silvicultural Technology of Zhejiang Province, Hangzhou, 311300, China
| | - Heikki Hänninen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Hangzhou, 311300, China; Key Laboratory of Modern Silvicultural Technology of Zhejiang Province, Hangzhou, 311300, China
| | | | - Muhammad Waheed Riaz
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Hangzhou, 311300, China
| | - Muhammad Sajjad
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Hangzhou, 311300, China
| | - Rui Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Hangzhou, 311300, China; Key Laboratory of Modern Silvicultural Technology of Zhejiang Province, Hangzhou, 311300, China.
| | - Jiasheng Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Hangzhou, 311300, China; Key Laboratory of Modern Silvicultural Technology of Zhejiang Province, Hangzhou, 311300, China.
| |
Collapse
|
43
|
Alcantara M, Acosta P, Azatian A, Calderon C, Candray K, Castillo N, Coria-Gomez L, Duran J, Fam J, Hernandez-Segura D, Hidalgo L, Huerta C, Jordan S, Kagan K, Loya K, Martinez E, Musaev K, Navarro R, Nazarians N, Paglia R, Robles G, Simmons T, Smith S, Soudani F, Valenzuela E, Villalobos J, Iftikhar H, Hanzawa Y. Experimental Verification of Inferred Regulatory Interactions of EARLY FLOWERING 3 ( GmELF3-1 ) in Glycine max. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000687. [PMID: 36506349 PMCID: PMC9729981 DOI: 10.17912/micropub.biology.000687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 10/28/2022] [Accepted: 11/18/2022] [Indexed: 12/15/2022]
Abstract
Understanding the roles of evening complex (EC) genes in the circadian clock of plants can inform how diurnal transcriptional loops in the clock gene network function to regulate key physiological and developmental events, including flowering transition. Gene regulatory interactions among soybean's circadian clock and flowering genes were inferred using time-series RNA-seq data and the network inference algorithmic package CausNet. In this study, we seek to clarify the inferred regulatory interactions of the EC gene GmELF3-1. A gene expression analysis using soybean protoplasts as a transient model indicated regulatory roles of GmELF3-1 in expression of selected flowering genes.
Collapse
Affiliation(s)
| | - Patrick Acosta
- Department of Biology, California State University Northridge
| | - Ara Azatian
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Carlos Calderon
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Kevin Candray
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Natalie Castillo
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Luis Coria-Gomez
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Jose Duran
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Justina Fam
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Diego Hernandez-Segura
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Lennix Hidalgo
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Carlos Huerta
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Shane Jordan
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Kimberly Kagan
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Karla Loya
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Eduardo Martinez
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Kirill Musaev
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Roxana Navarro
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Narek Nazarians
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Robert Paglia
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Gabriela Robles
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Taylor Simmons
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Shawn Smith
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Faisel Soudani
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Emily Valenzuela
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Jessica Villalobos
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Hira Iftikhar
- Department of Biology, California State University Northridge
| | - Yoshie Hanzawa
- Department of Biology, California State University Northridge
,
Correspondence to: Yoshie Hanzawa (
)
| |
Collapse
|
44
|
Careno DA, Perez Santangelo S, Macknight RC, Yanovsky MJ. The 5'-3' mRNA Decay Pathway Modulates the Plant Circadian Network in Arabidopsis. PLANT & CELL PHYSIOLOGY 2022; 63:1709-1719. [PMID: 36066193 DOI: 10.1093/pcp/pcac126] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/18/2022] [Accepted: 09/03/2022] [Indexed: 06/15/2023]
Abstract
Circadian rhythms enable organisms to anticipate and adjust their physiology to periodic environmental changes. These rhythms are controlled by biological clocks that consist of a set of clock genes that regulate each other's expression. Circadian oscillations in messenger RNA (mRNA) levels require the regulation of mRNA production and degradation. While transcription factors controlling clock function have been well characterized from cyanobacteria to humans, the role of factors controlling mRNA decay is largely unknown. Here, we show that mutations in SM-LIKE PROTEIN 1 (LSM1) and exoribonucleases 4 (XRN4), components of the 5'-3' mRNA decay pathway, alter clock function in Arabidopsis. We found that lsm1 and xrn4 mutants display long-period phenotypes for clock gene expression. In xrn4, these circadian defects were associated with changes in circadian phases of expression, but not overall mRNA levels, of several core-clock genes. We then used noninvasive transcriptome-wide mRNA stability analysis to identify genes and pathways regulated by XRN4. Among genes affected in the xrn4 mutant at the transcriptional and posttranscriptional level, we found an enrichment in genes involved in auxin, ethylene and drought recovery. Large effects were not observed for canonical core-clock genes, although the mRNAs of several auxiliary clock genes that control the pace of the clock were stabilized in xrn4 mutants. Our results establish that the 5'-3' mRNA decay pathway constitutes a novel posttranscriptional regulatory layer of the circadian gene network, which probably acts through a combination of small effects on mRNA stability of several auxiliary and some core-clock genes.
