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Bowman JL, Moyroud E. Reflections on the ABC model of flower development. Plant Cell 2024; 36:1334-1357. [PMID: 38345422 PMCID: PMC11062442 DOI: 10.1093/plcell/koae044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Wu C, Cai D, Li J, Lin Z, Wei W, Shan W, Chen J, Lu W, Su X, Kuang J. Banana MabHLH28 positively regulates the expression of softening-related genes to mediate fruit ripening independently or via cooperating with MaWRKY49/111. Hortic Res 2024; 11:uhae053. [PMID: 38706579 PMCID: PMC11069428 DOI: 10.1093/hr/uhae053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 02/17/2024] [Indexed: 05/07/2024]
Abstract
Texture softening is a physiological indicator of fruit ripening, which eventually contributes to fruit quality and the consumer's acceptance. Despite great progress having been made in identification of the genes related to fruit softening, the upstream transcriptional regulatory pathways of these softening-related genes are not fully elucidated. Here, a novel bHLH gene, designated as MabHLH28, was identified because of its significant upregulation in banana fruit ripening. DAP-Seq analysis revealed that MabHLH28 bound to the core sequence of 'CAYGTG' presented in promoter regions of fruit softening-associated genes, such as the genes related to cell wall modification (MaPG3, MaPE1, MaPL5, MaPL8, MaEXP1, MaEXP2, MaEXPA2, and MaEXPA15) and starch degradation (MaGWD1 and MaLSF2), and these bindings were validated by EMSA and DLR assays. Transient overexpression and knockdown of MabHLH28 in banana fruit resulted in up- and down-regulation of softening-related genes, thereby hastening and postponing fruit ripening. Furthermore, overexpression of MabHLH28 in tomato accelerated the ripening process by elevating the accumulation of softening-associated genes. In addition, MabHLH28 showed interaction withMaWRKY49/111 and itself to form protein complexes, which could combinatorically strengthen the transcription of softening-associated genes. Taken together, our findings suggest that MabHLH28 mediates fruit softening by upregulating the expression of softening-related genes either alone or in combination with MaWRKY49/111.
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Affiliation(s)
- Chaojie Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Danling Cai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Jun Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Zengxiang Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Wei Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Wei Shan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Jianye Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Wangjin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Xinguo Su
- Agronomy Dean, Guangdong AIB Polytechnic College, Guangzhou 510507, China
| | - Jianfei Kuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
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Zhao X, Li Y, Zhang MM, He X, Ahmad S, Lan S, Liu ZJ. Research advances on the gene regulation of floral development and color in orchids. Gene 2023; 888:147751. [PMID: 37657689 DOI: 10.1016/j.gene.2023.147751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/08/2023] [Accepted: 08/30/2023] [Indexed: 09/03/2023]
Abstract
Orchidaceae is one of the largest monocotyledon families and contributes significantly to worldwide biodiversity, with value in the fields of landscaping, medicine, and ecology. The diverse phenotypes and vibrant colors of orchid floral organs make them excellent research objects for investigating flower development and pigmentation. In recent years, a number of orchid genomes have been published, laying the molecular foundation for revealing flower development and color presentation. In this article, we review transcription factors, the structural genes responsible for the floral pigment synthesis pathways, the molecular mechanisms of flower morphogenesis, and the potential relationship between flower type and flower color. This study provides a theoretical reference for the research on molecular mechanisms related to flower morphogenesis and color presentation, genetic improvement, and new variety creation in orchids.
