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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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2
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Alique D, Redondo López A, González Schain N, Allona I, Wabnik K, Perales M. Core clock genes adjust growth cessation time to day-night switches in poplar. Nat Commun 2024; 15:1784. [PMID: 38413620 PMCID: PMC10899572 DOI: 10.1038/s41467-024-46081-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 02/14/2024] [Indexed: 02/29/2024] Open
Abstract
Poplar trees use photoperiod as a precise seasonal indicator, synchronizing plant phenology with the environment. Daylength cue determines FLOWERING LOCUS T 2 (FT2) daily expression, crucial for shoot apex development and establishment of the annual growing period. However, limited evidence exists for the molecular factors controlling FT2 transcription and the conservation with the photoperiodic control of Arabidopsis flowering. We demonstrate that FT2 expression mediates growth cessation response quantitatively, and we provide a minimal data-driven model linking core clock genes to FT2 daily levels. GIGANTEA (GI) emerges as a critical inducer of the FT2 activation window, time-bound by TIMING OF CAB EXPRESSION (TOC1) and LATE ELONGATED HYPOCOTYL (LHY2) repressions. CRISPR/Cas9 loss-of-function lines validate these roles, identifying TOC1 as a long-sought FT2 repressor. Additionally, model simulations predict that FT2 downregulation upon daylength shortening results from a progressive narrowing of this activation window, driven by the phase shift observed in the preceding clock genes. This circadian-mediated mechanism enables poplar to exploit FT2 levels as an accurate daylength-meter.
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Affiliation(s)
- Daniel Alique
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA) Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA, CSIC), Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Arturo Redondo López
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA) Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA, CSIC), Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Nahuel González Schain
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA) Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA, CSIC), Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
- Instituto de Biología Molecular y Celular de Rosario, CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Isabel Allona
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA) Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA, CSIC), Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, 28040, Spain
| | - Krzysztof Wabnik
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA) Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA, CSIC), Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain.
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, 28040, Spain.
| | - Mariano Perales
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA) Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA, CSIC), Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain.
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, 28040, Spain.
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3
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Huang X, Lyu T, Li Z, Lyu Y. Hydrangea arborescens 'Annabelle' Flower Formation and Flowering in the Current Year. PLANTS (BASEL, SWITZERLAND) 2023; 12:4103. [PMID: 38140430 PMCID: PMC10748224 DOI: 10.3390/plants12244103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/24/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023]
Abstract
The perennial woody plant Hydrangea arborescens 'Annabelle' is of great research value due to its unique mechanism of flower development that occurs in the current year, resulting in decorative flowers that can be enjoyed for a relatively long period of time. However, the mechanisms underlying the regulation of current-year flower development in H. arborescens 'Annabelle' are still not fully understood. In this study, we conducted an associated analysis to explore the core regulating network in H. arborescens 'Annabelle' by combining phenological observations, physiological assays, and transcriptome comparisons across seven flower developmental stages. Through this analysis, we constructed a gene co-expression network (GCN) based on the highest reciprocal rank (HRR), using 509 differentially expressed genes (DEGs) identified from seven flowering-related pathways, as well as the biosynthesis of eight flowering-related phytohormones and signal transduction in the transcriptomic analysis. According to the analysis of the GCN, we identified 14 key genes with the highest functional connectivity that played critical roles in specific development stages. We confirmed that 135 transcription factors (AP2/ERF, bHLH, CO-like, GRAS, MIKC, SBP, WRKY) were highly co-expressed with the 14 key genes, indicating their close associations with the development of current-year flowers. We further proposed a hypothetical model of a gene regulatory network for the development of the whole flower. This model suggested that the photoperiod, aging, and gibberellin pathways, along with the phytohormones abscisic acid (ABA), gibberellin (GA), brassinosteroid (BR), and jasmonic acid (JA), work synergistically to promote the floral transition. Additionally, auxin, GA, JA, ABA, and salicylic acid (SA) regulated the blooming process by involving the circadian clock. Cytokinin (CTK), ethylene (ETH), and SA were key regulators that affected flower senescence. Additionally, several floral integrators (HaLFY, HaSOC1-2, HaAP1, HaFULL, HaAGL24, HaFLC, etc.) were dominant contributors to the development of H. arborescens flowers. Overall, this research provides a comprehensive understanding of the dynamic mechanism underlying the entire process of current-year flower development, thereby offering valuable insights for further studies on the flower development of H. arborescens 'Annabelle'.
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Affiliation(s)
- Xiaoxu Huang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, China National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Tong Lyu
- Beijing Flower Engineering Technology Research Center, Plant Institute, China National Botanical Garden North Garden, Beijing 100093, China
| | - Zheng Li
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, China National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Yingmin Lyu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, China National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
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Horemans N, Kariuki J, Saenen E, Mysara M, Beemster GTS, Sprangers K, Pavlović I, Novak O, Van Hees M, Nauts R, Duarte GT, Cuypers A. Are Arabidopsis thaliana plants able to recover from exposure to gamma radiation? A molecular perspective. JOURNAL OF ENVIRONMENTAL RADIOACTIVITY 2023; 270:107304. [PMID: 37871537 DOI: 10.1016/j.jenvrad.2023.107304] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 09/15/2023] [Accepted: 09/29/2023] [Indexed: 10/25/2023]
Abstract
Most plant research focuses on the responses immediately after exposure to ionizing irradiation (IR). However, it is as important to investigate how plants recover after exposure since this has a profound effect on future plant growth and development and hence on the long-term consequences of exposure to stress. This study aimed to investigate the IR-induced responses after exposure and during recovery by exposing 1-week old A. thaliana seedlings to gamma dose rates ranging from 27 to 103.7 mGy/h for 2 weeks and allowing them to recover for 4 days. A high-throughput RNAsequencing analysis was carried out. An enrichment of GO terms related to the metabolism of hormones was observed both after irradiation and during recovery at all dose rates. While plants exposed to the lowest dose rate activate defence responses after irradiation, they recover from the IR by resuming normal growth during the recovery period. Plants exposed to the intermediate dose rate invest in signalling and defence after irradiation. During recovery, in the plants exposed to the highest dose rate, fundamental metabolic processes such as photosynthesis and RNA modification were still affected. This might lead to detrimental effects in the long-term or in the next generations of those irradiated plants.
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Affiliation(s)
- Nele Horemans
- Biosphere Impact Studies, SCK CEN, Boeretang 200, 2400, Mol, Belgium; Centre for Environmental Research, Hasselt University, Diepenbeek, Belgium.
| | - Jackline Kariuki
- Biosphere Impact Studies, SCK CEN, Boeretang 200, 2400, Mol, Belgium
| | - Eline Saenen
- Biosphere Impact Studies, SCK CEN, Boeretang 200, 2400, Mol, Belgium
| | - Mohamed Mysara
- Biosphere Impact Studies, SCK CEN, Boeretang 200, 2400, Mol, Belgium
| | - Gerrit T S Beemster
- Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Katrien Sprangers
- Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Iva Pavlović
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences & Faculty of Science of Palacký University, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Ondrej Novak
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences & Faculty of Science of Palacký University, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - May Van Hees
- Biosphere Impact Studies, SCK CEN, Boeretang 200, 2400, Mol, Belgium
| | - Robin Nauts
- Biosphere Impact Studies, SCK CEN, Boeretang 200, 2400, Mol, Belgium
| | | | - Ann Cuypers
- Centre for Environmental Research, Hasselt University, Diepenbeek, Belgium
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5
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Wang X, Zhang J, Liu X, Kong Y, Han L. The Roles of the PSEUDO-RESPONSE REGULATORs in Circadian Clock and Flowering Time in Medicago truncatula. Int J Mol Sci 2023; 24:16834. [PMID: 38069157 PMCID: PMC10706769 DOI: 10.3390/ijms242316834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/22/2023] [Accepted: 11/25/2023] [Indexed: 12/18/2023] Open
Abstract
PSEUDO-RESPONSE REGULATORs (PRRs) play key roles in the circadian rhythms and flowering in plants. Here, we identified the four members of the PRR family in Medicago truncatula, including MtPRR9a, MtPRR9b, MtPRR7 and MtPRR5, and isolated their Tnt1 retrotransposon-tagged mutants. They were expressed in different organs and were nuclear-localized. The four MtPRRs genes played important roles in normal clock rhythmicity maintenance by negatively regulating the expression of MtGI and MtLHY. Surprisingly, the four MtPRRs functioned redundantly in regulating flowering time under long-day conditions, and the quadruple mutant flowered earlier. Moreover, MtPRR can recruit the MtTPL/MtTPR corepressors and the other MtPRRs to form heterodimers to constitute the core mechanism of the circadian oscillator.