Collapse
Affiliation(s)
- Daniel A Careno
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1405BWE, Argentina
| | | | | | - Marcelo J Yanovsky
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1405BWE, Argentina
| |
Collapse
|
45
|
Meng Y, Zhang N, Li J, Shen X, Sheen J, Xiong Y. TOR kinase, a GPS in the complex nutrient and hormonal signaling networks to guide plant growth and development. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7041-7054. [PMID: 35781569 PMCID: PMC9664236 DOI: 10.1093/jxb/erac282] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 06/24/2022] [Indexed: 06/01/2023]
Abstract
To survive and sustain growth, sessile plants have developed sophisticated internal signalling networks that respond to various external and internal cues. Despite the central roles of nutrient and hormone signaling in plant growth and development, how hormone-driven processes coordinate with metabolic status remains largely enigmatic. Target of rapamycin (TOR) kinase is an evolutionarily conserved master regulator that integrates energy, nutrients, growth factors, hormones, and stress signals to promote growth in all eukaryotes. Inspired by recent comprehensive systems, chemical, genetic, and genomic studies on TOR in plants, this review discusses a potential role of TOR as a 'global positioning system' that directs plant growth and developmental programs both temporally and spatially by integrating dynamic information in the complex nutrient and hormonal signaling networks. We further evaluate and depict the possible functional and mechanistic models for how a single protein kinase, TOR, is able to recognize, integrate, and even distinguish a plethora of positive and negative input signals to execute appropriate and distinct downstream biological processes via multiple partners and effectors.
Collapse
Affiliation(s)
| | | | - Jiatian Li
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Haixia Institute of Science and Technology, Plant Synthetic Biology Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuehong Shen
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Haixia Institute of Science and Technology, Plant Synthetic Biology Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jen Sheen
- Department of Molecular Biology and Centre for Computational and Integrative Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | |
Collapse
|
46
|
Li Y, Zhang X, Zhu Y, Cai K, Li H, Zhao Q, Zhang Q, Jiang L, Li Y, Jiang T, Zhao X. Physiological and Transcriptomic Analysis Revealed the Molecular Mechanism of Pinus koraiensis Responses to Light. Int J Mol Sci 2022; 23:13608. [PMID: 36362393 PMCID: PMC9653891 DOI: 10.3390/ijms232113608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 10/31/2022] [Accepted: 11/01/2022] [Indexed: 10/28/2023] Open
Abstract
Korean pine (Pinus koraiensis Sieb. et Zucc.), as the main tree species in northeast China, has important economic and ecological values. Currently, supplementary light has been widely used in plant cultivation projects. However, the studies about different supplementary light sources on the growth and development of Korean pine are few. In this study, the one with no supplementary light was used as the control, and two kinds of light sources were set up: light-emitting diode (LED) and incandescent lamp, to supplement light treatment of Korean pine. The spectrum and intensity of these two light sources were different. The results showed that the growth and physiological-biochemical indicators were significantly different under different supplementary light treatments. The biomass of supplementary light treatment was significantly lower than the control. Compared with the control, IAA and GA were lower, and JA, ABA, ZT, and ETH were higher under supplementary light conditions. Photosynthetic parameters in supplementary light conditions were significantly lower than the control. Supplemental light induces chlorophyll a, chlorophyll b, total chlorophyll, and carotenoid accumulation. From RNA-seq data, differentially expressed genes (DEGs) were observed in all the comparison groups, and there were 487 common DEGs. The expression levels of DEGs encoding transcription factors were also changed. According to GO and KEGG analysis, the plant hormone signal transduction, circadian rhythm-plant, and flavonoid biosynthesis pathways were the most enriched. These results provided a theoretical basis for the response of Korean pine to different supplementary lights.