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Affiliation(s)
- Xuewei Zhao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuanyuan Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Meng-Meng Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xin He
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Sagheer Ahmad
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Siren Lan
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Zhong-Jian Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Suhaimi AH, Kobayashi MJ, Satake A, Ng CC, Lee SL, Muhammad N, Numata S, Otani T, Kondo T, Tani N, Yeoh SH. An ecological transcriptome approach to capture the molecular and physiological mechanisms of mass flowering in Shorea curtisii. PeerJ 2023; 11:e16368. [PMID: 38047035 PMCID: PMC10693236 DOI: 10.7717/peerj.16368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 10/08/2023] [Indexed: 12/05/2023] Open
Abstract
Climatic factors have commonly been attributed as the trigger of general flowering, a unique community-level mass flowering phenomenon involving most dipterocarp species that forms the foundation of Southeast Asian tropical rainforests. This intriguing flowering event is often succeeded by mast fruiting, which provides a temporary yet substantial burst of food resources for animals, particularly frugivores. However, the physiological mechanism that triggers general flowering, particularly in dipterocarp species, is not well understood largely due to its irregular and unpredictable occurrences in the tall and dense forests. To shed light on this mechanism, we employed ecological transcriptomic analyses on an RNA-seq dataset of a general flowering species, Shorea curtisii (Dipterocarpaceae), sequenced from leaves and buds collected at multiple vegetative and flowering phenological stages. We assembled 64,219 unigenes from the transcriptome of which 1,730 and 3,559 were differentially expressed in the leaf and the bud, respectively. Differentially expressed unigene clusters were found to be enriched with homologs of Arabidopsis thaliana genes associated with response to biotic and abiotic stresses, nutrient level, and hormonal treatments. When combined with rainfall data, our transcriptome data reveals that the trees were responding to a brief period of drought prior to the elevated expression of key floral promoters and followed by differential expression of unigenes that indicates physiological changes associated with the transition from vegetative to reproductive stages. Our study is timely for a representative general flowering dipterocarp species that occurs in forests that are under the constant threat of deforestation and climate change as it pinpoints important climate sensitive and flowering-related homologs and offers a glimpse into the cascade of gene expression before and after the onset of floral initiation.
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Affiliation(s)
- Ahmad Husaini Suhaimi
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Masaki J. Kobayashi
- Forestry Division, Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki, Japan
| | - Akiko Satake
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka, Japan
| | - Ching Ching Ng
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Soon Leong Lee
- Forestry Biotechnology Division, Forest Research Institute Malaysia, Selangor, Malaysia
| | - Norwati Muhammad
- Forestry Biotechnology Division, Forest Research Institute Malaysia, Selangor, Malaysia
| | - Shinya Numata
- Department of Tourism Science, Tokyo Metropolitan University, Tokyo, Japan
| | - Tatsuya Otani
- Shikoku Research Center, Forestry Research and Management Organization, Kochi, Japan
| | - Toshiaki Kondo
- Bio-Resources and Utilization Division, Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki, Japan
| | - Naoki Tani
- Forestry Division, Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Suat Hui Yeoh
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
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Wen C, Yuan Z, Zhang X, Chen H, Luo L, Li W, Li T, Ma N, Mao F, Lin D, Lin Z, Lin C, Xu T, Lü P, Lin J, Zhu F. Sea-ATI unravels novel vocabularies of plant active cistrome. Nucleic Acids Res 2023; 51:11568-11583. [PMID: 37850650 PMCID: PMC10681729 DOI: 10.1093/nar/gkad853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 08/11/2023] [Accepted: 09/25/2023] [Indexed: 10/19/2023] Open
Abstract
The cistrome consists of all cis-acting regulatory elements recognized by transcription factors (TFs). However, only a portion of the cistrome is active for TF binding in a specific tissue. Resolving the active cistrome in plants remains challenging. In this study, we report the assay sequential extraction assisted-active TF identification (sea-ATI), a low-input method that profiles the DNA sequences recognized by TFs in a target tissue. We applied sea-ATI to seven plant tissues to survey their active cistrome and generated 41 motif models, including 15 new models that represent previously unidentified cis-regulatory vocabularies. ATAC-seq and RNA-seq analyses confirmed the functionality of the cis-elements from the new models, in that they are actively bound in vivo, located near the transcription start site, and influence chromatin accessibility and transcription. Furthermore, comparing dimeric WRKY CREs between sea-ATI and DAP-seq libraries revealed that thermodynamics and genetic drifts cooperatively shaped their evolution. Notably, sea-ATI can identify not only positive but also negative regulatory cis-elements, thereby providing unique insights into the functional non-coding genome of plants.
