1
|
Jiang Z, Yao L, Zhu X, Hao G, Ding Y, Zhao H, Wang S, Wen CK, Xu X, Xin XF. Ethylene signaling modulates air humidity responses in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:653-668. [PMID: 37997486 DOI: 10.1111/tpj.16556] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 11/02/2023] [Accepted: 11/08/2023] [Indexed: 11/25/2023]
Abstract
Air humidity significantly impacts plant physiology. However, the upstream elements that mediate humidity sensing and adaptive responses in plants remain largely unexplored. In this study, we define high humidity-induced cellular features of Arabidopsis plants and take a quantitative phosphoproteomics approach to obtain a high humidity-responsive landscape of membrane proteins, which we reason are likely the early checkpoints of humidity signaling. We found that a brief high humidity exposure (i.e., 0.5 h) is sufficient to trigger extensive changes in membrane protein abundance and phosphorylation. Enrichment analysis of differentially regulated proteins reveals high humidity-sensitive processes such as 'transmembrane transport', 'response to abscisic acid', and 'stomatal movement'. We further performed a targeted screen of mutants, in which high humidity-responsive pathways/proteins are disabled, to uncover genes mediating high humidity sensitivity. Interestingly, ethylene pathway mutants (i.e., ein2 and ein3eil1) display a range of altered responses, including hyponasty, reactive oxygen species level, and responsive gene expression, to high humidity. Furthermore, we observed a rapid induction of ethylene biosynthesis genes and ethylene evolution after high humidity treatment. Our study sheds light on the potential early signaling events in humidity perception, a fundamental but understudied question in plant biology, and reveals ethylene as a key modulator of high humidity responses in plants.
Collapse
Affiliation(s)
- Zeyu Jiang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lingya Yao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiangmei Zhu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guodong Hao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanxia Ding
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hangwei Zhao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shanshan Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chi-Kuang Wen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoyan Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiu-Fang Xin
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- Chinese Academy of Sciences (CAS) and CAS John Innes Centre of Excellence for Plant and Microbial Sciences, Shanghai, China
| |
Collapse
|
2
|
Waheed A, Haxim Y, Islam W, Ahmad M, Muhammad M, Alqahtani FM, Hashem M, Salih H, Zhang D. Climate change reshaping plant-fungal interaction. ENVIRONMENTAL RESEARCH 2023; 238:117282. [PMID: 37783329 DOI: 10.1016/j.envres.2023.117282] [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: 08/07/2023] [Revised: 09/13/2023] [Accepted: 09/29/2023] [Indexed: 10/04/2023]
Abstract
Plant diseases pose a severe threat to modern agriculture, necessitating effective and lasting control solutions. Environmental factors significantly shape plant ecology. Human-induced greenhouse gas emissions have led to global temperature rise, impacting various aspects, including carbon dioxide (CO2) concentration, temperature, ozone (O3), and ultraviolet-B, all of which influence plant diseases. Altered pathogen ranges can accelerate disease transmission. This review explores environmental effects on plant diseases, with climate change affecting fungal biogeography, disease incidence, and severity, as well as agricultural production. Moreover, we have discussed how climate change influences pathogen development, host-fungal interactions, the emergence of new races of fungi, and the dissemination of emerging fungal diseases across the globe. The discussion about environment-mediated impact on pattern-triggered immunity (PTI), effector-triggered immunity (ETI), and RNA interference (RNAi) is also part of this review. In conclusion, the review underscores the critical importance of understanding how climate change is reshaping plant-fungal interactions. It highlights the need for continuous research efforts to elucidate the mechanisms driving these changes and their ecological consequences. As the global climate continues to evolve, it is imperative to develop innovative strategies for mitigating the adverse effects of fungal pathogens on plant health and food security.
Collapse
Affiliation(s)
- Abdul Waheed
- National Key Laboratory of Ecological Security and Resource Utilization in Arid Areas, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology & Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, 838008, China
| | - Yakoopjan Haxim
- National Key Laboratory of Ecological Security and Resource Utilization in Arid Areas, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology & Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, 838008, China
| | - Waqar Islam
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | | | - Murad Muhammad
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology & Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Fatmah M Alqahtani
- Department of Biology, College of Science, King Khalid University, Abha, 61413, Saudi Arabia
| | - Mohamed Hashem
- Department of Biology, College of Science, King Khalid University, Abha, 61413, Saudi Arabia
| | - Haron Salih
- National Key Laboratory of Ecological Security and Resource Utilization in Arid Areas, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology & Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, 838008, China
| | - Daoyuan Zhang
- National Key Laboratory of Ecological Security and Resource Utilization in Arid Areas, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology & Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, 838008, China.
| |
Collapse
|
3
|
Yao L, Jiang Z, Wang Y, Hu Y, Hao G, Zhong W, Wan S, Xin X. High air humidity dampens salicylic acid pathway and NPR1 function to promote plant disease. EMBO J 2023; 42:e113499. [PMID: 37728254 PMCID: PMC10620762 DOI: 10.15252/embj.2023113499] [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: 01/13/2023] [Revised: 08/16/2023] [Accepted: 08/18/2023] [Indexed: 09/21/2023] Open
Abstract
The occurrence of plant disease is determined by interactions among host, pathogen, and environment. Air humidity shapes various aspects of plant physiology and high humidity has long been known to promote numerous phyllosphere diseases. However, the molecular basis of how high humidity interferes with plant immunity to favor disease has remained elusive. Here we show that high humidity is associated with an "immuno-compromised" status in Arabidopsis plants. Furthermore, accumulation and signaling of salicylic acid (SA), an important defense hormone, are significantly inhibited under high humidity. NPR1, an SA receptor and central transcriptional co-activator of SA-responsive genes, is less ubiquitinated and displays a lower promoter binding affinity under high humidity. The cellular ubiquitination machinery, particularly the Cullin 3-based E3 ubiquitin ligase mediating NPR1 protein ubiquitination, is downregulated under high humidity. Importantly, under low humidity the Cullin 3a/b mutant plants phenocopy the low SA gene expression and disease susceptibility that is normally observed under high humidity. Our study uncovers a mechanism by which high humidity dampens a major plant defense pathway and provides new insights into the long-observed air humidity influence on diseases.
