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Zhang J, Jin H, Chen Y, Jiang Y, Gu L, Lin G, Lin C, Wang Q. The eukaryotic translation initiation factor eIF4E regulates flowering and circadian rhythm in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39145515 DOI: 10.1111/tpj.16975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 07/24/2024] [Accepted: 07/29/2024] [Indexed: 08/16/2024]
Abstract
Translation initiation is a critical, rate-limiting step in protein synthesis. The eukaryotic translation initiation factor 4E (eIF4E) plays an essential role in this process. However, the mechanisms by which eIF4E-dependent translation initiation regulates plant growth and development remain not fully understood. In this study, we found that Arabidopsis eIF4E proteins are distributed in both the nucleus and cytoplasm, with only the cytoplasmic eIF4E being involved in the control of photoperiodic flowering. Genome-wide translation profiling using Ribo-tag sequencing reveals that eIF4E may regulate plant flowering by maintaining the homeostatic translation of components in the photoperiodic flowering pathway. eIF4E not only regulates the translation of flowering genes such as FLOWERING LOCUS T (FT) and FLOWERING LOCUS D (FLD) but also influences the translation of circadian genes like CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and PSEUDO-RESPONSE REGULATOR 9 (PRR9). Consistently, our results show that the eIF4E modulates the rhythmic oscillation of the circadian clock. Together, our study provides mechanistic insights into how the protein translation regulates multiple developmental processes in Arabidopsis, including the circadian clock and photoperiodic flowering.
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Affiliation(s)
- Jing Zhang
- College of Life Sciences, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huanhuan Jin
- College of Life Sciences, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yadi Chen
- College of Life Sciences, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yonghong Jiang
- College of Life Sciences, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lianfeng Gu
- College of Life Sciences, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Guifang Lin
- College of Life Sciences, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chentao Lin
- College of Life Sciences, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qin Wang
- College of Life Sciences, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
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2
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Kulesza E, Thomas P, Prewitt SF, Shalit-Kaneh A, Wafula E, Knollenberg B, Winters N, Esteban E, Pasha A, Provart N, Praul C, Landherr L, dePamphilis C, Maximova SN, Guiltinan MJ. The cacao gene atlas: a transcriptome developmental atlas reveals highly tissue-specific and dynamically-regulated gene networks in Theobroma cacao L. BMC PLANT BIOLOGY 2024; 24:601. [PMID: 38926852 PMCID: PMC11201900 DOI: 10.1186/s12870-024-05171-9] [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: 09/05/2023] [Accepted: 05/19/2024] [Indexed: 06/28/2024]
Abstract
BACKGROUND Theobroma cacao, the cocoa tree, is a tropical crop grown for its highly valuable cocoa solids and fat which are the basis of a 200-billion-dollar annual chocolate industry. However, the long generation time and difficulties associated with breeding a tropical tree crop have limited the progress of breeders to develop high-yielding disease-resistant varieties. Development of marker-assisted breeding methods for cacao requires discovery of genomic regions and specific alleles of genes encoding important traits of interest. To accelerate gene discovery, we developed a gene atlas composed of a large dataset of replicated transcriptomes with the long-term goal of progressing breeding towards developing high-yielding elite varieties of cacao. RESULTS We describe the creation of the Cacao Transcriptome Atlas, its global characterization and define sets of genes co-regulated in highly organ- and temporally-specific manners. RNAs were extracted and transcriptomes sequenced from 123 different tissues and stages of development representing major organs and developmental stages of the cacao lifecycle. In addition, several experimental treatments and time courses were performed to measure gene expression in tissues responding to biotic and abiotic stressors. Samples were collected in replicates (3-5) to enable statistical analysis of gene expression levels for a total of 390 transcriptomes. To promote wide use of these data, all raw sequencing data, expression read mapping matrices, scripts, and other information used to create the resource are freely available online. We verified our atlas by analyzing the expression of genes with known functions and expression patterns in Arabidopsis (ACT7, LEA19, AGL16, TIP13, LHY, MYB2) and found their expression profiles to be generally similar between both species. We also successfully identified tissue-specific genes at two thresholds in many tissue types represented and a set of genes highly conserved across all tissues. CONCLUSION The Cacao Gene Atlas consists of a gene expression browser with graphical user interface and open access to raw sequencing data files as well as the unnormalized and CPM normalized read count data mapped to several cacao genomes. The gene atlas is a publicly available resource to allow rapid mining of cacao gene expression profiles. We hope this resource will be used to help accelerate the discovery of important genes for key cacao traits such as disease resistance and contribute to the breeding of elite varieties to help farmers increase yields.
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Affiliation(s)
- Evelyn Kulesza
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
- Huck Institute of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Patrick Thomas
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Sarah F Prewitt
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
- USDA Animal and Plant Health Inspection Service (APHIS), Riverdale, MD, 20737, USA
| | - Akiva Shalit-Kaneh
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
- Plant Sciences, Volcani-ARO (Agricultural and Rural Organization), Gilat, Israel
| | - Eric Wafula
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
- Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Benjamin Knollenberg
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
- Mars Inc, Davis, CA, 95616, USA
| | - Noah Winters
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
- Battelle Memorial Institute, Columbus, OH, 43201, USA
| | - Eddi Esteban
- Department of Cell & Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
| | - Asher Pasha
- Department of Cell & Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
| | - Nicholas Provart
- Department of Cell & Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
| | - Craig Praul
- Huck Institute of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Lena Landherr
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Claude dePamphilis
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
- Huck Institute of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Siela N Maximova
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
- Huck Institute of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Mark J Guiltinan
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA.
- Huck Institute of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.
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Touitou Y, Cermakian N, Touitou C. The environment and the internal clocks: The study of their relationships from prehistoric to modern times. Chronobiol Int 2024; 41:859-887. [PMID: 38757600 DOI: 10.1080/07420528.2024.2353857] [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: 02/14/2024] [Accepted: 05/03/2024] [Indexed: 05/18/2024]
Abstract
The origin of biological rhythms goes back to the very beginning of life. They are observed in the animal and plant world at all levels of organization, from cells to ecosystems. As early as the 18th century, plant scientists were the first to explain the relationship between flowering cycles and environmental cycles, emphasizing the importance of daily light-dark cycles and the seasons. Our temporal structure is controlled by external and internal rhythmic signals. Light is the main synchronizer of the circadian system, as daily exposure to light entrains our clock over 24 hours, the endogenous period of the circadian system being close to, but not exactly, 24 hours. In 1960, a seminal scientific meeting, the Cold Spring Harbor Symposium on Biological Rhythms, brought together all the biological rhythms scientists of the time, a number of whom are considered the founders of modern chronobiology. All aspects of biological rhythms were addressed, from the properties of circadian rhythms to their practical and ecological aspects. Birth of chronobiology dates from this period, with the definition of its vocabulary and specificities in metabolism, photoperiodism, animal physiology, etc. At around the same time, and right up to the present day, research has focused on melatonin, the circadian neurohormone of the pineal gland, with data on its pattern, metabolism, control by light and clinical applications. However, light has a double face, as it has positive effects as a circadian clock entraining agent, but also deleterious effects, as it can lead to chronodisruption when exposed chronically at night, which can increase the risk of cancer and other diseases. Finally, research over the past few decades has unraveled the anatomical location of circadian clocks and their cellular and molecular mechanisms. This recent research has in turn allowed us to explain how circadian rhythms control physiology and health.
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Affiliation(s)
- Yvan Touitou
- Unité de Chronobiologie, Fondation A. de Rothschild, Paris, France
| | - Nicolas Cermakian
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec, Canada
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Edet OU, Ubi BE, Ishii T. Genomic analysis of a spontaneous unifoliate mutant reveals gene candidates associated with compound leaf development in Vigna unguiculata [L] Walp. Sci Rep 2024; 14:10654. [PMID: 38724579 PMCID: PMC11082238 DOI: 10.1038/s41598-024-61062-x] [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: 01/29/2024] [Accepted: 04/30/2024] [Indexed: 05/12/2024] Open
Abstract
Molecular mechanisms which underpin compound leaf development in some legumes have been reported, but there is no previous study on the molecular genetic control of compound leaf formation in Vigna unguiculata (cowpea), an important dryland legume of African origin. In most studied species with compound leaves, class 1 KNOTTED-LIKE HOMEOBOX genes expressed in developing leaf primordia sustain morphogenetic activity, allowing leaf dissection and the development of leaflets. Other genes, such as, SINGLE LEAFLET1 in Medicago truncatula and Trifoliate in Solanum lycopersicum, are also implicated in regulating compound leaf patterning. To set the pace for an in-depth understanding of the genetics of compound leaf development in cowpea, we applied RNA-seq and whole genome shotgun sequence datasets of a spontaneous cowpea unifoliate mutant and its trifoliate wild-type cultivar to conduct comparative reference-based gene expression, de novo genome-wide isoform switch, and genome variant analyses between the two genotypes. Our results suggest that genomic variants upstream of LATE ELONGATED HYPOCOTYL and down-stream of REVEILLE4, BRASSINOSTERIOD INSENSITIVE1 and LATERAL ORGAN BOUNDARIES result in down-regulation of key components of cowpea circadian rhythm central oscillator and brassinosteroid signaling, resulting in unifoliate leaves and brassinosteroid-deficient-like phenotypes. We have stated hypotheses that will guide follow-up studies expected to provide more insights.
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Affiliation(s)
- Offiong Ukpong Edet
- Arid Land Research Center, Tottori University, Tottori, 680-0001, Japan.
- Department of Crop Science, University of Calabar, PMB 1115, Calabar, Cross River State, Nigeria.
| | - Benjamin Ewa Ubi
- Department of Biotechnology, Ebonyi State University, Abakaliki, Ebonyi State, Nigeria
| | - Takayoshi Ishii
- Arid Land Research Center, Tottori University, Tottori, 680-0001, Japan.
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Liu Y, Luo C, Lan M, Guo Y, Li R, Liang R, Chen S, Zhong J, Li B, Xie F, Chen C, He X. MiCOL6, MiCOL7A and MiCOL7B isolated from mango regulate flowering and stress response in transgenic Arabidopsis. PHYSIOLOGIA PLANTARUM 2024; 176:e14242. [PMID: 38439528 DOI: 10.1111/ppl.14242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/02/2024] [Accepted: 02/20/2024] [Indexed: 03/06/2024]
Abstract
The CONSTANS/CONSTANS-Like (CO/COL) family has been shown to play important roles in flowering, stress tolerance, fruit development and ripening in higher plants. In this study, three COL genes, MiCOL6, MiCOL7A and MiCOL7B, which each contain only one CCT domain, were isolated from mango (Mangifera indica), and their functions were investigated. MiCOL7A and MiCOL7B were expressed mainly at 20 days after flowering (DAF), and all three genes were highly expressed during the flowering induction period. The expression levels of the three genes were affected by light conditions, but only MiCOL6 exhibited a clear circadian rhythm. Overexpression of MiCOL6 promoted earlier flowering, while overexpression of MiCOL7A or MiCOL7B delayed flowering compared to that in the control lines of Arabidopsis thaliana under long-day (LD) and short-day (SD) conditions. Overexpressing MiCOL6, MiCOL7A or MiCOL7B in transgenic plants increased superoxide dismutase (SOD) and proline levels, decreased malondialdehyde (MAD) levels, and improved survival under drought and salt stress. In addition, yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) analyses showed that the MiCOL6, MiCOL7A and MiCOL7B proteins interact with several stress- and flower-related proteins. This work demonstrates the functions of MiCOL6, MiCOL7A and MiCOL7B and provides a foundation for further research on the role of mango COL genes in flowering regulation and the abiotic stress response.
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Affiliation(s)
- Yuan Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi
| | - Cong Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi
| | - Moying Lan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi
| | - Yihang Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi
- College of Agronomy and Horticulture, Huaihua Polytechnic College, Huaihua, Hunan
| | - Ruoyan Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi
| | - Rongzhen Liang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi
| | - Shuquan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi
| | - Junjie Zhong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi
| | - Baijun Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi
| | - Fangfang Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi
| | - Canbin Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi
| | - Xinhua He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi
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6
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Dwivedi SL, Quiroz LF, Spillane C, Wu R, Mattoo AK, Ortiz R. Unlocking allelic variation in circadian clock genes to develop environmentally robust and productive crops. PLANTA 2024; 259:72. [PMID: 38386103 PMCID: PMC10884192 DOI: 10.1007/s00425-023-04324-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/24/2023] [Indexed: 02/23/2024]
Abstract
MAIN CONCLUSION Molecular mechanisms of biological rhythms provide opportunities to harness functional allelic diversity in core (and trait- or stress-responsive) oscillator networks to develop more climate-resilient and productive germplasm. The circadian clock senses light and temperature in day-night cycles to drive biological rhythms. The clock integrates endogenous signals and exogenous stimuli to coordinate diverse physiological processes. Advances in high-throughput non-invasive assays, use of forward- and inverse-genetic approaches, and powerful algorithms are allowing quantitation of variation and detection of genes associated with circadian dynamics. Circadian rhythms and phytohormone pathways in response to endogenous and exogenous cues have been well documented the model plant Arabidopsis. Novel allelic variation associated with circadian rhythms facilitates adaptation and range expansion, and may provide additional opportunity to tailor climate-resilient crops. The circadian phase and period can determine adaptation to environments, while the robustness in the circadian amplitude can enhance resilience to environmental changes. Circadian rhythms in plants are tightly controlled by multiple and interlocked transcriptional-translational feedback loops involving morning (CCA1, LHY), mid-day (PRR9, PRR7, PRR5), and evening (TOC1, ELF3, ELF4, LUX) genes that maintain the plant circadian clock ticking. Significant progress has been made to unravel the functions of circadian rhythms and clock genes that regulate traits, via interaction with phytohormones and trait-responsive genes, in diverse crops. Altered circadian rhythms and clock genes may contribute to hybrid vigor as shown in Arabidopsis, maize, and rice. Modifying circadian rhythms via transgenesis or genome-editing may provide additional opportunities to develop crops with better buffering capacity to environmental stresses. Models that involve clock gene‒phytohormone‒trait interactions can provide novel insights to orchestrate circadian rhythms and modulate clock genes to facilitate breeding of all season crops.