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Affiliation(s)
- Xiao Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (X.W.); (J.Z.); (X.L.); (Y.K.)
| | - Juanjuan Zhang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (X.W.); (J.Z.); (X.L.); (Y.K.)
| | - Xiu Liu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (X.W.); (J.Z.); (X.L.); (Y.K.)
| | - Yiming Kong
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (X.W.); (J.Z.); (X.L.); (Y.K.)
- College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Lu Han
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (X.W.); (J.Z.); (X.L.); (Y.K.)
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6
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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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Lee SJ, Kang K, Lim JH, Paek NC. Natural alleles of CIRCADIAN CLOCK ASSOCIATED1 contribute to rice cultivation by fine-tuning flowering time. PLANT PHYSIOLOGY 2022; 190:640-656. [PMID: 35723564 PMCID: PMC9434239 DOI: 10.1093/plphys/kiac296] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 05/26/2022] [Indexed: 05/11/2023]
Abstract
The timing of flowering is a crucial factor for successful grain production at a wide range of latitudes. Domestication of rice (Oryza sativa) included selection for natural alleles of flowering-time genes that allow rice plants to adapt to broad geographic areas. Here, we describe the role of natural alleles of CIRCADIAN CLOCK ASSOCIATED1 (OsCCA1) in cultivated rice based on analysis of single-nucleotide polymorphisms deposited in the International Rice Genebank Collection Information System database. Rice varieties harboring japonica-type OsCCA1 alleles (OsCCA1a haplotype) flowered earlier than those harboring indica-type OsCCA1 alleles (OsCCA1d haplotype). In the japonica cultivar "Dongjin", a T-DNA insertion in OsCCA1a resulted in late flowering under long-day and short-day conditions, indicating that OsCCA1 is a floral inducer. Reverse transcription quantitative PCR analysis showed that the loss of OsCCA1a function induces the expression of the floral repressors PSEUDO-RESPONSE REGULATOR 37 (OsPRR37) and Days to Heading 8 (DTH8), followed by repression of the Early heading date 1 (Ehd1)-Heading date 3a (Hd3a)-RICE FLOWERING LOCUS T 1 (RFT1) pathway. Binding affinity assays indicated that OsCCA1 binds to the promoter regions of OsPRR37 and DTH8. Naturally occurring OsCCA1 alleles are evolutionarily conserved in cultivated rice (O. sativa). Oryza rufipogon-I (Or-I) and Or-III type accessions, representing the ancestors of O. sativa indica and japonica, harbored indica- and japonica-type OsCCA1 alleles, respectively. Taken together, our results demonstrate that OsCCA1 is a likely domestication locus that has contributed to the geographic adaptation and expansion of cultivated rice.
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Affiliation(s)
| | | | - Jung-Hyun Lim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea
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Ntambiyukuri A, Li X, Xiao D, Wang A, Zhan J, He L. Circadian Rhythm Regulates Reactive Oxygen Species Production and Inhibits Al-Induced Programmed Cell Death in Peanut. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081271. [PMID: 36013450 PMCID: PMC9410085 DOI: 10.3390/life12081271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/17/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022]
Abstract
Peanut is among the most important oil crops in the world. In the southern part of China, peanut is highly produced; however, the arable land is acidic. In acidic soils, aluminum (Al) inhibits plant growth and development by changing the properties of the cell wall and causing the disorder of the intracellular metabolic process. Circadian rhythm is an internal mechanism that occurs about every 24 h and enables plants to maintain internal biological processes with a daily cycle. To investigate the effect of photoperiod and Al stress on the Al-induced programmed cell death (PCD), two peanut varieties were treated with 100 μM AlCl3 under three photoperiodic conditions (8/16, SD; 12/12, ND; 16/8 h, LD). The results show that Al toxicity was higher in ZH2 than in 99-1507 and higher under LD than under SD. Root length decreased by 30, 37.5, and 50% in ZH2 and decreased by 26.08, 34.78, and 47.82% in 99-1507 under SD, ND, and LD, respectively, under Al stress. Photoperiod and Al induced cell death and ROS production. MDA content, PME activity, and LOX activity increased under SD, ND, and LD, respectively, under Al stress both in ZH2 and 99-1507. APX, SOD, CAT, and POD activities were higher under SD, ND, and LD, respectively. Al stress increased the level of AhLHY expression under SD and ND but decreased it under LD in both ZH2 and 99-1507. Contrastingly, AhSTS expression levels increased exponentially and were higher under SD, LD, and ND, respectively, under Al stress. Our results will be a useful platform to research PCD induced by Al and gain new insights into the genetic manipulation of the circadian clock for plant stress response.
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Affiliation(s)
- Aaron Ntambiyukuri
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Xia Li
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Dong Xiao
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, Nanning 530004, China
- Guangxi Colleges and Universities Key Laboratory of Crop Cultivation and Tillage, Nanning 530004, China
- Correspondence: (D.X.); (L.H.)
| | - Aiqin Wang
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, Nanning 530004, China
- Guangxi Colleges and Universities Key Laboratory of Crop Cultivation and Tillage, Nanning 530004, China
| | - Jie Zhan
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, Nanning 530004, China
- Guangxi Colleges and Universities Key Laboratory of Crop Cultivation and Tillage, Nanning 530004, China
| | - Longfei He
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, Nanning 530004, China
- Guangxi Colleges and Universities Key Laboratory of Crop Cultivation and Tillage, Nanning 530004, China
- Correspondence: (D.X.); (L.H.)
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9
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Song Y, Zhang R, Gao S, Pan Z, Guo Z, Yu S, Wang Y, Jin Q, Chen X, Zhang L. Transcriptome analysis and phenotyping of walnut seedling roots under nitrogen stresses. Sci Rep 2022; 12:12066. [PMID: 35835799 PMCID: PMC9283388 DOI: 10.1038/s41598-022-14850-2] [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: 05/12/2021] [Accepted: 05/03/2022] [Indexed: 11/15/2022] Open
Abstract
Nitrogen is an essential core element in walnut seedling growth and development. However, nitrogen starvation and excessive nitrogen stress can cause stunted growth and development of walnut seedlings, and environmental pollution is also of concern. Therefore, it is necessary to study the mechanism of walnut seedling resistance to nitrogen stress. In this study, morphological and physiological observations and transcriptome sequencing of walnut seedlings under nitrogen starvation and excess nitrogen stress were performed. The results showed that walnut seedlings under nitrogen starvation and excess stress could adapt to the changes in the nitrogen environment by changing the coordination of their root morphology and physiological indexes. Based on an analysis of transcriptome data, 4911 differential genes (DEGs) were obtained (2180 were upregulated and 2731 were downregulated) in a comparison of nitrogen starvation and control groups. A total of 9497 DEGs (5091 upregulated and 4406 downregulated) were obtained in the comparison between the nitrogen overdose and control groups. When these DEGs were analysed, the differential genes in both groups were found to be significantly enriched in the plant’s circadian pathway. Therefore, we selected the circadian rhythm as the focus for further analysis. We made some discoveries by analysing the gene co-expression network of nitrogen metabolism, circadian rhythm, and hormone signal transduction. (a) Nitrite nitrogen (NO2−) or Glu may act as a nitrogen signal to the circadian clock. (b) Nitrogen signalling may be input into the circadian clock by regulating changes in the abundance of the CRY1 gene. (c) After the nitrogen signal enters the circadian clock, the expression of the LHY gene is upregulated, which causes a phase shift in the circadian clock. (d) The RVE protein may send information about the circadian clock’s response to nitrogen stress back to the nitrogen metabolic pathway via the hormone transduction pathway. In conclusion, various metabolic pathways in the roots of walnut seedlings coordinated with one another to resist the ill effects of nitrogen stress on the root cells, and these coordination relationships were regulated by the circadian clock. This study is expected to provide valuable information on the circadian clock regulation of plant resistance to nitrogen stress.
