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Mineri L, Cerise M, Giaume F, Vicentini G, Martignago D, Chiara M, Galbiati F, Spada A, Horner D, Fornara F, Brambilla V. Rice florigens control a common set of genes at the shoot apical meristem including the F-BOX BROADER TILLER ANGLE 1 that regulates tiller angle and spikelet development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1647-1660. [PMID: 37285314 DOI: 10.1111/tpj.16345] [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: 02/21/2023] [Revised: 05/04/2023] [Accepted: 05/30/2023] [Indexed: 06/09/2023]
Abstract
Rice flowering is triggered by transcriptional reprogramming at the shoot apical meristem (SAM) mediated by florigenic proteins produced in leaves in response to changes in photoperiod. Florigens are more rapidly expressed under short days (SDs) compared to long days (LDs) and include the HEADING DATE 3a (Hd3a) and RICE FLOWERING LOCUS T1 (RFT1) phosphatidylethanolamine binding proteins. Hd3a and RFT1 are largely redundant at converting the SAM into an inflorescence, but whether they activate the same target genes and convey all photoperiodic information that modifies gene expression at the SAM is currently unclear. We uncoupled the contribution of Hd3a and RFT1 to transcriptome reprogramming at the SAM by RNA sequencing of dexamethasone-inducible over-expressors of single florigens and wild-type plants exposed to photoperiodic induction. Fifteen highly differentially expressed genes common to Hd3a, RFT1, and SDs were retrieved, 10 of which still uncharacterized. Detailed functional studies on some candidates revealed a role for LOC_Os04g13150 in determining tiller angle and spikelet development and the gene was renamed BROADER TILLER ANGLE 1 (BRT1). We identified a core set of genes controlled by florigen-mediated photoperiodic induction and defined the function of a novel florigen target controlling tiller angle and spikelet development.
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Affiliation(s)
- Lorenzo Mineri
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milan, Italy
| | - Martina Cerise
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milan, Italy
| | - Francesca Giaume
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milan, Italy
- Department of Agricultural and Environmental Sciences, University of Milan, via Celoria 2, 20133, Milan, Italy
| | - Giulio Vicentini
- Department of Agricultural and Environmental Sciences, University of Milan, via Celoria 2, 20133, Milan, Italy
| | - Damiano Martignago
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milan, Italy
| | - Matteo Chiara
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milan, Italy
| | - Francesca Galbiati
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milan, Italy
| | - Alberto Spada
- Department of Agricultural and Environmental Sciences, University of Milan, via Celoria 2, 20133, Milan, Italy
| | - David Horner
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milan, Italy
| | - Fabio Fornara
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milan, Italy
| | - Vittoria Brambilla
- Department of Agricultural and Environmental Sciences, University of Milan, via Celoria 2, 20133, Milan, Italy
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Li L, Ren X, Shao L, Huang X, Zhang C, Wang X, Yang J, Li C. Comprehensive Analysis of the NF-YB Gene Family and Expression under Abiotic Stress and Hormone Treatment in Larix kaempferi. Int J Mol Sci 2023; 24:ijms24108910. [PMID: 37240255 DOI: 10.3390/ijms24108910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/27/2023] [Accepted: 05/14/2023] [Indexed: 05/28/2023] Open
Abstract
NF-YB, a subfamily of Nuclear Factor Y (NF-Y) transcription factor, play crucial role in many biological processes of plant growth and development and abiotic stress responses, and they can therefore be good candidate factors for breeding stress-resistant plants. However, the NF-YB proteins have not yet been explored in Larix kaempferi, a tree species with high economic and ecological values in northeast China and other regions, limiting the breeding of anti-stress L. kaempferi. In order to explore the roles of NF-YB transcription factors in L. kaempferi, we identified 20 LkNF-YB family genes from L. kaempferi full-length transcriptome data and carried out preliminary characterization of them through series of analyses on their phylogenetic relationships, conserved motif structure, subcellular localization prediction, GO annotation, promoter cis-acting elements as well as expression profiles under treatment of phytohormones (ABA, SA, MeJA) and abiotic stresses (salt and drought). The LkNF-YB genes were classified into three clades through phylogenetic analysis and belong to non-LEC1 type NF-YB transcription factors. They have 10 conserved motifs; all genes contain a common motif, and their promoters have various phytohormones and abiotic stress related cis-acting elements. Quantitative real time reverse transcription PCR (RT-qPCR) analysis showed that the sensitivity of the LkNF-YB genes to drought and salt stresses was higher in leaves than roots. The sensitivity of LKNF-YB genes to ABA, MeJA, SA stresses was much lower than that to abiotic stress. Among the LkNF-YBs, LkNF-YB3 showed the strongest responses to drought and ABA treatments. Further protein interaction prediction analysis for LkNF-YB3 revealed that LkNF-YB3 interacts with various factors associated with stress responses and epigenetic regulation as well as NF-YA/NF-YC factors. Taken together, these results unveiled novel L. kaempferi NF-YB family genes and their characteristics, providing the basic knowledge for further in-depth studies on their roles in abiotic stress responses of L. kaempferi.