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Affiliation(s)
| | - Luis Felipe Quiroz
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, Galway, H91 REW4, Ireland
| | - Charles Spillane
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, Galway, H91 REW4, Ireland.
| | - Rongling Wu
- Beijing Yanqi Lake Institute of Mathematical Sciences and Applications, Beijing, 101408, China
| | - Autar K Mattoo
- USDA-ARS, Sustainable Agricultural Systems Laboratory, Beltsville, MD, 20705-2350, USA
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Sundsvagen, 10, Box 190, SE 23422, Lomma, Sweden.
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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.
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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
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Cuellar P, Castañeda-Ortiz EJ, Rosales-Zarza C, Martínez-Rodríguez CE, Canela-Pérez I, Rodríguez MA, Valdés J, Azuara-Liceaga E. Genome-Wide Classification of Myb Domain-Containing Protein Families in Entamoeba invadens. Genes (Basel) 2024; 15:201. [PMID: 38397191 PMCID: PMC10887745 DOI: 10.3390/genes15020201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 01/22/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
Entamoeba histolytica, the causative agent of amebiasis, is the third leading cause of death among parasitic diseases globally. Its life cycle includes encystation, which has been mostly studied in Entamoeba invadens, responsible for reptilian amebiasis. However, the molecular mechanisms underlying this process are not fully understood. Therefore, we focused on the identification and characterization of Myb proteins, which regulate the expression of encystation-related genes in various protozoan parasites. Through bioinformatic analysis, we identified 48 genes in E. invadens encoding MYB-domain-containing proteins. These were classified into single-repeat 1R (20), 2R-MYB proteins (27), and one 4R-MYB protein. The in-silico analysis suggests that these proteins are multifunctional, participating in transcriptional regulation, chromatin remodeling, telomere maintenance, and splicing. Transcriptomic data analysis revealed expression signatures of eimyb genes, suggesting a potential orchestration in the regulation of early and late encystation-excystation genes. Furthermore, we identified probable target genes associated with reproduction, the meiotic cell cycle, ubiquitin-dependent protein catabolism, and endosomal transport. In conclusion, our findings suggest that E. invadens Myb proteins regulate stage-specific proteins and a wide array of cellular processes. This study provides a foundation for further exploration of the molecular mechanisms governing encystation and unveils potential targets for therapeutic intervention in amebiasis.
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Affiliation(s)
- Patricia Cuellar
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City C.P. 03100, Mexico; (P.C.); (E.J.C.-O.)
| | - Elizabeth J. Castañeda-Ortiz
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City C.P. 03100, Mexico; (P.C.); (E.J.C.-O.)
| | - César Rosales-Zarza
- Licenciatura Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City C.P. 03100, Mexico;
| | | | - Israel Canela-Pérez
- Departamento de Bioquímica, CINVESTAV-IPN, Mexico City C.P. 07360, Mexico; (I.C.-P.); (J.V.)
| | - Mario Alberto Rodríguez
- Departamento de Infectómica y Patogénesis Molecular, CINVESTAV-IPN, Mexico City C.P. 07360, Mexico;
| | - Jesús Valdés
- Departamento de Bioquímica, CINVESTAV-IPN, Mexico City C.P. 07360, Mexico; (I.C.-P.); (J.V.)
| | - Elisa Azuara-Liceaga
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City C.P. 03100, Mexico; (P.C.); (E.J.C.-O.)
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9
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Lee J, Yang JH, Weber APM, Bhattacharya D, Kim WY, Yoon HS. Diurnal Rhythms in the Red Seaweed Gracilariopsis chorda are Characterized by Unique Regulatory Networks of Carbon Metabolism. Mol Biol Evol 2024; 41:msae012. [PMID: 38267085 PMCID: PMC10853006 DOI: 10.1093/molbev/msae012] [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: 09/09/2023] [Revised: 01/01/2024] [Accepted: 01/08/2024] [Indexed: 01/26/2024] Open
Abstract
Cellular and physiological cycles are driven by endogenous pacemakers, the diurnal and circadian rhythms. Key functions such as cell cycle progression and cellular metabolism are under rhythmic regulation, thereby maintaining physiological homeostasis. The photoreceptors phytochrome and cryptochrome, in response to light cues, are central input pathways for physiological cycles in most photosynthetic organisms. However, among Archaeplastida, red algae are the only taxa that lack phytochromes. Current knowledge about oscillatory rhythms is primarily derived from model species such as Arabidopsis thaliana and Chlamydomonas reinhardtii in the Viridiplantae, whereas little is known about these processes in other clades of the Archaeplastida, such as the red algae (Rhodophyta). We used genome-wide expression profiling of the red seaweed Gracilariopsis chorda and identified 3,098 rhythmic genes. Here, we characterized possible cryptochrome-based regulation and photosynthetic/cytosolic carbon metabolism in this species. We found a large family of cryptochrome genes in G. chorda that display rhythmic expression over the diurnal cycle and may compensate for the lack of phytochromes in this species. The input pathway gates regulatory networks of carbon metabolism which results in a compact and efficient energy metabolism during daylight hours. The system in G. chorda is distinct from energy metabolism in most plants, which activates in the dark. The green lineage, in particular, land plants, balance water loss and CO2 capture in terrestrial environments. In contrast, red seaweeds maintain a reduced set of photoreceptors and a compact cytosolic carbon metabolism to thrive in the harsh abiotic conditions typical of intertidal zones.
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Affiliation(s)
- JunMo Lee
- Department of Oceanography, Kyungpook National University, Daegu 41566, Korea
- Kyungpook Institute of Oceanography, Kyungpook National University, Daegu 41566, Korea
| | - Ji Hyun Yang
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Korea
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21 four), Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Korea
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Korea
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10
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Wang X, Hao Y, Altaf MA, Shu H, Cheng S, Wang Z, Zhu G. Evolution and Dynamic Transcriptome of Key Genes of Photoperiodic Flowering Pathway in Water Spinach ( Ipomoea aquatica). Int J Mol Sci 2024; 25:1420. [PMID: 38338699 PMCID: PMC10855745 DOI: 10.3390/ijms25031420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/09/2024] [Accepted: 01/16/2024] [Indexed: 02/12/2024] Open
Abstract
The photoperiod is a major environmental factor in flowering control. Water spinach flowering under the inductive short-day condition decreases the yield of vegetative tissues and the eating quality. To obtain an insight into the molecular mechanism of the photoperiod-dependent regulation of the flowering time in water spinach, we performed transcriptome sequencing on water spinach under long- and short-day conditions with eight time points. Our results indicated that there were 6615 circadian-rhythm-related genes under the long-day condition and 8691 under the short-day condition. The three key circadian-rhythm genes, IaCCA1, IaLHY, and IaTOC1, still maintained single copies and similar IaCCA1, IaLHY, and IaTOC1 feedback expression patterns, indicating the conservation of reverse feedback. In the photoperiod pathway, highly conserved GI genes were amplified into two copies (IaGI1 and IaGI2) in water spinach. The significant difference in the expression of the two genes indicates functional diversity. Although the photoperiod core gene FT was duplicated to three copies in water spinach, only IaFT1 was highly expressed and strongly responsive to the photoperiod and circadian rhythms, and the almost complete inhibition of IaFT1 in water spinach may be the reason why water spinach does not bloom, no matter how long it lasts under the long-day condition. Differing from other species (I. nil, I. triloba, I. trifida) of the Ipomoea genus that have three CO members, water spinach lacks one of them, and the other two CO genes (IaCO1 and IaCO2) encode only one CCT domain. In addition, through weighted correlation network analysis (WGCNA), some transcription factors closely related to the photoperiod pathway were obtained. This work provides valuable data for further in-depth analyses of the molecular regulation of the flowering time in water spinach and the Ipomoea genus.
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Affiliation(s)
- Xin Wang
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; (X.W.); (Y.H.); (M.A.A.); (H.S.); (S.C.)
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Yuanyuan Hao
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; (X.W.); (Y.H.); (M.A.A.); (H.S.); (S.C.)
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Muhammad Ahsan Altaf
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; (X.W.); (Y.H.); (M.A.A.); (H.S.); (S.C.)
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Huangying Shu
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; (X.W.); (Y.H.); (M.A.A.); (H.S.); (S.C.)
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Shanhan Cheng
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; (X.W.); (Y.H.); (M.A.A.); (H.S.); (S.C.)
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Zhiwei Wang
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; (X.W.); (Y.H.); (M.A.A.); (H.S.); (S.C.)
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Guopeng Zhu
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; (X.W.); (Y.H.); (M.A.A.); (H.S.); (S.C.)
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
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11
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Hu Z, Zhang N, Qin Z, Li J, Yang N, Chen Y, Kong J, Luo W, Xiong A, Zhuang J. Differential Response of MYB Transcription Factor Gene Transcripts to Circadian Rhythm in Tea Plants ( Camellia sinensis). Int J Mol Sci 2024; 25:657. [PMID: 38203827 PMCID: PMC10780195 DOI: 10.3390/ijms25010657] [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: 09/23/2023] [Revised: 12/31/2023] [Accepted: 01/02/2024] [Indexed: 01/12/2024] Open
Abstract
The circadian clock refers to the formation of a certain rule in the long-term evolution of an organism, which is an invisible 'clock' in the body of an organism. As one of the largest TF families in higher plants, the MYB transcription factor is involved in plant growth and development. MYB is also inextricably correlated with the circadian rhythm. In this study, the transcriptome data of the tea plant 'Baiyeyihao' were measured at a photoperiod interval of 4 h (24 h). A total of 25,306 unigenes were obtained, including 14,615 unigenes that were annotated across 20 functional categories within the GO classification. Additionally, 10,443 single-gene clusters were annotated to 11 sublevels of metabolic pathways using KEGG. Based on the results of gene annotation and differential gene transcript analysis, 22 genes encoding MYB transcription factors were identified. The G10 group in the phylogenetic tree had 13 members, of which 5 were related to the circadian rhythm, accounting for 39%. The G1, G2, G8, G9, G15, G16, G18, G19, G20, G21 and G23 groups had no members associated with the circadian rhythm. Among the 22 differentially expressed MYB transcription factors, 3 members of LHY, RVE1 and RVE8 were core circadian rhythm genes belonging to the G10, G12 and G10 groups, respectively. Real-time fluorescence quantitative PCR was used to detect and validate the expression of the gene transcripts encoding MYB transcription factors associated with the circadian rhythm.
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Affiliation(s)
- Zhihang Hu
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (Z.H.); (Z.Q.); (J.L.); (N.Y.); (Y.C.); (J.K.); (W.L.)
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China;
| | - Nan Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China;
| | - Zhiyuan Qin
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (Z.H.); (Z.Q.); (J.L.); (N.Y.); (Y.C.); (J.K.); (W.L.)
| | - Jinwen Li
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (Z.H.); (Z.Q.); (J.L.); (N.Y.); (Y.C.); (J.K.); (W.L.)
| | - Ni Yang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (Z.H.); (Z.Q.); (J.L.); (N.Y.); (Y.C.); (J.K.); (W.L.)
| | - Yi Chen
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (Z.H.); (Z.Q.); (J.L.); (N.Y.); (Y.C.); (J.K.); (W.L.)
| | - Jieyu Kong
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (Z.H.); (Z.Q.); (J.L.); (N.Y.); (Y.C.); (J.K.); (W.L.)
| | - Wei Luo
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (Z.H.); (Z.Q.); (J.L.); (N.Y.); (Y.C.); (J.K.); (W.L.)
| | - Aisheng Xiong
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China;
| | - Jing Zhuang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (Z.H.); (Z.Q.); (J.L.); (N.Y.); (Y.C.); (J.K.); (W.L.)