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Affiliation(s)
- Chenjin Wen
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Zhen Yuan
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Xiaotian Zhang
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Hao Chen
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Lin Luo
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Wanying Li
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Tian Li
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Nana Ma
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Fei Mao
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Dongmei Lin
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Zhanxi Lin
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Chentao Lin
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Tongda Xu
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Peitao Lü
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Juncheng Lin
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Fangjie Zhu
- College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
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Zumajo-Cardona C, Gabrieli F, Anire J, Albertini E, Ezquer I, Colombo L. Evolutionary studies of the bHLH transcription factors belonging to MBW complex: their role in seed development. Ann Bot 2023; 132:383-400. [PMID: 37467144 PMCID: PMC10667011 DOI: 10.1093/aob/mcad097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 07/17/2023] [Indexed: 07/21/2023]
Abstract
BACKGROUND AND AIMS The MBW complex consist of proteins belonging to three major families (MYB, bHLH and WDR) involved in various processes throughout plant development: epidermal cell development, mucilage secretory cells and flavonoid biosynthesis. Recently, it has been reported that TT8, encoding a bHLH transcription factor, is involved in the biosynthesis of flavonoids in the seed coat and it also plays a role in bypassing the postzygotic barrier resulting from an unbalance in genetic loads of the parental lines. Here, we focus on the functional evolution, in seed development, of the bHLH proteins that are part of the MBW complex, complemented with a literature review. METHODS Phylogenetic analyses performed across seed plants and expression analyses in the reproductive tissues of four selected angiosperms (Arabidopsis thaliana, Brassica napus, Capsella rubella and Solanum lycopersicum) allow us to hypothesize on the evolution of its functions. KEY RESULTS TT8 expression in the innermost layer of the seed coat is conserved in the selected angiosperms. However, except for Arabidopsis, TT8 is also expressed in ovules, carpels and fruits. The homologues belonging to the sister clade of TT8, EGL3/GL3, involved in trichome development, are expressed in the outermost layer of the seed coat, suggesting potential roles in mucilage. CONCLUSIONS The ancestral function of these genes appears to be flavonoid biosynthesis, and the conservation of TT8 expression patterns in the innermost layer of the seed coat in angiosperms suggests that their function in postzygotic barriers might also be conserved. Moreover, the literature review and the results of the present study suggest a sophisticated association, linking the mechanisms of action of these genes to the cross-communication activity between the different tissues of the seed. Thus, it provides avenues to study the mechanisms of action of TT8 in the postzygotic triploid block, which is crucial because it impacts seed development in unbalanced crosses.
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Affiliation(s)
- Cecilia Zumajo-Cardona
- Department of BioScience, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Flavio Gabrieli
- Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno 74, Perugia, Italy
- Dipartimento di Ingegneria Industriale DII, University of Padua, via Gradenigo, 6/a, Padova, Italy
| | - Jovannemar Anire
- Department of BioScience, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
- Wageningen UR Plant Breeding, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
- National Coconut Research Center – Visayas, Visayas State University, Baybay City, Leyte, Philippines
| | - Emidio Albertini
- Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno 74, Perugia, Italy
| | - Ignacio Ezquer
- Department of BioScience, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Lucia Colombo
- Department of BioScience, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
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Saavedra Núñez G, González-Villanueva E, Ramos P. Floral Development on Vitis vinifera Is Associated with MADS-Box Transcription Factors through the Transcriptional Regulation of VviZIP3. Plants (Basel) 2023; 12:3322. [PMID: 37765487 PMCID: PMC10535425 DOI: 10.3390/plants12183322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/11/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023]
Abstract
Several grapevine (Vitis vinifera L.) cultivars show a tendency to develop parthenocarpic seedless grapes, affecting fruit yield and quality. This reproductive disorder originates in defective ovule fertilization due to a failure in pollen tube growth. Zinc (Zn) is a crucial trace element, playing a vital role in various physiological and metabolic processes. It is particularly essential for the healthy growth of flowers and fruits. Insufficient zinc has been suggested as a potential reason for issues in this development process. This microelement is taken up through a mechanism that involves transporters, including the ZRT-IRT-like protein (ZIP) gene family, associated with the influx of Zn into the cell. In grapevines, 20 genes for ZIP-type transporters have been described. In this study, we analyzed the expression pattern of VviZIP3 during flower development and employ transgenic methods to assess its transcriptional regulation. Furthermore, through computational examination of the promoter region, we identified two CArG boxes, recognized as responsive elements to MADS transcription factors. These factors play a key role in shaping various components of a flower, such as pollen. Our investigation of the VviZIP3 promoter confirms the functionality of these CArG boxes. Overall, our results suggest that the increased expression of VviZIP3 during flowering is likely under the influence of MADS transcription factors.