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Affiliation(s)
- Lu Li
- State Key Laboratory of Forest Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Xi Ren
- State Key Laboratory of Forest Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Liying Shao
- State Key Laboratory of Forest Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Xun Huang
- State Key Laboratory of Forest Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Chunyan Zhang
- State Key Laboratory of Forest Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Xuhui Wang
- State Key Laboratory of Forest Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Jingli Yang
- State Key Laboratory of Forest Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Chenghao Li
- State Key Laboratory of Forest Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
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Bhattacharjee B, Hallan V. NF-YB family transcription factors in Arabidopsis: Structure, phylogeny, and expression analysis in biotic and abiotic stresses. Front Microbiol 2023; 13:1067427. [PMID: 36733773 PMCID: PMC9887194 DOI: 10.3389/fmicb.2022.1067427] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/22/2022] [Indexed: 01/18/2023] Open
Abstract
Nuclear factor-Y (NF-Y) transcription factors (TFs) are conserved heterotrimeric complexes present and widespread across eukaryotes. Three main subunits make up the structural and functional aspect of the NF-Y TFs: NF-YA, NF-YB and NF-YC, which bind to the conserved CCAAT- box of the promoter region of specific genes, while also interacting with each other, thereby forming myriad combinations. The NF-YBs are expressed differentially in various tissues and plant development stages, likely impacting many of the cellular processes constitutively and under stress conditions. In this study, ten members of NF-YB family from Arabidopsis thaliana were identified and expression profiles were mined from microarray data under different biotic and abiotic conditions, revealing key insights into the involvement of this class of proteins in the cellular and biological processes in Arabidopsis. Analysis of cis-acting regulatory elements (CAREs) indicated the presence of abiotic and biotic stress-related transcription factor binding sites (TFBs), shedding light on the multifaceted roles of these TFs. Microarray data analysis inferred distinct patterns of expression in various tissues under differing treatments such as drought, cold and heat stress as well as bacterial, fungal, and viral stress, indicating their likelihood of having an expansive range of regulatory functions under native and stressed conditions; while quantitative real-time PCR (qRT-PCR) based expression analysis revealed that these TFs get real-time-modulated in a stress dependent manner. This study, overall, provides an understanding of the AtNF-YB family of TFs in their regulation and participation in various morphogenetic and defense- related pathways and can provide insights for development of transgenic plants for trait dependent studies.
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Affiliation(s)
- Bipasha Bhattacharjee
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India,Plant Virology Laboratory, Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
| | - Vipin Hallan
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India,Plant Virology Laboratory, Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, India,*Correspondence: Vipin Hallan, ✉
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Lim CJ, Park KS, Ali A, Park J, Ryou SM, Shen M, Khan HA, Bader ZE, Zareen S, Bae MJ, Choi JH, Xu ZY, Pardo JM, Yun DJ. Negative regulation of floral transition in Arabidopsis by HOS15-PWR-HDA9 complex. FRONTIERS IN PLANT SCIENCE 2023; 13:1105988. [PMID: 36684790 PMCID: PMC9853073 DOI: 10.3389/fpls.2022.1105988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
Arabidopsis HOS15/PWR/HDA9 repressor complex, which is similar to the TBL1/NcoR1/HDAC complex in animals, plays a well-known role in epigenetic regulation. PWR and HDA9 have been reported to interact with each other and modulate the flowering time by repressing AGL19 expression, whereas HOS15 and HDA9, together with the photoperiodic evening complex, regulate flowering time through repression of GI transcription. However, the role of the HOS15/PWR/HDA9 core repressor complex as a functional unit in the regulation of flowering time is yet to be explored. In this study, we reported that the loss-of-function hos15-2/pwr/hda9 triple mutant accumulates higher transcript levels of AGL19 and exhibits an early flowering phenotype similar to those of hos15, pwr, and hda9 single mutants. Interestingly, the accumulation of HOS15 in the nucleus was drastically reduced in pwr and hda9 mutants. As a result, HOS15 could not perform its role in histone deacetylation or interaction with H3 in the nucleus. Furthermore, HOS15 is also associated with the same region of the AGL19 promoter known for PWR-HDA9 binding. The acetylation level of the AGL19 promoter was increased in the hos15-2 mutant, similar to the pwr and hda9 mutants. Therefore, our findings reveal that the HOS15/PWR/HDA9 repressor complex deacetylates the promoter region of AGL19, thereby negatively regulating AGL19 transcription, which leads to early flowering in Arabidopsis.