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Affiliation(s)
- Yan Song
- College of Plant Sciences, Tarim University, Alar, 843300, China.,National and Local Joint Engineering Laboratory for High-Efficiency and Quality Cultivation and Deep Processing Technology of Characteristic Fruit Trees in Southern Xinjiang, Alar, 843300, China.,Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Tarim University, Alar, 843300, China
| | - Rui Zhang
- College of Plant Sciences, Tarim University, Alar, 843300, China. .,National and Local Joint Engineering Laboratory for High-Efficiency and Quality Cultivation and Deep Processing Technology of Characteristic Fruit Trees in Southern Xinjiang, Alar, 843300, China. .,Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Tarim University, Alar, 843300, China.
| | - Shan Gao
- College of Plant Sciences, Tarim University, Alar, 843300, China.
| | - Zhiyong Pan
- College of Plant Sciences, Tarim University, Alar, 843300, China
| | - Zhongzhong Guo
- National and Local Joint Engineering Laboratory for High-Efficiency and Quality Cultivation and Deep Processing Technology of Characteristic Fruit Trees in Southern Xinjiang, Alar, 843300, China.,Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Tarim University, Alar, 843300, China.,College of Life Sciences, Tarim University, Alar, 843300, China
| | - Shangqi Yu
- National and Local Joint Engineering Laboratory for High-Efficiency and Quality Cultivation and Deep Processing Technology of Characteristic Fruit Trees in Southern Xinjiang, Alar, 843300, China.,Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Tarim University, Alar, 843300, China.,College of Life Sciences, Tarim University, Alar, 843300, China
| | - Yu Wang
- National and Local Joint Engineering Laboratory for High-Efficiency and Quality Cultivation and Deep Processing Technology of Characteristic Fruit Trees in Southern Xinjiang, Alar, 843300, China.,Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Tarim University, Alar, 843300, China.,College of Life Sciences, Tarim University, Alar, 843300, China
| | - Qiang Jin
- College of Plant Sciences, Tarim University, Alar, 843300, China.,National and Local Joint Engineering Laboratory for High-Efficiency and Quality Cultivation and Deep Processing Technology of Characteristic Fruit Trees in Southern Xinjiang, Alar, 843300, China
| | - Xiaofei Chen
- College of Plant Sciences, Tarim University, Alar, 843300, China
| | - Lei Zhang
- College of Plant Sciences, Tarim University, Alar, 843300, China
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10
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Lal M, Bhardwaj E, Chahar N, Yadav S, Das S. Comprehensive analysis of 1R- and 2R-MYBs reveals novel genic and protein features, complex organisation, selective expansion and insights into evolutionary tendencies. Funct Integr Genomics 2022; 22:371-405. [PMID: 35260976 DOI: 10.1007/s10142-022-00836-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 02/10/2022] [Accepted: 02/23/2022] [Indexed: 11/28/2022]
Abstract
Myeloblastosis (MYB) family, the largest plant transcription factor family, has been subcategorised based on the number and type of repeats in the MYB domain. In spite of several reports, evolution of MYB genes and repeats remains enigmatic. Brassicaceae members are endowed with complex genomes, including dysploidy because of its unique history with multiple rounds of polyploidisation, genomic fractionations and rearrangements. The present study is an attempt to gain insights into the complexities of MYB family diversity, understand impacts of genome evolution on gene families and develop an evolutionary framework to understand the origin of various subcategories of MYB gene family. We identified and analysed 1129 MYBs that included 1R-, 2R-, 3R- and atypical-MYBs across sixteen species representing protists, fungi, animals and plants and exclude MYB identified from Brassicaceae except Arabidopsis thaliana; in addition, a total of 1137 2R-MYB genes from six Brassicaceae species were also analysed. Comparative analysis revealed predominance of 1R-MYBs in protists, fungi, animals and lower plants. Phylogenetic reconstruction and analysis of selection pressure suggested ancestral nature of R1-type repeat containing 1R-MYBs that might have undergone intragenic duplication to form multi-repeat MYBs. Distinct differences in gene structure between 1R-MYB and 2R-MYBs were observed regarding intron number, the ratio of gene length to coding DNA sequence (CDS) length and the length of exons encoding the MYB domain. Conserved as well as novel and lineage-specific intron phases were identified. Analyses of physicochemical properties revealed drastic differences indicating functional diversification in MYBs. Phylogenetic reconstruction of 1R- and 2R-MYB genes revealed a shared structure-function relationship in clades which was supported when transcriptome data was analysed in silico. Comparative genomics to study distribution pattern and mapping of 2R-MYBs revealed congruency and greater degree of synteny and collinearity among closely related species. Micro-synteny analysis of genomic segments revealed high conservation of genes that are immediately flanking the surrounding tandemly organised 2R-MYBs along with instances of local duplication, reorganisations and genome fractionation. In summary, polyploidy, dysploidy, reshuffling and genome fractionation were found to cause loss or gain of 2R-MYB genes. The findings need to be supported with functional validation to understand gene structure-function relationship along the evolutionary lineage and adaptive strategies based on comparative functional genomics in plants.
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Affiliation(s)
- Mukund Lal
- Department of Botany, University of Delhi, Delhi, 110007, India
| | - Ekta Bhardwaj
- Department of Botany, University of Delhi, Delhi, 110007, India
| | - Nishu Chahar
- Department of Botany, University of Delhi, Delhi, 110007, India
| | - Shobha Yadav
- Department of Botany, University of Delhi, Delhi, 110007, India
| | - Sandip Das
- Department of Botany, University of Delhi, Delhi, 110007, India.
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11
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Hirohata A, Yamatsuta Y, Ogawa K, Kubota A, Suzuki T, Shimizu H, Kanesaka Y, Takahashi N, Endo M. Sulfanilamide Regulates Flowering Time through Expression of the Circadian Clock Gene LUX. PLANT & CELL PHYSIOLOGY 2022; 63:649-657. [PMID: 35238923 DOI: 10.1093/pcp/pcac027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/24/2022] [Accepted: 03/02/2022] [Indexed: 06/14/2023]
Abstract
Flowering time is an agriculturally important trait that can be manipulated by various approaches such as breeding, growth control and genetic modifications. Despite its potential advantages, including fine-tuning the regulation of flowering time, few reports have explored the use of chemical compounds to manipulate flowering. Here, we report that sulfanilamide, an inhibitor of folate biosynthesis, delays flowering by repressing the expression of florigen FLOWERING LOCUS T (FT) in Arabidopsis thaliana. Transcriptome deep sequencing and quantitative polymerase chain reaction analyses showed that the expression of the circadian clock gene LUX ARRYTHMO/PHYTOCLOCK1 (LUX/PCL1) is altered by sulfanilamide treatment. Furthermore, in the lux nox mutant harboring loss of function in both LUX and its homolog BROTHER OF LUX ARRHYTHMO (BOA, also named NOX), the inhibitory effect of sulfanilamide treatment on FT expression was weak and the flowering time was similar to that of the wild type, suggesting that the circadian clock may contribute to the FT-mediated regulation of flowering by sulfanilamide. Sulfanilamide also delayed flowering time in arugula (Eruca sativa), suggesting that it is involved in the regulation of flowering across Brassicaceae. We propose that sulfanilamide is a novel modulator of flowering.
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Affiliation(s)
- Atsuhiro Hirohata
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Takayama-Cho 8916-5, Ikoma, Nara, 630-0192 Japan
| | - Yuta Yamatsuta
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Takayama-Cho 8916-5, Ikoma, Nara, 630-0192 Japan
| | - Kaori Ogawa
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo, Kyoto, 606-8501 Japan
| | - Akane Kubota
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Takayama-Cho 8916-5, Ikoma, Nara, 630-0192 Japan
| | - Takamasa Suzuki
- College of Bioscience and Biotechnology, Chubu University, Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
| | - Hanako Shimizu
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, Shiga, 520-2113 Japan
| | - Yuki Kanesaka
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo, Kyoto, 606-8501 Japan
| | - Nozomu Takahashi
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Takayama-Cho 8916-5, Ikoma, Nara, 630-0192 Japan
| | - Motomu Endo
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Takayama-Cho 8916-5, Ikoma, Nara, 630-0192 Japan
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12
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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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13
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Kawash J, Colt K, Hartwick NT, Abramson BW, Vorsa N, Polashock JJ, Michael TP. Contrasting a reference cranberry genome to a crop wild relative provides insights into adaptation, domestication, and breeding. PLoS One 2022; 17:e0264966. [PMID: 35255111 PMCID: PMC8901128 DOI: 10.1371/journal.pone.0264966] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 02/19/2022] [Indexed: 11/24/2022] Open
Abstract
Cranberry (Vaccinium macrocarpon) is a member of the Heath family (Ericaceae) and is a temperate low-growing woody perennial native to North America that is both economically important and has significant health benefits. While some native varieties are still grown today, breeding programs over the past 50 years have made significant contributions to improving disease resistance, fruit quality and yield. An initial genome sequence of an inbred line of the wild selection ‘Ben Lear,’ which is parent to multiple breeding programs, provided insight into the gene repertoire as well as a platform for molecular breeding. Recent breeding efforts have focused on leveraging the circumboreal V. oxycoccos, which forms interspecific hybrids with V. macrocarpon, offering to bring in novel fruit chemistry and other desirable traits. Here we present an updated, chromosome-resolved V. macrocarpon reference genome, and compare it to a high-quality draft genome of V. oxycoccos. Leveraging the chromosome resolved cranberry reference genome, we confirmed that the Ericaceae has undergone two whole genome duplications that are shared with blueberry and rhododendron. Leveraging resequencing data for ‘Ben Lear’ inbred lines, as well as several wild and elite selections, we identified common regions that are targets of improvement. These same syntenic regions in V. oxycoccos, were identified and represent environmental response and plant architecture genes. These data provide insight into early genomic selection in the domestication of a native North American berry crop.