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12
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James AB, Sharples C, Laird J, Armstrong EM, Guo W, Tzioutziou N, Zhang R, Brown JWS, Nimmo HG, Jones MA. REVEILLE2 thermosensitive splicing: a molecular basis for the integration of nocturnal temperature information by the Arabidopsis circadian clock. THE NEW PHYTOLOGIST 2024; 241:283-297. [PMID: 37897048 DOI: 10.1111/nph.19339] [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: 05/07/2023] [Accepted: 09/27/2023] [Indexed: 10/29/2023]
Abstract
Cold stress is one of the major environmental factors that limit growth and yield of plants. However, it is still not fully understood how plants account for daily temperature fluctuations, nor how these temperature changes are integrated with other regulatory systems such as the circadian clock. We demonstrate that REVEILLE2 undergoes alternative splicing after chilling that increases accumulation of a transcript isoform encoding a MYB-like transcription factor. We explore the biological function of REVEILLE2 in Arabidopsis thaliana using a combination of molecular genetics, transcriptomics, and physiology. Disruption of REVEILLE2 alternative splicing alters regulatory gene expression, impairs circadian timing, and improves photosynthetic capacity. Changes in nuclear gene expression are particularly apparent in the initial hours following chilling, with chloroplast gene expression subsequently upregulated. The response of REVEILLE2 to chilling extends our understanding of plants immediate response to cooling. We propose that the circadian component REVEILLE2 restricts plants responses to nocturnal reductions in temperature, thereby enabling appropriate responses to daily environmental changes.
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Affiliation(s)
- Allan B James
- School of Molecular Biosciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Chantal Sharples
- School of Molecular Biosciences, University of Glasgow, Glasgow, G12 8QQ, UK
- RNA Biology and Molecular Physiology, Faculty for Biology, Bielefeld University, Universitaetsstrasse 25, 33615, Bielefeld, Germany
| | - Janet Laird
- School of Molecular Biosciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Emily May Armstrong
- School of Molecular Biosciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Wenbin Guo
- Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Nikoleta Tzioutziou
- Plant Sciences Division, College of Life Sciences, University of Dundee, Invergowrie, Dundee, DD2 5DA, UK
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Runxuan Zhang
- Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - John W S Brown
- Plant Sciences Division, College of Life Sciences, University of Dundee, Invergowrie, Dundee, DD2 5DA, UK
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Hugh G Nimmo
- School of Molecular Biosciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Matthew A Jones
- School of Molecular Biosciences, University of Glasgow, Glasgow, G12 8QQ, UK
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13
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Liu F, Cai S, Ma Z, Yue H, Xing L, Wang Y, Feng S, Wang L, Dai L, Wan H, Gao J, Chen M, Rahman M, Zhou B. RVE2, a new regulatory factor in jasmonic acid pathway, orchestrates resistance to Verticillium wilt. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2507-2524. [PMID: 37553251 PMCID: PMC10651145 DOI: 10.1111/pbi.14149] [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: 09/12/2022] [Revised: 07/06/2023] [Accepted: 07/27/2023] [Indexed: 08/10/2023]
Abstract
Verticillium dahliae, one of the most destructive fungal pathogens of several crops, challenges the sustainability of cotton productivity worldwide because very few widely-cultivated Upland cotton varieties are resistant to Verticillium wilt (VW). Here, we report that REVEILLE2 (RVE2), the Myb-like transcription factor, confers the novel function in resistance to VW by regulating the jasmonic acid (JA) pathway in cotton. RVE2 expression was essentially required for the activation of JA-mediated disease-resistance response. RVE2 physically interacted with TPL/TPRs and disturbed JAZ proteins to recruit TPL and TPR1 in NINJA-dependent manner, which regulated JA response by relieving inhibited-MYC2 activity. The MYC2 then bound to RVE2 promoter for the activation of its transcription, forming feedback loop. Interestingly, a unique truncated RVE2 widely existing in D-subgenome (GhRVE2D) of natural Upland cotton represses the ability of the MYC2 to activate GhRVE2A promoter but not GausRVE2 or GbRVE2. The result could partially explain why Gossypium barbadense popularly shows higher resistance than Gossypium hirsutum. Furthermore, disturbing the JA-signalling pathway resulted into the loss of RVE2-mediated disease-resistance in various plants (Arabidopsis, tobacco and cotton). RVE2 overexpression significantly enhanced the resistance to VW. Collectively, we conclude that RVE2, a new regulatory factor, plays a pivotal role in fine-tuning JA-signalling, which would improve our understanding the mechanisms underlying the resistance to VW.
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Affiliation(s)
- Fujie Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production co‐sponsored by Jiangsu Province and Ministry of Education, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education)Nanjing Agricultural UniversityNanjingJiangsuChina
| | - Sheng Cai
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production co‐sponsored by Jiangsu Province and Ministry of Education, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education)Nanjing Agricultural UniversityNanjingJiangsuChina
| | - Zhifeng Ma
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production co‐sponsored by Jiangsu Province and Ministry of Education, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education)Nanjing Agricultural UniversityNanjingJiangsuChina
| | - Haoran Yue
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production co‐sponsored by Jiangsu Province and Ministry of Education, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education)Nanjing Agricultural UniversityNanjingJiangsuChina
| | - Liangshuai Xing
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production co‐sponsored by Jiangsu Province and Ministry of Education, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education)Nanjing Agricultural UniversityNanjingJiangsuChina
| | - Yingying Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production co‐sponsored by Jiangsu Province and Ministry of Education, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education)Nanjing Agricultural UniversityNanjingJiangsuChina
| | - Shouli Feng
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production co‐sponsored by Jiangsu Province and Ministry of Education, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education)Nanjing Agricultural UniversityNanjingJiangsuChina
| | - Liang Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production co‐sponsored by Jiangsu Province and Ministry of Education, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education)Nanjing Agricultural UniversityNanjingJiangsuChina
| | - Lingjun Dai
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production co‐sponsored by Jiangsu Province and Ministry of Education, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education)Nanjing Agricultural UniversityNanjingJiangsuChina
| | - Hui Wan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production co‐sponsored by Jiangsu Province and Ministry of Education, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education)Nanjing Agricultural UniversityNanjingJiangsuChina
| | - Jianbo Gao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production co‐sponsored by Jiangsu Province and Ministry of Education, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education)Nanjing Agricultural UniversityNanjingJiangsuChina
| | - Mengfei Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production co‐sponsored by Jiangsu Province and Ministry of Education, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education)Nanjing Agricultural UniversityNanjingJiangsuChina
| | - Mehboob‐ur‐ Rahman
- Plant Genomics & Mol. Breeding LabNational Institute for Biotechnology & Genetic Engineering (NIBGE)FaisalabadPakistan
| | - Baoliang Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production co‐sponsored by Jiangsu Province and Ministry of Education, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education)Nanjing Agricultural UniversityNanjingJiangsuChina
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14
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Faehn C, Reichelt M, Mithöfer A, Hytönen T, Mølmann J, Jaakola L. Acclimation of circadian rhythms in woodland strawberries (Fragaria vesca L.) to Arctic and mid-latitude photoperiods. BMC PLANT BIOLOGY 2023; 23:483. [PMID: 37817085 PMCID: PMC10563271 DOI: 10.1186/s12870-023-04491-6] [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: 12/09/2022] [Accepted: 09/27/2023] [Indexed: 10/12/2023]
Abstract
BACKGROUND Though many abiotic factors are constantly changing, the photoperiod is a predictable factor that enables plants to time many physiological responses. This timing is regulated by the circadian clock, yet little is known about how the clock adapts to the differences in photoperiod between mid-latitudes and high latitudes. The primary objective of this study was to compare how clock gene expression is modified in four woodland strawberry (Fragaria vesca L.) accessions originating from two different populations in Italy (IT1: Tenno, Italy, 45°N, IT4: Salorno, Italy, 46°N) and two in Northern Norway (NOR2: Alta, Norway, 69°N, NOR13: Indre Nordnes, Norway 69°N) when grown under simulated daylength conditions of an Arctic or mid-latitude photoperiod. The second objective was to investigate whether population origin or the difference in photoperiod influenced phytohormone accumulation. RESULTS The Arctic photoperiod induced lower expression in IT4 and NOR13 for six clock genes (FvLHY, FvRVE8, FvPRR9, FvPRR7, FvPRR5, and FvLUX), in IT1 for three genes (FvLHY, FvPRR9, and FvPRR5) and in NOR2 for one gene (FvPRR9). Free-running rhythms for FvLHY in IT1 and IT4 were higher after the Arctic photoperiod, while the free-running rhythm for FvLUX in IT4 was higher after the mid-latitude photoperiod. IT1 showed significantly higher expression of FvLHY and FvPRR9 than all other accessions, as well as significantly higher expression of the circadian regulated phytohormone, abscisic acid (ABA), but low levels of salicylic acid (SA). NOR13 had significantly higher expression of FvRVE8, FvTOC1, and FvLUX than all other accessions. NOR2 had extremely low levels of auxin (IAA) and high levels of the jasmonate catabolite, hydroxyjasmonic acid (OH-JA). CONCLUSIONS Our study shows that circadian rhythms in Fragaria vesca are driven by both the experienced photoperiod and genetic factors, while phytohormone levels are primarily determined by specific accessions' genetic factors rather than the experienced photoperiod.
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Affiliation(s)
- Corine Faehn
- Department of Arctic and Marine Biology, The Arctic University of Norway, Tromsø, 9037, Norway.
| | - Michael Reichelt
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, 07745, Jena, Germany
| | - Axel Mithöfer
- Research Group Plant Defense Physiology, Max Planck Institute for Chemical Ecology, 07745, Jena, Germany
| | - Timo Hytönen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, 00790, Finland
| | - Jørgen Mølmann
- NIBIO, Norwegian Institute of Bioeconomy Research, P.O. Box 115, Ås, 1431, Norway
| | - Laura Jaakola
- Department of Arctic and Marine Biology, The Arctic University of Norway, Tromsø, 9037, Norway
- NIBIO, Norwegian Institute of Bioeconomy Research, P.O. Box 115, Ås, 1431, Norway
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15
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Grant NP, Toy JJ, Funnell-Harris DL, Sattler SE. Deleterious mutations predicted in the sorghum (Sorghum bicolor) Maturity (Ma) and Dwarf (Dw) genes from whole-genome resequencing. Sci Rep 2023; 13:16638. [PMID: 37789045 PMCID: PMC10547693 DOI: 10.1038/s41598-023-42306-8] [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: 05/10/2023] [Accepted: 09/07/2023] [Indexed: 10/05/2023] Open
Abstract
In sorghum [Sorghum bicolor (L.) Moench] the Maturity (Ma1, Ma2, Ma3, Ma4, Ma5, Ma6) and Dwarf (Dw1, Dw2, Dw3, Dw4) loci, encode genes controlling flowering time and plant height, respectively, which are critical for designing sorghum ideotypes for a maturity timeframe and a harvest method. Publicly available whole-genome resequencing data from 860 sorghum accessions was analyzed in silico to identify genomic variants at 8 of these loci (Ma1, Ma2, Ma3, Ma5, Ma6, Dw1, Dw2, Dw3) to identify novel loss of function alleles and previously characterized ones in sorghum germplasm. From ~ 33 million SNPs and ~ 4.4 million InDels, 1445 gene variants were identified within these 8 genes then evaluated for predicted effect on the corresponding encoded proteins, which included newly identified mutations (4 nonsense, 15 frameshift, 28 missense). Likewise, most accessions analyzed contained predicted loss of function alleles (425 ma1, 22 ma2, 40 ma3, 74 ma5, 414 ma6, 289 dw1, 268 dw2 and 45 dw3) at multiple loci, but 146 and 463 accessions had no predicted ma or dw mutant alleles, respectively. The ma and dw alleles within these sorghum accessions represent a valuable source for manipulating flowering time and plant height to develop the full range of sorghum types: grain, sweet and forage/biomass.
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Affiliation(s)
- Nathan P Grant
- Wheat, Sorghum and Forage Research Unit, Agricultural Research Service, United States Department of Agriculture, Lincoln, NE, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - John J Toy
- Wheat, Sorghum and Forage Research Unit, Agricultural Research Service, United States Department of Agriculture, Lincoln, NE, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Deanna L Funnell-Harris
- Wheat, Sorghum and Forage Research Unit, Agricultural Research Service, United States Department of Agriculture, Lincoln, NE, USA
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Scott E Sattler
- Wheat, Sorghum and Forage Research Unit, Agricultural Research Service, United States Department of Agriculture, Lincoln, NE, USA.
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA.
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16
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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.
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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
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17
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Cai Y, Liu Y, Fan Y, Li X, Yang M, Xu D, Wang H, Deng XW, Li J. MYB112 connects light and circadian clock signals to promote hypocotyl elongation in Arabidopsis. THE PLANT CELL 2023; 35:3485-3503. [PMID: 37335905 PMCID: PMC10473211 DOI: 10.1093/plcell/koad170] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/05/2023] [Accepted: 06/13/2023] [Indexed: 06/21/2023]
Abstract
Ambient light and the endogenous circadian clock play key roles in regulating Arabidopsis (Arabidopsis thaliana) seedling photomorphogenesis. PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) acts downstream of both light and the circadian clock to promote hypocotyl elongation. Several members of the R2R3-MYB transcription factor (TF) family, the most common type of MYB TF family in Arabidopsis, have been shown to be involved in regulating photomorphogenesis. Nonetheless, whether R2R3-MYB TFs are involved in connecting the light and clock signaling pathways during seedling photomorphogenesis remains unknown. Here, we report that MYB112, a member of the R2R3-MYB family, acts as a negative regulator of seedling photomorphogenesis in Arabidopsis. The light signal promotes the transcription and protein accumulation of MYB112. myb112 mutants exhibit short hypocotyls in both constant light and diurnal cycles. MYB112 physically interacts with PIF4 to enhance the transcription of PIF4 target genes involved in the auxin pathway, including YUCCA8 (YUC8), INDOLE-3-ACETIC ACID INDUCIBLE 19 (IAA19), and IAA29. Furthermore, MYB112 directly binds to the promoter of LUX ARRHYTHMO (LUX), the central component of clock oscillators, to repress its expression mainly in the afternoon and relieve LUX-inhibited expression of PIF4. Genetic evidence confirms that LUX acts downstream of MYB112 in regulating hypocotyl elongation. Thus, the enhanced transcript accumulation and transcriptional activation activity of PIF4 by MYB112 additively promotes the expression of auxin-related genes, thereby increasing auxin synthesis and signaling and fine-tuning hypocotyl growth under diurnal cycles.