Collapse
Affiliation(s)
- Lingya Yao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
- University of the Chinese Academy of SciencesBeijingChina
| | - Zeyu Jiang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
- University of the Chinese Academy of SciencesBeijingChina
| | - Yiping Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
- University of the Chinese Academy of SciencesBeijingChina
| | - Yezhou Hu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
- University of the Chinese Academy of SciencesBeijingChina
| | - Guodong Hao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
- University of the Chinese Academy of SciencesBeijingChina
| | - Weili Zhong
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
- University of the Chinese Academy of SciencesBeijingChina
| | - Shiwei Wan
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
- University of the Chinese Academy of SciencesBeijingChina
| | - Xiu‐Fang Xin
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
- University of the Chinese Academy of SciencesBeijingChina
- Chinese Academy of Sciences (CAS) and CAS John Innes Centre of Excellence for Plant and Microbial SciencesShanghaiChina
| |
Collapse
|
4
|
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
|
5
|
Masuda K, Yamada T, Kagawa Y, Fukuda H. Application of time lags between light and temperature cycles for growth control based on the circadian clock of Lactuca sativa L. seedlings. FRONTIERS IN PLANT SCIENCE 2022; 13:994555. [PMID: 36589103 PMCID: PMC9802636 DOI: 10.3389/fpls.2022.994555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/26/2022] [Indexed: 06/17/2023]
Abstract
The circadian clock plays an important role in agriculture, especially in highly controlled environments, such as plant factories. However, multiple environmental factors have an extremely high degree of freedom, and it is difficult to experimentally search for the optimal design conditions. A recent study demonstrated that the effect of time lags between light and temperature cycles on plant growth could be predicted by the entrainment properties of the circadian clock in Arabidopsis thaliana. Based on this prediction, it was possible to control plant growth by adjusting the time lag. However, for application in plant factories, it is necessary to verify the effectiveness of this method using commercial vegetables, such as leaf lettuce. In this study, we investigated the entrainment properties of the circadian clock and the effect of the time lag between light and temperature cycles on circadian rhythms and plant growth in Lactuca sativa L. seedlings. For evaluation of circadian rhythms, we used transgenic L. sativa L. with a luciferase reporter in the experiment and a phase oscillator model in the simulation. We found that the entrainment properties for the light and temperature stimuli and the effects of time lags on circadian rhythm and growth were similar to those of A. thaliana. Moreover, we demonstrated that changes in growth under different time lags could be predicted by simulation based on the entrainment properties of the circadian clock. These results showed the importance of designing a cultivation environment that considers the circadian clock and demonstrated a series of methods to achieve this.
Collapse
Affiliation(s)
- Kosaku Masuda
- Department of Mechanical Engineering, Graduate School of Engineering, Osaka Prefecture University, Sakai, Japan
| | - Tatsuya Yamada
- Department of Mechanical Engineering, Graduate School of Engineering, Osaka Prefecture University, Sakai, Japan
| | - Yuya Kagawa
- Department of Mechanical Engineering, Graduate School of Engineering, Osaka Prefecture University, Sakai, Japan
| | - Hirokazu Fukuda
- Department of Mechanical Engineering, Graduate School of Engineering, Osaka Prefecture University, Sakai, Japan
- Department of Mechanical Engineering, Graduate School of Engineering, Osaka Metropolitan University, Sakai, Japan
| |
Collapse
|
6
|
Wang S, Steed G, Webb AAR. Circadian entrainment in Arabidopsis. PLANT PHYSIOLOGY 2022; 190:981-993. [PMID: 35512209 PMCID: PMC9516740 DOI: 10.1093/plphys/kiac204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 03/29/2022] [Indexed: 06/14/2023]
Abstract
Circadian clocks coordinate physiology and development as an adaption to the oscillating day/night cycle caused by the rotation of Earth on its axis and the changing length of day and night away from the equator caused by orbiting the sun. Circadian clocks confer advantages by entraining to rhythmic environmental cycles to ensure that internal events within the plant occur at the correct time with respect to the cyclic external environment. Advances in determining the structure of circadian oscillators and the pathways that allow them to respond to light, temperature, and metabolic signals have begun to provide a mechanistic insight to the process of entrainment in Arabidopsis (Arabidopsis thaliana). We describe the concepts of entrainment and how it occurs. It is likely that a thorough mechanistic understanding of the genetic and physiological basis of circadian entrainment will provide opportunities for crop improvement.
Collapse
Affiliation(s)
- Shouming Wang
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
- School of Life Science and Technology, Hubei Engineering University, Xiaogan 432000, China
| | - Gareth Steed
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | | |
Collapse
|
7
|
Lu Y, Yang G, Shen Y, Yang H, Xu K. Multifunctional Flexible Humidity Sensor Systems Towards Noncontact Wearable Electronics. NANO-MICRO LETTERS 2022; 14:150. [PMID: 35869398 PMCID: PMC9307709 DOI: 10.1007/s40820-022-00895-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/02/2022] [Indexed: 05/14/2023]
Abstract
In the past decade, the global industry and research attentions on intelligent skin-like electronics have boosted their applications in diverse fields including human healthcare, Internet of Things, human-machine interfaces, artificial intelligence and soft robotics. Among them, flexible humidity sensors play a vital role in noncontact measurements relying on the unique property of rapid response to humidity change. This work presents an overview of recent advances in flexible humidity sensors using various active functional materials for contactless monitoring. Four categories of humidity sensors are highlighted based on resistive, capacitive, impedance-type and voltage-type working mechanisms. Furthermore, typical strategies including chemical doping, structural design and Joule heating are introduced to enhance the performance of humidity sensors. Drawing on the noncontact perception capability, human/plant healthcare management, human-machine interactions as well as integrated humidity sensor-based feedback systems are presented. The burgeoning innovations in this research field will benefit human society, especially during the COVID-19 epidemic, where cross-infection should be averted and contactless sensation is highly desired.