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Affiliation(s)
- Joseph Kawash
- USDA, Agricultural Research Service, Genetic Improvement of Fruits and Vegetables Lab, Chatsworth, New Jersey, United States of America
| | - Kelly Colt
- Plant Molecular and Cellular Biology, Salk Institute of Biological Sciences, La Jolla, California, United States of America
| | - Nolan T. Hartwick
- Plant Molecular and Cellular Biology, Salk Institute of Biological Sciences, La Jolla, California, United States of America
| | - Bradley W. Abramson
- Plant Molecular and Cellular Biology, Salk Institute of Biological Sciences, La Jolla, California, United States of America
| | - Nicholi Vorsa
- P.E. Marucci Center for Blueberry and Cranberry Research, Chatsworth, New Jersey, United States of America
- Department of Plant Biology and Pathology, Rutgers University, New Brunswick, New Jersey, United States of America
| | - James J. Polashock
- USDA, Agricultural Research Service, Genetic Improvement of Fruits and Vegetables Lab, Chatsworth, New Jersey, United States of America
- * E-mail: (JJP); (TPM)
| | - Todd P. Michael
- Plant Molecular and Cellular Biology, Salk Institute of Biological Sciences, La Jolla, California, United States of America
- * E-mail: (JJP); (TPM)
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14
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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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15
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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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16
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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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17
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Gutiérrez-Larruscain D, Abeyawardana OAJ, Krüger M, Belz C, Juříček M, Štorchová H. Transcriptomic study of the night break in Chenopodium rubrum reveals possible upstream regulators of the floral activator CrFTL1. JOURNAL OF PLANT PHYSIOLOGY 2021; 265:153492. [PMID: 34385120 DOI: 10.1016/j.jplph.2021.153492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/23/2021] [Accepted: 08/04/2021] [Indexed: 06/13/2023]
Abstract
The transition from vegetative to reproductive phases is the most fundamental and tightly controlled switch in the life of flowering plants. The short-day plant Chenopodium rubrum is a fast cycling annual plant lacking a juvenile phase. It can be induced to flowering at the seedling stage by exposure to a single period of darkness. This floral induction may then be cancelled by a short pulse of red light at midnight called night break (NB), which also inhibits the floral activator FLOWERING LOCUS T LIKE 1 (CrFTL1). We performed a comparative transcriptomic study between C. rubrum seedlings treated by NB and ones growing through uninterrupted night, and found about six hundred differentially expressed genes, including the B-BOX DOMAIN (BBX) genes. We focused on the CrBBX19 and BOLTING TIME CONTROL 1 (BTC1) genes, homologous to the upstream regulators of the BvFT2, a floral inducer in sugar beet. The transcription patterns of the two genes were compatible with their putative role as a sensor of the dark period length optimal for flowering (CrBBX19), and a signal of lights-on (CrBTC1), but the participation of other genes cannot be excluded. The expression profiles of CrBBX19 and the homolog of the core endogenous clock gene LATE ELONGATED HYPOCOTYL (LHY) were highly similar, which suggested their co-regulation.
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Affiliation(s)
- David Gutiérrez-Larruscain
- Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 263, 16502, Prague, Czech Republic.
| | - Oushadee A J Abeyawardana
- Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 263, 16502, Prague, Czech Republic; Department of Horticulture, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 16500, Prague, Czech Republic.
| | - Manuela Krüger
- Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 263, 16502, Prague, Czech Republic.
| | - Claudia Belz
- Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 263, 16502, Prague, Czech Republic.
| | - Miloslav Juříček
- Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 263, 16502, Prague, Czech Republic.
| | - Helena Štorchová
- Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 263, 16502, Prague, Czech Republic.
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18
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Beathard C, Mooney S, Al-Saharin R, Goyer A, Hellmann H. Characterization of Arabidopsis thaliana R2R3 S23 MYB Transcription Factors as Novel Targets of the Ubiquitin Proteasome-Pathway and Regulators of Salt Stress and Abscisic Acid Response. FRONTIERS IN PLANT SCIENCE 2021; 12:629208. [PMID: 34489986 PMCID: PMC8417012 DOI: 10.3389/fpls.2021.629208] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 07/30/2021] [Indexed: 05/27/2023]
Abstract
Rapid response to environmental changes and abiotic stress to coordinate developmental programs is critical for plants. To accomplish this, plants use the ubiquitin proteasome pathway as a flexible and efficient mechanism to control protein stability and to direct cellular reactions. Here, we show that all three members of the R2R3 S23 MYB transcription factor subfamily, MYB1, MYB25, and MYB109, are degraded by the 26S proteasome, likely facilitated by a CUL3-based E3 ligase that uses MATH-BTB/POZ proteins as substrate adaptors. A detailed description of MYB1, MYB25, and MYB109 expression shows their nuclear localization and specific tissue specific expression patterns. It further demonstrates that elevated expression of MYB25 reduces sensitivities toward abscisic acid, osmotic and salt stress in Arabidopsis, while downregulation of all S23 members results in hypersensitivities. Transcriptional profiling in root and shoot of seedlings overexpressing MYB25 shows that the transcription factor widely affects cellular stress pathways related to biotic and abiotic stress control. Overall, the work extends our knowledge on proteins targeted by CUL3-based E3 ligases that use MATH-BTB/POZ proteins as substrate adaptors and provides first information on all members of the MYB S23 subfamily.
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Affiliation(s)
- Chase Beathard
- School of Biological Sciences, Washington State University, Pullman, WA, United States
| | - Sutton Mooney
- School of Biological Sciences, Washington State University, Pullman, WA, United States
| | - Raed Al-Saharin
- School of Biological Sciences, Washington State University, Pullman, WA, United States
- Department of Applied Biology, Tafila Technical University, At-Tafilah, Jordan
| | - Aymeric Goyer
- Department of Botany and Plant Pathology, Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston, OR, United States
| | - Hanjo Hellmann
- School of Biological Sciences, Washington State University, Pullman, WA, United States
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19
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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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20
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Zhang S, Zhang Y, Li K, Yan M, Zhang J, Yu M, Tang S, Wang L, Qu H, Luo L, Xuan W, Xu G. Nitrogen Mediates Flowering Time and Nitrogen Use Efficiency via Floral Regulators in Rice. Curr Biol 2020; 31:671-683.e5. [PMID: 33278354 DOI: 10.1016/j.cub.2020.10.095] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 10/10/2020] [Accepted: 10/30/2020] [Indexed: 11/29/2022]
Abstract
High nitrogen (N) fertilization for maximizing crop yield commonly leads to postponed flowering time (heading date in rice) and ripening, thus affecting resources use efficiency and followed planting time. We found that N-mediated heading date-1 (Nhd1) can directly activate florigen gene OsHd3a in rice. Inactivation of either Nhd1 or OsHd3a results in delay and insensitivity to N supply of flowering time. Knockout of Nhd1 increases N uptake and utilization efficiency at low-to-moderate N level under both short- and long-day field conditions. Increasing glutamine, the product of N assimilation, can upregulate expression of Nhd1, which in turn downregulates OsFd-GOGAT expression and OsFd-GOGAT activity, displaying a Nhd1-controlled negative feedback regulatory pathway of N assimilation. Moreover, N fertilization effect on rice flowering time shows genetically controlled diversity, and single-nucleotide polymorphism in Nhd1 promoter may relate to different responses of flowering time to N application. Nhd1 thus balances flowering time and N use efficiency in addition to photoperiod in rice.
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Affiliation(s)
- Shunan Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuyi Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Kangning Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ming Yan
- Shanghai Agrobiological Gene Center, Shanghai 201106, China
| | - Jinfei Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ming Yu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuo Tang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Luyang Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Hongye Qu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Le Luo
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Wei Xuan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Guohua Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.
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21
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de María N, Guevara MÁ, Perdiguero P, Vélez MD, Cabezas JA, López‐Hinojosa M, Li Z, Díaz LM, Pizarro A, Mancha JA, Sterck L, Sánchez‐Gómez D, Miguel C, Collada C, Díaz‐Sala MC, Cervera MT. Molecular study of drought response in the Mediterranean conifer Pinus pinaster Ait.: Differential transcriptomic profiling reveals constitutive water deficit-independent drought tolerance mechanisms. Ecol Evol 2020; 10:9788-9807. [PMID: 33005345 PMCID: PMC7520194 DOI: 10.1002/ece3.6613] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/19/2020] [Accepted: 06/29/2020] [Indexed: 12/27/2022] Open
Abstract
Adaptation of long-living forest trees to respond to environmental changes is essential to secure their performance under adverse conditions. Water deficit is one of the most significant stress factors determining tree growth and survival. Maritime pine (Pinus pinaster Ait.), the main source of softwood in southwestern Europe, is subjected to recurrent drought periods which, according to climate change predictions for the years to come, will progressively increase in the Mediterranean region. The mechanisms regulating pine adaptive responses to environment are still largely unknown. The aim of this work was to go a step further in understanding the molecular mechanisms underlying maritime pine response to water stress and drought tolerance at the whole plant level. A global transcriptomic profiling of roots, stems, and needles was conducted to analyze the performance of siblings showing contrasted responses to water deficit from an ad hoc designed full-sib family. Although P. pinaster is considered a recalcitrant species for vegetative propagation in adult phase, the analysis was conducted using vegetatively propagated trees exposed to two treatments: well-watered and moderate water stress. The comparative analyses led us to identify organ-specific genes, constitutively expressed as well as differentially expressed when comparing control versus water stress conditions, in drought-sensitive and drought-tolerant genotypes. Different response strategies can point out, with tolerant individuals being pre-adapted for coping with drought by constitutively expressing stress-related genes that are detected only in latter stages on sensitive individuals subjected to drought.