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Affiliation(s)
- Yupeng Cai
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yongting Liu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yangyang Fan
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center for Edible Mushroom, Beijing 100097, China
| | - Xitao Li
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
- School of Life Science, Huizhou University, Huizhou 516007, China
| | - Maosheng Yang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Dongqing Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Haiyang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
| | - Xing Wang Deng
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
- State Key Laboratory of Protein and Plant Gene Research, Peking–Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Jian Li
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
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18
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Abstract
Photoperiod-measuring mechanisms allow organisms to anticipate seasonal changes to align reproduction and growth with appropriate times of the year. This review provides historical and modern context to studies of plant photoperiodism. We describe how studies of photoperiodic flowering in plants led to the first theoretical models of photoperiod-measuring mechanisms in any organism. We discuss how more recent molecular genetic studies in Arabidopsis and rice have revisited these concepts. We then discuss how photoperiod transcriptomics provides new lessons about photoperiodic gene regulatory networks and the discovery of noncanonical photoperiod-measuring systems housed in metabolic networks of plants. This leads to an examination of nonflowering developmental processes controlled by photoperiod, including metabolism and growth. Finally, we highlight the importance of understanding photoperiodism in the context of climate change, delving into the rapid latitudinal migration of plant species and the potential role of photoperiod-measuring systems in generating photic barriers during migration.
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Affiliation(s)
- Joshua M Gendron
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA;
| | - Dorothee Staiger
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany;
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19
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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.
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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
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20
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Awuni GA, Reynolds DB, Dodds D, Denwar NN, Abdulai AL, Asungre PA, Yahaya I, Goldsmith PD. Lime, inoculum, and phosphorous input supplementation under rain-fed soybean in Ghana's northern savannas. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2023. [DOI: 10.3389/fsufs.2023.992644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Abstract
IntroductionRecent prices in soybean have spurred interest in motivating growers into input integration to improve yields across the northern savannas of Ghana. This requires more knowledge of input integration to increase soybean yield and profitability across production areas.Materials and methodA 3-yr study was conducted in three locations at Manga, Nyankpala, and Wa in Ghana's northern savanna to identify the best-yielding input combination under a rain-fed environment. The experiment used “Jenguma” soybean cultivar with lime, inoculum, and phosphorus in a 2 × 2 × 2 factorial arrangement with four replications. Eight treatment combinations (control included) were used to assess soybean yield, yield components, rain use efficiency, and economic profitability. The single-input application of lime (T1), inoculum (T2), and phosphorus (T4) was the low-input, lime × inoculum (T3), lime × phosphorus (T5), and (inoculum × phosphorus) (T6) as medium input, T7 (lime × inoculum × phosphorus) was high input, and a no-input treatment (control).ResultsThe soils were inherently low in fertility, and weather variability during the reproductive stages was a significant limiting factor to improving grain yield across locations. Grain yield was highest in 2017 at Manga and Nyankpala, but in 2019 at Wa. Except at Manga, grain yield and rain use efficiency (RUE) were highest in the high input system (T7). However, marginal net benefits (MNB) and marginal rate of returns (MRR) were highest in the low input system (T2) across locations. The low (T1) and medium (T3) input systems (except Nyankpala) were dominant for MNB and MRR due to the high cost of the lime product.DiscussionThese results suggest that smallholder farmers prefer low input (T2) with the least cost of production and the highest marginal net benefit and marginal rate of returns. Nevertheless, producers would have to evaluate their resource base and the cost of nutrient integration for sustainability.ConclusionThis paper recommends further studies on lime rates to determine profitability, lime's long-term (residual) effect, and the synergic impact of inoculum and phosphorus.
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21
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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.
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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
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22
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Kim K, Shin J, Kang TA, Kim B, Kim WC. CRISPR/Cas9-mediated AtGATA25 mutant represents a novel model for regulating hypocotyl elongation in Arabidopsis thaliana. Mol Biol Rep 2023; 50:31-41. [PMID: 36301462 PMCID: PMC9884261 DOI: 10.1007/s11033-022-07926-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/06/2022] [Indexed: 02/01/2023]
Abstract
BACKGROUND Plants have evolved to adapt to the ever-changing environments through various morphological changes. An organism anticipates and responds to changes in its environment via the circadian clock, an endogenous oscillator lasting approximately 24 h. The circadian clock regulates various physiological processes, such as hypocotyl elongation in Arabidopsis thaliana. Phytochrome interacting factor 4 (PIF4), a member of the bHLH protein family, plays a vital hub role in light signaling pathways and temperature-mediated growth response mechanisms. PIF4 is controlled by the circadian clock and interacts with several factors. However, the components that regulate PIF4 transcription and activity are not clearly understood. METHODS AND RESULTS Here, we showed that the Arabidopsis thaliana GATA25 (AtGATA25) transcription factor plays a fundamental role in promoting hypocotyl elongation by positively regulating the expression of PIF4. This was confirmed to in the loss-of-function mutant of AtGATA25 via CRISPR/Cas9-mediated gene editing, which inhibits hypocotyl elongation and decreases the expression of PIF4. In contrast, the overexpression of AtGATA25 in transgenic plants resulted in increased expression of PIF4 and enhanced hypocotyl elongation. To better understand AtGATA25-mediated PIF4 transcriptional regulation, we analyzed the promoter region of the target gene PIF4 and characterized the role of GATA25 through transcriptional activation analysis. CONCLUSION Our findings suggest a novel role of the AtGATA25 transcription factor in hypocotyl elongation.
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Affiliation(s)
- Kihwan Kim
- Department of Applied Biosciences, Kyungpook National University, 41566 Daegu, Republic of Korea
| | - Juhyung Shin
- Department of Integrative Biology, Kyungpook National University, 41566 Daegu, Republic of Korea
| | - Tae-An Kang
- Department of Applied Biosciences, Kyungpook National University, 41566 Daegu, Republic of Korea
| | - Byeonggyu Kim
- Department of Integrative Biology, Kyungpook National University, 41566 Daegu, Republic of Korea
| | - Won-Chan Kim
- Department of Applied Biosciences, Kyungpook National University, 41566 Daegu, Republic of Korea ,Department of Integrative Biology, Kyungpook National University, 41566 Daegu, Republic of Korea
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23
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Michael TP. Time of Day Analysis over a Field Grown Developmental Time Course in Rice. PLANTS (BASEL, SWITZERLAND) 2022; 12:166. [PMID: 36616295 PMCID: PMC9823482 DOI: 10.3390/plants12010166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Plants integrate time of day (TOD) information over an entire season to ensure optimal growth, flowering time, and grain fill. However, most TOD expression studies have focused on a limited number of combinations of daylength and temperature under laboratory conditions. Here, an Oryza sativa (rice) expression study that followed TOD expression in the field over an entire growing season was re-analyzed. Similar to Arabidopsis thaliana, almost all rice genes have a TOD-specific expression over the developmental time course. As has been suggested in other grasses, thermocycles were a stronger cue for TOD expression than the photocycles over the growing season. All the core circadian clock genes display consistent TOD expression over the season with the interesting exception that the two grass paralogs of EARLY FLOWERING 3 (ELF3) display a distinct phasing based on the interaction between thermo- and photo-cycles. The dataset also revealed how specific pathways are modulated to distinct TOD over the season consistent with the changing biology. The data presented here provide a resource for researchers to study how TOD expression changes under natural conditions over a developmental time course, which will guide approaches to engineer more resilient and prolific crops.
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Affiliation(s)
- Todd P Michael
- The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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24
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Luklová M, Novák J, Kopecká R, Kameniarová M, Gibasová V, Brzobohatý B, Černý M. Phytochromes and Their Role in Diurnal Variations of ROS Metabolism and Plant Proteome. Int J Mol Sci 2022; 23:ijms232214134. [PMID: 36430613 PMCID: PMC9695588 DOI: 10.3390/ijms232214134] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/12/2022] [Accepted: 11/13/2022] [Indexed: 11/18/2022] Open
Abstract
Plants are sessile organisms forced to adapt to environmental variations recurring in a day-night cycle. Extensive research has uncovered the transcriptional control of plants' inner clock and has revealed at least some part of the intricate and elaborate regulatory mechanisms that govern plant diel responses and provide adaptation to the ever-changing environment. Here, we analyzed the proteome of the Arabidopsis thaliana mutant genotypes collected in the middle of the day and the middle of the night, including four mutants in the phytochrome (phyA, phyB, phyC, and phyD) and the circadian clock protein LHY. Our approach provided a novel insight into the diel regulations, identifying 640 significant changes in the night-day protein abundance. The comparison with previous studies confirmed that a large portion of identified proteins was a known target of diurnal regulation. However, more than 300 were novel oscillations hidden under standard growth chamber conditions or not manifested in the wild type. Our results indicated a prominent role for ROS metabolism and phytohormone cytokinin in the observed regulations, and the consecutive analyses confirmed that. The cytokinin signaling significantly increased at night, and in the mutants, the hydrogen peroxide content was lower, and the night-day variation seemed to be lost in the phyD genotype. Furthermore, regulations in the lhy and phyB mutants were partially similar to those found in the catalase mutant cat2, indicating shared ROS-mediated signaling pathways. Our data also shed light on the role of the relatively poorly characterized Phytochrome D, pointing to its connection to glutathione metabolism and the regulation of glutathione S-transferases.
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25
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Newman A, Picot E, Davies S, Hilton S, Carré IA, Bending GD. Circadian rhythms in the plant host influence rhythmicity of rhizosphere microbiota. BMC Biol 2022; 20:235. [PMID: 36266698 PMCID: PMC9585842 DOI: 10.1186/s12915-022-01430-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 09/30/2022] [Indexed: 11/18/2022] Open
Abstract
Background Recent studies demonstrated that microbiota inhabiting the plant rhizosphere exhibit diel changes in abundance. To investigate the impact of plant circadian rhythms on bacterial and fungal rhythms in the rhizosphere, we analysed temporal changes in fungal and bacterial communities in the rhizosphere of Arabidopsis plants overexpressing or lacking function of the circadian clock gene LATE ELONGATED HYPOCOTYL (LHY). Results Under diel light–dark cycles, the knock-out mutant lhy-11 and the gain-of-function mutant lhy-ox both exhibited gene expression rhythms with altered timing and amplitude compared to wild-type plants. Distinct sets of bacteria and fungi were found to display rhythmic changes in abundance in the rhizosphere of both of these mutants, suggesting that abnormal patterns of rhythmicity in the plant host caused temporal reprogramming of the rhizosphere microbiome. This was associated with changes in microbial community structure, including changes in the abundance of fungal guilds known to impact on plant health. Under constant environmental conditions, microbial rhythmicity persisted in the rhizosphere of wild-type plants, indicating control by a circadian oscillator. In contrast, loss of rhythmicity in lhy-ox plants was associated with disrupted rhythms for the majority of rhizosphere microbiota. Conclusions These results show that aberrant function of the plant circadian clock is associated with altered rhythmicity of rhizosphere bacteria and fungi. In the long term, this leads to changes in composition of the rhizosphere microbiome, with potential consequences for plant health. Further research will be required to understand the functional implications of these changes and how they impact on plant health and productivity. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01430-z.
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Affiliation(s)
- Amy Newman
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, West Midlands, UK.,Present address: National STEM Learning Centre, University of York, York, YO10 5DD, UK
| | - Emma Picot
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, West Midlands, UK
| | - Sian Davies
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, West Midlands, UK.,Present address: Micropathology Ltd, Venture Centre, Sir William Lyons Road, Coventry, CV4 7EZ, UK
| | - Sally Hilton
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, West Midlands, UK.,Present address: Micropathology Ltd, Venture Centre, Sir William Lyons Road, Coventry, CV4 7EZ, UK
| | - Isabelle A Carré
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, West Midlands, UK.
| | - Gary D Bending
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, West Midlands, UK
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26
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Guan J, Zhang J, Gong D, Zhang Z, Yu Y, Luo G, Somta P, Hu Z, Wang S, Yuan X, Zhang Y, Wang Y, Chen Y, Laosatit K, Chen X, Chen H, Sha A, Cheng X, Xie H, Wang L. Genomic analyses of rice bean landraces reveal adaptation and yield related loci to accelerate breeding. Nat Commun 2022; 13:5707. [PMID: 36175442 PMCID: PMC9523027 DOI: 10.1038/s41467-022-33515-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 09/21/2022] [Indexed: 11/29/2022] Open
Abstract
Rice bean (Vigna umbellata) is an underexploited domesticated legume crop consumed for dietary protein in Asia, yet little is known about the genetic diversity of this species. Here, we present a high-quality reference genome for a rice bean landrace (FF25) built using PacBio long-read data and a Hi-C chromatin interaction map, and assess the phylogenetic position and speciation time of rice bean within the Vigna genus. We sequence 440 landraces (two core collections), and GWAS based on data for growth sites at three widely divergent latitudes reveal loci associated with flowering and yield. Loci harboring orthologs of FUL (FRUITFULL), FT (FLOWERING LOCUS T), and PRR3 (PSEUDO-RESPONSE REGULATOR 3) contribute to the adaptation of rice bean from its low latitude center of origin towards higher latitudes, and the landraces which pyramid early-flowering alleles for these loci display maximally short flowering times. We also demonstrate that copy-number-variation for VumCYP78A6 can regulate seed-yield traits. Intriguingly, 32 landraces collected from a mountainous region in South-Central China harbor a recently acquired InDel in TFL1 (TERMINAL FLOWER1) affecting stem determinacy; these materials also have exceptionally high values for multiple human-desired traits and could therefore substantially advance breeding efforts to improve rice bean. Rice bean is an underexploited legume crop that has many desirable properties against bio and abiotic stresses. Here, the authors report the genome assembly of this species, conduct population genetics studies and reveal the genetic variations associated with adaptation and yield traits.