Collapse
Affiliation(s)
- Yuyao Lu
- State Key Laboratory of Fluid Power and Mechatronic Systems, School of Mechanical Engineering, Zhejiang University, Hangzhou, 310027, People's Republic of China
| | - Geng Yang
- State Key Laboratory of Fluid Power and Mechatronic Systems, School of Mechanical Engineering, Zhejiang University, Hangzhou, 310027, People's Republic of China.
| | - Yajing Shen
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, People's Republic of China
| | - Huayong Yang
- State Key Laboratory of Fluid Power and Mechatronic Systems, School of Mechanical Engineering, Zhejiang University, Hangzhou, 310027, People's Republic of China
| | - Kaichen Xu
- State Key Laboratory of Fluid Power and Mechatronic Systems, School of Mechanical Engineering, Zhejiang University, Hangzhou, 310027, People's Republic of China.
| |
Collapse
|
8
|
Yi F, Huo M, Li J, Yu J. Time-series transcriptomics reveals a drought-responsive temporal network and crosstalk between drought stress and the circadian clock in foxtail millet. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1213-1228. [PMID: 35262997 DOI: 10.1111/tpj.15725] [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: 03/01/2021] [Revised: 02/23/2022] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
Drought stress is a serious factor affecting crop growth and production worldwide. The circadian clock has been identified as key to improving regional adaptability of plants. However, our understanding of the contribution of the circadian clock to drought response and the impacts of drought stress on the circadian clock in plants is still limited. To explore the interactions between the circadian clock and drought stress, foxtail millet seedlings were treated with simulated drought (20% polyethylene glycol-6000) treatment starting at the day (DD) onset zeitgeber time 0 (ZT0, lights on) and at the night (DN) onset zeitgeber time 16 (ZT16, lights off). A high temporal-resolution transcriptomic investigation was performed using DD and DN samples collected at intervals of 2 or 4 h within a 24-h drought-treatment period. Overall, we identified 13 294 drought-responsive genes (DRGs). Among these DRGs, 7931 were common between DD and DN samples, 2638 were specific to DD, and 2725 were specific to DN. Additionally, we identified 1257 circadian genes, of which 67% were DRGs. Interestingly, with drought treatment starting at the day for 8, 12 or 16 h, the circadian phase shifted to 12 h. We also found that the circadian clock led to different day and night drought-responsive pathways. The identification of DRG_Clock (DRG and circadian clock) and DRG_NonClock (DRG and not circadian clock) genes provides a reference for selecting candidate drought resistance genes. Our work reveals the temporal drought-response process and crosstalk between drought stress and the circadian clock in foxtail millet.
Collapse
Affiliation(s)
- Fei Yi
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- State Key Laboratory of Plant Physiology and Biochemistry, Engineering Research Center of Plant Growth Regulator, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Mingyue Huo
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jianrui Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Jingjuan Yu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| |
Collapse
|
9
|
Reynolds M, de Oliveira L, Vosburg C, Paris T, Massimino C, Norus J, Ortiz Y, Espino M, Davis N, Masse R, Neiman A, Holcomb R, Gervais K, Kemp M, Hoang M, Shippy TD, Hosmani PS, Flores-Gonzalez M, Pelz-Stelinski K, Qureshi JA, Mueller LA, Hunter WB, Benoit JB, Brown SJ, D’Elia T, Saha S. Annotation of putative circadian rhythm-associated genes in Diaphorina citri (Hemiptera: Liviidae). GIGABYTE 2022; 2022:gigabyte48. [PMID: 36824532 PMCID: PMC9662589 DOI: 10.46471/gigabyte.48] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 03/28/2022] [Indexed: 11/09/2022] Open
Abstract
The circadian rhythm involves multiple genes that generate an internal molecular clock, allowing organisms to anticipate environmental conditions produced by the Earth's rotation on its axis. Here, we present the results of the manual curation of 27 genes that are associated with circadian rhythm in the genome of Diaphorina citri, the Asian citrus psyllid. This insect is the vector for the bacterial pathogen Candidatus Liberibacter asiaticus (CLas), the causal agent of citrus greening disease (Huanglongbing). This disease severely affects citrus industries and has drastically decreased crop yields worldwide. Based on cry1 and cry2 identified in the psyllid genome, D. citri likely possesses a circadian model similar to the lepidopteran butterfly, Danaus plexippus. Manual annotation will improve the quality of circadian rhythm gene models, allowing the future development of molecular therapeutics, such as RNA interference or antisense technologies, to target these genes to disrupt the psyllid biology.