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Affiliation(s)
- Germán Saavedra Núñez
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca 3460787, Chile; (G.S.N.); (E.G.-V.)
| | | | - Patricio Ramos
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca 3460787, Chile; (G.S.N.); (E.G.-V.)
- Vicerrectoría de Investigación y Postgrado, Universidad Católica del Maule, Talca 3480112, Chile
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Zahn IE, Roelofsen C, Angenent GC, Bemer M. TM3 and STM3 Promote Flowering Together with FUL2 and MBP20, but Act Antagonistically in Inflorescence Branching in Tomato. Plants (Basel) 2023; 12:2754. [PMID: 37570908 PMCID: PMC10420972 DOI: 10.3390/plants12152754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 08/13/2023]
Abstract
The moment at which a plant transitions to reproductive development is paramount to its life cycle and is strictly controlled by many genes. The transcription factor SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) plays a central role in this process in Arabidopsis. However, the role of SOC1 in tomato (Solanum lycopersicum) has been sparsely studied. Here, we investigated the function of four tomato SOC1 homologs in the floral transition and inflorescence development. We thoroughly characterized the SOC1-like clade throughout the Solanaceae and selected four tomato homologs that are dynamically expressed upon the floral transition. We show that of these homologs, TOMATO MADS 3 (TM3) and SISTER OF TM3 (STM3) promote the primary and sympodial transition to flowering, while MADS-BOX PROTEIN 23 (MBP23) and MBP18 hardly contribute to flowering initiation in the indeterminate cultivar Moneyberg. Protein-protein interaction assays and whole-transcriptome analysis during reproductive meristem development revealed that TM3 and STM3 interact and share many targets with FRUITFULL (FUL) homologs, including cytokinin regulators. Furthermore, we observed that mutating TM3/STM3 affects inflorescence development, but counteracts the inflorescence-branching phenotype of ful2 mbp20. Collectively, this indicates that TM3/STM3 promote the floral transition together with FUL2/MBP20, while these transcription factors have opposite functions in inflorescence development.
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Affiliation(s)
- Iris E. Zahn
- Laboratory of Molecular Biology, Wageningen University & Research, 6708 PB Wageningen, The Netherlands; (I.E.Z.); (G.C.A.)
| | - Chris Roelofsen
- Laboratory of Molecular Biology, Wageningen University & Research, 6708 PB Wageningen, The Netherlands; (I.E.Z.); (G.C.A.)
| | - Gerco C. Angenent
- Laboratory of Molecular Biology, Wageningen University & Research, 6708 PB Wageningen, The Netherlands; (I.E.Z.); (G.C.A.)
