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An F, Yin X, Jueraiti K, Yang Y, Yan Z, Li J, Shan D. Genome-Wide Identification, Characterization, and Expression Analysis of the NAC Transcription Factor Family in Sweet Cherry ( Prunus avium L.). PLANTS (BASEL, SWITZERLAND) 2025; 14:1201. [PMID: 40284089 PMCID: PMC12030308 DOI: 10.3390/plants14081201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2025] [Revised: 03/31/2025] [Accepted: 04/07/2025] [Indexed: 04/29/2025]
Abstract
The NAC (NAM, ATAF1/2, and CUC2) family is one of the largest plant-specific transcription factor families, playing a crucial role in adaptation to abiotic stresses. However, the NAC gene family in sweet cherry (Prunus avium L.) remains poorly understood. In this study, we identified 130 NAC genes (PaNAC) from the sweet cherry genome, which were unevenly distributed across eight chromosomes. Phylogenetic analysis classified the PaNACs into 21 distinct groups, including 2 sweet cherry-specific groups. Comparative analysis revealed significant variations in gene proportions, exon-intron structures, and motif compositions among different groups. Furthermore, cis-element analysis suggested the potential roles of PaNACs in regulating plant growth, development, hormone signaling, and stress responses. Transcriptomic data revealed tissue-specific expression patterns for several PaNAC genes. qRT-PCR further confirmed that eight selected PaNACs were responsive to various abiotic stresses in Gisela 6, a widely used hybrid rootstock in sweet cherry production that shares high sequence similarity in NAC genes with P. avium. These findings provide valuable insights for future research on the functional characteristics of the PaNAC genes in the growth, development, and responses to abiotic stress in sweet cherry.
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Affiliation(s)
| | | | | | | | | | | | - Dongqian Shan
- College of Horticulture, Northwest A & F University, Yangling 712100, China; (F.A.); (X.Y.); (K.J.); (Y.Y.); (Z.Y.); (J.L.)
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2
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Li T, Chen H, Ma N, Jiang D, Wu J, Zhang X, Li H, Su J, Chen P, Liu Q, Guan Y, Zhu X, Lin J, Zhang J, Wang Q, Guo H, Zhu F. Specificity landscapes of 40 R2R3-MYBs reveal how paralogs target different cis-elements by homodimeric binding. IMETA 2025; 4:e70009. [PMID: 40236784 PMCID: PMC11995187 DOI: 10.1002/imt2.70009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2024] [Revised: 02/11/2025] [Accepted: 02/17/2025] [Indexed: 04/17/2025]
Abstract
Paralogous transcription factors (TFs) frequently recognize highly similar DNA motifs. Homodimerization can help distinguish them according to their different dimeric configurations. Here, by studying R2R3-MYB TFs, we show that homodimerization can also directly change the recognized DNA motifs to distinguish between similar TFs. By high-throughput SELEX, we profiled the specificity landscape for 40 R2R3-MYBs of subfamily VIII and curated 833 motif models. The dimeric models show that homodimeric binding has evoked specificity changes for AtMYBs. Focusing on AtMYB2 as an example, we show that homodimerization has modified its specificity and allowed it to recognize additional cis-regulatory sequences that are different from the closely related CCWAA-box AtMYBs and are unique among all AtMYBs. Genomic sites described by the modified dimeric specificities of AtMYB2 are conserved in evolution and involved in AtMYB2-specific transcriptional activation. Collectively, this study provides rich data on sequence preferences of VIII R2R3-MYBs and suggests an alternative mechanism that guides closely related TFs to respective cis-regulatory sites.
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Affiliation(s)
- Tian Li
- Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, College of JUNCAO Science and Ecology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Hao Chen
- Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, College of JUNCAO Science and Ecology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Nana Ma
- Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, College of JUNCAO Science and Ecology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry UniversityFuzhouChina
- College of Life ScienceFujian Agriculture and Forestry UniversityFuzhouChina
| | - Dingkun Jiang
- Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, College of JUNCAO Science and Ecology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry UniversityFuzhouChina
- College of Life ScienceFujian Agriculture and Forestry UniversityFuzhouChina
| | - Jiacheng Wu
- Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, College of JUNCAO Science and Ecology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Xinfeng Zhang
- Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, College of JUNCAO Science and Ecology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Hao Li
- Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, College of JUNCAO Science and Ecology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry UniversityFuzhouChina
- College of Life ScienceFujian Agriculture and Forestry UniversityFuzhouChina
| | - Jiaqing Su
- College of Resources and EnvironmentFujian Agriculture and Forestry UniversityFuzhouChina
| | - Piaojuan Chen
- Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, College of JUNCAO Science and Ecology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Qing Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
| | - Yuefeng Guan
- College of Resources and EnvironmentFujian Agriculture and Forestry UniversityFuzhouChina
| | - Xiaoyue Zhu
- Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, College of JUNCAO Science and Ecology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Juncheng Lin
- Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, College of JUNCAO Science and Ecology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Jilin Zhang
- Department of Biomedical SciencesCity University of Hong KongHong KongChina
- Tung Biomedical Sciences CentreCity University of Hong KongHong KongChina
- Department of Precision Diagnostic and Therapeutic TechnologyThe City University of Hong Kong Shenzhen Futian Research InstituteShenzhenChina
| | - Qin Wang
- Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, College of JUNCAO Science and Ecology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Honghong Guo
- Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, College of JUNCAO Science and Ecology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry UniversityFuzhouChina
- College of Life ScienceFujian Agriculture and Forestry UniversityFuzhouChina
| | - Fangjie Zhu
- Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, College of JUNCAO Science and Ecology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry UniversityFuzhouChina
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3
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Wetters S, Nick P. B-class gene GLOBOSA - a facilitator for enriched species diversity of Salvia in the New World? PLANT BIOLOGY (STUTTGART, GERMANY) 2025; 27:333-346. [PMID: 39964076 PMCID: PMC11950904 DOI: 10.1111/plb.70002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Accepted: 01/23/2025] [Indexed: 03/29/2025]
Abstract
The genus Salvia, comprising around 1000 species, half of which are found in the New World, belongs to the taxonomically most challenging genera within the Lamiaceae. A part of this diversity can be ascribed to the shape and expansion of the corolla and stamen structures, because changes in geometry of the sexual organs and attractance of pollinators might establish propagation barriers. However, the structural, functional, and evolutionary context of the underlying genes has not yet been elaborated. In this study, we analyse a large set of flowers from Salvia species of different geographic origin and use this morphometric framework to address gene expression and phylogenetic analysis of the MADS-box B-class gene, GLOBOSA. We examined expression of GLOBOSA in petals and anthers throughout anthesis for both Salvia pratensis L., as species from Europe, and the American Salvia elegans Vahl. Structural analysis of the B-class genes reveals typical MADS-MIKC-type composition. When we infer phylogenies for GLOBOSA and its binding partner DEFICIENS, we see a genus-wide duplication of DEFICIENS in Salvia and a specific duplication of GLOBOSA in Salvia species from the New World. Based on the first description of flowering genes in the genus Salvia, we arrive at a working model, where a duplication of GLOBOSA enabled the intense radiation of New World Salvia by neo-functionalization of a flower identity gene for morphogenetic control of corolla and anther geometry. We propose that the genus Salvia can be used as paradigm to address the role of EvoDevo for plant speciation.
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Affiliation(s)
- S. Wetters
- Department of Molecular Cell BiologyJoseph Gottlieb Kölreuter Institute of Plant Science (JKIP), Karlsruhe Institute of TechnologyKarlsruheGermany
| | - P. Nick
- Department of Molecular Cell BiologyJoseph Gottlieb Kölreuter Institute of Plant Science (JKIP), Karlsruhe Institute of TechnologyKarlsruheGermany
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Basak M, Chakraborty S, Kundu S, Dey S, Das M. Identification, expression analyses of APETALA1 gene homologs in Bambusa tulda and heterologous validation of BtMADS14 in Arabidopsis thaliana. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2025; 31:389-404. [PMID: 40256271 PMCID: PMC12006657 DOI: 10.1007/s12298-025-01569-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2024] [Revised: 02/19/2025] [Accepted: 02/21/2025] [Indexed: 04/22/2025]
Abstract
Bamboos belong to the grass family Poaceae, sub-family Bambusoideae and possess many interesting developmental features including a long vegetative period before flowering. Previously, transcriptome based analyses have identified differentially expressed transcripts in flowering and vegetative tissues to predict gene clusters of functional relevance. In contrast, limited studies were conducted to characterize individual genes to decipher their precise role to induce flowering. This was primarily due to the unavailability of sufficient genomic resources, which has lately been overcome by the release of additional bamboo genomes. In this study, the APETALA1 gene homologs (MADS14, MADS15, MADS18 and MADS20) have been identified from five sequenced bamboo species (Bonia amplexicaulis, Guadua angustifolia, Raddia guianensis, Olyra latifolia, Phyllostachys edulis). In addition, APETALA1 homologs from a tropical bamboo (Bambusa tulda) have been PCR amplified, sequenced and included in the analyses to widen spectrum of sampling. Assessment of their phylogenetic and syntenic relationship with related Poaceae neighbours revealed closer relationship between MADS14 and MADS15 members than MADS18 and MADS20. Transcriptional expression patterns of B. tulda BtMADS14, BtMADS15, BtMADS18 and BtMADS20 in vegetative and floral tissues indicated a possible role of BtMADS14 and BtMADS15 in flower induction and differentiation, while BtMADS18 might be associated with seed development. Total 24 proteins were predicted to interact with the Phyllostachys edulis homolog of BtMADS14 protein and 8 of them were members of the MADS-box family. The p35S::BtMADS14 overexpressing Arabidopsis plants flowered 8-10 days earlier than the wild type plants suggesting its possible involvement in the floral induction of B. tulda. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-025-01569-3.