Collapse
Affiliation(s)
- Max Reynolds
- Indian River State College, Fort Pierce, FL 34981, USA
| | | | - Chad Vosburg
- Indian River State College, Fort Pierce, FL 34981, USA,Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, USA
| | - Thomson Paris
- Entomology and Nematology Department, University of Florida, North Florida Research and Education Center, Research Road, Quincy 32351, Florida, USA
| | | | - Jordan Norus
- Indian River State College, Fort Pierce, FL 34981, USA
| | - Yasmin Ortiz
- Indian River State College, Fort Pierce, FL 34981, USA
| | | | - Nina Davis
- Indian River State College, Fort Pierce, FL 34981, USA
| | - Ron Masse
- Indian River State College, Fort Pierce, FL 34981, USA
| | - Alan Neiman
- Indian River State College, Fort Pierce, FL 34981, USA
| | | | - Kylie Gervais
- Indian River State College, Fort Pierce, FL 34981, USA
| | - Melissa Kemp
- Indian River State College, Fort Pierce, FL 34981, USA
| | - Maria Hoang
- Indian River State College, Fort Pierce, FL 34981, USA
| | - Teresa D. Shippy
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | | | | | - Kirsten Pelz-Stelinski
- Department of Entomology and Nematology, University of Florida, Lake Alfred, FL 33850, USA
| | - Jawwad A. Qureshi
- Indian River Research and Education Center, University of Florida, IFAS, 2199 South Rock Road, Fort Pierce, FL 34945-3138, USA,Southwest Florida Research and Education Center, University of Florida, IFAS, 2685 State Road 29 North, Immokalee, FL 34142, USA
| | | | - Wayne B. Hunter
- USDA-ARS, US Horticultural Research Laboratory, Fort Pierce, FL 34945, USA
| | - Joshua B. Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Susan J. Brown
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Tom D’Elia
- Indian River State College, Fort Pierce, FL 34981, USA
| | - Surya Saha
- Boyce Thompson Institute, Ithaca, NY 14853, USA,Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USA, Corresponding author. E-mail:
| |
Collapse
|
10
|
Xu X, Yuan L, Yang X, Zhang X, Wang L, Xie Q. Circadian clock in plants: Linking timing to fitness. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:792-811. [PMID: 35088570 DOI: 10.1111/jipb.13230] [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: 11/19/2021] [Accepted: 01/25/2022] [Indexed: 05/12/2023]
Abstract
Endogenous circadian clock integrates cyclic signals of environment and daily and seasonal behaviors of organisms to achieve spatiotemporal synchronization, which greatly improves genetic diversity and fitness of species. This review addresses recent studies on the plant circadian system in the field of chronobiology, covering topics on molecular mechanisms, internal and external Zeitgebers, and hierarchical regulation of physiological outputs. The architecture of the circadian clock involves the autoregulatory transcriptional feedback loops, post-translational modifications of core oscillators, and epigenetic modifications of DNA and histones. Here, light, temperature, humidity, and internal elemental nutrients are summarized to illustrate the sensitivity of the circadian clock to timing cues. In addition, the circadian clock runs cell-autonomously, driving independent circadian rhythms in various tissues. The core oscillators responds to each other with biochemical factors including calcium ions, mineral nutrients, photosynthetic products, and hormones. We describe clock components sequentially expressed during a 24-h day that regulate rhythmic growth, aging, immune response, and resistance to biotic and abiotic stresses. Notably, more data have suggested the circadian clock links chrono-culture to key agronomic traits in crops.
Collapse
Affiliation(s)
- Xiaodong Xu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Li Yuan
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Xin Yang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Xiao Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Lei Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Qiguang Xie
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| |
Collapse
|
11
|
Tang J, Zhao Y, Wang M, Wang D, Yang X, Hao R, Wang M, Wang Y, He H, Xin JH, Zheng S. Circadian humidity fluctuation induced capillary flow for sustainable mobile energy. Nat Commun 2022; 13:1291. [PMID: 35277510 PMCID: PMC8917138 DOI: 10.1038/s41467-022-28998-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 02/23/2022] [Indexed: 11/09/2022] Open
Abstract
Circadian humidity fluctuation is an important factor that affects human life all over the world. Here we show that spherical cap-shaped ionic liquid drops sitting on nanowire array are able to continuously output electricity when exposed to outdoor air, which we attribute to the daily humidity fluctuation induced directional capillary flow. Specifically, ionic liquid drops could absorb/desorb water around the liquid/vapor interface and swell/shrink depending on air humidity fluctuation. While pinning of the drop by nanowire array suppresses advancing/receding of triple-phase contact line. To maintain the surface tension-regulated spherical cap profile, inward/outward flow arises for removing excess fluid from the edge or filling the perimeter with fluid from center. This moisture absorption/desorption-caused capillary flow is confirmed by in-situ microscope imaging. We conduct further research to reveal how environmental humidity affects flow rate and power generation performance. To further illustrate feasibility of our strategy, we combine the generators to light up a red diode and LCD screen. All these results present the great potential of tiny humidity fluctuation as an easily accessible anytime-and-anywhere small-scale green energy resource. Droplet generators convert mechanical movements of droplets into small-scale electricity. Here, Tang et al. report a humidity-driven power generator by utilizing daily humidity fluctuation in atmosphere enabling continuous generation of electricity upon moisture absorption and desorption cycles.
Collapse
|
12
|
Mechanosensory trichome cells evoke a mechanical stimuli-induced immune response in Arabidopsis thaliana. Nat Commun 2022; 13:1216. [PMID: 35260555 PMCID: PMC8904797 DOI: 10.1038/s41467-022-28813-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 02/08/2022] [Indexed: 12/13/2022] Open
Abstract
Perception of pathogen-derived ligands by corresponding host receptors is a pivotal strategy in eukaryotic innate immunity. In plants, this is complemented by circadian anticipation of infection timing, promoting basal resistance even in the absence of pathogen threat. Here, we report that trichomes, hair-like structures on the epidermis, directly sense external mechanical forces, including raindrops, to anticipate pathogen infections in Arabidopsis thaliana. Exposure of leaf surfaces to mechanical stimuli initiates the concentric propagation of intercellular calcium waves away from trichomes to induce defence-related genes. Propagating calcium waves enable effective immunity against pathogenic microbes through the CALMODULIN-BINDING TRANSCRIPTION ACTIVATOR 3 (CAMTA3) and mitogen-activated protein kinases. We propose an early layer of plant immunity in which trichomes function as mechanosensory cells that detect potential risks.
Collapse
|
13
|
Giannoni-Guzmán MA, Rivera-Rodriguez EJ, Aleman-Rios J, Melendez Moreno AM, Pérez Ramos M, Pérez-Claudio E, Loubriel D, Moore D, Giray T, Agosto-Rivera JL. The Role of Colony Temperature in the Entrainment of Circadian Rhythms of Honey Bee Foragers. ANNALS OF THE ENTOMOLOGICAL SOCIETY OF AMERICA 2021; 114:596-605. [PMID: 34512858 PMCID: PMC8423108 DOI: 10.1093/aesa/saab021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Indexed: 06/13/2023]
Abstract
Honey bees utilize their circadian rhythms to accurately predict the time of day. This ability allows foragers to remember the specific timing of food availability and its location for several days. Previous studies have provided strong evidence toward light/dark cycles being the primary Zeitgeber for honey bees. Work in our laboratory described large individual variation in the endogenous period length of honey bee foragers from the same colony and differences in the endogenous rhythms under different constant temperatures. In this study, we further this work by examining the temperature inside the honey bee colony. By placing temperature and light data loggers at different locations inside the colony we measured temperature at various locations within the colony. We observed significant oscillations of the temperature inside the hive, that show seasonal patterns. We then simulated the observed temperature oscillations in the laboratory and found that using the temperature cycle as a Zeitgeber, foragers present large individual differences in the phase of locomotor rhythms for temperature. Moreover, foragers successfully synchronize their locomotor rhythms to these simulated temperature cycles. Advancing the cycle by six hours, resulting in changes in the phase of activity in some foragers in the assay. The results are shown in this study highlight the importance of temperature as a potential Zeitgeber in the field. Future studies will examine the possible functional and evolutionary role of the observed phase differences of circadian rhythms.