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Affiliation(s)
- Chae Jin Lim
- Institute of Global Disease Control, Konkuk University, Seoul, Republic of Korea
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Ki Suk Park
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Akhtar Ali
- Institute of Global Disease Control, Konkuk University, Seoul, Republic of Korea
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Junghoon Park
- Institute of Global Disease Control, Konkuk University, Seoul, Republic of Korea
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Seung Min Ryou
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Mingzhe Shen
- Department of Agronomy, Agricultural College, Yanbian University, Yanji, China
| | - Haris Ali Khan
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Zein Eddin Bader
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Shah Zareen
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Min Jae Bae
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Jong Hyoo Choi
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Jose M. Pardo
- Institute of Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones 17 Cientificas and Universidad de Sevilla, Seville, Spain
| | - Dae-Jin Yun
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
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Liu H, Guo Y, Wang H, Yang W, Yang J, Zhang J, Liu D, El-Kassaby YA, Li W. Involvement of PtCOL5-PtNF-YC4 in reproductive cone development and gibberellin signaling in Chinese pine. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 323:111383. [PMID: 35850285 DOI: 10.1016/j.plantsci.2022.111383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/10/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
It is well documented that the CO/NF-YB/NF-YC trimer (NF-Y-CO) binds and regulates the FT promoter. However, the FT/TFL1-like (FLOWERING LOCUS T/TERMINALFLOWER1-like) genes in gymnosperms are all flowering suppressors, and the regulation model of NF-Y in gymnosperms is different from that in angiosperms. Here, using Chinese pine (Pinus tabuliformis), we identified a CONSTANS-LIKE gene, PtCOL5, the expression of which was strongly induced during cones development and it functioned as a repressor of flowering. PtNF-YC4, which interacted with PtCOL5, was highly correlated with PtCOL5 during growth and development, has been demonstrated. Moreover, PtNF-YC4 and PtCOL5 can bind to PtTFL2 promoter, and their interaction can enhance PtTFL2 expression. Interestingly, we found PtNF-YC4 and PtCOL5 were involved in gibberellin signaling and their interaction was inhibited by PtDELLA protein, thus affecting PtTFL2 expression. Collectively, PtCOL5-PtNF-YC4 was involved in reproductive cone development and gibberellin signaling in Chinese pine. Our findings uncovered reproductive cone development and signal transduction mechanism of COL-NF-Y in gymnosperms.
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Affiliation(s)
- Hongmei Liu
- National Engineering Laboratory of Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People's Republic of China.
| | - Yingtian Guo
- National Engineering Laboratory of Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People's Republic of China.
| | - Huili Wang
- National Engineering Laboratory of Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People's Republic of China.
| | - Wenbin Yang
- National Engineering Laboratory of Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People's Republic of China.
| | - Junhe Yang
- National Engineering Laboratory of Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People's Republic of China.
| | - Jingxing Zhang
- National Engineering Laboratory of Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People's Republic of China.
| | - Dan Liu
- National Engineering Laboratory of Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People's Republic of China.
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4, Canada.
| | - Wei Li
- National Engineering Laboratory of Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, People's Republic of China.
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6
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Sun K, Huang M, Zong W, Xiao D, Lei C, Luo Y, Song Y, Li S, Hao Y, Luo W, Xu B, Guo X, Wei G, Chen L, Liu YG, Guo J. Hd1, Ghd7, and DTH8 synergistically determine rice heading date and yield-related agronomic traits. J Genet Genomics 2022; 49:437-447. [DOI: 10.1016/j.jgg.2022.02.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 02/13/2022] [Accepted: 02/16/2022] [Indexed: 10/18/2022]
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7
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Zeng X, Lv X, Liu R, He H, Liang S, Chen L, Zhang F, Chen L, He Y, Du J. Molecular basis of CONSTANS oligomerization in FLOWERING LOCUS T activation. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:731-740. [PMID: 35023269 DOI: 10.1111/jipb.13223] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
The transcription factor CONSTANS (CO) integrates day-length information to induce the expression of florigen FLOWERING LOCUS T (FT) in Arabidopsis. We recently reported that the C-terminal CCT domain of CO forms a complex with NUCLEAR FACTOR-YB/YC to recognize multiple cis-elements in the FT promoter, and the N-terminal tandem B-box domains form a homomultimeric assembly. However, the mechanism and biological function of CO multimerization remained unclear. Here, we report that CO takes on a head-to-tail oligomeric configuration via its B-boxes to mediate FT activation in long days. The crystal structure of B-boxesCO reveals a closely connected tandem B-box fold forming a continuous head-to-tail assembly through unique CDHH zinc fingers. Mutating the key residues involved in CO oligomerization resulted in a non-functional CO, as evidenced by the inability to rescue co mutants. By contrast, a transgene encoding a human p53-derived tetrameric peptide in place of the B-boxesCO rescued co mutant, emphasizing the essential role of B-boxesCO -mediated oligomerization. Furthermore, we found that the four TGTG-bearing cis-elements in FT proximal promoter are required for FT activation in long days. Our results suggest that CO forms a multimer to bind to the four TGTG motifs in the FT promoter to mediate FT activation.