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Affiliation(s)
- Mridushree Basak
- Plant Genomics Laboratory, Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, West Bengal 700073 India
| | - Sukanya Chakraborty
- Plant Genomics Laboratory, Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, West Bengal 700073 India
- Department of Botany, Scottish Church College, 1 & 3, Urquhart Square, Manicktala, Azad Hind Bag, Kolkata, West Bengal 700006 India
| | - Sutrisha Kundu
- Plant Genomics Laboratory, Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, West Bengal 700073 India
| | - Sonali Dey
- Plant Genomics Laboratory, Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, West Bengal 700073 India
| | - Malay Das
- Plant Genomics Laboratory, Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, West Bengal 700073 India
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Ji L, Huang B, Ren D, Wei X, Liu L, Bi Y, Li Z, Yuan F, Han K, Li K, Yang F, Li X, Yu T, Shi Y, He L, Lu Q, He G. Identification of Schizophrenia-Risk Regulatory Variant rs1399178 in the Non-coding Region With Its Impact on NRF1 Binding. CNS Neurosci Ther 2025; 31:e70275. [PMID: 40019038 PMCID: PMC11868986 DOI: 10.1111/cns.70275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2024] [Revised: 11/28/2024] [Accepted: 01/31/2025] [Indexed: 03/01/2025] Open
Abstract
AIMS The challenges in identifying functional variants from genome-wide association studies (GWAS) and unraveling regulatory mechanisms in schizophrenia research persist, particularly in intronic regions. A non-coding regulatory variant, rs1399178, associated with schizophrenia risk, is identified and its impact on NRF1 binding is investigated. METHODS This study focuses on schizophrenia GWAS risk loci, using functional genomics, expression analyses and structural analysis to identify 736 schizophrenia risk single-nucleotide polymorphisms (SNPs) that disrupt transcription factor (TF) binding. RESULTS Among these SNPs, rs1399178 stands out as a bifunctional intergenic SNP that can switch between acting as a promoter and an enhancer, potentially influencing MLH1 and LRRFIP2 expression via expression quantitative trait loci analysis. Importantly, mutation of the G allele of rs1399178 to A significantly diminishes its binding affinity to nuclear respiratory factor 1 (NRF1). Structural analysis provides further insight into this alteration in the protein-nucleic acid complex formation. CONCLUSION Based on our data, a model is proposed in which rs1399178 confers schizophrenia risk by modifying NRF1 binding profiles, thereby regulating the abundance of target genes through promoter-enhancer switching. This study provides novel insights into the regulatory mechanisms of schizophrenia risk variants, highlighting the intricate nature of genetic interactions and potential therapeutic targets.
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Affiliation(s)
- Lei Ji
- Bio‐X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric DisordersShanghai Jiao Tong UniversityShanghaiChina
- The Collaborative Innovation Center for Brain Science, and Brain Science and Technology Research CenterShanghai Jiao Tong UniversityShanghaiChina
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health CenterShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Bojian Huang
- Bio‐X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric DisordersShanghai Jiao Tong UniversityShanghaiChina
- The Collaborative Innovation Center for Brain Science, and Brain Science and Technology Research CenterShanghai Jiao Tong UniversityShanghaiChina
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health CenterShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Decheng Ren
- Bio‐X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric DisordersShanghai Jiao Tong UniversityShanghaiChina
- The Collaborative Innovation Center for Brain Science, and Brain Science and Technology Research CenterShanghai Jiao Tong UniversityShanghaiChina
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health CenterShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Xiaoxi Wei
- Bio‐X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric DisordersShanghai Jiao Tong UniversityShanghaiChina
- The Collaborative Innovation Center for Brain Science, and Brain Science and Technology Research CenterShanghai Jiao Tong UniversityShanghaiChina
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health CenterShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Liangjie Liu
- Bio‐X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric DisordersShanghai Jiao Tong UniversityShanghaiChina
- The Collaborative Innovation Center for Brain Science, and Brain Science and Technology Research CenterShanghai Jiao Tong UniversityShanghaiChina
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health CenterShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Yan Bi
- Bio‐X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric DisordersShanghai Jiao Tong UniversityShanghaiChina
- The Collaborative Innovation Center for Brain Science, and Brain Science and Technology Research CenterShanghai Jiao Tong UniversityShanghaiChina
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health CenterShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Zhiqiang Li
- Bio‐X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric DisordersShanghai Jiao Tong UniversityShanghaiChina
- The Collaborative Innovation Center for Brain Science, and Brain Science and Technology Research CenterShanghai Jiao Tong UniversityShanghaiChina
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health CenterShanghai Jiao Tong University School of MedicineShanghaiChina
- Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio‐X Institutes)Qingdao UniversityQingdaoChina
| | - Fan Yuan
- Bio‐X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric DisordersShanghai Jiao Tong UniversityShanghaiChina
- The Collaborative Innovation Center for Brain Science, and Brain Science and Technology Research CenterShanghai Jiao Tong UniversityShanghaiChina
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health CenterShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Ke Han
- Bio‐X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric DisordersShanghai Jiao Tong UniversityShanghaiChina
- The Collaborative Innovation Center for Brain Science, and Brain Science and Technology Research CenterShanghai Jiao Tong UniversityShanghaiChina
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health CenterShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Keyi Li
- Bio‐X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric DisordersShanghai Jiao Tong UniversityShanghaiChina
- The Collaborative Innovation Center for Brain Science, and Brain Science and Technology Research CenterShanghai Jiao Tong UniversityShanghaiChina
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health CenterShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Fengping Yang
- Bio‐X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric DisordersShanghai Jiao Tong UniversityShanghaiChina
- The Collaborative Innovation Center for Brain Science, and Brain Science and Technology Research CenterShanghai Jiao Tong UniversityShanghaiChina
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health CenterShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Xingwang Li
- Bio‐X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric DisordersShanghai Jiao Tong UniversityShanghaiChina
- The Collaborative Innovation Center for Brain Science, and Brain Science and Technology Research CenterShanghai Jiao Tong UniversityShanghaiChina
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health CenterShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Tao Yu
- Bio‐X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric DisordersShanghai Jiao Tong UniversityShanghaiChina
- The Collaborative Innovation Center for Brain Science, and Brain Science and Technology Research CenterShanghai Jiao Tong UniversityShanghaiChina
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health CenterShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Yi Shi
- Bio‐X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric DisordersShanghai Jiao Tong UniversityShanghaiChina
- The Collaborative Innovation Center for Brain Science, and Brain Science and Technology Research CenterShanghai Jiao Tong UniversityShanghaiChina
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health CenterShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Lin He
- Bio‐X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric DisordersShanghai Jiao Tong UniversityShanghaiChina
- The Collaborative Innovation Center for Brain Science, and Brain Science and Technology Research CenterShanghai Jiao Tong UniversityShanghaiChina
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health CenterShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Qing Lu
- Bio‐X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric DisordersShanghai Jiao Tong UniversityShanghaiChina
- Department of Otorhinolaryngology‐Head and Neck SurgeryChongqing General HospitalChongqingChina
- Ear InstituteShanghai Jiao Tong University School of MedicineShanghaiChina
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose DiseasesShanghaiChina
| | - Guang He
- Bio‐X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric DisordersShanghai Jiao Tong UniversityShanghaiChina
- The Collaborative Innovation Center for Brain Science, and Brain Science and Technology Research CenterShanghai Jiao Tong UniversityShanghaiChina
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health CenterShanghai Jiao Tong University School of MedicineShanghaiChina
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Zhang L, Yang Y, Zhang Y, Yang F. Genome-Wide Investigation of MADS-Box Genes in Flower Development and Environmental Acclimation of Lumnitzera littorea (Jack) Voigt. Int J Mol Sci 2025; 26:1680. [PMID: 40004145 PMCID: PMC11855919 DOI: 10.3390/ijms26041680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2024] [Revised: 02/13/2025] [Accepted: 02/14/2025] [Indexed: 02/27/2025] Open
Abstract
Lumnitzera littorea (Jack) Voigt is an endangered mangrove species in China. Low fecundity and environmental pressure are supposed to be key factors limiting the population expansion of L. littorea. Transcription factors with the MADS-box domain are crucial regulators of plant flower development, reproduction, and stress response. In this study, we performed a comprehensive investigation into the features and functions of MADS-box genes of L. littorea. Sixty-three LlMADS genes with similar structure and motif composition were identified in the L. littorea genome, and these genes were unevenly distributed on the 11 chromosomes. Segmental duplication was suggested to make a main contribution to the expansion of the LlMADS gene family. Some LIMADS genes exhibited differential expression in different flower types or in response to cold stress. Overexpression of the B-class gene LlMADS37 had substantial effects on the flower morphology and flowering time of transgenic Arabidopsis plants, demonstrating its key role in regulating flower morphogenesis and inflorescence. These findings largely enrich our understanding of the functional importance of MADS-box genes in the inflorescence and stress acclimation of L. littorea and provide valuable resources for future genetic research to improve the conservation of this species.
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Affiliation(s)
- Linbi Zhang
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China;
| | - Yuchen Yang
- School of Ecology, Sun Yat-sen University, Shenzhen 518107, China;
| | - Ying Zhang
- School of Life Science and Technology, Lingnan Normal University, Zhanjiang 524048, China
| | - Fusun Yang
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China;
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7
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Duan E, Teng X, Xu H, Ma W, Zhang D, Zhang R, Gu C, Zhang Y, Chen R, Chen X, Feng M, Lin Q, Dong H, Zhang Y, Yang X, Zhou L, Liu S, Liu X, Tian Y, Jiang L, Wang H, Wang Y, Wan J. SHORT INTERNODE1 regulates the activity of MADS transcription factors during rice floral organ development. PLANT PHYSIOLOGY 2025; 197:kiaf034. [PMID: 39964839 DOI: 10.1093/plphys/kiaf034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 12/10/2024] [Accepted: 12/18/2024] [Indexed: 02/20/2025]
Abstract
Floral organ identity is fundamental to species diversity and reproductive success in plants and is mainly determined by the combinatorial action of MADS homeotic factors. However, despite their conserved roles in specifying floral organ identity, the regulation of MADS transcription factors remains elusive. Here, we show that the rice (Oryza sativa L.) short internode1 (shi1) mutant displays pleiotropic defects in floral organ development, resulting in severe penalties to yield and grain quality. OsSHI1 mRNA accumulates in each floral organ whorl, and OsSHI1 interacts with multiple MADS transcription factors, especially the Class E members. This physical interaction occurs through the intrinsic MADS domains, thus regulating the transcriptional activity of the MADS transcription factors. This study provides insight into the molecular and genetic regulatory mechanisms underlying the roles of OsSHI1 and MADS transcription factors in rice floral organ development and, consequently, grain yield and quality.