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Affiliation(s)
- Nuria de María
- Departamento de Ecología y Genética ForestalCentro de Investigación Forestal (CIFOR)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)MadridSpain
- Unidad Mixta de Genómica y Ecofisiología ForestalInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Universidad Politécnica de Madrid (UPM)MadridSpain
| | - María Ángeles Guevara
- Departamento de Ecología y Genética ForestalCentro de Investigación Forestal (CIFOR)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)MadridSpain
- Unidad Mixta de Genómica y Ecofisiología ForestalInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Universidad Politécnica de Madrid (UPM)MadridSpain
| | - Pedro Perdiguero
- Departamento de Ecología y Genética ForestalCentro de Investigación Forestal (CIFOR)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)MadridSpain
- Centro de Investigación en Sanidad Animal (CISA‐INIA)MadridSpain
- Departamento de Cultivos HerbáceosCentro de Investigación Agroforestal de AlbaladejitoCuencaSpain
| | - María Dolores Vélez
- Departamento de Ecología y Genética ForestalCentro de Investigación Forestal (CIFOR)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)MadridSpain
- Unidad Mixta de Genómica y Ecofisiología ForestalInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Universidad Politécnica de Madrid (UPM)MadridSpain
| | - José Antonio Cabezas
- Departamento de Ecología y Genética ForestalCentro de Investigación Forestal (CIFOR)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)MadridSpain
- Unidad Mixta de Genómica y Ecofisiología ForestalInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Universidad Politécnica de Madrid (UPM)MadridSpain
| | - Miriam López‐Hinojosa
- Departamento de Ecología y Genética ForestalCentro de Investigación Forestal (CIFOR)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)MadridSpain
- Unidad Mixta de Genómica y Ecofisiología ForestalInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Universidad Politécnica de Madrid (UPM)MadridSpain
| | - Zhen Li
- Ghent University Department of Plant Biotechnology and BioinformaticsGhentBelgium
- VIB‐UGent Center for Plant Systems BiologyGhentBelgium
- Bioinformatics Institute GhentGhent UniversityGhentBelgium
| | - Luís Manuel Díaz
- Departamento de Ecología y Genética ForestalCentro de Investigación Forestal (CIFOR)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)MadridSpain
- Unidad Mixta de Genómica y Ecofisiología ForestalInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Universidad Politécnica de Madrid (UPM)MadridSpain
| | - Alberto Pizarro
- Departamento de Ciencias de la VidaUniversidad de AlcaláAlcalá de HenaresSpain
| | - José Antonio Mancha
- Departamento de Ecología y Genética ForestalCentro de Investigación Forestal (CIFOR)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)MadridSpain
| | - Lieven Sterck
- Ghent University Department of Plant Biotechnology and BioinformaticsGhentBelgium
- VIB‐UGent Center for Plant Systems BiologyGhentBelgium
- Bioinformatics Institute GhentGhent UniversityGhentBelgium
| | - David Sánchez‐Gómez
- Departamento de Ecología y Genética ForestalCentro de Investigación Forestal (CIFOR)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)MadridSpain
- Unidad Mixta de Genómica y Ecofisiología ForestalInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Universidad Politécnica de Madrid (UPM)MadridSpain
- Departamento de Cultivos HerbáceosCentro de Investigación Agroforestal de AlbaladejitoCuencaSpain
| | - Célia Miguel
- BioISI‐Biosystems & Integrative Sciences InstituteFaculdade de CiênciasUniversidade de LisboaLisboaPortugal
- Instituto de Biologia Experimental e Tecnológica (iBET)OeirasPortugal
| | - Carmen Collada
- Unidad Mixta de Genómica y Ecofisiología ForestalInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Universidad Politécnica de Madrid (UPM)MadridSpain
- Grupo de investigación Sistemas Naturales e Historia ForestalUPMMadridSpain
| | | | - María Teresa Cervera
- Departamento de Ecología y Genética ForestalCentro de Investigación Forestal (CIFOR)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)MadridSpain
- Unidad Mixta de Genómica y Ecofisiología ForestalInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Universidad Politécnica de Madrid (UPM)MadridSpain
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22
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Bae SY, Kim MH, Cho JS, Park EJ, Lee H, Kim JH, Ko JH. Overexpression of Populus transcription factor PtrTALE12 increases axillary shoot development by regulating WUSCHEL expression. TREE PHYSIOLOGY 2020; 40:1232-1246. [PMID: 32420604 DOI: 10.1093/treephys/tpaa062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 03/26/2020] [Accepted: 05/13/2020] [Indexed: 06/11/2023]
Abstract
The TALE (Three Amino acid Loop Extension) transcription factor family has been shown to control meristem formation and organogenesis in plants. To understand the functional roles of the TALE family in woody perennials, each of the TALE members of Populus trichocarpa was overexpressed in Arabidopsis as a proxy. Among them, the overexpression of PtrTALE12 (i.e., 35S::PtrTALE12) resulted in a dramatic increase of axillary shoot development with early flowering. Interestingly, expression of WUSCHEL (WUS), a central regulator of both apical and axillary meristem formation, was significantly increased in the 35S::PtrTALE12 Arabidopsis plants. Conversely, WUS expression was downregulated in 35S::PtrTALE12-SRDX (short transcriptional repressor domain) plants. Further analysis found that PtrTALE12, expressed preferentially in meristem tissues, directly regulates WUS expression in transient activation assays using Arabidopsis leaf protoplast. Yeast two-hybrid assays showed that PtrTALE12 interacts with SHOOT MERISTEMLESS (STM); however, the interaction does not affect the WUS expression. In addition, expression of both CIRCADIAN CLOCK ASSOCIATED1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY) genes was suppressed accordingly for early flowering 35S::PtrTALE12 Arabidopsis. Indeed, transgenic poplars overexpressing PtrTALE12 as well as Arabidopsis plants overexpressing AtBLH11, a close homolog of PtrTALE12, phenocopied the 35S::PtrTALE12 Arabidopsis (i.e., increased axillary shoot development). Taken together, our results suggest that PtrTALE12 functions as a positive regulator of axillary shoot formation in both Arabidopsis and poplar.
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Affiliation(s)
- So-Young Bae
- Department of Plant & Environmental New Resources, Kyung Hee University, 1732 Deogyeong-daero, Yongin 17104, Republic of Korea
| | - Min-Ha Kim
- Department of Plant & Environmental New Resources, Kyung Hee University, 1732 Deogyeong-daero, Yongin 17104, Republic of Korea
| | - Jin-Seong Cho
- Department of Plant & Environmental New Resources, Kyung Hee University, 1732 Deogyeong-daero, Yongin 17104, Republic of Korea
| | - Eung-Jun Park
- Division of Forest Biotechnology, National Institute of Forest Science, 39 Onjeong-ro, Suwon 16631, Republic of Korea
| | - Hyoshin Lee
- Division of Forest Biotechnology, National Institute of Forest Science, 39 Onjeong-ro, Suwon 16631, Republic of Korea
| | - Jeong-Hoe Kim
- Department of Biology, School of Biological Sciences, Kyungpook National University, Daegu 41566, Korea
| | - Jae-Heung Ko
- Department of Plant & Environmental New Resources, Kyung Hee University, 1732 Deogyeong-daero, Yongin 17104, Republic of Korea
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23
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Khokhar W, Hassan MA, Reddy ASN, Chaudhary S, Jabre I, Byrne LJ, Syed NH. Genome-Wide Identification of Splicing Quantitative Trait Loci (sQTLs) in Diverse Ecotypes of Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2019; 10:1160. [PMID: 31632417 PMCID: PMC6785726 DOI: 10.3389/fpls.2019.01160] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 08/26/2019] [Indexed: 05/27/2023]
Abstract
Alternative splicing (AS) of pre-mRNAs contributes to transcriptome diversity and enables plants to generate different protein isoforms from a single gene and/or fine-tune gene expression during different development stages and environmental changes. Although AS is pervasive, the genetic basis for differential isoform usage in plants is still emerging. In this study, we performed genome-wide analysis in 666 geographically distributed diverse ecotypes of Arabidopsis thaliana to identify genomic regions [splicing quantitative trait loci (sQTLs)] that may regulate differential AS. These ecotypes belong to different microclimatic conditions and are part of the relict and non-relict populations. Although sQTLs were spread across the genome, we observed enrichment for trans-sQTL (trans-sQTLs hotspots) on chromosome one. Furthermore, we identified several sQTL (911) that co-localized with trait-linked single nucleotide polymorphisms (SNP) identified in the Arabidopsis genome-wide association studies (AraGWAS). Many sQTLs were enriched among circadian clock, flowering, and stress-responsive genes, suggesting a role for differential isoform usage in regulating these important processes in diverse ecotypes of Arabidopsis. In conclusion, the current study provides a deep insight into SNPs affecting isoform ratios/genes and facilitates a better mechanistic understanding of trait-associated SNPs in GWAS studies. To the best of our knowledge, this is the first report of sQTL analysis in a large set of Arabidopsis ecotypes and can be used as a reference to perform sQTL analysis in the Brassicaceae family. Since whole genome and transcriptome datasets are available for these diverse ecotypes, it could serve as a powerful resource for the biological interpretation of trait-associated loci, splice isoform ratios, and their phenotypic consequences to help produce more resilient and high yield crop varieties.