- Business Unit Bioscience, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Marian Bemer
- Business Unit Bioscience, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
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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:ijms24098253. [PMID: 37175955 PMCID: PMC10178880 DOI: 10.3390/ijms24098253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [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)
- Sandra Käppel
- Matthias Schleiden Institute/Genetics, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Florian Rümpler
- Matthias Schleiden Institute/Genetics, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Günter Theißen
- Matthias Schleiden Institute/Genetics, Friedrich Schiller University Jena, 07743 Jena, Germany
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10
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Goslin K, Finocchio A, Wellmer F. Floral Homeotic Factors: A Question of Specificity. Plants (Basel) 2023; 12:plants12051128. [PMID: 36903987 PMCID: PMC10004826 DOI: 10.3390/plants12051128] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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11
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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. Nat Plants 2023; 9:473-485. [PMID: 36797351 DOI: 10.1038/s41477-023-01351-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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12
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Yasmeen E, Wang J, Riaz M, Zhang L, Zuo K. Designing artificial synthetic promoters for accurate, smart, and versatile gene expression in plants. Plant Commun 2023:100558. [PMID: 36760129 PMCID: PMC10363483 DOI: 10.1016/j.xplc.2023.100558] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
With the development of high-throughput biology techniques and artificial intelligence, it has become increasingly feasible to design and construct artificial biological parts, modules, circuits, and even whole systems. To overcome the limitations of native promoters in controlling gene expression, artificial promoter design aims to synthesize short, inducible, and conditionally controlled promoters to coordinate the expression of multiple genes in diverse plant metabolic and signaling pathways. Synthetic promoters are versatile and can drive gene expression accurately with smart responses; they show potential for enhancing desirable traits in crops, thereby improving crop yield, nutritional quality, and food security. This review first illustrates the importance of synthetic promoters, then introduces promoter architecture and thoroughly summarizes advances in synthetic promoter construction. Restrictions to the development of synthetic promoters and future applications of such promoters in synthetic plant biology and crop improvement are also discussed.
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Affiliation(s)
- Erum Yasmeen
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Muhammad Riaz
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lida Zhang
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Kaijing Zuo
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
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13
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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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14
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Chen P, Smaczniak C, Haffner J, Muino JM, Kaufmann K. Estimating DNA-Binding Specificities of Transcription Factors Using SELEX-Seq. Methods Mol Biol 2023; 2698:147-161. [PMID: 37682474 DOI: 10.1007/978-1-0716-3354-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Here we provide an updated protocol for the Systematic Evolution of Ligands followed by massively parallel sequencing (SELEX-seq) method to study protein-DNA interaction specificities. This in vitro method is used to characterize DNA-binding specificities of transcription factors (TFs). The procedure is based on cycles of immunoprecipitation of protein-DNA complexes, starting with a randomized DNA library of defined fragment length, followed by massively parallel sequencing. The updated protocol includes aspects of experimental design and procedure as well as basic instructions on data analysis.
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Affiliation(s)
- Peilin Chen
- Institute for Biology, Plant Cell and Molecular Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Cezary Smaczniak
- Institute for Biology, Plant Cell and Molecular Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Johanna Haffner
- Institute for Biology, Plant Cell and Molecular Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jose M Muino
- Institute for Biology, Plant Cell and Molecular Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Kerstin Kaufmann
- Institute for Biology, Plant Cell and Molecular Biology, Humboldt-Universität zu Berlin, Berlin, Germany.