Collapse
Affiliation(s)
- Yuxi Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Forestry and Grassland, Jilin Agricultural University, Changchun 130118, China
| | - Xinxin Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Forestry and Grassland, Jilin Agricultural University, Changchun 130118, China
| | - Yan Zhu
- College of Forestry and Grassland, Jilin Agricultural University, Changchun 130118, China
| | - Kewei Cai
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Hanxi Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Forestry and Grassland, Jilin Agricultural University, Changchun 130118, China
| | - Qiushuang Zhao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Qinhui Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Luping Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Yan Li
- College of Forestry and Grassland, Jilin Agricultural University, Changchun 130118, China
| | - Tingbo Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Xiyang Zhao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Forestry and Grassland, Jilin Agricultural University, Changchun 130118, China
| |
Collapse
|
47
|
Yang MK, Zhu XJ, Chen CM, Guo X, Xu SX, Xu YR, Du SX, Xiao S, Mueller-Roeber B, Huang W, Chen L. The plant circadian clock regulates autophagy rhythm through transcription factor LUX ARRHYTHMO. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2135-2149. [PMID: 35962716 DOI: 10.1111/jipb.13343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 08/10/2022] [Indexed: 06/15/2023]
Abstract
Autophagy is an evolutionarily conserved degradation pathway in eukaryotes; it plays a critical role in nutritional stress tolerance. The circadian clock is an endogenous timekeeping system that generates biological rhythms to adapt to daily changes in the environment. Accumulating evidence indicates that the circadian clock and autophagy are intimately interwoven in animals. However, the role of the circadian clock in regulating autophagy has been poorly elucidated in plants. Here, we show that autophagy exhibits a robust circadian rhythm in both light/dark cycle (LD) and in constant light (LL) in Arabidopsis. However, autophagy rhythm showed a different pattern with a phase-advance shift and a lower amplitude in LL compared to LD. Moreover, mutation of the transcription factor LUX ARRHYTHMO (LUX) removed autophagy rhythm in LL and led to an enhanced amplitude in LD. LUX represses expression of the core autophagy genes ATG2, ATG8a, and ATG11 by directly binding to their promoters. Phenotypic analysis revealed that LUX is responsible for improved resistance of plants to carbon starvation, which is dependent on moderate autophagy activity. Comprehensive transcriptomic analysis revealed that the autophagy rhythm is ubiquitous in plants. Taken together, our findings demonstrate that the LUX-mediated circadian clock regulates plant autophagy rhythms.
Collapse
Affiliation(s)
- Ming-Kang Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, South China Agricultural University, Guangzhou, 510642, China
| | - Xiao-Jie Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Chu-Min Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Xu Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Shu-Xuan Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Ya-Rou Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Shen-Xiu Du
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Shi Xiao
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Bernd Mueller-Roeber
- Department of Molecular Biology, Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam-Golm, Germany
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
| | - Wei Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, South China Agricultural University, Guangzhou, 510642, China
| | - Liang Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, South China Agricultural University, Guangzhou, 510642, China
| |
Collapse
|
48
|
Fan T, Aslam MM, Zhou JL, Chen MX, Zhang J, Du S, Zhang KL, Chen YS. A crosstalk of circadian clock and alternative splicing under abiotic stresses in the plants. FRONTIERS IN PLANT SCIENCE 2022; 13:976807. [PMID: 36275558 PMCID: PMC9583901 DOI: 10.3389/fpls.2022.976807] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/05/2022] [Indexed: 06/16/2023]
Abstract
The circadian clock is an internal time-keeping mechanism that synchronizes the physiological adaptation of an organism to its surroundings based on day and night transition in a period of 24 h, suggesting the circadian clock provides fitness by adjusting environmental constrains. The circadian clock is driven by positive and negative elements that regulate transcriptionally and post-transcriptionally. Alternative splicing (AS) is a crucial transcriptional regulator capable of generating large numbers of mRNA transcripts from limited numbers of genes, leading to proteome diversity, which is involved in circadian to deal with abiotic stresses. Over the past decade, AS and circadian control have been suggested to coordinately regulate plant performance under fluctuating environmental conditions. However, only a few reports have reported the regulatory mechanism of this complex crosstalk. Based on the emerging evidence, this review elaborates on the existing links between circadian and AS in response to abiotic stresses, suggesting an uncovered regulatory network among circadian, AS, and abiotic stresses. Therefore, the rhythmically expressed splicing factors and core clock oscillators fill the role of temporal regulators participating in improving plant growth, development, and increasing plant tolerance against abiotic stresses.