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Affiliation(s)
- Xiaolin Zeng
- Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
- National Key Laboratory of Plant Molecular Genetics & Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai, 201602, China
| | - Xinchen Lv
- National Key Laboratory of Plant Molecular Genetics & Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai, 201602, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Rui Liu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Hang He
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Shiqi Liang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Lixian Chen
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Fan Zhang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Liu Chen
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yuehui He
- Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
- National Key Laboratory of Plant Molecular Genetics & Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai, 201602, China
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261000, China
| | - Jiamu Du
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
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Genome-wide screening and identification of nuclear Factor-Y family genes and exploration their function on regulating abiotic and biotic stress in potato (Solanum tuberosum L.). Gene 2021; 812:146089. [PMID: 34896520 DOI: 10.1016/j.gene.2021.146089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/21/2021] [Accepted: 11/16/2021] [Indexed: 12/30/2022]
Abstract
The Nuclear Factor-Y (NF-Y) transcription factor (TF), which includes three distinct subunits (NF-YA, NF-YB and NF-YC), is known to manipulate various aspects of plant growth, development, and stress responses. Although the NF-Y gene family was well studied in many species, little is known about their functions in potato. In this study, a total of 37 potato NF-Y genes were identified, including 11 StNF-YAs, 20 StNF-YBs, and 6 StNF-YCs. The genetic features of these StNF-Y genes were investigated by comparing their evolutionary relationship, intron/exon organization and motif distribution pattern. Multiple alignments showed that all StNF-Y proteins possessed clearly conserved core regions that were flanked by non-conserved sequences. Gene duplication analysis indicated that nine StNF-Y genes were subjected to tandem duplication and eight StNF-Ys arose from segmental duplication events. Synteny analysis suggested that most StNF-Y genes (33 of 37) were orthologous to potato's close relative tomato (Solanum lycopersicum L.). Tissue-specific expression of the StNF-Y genes suggested their potential roles in controlling potato growth and development. The role of StNF-Ys in regulating potato responses to abiotic stress (ABA, drought and salinity) was also confirmed: twelve StNF-Y genes were up-regulated and another two were down-regulated under different abiotic treatments. In addition, genes responded differently to pathogen challenges, suggesting that StNF-Y genes may play distinct roles under certain biotic stress. In summary, insights into the evolution of NF-Y family members and their functions in potato development and stress responses are provided.
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Lv X, Zeng X, Hu H, Chen L, Zhang F, Liu R, Liu Y, Zhou X, Wang C, Wu Z, Kim C, He Y, Du J. Structural insights into the multivalent binding of the Arabidopsis FLOWERING LOCUS T promoter by the CO-NF-Y master transcription factor complex. THE PLANT CELL 2021; 33:1182-1195. [PMID: 33693873 DOI: 10.1093/plcell/koab016] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 01/09/2021] [Indexed: 05/19/2023]
Abstract
Flowering plants sense various environmental and endogenous signals to trigger the floral transition and start the reproductive growth cycle. CONSTANS (CO) is a master transcription factor in the photoperiod floral pathway that integrates upstream signals and activates the florigen gene FLOWERING LOCUS T (FT). Here, we performed comprehensive structural and biochemical analyses to study the molecular mechanism underlying the regulation of FT by CO in Arabidopsis thaliana. We show that the four previously characterized cis-elements in the FT promoter proximal region, CORE1, CORE2, P1, and P2, are all direct CO binding sites. Structural analysis of CO in complex with NUCLEAR FACTOR-YB/YC (NF-YB/YC) and the CORE2 or CORE1 elements revealed the molecular basis for the specific recognition of the shared TGTG motifs. Biochemical analysis suggested that CO might form a homomultimeric assembly via its N-terminal B-Box domain and simultaneously occupy multiple cis-elements within the FT promoter. We suggest that this multivalent binding gives the CO-NF-Y complex high affinity and specificity for FT promoter binding. Overall, our data provide a detailed molecular model for the regulation of FT by the master transcription factor complex CO-NF-Y during the floral transition.