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Affiliation(s)
- Jiantao Guan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.,Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jintao Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Agriculture, Yangtze University, Jingzhou, China
| | - Dan Gong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Agriculture, Yangtze University, Jingzhou, China
| | - Zhengquan Zhang
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yang Yu
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Gaoling Luo
- Institute of Rice Research, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Prakit Somta
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
| | - Zheng Hu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Suhua Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xingxing Yuan
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yaowen Zhang
- College of Agriculture, Shanxi Agricultural University, Taiyuan, China
| | - Yanlan Wang
- Crop Research Institute of Hunan Province, Changsha, China
| | - Yanhua Chen
- Institute of Rice Research, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Kularb Laosatit
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
| | - Xin Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Honglin Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Aihua Sha
- College of Agriculture, Yangtze University, Jingzhou, China
| | - Xuzhen Cheng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hua Xie
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.
| | - Lixia Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
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Petersen J, Rredhi A, Szyttenholm J, Mittag M. Evolution of circadian clocks along the green lineage. PLANT PHYSIOLOGY 2022; 190:924-937. [PMID: 35325228 PMCID: PMC9516769 DOI: 10.1093/plphys/kiac141] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/04/2022] [Indexed: 05/10/2023]
Abstract
Circadian clocks govern temporal programs in the green lineage (Chloroplastida) as they do in other photosynthetic pro- and eukaryotes, bacteria, fungi, animals, and humans. Their physiological properties, including entrainment, phase responses, and temperature compensation, are well conserved. The involvement of transcriptional/translational feedback loops in the oscillatory machinery and reversible phosphorylation events are also maintained. Circadian clocks control a large variety of output rhythms in green algae and terrestrial plants, adjusting their metabolism and behavior to the day-night cycle. The angiosperm Arabidopsis (Arabidopsis thaliana) represents a well-studied circadian clock model. Several molecular components of its oscillatory machinery are conserved in other Chloroplastida, but their functions may differ. Conserved clock components include at least one member of the CIRCADIAN CLOCK ASSOCIATED1/REVEILLE and one of the PSEUDO RESPONSE REGULATOR family. The Arabidopsis evening complex members EARLY FLOWERING3 (ELF3), ELF4, and LUX ARRHYTHMO are found in the moss Physcomitrium patens and in the liverwort Marchantia polymorpha. In the flagellate chlorophyte alga Chlamydomonas reinhardtii, only homologs of ELF4 and LUX (named RHYTHM OF CHLOROPLAST ROC75) are present. Temporal ROC75 expression in C. reinhardtii is opposite to that of the angiosperm LUX, suggesting different clock mechanisms. In the picoalga Ostreococcus tauri, both ELF genes are missing, suggesting that it has a progenitor circadian "green" clock. Clock-relevant photoreceptors and thermosensors vary within the green lineage, except for the CRYPTOCHROMEs, whose variety and functions may differ. More genetically tractable models of Chloroplastida are needed to draw final conclusions about the gradual evolution of circadian clocks within the green lineage.
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Affiliation(s)
- Jan Petersen
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Anxhela Rredhi
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Julie Szyttenholm
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Jena 07743, Germany
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Michael TP. Core circadian clock and light signaling genes brought into genetic linkage across the green lineage. PLANT PHYSIOLOGY 2022; 190:1037-1056. [PMID: 35674369 PMCID: PMC9516744 DOI: 10.1093/plphys/kiac276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
The circadian clock is conserved at both the level of transcriptional networks as well as core genes in plants, ensuring that biological processes are phased to the correct time of day. In the model plant Arabidopsis (Arabidopsis thaliana), the core circadian SHAQKYF-type-MYB (sMYB) genes CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and REVEILLE (RVE4) show genetic linkage with PSEUDO-RESPONSE REGULATOR 9 (PRR9) and PRR7, respectively. Leveraging chromosome-resolved plant genomes and syntenic ortholog analysis enabled tracing this genetic linkage back to Amborella trichopoda, a sister lineage to the angiosperm, and identifying an additional evolutionarily conserved genetic linkage in light signaling genes. The LHY/CCA1-PRR5/9, RVE4/8-PRR3/7, and PIF3-PHYA genetic linkages emerged in the bryophyte lineage and progressively moved within several genes of each other across an array of angiosperm families representing distinct whole-genome duplication and fractionation events. Soybean (Glycine max) maintained all but two genetic linkages, and expression analysis revealed the PIF3-PHYA linkage overlapping with the E4 maturity group locus was the only pair to robustly cycle with an evening phase, in contrast to the sMYB-PRR morning and midday phase. While most monocots maintain the genetic linkages, they have been lost in the economically important grasses (Poaceae), such as maize (Zea mays), where the genes have been fractionated to separate chromosomes and presence/absence variation results in the segregation of PRR7 paralogs across heterotic groups. The environmental robustness model is put forward, suggesting that evolutionarily conserved genetic linkages ensure superior microhabitat pollinator synchrony, while wide-hybrids or unlinking the genes, as seen in the grasses, result in heterosis, adaptation, and colonization of new ecological niches.
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Maeda AE, Nakamichi N. Plant clock modifications for adapting flowering time to local environments. PLANT PHYSIOLOGY 2022; 190:952-967. [PMID: 35266545 PMCID: PMC9516756 DOI: 10.1093/plphys/kiac107] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/09/2022] [Indexed: 05/25/2023]
Abstract
During and after the domestication of crops from ancestral wild plants, humans selected cultivars that could change their flowering time in response to seasonal daylength. Continuous selection of this trait eventually allowed the introduction of crops into higher or lower latitudes and different climates from the original regions where domestication initiated. In the past two decades, numerous studies have found the causal genes or alleles that change flowering time and have assisted in adapting crop species such as barley (Hordeum vulgare), wheat (Triticum aestivum L.), rice (Oryza sativa L.), pea (Pisum sativum L.), maize (Zea mays spp. mays), and soybean (Glycine max (L.) Merr.) to new environments. This updated review summarizes the genes or alleles that contributed to crop adaptation in different climatic areas. Many of these genes are putative orthologs of Arabidopsis (Arabidopsis thaliana) core clock genes. We also discuss how knowledge of the clock's molecular functioning can facilitate molecular breeding in the future.
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Affiliation(s)
- Akari E Maeda
- Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Norihito Nakamichi
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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Harmer SL, Fankhauser C, Webb AAR. Focus on circadian rhythms. PLANT PHYSIOLOGY 2022; 190:921-923. [PMID: 35900174 PMCID: PMC9516718 DOI: 10.1093/plphys/kiac353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Affiliation(s)
| | - Christian Fankhauser
- Faculty of Biology and Medicine, Centre for Integrative Genomics, University of Lausanne, Génopode Building, Lausanne CH-1015, Switzerland
| | - Alex A R Webb
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
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31
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Yan J, He J, Li J, Ren S, Wang Y, Zhou J, Tan X. Analysis of Camellia oleifera transcriptome reveals key pathways and hub genes involved during different photoperiods. BMC PLANT BIOLOGY 2022; 22:435. [PMID: 36089577 PMCID: PMC9465947 DOI: 10.1186/s12870-022-03798-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/09/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Camellia oleifera Abel. (C. oleifera) is an important traditional woody species in China that produces edible oil. However, the current literature lacks a proper understanding of C. oleifera's ability to adapt to different photoperiods. RESULTS Our results indicate that the photoperiod can significantly impact flowering time in C. oleifera. We grew a total of nine samples under the short day condition (SD), middle day condition (MD) and long day condition (LD). Transcriptome analysis yielded 66.94 Gb of high-quality clean reads, with an average of over 6.73 Gb of reads for per sample. Following assembly, a total of 120,080 transcripts were obtained and 94,979 unigenes annotated. A total of 3475 differentially expressed genes (DEGs) were identified between the SD_MD, SD_LD, and MD_LD gene sets. Moreover, WGCNA identified ten gene modules. Genes in pink module (92 genes) were positively correlated with SD, and negatively correlated with both MD and LD. Genes in the magenta module (42 genes) were positively correlated with MD and negatively correlated with both LD and SD. Finally, genes in the yellow module (1758 genes) were positively correlated with both SD and MD, but negatively correlated with LD. KEGG enrichment analysis revealed that genes in the pink, magenta, and yellow modules were involved in flavonoid biosynthesis, amino sugar and nucleotide sugar metabolism and circadian rhythm pathways. Additionally, eight hub genes (GI, AP2, WRKY65, SCR, SHR, PHR1, ERF106, and SCL3) were obtained through network analysis. The hub genes had high connectivity with other photoperiod-sensitive DEGs. The expression levels of hub genes were verified by qRT-PCR analysis. CONCLUSION An increase in light duration promotes earlier flowering of C. oleifera. Flavonoid biosynthesis, amino sugar and nucleotide sugar metabolism, and circadian rhythm pathways may function in the photoperiodic flowering pathway of C. oleifera. We also identified eight hub genes that may play a role in this pathway. Ultimately, this work contributes to our understanding of the photoperiodic flowering pathway of C. oleifera and further informs molecular breeding programs on the plant's photoperiodic sensitivity.
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Affiliation(s)
- Jindong Yan
- Key Laboratory of Cultivation and Protection for Non-wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, 410004, Changsha, China
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, 410004, Changsha, China
| | - Jiacheng He
- Key Laboratory of Cultivation and Protection for Non-wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, 410004, Changsha, China
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, 410004, Changsha, China
| | - Jian'an Li
- Key Laboratory of Cultivation and Protection for Non-wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, 410004, Changsha, China.
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, 410004, Changsha, China.
| | - Shuangshuang Ren
- Key Laboratory of Cultivation and Protection for Non-wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, 410004, Changsha, China
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, 410004, Changsha, China
| | - Ying Wang
- Key Laboratory of Cultivation and Protection for Non-wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, 410004, Changsha, China
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, 410004, Changsha, China
| | - Junqin Zhou
- Key Laboratory of Cultivation and Protection for Non-wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, 410004, Changsha, China
| | - Xiaofeng Tan
- Key Laboratory of Cultivation and Protection for Non-wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, 410004, Changsha, China.
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forest Industry of Hunan Province, 410004, Changsha, China.
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32
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Cha JY, Kim J, Jeong SY, Shin GI, Ji MG, Hwang JW, Khaleda L, Liao X, Ahn G, Park HJ, Kim DY, Pardo JM, Lee SY, Yun DJ, Somers DE, Kim WY. The Na +/H + antiporter SALT OVERLY SENSITIVE 1 regulates salt compensation of circadian rhythms by stabilizing GIGANTEA in Arabidopsis. Proc Natl Acad Sci U S A 2022; 119:e2207275119. [PMID: 35939685 PMCID: PMC9388102 DOI: 10.1073/pnas.2207275119] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/14/2022] [Indexed: 12/27/2022] Open
Abstract
The circadian clock is a timekeeping, homeostatic system that temporally coordinates all major cellular processes. The function of the circadian clock is compensated in the face of variable environmental conditions ranging from normal to stress-inducing conditions. Salinity is a critical environmental factor affecting plant growth, and plants have evolved the SALT OVERLY SENSITIVE (SOS) pathway to acquire halotolerance. However, the regulatory systems for clock compensation under salinity are unclear. Here, we show that the plasma membrane Na+/H+ antiporter SOS1 specifically functions as a salt-specific circadian clock regulator via GIGANTEA (GI) in Arabidopsis thaliana. SOS1 directly interacts with GI in a salt-dependent manner and stabilizes this protein to sustain a proper clock period under salinity conditions. SOS1 function in circadian clock regulation requires the salt-mediated secondary messengers cytosolic free calcium and reactive oxygen species, pointing to a distinct regulatory role for SOS1 in addition to its function as a transporter to maintain Na+ homeostasis. Our results demonstrate that SOS1 maintains homeostasis of the salt response under high or daily fluctuating salt levels. These findings highlight the genetic capacity of the circadian clock to maintain timekeeping activity over a broad range of salinity levels.