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Affiliation(s)
- Waqas Khokhar
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, United Kingdom
| | - Musa A. Hassan
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Tropical Livestock Genetics and Health, University of Edinburgh, Edinburgh, United Kingdom
| | - Anireddy S. N. Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, United States
| | - Saurabh Chaudhary
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, United Kingdom
| | - Ibtissam Jabre
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, United Kingdom
| | - Lee J. Byrne
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, United Kingdom
| | - Naeem H. Syed
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, United Kingdom
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24
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Sternberger AL, Bowman MJ, Kruse CPS, Childs KL, Ballard HE, Wyatt SE. Transcriptomics Identifies Modules of Differentially Expressed Genes and Novel Cyclotides in Viola pubescens. FRONTIERS IN PLANT SCIENCE 2019; 10:156. [PMID: 30828342 PMCID: PMC6384259 DOI: 10.3389/fpls.2019.00156] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 01/29/2019] [Indexed: 05/24/2023]
Abstract
Viola is a large genus with worldwide distribution and many traits not currently exemplified in model plants including unique breeding systems and the production of cyclotides. Here we report de novo genome assembly and transcriptomic analyses of the non-model species Viola pubescens using short-read DNA sequencing data and RNA-Seq from eight diverse tissues. First, V. pubescens genome size was estimated through flow cytometry, resulting in an approximate haploid genome of 455 Mbp. Next, the draft V. pubescens genome was sequenced and assembled resulting in 264,035,065 read pairs and 161,038 contigs with an N50 length of 3,455 base pairs (bp). RNA-Seq data were then assembled into tissue-specific transcripts. Together, the DNA and transcript data generated 38,081 ab initio gene models which were functionally annotated based on homology to Arabidopsis thaliana genes and Pfam domains. Gene expression was visualized for each tissue via principal component analysis and hierarchical clustering, and gene co-expression analysis identified 20 modules of tissue-specific transcriptional networks. Some of these modules highlight genetic differences between chasmogamous and cleistogamous flowers and may provide insight into V. pubescens' mixed breeding system. Orthologous clustering with the proteomes of A. thaliana and Populus trichocarpa revealed 8,531 sequences unique to V. pubescens, including 81 novel cyclotide precursor sequences. Cyclotides are plant peptides characterized by a stable, cyclic cystine knot motif, making them strong candidates for drug scaffolding and protein engineering. Analysis of the RNA-Seq data for these cyclotide transcripts revealed diverse expression patterns both between transcripts and tissues. The diversity of these cyclotides was also highlighted in a maximum likelihood protein cladogram containing V. pubescens cyclotides and published cyclotide sequences from other Violaceae and Rubiaceae species. Collectively, this work provides the most comprehensive sequence resource for Viola, offers valuable transcriptomic insight into V. pubescens, and will facilitate future functional genomics research in Viola and other diverse plant groups.
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Affiliation(s)
- Anne L. Sternberger
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, United States
| | - Megan J. Bowman
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
| | - Colin P. S. Kruse
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, United States
- Interdisciplinary Molecular and Cellular Biology Program, Ohio University, Athens, OH, United States
| | - Kevin L. Childs
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
| | - Harvey E. Ballard
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, United States
| | - Sarah E. Wyatt
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, United States
- Interdisciplinary Molecular and Cellular Biology Program, Ohio University, Athens, OH, United States
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25
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Kryvokhyzha MV, Krutovsky KV, Rashydov NM. Differential expression of flowering genes in Arabidopsis thaliana under chronic and acute ionizing radiation. Int J Radiat Biol 2018; 95:626-634. [PMID: 30570374 DOI: 10.1080/09553002.2019.1562251] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
PURPOSE Chronic and acute irradiations have drastic effects on flowering stage that plays an important role in further seed development and can determine seed yield. The expression of the key flowering genes, AP1, CO, GI, FT, FLC, and LFY, sensitive to irradiation repair gene RAD51 and the proliferation gene PCNA2 were studied in the wild-type Arabidopsis thaliana (Columbia ecotype) under chronic and acute irradiations. MATERIALS AND METHODS Chronic irradiation was performed using the radioactive isotope 137СsCl in two total doses of 3 cGy and 17 cGy, with the dose rate of 10-7 cGy/s and 6.8 10-6 cGy/s, respectively. The plants were grown under chronic irradiation during 6 weeks, from seeds till the 6.3 stage of flowering. For acute exposure, the plants were X-ray irradiated one time at the 5.0 development stage (20 days old) by a total dose of 15 Gy with the dose rate of 89 cGy/s. RESULTS After chronic irradiation with the 3 cGy dose the irradiated plants demonstrated 8 ± 2.8 days earlier flowering than in the control group. However, at the 17 cGy chronic and at the 15 Gy acute doses plants showed 14 ± 3.7 and 2 ± 1.4 days later flowering, respectively. The 3 cGy chronic exposure significantly increased the expression of the CO gene by a factor of 1.152 (1.087-1.217 95% C.I.) and decreased the expression of the FT gene by a factor of 0.128 (0.021-0.396 95% C.I.). The 17 cGy chronic exposure decreased expression of the AP1 gene by a factor of 0.872 (0.803-0.940 95% C.I.) and the LFY gene by a factor of 0.471 (0.306-0.687 95% C.I.). The 15 Gy acute exposure decreased the expression of the AP1 gene by a factor of 0.104 (0.074-0.144 95% C.I.) and the PCNA2 gene by a factor of 0.346 (0.238-0.488 95% C.I.). CONCLUSIONS The increased expression of the CO gene and decreased expression of the AP1 and FT genes under the lower dose of chronic exposure were associated with earlier flowering. The acute exposure increased the expression of the PCNA2 gene and decreased the expression of the flowering genes, except AP1. The flowering was delayed under both the higher dose of chronic exposure and under acute exposure, but it was less affected by the latter. Presumably, it was related to the activation of DNA repair under the 3 cGy chronic and 15 Gy acute irradiations.
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Affiliation(s)
- Maryna V Kryvokhyzha
- a Institute of Cell Biology and Genetic Engineering , National Academy of Sciences of Ukraine , Kiev , Ukraine
| | - Konstantin V Krutovsky
- b Department of Forest Genetics and Forest Tree Breeding , Georg-August University of Göttingen , Göttingen , Germany.,c Vavilov Institute of General Genetics , Russian Academy of Sciences , Moscow , Russia.,d Genome Research and Education Center , Siberian Federal University , Krasnoyarsk , Russia.,e Department of Ecosystem Science and Management , Texas A&M University , College Station , TX , USA
| | - Namik M Rashydov
- a Institute of Cell Biology and Genetic Engineering , National Academy of Sciences of Ukraine , Kiev , Ukraine
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Prudencio ÁS, Werner O, Martínez-García PJ, Dicenta F, Ros RM, Martínez-Gómez P. DNA Methylation Analysis of Dormancy Release in Almond ( Prunus dulcis) Flower Buds Using Epi-Genotyping by Sequencing. Int J Mol Sci 2018; 19:ijms19113542. [PMID: 30423798 PMCID: PMC6274898 DOI: 10.3390/ijms19113542] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/05/2018] [Accepted: 11/07/2018] [Indexed: 01/26/2023] Open
Abstract
DNA methylation and histone post-translational modifications have been described as epigenetic regulation mechanisms involved in developmental transitions in plants, including seasonal changes in fruit trees. In species like almond (Prunus dulcis (Mill.) D.A: Webb), prolonged exposure to cold temperatures is required for dormancy release and flowering. Aiming to identify genomic regions with differential methylation states in response to chill accumulation, we carried out Illumina reduced-representation genome sequencing on bisulfite-treated DNA from floral buds. To do this, we analyzed almond genotypes with different chilling requirements and flowering times both before and after dormancy release for two consecutive years. The study was performed using epi-Genotyping by Sequencing (epi-GBS). A total of 7317 fragments were sequenced and the samples compared. Out of these fragments, 677 were identified as differentially methylated between the almond genotypes. Mapping these fragments using the Prunus persica (L.) Batsch v.2 genome as reference provided information about coding regions linked to early and late flowering methylation markers. Additionally, the methylation state of ten gene-coding sequences was found to be linked to the dormancy release process.