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Affiliation(s)
- Xinchen Lv
- National Key Laboratory of Plant Molecular Genetics and Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, School of Life Sciences, Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen 518055, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaolin Zeng
- National Key Laboratory of Plant Molecular Genetics and Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Hongmiao Hu
- National Key Laboratory of Plant Molecular Genetics and Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, School of Life Sciences, Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen 518055, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lixian Chen
- National Key Laboratory of Plant Molecular Genetics and Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fan Zhang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, School of Life Sciences, Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Rui Liu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, School of Life Sciences, Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yue Liu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, School of Life Sciences, Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xuelin Zhou
- National Key Laboratory of Plant Molecular Genetics and Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, School of Life Sciences, Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen 518055, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Changshi Wang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, School of Life Sciences, Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Zhe Wu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, School of Life Sciences, Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Chanhong Kim
- National Key Laboratory of Plant Molecular Genetics and Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Yuehui He
- National Key Laboratory of Plant Molecular Genetics and Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Jiamu Du
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, School of Life Sciences, Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen 518055, China
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10
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González AM, Vander Schoor JK, Fang C, Kong F, Wu J, Weller JL, Santalla M. Ancient relaxation of an obligate short-day requirement in common bean through loss of CONSTANS-like gene function. Curr Biol 2021; 31:1643-1652.e2. [PMID: 33609454 DOI: 10.1016/j.cub.2021.01.075] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 01/18/2021] [Accepted: 01/21/2021] [Indexed: 01/24/2023]
Abstract
Common bean (Phaseolus vulgaris L.) is a major global food staple and source of dietary protein that was domesticated independently in Mexico and Andean South America. Its subsequent development as a crop of importance worldwide has been enabled by genetic relaxation of the strict short-day requirement typical of wild forms, but the genetic basis for this change is not well understood. Recently, a loss of photoperiod sensitivity was shown to result from mutations in the phytochrome photoreceptor gene Ppd/PHYA3 that arose independently within the two major domesticated lineages. Here, we define a second major photoperiod sensitivity locus, at which recessive alleles associate with deleterious mutations affecting the CONSTANS-like gene COL2. A wider survey of sequence variation in over 800 diverse lines, including wild, landrace, and domesticated accessions, show that distinct col2 haplotypes are associated with early flowering in Andean and Mesoamerican germplasm. The relative frequencies and distributions of COL2 and PHYA3 haplotypes imply that photoperiod adaptation developed in two phases within each gene pool: an initial reduction in sensitivity through impairment of COL2 function and subsequent complete loss through PHYA3. Gene expression analyses indicate that COL2 functions downstream of PHYA3 to repress expression of FT genes and may function in parallel with PvE1, the bean ortholog of a key legume-specific flowering repressor. Collectively, these results define the molecular basis for a key phenological adaptation, reveal a striking convergence in the naturally replicated evolution of this major crop, and further emphasize the wider evolutionary lability of CONSTANS effects on flowering time control.
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Affiliation(s)
- Ana M González
- Grupo de Genética del Desarrollo de Plantas, Misión Biológica de Galicia-CSIC, PO Box 28, 36080 Pontevedra, Spain
| | | | - Chao Fang
- Innovation Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Fanjiang Kong
- Innovation Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Jing Wu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - James L Weller
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia.
| | - Marta Santalla
- Grupo de Genética del Desarrollo de Plantas, Misión Biológica de Galicia-CSIC, PO Box 28, 36080 Pontevedra, Spain.
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11
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Zong W, Ren D, Huang M, Sun K, Feng J, Zhao J, Xiao D, Xie W, Liu S, Zhang H, Qiu R, Tang W, Yang R, Chen H, Xie X, Chen L, Liu Y, Guo J. Strong photoperiod sensitivity is controlled by cooperation and competition among Hd1, Ghd7 and DTH8 in rice heading. THE NEW PHYTOLOGIST 2021; 229:1635-1649. [PMID: 33089895 PMCID: PMC7821112 DOI: 10.1111/nph.16946] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 09/05/2020] [Indexed: 05/19/2023]
Abstract
Rice (Oryza sativa) is a short-day (SD) plant originally having strong photoperiod sensitivity (PS), with SDs promoting and long days (LDs) suppressing flowering. Although the evolution of PS in rice has been extensively studied, there are few studies that combine the genetic effects and underlying mechanism of different PS gene combinations with variations in PS. We created a set of isogenic lines among the core PS-flowering genes Hd1, Ghd7 and DTH8 using CRISPR mutagenesis, to systematically dissect their genetic relationships under different day-lengths. We investigated their monogenic, digenic, and trigenic effects on target gene regulation and PS variation. We found that Hd1 and Ghd7 have the primary functions for promoting and repressing flowering, respectively, regardless of day-length. However, under LD conditions, Hd1 promotes Ghd7 expression and is recruited by Ghd7 and/or DTH8 to form repressive complexes that collaboratively suppress the Ehd1-Hd3a/RFT1 pathway to block heading, but under SD conditions Hd1 competes with the complexes to promote Hd3a/RFT1 expression, playing a tradeoff relationship with PS flowering. Natural allelic variations of Hd1, Ghd7 and DTH8 in rice populations have resulted in various PS performances. Our findings reveal that rice PS flowering is controlled by crosstalk of two modules - Hd1-Hd3a/RFT1 in SD conditions and (Hd1/Ghd7/DTH8)-Ehd1-Hd3a/RFT1 in LD conditions - and the divergences of these genes provide the basis for rice adaptation to broad regions.