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Affiliation(s)
- Erchao Duan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, Jiangsu Nanjing Rice Germplasm Resources National Field Observation and Research Station, Key Laboratory of Biology, Genetics and Breeding of Japonica Rice in Mid-lower Yangtze River, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
| | - Xuan Teng
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, Jiangsu Nanjing Rice Germplasm Resources National Field Observation and Research Station, Key Laboratory of Biology, Genetics and Breeding of Japonica Rice in Mid-lower Yangtze River, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
| | - Huan Xu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, Jiangsu Nanjing Rice Germplasm Resources National Field Observation and Research Station, Key Laboratory of Biology, Genetics and Breeding of Japonica Rice in Mid-lower Yangtze River, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenyu Ma
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, Jiangsu Nanjing Rice Germplasm Resources National Field Observation and Research Station, Key Laboratory of Biology, Genetics and Breeding of Japonica Rice in Mid-lower Yangtze River, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
| | - Desheng Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, Jiangsu Nanjing Rice Germplasm Resources National Field Observation and Research Station, Key Laboratory of Biology, Genetics and Breeding of Japonica Rice in Mid-lower Yangtze River, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
| | - Rushuang Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, Jiangsu Nanjing Rice Germplasm Resources National Field Observation and Research Station, Key Laboratory of Biology, Genetics and Breeding of Japonica Rice in Mid-lower Yangtze River, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
| | - Chuanwei Gu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, Jiangsu Nanjing Rice Germplasm Resources National Field Observation and Research Station, Key Laboratory of Biology, Genetics and Breeding of Japonica Rice in Mid-lower Yangtze River, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
| | - Yipeng Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, Jiangsu Nanjing Rice Germplasm Resources National Field Observation and Research Station, Key Laboratory of Biology, Genetics and Breeding of Japonica Rice in Mid-lower Yangtze River, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
| | - Rongbo Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, Jiangsu Nanjing Rice Germplasm Resources National Field Observation and Research Station, Key Laboratory of Biology, Genetics and Breeding of Japonica Rice in Mid-lower Yangtze River, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoli Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, Jiangsu Nanjing Rice Germplasm Resources National Field Observation and Research Station, Key Laboratory of Biology, Genetics and Breeding of Japonica Rice in Mid-lower Yangtze River, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
| | - Miao Feng
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qibing Lin
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hui Dong
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, Jiangsu Nanjing Rice Germplasm Resources National Field Observation and Research Station, Key Laboratory of Biology, Genetics and Breeding of Japonica Rice in Mid-lower Yangtze River, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuanyan Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, Jiangsu Nanjing Rice Germplasm Resources National Field Observation and Research Station, Key Laboratory of Biology, Genetics and Breeding of Japonica Rice in Mid-lower Yangtze River, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
| | - Xue Yang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, Jiangsu Nanjing Rice Germplasm Resources National Field Observation and Research Station, Key Laboratory of Biology, Genetics and Breeding of Japonica Rice in Mid-lower Yangtze River, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
| | - Lei Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, Jiangsu Nanjing Rice Germplasm Resources National Field Observation and Research Station, Key Laboratory of Biology, Genetics and Breeding of Japonica Rice in Mid-lower Yangtze River, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
| | - Shijia Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, Jiangsu Nanjing Rice Germplasm Resources National Field Observation and Research Station, Key Laboratory of Biology, Genetics and Breeding of Japonica Rice in Mid-lower Yangtze River, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
| | - Xi Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, Jiangsu Nanjing Rice Germplasm Resources National Field Observation and Research Station, Key Laboratory of Biology, Genetics and Breeding of Japonica Rice in Mid-lower Yangtze River, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
| | - Yunlu Tian
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, Jiangsu Nanjing Rice Germplasm Resources National Field Observation and Research Station, Key Laboratory of Biology, Genetics and Breeding of Japonica Rice in Mid-lower Yangtze River, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
| | - Ling Jiang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, Jiangsu Nanjing Rice Germplasm Resources National Field Observation and Research Station, Key Laboratory of Biology, Genetics and Breeding of Japonica Rice in Mid-lower Yangtze River, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
| | - Haiyang Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
| | - Yihua Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, Jiangsu Nanjing Rice Germplasm Resources National Field Observation and Research Station, Key Laboratory of Biology, Genetics and Breeding of Japonica Rice in Mid-lower Yangtze River, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
| | - Jianmin Wan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Zhongshan Biological Breeding Laboratory, Jiangsu Nanjing Rice Germplasm Resources National Field Observation and Research Station, Key Laboratory of Biology, Genetics and Breeding of Japonica Rice in Mid-lower Yangtze River, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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8
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Liu Y, Xu X, He C, Jin L, Zhou Z, Gao J, Guo M, Wang X, Chen C, Ayaad MH, Li X, Yan W. Chromatin loops gather targets of upstream regulators together for efficient gene transcription regulation during vernalization in wheat. Genome Biol 2024; 25:306. [PMID: 39623466 PMCID: PMC11613916 DOI: 10.1186/s13059-024-03437-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 11/18/2024] [Indexed: 12/06/2024] Open
Abstract
BACKGROUND Plants respond to environmental stimuli by altering gene transcription that is highly related with chromatin status, including histone modification, chromatin accessibility, and three-dimensional chromatin interaction. Vernalization is essential for the transition to reproductive growth for winter wheat. How wheat reshapes its chromatin features, especially chromatin interaction during vernalization, remains unknown. RESULTS Combinatory analysis of gene transcription and histone modifications in winter wheat under different vernalization conditions identifies 17,669 differential expressed genes and thousands of differentially enriched peaks of H3K4me3, H3K27me3, and H3K9ac. We find dynamic gene expression across the vernalization process is highly associated with H3K4me3. More importantly, the dynamic H3K4me3- and H3K9ac-associated chromatin-chromatin interactions demonstrate that vernalization leads to increased chromatin interactions and gene activation. Remarkably, spatially distant targets of master regulators like VRN1 and VRT2 are gathered together by chromatin loops to achieve efficient transcription regulation, which is designated as a "shepherd" model. Furthermore, by integrating gene regulatory network for vernalization and natural variation of flowering time, TaZNF10 is identified as a negative regulator for vernalization-related flowering time in wheat. CONCLUSIONS We reveal dynamic gene transcription network during vernalization and find that the spatially distant genes can be recruited together via chromatin loops associated with active histone mark thus to be more efficiently found and bound by upstream regulator. It provides new insights into understanding vernalization and response to environmental stimuli in wheat and other plants.
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Affiliation(s)
- Yanyan Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xintong Xu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chao He
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Liujie Jin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ziru Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jie Gao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Minrong Guo
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xin Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chuanye Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mohammed H Ayaad
- Plant Research Department, Nuclear Research Center, Egyptian Atomic Energy Authority, Cairo, 13759, Egypt
| | - Xingwang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenhao Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
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9
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Ali A, Khan NM, Jiang Y, Zhou G, Wan Y. Comprehensive Genome-Wide Identification and Expression Profiling of bHLH Transcription Factors in Areca catechu Under Abiotic Stress. Int J Mol Sci 2024; 25:12936. [PMID: 39684646 DOI: 10.3390/ijms252312936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2024] [Revised: 11/25/2024] [Accepted: 11/29/2024] [Indexed: 12/18/2024] Open
Abstract
The basic helix-loop-helix (bHLH) transcription factor (TF) family, the second-largest among eukaryotes, is known for its evolutionary and functional diversity across plant species. However, bHLH genes have not yet been characterized in Areca catechu. In this study, we identified 76 AcbHLH genes, which exhibit a variety of physicochemical properties. Phylogenetic analysis revealed evolutionary relationships between Arabidopsis thaliana bHLH genes (AtbHLH) and their counterparts in A. catechu (AcbHLH). These analyses also highlighted conserved amino acid motifs (S, R, K, P, L, A, G, and D), conserved domains, and evolutionary changes, such as insertions, deletions, and exon gains or losses. Promoter analysis of AcbHLH genes revealed 76 cis-elements related to growth, phytohormones, light, and stress. Gene duplication analysis revealed four tandem duplications and twenty-three segmental duplications, while AcbHLH63 in the Areca genome exhibited significant synteny with bHLH genes from A. thaliana, Vitis vinifera, Solanum lycopersicum, Brachypodium distachyon, Oryza sativa, and Zea mays. Furthermore, relative expression analysis showed that under drought stress (DS), AcbHLH22, AcbHLH39, AcbHLH45, and AcbHLH58 showed distinct upregulation in leaves at specific time points, while all nine AcbHLH genes were upregulated in roots. Under salt stress (SS), AcbHLH22, AcbHLH39, AcbHLH45, and AcbHLH58 were upregulated in leaves, and AcbHLH22, AcbHLH34, and AcbHLH39 exhibited differential expression in roots at various time points. This study provides valuable insights into the bHLH superfamily in A. catechu, offering a solid foundation for further investigation into its role in responding to abiotic stresses.
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Affiliation(s)
- Akhtar Ali
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Noor Muhammad Khan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Yiqi Jiang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Guangzhen Zhou
- The Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou 571158, China
| | - Yinglang Wan
- The Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou 571158, China
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10
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Thoris K, Correa Marrero M, Fiers M, Lai X, Zahn I, Jiang X, Mekken M, Busscher S, Jansma S, Nanao M, de Ridder D, van Dijk AJ, Angenent G, Immink RH, Zubieta C, Bemer M. Uncoupling FRUITFULL's functions through modification of a protein motif identified by co-ortholog analysis. Nucleic Acids Res 2024; 52:13290-13304. [PMID: 39475190 PMCID: PMC11602133 DOI: 10.1093/nar/gkae963] [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: 06/14/2024] [Revised: 10/04/2024] [Accepted: 10/15/2024] [Indexed: 11/29/2024] Open
Abstract
Many plant transcription factors (TFs) are multifunctional and regulate growth and development in more than one tissue. These TFs can generally associate with different protein partners depending on the tissue type, thereby regulating tissue-specific target gene sets. However, how interaction specificity is ensured is still largely unclear. Here, we examine protein-protein interaction specificity using subfunctionalized co-orthologs of the FRUITFULL (FUL) subfamily of MADS-domain TFs. In Arabidopsis, FUL is multifunctional, playing important roles in flowering and fruiting, whereas these functions have partially been divided in the tomato co-orthologs FUL1 and FUL2. By linking protein sequence and function, we discovered a key amino acid motif that determines interaction specificity of MADS-domain TFs, which in Arabidopsis FUL determines the interaction with AGAMOUS and SEPALLATA proteins, linked to the regulation of a subset of targets. This insight offers great opportunities to dissect the biological functions of multifunctional MADS TFs.