Collapse
Affiliation(s)
- Tao Fan
- Clinical Laboratory, Shenzhen Children’s Hospital, Shenzhen, China
- Co-Innovation Center for Sustainable Forestry in Southern China & Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Mehtab Muhammad Aslam
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Jian-Li Zhou
- Clinical Laboratory, Shenzhen Children’s Hospital, Shenzhen, China
| | - Mo-Xian Chen
- Co-Innovation Center for Sustainable Forestry in Southern China & Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Shenxiu Du
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Kai-Lu Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China & Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Yun-Sheng Chen
- Clinical Laboratory, Shenzhen Children’s Hospital, Shenzhen, China
| |
Collapse
|
49
|
Kattenborn T, Richter R, Guimarães‐Steinicke C, Feilhauer H, Wirth C. AngleCam
: Predicting the temporal variation of leaf angle distributions from image series with deep learning. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Teja Kattenborn
- Remote Sensing Centre for Earth System Research (RSC4Earth) Leipzig University Leipzig Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Germany
| | - Ronny Richter
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Germany
- Systematic Botany and Functional Biodiversity Institute of Biology Leipzig University Leipzig Germany
| | - Claudia Guimarães‐Steinicke
- Remote Sensing Centre for Earth System Research (RSC4Earth) Leipzig University Leipzig Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Germany
| | - Hannes Feilhauer
- Remote Sensing Centre for Earth System Research (RSC4Earth) Leipzig University Leipzig Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Germany
| | - Christian Wirth
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Germany
- Systematic Botany and Functional Biodiversity Institute of Biology Leipzig University Leipzig Germany
| |
Collapse
|
50
|
He Y, Yu Y, Wang X, Qin Y, Su C, Wang L. Aschoff's rule on circadian rhythms orchestrated by blue light sensor CRY2 and clock component PRR9. Nat Commun 2022; 13:5869. [PMID: 36198686 PMCID: PMC9535003 DOI: 10.1038/s41467-022-33568-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 09/22/2022] [Indexed: 11/09/2022] Open
Abstract
Circadian pace is modulated by light intensity, known as the Aschoff’s rule, with largely unrevealed mechanisms. Here we report that photoreceptor CRY2 mediates blue light input to the circadian clock by directly interacting with clock core component PRR9 in blue light dependent manner. This physical interaction dually blocks the accessibility of PRR9 protein to its co-repressor TPL/TPRs and the resulting kinase PPKs. Notably, phosphorylation of PRR9 by PPKs is critical for its DNA binding and repressive activity, hence to ensure proper circadian speed. Given the labile nature of CRY2 in strong blue light, our findings provide a mechanistic explanation for Aschoff’s rule in plants, i.e., blue light triggers CRY2 turnover in proportional to its intensity, which accordingly releasing PRR9 to fine tune circadian speed. Our findings not only reveal a network mediating light input into the circadian clock, but also unmask a mechanism by which the Arabidopsis circadian clock senses light intensity. Circadian pace is modulated by light intensity. Here the authors show that CRY2 interacts with PRR9 to mediate blue light input to the circadian clock and is degraded at higher light intensity offering a mechanistic explanation as to how intensity can modify clock place.
Collapse
Affiliation(s)
- Yuqing He
- Key laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yingjun Yu
- Key laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiling Wang
- Key laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yumei Qin
- Key laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chen Su
- Key laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lei Wang
- Key laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|