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Affiliation(s)
- Joon-Yung Cha
- Division of Applied Life Science (BK21four), Plant Molecular Biology and Biotechnology Research Center, Graduate School of Gyeongsang National University, Jinju 52828, Republic of Korea
- Research Institute of Life Science, Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Jeongsik Kim
- Faculty of Science Education and Interdisciplinary Graduate Program in Advanced Convergence Technology and Science, Jeju National University, Jeju 63243, Republic of Korea
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210
| | - Song Yi Jeong
- Division of Applied Life Science (BK21four), Plant Molecular Biology and Biotechnology Research Center, Graduate School of Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Gyeong-Im Shin
- Division of Applied Life Science (BK21four), Plant Molecular Biology and Biotechnology Research Center, Graduate School of Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Myung Geun Ji
- Division of Applied Life Science (BK21four), Plant Molecular Biology and Biotechnology Research Center, Graduate School of Gyeongsang National University, Jinju 52828, Republic of Korea
- Research Institute of Life Science, Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Ji-Won Hwang
- Division of Applied Life Science (BK21four), Plant Molecular Biology and Biotechnology Research Center, Graduate School of Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Laila Khaleda
- Division of Applied Life Science (BK21four), Plant Molecular Biology and Biotechnology Research Center, Graduate School of Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Xueji Liao
- Division of Applied Life Science (BK21four), Plant Molecular Biology and Biotechnology Research Center, Graduate School of Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Gyeongik Ahn
- Research Institute of Life Science, Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Hee-Jin Park
- Department of Biological Sciences, College of Natural Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Dong Young Kim
- College of Pharmacy, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Jose M. Pardo
- Institute of Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Cientificas and Universidad de Sevilla, Seville 41092, Spain
| | - Sang Yeol Lee
- Division of Applied Life Science (BK21four), Plant Molecular Biology and Biotechnology Research Center, Graduate School of Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Dae-Jin Yun
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - David E. Somers
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21four), Plant Molecular Biology and Biotechnology Research Center, Graduate School of Gyeongsang National University, Jinju 52828, Republic of Korea
- Research Institute of Life Science, Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
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Gong J, Tang Y, Liu Y, Sun R, Li Y, Ma J, Zhang S, Zhang F, Chen Z, Liao X, Sun H, Lu Z, Zhao C, Gao S. The Central Circadian Clock Protein TaCCA1 Regulates Seedling Growth and Spike Development in Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:946213. [PMID: 35923880 PMCID: PMC9340162 DOI: 10.3389/fpls.2022.946213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/20/2022] [Indexed: 05/14/2023]
Abstract
The biological functions of the circadian clock on growth and development have been well elucidated in model plants, while its regulatory roles in crop species, especially the roles on yield-related traits, are poorly understood. In this study, we characterized the core clock gene CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1) homoeologs in wheat and studied their biological functions in seedling growth and spike development. TaCCA1 homoeologs exhibit typical diurnal expression patterns, which are positively regulated by rhythmic histone modifications including histone H3 lysine 4 trimethylation (H3K4me3), histone H3 lysine 9 acetylation (H3K9Ac), and histone H3 lysine 36 trimethylation (H3K36me3). TaCCA1s are preferentially located in the nucleus and tend to form both homo- and heterodimers. TaCCA1 overexpression (TaCCA1-OE) transgenic wheat plants show disrupted circadian rhythmicity coupling with reduced chlorophyll and starch content, as well as biomass at seedling stage, also decreased spike length, grain number per spike, and grain size at the ripening stage. Further studies using DNA affinity purification followed by deep sequencing [DNA affinity purification and sequencing (DAP-seq)] indicated that TaCCA1 preferentially binds to sequences similarly to "evening elements" (EE) motif in the wheat genome, particularly genes associated with photosynthesis, carbon utilization, and auxin homeostasis, and decreased transcriptional levels of these target genes are observed in TaCCA1-OE transgenic wheat plants. Collectively, our study provides novel insights into a circadian-mediated mechanism of gene regulation to coordinate photosynthetic and metabolic activities in wheat, which is important for optimal plant growth and crop yield formation.
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Affiliation(s)
- Jie Gong
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yimiao Tang
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yongjie Liu
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Renwei Sun
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yanhong Li
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jinxiu Ma
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Shengquan Zhang
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Fengting Zhang
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Zhaobo Chen
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Xiangzheng Liao
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Hui Sun
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Zefu Lu
- National Key Facility of Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Changping Zhao
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Shiqing Gao
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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34
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A guiding role of the Arabidopsis circadian clock in cell differentiation revealed by time-series single-cell RNA sequencing. Cell Rep 2022; 40:111059. [PMID: 35830805 DOI: 10.1016/j.celrep.2022.111059] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 04/01/2022] [Accepted: 06/14/2022] [Indexed: 11/21/2022] Open
Abstract
Circadian rhythms and progression of cell differentiation are closely coupled in multicellular organisms. However, whether establishment of circadian rhythms regulates cell differentiation or vice versa has not been elucidated due to technical limitations. Here, we exploit high cell fate plasticity of plant cells to perform single-cell RNA sequencing during the entire process of cell differentiation. By analyzing reconstructed actual time series of the differentiation processes at single-cell resolution using a method we developed (PeakMatch), we find that the expression profile of clock genes is changed prior to cell differentiation, including induction of the clock gene LUX ARRYTHMO (LUX). ChIP sequencing analysis reveals that LUX induction in early differentiating cells directly targets genes involved in cell-cycle progression to regulate cell differentiation. Taken together, these results not only reveal a guiding role of the plant circadian clock in cell differentiation but also provide an approach for time-series analysis at single-cell resolution.
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35
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Siqueira JA, Wakin T, Batista-Silva W, Silva JCF, Vicente MH, Silva JC, Clarindo WR, Zsögön A, Peres LEP, De Veylder L, Fernie AR, Nunes-Nesi A, Araújo WL. A long and stressful day: Photoperiod shapes aluminium tolerance in plants. JOURNAL OF HAZARDOUS MATERIALS 2022; 432:128704. [PMID: 35313159 DOI: 10.1016/j.jhazmat.2022.128704] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/06/2022] [Accepted: 03/12/2022] [Indexed: 06/14/2023]
Abstract
Aluminium (Al), a limiting factor for crop productivity in acidic soils (pH ≤ 5.5), imposes drastic constraints for food safety in developing countries. The major mechanisms that allow plants to cope with Al involve manipulations of organic acids metabolism and DNA-checkpoints. When assumed individually both approaches have been insufficient to overcome Al toxicity. On analysing the centre of origin of most cultivated plants, we hypothesised that day-length seems to be a pivotal agent modulating Al tolerance across distinct plant species. We observed that with increasing distance from the Equator, Al tolerance decreases, suggesting a relationship with the photoperiod. We verified that long-day (LD) species are generally more Al-sensitive than short-day (SD) species, whereas genetic conversion of tomato for SD growth habit boosts Al tolerance. Reduced Al tolerance correlates with DNA-checkpoint activation under LD. Furthermore, DNA-checkpoint-related genes are under positive selection in Arabidopsis accessions from regions with shorter days, suggesting that photoperiod act as a selective barrier for Al tolerance. A diel regulation and genetic diversity affect Al tolerance, suggesting that day-length orchestrates Al tolerance. Altogether, photoperiodic control of Al tolerance might contribute to solving the historical obstacle that imposes barriers for developing countries to reach a sustainable agriculture.
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Affiliation(s)
- João Antonio Siqueira
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Thiago Wakin
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Willian Batista-Silva
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - José Cleydson F Silva
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Matheus H Vicente
- Laboratory of Hormonal Control of Plant Development. Departamento de Ciências Biológicas (LCB), Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, SP 13418-900, Brazil
| | - Jéssica C Silva
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Wellington R Clarindo
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Agustin Zsögön
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Lazaro E P Peres
- Laboratory of Hormonal Control of Plant Development. Departamento de Ciências Biológicas (LCB), Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, SP 13418-900, Brazil
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium; VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
| | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Wagner L Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil.
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36
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Tobin E. Adventures in Life and Science, from Light to Rhythms. ANNUAL REVIEW OF PLANT BIOLOGY 2022; 73:1-16. [PMID: 35130444 DOI: 10.1146/annurev-arplant-090921-091346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The author describes her life's pathway from her beginnings at a time when women were not well represented in the sciences. Her grandparents were immigrants to the United States. Although her parents were not able to go to college because of the Great Depression, they supported her education and other adventures. In addition to her interest in science, she describes her interest and involvement in politics. Her education at Oberlin, Stanford, and Harvard prepared her for her independent career at the University of California, Los Angeles, where she was an affirmative action appointment. Her research initially centered on the plant photoreceptor phytochrome, but later in her career she investigated circadian rhythms in plants, discovering and characterizing one of the members of the central oscillator.
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Affiliation(s)
- Elaine Tobin
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, USA;
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37
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Liu C, Zhang Q, Dong J, Cai C, Zhu H, Li S. Genome-wide identification and characterization of mungbean CIRCADIAN CLOCK ASSOCIATED 1 like genes reveals an important role of VrCCA1L26 in flowering time regulation. BMC Genomics 2022; 23:374. [PMID: 35581536 PMCID: PMC9115955 DOI: 10.1186/s12864-022-08620-7] [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: 01/06/2022] [Accepted: 05/11/2022] [Indexed: 11/22/2022] Open
Abstract
Background CIRCADIAN CLOCK ASSOCIATED 1 like (CCA1L) proteins are important components that participate in plant growth and development, and now have been characterized in multiple plant species. However, information on mungbean CCA1L genes is limited. Results In this study, we identified 27 VrCCA1L genes from the mungbean genome. VrCCA1L genes were unevenly distributed on 10 of the 11 chromosomes and showed one tandem and two interchromosomal duplication events. Two distinct kinds of conserved MYB domains, MYB 1 and MYB 2, were found, and the conserved SHAQK(Y/F) F sequence was found at the C terminus of each MYB 2 domain. The VrCCA1Ls displayed a variety of exon-intron organizations, and 24 distinct motifs were found among these genes. Based on phylogenetic analysis, VrCCA1L proteins were classified into five groups; group I contained the most members, with 11 VrCCA1Ls. VrCCA1L promoters contained different types and numbers of cis-acting elements, and VrCCA1Ls showed different expression levels in different tissues. The VrCCA1Ls also displayed distinct expression patterns under different photoperiod conditions throughout the day in leaves. VrCCA1L26 shared greatest homology to Arabidopsis CCA1 and LATE ELONGATED HYPOCOTYL (LHY). It delayed the flowering time in Arabidopsis by affecting the expression levels of CONSTANS (CO), FLOWERING LOCUS T (FT), and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1). Conclusion We identified and characterized 27 VrCCA1L genes from mungbean genome, and investigated their spatio-temporal expression patterns. Further analysis revealed that VrCCA1L26 delayed flowering time in transgenic Arabidopsis plants. Our results provide useful information for further functional characterization of the VrCCA1L genes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08620-7.
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Affiliation(s)
- Chenyang Liu
- College of Life Sciences, Key Lab of Plant Biotechnology in Universities of Shandong Province, Qingdao Agricultural University, Qingdao, 266109, China
| | - Qianqian Zhang
- College of Life Sciences, Key Lab of Plant Biotechnology in Universities of Shandong Province, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jing Dong
- College of Life Sciences, Key Lab of Plant Biotechnology in Universities of Shandong Province, Qingdao Agricultural University, Qingdao, 266109, China
| | - Chunmei Cai
- College of Life Sciences, Key Lab of Plant Biotechnology in Universities of Shandong Province, Qingdao Agricultural University, Qingdao, 266109, China
| | - Hong Zhu
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China.
| | - Shuai Li
- College of Life Sciences, Key Lab of Plant Biotechnology in Universities of Shandong Province, Qingdao Agricultural University, Qingdao, 266109, China.
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Huang Y, Xing X, Tang Y, Jin J, Ding L, Song A, Chen S, Chen F, Jiang J, Fang W. An ethylene-responsive transcription factor and a flowering locus KH domain homologue jointly modulate photoperiodic flowering in chrysanthemum. PLANT, CELL & ENVIRONMENT 2022; 45:1442-1456. [PMID: 35040157 DOI: 10.1111/pce.14261] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 10/30/2021] [Accepted: 11/03/2021] [Indexed: 06/14/2023]
Abstract
The timely transition from vegetative to reproductive development is coordinated through the quantitative regulation of floral pathway genes in response to physiological and environmental cues. The function of ethylene-responsive element-binding protein (ERF) transcription factors in the regulation of flowering in chrysanthemum (Chrysanthemum morifolium Ramat.) is not well understood. Here, chrysanthemum overexpressing CmERF110 flowered earlier than the wild-type plants, while those in which CmERF110 was suppressed flowered later. RNA-seq results revealed that several genes involved in the circadian rhythm were transcribed differently in CmERF110 transgenic plants from that of the wild-type plants. The rhythm peak of the circadian clock genes in transgenic plants was delayed. Yeast two-hybrid screening of CmERF110 interactors identified a chrysanthemum FLOWERING LOCUS KH DOMAIN (FLK) homologue CmFLK, which was further confirmed with both in vitro and in vivo assays. KEGG pathway enrichment also revealed that CmFLK is involved in the regulation of circadian rhythm-related genes. CmFLK transgenic plants showed a change in flowering time and delayed rhythm peak of the circadian rhythm genes. Taken together, the present data not only suggest that CmERF110 interacts with CmFLK to promote floral transition by tuning the circadian clock, but also provides evidence for the evolutionary conservation of the components in the autonomous pathway in chrysanthemum.