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Affiliation(s)
- Kai Thoris
- Laboratory of Molecular Biology, Wageningen University & Research, 6708 PB Wageningen, the Netherlands
| | - Miguel Correa Marrero
- Bioinformatics Group, Wageningen University & Research, 6708 PB Wageningen, the Netherlands
| | - Martijn Fiers
- Business Unit Bioscience, Wageningen University & Research, 6708 PB Wageningen, the Netherlands
| | - Xuelei Lai
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, Université Grenoble Alpes, INRAE, IRIG, CEA, 38000 Grenoble, Grenoble, France
| | - Iris E Zahn
- Laboratory of Molecular Biology, Wageningen University & Research, 6708 PB Wageningen, the Netherlands
| | - Xiaobing Jiang
- Laboratory of Molecular Biology, Wageningen University & Research, 6708 PB Wageningen, the Netherlands
| | - Mark Mekken
- Laboratory of Molecular Biology, Wageningen University & Research, 6708 PB Wageningen, the Netherlands
| | - Stefan Busscher
- Laboratory of Molecular Biology, Wageningen University & Research, 6708 PB Wageningen, the Netherlands
| | - Stuart Jansma
- Laboratory of Molecular Biology, Wageningen University & Research, 6708 PB Wageningen, the Netherlands
| | - Max Nanao
- Structural Biology, European Synchrotron Radiation Facility, 71 ave. des Martyrs, 38000 Grenoble, France
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University & Research, 6708 PB Wageningen, the Netherlands
| | - Aalt D J van Dijk
- Bioinformatics Group, Wageningen University & Research, 6708 PB Wageningen, the Netherlands
| | - Gerco C Angenent
- Laboratory of Molecular Biology, Wageningen University & Research, 6708 PB Wageningen, the Netherlands
- Business Unit Bioscience, Wageningen University & Research, 6708 PB Wageningen, the Netherlands
| | - Richard G H Immink
- Laboratory of Molecular Biology, Wageningen University & Research, 6708 PB Wageningen, the Netherlands
- Business Unit Bioscience, Wageningen University & Research, 6708 PB Wageningen, the Netherlands
| | - Chloe Zubieta
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, Université Grenoble Alpes, INRAE, IRIG, CEA, 38000 Grenoble, Grenoble, France
| | - Marian Bemer
- Business Unit Bioscience, Wageningen University & Research, 6708 PB Wageningen, the Netherlands
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11
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Zamorano-Curaqueo M, Valenzuela-Riffo F, Herrera R, Moya-León MA. Characterization of FchAGL9 and FchSHP, two MADS-boxes related to softening of Fragaria chiloensis fruit. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 215:108985. [PMID: 39084168 DOI: 10.1016/j.plaphy.2024.108985] [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: 05/06/2024] [Revised: 07/25/2024] [Accepted: 07/28/2024] [Indexed: 08/02/2024]
Abstract
Fragaria chiloensis is a Chilean native species that softens intensively during its ripening. Its softening is related to cell wall disassembly due to the participation of cell wall degrading enzymes. Softening of F. chiloensis fruit can be accelerated by ABA treatment which is accompanied by the increment in the expression of key cell wall degrading genes, however the molecular machinery involved in the transcriptional regulation has not been studied until now. Therefore, the participation of two MADS-box transcription factors belonging to different subfamilies, FchAGL9 and FchSHP, was addressed. Both TFs are members of type-II MADS-box family (MIKC-type) and localized in the nucleus. FchAGL9 and FchSHP are expressed only in flower and fruit tissues, rising as the fruit softens with the highest expression level at C3-C4 stages. EMSA assays demonstrated that FchAGL9 binds to CArG sequences of RIN and SQM, meanwhile FchSHP interacts only with RIN. Bimolecular fluorescence complementation and yeast two-hybrid assays confirmed FchAGL9-FchAGL9 and FchAGL9-FchSHP interactions. Hetero-dimer structure was built through homology modeling concluding that FchSHP monomer binds to DNA. Functional validation by Luciferase-dual assays indicated that FchAGL9 transactivates FchRGL and FchPG's promoters, meanwhile FchSHP transactivates those of FchEXP2, FchRGL and FchPG. Over-expression of FchAGL9 in C2 F. chiloensis fruit rises FchEXP2 and FchEXP5 transcripts, meanwhile the over-expression of FchSHP also increments FchXTH1 and FchPL; in both cases there is a down-regulation of FchRGL and FchPG. In summary, we provided evidence of FchAGL9 and FchSHP participating in the transcription regulation associated to F. chiloensis's softening.
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Affiliation(s)
- Macarena Zamorano-Curaqueo
- Laboratorio de Fisiología Vegetal y Genética Molecular, Instituto de Ciencias Biológicas, Universidad de Talca, Avenida Lircay s/n, Talca, Chile
| | - Felipe Valenzuela-Riffo
- Laboratorio de Fisiología Vegetal y Genética Molecular, Instituto de Ciencias Biológicas, Universidad de Talca, Avenida Lircay s/n, Talca, Chile
| | - Raúl Herrera
- Laboratorio de Fisiología Vegetal y Genética Molecular, Instituto de Ciencias Biológicas, Universidad de Talca, Avenida Lircay s/n, Talca, Chile
| | - María A Moya-León
- Laboratorio de Fisiología Vegetal y Genética Molecular, Instituto de Ciencias Biológicas, Universidad de Talca, Avenida Lircay s/n, Talca, Chile.
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12
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Hugouvieux V, Blanc-Mathieu R, Janeau A, Paul M, Lucas J, Xu X, Ye H, Lai X, Le Hir S, Guillotin A, Galien A, Yan W, Nanao M, Kaufmann K, Parcy F, Zubieta C. SEPALLATA-driven MADS transcription factor tetramerization is required for inner whorl floral organ development. THE PLANT CELL 2024; 36:3435-3450. [PMID: 38771250 PMCID: PMC11371193 DOI: 10.1093/plcell/koae151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 04/10/2024] [Accepted: 04/20/2024] [Indexed: 05/22/2024]
Abstract
MADS transcription factors are master regulators of plant reproduction and flower development. The SEPALLATA (SEP) subfamily of MADS transcription factors is required for the development of floral organs and plays roles in inflorescence architecture and development of the floral meristem. SEPALLATAs act as organizers of MADS complexes, forming both heterodimers and heterotetramers in vitro. To date, the MADS complexes characterized in angiosperm floral organ development contain at least 1 SEPALLATA protein. Whether DNA binding by SEPALLATA-containing dimeric MADS complexes is sufficient for launching floral organ identity programs, however, is not clear as only defects in floral meristem determinacy were observed in tetramerization-impaired SEPALLATA mutant proteins. Here, we used a combination of genome-wide-binding studies, high-resolution structural studies of the SEP3/AGAMOUS (AG) tetramerization domain, structure-based mutagenesis and complementation experiments in Arabidopsis (Arabidopsis thaliana) sep1 sep2 sep3 and sep1 sep2 sep3 ag-4 plants transformed with versions of SEP3 encoding tetramerization mutants. We demonstrate that while SEP3 heterodimers can bind DNA both in vitro and in vivo and recognize the majority of SEP3 wild-type-binding sites genome-wide, tetramerization is required not only for floral meristem determinacy but also for floral organ identity in the second, third, and fourth whorls.
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Affiliation(s)
- Veronique Hugouvieux
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble-Alpes, CNRS, CEA, INRAE, IRIG-DBSCI, 17 rue des Martyrs, 38000 Grenoble, France
| | - Romain Blanc-Mathieu
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble-Alpes, CNRS, CEA, INRAE, IRIG-DBSCI, 17 rue des Martyrs, 38000 Grenoble, France
| | - Aline Janeau
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble-Alpes, CNRS, CEA, INRAE, IRIG-DBSCI, 17 rue des Martyrs, 38000 Grenoble, France
| | - Michel Paul
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble-Alpes, CNRS, CEA, INRAE, IRIG-DBSCI, 17 rue des Martyrs, 38000 Grenoble, France
| | - Jeremy Lucas
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble-Alpes, CNRS, CEA, INRAE, IRIG-DBSCI, 17 rue des Martyrs, 38000 Grenoble, France
| | - Xiaocai Xu
- Plant Cell and Molecular Biology, Institute of Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Hailong Ye
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuelei Lai
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Sarah Le Hir
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble-Alpes, CNRS, CEA, INRAE, IRIG-DBSCI, 17 rue des Martyrs, 38000 Grenoble, France
| | - Audrey Guillotin
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble-Alpes, CNRS, CEA, INRAE, IRIG-DBSCI, 17 rue des Martyrs, 38000 Grenoble, France
| | - Antonin Galien
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble-Alpes, CNRS, CEA, INRAE, IRIG-DBSCI, 17 rue des Martyrs, 38000 Grenoble, France
| | - Wenhao Yan
- Plant Cell and Molecular Biology, Institute of Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Max Nanao
- Structural Biology Group, European Synchrotron Radiation Facility, 38000 Grenoble, France
| | - Kerstin Kaufmann
- Plant Cell and Molecular Biology, Institute of Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - François Parcy
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble-Alpes, CNRS, CEA, INRAE, IRIG-DBSCI, 17 rue des Martyrs, 38000 Grenoble, France
| | - Chloe Zubieta
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble-Alpes, CNRS, CEA, INRAE, IRIG-DBSCI, 17 rue des Martyrs, 38000 Grenoble, France
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13
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Yu Y, Chu X, Ma X, Hu Z, Wang M, Li J, Yin H. Genome-Wide Analysis of MADS-Box Gene Family Reveals CjSTK as a Key Regulator of Seed Abortion in Camellia japonica. Int J Mol Sci 2024; 25:5770. [PMID: 38891958 PMCID: PMC11171818 DOI: 10.3390/ijms25115770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/20/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024] Open
Abstract
The plant MADS-box transcription factor family is a major regulator of plant flower development and reproduction, and the AGAMOUS-LIKE11/SEEDSTICK (AGL11/STK) subfamily plays conserved functions in the seed development of flowering plants. Camellia japonica is a world-famous ornamental flower, and its seed kernels are rich in highly valuable fatty acids. Seed abortion has been found to be common in C. japonica, but little is known about how it is regulated during seed development. In this study, we performed a genome-wide analysis of the MADS-box gene the in C. japonica genome and identified 126 MADS-box genes. Through gene expression profiling in various tissue types, we revealed the C/D-class MADS-box genes were preferentially expressed in seed-related tissues. We identified the AGL11/STK-like gene, CjSTK, and showed that it contained a typical STK motif and exclusively expressed during seed development. We found a significant increase in the CjSTK expression level in aborted seeds compared with normally developing seeds. Furthermore, overexpression of CjSTK in Arabidopsis thaliana caused shorter pods and smaller seeds. Taken together, we concluded that the fine regulation of the CjSTK expression at different stages of seed development is critical for ovule formation and seed abortion in C. japonica. The present study provides evidence revealing the regulation of seed development in Camellia.
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Affiliation(s)
- Yifan Yu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (Y.Y.); (X.C.); (X.M.); (Z.H.); (M.W.); (J.L.)
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, China
| | - Xian Chu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (Y.Y.); (X.C.); (X.M.); (Z.H.); (M.W.); (J.L.)
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, China
| | - Xianjin Ma
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (Y.Y.); (X.C.); (X.M.); (Z.H.); (M.W.); (J.L.)
| | - Zhikang Hu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (Y.Y.); (X.C.); (X.M.); (Z.H.); (M.W.); (J.L.)
| | - Minyan Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (Y.Y.); (X.C.); (X.M.); (Z.H.); (M.W.); (J.L.)
| | - Jiyuan Li
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (Y.Y.); (X.C.); (X.M.); (Z.H.); (M.W.); (J.L.)
| | - Hengfu Yin
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (Y.Y.); (X.C.); (X.M.); (Z.H.); (M.W.); (J.L.)
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14
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Bowman JL, Moyroud E. Reflections on the ABC model of flower development. THE PLANT CELL 2024; 36:1334-1357. [PMID: 38345422 PMCID: PMC11062442 DOI: 10.1093/plcell/koae044] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 02/07/2024] [Indexed: 05/02/2024]
Abstract
The formulation of the ABC model by a handful of pioneer plant developmental geneticists was a seminal event in the quest to answer a seemingly simple question: how are flowers formed? Fast forward 30 years and this elegant model has generated a vibrant and diverse community, capturing the imagination of developmental and evolutionary biologists, structuralists, biochemists and molecular biologists alike. Together they have managed to solve many floral mysteries, uncovering the regulatory processes that generate the characteristic spatio-temporal expression patterns of floral homeotic genes, elucidating some of the mechanisms allowing ABC genes to specify distinct organ identities, revealing how evolution tinkers with the ABC to generate morphological diversity, and even shining a light on the origins of the floral gene regulatory network itself. Here we retrace the history of the ABC model, from its genesis to its current form, highlighting specific milestones along the way before drawing attention to some of the unsolved riddles still hidden in the floral alphabet.