Collapse
Affiliation(s)
| | | | - Janpierre Aleman-Rios
- Department of Biology, University of Puerto Rico Rio Piedras Campus, San Juan, PR, USA
| | | | | | - Eddie Pérez-Claudio
- Department of Biomedical Informatics, University of Pittsburgh, School of Medicine, Pittsburgh, PA, USA
| | - Darimar Loubriel
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Darrell Moore
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, USA
| | - Tugrul Giray
- Department of Biology, University of Puerto Rico Rio Piedras Campus, San Juan, PR, USA
| | - Jose L Agosto-Rivera
- Department of Biology, University of Puerto Rico Rio Piedras Campus, San Juan, PR, USA
| |
Collapse
|
14
|
Masuda K, Fukuda H. Unstable Phase Response Curves Shown by Spatiotemporal Patterns in the Plant Root Circadian Clock. J Biol Rhythms 2021; 36:432-441. [PMID: 34313451 DOI: 10.1177/07487304211028440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Phase response curves (PRCs) play important roles in the entrainment of periodic environmental cycles. Measuring the PRC is necessary to elucidate the relationship between environmental cues and the circadian clock. Conversely, the PRCs of plant circadian clocks are unstable due to multiple factors such as biotic/abiotic noise, individual differences, changes in amplitude, growth stage, and organ/tissue specificity. However, evaluating the effect of each factor is important because PRCs are commonly obtained by determining the response of many individuals, which include different amplitude states and organs. The plant root circadian clock spontaneously generates a spatiotemporal pattern called a stripe pattern, whereby all phases of the circadian rhythm exist within an individual root. Therefore, stimulating a plant root expressing this pattern enables phase responses at all phases to be measured using an individual root. In this study, we measured PRCs for thermal stimuli using this spatiotemporal pattern method and found that the PRC changed asymmetrically with positive and negative temperature stimuli. Individual differences were observed for weak but not for strong temperature stimuli. The root PRC changed depending on the amplitude of the circadian rhythm. The PRC in the young root near the hypocotyl was more sensitive than those in older roots or near the tip. Simulation with a phase oscillator model revealed the effect of measurement and internal noises on the PRC. These results indicate that instability in the entrainment of the plant circadian clock involves multiple factors, each having different characteristics. These results may help us understand how plant circadian clocks adapt to unstable environments and how plant circadian clocks with different characteristics, such as organ, age, and amplitude, are integrated within individuals.
Collapse
Affiliation(s)
- Kosaku Masuda
- Graduate School of Engineering, Osaka Prefecture University, Osaka, Japan.,Japan Society for the Promotion of Science, Tokyo, Japan
| | - Hirokazu Fukuda
- Graduate School of Engineering, Osaka Prefecture University, Osaka, Japan
| |
Collapse
|
15
|
Balcerowicz M, Mahjoub M, Nguyen D, Lan H, Stoeckle D, Conde S, Jaeger KE, Wigge PA, Ezer D. An early-morning gene network controlled by phytochromes and cryptochromes regulates photomorphogenesis pathways in Arabidopsis. MOLECULAR PLANT 2021; 14:983-996. [PMID: 33766657 DOI: 10.1016/j.molp.2021.03.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/04/2021] [Accepted: 03/22/2021] [Indexed: 06/12/2023]
Abstract
Light perception at dawn plays a key role in coordinating multiple molecular processes and in entraining the plant circadian clock. The Arabidopsis mutant lacking the main photoreceptors, however, still shows clock entrainment, indicating that the integration of light into the morning transcriptome is not well understood. In this study, we performed a high-resolution RNA-sequencing time-series experiment, sampling every 2 min beginning at dawn. In parallel experiments, we perturbed temperature, the circadian clock, photoreceptor signaling, and chloroplast-derived light signaling. We used these data to infer a gene network that describes the gene expression dynamics after light stimulus in the morning, and then validated key edges. By sampling time points at high density, we are able to identify three light- and temperature-sensitive bursts of transcription factor activity, one of which lasts for only about 8 min. Phytochrome and cryptochrome mutants cause a delay in the transcriptional bursts at dawn, and completely remove a burst of expression in key photomorphogenesis genes (HY5 and BBX family). Our complete network is available online (http://www-users.york.ac.uk/∼de656/dawnBurst/dawnBurst.html). Taken together, our results show that phytochrome and cryptochrome signaling is required for fine-tuning the dawn transcriptional response to light, but separate pathways can robustly activate much of the program in their absence.
Collapse
Affiliation(s)
| | - Mahiar Mahjoub
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Duy Nguyen
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Hui Lan
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | | | - Susana Conde
- Department of Statistics, University of Warwick, Coventry, UK; Alan Turing Institute, London, UK
| | - Katja E Jaeger
- Leibniz-Institute of Vegetable and Ornamental Crops (IGZ), 14979 Großbeeren, Germany
| | - Philip A Wigge
- Leibniz-Institute of Vegetable and Ornamental Crops (IGZ), 14979 Großbeeren, Germany; Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Daphne Ezer
- Alan Turing Institute, London, UK; Department of Biology, University of York, York YO10 5DD, UK.
| |
Collapse
|
16
|
Spatial Organization and Coordination of the Plant Circadian System. Genes (Basel) 2021; 12:genes12030442. [PMID: 33804638 PMCID: PMC8003751 DOI: 10.3390/genes12030442] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 12/21/2022] Open
Abstract
The plant circadian clock has a pervasive influence on many aspects of plant biology and is proposed to function as a developmental manager. To do so, the circadian oscillator needs to be able to integrate a multiplicity of environmental signals and coordinate an extensive and diverse repertoire of endogenous rhythms accordingly. Recent studies on tissue-specific characteristics and spatial structure of the plant circadian clock suggest that such plasticity may be achieved through the function of distinct oscillators, which sense the environment locally and are then coordinated across the plant through both intercellular coupling and long-distance communication. This review summarizes the current knowledge on tissue-specific features of the clock in plants and their spatial organization and synchronization at the organismal level.