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Affiliation(s)
- Yaoyao Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xiaojuan Xing
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yun Tang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Jinyu Jin
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Lian Ding
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Aiping Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Sumei Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Fadi Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Jiafu Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Weimin Fang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, China
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Venkat A, Muneer S. Role of Circadian Rhythms in Major Plant Metabolic and Signaling Pathways. FRONTIERS IN PLANT SCIENCE 2022; 13:836244. [PMID: 35463437 PMCID: PMC9019581 DOI: 10.3389/fpls.2022.836244] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/23/2022] [Indexed: 05/10/2023]
Abstract
Plants require an endogenous regulatory network and mechanism to cope with diurnal environmental changes and compensate for their sessile nature. Plants use the circadian clock to anticipate diurnal changes. Circadian rhythm predicts a 24-h cycle with 16 h of light and 8 h of darkness in response to abiotic and biotic factors as well as the appropriate temperature. For a plant's fitness, proper growth, and development, these rhythms synchronize the diurnal photoperiodic changes. Input pathway, central oscillator, and output pathway are the three components that make up the endogenous clock. There are also transcriptional and translational feedback loops (TTFLs) in the clock, which are dependent on the results of gene expression. Several physiological processes, such as stress acclimatization, hormone signaling, morphogenesis, carbon metabolism, and defense response, are currently being investigated for their interactions with the circadian clock using phenotypic, genomic, and metabolic studies. This review examines the role of circadian rhythms in the regulation of plant metabolic pathways, such as photosynthesis and carbon metabolism, as well as developmental and degenerative processes, such as flowering and senescence. Furthermore, we summarized signaling pathways related to circadian rhythms, such as defense response and gene regulatory pathways.
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Affiliation(s)
- Ajila Venkat
- Horticulture and Molecular Physiology Lab, School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore, India
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Sowbiya Muneer
- Horticulture and Molecular Physiology Lab, School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore, India
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Wang Z, Jiang Y, Yang X, Bi H, Li J, Mao X, Ma Y, Ru D, Zhang C, Hao G, Wang J, Abbott RJ, Liu J. Molecular signatures of parallel adaptive divergence causing reproductive isolation and speciation across two genera. Innovation (N Y) 2022; 3:100247. [PMID: 35519515 PMCID: PMC9065898 DOI: 10.1016/j.xinn.2022.100247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 04/16/2022] [Indexed: 11/18/2022] Open
Abstract
Parallel evolution of reproductive isolation (PERI) provides strong evidence for natural selection playing a fundamental role in the origin of species. However, PERI has been rarely demonstrated for well established species drawn from different genera. In particular, parallel molecular signatures for the same genes in response to similar habitat divergence in such different lineages is lacking. Here, based on whole-genome sequencing data, we first explore the speciation process in two sister species of Carpinus (Betulaceae) in response to divergence for temperature and soil-iron concentration in habitats they occupy in northern and southwestern China, respectively. We then determine whether parallel molecular mutations occur during speciation in this pair of species and also in another sister-species pair of the related genus, Ostryopsis, which occupy similarly divergent habitats in China. We show that gene flow occurred during the origin of both pairs of sister species since approximately 9.8 or approximately 2 million years ago, implying strong natural selection during divergence. Also, in both species pairs we detected concurrent positive selection in a gene (LHY) for flowering time and in two paralogous genes (FRO4 and FRO7) of a gene family known to be important for iron tolerance. These changes were in addition to changes in other major genes related to these two traits. The different alleles of these particular candidate genes possessed by the sister species of Carpinus were functionally tested and indicated likely to alter flowering time and iron tolerance as previously demonstrated in the pair of Ostryopsis sister species. Allelic changes in these genes may have effectively resulted in high levels of prezygotic reproductive isolation to evolve between sister species of each pair. Our results show that PERI can occur in different genera at different timescales and involve similar signatures of molecular evolution at genes or paralogues of the same gene family, causing reproductive isolation as a consequence of adaptation to similarly divergent habitats. PERI provides strong evidence for natural selection playing a fundamental role in the origin of species PERI is rarely demonstrated for well-established species drawn from different genera We detected PERI across two genera (Carpinus and Ostryopsis) in the family Betulaceae PERI can occur in different genera at different timescales and involve molecular signatures at similar pathways
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Affiliation(s)
- Zefu Wang
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yuanzhong Jiang
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Xiaoyue Yang
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Hao Bi
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Jialiang Li
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Xingxing Mao
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yazhen Ma
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Dafu Ru
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Cheng Zhang
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Guoqian Hao
- Sichuan Tea College, Yibin University, Yibin 644000, China
| | - Jing Wang
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | | | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
- Corresponding author
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Kyung J, Jeon M, Jeong G, Shin Y, Seo E, Yu J, Kim H, Park CM, Hwang D, Lee I. The two clock proteins CCA1 and LHY activate VIN3 transcription during vernalization through the vernalization-responsive cis-element. THE PLANT CELL 2022; 34:1020-1037. [PMID: 34931682 PMCID: PMC8894950 DOI: 10.1093/plcell/koab304] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 11/22/2021] [Indexed: 05/20/2023]
Abstract
Vernalization, a long-term cold-mediated acquisition of flowering competence, is critically regulated by VERNALIZATION INSENSITIVE 3 (VIN3), a gene induced by vernalization in Arabidopsis. Although the function of VIN3 has been extensively studied, how VIN3 expression itself is upregulated by long-term cold is not well understood. In this study, we identified a vernalization-responsive cis-element in the VIN3 promoter, VREVIN3, composed of a G-box and an evening element (EE). Mutations in either the G-box or the EE prevented VIN3 expression from being fully induced upon vernalization, leading to defects in the vernalization response. We determined that the core clock proteins CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1) and LATE-ELONGATED HYPOCOTYL (LHY) associate with the EE of VREVIN3, both in vitro and in vivo. In a cca1 lhy double mutant background harboring a functional FRIGIDA allele, long-term cold-mediated VIN3 induction and acceleration of flowering were impaired, especially under mild cold conditions such as at 12°C. During prolonged cold exposure, oscillations of CCA1/LHY transcripts were altered, while CCA1 abundance increased at dusk, coinciding with the diurnal peak of VIN3 transcripts. We propose that modulation of the clock proteins CCA1 and LHY participates in the systems involved in sensing long-term cold for the activation of VIN3 transcription.
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Affiliation(s)
- Jinseul Kyung
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Myeongjune Jeon
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Goowon Jeong
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Yourae Shin
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Eunjoo Seo
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Jihyeon Yu
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Hoyeun Kim
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Chung-Mo Park
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Daehee Hwang
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Ilha Lee
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul 08826, Korea
- Author for correspondence:
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Li C, Liu XJ, Yan Y, Alam MS, Liu Z, Yang ZK, Tao RF, Yue EK, Duan MH, Xu JH. OsLHY is involved in regulating flowering through the Hd1- and Ehd1- mediated pathways in rice (Oryza sativa L.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 315:111145. [PMID: 35067308 DOI: 10.1016/j.plantsci.2021.111145] [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: 07/14/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 06/14/2023]
Abstract
Flowering time (or heading date in crops) is a critical agronomic trait for rice reproduction and adaptation. The circadian clock is an endogenous oscillator that is involved in controlling photoperiodic flowering. The rice LATE ELONGATED HYPOCOTYL (OsLHY), the core oscillator component of circadian clock, is a homolog of the LHY/CCA1 in Arabidopsis. Here we showed that CRISPR/Cas9-engineered mutations in OsLHY caused late flowering in rice only under natural long-day (nLD) and short-day (nSD) conditions, but not artificial SD (10 h light/14 h dark) conditions. In the oslhy mutant, the diurnal expression of circadian clock-related genes was seriously affected under both LD and SD conditions. Furthermore, the expression of the flowering activators Ehd1, Hd3a and RFT1 was down-regulated and flowering repressors Hd1 and Ghd7 was up-regulated in the oslhy mutant under LD conditions. While the transcripts of flowering-related genes were not dramatically influenced under SD conditions. Dual-luciferase assays showed that OsLHY repressed the transcription of OsGI, Hd1, Ghd7, Hd3a, RFT1 and OsELF3, and activated the transcription of Ehd1. Moreover, the yeast one hybrid assay and electrophoretic mobility shift assay confirmed that OsLHY directly repressed OsGI, RFT1 and OsELF3 by binding to their promoters, which is consistent with that in Arabidopsis. These results suggested that the OsLHY can promote rice flowering mainly through regulating Hd1 and Ehd1.
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Affiliation(s)
- Chao Li
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China; Shandong (Linyi) Institute of Modern Agriculture, Zhejiang University, Shandong, 276034, China
| | - Xue-Jiao Liu
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
| | - Yan Yan
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
| | - Mohammad Shah Alam
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
| | - Zhen Liu
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
| | - Zhen-Kun Yang
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
| | - Ruo-Fu Tao
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
| | - Er-Kui Yue
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
| | - Ming-Hua Duan
- Zhejiang Zhengjingyuan Pharmacy Chain Co., Ltd. & Hangzhou Zhengcaiyuan Pharmaceutical Co., Ltd., Hangzhou, 310021, China
| | - Jian-Hong Xu
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China; Shandong (Linyi) Institute of Modern Agriculture, Zhejiang University, Shandong, 276034, China.
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GUN4 Affects the Circadian Clock and Seedlings Adaptation to Changing Light Conditions. Int J Mol Sci 2021; 23:ijms23010194. [PMID: 35008619 PMCID: PMC8745339 DOI: 10.3390/ijms23010194] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/16/2021] [Accepted: 12/20/2021] [Indexed: 01/13/2023] Open
Abstract
The chloroplast is a key organelle for photosynthesis and perceiving environmental information. GENOME UNCOUPLED 4 (GUN4) has been shown to be required for the regulation of both chlorophyll synthesis, reactive oxygen species (ROS) homeostasis and plastid retrograde signaling. In this study, we found that growth of the gun4 mutant was significantly improved under medium strong light (200 μmol photons m−2s−1) compared to normal light (100 μmol photons m−2s−1), in marked contrast to wild-type (WT). Further analysis revealed that GUN4 interacts with SIGNAL RECOGNITION PARTICLE 54 KDA SUBUNIT (SRP43) and SRP54. RNA-seq analysis indicated that the expression of genes for light signaling and the circadian clock is altered in gun4 compared with (WT). qPCR analysis confirmed that the expression of the clock genes CLOCK-RELATED 1 (CCA1), LATE ELONGATION HYPOCOTYL (LHY), TIMING OF CAB EXPRESSION 1 (TOC1) and PSEUDO RESPONSE REGULATOR 7 (PRR7) is significantly changed in the gun4 and srp54 mutants under normal and medium strong light conditions. These results suggest that GUN4 may coordinate the adaptation of plants to changing light conditions by regulating the biological clock, although it is not clear whether the effect is direct or indirect.
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Gao W, Zhang L, Wang J, Liu Z, Zhang Y, Xue C, Liu M, Zhao J. ZjSEP3 modulates flowering time by regulating the LHY promoter. BMC PLANT BIOLOGY 2021; 21:527. [PMID: 34763664 PMCID: PMC8582215 DOI: 10.1186/s12870-021-03305-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND SEPALLATA3 (SEP3), which is conserved across various plant species, plays essential and various roles in flower and fruit development. However, the regulatory network of the role of SEP3 in flowering time at the molecular level remained unclear. RESULTS Here, we investigated that SEP3 in Ziziphus jujuba Mill. (ZjSEP3) was expressed in four floral organs and exhibited strong transcriptional activation activity. ZjSEP3 transgenic Arabidopsis showed an early-flowering phenotype and altered the expression of some genes related to flowering. Among them, the expression of LATE ELONGATED HYPOCOTYL (AtLHY), the key gene of circadian rhythms, was significantly suppressed. Yeast one-hybrid (Y1H) and electrophoretic mobility shift assays (EMSAs) further verified that ZjSEP3 inhibited the transcription of AtLHY by binding to the CArG-boxes in its promoter. Moreover, ZjSEP3 also could bind to the ZjLHY promoter and the conserved binding regions of ZjSEP3 were found in the LHY promoter of various plant species. The ectopic regulatory pathway of ZjSEP3-AtLHY was further supported by the ability of 35S::AtLHY to rescue the early-flowering phenotype in ZjSEP3 transgenic plants. In ZjSEP3 transgenic plants, total chlorophyll content and the expression of genes involved in chlorophyll synthesis increased during vegetative stages, which should contribute to its early flowering and relate to the regulatory of AtLHY. CONCLUSION Overall, ZjSEP3-AtLHY pathway represents a novel regulatory mechanism that is involved in the regulation of flowering time.