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Affiliation(s)
- John L Bowman
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Melbourne, VIC 3800, Australia
| | - Edwige Moyroud
- The Sainsbury Laboratory, Cambridge University, Cambridge CB2 1LR, UK
- Department of Genetics, University of Cambridge, Cambridge CB2 3EJ, UK
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15
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Poulet A, Zhao M, Peng Y, Tham F, Jaudal M, Zhang L, van Wolfswinkel JC, Putterill J. Gene-edited Mtsoc1 triple mutant Medicago plants do not flower. FRONTIERS IN PLANT SCIENCE 2024; 15:1357924. [PMID: 38469328 PMCID: PMC10926907 DOI: 10.3389/fpls.2024.1357924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 02/02/2024] [Indexed: 03/13/2024]
Abstract
Optimized flowering time is an important trait that ensures successful plant adaptation and crop productivity. SOC1-like genes encode MADS transcription factors, which are known to play important roles in flowering control in many plants. This includes the best-characterized eudicot model Arabidopsis thaliana (Arabidopsis), where SOC1 promotes flowering and functions as a floral integrator gene integrating signals from different flowering-time regulatory pathways. Medicago truncatula (Medicago) is a temperate reference legume with strong genomic and genetic resources used to study flowering pathways in legumes. Interestingly, despite responding to similar floral-inductive cues of extended cold (vernalization) followed by warm long days (VLD), such as in winter annual Arabidopsis, Medicago lacks FLC and CO which are key regulators of flowering in Arabidopsis. Unlike Arabidopsis with one SOC1 gene, multiple gene duplication events have given rise to three MtSOC1 paralogs within the Medicago genus in legumes: one Fabaceae group A SOC1 gene, MtSOC1a, and two tandemly repeated Fabaceae group B SOC1 genes, MtSOC1b and MtSOC1c. Previously, we showed that MtSOC1a has unique functions in floral promotion in Medicago. The Mtsoc1a Tnt1 retroelement insertion single mutant showed moderately delayed flowering in long- and short-day photoperiods, with and without prior vernalization, compared to the wild-type. In contrast, Mtsoc1b Tnt1 single mutants did not have altered flowering time or flower development, indicating that it was redundant in an otherwise wild-type background. Here, we describe the generation of Mtsoc1a Mtsoc1b Mtsoc1c triple mutant lines using CRISPR-Cas9 gene editing. We studied two independent triple mutant lines that segregated plants that did not flower and were bushy under floral inductive VLD. Genotyping indicated that these non-flowering plants were homozygous for the predicted strong mutant alleles of the three MtSOC1 genes. Gene expression analyses using RNA-seq and RT-qPCR indicated that these plants remained vegetative. Overall, the non-flowering triple mutants were dramatically different from the single Mtsoc1a mutant and the Arabidopsis soc1 mutant; implicating multiple MtSOC1 genes in critical overlapping roles in the transition to flowering in Medicago.
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Affiliation(s)
- Axel Poulet
- Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, CT, United States
| | - Min Zhao
- Flowering Lab, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Yongyan Peng
- Flowering Lab, School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Mt Albert Research Centre, The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - FangFei Tham
- Flowering Lab, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Mauren Jaudal
- Flowering Lab, School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Mt Albert Research Centre, The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Lulu Zhang
- Flowering Lab, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Josien C. van Wolfswinkel
- Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, CT, United States
| | - Joanna Putterill
- Flowering Lab, School of Biological Sciences, University of Auckland, Auckland, New Zealand
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16
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Hutin S, Wigge PA, Zubieta C. In Vitro Determination of Temperature-Dependent DNA Binding of the Evening Complex Using Electrophoretic Mobility Shift Assays. Methods Mol Biol 2024; 2795:135-147. [PMID: 38594535 DOI: 10.1007/978-1-0716-3814-9_14] [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] [Indexed: 04/11/2024]
Abstract
Electrophoretic mobility shift assays (EMSAs) of DNA-binding proteins and labeled DNA allow the qualitative and quantitative characterization of protein-DNA complex formation using native (nondenaturing) polyacrylamide or agarose gel electrophoresis. By varying the incubation temperature of the protein-DNA binding reaction and maintaining this temperature during electrophoresis, temperature-dependent protein-DNA interactions can be investigated. Here, we provide examples of the binding of a transcriptional repressor complex called the Evening Complex, comprising the DNA-binding protein LUX ARRYTHMO (LUX), the scaffold protein EARLY FLOWERING 3 (ELF3), and the adapter protein ELF4, to its cognate DNA and demonstrate direct detection and visualization of thermoresponsive binding in vitro. As negative controls we use the LUX DNA-binding domain and LUX full length protein, which do not exhibit temperature-dependent DNA binding.
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Affiliation(s)
- Stephanie Hutin
- Laboratoire Physiologie Cellulaire et Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI, Grenoble, France
| | - Philip A Wigge
- Leibniz-Institut für Gemüse- und Zierpflanzenbau, Großbeeren, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Chloe Zubieta
- Laboratoire Physiologie Cellulaire et Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI, Grenoble, France.
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17
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Blanc-Mathieu R, Dumas R, Turchi L, Lucas J, Parcy F. Plant-TFClass: a structural classification for plant transcription factors. TRENDS IN PLANT SCIENCE 2024; 29:40-51. [PMID: 37482504 DOI: 10.1016/j.tplants.2023.06.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/25/2023]
Abstract
Transcription factors (TFs) bind DNA at specific sequences to regulate gene expression. This universal process is achieved via their DNA-binding domain (DBD). In mammals, the vast diversity of DBD structural conformations and the way in which they contact DNA has been used to organize TFs in the TFClass hierarchical classification. However, the numerous DBD types present in plants but absent from mammalian genomes were missing from this classification. We reviewed DBD 3D structures and models available for plant TFs to classify most of the 56 recognized plant TF types within the TFClass framework. This extended classification adds eight new classes and 37 new families corresponding to DBD structures absent in mammals. Plant-TFClass provides a unique resource for TF comparison across families and organisms.
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Affiliation(s)
- Romain Blanc-Mathieu
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 Avenue des Martyrs, F-38054, Grenoble, France
| | - Renaud Dumas
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 Avenue des Martyrs, F-38054, Grenoble, France
| | - Laura Turchi
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 Avenue des Martyrs, F-38054, Grenoble, France
| | - Jérémy Lucas
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 Avenue des Martyrs, F-38054, Grenoble, France
| | - François Parcy
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 Avenue des Martyrs, F-38054, Grenoble, France.
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18
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Qiu Y, Li Z, Walther D, Köhler C. Updated Phylogeny and Protein Structure Predictions Revise the Hypothesis on the Origin of MADS-box Transcription Factors in Land Plants. Mol Biol Evol 2023; 40:msad194. [PMID: 37652031 PMCID: PMC10484287 DOI: 10.1093/molbev/msad194] [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: 07/10/2023] [Revised: 08/16/2023] [Accepted: 08/25/2023] [Indexed: 09/02/2023] Open
Abstract
MADS-box transcription factors (TFs), among the first TFs extensively studied, exhibit a wide distribution across eukaryotes and play diverse functional roles. Varying by domain architecture, MADS-box TFs in land plants are categorized into Type I (M-type) and Type II (MIKC-type). Type I and II genes have been considered orthologous to the SRF and MEF2 genes in animals, respectively, presumably originating from a duplication before the divergence of eukaryotes. Here, we exploited the increasing availability of eukaryotic MADS-box sequences and reassessed their evolution. While supporting the ancient duplication giving rise to SRF- and MEF2-types, we found that Type I and II genes originated from the MEF2-type genes through another duplication in the most recent common ancestor (MRCA) of land plants. Protein structures predicted by AlphaFold2 and OmegaFold support our phylogenetic analyses, with plant Type I and II TFs resembling the MEF2-type structure, rather than SRFs. We hypothesize that the ancestral SRF-type TFs were lost in the MRCA of Archaeplastida (the kingdom Plantae sensu lato). The retained MEF2-type TFs acquired a Keratin-like domain and became MIKC-type before the divergence of Streptophyta. Subsequently in the MRCA of land plants, M-type TFs evolved from a duplicated MIKC-type precursor through loss of the Keratin-like domain, leading to the Type I clade. Both Type I and II TFs expanded and functionally differentiated in concert with the increasing complexity of land plant body architecture. The recruitment of these originally stress-responsive TFs into developmental programs, including those underlying reproduction, may have facilitated the adaptation to the terrestrial environment.
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Affiliation(s)
- Yichun Qiu
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- Swedish University of Agricultural Sciences & Linnean Center for Plant Biology, Uppsala BioCenter, Uppsala, Sweden
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Dirk Walther
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Claudia Köhler
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- Swedish University of Agricultural Sciences & Linnean Center for Plant Biology, Uppsala BioCenter, Uppsala, Sweden
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19
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Lin Y, Qi X, Wan Y, Chen Z, Fang H, Liang C. Genome-wide analysis of the MADS-box gene family in Lonicera japonica and a proposed floral organ identity model. BMC Genomics 2023; 24:447. [PMID: 37553575 PMCID: PMC10408238 DOI: 10.1186/s12864-023-09509-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 07/08/2023] [Indexed: 08/10/2023] Open
Abstract
BACKGROUND Lonicera japonica Thunb. is widely used in traditional Chinese medicine. Medicinal L. japonica mainly consists of dried flower buds and partially opened flowers, thus flowers are an important quality indicator. MADS-box genes encode transcription factors that regulate flower development. However, little is known about these genes in L. japonica. RESULTS In this study, 48 MADS-box genes were identified in L. japonica, including 20 Type-I genes (8 Mα, 2 Mβ, and 10 Mγ) and 28 Type-II genes (26 MIKCc and 2 MIKC*). The Type-I and Type-II genes differed significantly in gene structure, conserved domains, protein structure, chromosomal distribution, phylogenesis, and expression pattern. Type-I genes had a simpler gene structure, lacked the K domain, had low protein structure conservation, were tandemly distributed on the chromosomes, had more frequent lineage-specific duplications, and were expressed at low levels. In contrast, Type-II genes had a more complex gene structure; contained conserved M, I, K, and C domains; had highly conserved protein structure; and were expressed at high levels throughout the flowering period. Eleven floral homeotic MADS-box genes that are orthologous to the proposed Arabidopsis ABCDE model of floral organ identity determination, were identified in L. japonica. By integrating expression pattern and protein interaction data for these genes, we developed a possible model for floral organ identity determination. CONCLUSION This study genome-widely identified and characterized the MADS-box gene family in L. japonica. Eleven floral homeotic MADS-box genes were identified and a possible model for floral organ identity determination was also developed. This study contributes to our understanding of the MADS-box gene family and its possible involvement in floral organ development in L. japonica.