Collapse
|
17
|
Zhang S, Liu H, Yuan L, Li X, Wang L, Xu X, Xie Q. Recognition of CCA1 alternative protein isoforms during temperature acclimation. PLANT CELL REPORTS 2021; 40:421-432. [PMID: 33398474 DOI: 10.1007/s00299-020-02644-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 11/26/2020] [Indexed: 05/14/2023]
Abstract
CCA1α and CCA1β protein variants respond to environmental light and temperature cues, and higher temperature promotes CCA1β protein production and causes its retention detectable in the cytoplasm. CIRCADIAN CLOCK ASSOCIATED1 (CCA1), as the core transcription factor of circadian clock, is involved in the regulation of endogenous circadian rhythm in Arabidopsis. Previous studies have shown that CCA1 consists of two abundant splice variants, fully spliced CCA1α and intron-retaining CCA1β. CCA1β is believed to form a nonfunctional heterodimer with CCA1α and its closed-related homolog LHY. Many studies have established that CCA1β is a transcription product, while how CCA1β protein is produced and how two CCA1 isoforms respond to environmental cues have not been elucidated. In this study, we identified CCA1α and CCA1β protein variants under different photoperiods with warm or cold temperature cycles, respectively. Our results showed that CCA1 protein production is regulated by prolonged light exposure and warm temperature. The protein levels of CCA1α and CCA1β peak in the morning, but the detection of CCA1β is dependent on immunoprecipitation enrichment at 22 °C. Higher temperature of 37 °C promotes CCA1β protein production and causes its retention to be detectable in the cytoplasm. Overall, our results indicate that two splice variants of the CCA1 protein respond to environmental light and temperature signals and may, therefore, maintain the circadian rhythms and give individuals the ability to adapt to environment.
Collapse
Affiliation(s)
- Shijia Zhang
- Key Laboratory of Molecular and Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Huili Liu
- Key Laboratory of Molecular and Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Li Yuan
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Xiaojing Li
- Key Laboratory of Molecular and Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Lingbao Wang
- Key Laboratory of Molecular and Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Xiaodong Xu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China.
| | - Qiguang Xie
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China.
| |
Collapse
|
18
|
Zhang J, Coaker G, Zhou JM, Dong X. Plant Immune Mechanisms: From Reductionistic to Holistic Points of View. MOLECULAR PLANT 2020; 13:1358-1378. [PMID: 32916334 PMCID: PMC7541739 DOI: 10.1016/j.molp.2020.09.007] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 09/05/2020] [Accepted: 09/08/2020] [Indexed: 05/19/2023]
Abstract
After three decades of the amazing progress made on molecular studies of plant-microbe interactions (MPMI), we have begun to ask ourselves "what are the major questions still remaining?" as if the puzzle has only a few pieces missing. Such an exercise has ultimately led to the realization that we still have many more questions than answers. Therefore, it would be an impossible task for us to project a coherent "big picture" of the MPMI field in a single review. Instead, we provide our opinions on where we would like to go in our research as an invitation to the community to join us in this exploration of new MPMI frontiers.
Collapse
Affiliation(s)
- Jie Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, College of Advanced Agricutural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gitta Coaker
- Department of Plant Pathology, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Jian-Min Zhou
- CAS Center for Excellence in Biotic Interactions, College of Advanced Agricutural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xinnian Dong
- Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA; Department of Biology, Duke University, PO Box 90338, Durham, NC 27708, USA.
| |
Collapse
|
19
|
Greenwood M, Locke JC. The circadian clock coordinates plant development through specificity at the tissue and cellular level. CURRENT OPINION IN PLANT BIOLOGY 2020; 53:65-72. [PMID: 31783323 DOI: 10.1016/j.pbi.2019.09.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/20/2019] [Accepted: 09/23/2019] [Indexed: 05/27/2023]
Abstract
The circadian clock is a genetic circuit that allows organisms to anticipate daily events caused by the rotation of the Earth. The plant clock regulates physiology at multiple scales, from cell division to ecosystem-scale interactions. It is becoming clear that rather than being a single perfectly synchronised timer throughout the plant, the clock can be sensitive to different cues, run at different speeds, and drive distinct processes in different cell types and tissues. This flexibility may help the plant clock to regulate such a range of developmental and physiological processes. In this review, using examples from the literature, we describe how the clock regulates development at multiple scales and discuss how the clock might allow local flexibility in regulation whilst remaining coordinated across the plant.
Collapse
Affiliation(s)
- Mark Greenwood
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge, UK; Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, UK
| | - James Cw Locke
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge, UK.
| |
Collapse
|
20
|
Saijo Y, Loo EPI. Plant immunity in signal integration between biotic and abiotic stress responses. THE NEW PHYTOLOGIST 2020; 225:87-104. [PMID: 31209880 DOI: 10.1111/nph.15989] [Citation(s) in RCA: 178] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 06/04/2019] [Indexed: 05/20/2023]
Abstract
Plants constantly monitor and cope with the fluctuating environment while hosting a diversity of plant-inhabiting microbes. The mode and outcome of plant-microbe interactions, including plant disease epidemics, are dynamically and profoundly influenced by abiotic factors, such as light, temperature, water and nutrients. Plants also utilize associations with beneficial microbes during adaptation to adverse conditions. Elucidation of the molecular bases for the plant-microbe-environment interactions is therefore of fundamental importance in the plant sciences. Following advances into individual stress signaling pathways, recent studies are beginning to reveal molecular intersections between biotic and abiotic stress responses and regulatory principles in combined stress responses. We outline mechanisms underlying environmental modulation of plant immunity and emerging roles for immune regulators in abiotic stress tolerance. Furthermore, we discuss how plants coordinate conflicting demands when exposed to combinations of different stresses, with attention to a possible determinant that links initial stress response to broad-spectrum stress tolerance or prioritization of specific stress tolerance.