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Affiliation(s)
- Wubei Zong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesCollege of Life SciencesSouth China Agricultural University, SCAUGuangzhou510642China
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhou510642China
| | - Ding Ren
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesCollege of Life SciencesSouth China Agricultural University, SCAUGuangzhou510642China
| | - Minghui Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesCollege of Life SciencesSouth China Agricultural University, SCAUGuangzhou510642China
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhou510642China
| | - Kangli Sun
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesCollege of Life SciencesSouth China Agricultural University, SCAUGuangzhou510642China
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhou510642China
| | - Jinglei Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesCollege of Life SciencesSouth China Agricultural University, SCAUGuangzhou510642China
| | - Jing Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesCollege of Life SciencesSouth China Agricultural University, SCAUGuangzhou510642China
| | - Dongdong Xiao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesCollege of Life SciencesSouth China Agricultural University, SCAUGuangzhou510642China
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhou510642China
| | - Wenhao Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesCollege of Life SciencesSouth China Agricultural University, SCAUGuangzhou510642China
| | - Shiqi Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesCollege of Life SciencesSouth China Agricultural University, SCAUGuangzhou510642China
| | - Han Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesCollege of Life SciencesSouth China Agricultural University, SCAUGuangzhou510642China
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhou510642China
| | - Rong Qiu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesCollege of Life SciencesSouth China Agricultural University, SCAUGuangzhou510642China
| | - Wenjing Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesCollege of Life SciencesSouth China Agricultural University, SCAUGuangzhou510642China
| | - Ruqi Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesCollege of Life SciencesSouth China Agricultural University, SCAUGuangzhou510642China
| | - Hongyi Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesCollege of Life SciencesSouth China Agricultural University, SCAUGuangzhou510642China
| | - Xianrong Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesCollege of Life SciencesSouth China Agricultural University, SCAUGuangzhou510642China
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhou510642China
| | - Letian Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesCollege of Life SciencesSouth China Agricultural University, SCAUGuangzhou510642China
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhou510642China
| | - Yao‐Guang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesCollege of Life SciencesSouth China Agricultural University, SCAUGuangzhou510642China
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhou510642China
| | - Jingxin Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesCollege of Life SciencesSouth China Agricultural University, SCAUGuangzhou510642China
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhou510642China
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12
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Mengarelli DA, Zanor MI. Genome-wide characterization and analysis of the CCT motif family genes in soybean (Glycine max). PLANTA 2021; 253:15. [PMID: 33392793 DOI: 10.1007/s00425-020-03537-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 12/11/2020] [Indexed: 05/27/2023]
Abstract
MAIN CONCLUSION Soybean possesses 19 CMF genes which mainly arose from duplication events. Their features and motifs are highly conserved but transcriptional data indicated functional diversity in metabolism and stress responses. CCT [for CONSTANS, CONSTANS-like (CO-like), and timing of CAB expression1 (TOC1)] domain-containing genes play important roles in regulating flowering, plant growth, and grain yield and are also involved in stress responses. The CMF (CCT motif family) genes, included in the CCT family, contain a single CCT domain as the only identifiable domain in their predicted protein sequence and are interesting targets for breeding programs. In this study, we identified 19 putative GmCMF genes, based on the latest soybean (Glycine max) genome annotation. The predicted GmCMF proteins were characterized based on conserved structural features, and a phylogenetic tree was constructed including all CMF proteins from rice and Arabidopsis as representative examples of the monocotyledonous (monocot) and dicotyledonous (dicot) plants, respectively. High similarities in the conserved motifs of the protein sequences and the gene structures were found. In addition, by analyzing the CMF gene family in soybean, we identified seven pairs of genes that originated from segmental chromosomal duplication events attributable to the most recent whole-genome duplication (WGD) event in the Glycine lineage. Expression analysis of GmCMF genes in various tissues and after specific treatments demonstrated tissue and stress-response specific differential expression. Gene expression analysis was complemented by the identification of putative cis-elements present in the promoter regions of the genes through a bioinformatics approach, using the existing soybean reference genome sequence and gene models. Co-functional networks inferred from distinct types of genomics data-including microarrays and RNA-seq samples from soybean-revealed that GmCMF genes might play crucial roles in metabolism and transport processes. The results of this study, the first systematic analysis of the soybean CCT gene family, can serve as a strong foundation for further elucidation of their physiological functions and biological roles.
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Guo Y, Niu S, El-Kassaby YA, Li W. Transcriptome-wide isolation and expression of NF-Y gene family in male cone development and hormonal treatment of Pinus tabuliformis. PHYSIOLOGIA PLANTARUM 2021; 171:34-47. [PMID: 32770551 DOI: 10.1111/ppl.13183] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 08/03/2020] [Indexed: 06/11/2023]
Abstract
It is known that nuclear factor Y (NF-Y) transcription factors play an important role in flowering time regulation and hormone response (ABA, GA) in angiosperms, but, little known in conifers. Moreover, the NF-Y gene family has not been comprehensively reported in conifers. Here, we identified 9 NF-YA, 9 NF-YB and 10 NF-YC genes in Pinus tabuliformis using Arabidopsis NF-Y protein sequences as queries. Additionally, by comparing conserved regions and phylogenetic relationships of the PtNF-Ys, we found that NF-Ys were both conserved and altered during evolution. PtTFL2, PtCO, PtNF-YC1 and PtNF-YC4 were exploited by expression profile in male cone development and correlation analysis. Furthermore, NF-YC1/4 and DPL (DELLA protein of P. tabuliformis) were interacted by yeast two-hybrid and BiFC assays, which suggested that NF-YC1/4 may be involved in gibberellins signaling pathway. Moreover, the multiple types of phytohormones-responsive cis-elements (ABA, JA, IAA, SA) have been found, and gene expression profile analysis showed that many NF-Y genes responded positively to SA and as opposed to IAA and JA, revealing the potential role of NF-Ys in conifers resistance. In summary, this study provided the basis for further investigation of the function of NF-Y genes in conifers.