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Affiliation(s)
- Yi Lin
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Nanjing, 210014, Jiangsu Province, China
- Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Xiwu Qi
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Nanjing, 210014, Jiangsu Province, China
| | - Yan Wan
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Nanjing, 210014, Jiangsu Province, China
- Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Zequn Chen
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Nanjing, 210014, Jiangsu Province, China
| | - Hailing Fang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Nanjing, 210014, Jiangsu Province, China
| | - Chengyuan Liang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Nanjing, 210014, Jiangsu Province, China.
- Nanjing University of Chinese Medicine, Nanjing, 210023, China.
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20
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Yang H, Zhang P, Guo D, Wang N, Lin H, Wang X, Niu L. Transcriptional repressor AGL79 positively regulates flowering time in Arabidopsis. JOURNAL OF PLANT PHYSIOLOGY 2023; 285:153985. [PMID: 37148653 DOI: 10.1016/j.jplph.2023.153985] [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: 02/17/2023] [Revised: 04/16/2023] [Accepted: 04/18/2023] [Indexed: 05/08/2023]
Abstract
The MADS-box gene family is widely distributed in higher plants and the members of the angiosperm-specific APETALA1/FRUITFULL (AP1/FUL) subfamily plays important roles in the regulation of plant reproductive development. Recent studies revealed that the AP1/FUL subfamily member Dt2, VEGETATIVE1/PsFRUITFULc (VEG1/PsFULc) and MtFRUITFULc (MtFULc) are essential for the stem growth, branching and inflorescence development in legume species soybean (Glycine max), pea (Pisum sativum) and Medicago truncatula. However, the biological function of their homologue in Arabidopsis thaliana, AGAMOUS-LIKE 79 (AGL79), has not been well elucidated. In this study, we investigated the developmental roles of Arabidopsis AGL79 by CRISPR/Cas9-mutagenesis and molecular and physiological analyses. We found that AGL79 mainly acts as a transcriptional repressor and positively regulates Arabidopsis flowering time. We further revealed that AGL79 interacts with SUPPRESSOR OF OVEREXPRESSION OF CO1 (SOC1) and represses the expression of TERMINAL FLOWER 1 (TFL1). Our results demonstrated the AGL79-mediated flowering regulation in Arabidopsis and added an additional layer of complexity to the understanding of flowering time regulation in dicot plants.
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Affiliation(s)
- Haibo Yang
- College of Life Sciences, Shanxi Agriculture University, Taigu, 030801, China; Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Pengcheng Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Diandian Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Na Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hao Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xingchun Wang
- College of Life Sciences, Shanxi Agriculture University, Taigu, 030801, China.
| | - Lifang Niu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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21
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Xia H, Lin Z, He Z, Guo Y, Liu X, Deng H, Li M, Xie Y, Zhang M, Wang J, Lv X, Deng Q, Luo X, Tang Y, Lin L, Liang D. AcMADS32 positively regulates carotenoid biosynthesis in kiwifruit by activating AcBCH1/2 expression. Int J Biol Macromol 2023; 242:124928. [PMID: 37224896 DOI: 10.1016/j.ijbiomac.2023.124928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 04/28/2023] [Accepted: 05/06/2023] [Indexed: 05/26/2023]
Abstract
Fruits provide abundant carotenoid nutrients for humans, whereas the understanding of the transcriptional regulatory mechanisms of carotenoids in fruits is still limited. Here, we identified a transcription factor AcMADS32 in kiwifruit, which was highly expressed in the fruit, correlated with carotenoid content and localized in the nucleus. The silencing expression of AcMADS32 significantly reduced the content of β-carotene and zeaxanthin and expression of β-carotene hydroxylase gene AcBCH1/2 in kiwifruit, while transient overexpression increased the accumulation of zeaxanthin, suggesting that AcMADS32 was an activator involved in the transcriptional regulation of carotenoid in fruit. When AcMADS32 was further stably transformed into kiwifruit, the content of total carotenoid and components in the leaves of transgenic lines significantly increased, and the expression level of carotenogenic genes was up-regulated. Moreover, Y1H and dual luciferase reporter experiments confirmed that AcMADS32 directly bound the AcBCH1/2 promoter and activated its expression. Through Y2H assays, AcMADS32 can interact with other MADS transcription factor AcMADS30, AcMADS64 and AcMADS70. These findings will contribute to our understanding of the transcriptional regulation mechanisms underlying carotenoid biosynthesis in plants.
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Affiliation(s)
- Hui Xia
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhiyi Lin
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Zunzhen He
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Yuqi Guo
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Xinling Liu
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Honghong Deng
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Minzhang Li
- Sichuan Provincial Academy of Natural Resources Sciences, Chengdu 610015, China
| | - Yue Xie
- Sichuan Provincial Academy of Natural Resources Sciences, Chengdu 610015, China
| | - Mingfei Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Jin Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiulan Lv
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Qunxian Deng
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Xian Luo
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Yi Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Lijin Lin
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Dong Liang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China.
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22
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Käppel S, Rümpler F, Theißen G. Cracking the Floral Quartet Code: How Do Multimers of MIKC C-Type MADS-Domain Transcription Factors Recognize Their Target Genes? Int J Mol Sci 2023; 24:8253. [PMID: 37175955 PMCID: PMC10178880 DOI: 10.3390/ijms24098253] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/28/2023] [Accepted: 05/01/2023] [Indexed: 05/15/2023] Open
Abstract
MADS-domain transcription factors (MTFs) are involved in the control of many important processes in eukaryotes. They are defined by the presence of a unique and highly conserved DNA-binding domain, the MADS domain. MTFs bind to double-stranded DNA as dimers and recognize specific sequences termed CArG boxes (such as 5'-CC(A/T)6GG-3') and similar sequences that occur hundreds of thousands of times in a typical flowering plant genome. The number of MTF-encoding genes increased by around two orders of magnitude during land plant evolution, resulting in roughly 100 genes in flowering plant genomes. This raises the question as to how dozens of different but highly similar MTFs accurately recognize the cis-regulatory elements of diverse target genes when the core binding sequence (CArG box) occurs at such a high frequency. Besides the usual processes, such as the base and shape readout of individual DNA sequences by dimers of MTFs, an important sublineage of MTFs in plants, termed MIKCC-type MTFs (MC-MTFs), has evolved an additional mechanism to increase the accurate recognition of target genes: the formation of heterotetramers of closely related proteins that bind to two CArG boxes on the same DNA strand involving DNA looping. MC-MTFs control important developmental processes in flowering plants, ranging from root and shoot to flower, fruit and seed development. The way in which MC-MTFs bind to DNA and select their target genes is hence not only of high biological interest, but also of great agronomic and economic importance. In this article, we review the interplay of the different mechanisms of target gene recognition, from the ordinary (base readout) via the extravagant (shape readout) to the idiosyncratic (recognition of the distance and orientation of two CArG boxes by heterotetramers of MC-MTFs). A special focus of our review is on the structural prerequisites of MC-MTFs that enable the specific recognition of target genes.
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Affiliation(s)
| | | | - Günter Theißen
- Matthias Schleiden Institute/Genetics, Friedrich Schiller University Jena, 07743 Jena, Germany; (S.K.); (F.R.)
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23
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Goslin K, Finocchio A, Wellmer F. Floral Homeotic Factors: A Question of Specificity. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12051128. [PMID: 36903987 PMCID: PMC10004826 DOI: 10.3390/plants12051128] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/23/2023] [Accepted: 02/25/2023] [Indexed: 05/27/2023]
Abstract
MADS-domain transcription factors are involved in the control of a multitude of processes in eukaryotes, and in plants, they play particularly important roles during reproductive development. Among the members of this large family of regulatory proteins are the floral organ identity factors, which specify the identities of the different types of floral organs in a combinatorial manner. Much has been learned over the past three decades about the function of these master regulators. For example, it has been shown that they have similar DNA-binding activities and that their genome-wide binding patterns exhibit large overlaps. At the same time, it appears that only a minority of binding events lead to changes in gene expression and that the different floral organ identity factors have distinct sets of target genes. Thus, binding of these transcription factors to the promoters of target genes alone may not be sufficient for their regulation. How these master regulators achieve specificity in a developmental context is currently not well understood. Here, we review what is known about their activities and highlight open questions that need to be addressed to gain more detailed insights into the molecular mechanisms underlying their functions. We discuss evidence for the involvement of cofactors as well as the results from studies on transcription factors in animals that may be instructive for a better understanding of how the floral organ identity factors achieve regulatory specificity.
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24
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van Mourik H, Chen P, Smaczniak C, Boeren S, Kaufmann K, Bemer M, Angenent GC, Muino JM. Dual specificity and target gene selection by the MADS-domain protein FRUITFULL. NATURE PLANTS 2023; 9:473-485. [PMID: 36797351 DOI: 10.1038/s41477-023-01351-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 01/11/2023] [Indexed: 05/18/2023]
Abstract
How transcription factors attain their target gene specificity and how this specificity may be modulated, acquiring different regulatory functions through the development of plant tissues, is an open question. Here we characterized different regulatory roles of the MADS-domain transcription factor FRUITFULL (FUL) in flower development and mechanisms modulating its activity. We found that the dual role of FUL in regulating floral transition and pistil development is associated with its different in vivo patterns of DNA binding in both tissues. Characterization of FUL protein complexes by liquid chromatography-tandem mass spectrometry and SELEX-seq experiments shows that aspects of tissue-specific target site selection can be predicted by tissue-specific variation in the composition of FUL protein complexes with different DNA binding specificities, without considering the chromatin status of the target region. This suggests a role for dynamic changes in FUL TF complex composition in reshaping the regulatory functions of FUL during flower development.
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Affiliation(s)
- Hilda van Mourik
- Laboratory of Molecular Biology, Wageningen University & Research, Wageningen, the Netherlands
| | - Peilin Chen
- Plant Cell and Molecular Biology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Cezary Smaczniak
- Plant Cell and Molecular Biology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, the Netherlands
| | - Kerstin Kaufmann
- Plant Cell and Molecular Biology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Marian Bemer
- Laboratory of Molecular Biology, Wageningen University & Research, Wageningen, the Netherlands
- Department of Bioscience, Wageningen University & Research, Wageningen, the Netherlands
| | - Gerco C Angenent
- Laboratory of Molecular Biology, Wageningen University & Research, Wageningen, the Netherlands
- Department of Bioscience, Wageningen University & Research, Wageningen, the Netherlands
| | - Jose M Muino
- Plant Cell and Molecular Biology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany.