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Affiliation(s)
- Ángela S Prudencio
- Department of Plant Breeding, CEBAS-CSIC, P.O. Box 164, Espinardo, 30100 Murcia, Spain.
| | - Olaf Werner
- Department of Plant Biology, Faculty of Biology, University of Murcia, Espinardo, 30100 Murcia, Spain.
| | | | - Federico Dicenta
- Department of Plant Breeding, CEBAS-CSIC, P.O. Box 164, Espinardo, 30100 Murcia, Spain.
| | - Rosa M Ros
- Department of Plant Biology, Faculty of Biology, University of Murcia, Espinardo, 30100 Murcia, Spain.
| | - Pedro Martínez-Gómez
- Department of Plant Breeding, CEBAS-CSIC, P.O. Box 164, Espinardo, 30100 Murcia, Spain.
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27
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Prudencio ÁS, Werner O, Martínez-García PJ, Dicenta F, Ros RM, Martínez-Gómez P. DNA Methylation Analysis of Dormancy Release in Almond ( Prunus dulcis) Flower Buds Using Epi-Genotyping by Sequencing. Int J Mol Sci 2018. [PMID: 30423798 DOI: 10.3542/ijms19113542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
DNA methylation and histone post-translational modifications have been described as epigenetic regulation mechanisms involved in developmental transitions in plants, including seasonal changes in fruit trees. In species like almond (Prunus dulcis (Mill.) D.A: Webb), prolonged exposure to cold temperatures is required for dormancy release and flowering. Aiming to identify genomic regions with differential methylation states in response to chill accumulation, we carried out Illumina reduced-representation genome sequencing on bisulfite-treated DNA from floral buds. To do this, we analyzed almond genotypes with different chilling requirements and flowering times both before and after dormancy release for two consecutive years. The study was performed using epi-Genotyping by Sequencing (epi-GBS). A total of 7317 fragments were sequenced and the samples compared. Out of these fragments, 677 were identified as differentially methylated between the almond genotypes. Mapping these fragments using the Prunus persica (L.) Batsch v.2 genome as reference provided information about coding regions linked to early and late flowering methylation markers. Additionally, the methylation state of ten gene-coding sequences was found to be linked to the dormancy release process.
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Affiliation(s)
- Ángela S Prudencio
- Department of Plant Breeding, CEBAS-CSIC, P.O. Box 164, Espinardo, 30100 Murcia, Spain.
| | - Olaf Werner
- Department of Plant Biology, Faculty of Biology, University of Murcia, Espinardo, 30100 Murcia, Spain.
| | | | - Federico Dicenta
- Department of Plant Breeding, CEBAS-CSIC, P.O. Box 164, Espinardo, 30100 Murcia, Spain.
| | - Rosa M Ros
- Department of Plant Biology, Faculty of Biology, University of Murcia, Espinardo, 30100 Murcia, Spain.
| | - Pedro Martínez-Gómez
- Department of Plant Breeding, CEBAS-CSIC, P.O. Box 164, Espinardo, 30100 Murcia, Spain.
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28
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Song YH, Kubota A, Kwon MS, Covington MF, Lee N, Taagen ER, Laboy Cintrón D, Hwang DY, Akiyama R, Hodge SK, Huang H, Nguyen NH, Nusinow DA, Millar AJ, Shimizu KK, Imaizumi T. Molecular basis of flowering under natural long-day conditions in Arabidopsis. NATURE PLANTS 2018; 4:824-835. [PMID: 30250277 PMCID: PMC6195122 DOI: 10.1038/s41477-018-0253-3] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 08/16/2018] [Indexed: 05/18/2023]
Abstract
Plants sense light and temperature changes to regulate flowering time. Here, we show that expression of the Arabidopsis florigen gene, FLOWERING LOCUS T (FT), peaks in the morning during spring, a different pattern than we observe in the laboratory. Providing our laboratory growth conditions with a red/far-red light ratio similar to open-field conditions and daily temperature oscillation is sufficient to mimic the FT expression and flowering time in natural long days. Under the adjusted growth conditions, key light signalling components, such as phytochrome A and EARLY FLOWERING 3, play important roles in morning FT expression. These conditions stabilize CONSTANS protein, a major FT activator, in the morning, which is probably a critical mechanism for photoperiodic flowering in nature. Refining the parameters of our standard growth conditions to more precisely mimic plant responses in nature can provide a powerful method for improving our understanding of seasonal response.
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Affiliation(s)
- Young Hun Song
- Department of Biology, University of Washington, Seattle, WA, USA.
- Department of Life Sciences, Ajou University, Suwon, Korea.
| | - Akane Kubota
- Department of Biology, University of Washington, Seattle, WA, USA
| | - Michael S Kwon
- Department of Biology, University of Washington, Seattle, WA, USA
| | | | - Nayoung Lee
- Department of Biology, University of Washington, Seattle, WA, USA
| | - Ella R Taagen
- Department of Biology, University of Washington, Seattle, WA, USA
| | | | - Dae Yeon Hwang
- Department of Life Sciences, Ajou University, Suwon, Korea
| | - Reiko Akiyama
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Sarah K Hodge
- School of Biological Sciences and SynthSys, University of Edinburgh, Edinburgh, UK
| | - He Huang
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Nhu H Nguyen
- Department of Biology, University of Washington, Seattle, WA, USA
| | | | - Andrew J Millar
- School of Biological Sciences and SynthSys, University of Edinburgh, Edinburgh, UK
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Takato Imaizumi
- Department of Biology, University of Washington, Seattle, WA, USA.
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29
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Triozzi PM, Ramos-Sánchez JM, Hernández-Verdeja T, Moreno-Cortés A, Allona I, Perales M. Photoperiodic Regulation of Shoot Apical Growth in Poplar. FRONTIERS IN PLANT SCIENCE 2018; 9:1030. [PMID: 30057588 PMCID: PMC6053638 DOI: 10.3389/fpls.2018.01030] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 06/25/2018] [Indexed: 05/19/2023]
Abstract
Woody perennials adapt their genetic traits to local climate conditions. Day length plays an essential role in the seasonal growth of poplar trees. When photoperiod falls below a given critical day length, poplars undergo growth cessation and bud set. A leaf-localized mechanism of photoperiod measurement triggers the transcriptional modulation of a long distance signaling molecule, FLOWERING LOCUS T (FT). This molecule targets meristem function giving rise to these seasonal responses. Studies over the past decade have identified conserved orthologous genes involved in photoperiodic flowering in Arabidopsis that regulate poplar vegetative growth. However, phenological and molecular examination of key photoperiod signaling molecules reveals functional differences between these two plant model systems suggesting alternative components and/or regulatory mechanisms operating during poplar vegetative growth. Here, we review current knowledge and provide new data regarding the molecular components of the photoperiod measuring mechanism that regulates annual growth in poplar focusing on main achievements and new perspectives.
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Affiliation(s)
- Paolo M. Triozzi
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y AlimentariaMadrid, Spain
| | - José M. Ramos-Sánchez
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y AlimentariaMadrid, Spain
| | - Tamara Hernández-Verdeja
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y AlimentariaMadrid, Spain
| | - Alicia Moreno-Cortés
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y AlimentariaMadrid, Spain
| | - Isabel Allona
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y AlimentariaMadrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de MadridMadrid, Spain
- *Correspondence: Isabel Allona
| | - Mariano Perales
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y AlimentariaMadrid, Spain
- Mariano Perales
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30
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Henríquez-Valencia C, Arenas-M A, Medina J, Canales J. Integrative Transcriptomic Analysis Uncovers Novel Gene Modules That Underlie the Sulfate Response in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2018; 9:470. [PMID: 29692794 PMCID: PMC5902692 DOI: 10.3389/fpls.2018.00470] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 03/26/2018] [Indexed: 05/10/2023]
Abstract
Sulfur is an essential nutrient for plant growth and development. Sulfur is a constituent of proteins, the plasma membrane and cell walls, among other important cellular components. To obtain new insights into the gene regulatory networks underlying the sulfate response, we performed an integrative meta-analysis of transcriptomic data from five different sulfate experiments available in public databases. This bioinformatic approach allowed us to identify a robust set of genes whose expression depends only on sulfate availability, indicating that those genes play an important role in the sulfate response. In relation to sulfate metabolism, the biological function of approximately 45% of these genes is currently unknown. Moreover, we found several consistent Gene Ontology terms related to biological processes that have not been extensively studied in the context of the sulfate response; these processes include cell wall organization, carbohydrate metabolism, nitrogen compound transport, and the regulation of proteolysis. Gene co-expression network analyses revealed relationships between the sulfate-responsive genes that were distributed among seven function-specific co-expression modules. The most connected genes in the sulfate co-expression network belong to a module related to the carbon response, suggesting that this biological function plays an important role in the control of the sulfate response. Temporal analyses of the network suggest that sulfate starvation generates a biphasic response, which involves that major changes in gene expression occur during both the early and late responses. Network analyses predicted that the sulfate response is regulated by a limited number of transcription factors, including MYBs, bZIPs, and NF-YAs. In conclusion, our analysis identified new candidate genes and provided new hypotheses to advance our understanding of the transcriptional regulation of sulfate metabolism in plants.