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Affiliation(s)
- Weilin Gao
- College of Life Science, Hebei Agricultural University, Baoding, 071000, China
| | - Liman Zhang
- College of Life Science, Hebei Agricultural University, Baoding, 071000, China
| | - Jiurui Wang
- College of Forestry, Hebei Agricultural University, Baoding, 071000, China
| | - Zhiguo Liu
- Research Center of Chinese Jujube, College of Horticulture, Hebei Agricultural University, Baoding, 071000, China
| | - Yao Zhang
- College of Life Science, Hebei Agricultural University, Baoding, 071000, China
| | - Chaoling Xue
- College of Life Science, Hebei Agricultural University, Baoding, 071000, China
| | - Mengjun Liu
- Research Center of Chinese Jujube, College of Horticulture, Hebei Agricultural University, Baoding, 071000, China
| | - Jin Zhao
- College of Life Science, Hebei Agricultural University, Baoding, 071000, China.
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Shim S, Park CM, Seo PJ. iRegNet: an integrative Regulatory Network analysis tool for Arabidopsis thaliana. PLANT PHYSIOLOGY 2021; 187:1292-1309. [PMID: 34618085 PMCID: PMC8566287 DOI: 10.1093/plphys/kiab389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/09/2021] [Indexed: 05/24/2023]
Abstract
Gene expression is delicately controlled via multilayered genetic and/or epigenetic regulatory mechanisms. Rapid development of the high-throughput sequencing (HTS) technology and its derivative methods including chromatin immunoprecipitation sequencing (ChIP-seq) and DNA affinity purification sequencing (DAP-seq) have generated a large volume of data on DNA-protein interactions (DPIs) and histone modifications on a genome-wide scale. However, the ability to comprehensively retrieve empirically validated upstream regulatory networks of genes of interest (GOIs) and genomic regions of interest (ROIs) remains limited. Here, we present integrative Regulatory Network (iRegNet), a web application that analyzes the upstream regulatory network for user-queried GOIs or ROIs in the Arabidopsis (Arabidopsis thaliana) genome. iRegNet covers the largest empirically proven DNA-binding profiles of Arabidopsis transcription factors (TFs) and non-TF proteins, and histone modifications obtained from all currently available Arabidopsis ChIP-seq and DAP-seq data. iRegNet not only catalogs upstream regulomes and epigenetic chromatin states for single-query gene/genomic region but also suggests significantly overrepresented upstream genetic regulators and epigenetic chromatin states of user-submitted multiple query genes/genomic regions. Furthermore, gene-to-gene coexpression index and protein-protein interaction information were also integrated into iRegNet for a more reliable identification of upstream regulators and realistic regulatory networks. Thus, iRegNet will help discover upstream regulators as well as molecular regulatory networks of GOI(s) and/or ROI(s), and is freely available at http://chromatindynamics.snu.ac.kr:8082/iRegNet_main.
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Affiliation(s)
- Sangrea Shim
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea
| | - Chung-Mo Park
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea
- Research Institute of Basic Sciences, Seoul National University, Seoul 08826, Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea
- Research Institute of Basic Sciences, Seoul National University, Seoul 08826, Korea
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Abstract
Circadian clocks are important to much of life on Earth and are of inherent interest to humanity, implicated in fields ranging from agriculture and ecology to developmental biology and medicine. New techniques show that it is not simply the presence of clocks, but coordination between them that is critical for complex physiological processes across the kingdoms of life. Recent years have also seen impressive advances in synthetic biology to the point where parallels can be drawn between synthetic biological and circadian oscillators. This review will emphasize theoretical and experimental studies that have revealed a fascinating dichotomy of coupling and heterogeneity among circadian clocks. We will also consolidate the fields of chronobiology and synthetic biology, discussing key design principles of their respective oscillators.
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Affiliation(s)
- Chris N Micklem
- The Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK.,The Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge CH3 0HE, UK
| | - James C W Locke
- The Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK
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47
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Zhu C, Li Z, Tang Y, Zhang L, Wen J, Wang Z, Su Y, Chen Y, Zhang H. TaWRKY10 plays a key role in the upstream of circadian gene TaLHY in wheat. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 310:110973. [PMID: 34315591 DOI: 10.1016/j.plantsci.2021.110973] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/17/2021] [Accepted: 06/09/2021] [Indexed: 06/13/2023]
Abstract
TaLHY is an MYB transcription factor (TF) that is upregulated by salicylic acid induction and shows circadian rhythms. However, the study of the upstream regulatory factors is still unclear. In this study, we cloned the promoter sequence of the TaLHY homologous genes, verified the activity of the promoters, and identified important regions that affect promoter activity. Furthermore, we explored a possible upstream regulator of TaLHY, named TaWRKY10, which played a key role in the expression of TaLHY. We found that the three promoters pTaLHYa, pTaLHYb, and pTaLHYd had transcriptional activity in wheat protoplasts. All three promoters have W-Box, which can bind to WRKY TFs. Using virus-induced gene silencing (VIGS), after silencing TaWRKY10, the resistance of ChuanNong 19 (CN19) to stripe rust pathogen strain CYR32 was lost, and the expression level of the TaLHY homologous gene decreased. At the same time, in wheat protoplasts, the transcriptional activity of TaLHY homologous promoters improved after TaWRKY10 overexpression. This indicates that TaWRKY10 is a key gene for wheat immune response to stripe rust, and this gene may bind to TaLHYa, TaLHYb, and TaLHYd promoters to regulate the expression of TaLHY.
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Affiliation(s)
- Chaoyang Zhu
- College of Life Sciences, Sichuan Agricultural University, Ya'an, 625014, PR China
| | - Zhongyuan Li
- College of Life Sciences, Sichuan Agricultural University, Ya'an, 625014, PR China
| | - Yizhen Tang
- College of Life Sciences, Sichuan Agricultural University, Ya'an, 625014, PR China
| | - Liqiang Zhang
- College of Life Sciences, Sichuan Agricultural University, Ya'an, 625014, PR China
| | - Jiahe Wen
- College of Life Sciences, Sichuan Agricultural University, Ya'an, 625014, PR China
| | - Zhiming Wang
- College of Life Sciences, Sichuan Agricultural University, Ya'an, 625014, PR China
| | - Yongying Su
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Yang'er Chen
- College of Life Sciences, Sichuan Agricultural University, Ya'an, 625014, PR China
| | - Huaiyu Zhang
- College of Life Sciences, Sichuan Agricultural University, Ya'an, 625014, PR China.
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48
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Cao Z, Zhao T, Wang L, Han J, Chen J, Hao Y, Guan X. The lincRNA XH123 is involved in cotton cold-stress regulation. PLANT MOLECULAR BIOLOGY 2021; 106:521-531. [PMID: 34224063 DOI: 10.1007/s11103-021-01169-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 06/27/2021] [Indexed: 06/13/2023]
Abstract
We characterize a functional lincRNA, XH123 in cotton seedling in defense of cold stress. The silencing of XH123 leads to increased sensitivity to cold stress and the decay of chloroplast. Cotton, which originated from the arid mid-American region, is one of the most important cash crops worldwide. Cultivated cotton is now widely spread throughout high-altitude regions such as those in the far northwest of Asia. In such areas, spring temperatures below 12 ℃ impose cold stress on cotton seedlings, with concomitant threat of lost yield and productivity. It is documented that cold stress can induce differential expression of long noncoding RNAs (lncRNAs) in cotton; however, it is not yet clear if these cold-responsive lncRNAs are actively involved with tolerance of cold stress at the molecular level. Here, we select ten long intergenic non-coding RNAs as candidate genes and use virus-induced gene silencing and additional cold treatments to examine their roles in the response to cold stress during the cotton seedling stage. One such gene, XH123, was revealed to be involved in tolerance of cold stress. Specifically, XH123-silenced plants demonstrated sensitivity to cold stress, exhibiting chloroplast damage and increased endogenous levels of reactive oxygen species. The transcriptome profile of XH123-silenced seedlings was similar to that of cold-stressed seedlings having the known cold stress gene PIF3 silenced. These results imply that the lincRNA XH123 is actively involved with cold stress regulation in cotton during the seedling stage.
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Affiliation(s)
- Zeyi Cao
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Ting Zhao
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Luyao Wang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- College of Agriculture, Engineering Research Center of Ministry of Cotton Education, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Jin Han
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Jinwen Chen
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yupeng Hao
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Building 11, Yonyou Industrial Park, Yazhou Bay Science and Technology City, Yazhou District, Sanya, 572025, Hainan, China
| | - Xueying Guan
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
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49
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Sun C, Zhang K, Zhou Y, Xiang L, He C, Zhong C, Li K, Wang Q, Yang C, Wang Q, Chen C, Chen D, Wang Y, Liu C, Yang B, Wu H, Chen X, Li W, Wang J, Xu P, Wang P, Fang J, Chu C, Deng X. Dual function of clock component OsLHY sets critical day length for photoperiodic flowering in rice. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1644-1657. [PMID: 33740293 PMCID: PMC8384598 DOI: 10.1111/pbi.13580] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/18/2021] [Accepted: 03/08/2021] [Indexed: 05/11/2023]
Abstract
Circadian clock, an endogenous time-setting mechanism, allows plants to adapt to unstable photoperiod conditions and induces flowering with proper timing. In Arabidopsis, the central clock oscillator was formed by a series of interlocked transcriptional feedback loops, but little is known in rice so far. By MutMap technique, we identified the candidate gene OsLHY from a later flowering mutant lem1 and further confirmed it through genetic complementation, RNA interference knockdown, and CRISPR/Cas9-knockout. Global transcriptome profiling and expression analyses revealed that OsLHY might be a vital circadian rhythm component. Interestingly, oslhy flowered later under ≥12 h day length but headed earlier under ≤11 h day length. qRT-PCR results exhibited that OsLHY might function through OsGI-Hd1 pathway. Subsequent one-hybrid assays in yeast, DNA affinity purification qPCR, and electrophoretic mobility shift assays confirmed OsLHY could directly bind to the CBS element in OsGI promoter. Moreover, the critical day length (CDL) for function reversal of OsLHY in oslhy (11-12 h) was prolonged in the double mutant oslhy osgi (about 13.5 h), indicating that the CDL set by OsLHY was OsGI dependent. Additionally, the dual function of OsLHY entirely relied on Hd1, as the double mutant oslhy hd1 showed the same heading date with hd1 under about 11.5, 13.5, and 14 h day lengths. Together, OsLHY could fine-tune the CDL by directly regulating OsGI, and Hd1 acts as the final effector of CDL downstream of OsLHY. Our study illustrates a new regulatory mechanism between the circadian clock and photoperiodic flowering.
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Affiliation(s)
- Changhui Sun
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Kuan Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Yi Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Lin Xiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Changcai He
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Chao Zhong
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Ke Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Qiuxia Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Chuanpeng Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Qian Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Congping Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Dan Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Yang Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Chuanqiang Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Bin Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Hualin Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Xiaoqiong Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Weitao Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Jing Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Peizhou Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Pingrong Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Jun Fang
- Key Laboratory of Soybean Molecular Design BreedingNortheast Institute of Geography and AgroecologyChinese Academy of SciencesHarbinChina
| | - Chengcai Chu
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyThe Innovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Xiaojian Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
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50
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Palm D, Uzoni A, Simon F, Fischer M, Coogan A, Tucha O, Thome J, Faltraco F. Evolutionary conservations, changes of circadian rhythms and their effect on circadian disturbances and therapeutic approaches. Neurosci Biobehav Rev 2021; 128:21-34. [PMID: 34102148 DOI: 10.1016/j.neubiorev.2021.06.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 02/04/2021] [Accepted: 06/01/2021] [Indexed: 12/21/2022]
Abstract
The circadian rhythm is essential for the interaction of all living organisms with their environments. Several processes, such as thermoregulation, metabolism, cognition and memory, are regulated by the internal clock. Disturbances in the circadian rhythm have been shown to lead to the development of neuropsychiatric disorders, including attention-deficit hyperactivity disorder (ADHD). Interestingly, the mechanism of the circadian rhythms has been conserved in many different species, and misalignment between circadian rhythms and the environment results in evolutionary regression and lifespan reduction. This review summarises the conserved mechanism of the internal clock and its major interspecies differences. In addition, it focuses on effects the circadian rhythm disturbances, especially in cases of ADHD, and describes the possibility of recombinant proteins generated by eukaryotic expression systems as therapeutic agents as well as CRISPR/Cas9 technology as a potential tool for research and therapy. The aim is to give an overview about the evolutionary conserved mechanism as well as the changes of the circadian clock. Furthermore, current knowledge about circadian rhythm disturbances and therapeutic approaches is discussed.
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Affiliation(s)
- Denise Palm
- Department of Psychiatry and Psychotherapy, University Medical Center Rostock, Rostock, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Adriana Uzoni
- Department of Psychiatry and Psychotherapy, University Medical Center Rostock, Rostock, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Frederick Simon
- Department of Psychiatry and Psychotherapy, University Medical Center Rostock, Rostock, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Matthias Fischer
- Department of Psychiatry and Psychotherapy, University Medical Center Rostock, Rostock, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Andrew Coogan
- Department of Psychology, Maynooth University, National University of Ireland, Ireland
| | - Oliver Tucha
- Department of Psychiatry and Psychotherapy, University Medical Center Rostock, Rostock, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Johannes Thome
- Department of Psychiatry and Psychotherapy, University Medical Center Rostock, Rostock, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Frank Faltraco
- Department of Psychiatry and Psychotherapy, University Medical Center Rostock, Rostock, Gehlsheimer Str. 20, 18147, Rostock, Germany.
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