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Strejčková B, Mazzucotelli E, Čegan R, Milec Z, Brus J, Çakır E, Mastrangelo AM, Özkan H, Šafář J. Wild emmer wheat, the progenitor of modern bread wheat, exhibits great diversity in the VERNALIZATION1 gene. FRONTIERS IN PLANT SCIENCE 2023; 13:1106164. [PMID: 36684759 PMCID: PMC9853909 DOI: 10.3389/fpls.2022.1106164] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
Wild emmer wheat is an excellent reservoir of genetic variability that can be utilized to improve cultivated wheat to address the challenges of the expanding world population and climate change. Bearing this in mind, we have collected a panel of 263 wild emmer wheat (WEW) genotypes across the Fertile Crescent. The genotypes were grown in different locations and phenotyped for heading date. Genome-wide association mapping (GWAS) was carried out, and 16 SNPs were associated with the heading date. As the flowering time is controlled by photoperiod and vernalization, we sequenced the VRN1 gene, the most important of the vernalization response genes, to discover new alleles. Unlike most earlier attempts, which characterized known VRN1 alleles according to a partial promoter or intron sequences, we obtained full-length sequences of VRN-A1 and VRN-B1 genes in a panel of 95 wild emmer wheat from the Fertile Crescent and uncovered a significant sequence variation. Phylogenetic analysis of VRN-A1 and VRN-B1 haplotypes revealed their evolutionary relationships and geographic distribution in the Fertile Crescent region. The newly described alleles represent an attractive resource for durum and bread wheat improvement programs.
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Affiliation(s)
- Beáta Strejčková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University Olomouc, Olomouc, Czechia
| | - Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics (CREA) Research Centre for Genomics and Bioinformatics via San Protaso 302, Fiorenzuola d’Arda, Italy
| | - Radim Čegan
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, ;Czechia
| | - Zbyněk Milec
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Jan Brus
- Department of Geoinformatics, Faculty of Science, Palacký University Olomouc, Olomouc, Czechia
| | - Esra Çakır
- Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana, Turkey
| | - Anna Maria Mastrangelo
- Council for Agricultural Research and Economics (CREA) Research Centre for Cereal and Industrial Crops, Foggia, Italy
| | - Hakan Özkan
- Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana, Turkey
| | - Jan Šafář
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
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26
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Chahtane H, Lai X, Tichtinsky G, Rieu P, Arnoux-Courseaux M, Cancé C, Marondedze C, Parcy F. Flower Development in Arabidopsis. Methods Mol Biol 2023; 2686:3-38. [PMID: 37540352 DOI: 10.1007/978-1-0716-3299-4_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Like in other angiosperms, the development of flowers in Arabidopsis starts right after the floral transition, when the shoot apical meristem (SAM) stops producing leaves and makes flowers instead. On the flanks of the SAM emerge the flower meristems (FM) that will soon differentiate into the four main floral organs, sepals, petals, stamens, and pistil, stereotypically arranged in concentric whorls. Each phase of flower development-floral transition, floral bud initiation, and floral organ development-is under the control of specific gene networks. In this chapter, we describe these different phases and the gene regulatory networks involved, from the floral transition to the floral termination.
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Affiliation(s)
- Hicham Chahtane
- CNRS, Université Grenoble Alpes, CEA, INRAE, IRIG, BIG-LPCV, Grenoble, France
- Institut de Recherche Pierre Fabre, Green Mission Pierre Fabre, Conservatoire Botanique Pierre Fabre, Soual, France
| | - Xuelei Lai
- CNRS, Université Grenoble Alpes, CEA, INRAE, IRIG, BIG-LPCV, Grenoble, France
- Huazhong Agricultural University, National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Wuhan, China
| | | | - Philippe Rieu
- CNRS, Université Grenoble Alpes, CEA, INRAE, IRIG, BIG-LPCV, Grenoble, France
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | | | - Coralie Cancé
- CNRS, Université Grenoble Alpes, CEA, INRAE, IRIG, BIG-LPCV, Grenoble, France
| | - Claudius Marondedze
- CNRS, Université Grenoble Alpes, CEA, INRAE, IRIG, BIG-LPCV, Grenoble, France
- Department of Biochemistry, Faculty of Medicine, Midlands State University, Senga, Gweru, Zimbabwe
| | - François Parcy
- CNRS, Université Grenoble Alpes, CEA, INRAE, IRIG, BIG-LPCV, Grenoble, France.
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Hutin S, Blanc-Mathieu R, Rieu P, Parcy F, Lai X, Zubieta C. Identification of Plant Transcription Factor DNA-Binding Sites Using seq-DAP-seq. Methods Mol Biol 2023; 2698:119-145. [PMID: 37682473 DOI: 10.1007/978-1-0716-3354-0_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
The identification of genome-wide transcription factor binding sites (TFBS) is a critical step in deciphering gene and transcriptional regulatory networks. However, determining the genome-wide binding of specific TFs or TF complexes remains a technical challenge. DNA affinity purification sequencing (DAP-seq) and modifications such as sequential DAP-seq (seq-DAP-seq) are robust in vitro methods for mapping individual TF or TF complex binding sites in a genome-wide manner. DAP-seq protocols use a genomic DNA (gDNA) library from any target organism with or without amplification, allowing the determination of TF binding on naked or endogenously modified DNA, respectively. As a first step, the gDNA is fragmented to ~200 bp, end-repaired, and sequencing adaptors are added. This gDNA library can be used directly or an amplification step may be performed to remove DNA modifications such as cytosine methylation. DNA libraries are then incubated with an affinity-tagged TF or TF- complex immobilized on magnetic beads. The TF or TF complex of interest is generally produced using recombinant protein expression and purified prior to DNA affinity purification. After incubation of the DNA library with the immobilized TF of interest, multiple wash steps are performed to reduce non-specific DNA binding and the TF-DNA complexes eluted. The eluted DNA is PCR-amplified and sequenced using next-generation sequencing. The resulting sequence reads are mapped to the corresponding reference genome, identifying direct potential bound regions and binding sites of the TF or TF complex of interest. Predictive TFBS models are generated from the bound regions using downstream bioinformatics analysis pipelines. Here, we present a detailed protocol outlining the steps required for seq-DAP-seq of a heterooligomeric TF complex (Fig. 1) and briefly describe the downstream bioinformatics pipeline used to develop a robust TFBS model from sequencing data generated from a DAP-seq experiment.
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Affiliation(s)
- Stephanie Hutin
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, Université Grenoble Alpes, INRAE, IRIG, CEA Grenoble, Grenoble, France
| | - Romain Blanc-Mathieu
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, Université Grenoble Alpes, INRAE, IRIG, CEA Grenoble, Grenoble, France
| | - Philippe Rieu
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, Université Grenoble Alpes, INRAE, IRIG, CEA Grenoble, Grenoble, France
| | - François Parcy
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, Université Grenoble Alpes, INRAE, IRIG, CEA Grenoble, Grenoble, France
| | - Xuelei Lai
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, Université Grenoble Alpes, INRAE, IRIG, CEA Grenoble, Grenoble, France
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Chloe Zubieta
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, Université Grenoble Alpes, INRAE, IRIG, CEA Grenoble, Grenoble, France.
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28
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Liao L, Li Y, Bi X, Xiong B, Wang X, Deng H, Zhang M, Sun G, Jin Z, Huang Z, Wang Z. Transcriptome analysis of Harumi tangor fruits: Insights into interstock-mediated fruit quality. FRONTIERS IN PLANT SCIENCE 2022; 13:995913. [PMID: 36311145 PMCID: PMC9608513 DOI: 10.3389/fpls.2022.995913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 09/30/2022] [Indexed: 05/27/2023]
Abstract
Harumi tangor fruit with Ponkan as an interstock contains significantly higher levels of total soluble solids compared to Harumi tangor fruit cv.with no interstock. Transcriptome analysis of two graft combinations (Harumi/Hongjv (HP) and cv. cv.Harumi/Ponkan/Hongjv (HPP)) was conducted to identify the genes related to use of the Ponkan interstock. Soluble sugars and organic acids were also measured in the two graft combinations. The results showed that the contents of sucrose, glucose, and fructose were higher in the fruits of HPP than in those of HP; additionally, the titratable acid levels were lower in grafts with interstocks than in grafts without interstocks. Transcriptome analysis of HPP and HP citrus revealed that the interstock regulated auxin and ethylene signals, sugar and energy metabolism, and cell wall metabolism. Trend and Venn analyses suggested that genes related to carbohydrate-, energy-, and hormone-metabolic activities were more abundant in HPP plants than in HP plants during different periods. Moreover, weighted gene co-expression network analysis demonstrated that carbohydrates, hormones, cell wall, and transcription factors may be critical for interstock-mediated citrus fruit development and ripening. The contents of ethylene, auxin, cytokinin, transcription factors, starch, sucrose, glucose, fructose, and total sugar in HPP plants differed considerably than those in HP fruits. Interstocks may help to regulate the early ripening and quality of citrus fruit through the above-mentioned pathways. These findings provide information on the effects of interstock on plant growth and development.
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Affiliation(s)
- Ling Liao
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Yunjie Li
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Xiaoyi Bi
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Bo Xiong
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Xun Wang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Honghong Deng
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Mingfei Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Guochao Sun
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Zhenghua Jin
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Zehao Huang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Zhihui Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
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29
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Heisler MG, Jönsson H, Wenkel S, Kaufmann K. Context-specific functions of transcription factors controlling plant development: From leaves to flowers. CURRENT OPINION IN PLANT BIOLOGY 2022; 69:102262. [PMID: 35952407 DOI: 10.1016/j.pbi.2022.102262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 06/14/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Plant development is regulated by transcription factors that often act in more than one process and stage of development. Yet the molecular mechanisms that govern the functional diversity and specificity of these proteins remains far from understood. Flower development provides an ideal context to study these mechanisms since the development of distinct floral organs depends on similar but distinct combinations of transcriptional regulators. Recent work also highlights the importance of leaf polarity regulators as additional key factors in flower initiation, floral organ morphogenesis, and possibly floral organ positioning. A detailed understanding of how these factors work in combination will enable us to address outstanding questions in flower development including how distinct shapes and positions of floral organs are generated. Experimental approaches and computer-based modeling will be required to characterize gene-regulatory networks at the level of single cells.
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Affiliation(s)
- Marcus G Heisler
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Henrik Jönsson
- Sainsbury Laboratory, University of Cambridge, UK; Department of Applied Mathematics and Theoretical Physics, University of Cambridge, UK; Computational Biology and Biological Physics, Lund University, Sweden
| | - Stephan Wenkel
- Department of Plant & Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Kerstin Kaufmann
- Humboldt-Universität zu Berlin, Institute of Biology, Philippstr. 13, 10115, Berlin, Germany.