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Affiliation(s)
- Yingtian Guo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Forest Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Shihui Niu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Forest Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, 2424 Main Mall, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Wei Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Forest Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
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14
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Martignago D, Siemiatkowska B, Lombardi A, Conti L. Abscisic Acid and Flowering Regulation: Many Targets, Different Places. Int J Mol Sci 2020; 21:ijms21249700. [PMID: 33353251 PMCID: PMC7767233 DOI: 10.3390/ijms21249700] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/14/2020] [Accepted: 12/17/2020] [Indexed: 12/13/2022] Open
Abstract
Plants can react to drought stress by anticipating flowering, an adaptive strategy for plant survival in dry climates known as drought escape (DE). In Arabidopsis, the study of DE brought to surface the involvement of abscisic acid (ABA) in controlling the floral transition. A central question concerns how and in what spatial context can ABA signals affect the floral network. In the leaf, ABA signaling affects flowering genes responsible for the production of the main florigen FLOWERING LOCUS T (FT). At the shoot apex, FD and FD-like transcription factors interact with FT and FT-like proteins to regulate ABA responses. This knowledge will help separate general and specific roles of ABA signaling with potential benefits to both biology and agriculture.
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15
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Gnesutta N, Chiara M, Bernardini A, Balestra M, Horner DS, Mantovani R. The Plant NF-Y DNA Matrix In Vitro and In Vivo. PLANTS 2019; 8:plants8100406. [PMID: 31658622 PMCID: PMC6843132 DOI: 10.3390/plants8100406] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/24/2019] [Accepted: 10/08/2019] [Indexed: 01/17/2023]
Abstract
Nuclear Factor Y (NF-Y) is an evolutionarily conserved trimer formed by a Histone-Fold Domain (HFD) heterodimeric module shared by core histones, and the sequence-specific NF-YA subunit. In plants, the genes encoding each of the three subunits have expanded in number, giving rise to hundreds of potential trimers. While in mammals NF-Y binds a well-characterized motif, with a defined matrix centered on the CCAAT box, the specificity of the plant trimers has yet to be determined. Here we report that Arabidopsis thaliana NF-Y trimeric complexes, containing two different NF-YA subunits, bind DNA in vitro with similar affinities. We assayed precisely sequence-specificity by saturation mutagenesis, and analyzed genomic DNA sites bound in vivo by selected HFDs. The plant NF-Y CCAAT matrix is different in nucleotides flanking CCAAT with respect to the mammalian matrix, in vitro and in vivo. Our data point to flexible DNA-binding rules by plant NF-Ys, serving the scope of adapting to a diverse audience of genomic motifs.
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Affiliation(s)
- Nerina Gnesutta
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy.
| | - Matteo Chiara
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy.
| | - Andrea Bernardini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy.
| | - Matteo Balestra
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy.
| | - David S Horner
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy.
| | - Roberto Mantovani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy.
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16
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Quan S, Niu J, Zhou L, Xu H, Ma L, Qin Y. Identification and characterization of NF-Y gene family in walnut (Juglans regia L.). BMC PLANT BIOLOGY 2018; 18:255. [PMID: 30352551 PMCID: PMC6199752 DOI: 10.1186/s12870-018-1459-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 10/03/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND The eukaryotic transcription factor NF-Y (which consists of NF-YA, NF-YB and NF-YC subunits) is involved in many important plant development processes. There are many reports about the NF-Y family in Arabidopsis and other plant species. However, there are no reports about the NF-Y family in walnut (Juglans regia L.). RESULTS Thirty-three walnut NF-Y genes (JrNF-Ys) were identified and mapped on the walnut genome. The JrNF-Y gene family consisted of 17 NF-YA genes, 9 NF-YB genes, and 7 NF-YC genes. The structural features of the JrNF-Y genes were investigated by comparing their evolutionary relationship and motif distributions. The comparisons indicated the NF-Y gene structure was both conserved and altered during evolution. Functional prediction and protein interaction analysis were performed by comparing the JrNF-Y protein structure with that in Arabidopsis. Two differentially expressed JrNF-Y genes were identified. Their expression was compared with that of three JrCOs and two JrFTs using quantitative real-time PCR (qPCR). The results revealed that the expression of JrCO2 was positively correlated with the expression of JrNF-YA11 and JrNF-YA12. In contrast, JrNF-CO1 and JrNF-YA12 were negatively correlated. CONCLUSIONS Thirty-three JrNF-Ys were identified and their evolutionary, structure, biological function and expression pattern were analyzed. Two of the JrNF-Ys were screened out, their expression was differentially expressed in different development periods of female flower buds, and in different tissues (female flower buds and leaf buds). Based on prediction and experimental data, JrNF-Ys may be involved in flowering regulation by co-regulate the expression of flowering genes with other transcription factors (TFs). The results of this study may make contribution to the further investigation of JrNF-Y family.