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Affiliation(s)
- Carlos Henríquez-Valencia
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Anita Arenas-M
- Instituto de Producción y Sanidad Vegetal, Facultad de Ciencias Agrarias, Universidad Austral de Chile, Valdivia, Chile
| | - Joaquín Medina
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid, Spain
| | - Javier Canales
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Millennium Institute for Integrative Systems and Synthetic Biology (MIISSB), Santiago, Chile
- *Correspondence: Javier Canales,
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31
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Bian S, Jin D, Li R, Xie X, Gao G, Sun W, Li Y, Zhai L, Li X. Genome-Wide Analysis of CCA1-Like Proteins in Soybean and Functional Characterization of GmMYB138a. Int J Mol Sci 2017; 18:E2040. [PMID: 28937654 PMCID: PMC5666722 DOI: 10.3390/ijms18102040] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 09/10/2017] [Accepted: 09/20/2017] [Indexed: 12/31/2022] Open
Abstract
Plant CIRCADIAN CLOCK ASSOCIATED1 (CCA1)-like proteins are a class of single-repeat MYELOBLASTOSIS ONCOGENE (MYB) transcription factors generally featured by a highly conserved motif SHAQK(Y/F)F, which play important roles in multiple biological processes. Soybean is an important grain legume for seed protein and edible vegetable oil. However, essential understandings regarding CCA1-like proteins are very limited in soybean. In this study, 54 CCA1-like proteins were identified by data mining of soybean genome. Phylogenetic analysis indicated that soybean CCA1-like subfamily showed evolutionary conservation and diversification. These CCA1-like genes displayed tissue-specific expression patterns, and analysis of genomic organization and evolution revealed 23 duplicated gene pairs. Among them, GmMYB138a was chosen for further investigation. Our protein-protein interaction studies revealed that GmMYB138a, but not its alternatively spliced isoform, interacts with a 14-3-3 protein (GmSGF14l). Although GmMYB138a was predominately localized in nucleus, the resulting complex of GmMYB138a and GmSGF14l was almost evenly distributed in nucleus and cytoplasm, supporting that 14-3-3s interact with their clients to alter their subcellular localization. Additionally, qPCR analysis suggested that GmMYB138a and GmSGF14l synergistically or antagonistically respond to drought, cold and salt stresses. Our findings will contribute to future research in regard to functions of soybean CCA1-like subfamily, especially regulatory mechanisms of GmMYB138a in response to abiotic stresses.
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Affiliation(s)
| | - Donghao Jin
- College of Plant Science, Jilin University, Changchun 130062, China.
| | - Ruihua Li
- College of Plant Science, Jilin University, Changchun 130062, China.
| | - Xin Xie
- College of Plant Science, Jilin University, Changchun 130062, China.
| | - Guoli Gao
- College of Plant Science, Jilin University, Changchun 130062, China.
| | - Weikang Sun
- College of Plant Science, Jilin University, Changchun 130062, China.
| | - Yuejia Li
- College of Plant Science, Jilin University, Changchun 130062, China.
| | - Lulu Zhai
- College of Plant Science, Jilin University, Changchun 130062, China.
| | - Xuyan Li
- College of Plant Science, Jilin University, Changchun 130062, China.
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32
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Park YJ, Lee HJ, Ha JH, Kim JY, Park CM. COP1 conveys warm temperature information to hypocotyl thermomorphogenesis. THE NEW PHYTOLOGIST 2017; 215:269-280. [PMID: 28418582 DOI: 10.1111/nph.14581] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 03/21/2017] [Indexed: 05/19/2023]
Abstract
Plants adjust their architecture to optimize growth and reproductive success under changing climates. Hypocotyl elongation is a pivotal morphogenic trait that is profoundly influenced by light and temperature conditions. While hypocotyl photomorphogenesis has been well characterized at the molecular level, molecular mechanisms underlying hypocotyl thermomorphogenesis remains elusive. Here, we demonstrate that the E3 ubiquitin ligase CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) conveys warm temperature signals to hypocotyl thermomorphogenesis. To investigate the roles of COP1 and its target ELONGATED HYPOCOTYL 5 (HY5) during hypocotyl thermomorphogenesis, we employed Arabidopsis mutants that are defective in their genes. Transgenic plants overexpressing the genes were also produced. We examined hypocotyl growth and thermoresponsive turnover rate of HY5 protein at warm temperatures under both light and dark conditions. Elevated temperatures trigger the nuclear import of COP1, thereby alleviating the suppression of hypocotyl growth by HY5. While the thermal induction of hypocotyl growth is circadian-gated, the degradation of HY5 by COP1 is uncoupled from light responses and timing information. We propose that thermal activation of COP1 enables coincidence between warm temperature signaling and circadian rhythms, which allows plants to gate hypocotyl thermomorphogenesis at the most profitable time at warm temperatures.
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Affiliation(s)
- Young-Joon Park
- Department of Chemistry, Seoul National University, Seoul, 151-742, Korea
| | - Hyo-Jun Lee
- Department of Chemistry, Seoul National University, Seoul, 151-742, Korea
| | - Jun-Ho Ha
- Department of Chemistry, Seoul National University, Seoul, 151-742, Korea
| | - Jae Young Kim
- Department of Chemistry, Seoul National University, Seoul, 151-742, Korea
| | - Chung-Mo Park
- Department of Chemistry, Seoul National University, Seoul, 151-742, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 151-742, Korea
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33
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Ramos-Sánchez JM, Triozzi PM, Moreno-Cortés A, Conde D, Perales M, Allona I. Real-time monitoring of PtaHMGB activity in poplar transactivation assays. PLANT METHODS 2017; 13:50. [PMID: 28638438 PMCID: PMC5472981 DOI: 10.1186/s13007-017-0199-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 06/08/2017] [Indexed: 05/06/2023]
Abstract
BACKGROUND Precise control of gene expression is essential to synchronize plant development with the environment. In perennial plants, transcriptional regulation remains poorly understood, mainly due to the long time required to perform functional studies. Transcriptional reporters based on luciferase have been useful to study circadian and diurnal regulation of gene expression, both by transcription factors and chromatin remodelers. The high mobility group proteins are considered transcriptional chaperones that also modify the chromatin architecture. They have been found in several species, presenting in some cases a circadian expression of their mRNA or protein. RESULTS Transactivation experiments have been shown as a powerful and fast method to obtain information about the potential role of transcription factors upon a certain reporter. We designed and validated a luciferase transcriptional reporter using the 5' sequence upstream ATG of Populus tremula × alba LHY2 gene. We showed the robustness of this reporter line under long day and continuous light conditions. Moreover, we confirmed that pPtaLHY2::LUC activity reproduces the accumulation of PtaLHY2 mRNA. We performed transactivation studies by transient expression, using the reporter line as a genetic background, unraveling a new function of a high mobility group protein in poplar, which can activate the PtaLHY2 promoter in a gate-dependent manner. We also showed PtaHMGB2/3 needs darkness to produce that activation and exhibits an active degradation after dawn, mediated by the 26S proteasome. CONCLUSIONS We generated a stable luciferase reporter poplar line based on the circadian clock gene PtaLHY2, which can be used to investigate transcriptional regulation and signal transduction pathway. Using this reporter line as a genetic background, we established a methodology to rapidly assess potential regulators of diurnal and circadian rhythms. This tool allowed us to demonstrate that PtaHMGB2/3 promotes the transcriptional activation of our reporter in a gate-dependent manner. Moreover, we added new information about the PtaHMGB2/3 protein regulation along the day. This methodology can be easily adapted to other transcription factors and reporters.
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Affiliation(s)
- José M. Ramos-Sánchez
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Paolo M. Triozzi
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Alicia Moreno-Cortés
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Daniel Conde
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Mariano Perales
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Isabel Allona
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
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