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30
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Lavrekha VV, Levitsky VG, Tsukanov AV, Bogomolov AG, Grigorovich DA, Omelyanchuk N, Ubogoeva EV, Zemlyanskaya EV, Mironova V. CisCross: A gene list enrichment analysis to predict upstream regulators in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2022; 13:942710. [PMID: 36061801 PMCID: PMC9434332 DOI: 10.3389/fpls.2022.942710] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
Having DNA-binding profiles for a sufficient number of genome-encoded transcription factors (TFs) opens up the perspectives for systematic evaluation of the upstream regulators for the gene lists. Plant Cistrome database, a large collection of TF binding profiles detected using the DAP-seq method, made it possible for Arabidopsis. Here we re-processed raw DAP-seq data with MACS2, the most popular peak caller that leads among other ones according to quality metrics. In the benchmarking study, we confirmed that the improved collection of TF binding profiles supported a more precise gene list enrichment procedure, and resulted in a more relevant ranking of potential upstream regulators. Moreover, we consistently recovered the TF binding profiles that were missing in the previous collection of DAP-seq peak sets. We developed the CisCross web service (https://plamorph.sysbio.ru/ciscross/) that gives more flexibility in the analysis of potential upstream TF regulators for Arabidopsis thaliana genes.
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Affiliation(s)
- Viktoriya V. Lavrekha
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Victor G. Levitsky
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Anton V. Tsukanov
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Anton G. Bogomolov
- Department of Cell Biology, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Dmitry A. Grigorovich
- Service of Information Technologies, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Nadya Omelyanchuk
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Elena V. Ubogoeva
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Elena V. Zemlyanskaya
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Victoria Mironova
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Department of Plant Systems Physiology, RIBES, Radboud University, Nijmegen, Netherlands
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31
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Lee YK, Kumari S, Olson A, Hauser F, Ware D. Role of a ZF-HD Transcription Factor in miR157-Mediated Feed-Forward Regulatory Module That Determines Plant Architecture in Arabidopsis. Int J Mol Sci 2022; 23:ijms23158665. [PMID: 35955798 PMCID: PMC9369202 DOI: 10.3390/ijms23158665] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/27/2022] [Accepted: 07/28/2022] [Indexed: 02/05/2023] Open
Abstract
In plants, vegetative and reproductive development are associated with agronomically important traits that contribute to grain yield and biomass. Zinc finger homeodomain (ZF-HD) transcription factors (TFs) constitute a relatively small gene family that has been studied in several model plants, including Arabidopsis thaliana L. and Oryza sativa L. The ZF-HD family members play important roles in plant growth and development, but their contribution to the regulation of plant architecture remains largely unknown due to their functional redundancy. To understand the gene regulatory network controlled by ZF-HD TFs, we analyzed multiple loss-of-function mutants of ZF-HD TFs in Arabidopsis that exhibited morphological abnormalities in branching and flowering architecture. We found that ZF-HD TFs, especially HB34, negatively regulate the expression of miR157 and positively regulate SQUAMOSA PROMOTER BINDING-LIKE 10 (SPL10), a target of miR157. Genome-wide chromatin immunoprecipitation sequencing (ChIP-Seq) analysis revealed that miR157D and SPL10 are direct targets of HB34, creating a feed-forward loop that constitutes a robust miRNA regulatory module. Network motif analysis contains overrepresented coherent type IV feedforward motifs in the amiR zf-HD and hbq mutant background. This finding indicates that miRNA-mediated ZF-HD feedforward modules modify branching and inflorescence architecture in Arabidopsis. Taken together, these findings reveal a guiding role of ZF-HD TFs in the regulatory network module and demonstrate its role in plant architecture in Arabidopsis.
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Affiliation(s)
- Young Koung Lee
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
- Institute of Plasma Technology, Korea Institute of Fusion Energy, 37, Dongjangsan-ro, Gunsan-si 54004, Korea
- Correspondence: (Y.K.L.); (D.W.)
| | - Sunita Kumari
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Andrew Olson
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Felix Hauser
- Division of Biological Sciences, University of California–San Diego, La Jolla, CA 92093, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
- USDA-ARS, Robert W. Holley Center, Ithaca, NY 14853, USA
- Correspondence: (Y.K.L.); (D.W.)
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32
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Hajheidari M, Huang SSC. Elucidating the biology of transcription factor-DNA interaction for accurate identification of cis-regulatory elements. CURRENT OPINION IN PLANT BIOLOGY 2022; 68:102232. [PMID: 35679803 PMCID: PMC10103634 DOI: 10.1016/j.pbi.2022.102232] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/26/2022] [Accepted: 05/02/2022] [Indexed: 05/03/2023]
Abstract
Transcription factors (TFs) play a critical role in determining cell fate decisions by integrating developmental and environmental signals through binding to specific cis-regulatory modules and regulating spatio-temporal specificity of gene expression patterns. Precise identification of functional TF binding sites in time and space not only will revolutionize our understanding of regulatory networks governing cell fate decisions but is also instrumental to uncover how genetic variations cause morphological diversity or disease. In this review, we discuss recent advances in mapping TF binding sites and characterizing the various parameters underlying the complexity of binding site recognition by TFs.
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Affiliation(s)
- Mohsen Hajheidari
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Pl, New York, NY 10003, USA
| | - Shao-Shan Carol Huang
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Pl, New York, NY 10003, USA.
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Li C, Lei C, Wang K, Tan M, Xu F, Wang J, Zheng Y. MADS2 regulates priming defence in postharvest peach through combined salicylic acid and abscisic acid signaling. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3787-3806. [PMID: 35266534 DOI: 10.1093/jxb/erac099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
MADS-box genes play well-documented roles in plant development, but relatively little is known regarding their involvement in defence responses. In this study, pre-treatment of peach (Prunus persica) fruit with β-aminobutyric acid (BABA) activated resistance against Rhizopus stolonifer, leading to a significant delay in the symptomatic appearance of disease. This was associated with an integrated defence response that included a H2O2 burst, ABA accumulation, and callose deposition. cDNA library screening identified nucleus-localized MADS2 as an interacting partner with NPR1, and this was further confirmed by yeast two-hybrid, luciferase complementation imaging, and co-immunoprecipitation assays. The DNA-binding activity of NPR1 conferred by the NPR1-MADS2 complex was required for the transcription of SA-dependent pathogenesis-related (PR) and ABA-inducible CalS genes in order to gain the BABA-induced resistance, in which MAPK1-induced post-translational modification of MADS2 was also involved. In accordance with this, overexpression of PpMADS2 in Arabidopsis potentiated the transcription of a group of PR genes and conferred fungal resistance in the transgenic plants. Conversely, Arabidopsis mads2-knockout lines showed high sensitivity to the fungal pathogen. Our results indicate that MADS2 positively participates in BABA-elicited defence in peach through a combination of SA-dependent NPR1 activation and ABA signaling-induced callose accumulation, and that this defence is also related to the post-translational modification of MADS2 by MAPK1 for signal amplification.
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Affiliation(s)
- Chunhong Li
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095 Jiangsu, P.R. China
- College of Biology and Food Science, Chongqing Three Gorges University, Chongqing 404000, P.R. China
| | - Changyi Lei
- College of Biology and Food Science, Chongqing Three Gorges University, Chongqing 404000, P.R. China
| | - Kaituo Wang
- College of Biology and Food Science, Chongqing Three Gorges University, Chongqing 404000, P.R. China
| | - Meilin Tan
- College of Biology and Food Science, Chongqing Three Gorges University, Chongqing 404000, P.R. China
| | - Feng Xu
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315211, P.R. China
| | - Jinsong Wang
- College of Biology and Food Science, Chongqing Three Gorges University, Chongqing 404000, P.R. China
| | - Yonghua Zheng
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095 Jiangsu, P.R. China
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Li X, Cai K, Pei X, Li Y, Hu Y, Meng F, Song X, Tigabu M, Ding C, Zhao X. Genome-Wide Identification of NAC Transcription Factor Family in Juglans mandshurica and Their Expression Analysis during the Fruit Development and Ripening. Int J Mol Sci 2021; 22:ijms222212414. [PMID: 34830294 PMCID: PMC8625062 DOI: 10.3390/ijms222212414] [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: 10/12/2021] [Revised: 11/03/2021] [Accepted: 11/15/2021] [Indexed: 12/17/2022] Open
Abstract
The NAC (NAM, ATAF and CUC) gene family plays a crucial role in the transcriptional regulation of various biological processes and has been identified and characterized in multiple plant species. However, genome-wide identification of this gene family has not been implemented in Juglans mandshurica, and specific functions of these genes in the development of fruits remain unknown. In this study, we performed genome-wide identification and functional analysis of the NAC gene family during fruit development and identified a total of 114 JmNAC genes in the J. mandshurica genome. Chromosomal location analysis revealed that JmNAC genes were unevenly distributed in 16 chromosomes; the highest numbers were found in chromosomes 2 and 4. Furthermore, according to the homologues of JmNAC genes in Arabidopsis thaliana, a phylogenetic tree was constructed, and the results demonstrated 114 JmNAC genes, which were divided into eight subgroups. Four JmNAC gene pairs were identified as the result of tandem duplicates. Tissue-specific analysis of JmNAC genes during different developmental stages revealed that 39 and 25 JmNAC genes exhibited upregulation during the mature stage in walnut exocarp and embryos, indicating that they may serve key functions in fruit development. Furthermore, 12 upregulated JmNAC genes were common in fruit ripening stage in walnut exocarp and embryos, which demonstrated that these genes were positively correlated with fruit development in J. mandshurica. This study provides new insights into the regulatory functions of JmNAC genes during fruit development in J. mandshurica, thereby improving the understanding of characteristics and evolution of the JmNAC gene family.
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Affiliation(s)
- Xiang Li
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China; (X.L.); (K.C.); (Y.L.); (Y.H.); (F.M.); (X.S.)
| | - Kewei Cai
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China; (X.L.); (K.C.); (Y.L.); (Y.H.); (F.M.); (X.S.)
| | - Xiaona Pei
- College of Forestry and Grassland, Jilin Agricultural University, Changchun 130118, China;
| | - Yan Li
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China; (X.L.); (K.C.); (Y.L.); (Y.H.); (F.M.); (X.S.)
| | - Yanbo Hu
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China; (X.L.); (K.C.); (Y.L.); (Y.H.); (F.M.); (X.S.)
| | - Fanjuan Meng
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China; (X.L.); (K.C.); (Y.L.); (Y.H.); (F.M.); (X.S.)
| | - Xingshun Song
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China; (X.L.); (K.C.); (Y.L.); (Y.H.); (F.M.); (X.S.)
| | - Mulualem Tigabu
- Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, 230 53 Alnarp, Sweden;
| | - Changjun Ding
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Correspondence: (C.D.); (X.Z.); Tel.: +86-15246668860 (X.Z.)
| | - Xiyang Zhao
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China; (X.L.); (K.C.); (Y.L.); (Y.H.); (F.M.); (X.S.)
- College of Forestry and Grassland, Jilin Agricultural University, Changchun 130118, China;
- Correspondence: (C.D.); (X.Z.); Tel.: +86-15246668860 (X.Z.)
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