Collapse
Affiliation(s)
- Yusuke Saijo
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan
| | - Eliza Po-Iian Loo
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan
| |
Collapse
|
21
|
Mayol M, Riba M, Cavers S, Grivet D, Vincenot L, Cattonaro F, Vendramin GG, González‐Martínez SC. A multiscale approach to detect selection in nonmodel tree species: Widespread adaptation despite population decline in Taxus baccata L. Evol Appl 2020; 13:143-160. [PMID: 31892949 PMCID: PMC6935595 DOI: 10.1111/eva.12838] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 06/18/2019] [Accepted: 06/24/2019] [Indexed: 01/03/2023] Open
Abstract
Detecting the molecular basis of local adaptation and identifying selective drivers is still challenging in nonmodel species. The use of purely population genetic approaches is limited by some characteristics of genetic systems, such as pleiotropy and polygenic control, and parallel evidence from phenotypic-based experimental comparisons is required. In long-lived organisms, the detection of selective pressures might also be precluded by evolutionary lag times in response to the environment. Here, we used the English yew to showcase an example of a multiscale integrative approach in a nonmodel species with limited plant and genomic resources. We combined information from two independent sources, phenotypes in a common environment and genomic data in natural populations, to investigate the signature of selection. Growth differences among populations in a common environment, and phenological patterns of both shoot elongation and male strobili maturation, were associated with climate clines, providing evidence for local adaptation and guiding us in the selection of populations for genomic analyses. We used information on over 25,000 SNPs from c. 1,200 genes to infer the demographic history and to test for molecular signatures of selection at different levels: SNP, gene, and biological pathway. Our results confirmed an overall demographic history of population decline, but we also found evidence for putative local adaptation at the molecular level. We identified or confirmed several candidate genes for positive and negative selection in forest trees, including the pseudo-response regulator 7 (PRR7), an essential component of the circadian clock in plants. In addition, we successfully tested an approach to detect polygenic adaptation in biological pathways, allowing us to identify the flavonoid biosynthesis pathway as a candidate stress-response pathway that deserves further attention in other plants. Finally, our study contributes to the emerging view that explaining contemporary standing genetic variation requires considering adaptation to past climates, especially for long-lived trees.
Collapse
Affiliation(s)
| | - Miquel Riba
- CREAFCerdanyola del VallèsSpain
- Univ. Autònoma BarcelonaCerdanyola del VallèsSpain
| | | | - Delphine Grivet
- Department of Forest Ecology and Genetics, Forest Research CentreINIA‐CIFORMadridSpain
- Sustainable Forest Management Research Institute, INIA‐University of ValladolidMadridSpain
| | | | | | - Giovanni G. Vendramin
- Institute of Biosciences and Bioresources, Division of FlorenceNational Research CouncilSesto FiorentinoItaly
| | | |
Collapse
|
22
|
Abstract
In the past four decades, tremendous progress has been made in understanding how plants respond to microbial colonization and how microbial pathogens and symbionts reprogram plant cellular processes. In contrast, our knowledge of how environmental conditions impact plant-microbe interactions is less understood at the mechanistic level, as most molecular studies are performed under simple and static laboratory conditions. In this review, we highlight research that begins to shed light on the mechanisms by which environmental conditions influence diverse plant-pathogen, plant-symbiont, and plant-microbiota interactions. There is a great need to increase efforts in this important area of research in order to reach a systems-level understanding of plant-microbe interactions that are more reflective of what occurs in nature.
Collapse
Affiliation(s)
- Yu Ti Cheng
- Howard Hughes Medical Institute, Michigan State University, East Lansing, MI 48824, USA; Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA.
| | - Li Zhang
- Howard Hughes Medical Institute, Michigan State University, East Lansing, MI 48824, USA; Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA.
| | - Sheng Yang He
- Howard Hughes Medical Institute, Michigan State University, East Lansing, MI 48824, USA; Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA; Plant Resilient Institute, Michigan State University, East Lansing, MI 48824, USA.
| |
Collapse
|
23
|
Dakhiya Y, Green RM. Thermal imaging as a noninvasive technique for analyzing circadian rhythms in plants. THE NEW PHYTOLOGIST 2019; 224:1685-1696. [PMID: 31411748 DOI: 10.1111/nph.16124] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 07/17/2019] [Indexed: 06/10/2023]
Abstract
Endogenous (˜24 circadian) rhythms control an enormously diverse range of processes in plants and are, increasingly, the target of studies aimed at understanding plant performance. Although in the previous few decades most plant circadian research has focused on Arabidopsis, there is a pressing need for low-cost, high-throughput tools for analyzing rhythms in a wider variety of species. The present contribution investigates using circadian temperature oscillations as a novel marker for assaying plant circadian rhythms. A thermal imaging platform was set up to measure diel and circadian rhythms in different plant species, in wild-type and circadian mutant plants, and in leaves and flowers. Results from the thermal imaging technique were compared with those from other established circadian assay techniques. All of the dicot and monocot species examined showed robust circadian rhythms of leaf surface temperature; the effects of circadian mutations on thermocycles were similar to those reported using other techniques. In Petunia × atkinsiana plants circadian oscillations were observed in both leaves and flowers. Thermal imaging is an extremely useful technique for analyzing circadian rhythms in plants. It is predicted that the ability to make very high temporal resolution measurements may facilitate the discovery of novel aspects of circadian control.