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Affiliation(s)
- Shaowen Quan
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, Xinjiang, 832003 China
- Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, Xinjiang, 832003 China
| | - Jianxin Niu
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, Xinjiang, 832003 China
- Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, Xinjiang, 832003 China
| | - Li Zhou
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, Xinjiang, 832003 China
- Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, Xinjiang, 832003 China
| | - Hang Xu
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, Xinjiang, 832003 China
- Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, Xinjiang, 832003 China
| | - Li Ma
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, Xinjiang, 832003 China
- Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, Xinjiang, 832003 China
| | - Yang Qin
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, Xinjiang, 832003 China
- Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, Xinjiang, 832003 China
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17
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Gnesutta N, Mantovani R, Fornara F. Plant Flowering: Imposing DNA Specificity on Histone-Fold Subunits. TRENDS IN PLANT SCIENCE 2018; 23:293-301. [PMID: 29331540 DOI: 10.1016/j.tplants.2017.12.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Revised: 12/11/2017] [Accepted: 12/14/2017] [Indexed: 05/27/2023]
Abstract
CONSTANS (CO) is a master regulator of flowering time, although the mechanisms underlying its role as a transcriptional regulator are not well understood. The DNA-binding domain of CO shares homology with that of NUCLEAR FACTOR YA (NF-YA), a subunit of the CCAAT-binding trimer NF-Y. Recent publications indicate that CO and its rice homolog HEADING DATE 1 (Hd1) form heterotrimers with the histone-fold subunits of NF-Y to efficiently bind promoter elements in the florigen genes. Differences in the DNA-binding specificities of NF-Y and NF-CO can be conceptualized based on our knowledge of the 3D structure of the NF-Y/CCAAT complex. Here we discuss the modes of assembly of NF-Y-like heterotrimers and possible models for their activity as flexible sequence-specific transcriptional regulators.
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Affiliation(s)
- Nerina Gnesutta
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy.
| | - Roberto Mantovani
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Fabio Fornara
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy.
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18
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Mantovani R. Nuclear factor Y in development and disease. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:523-524. [PMID: 28279783 DOI: 10.1016/j.bbagrm.2017.03.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Roberto Mantovani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
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Brambilla V, Gomez-Ariza J, Cerise M, Fornara F. The Importance of Being on Time: Regulatory Networks Controlling Photoperiodic Flowering in Cereals. FRONTIERS IN PLANT SCIENCE 2017; 8:665. [PMID: 28491078 PMCID: PMC5405123 DOI: 10.3389/fpls.2017.00665] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 04/11/2017] [Indexed: 05/04/2023]
Abstract
Flowering is the result of the coordination between genetic information and environmental cues. Gene regulatory networks have evolved in plants in order to measure diurnal and seasonal variation of day length (or photoperiod), thus aligning the reproductive phase with the most favorable season of the year. The capacity of plants to discriminate distinct photoperiods classifies them into long and short day species, depending on the conditions that induce flowering. Plants of tropical origin and adapted to short day lengths include rice, maize, and sorghum, whereas wheat and barley were originally domesticated in the Fertile Crescent and are considered long day species. In these and other crops, day length measurement mechanisms have been artificially modified during domestication and breeding to adapt plants to novel areas, to the extent that a wide diversity of responses exists within any given species. Notwithstanding the ample natural and artificial variation of day length responses, some of the basic molecular elements governing photoperiodic flowering are widely conserved. However, as our understanding of the underlying mechanisms improves, it becomes evident that specific regulators exist in many lineages that are not shared by others, while apparently conserved components can be recruited to novel functions during evolution.
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Zhao H, Wu D, Kong F, Lin K, Zhang H, Li G. The Arabidopsis thaliana Nuclear Factor Y Transcription Factors. FRONTIERS IN PLANT SCIENCE 2016; 7:2045. [PMID: 28119722 PMCID: PMC5222873 DOI: 10.3389/fpls.2016.02045] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 12/21/2016] [Indexed: 05/03/2023]
Abstract
Nuclear factor Y (NF-Y) is an evolutionarily conserved trimeric transcription factor complex present in nearly all eukaryotes. The heterotrimeric NF-Y complex consists of three subunits, NF-YA, NF-YB, and NF-YC, and binds to the CCAAT box in the promoter regions of its target genes to regulate their expression. Yeast and mammal genomes generally have single genes with multiple splicing isoforms that encode each NF-Y subunit. By contrast, plant genomes generally have multi-gene families encoding each subunit and these genes are differentially expressed in various tissues or stages. Therefore, different subunit combinations can lead to a wide variety of NF-Y complexes in various tissues, stages, and growth conditions, indicating the potentially diverse functions of this complex in plants. Indeed, many recent studies have proved that the NF-Y complex plays multiple essential roles in plant growth, development, and stress responses. In this review, we highlight recent progress on NF-Y in Arabidopsis thaliana, including NF-Y protein structure, heterotrimeric complex formation, and the molecular mechanism by which NF-Y regulates downstream target gene expression. We then focus on its biological functions and underlying molecular mechanisms. Finally, possible directions for future research on NF-Y are also presented.
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