Collapse
Affiliation(s)
- Yuri Dakhiya
- Department of Plant and Environmental Sciences, The Silberman Institute for Life Sciences, The Hebrew University, Givat Ram, Jerusalem, 91904, Israel
| | - Rachel M Green
- Department of Plant and Environmental Sciences, The Silberman Institute for Life Sciences, The Hebrew University, Givat Ram, Jerusalem, 91904, Israel
| |
Collapse
|
24
|
Panter PE, Muranaka T, Cuitun-Coronado D, Graham CA, Yochikawa A, Kudoh H, Dodd AN. Circadian Regulation of the Plant Transcriptome Under Natural Conditions. Front Genet 2019; 10:1239. [PMID: 31850080 PMCID: PMC6895068 DOI: 10.3389/fgene.2019.01239] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 11/08/2019] [Indexed: 11/16/2022] Open
Abstract
Circadian rhythms produce a biological measure of the time of day. In plants, circadian regulation forms an essential adaptation to the fluctuating environment. Most of our knowledge of the molecular aspects of circadian regulation in plants is derived from laboratory experiments that are performed under controlled conditions. However, it is emerging that the circadian clock has complex roles in the coordination of the transcriptome under natural conditions, in both naturally occurring populations of plants and in crop species. In this review, we consider recent insights into circadian regulation under natural conditions. We examine how circadian regulation is integrated with the acute responses of plants to the daily and seasonally fluctuating environment that also presents environmental stresses, in order to coordinate the transcriptome and dynamically adapt plants to their continuously changing environment.
Collapse
Affiliation(s)
- Paige E. Panter
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | | | - David Cuitun-Coronado
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Calum A. Graham
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Aline Yochikawa
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Otsu, Japan
| | - Antony N. Dodd
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| |
Collapse
|
25
|
Mwimba M, Dong X. Quantification of the humidity effect on HR by Ion leakage assay. Bio Protoc 2019; 9:e3203. [PMID: 33654999 PMCID: PMC7854056 DOI: 10.21769/bioprotoc.3203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 03/24/2019] [Accepted: 03/18/2019] [Indexed: 11/02/2022] Open
Abstract
We describe a protocol to measure the contribution of humidity on cell death during the effector-triggered immunity (ETI), the plant immune response triggered by the recognition of pathogen effectors by plant resistance genes. This protocol quantifies tissue cell death by measuring ion leakage due to loss of membrane integrity during the hypersensitive response (HR), the ETI-associated cell death. The method is simple and short enough to handle many biological replicates, which improves the power of test of statistical significance. The protocol is easily applicable to other environmental cues, such as light and temperature, or treatment with chemicals.
Collapse
Affiliation(s)
- Musoki Mwimba
- Department of Biology, PO Box 90338, Duke University, Durham, North Carolina 27708, USA
| | - Xinnian Dong
- Department of Biology, PO Box 90338, Duke University, Durham, North Carolina 27708, USA
| |
Collapse
|
26
|
Feke A, Liu W, Hong J, Li MW, Lee CM, Zhou EK, Gendron JM. Decoys provide a scalable platform for the identification of plant E3 ubiquitin ligases that regulate circadian function. eLife 2019; 8:44558. [PMID: 30950791 PMCID: PMC6483598 DOI: 10.7554/elife.44558] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/04/2019] [Indexed: 12/30/2022] Open
Abstract
The circadian clock relies on regulated degradation of clock proteins to maintain rhythmicity. Despite this, we know few components that mediate protein degradation. This is due to high levels of functional redundancy within plant E3 ubiquitin ligase families. In order to overcome this issue and discover E3 ubiquitin ligases that control circadian function, we generated a library of transgenic Arabidopsis plants expressing dominant-negative ‘decoy’ E3 ubiquitin ligases. We determined their effects on the circadian clock and identified dozens of new potential regulators of circadian function. To demonstrate the potency of the decoy screening methodology to overcome redundancy and identify bona fide clock regulators, we performed follow-up studies on MAC3A (PUB59) and MAC3B (PUB60). We show that they redundantly control circadian period by regulating splicing. This work demonstrates the viability of ubiquitin ligase decoys as a screening platform to overcome genetic challenges and discover E3 ubiquitin ligases that regulate plant development. Plants have an internal time keeper known as the circadian clock that operates in 24-hour cycles to coordinate the plants behaviors with the environment. The clock is made of many different proteins and plants carefully control when they make and destroy these proteins to regulate the cycle. Inside plant cells, enzymes known as E3 ubiquitin ligases determine which proteins are destroyed by labelling target proteins with a small tag. Plants have hundreds of different E3 ubiquitin ligases, leading to overlaps in the roles the different enzymes play. These overlaps make it difficult to identify the specific E3 ubiquitin ligases that are involved in a particular process. As a result, only few E3 ubiquitin ligases implicated in the circadian clock have been identified so far. A small weed known as Arabidopsis is often used in research studies because it grows quickly and the genes can be easily manipulated. Here, Feke et al. set out to develop a new tool to identify the specific E3 ubiquitin ligases involved in regulating the circadian clock in Arabidopsis. The team created a library of hundreds of Arabidopsis plants producing different decoy E3 ubiquitin ligases that retained their ability to bind to target proteins but were unable to degrade them. Nearly a quarter of the E3 ligases found in Arabidopsis were represented in this library. The decoy enzymes protected the target proteins from being degraded by the normal E3 ubiquitin ligases, resulting in the library plants having presumably higher levels of these target proteins compared to normal Arabidopsis plants. By tracking circadian rhythms in these plants, the team was able to identify the individual E3 ligases that control the circadian clock. The experiments revealed several E3 ligases that may regulate the circadian clock, including two enzymes called MAC3A and MAC3B. Further experiments demonstrated that MAC3A and MAC3B have similar roles in regulating the circadian clock and can compensate for the absence of the other. The library of Arabidopsis plants generated by Feke et al. is now available for other researchers to use in their studies. In the future this approach could be adapted to make similar libraries for crops and other plants that have even more E3 ligase enzymes than Arabidopsis.
Collapse
Affiliation(s)
- Ann Feke
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
| | - Wei Liu
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
| | - Jing Hong
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States.,School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Man-Wah Li
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
| | - Chin-Mei Lee
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
| | - Elton K Zhou
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
| | - Joshua M Gendron
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
| |
Collapse
|