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15
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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. Curr Opin Plant Biol 2022; 69:102262. [PMID: 35952407 DOI: 10.1016/j.pbi.2022.102262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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16
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Hajheidari M, Huang SSC. Elucidating the biology of transcription factor-DNA interaction for accurate identification of cis-regulatory elements. Curr Opin Plant Biol 2022; 68:102232. [PMID: 35679803 PMCID: PMC10103634 DOI: 10.1016/j.pbi.2022.102232] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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17
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da Silveira Falavigna V, Severing E, Lai X, Estevan J, Farrera I, Hugouvieux V, Revers LF, Zubieta C, Coupland G, Costes E, Andrés F. Unraveling the role of MADS transcription factor complexes in apple tree dormancy. New Phytol 2021; 232:2071-2088. [PMID: 34480759 PMCID: PMC9292984 DOI: 10.1111/nph.17710] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/19/2021] [Indexed: 05/27/2023]
Abstract
A group of MADS transcription factors (TFs) are believed to control temperature-mediated bud dormancy. These TFs, called DORMANCY-ASSOCIATED MADS-BOX (DAM), are encoded by genes similar to SHORT VEGETATIVE PHASE (SVP) from Arabidopsis. MADS proteins form transcriptional complexes whose combinatory composition defines their molecular function. However, how MADS multimeric complexes control the dormancy cycle in trees is unclear. Apple MdDAM and other dormancy-related MADS proteins form complexes with MdSVPa, which is essential for the ability of transcriptional complexes to bind to DNA. Sequential DNA-affinity purification sequencing (seq-DAP-seq) was performed to identify the genome-wide binding sites of apple MADS TF complexes. Target genes associated with the binding sites were identified by combining seq-DAP-seq data with transcriptomics datasets obtained using a glucocorticoid receptor fusion system, and RNA-seq data related to apple dormancy. We describe a gene regulatory network (GRN) formed by MdSVPa-containing complexes, which regulate the dormancy cycle in response to environmental cues and hormonal signaling pathways. Additionally, novel molecular evidence regarding the evolutionary functional segregation between DAM and SVP proteins in the Rosaceae is presented. MdSVPa sequentially forms complexes with the MADS TFs that predominate at each dormancy phase, altering its DNA-binding specificity and, therefore, the transcriptional regulation of its target genes.
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Affiliation(s)
- Vítor da Silveira Falavigna
- UMR AGAP InstitutUniv MontpellierCIRADINRAEInstitut AgroF‐34398MontpellierFrance
- Department of Plant Developmental BiologyMax Planck Institute for Plant Breeding Research50829CologneGermany
| | - Edouard Severing
- Department of Plant Developmental BiologyMax Planck Institute for Plant Breeding Research50829CologneGermany
| | - Xuelei Lai
- Laboratoire de Physiologie Cellulaire et VégétaleUniversité Grenoble‐AlpesCNRSCEAINRAEIRIG‐DBSCI38000GrenobleFrance
| | - Joan Estevan
- UMR AGAP InstitutUniv MontpellierCIRADINRAEInstitut AgroF‐34398MontpellierFrance
| | - Isabelle Farrera
- UMR AGAP InstitutUniv MontpellierCIRADINRAEInstitut AgroF‐34398MontpellierFrance
| | - Véronique Hugouvieux
- Laboratoire de Physiologie Cellulaire et VégétaleUniversité Grenoble‐AlpesCNRSCEAINRAEIRIG‐DBSCI38000GrenobleFrance
| | | | - Chloe Zubieta
- Laboratoire de Physiologie Cellulaire et VégétaleUniversité Grenoble‐AlpesCNRSCEAINRAEIRIG‐DBSCI38000GrenobleFrance
| | - George Coupland
- Department of Plant Developmental BiologyMax Planck Institute for Plant Breeding Research50829CologneGermany
| | - Evelyne Costes
- UMR AGAP InstitutUniv MontpellierCIRADINRAEInstitut AgroF‐34398MontpellierFrance
| | - Fernando Andrés
- UMR AGAP InstitutUniv MontpellierCIRADINRAEInstitut AgroF‐34398MontpellierFrance
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18
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Sunaga-Franze DY, Muino JM, Braeuning C, Xu X, Zong M, Smaczniak C, Yan W, Fischer C, Vidal R, Kliem M, Kaufmann K, Sauer S. Single-nucleus RNA sequencing of plant tissues using a nanowell-based system. Plant J 2021; 108:859-869. [PMID: 34390289 DOI: 10.1111/tpj.15458] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 07/16/2021] [Accepted: 08/02/2021] [Indexed: 05/25/2023]
Abstract
Single-cell genomics provides unprecedented potential for research on plant development and environmental responses. Here, we introduce a generic procedure for plant nucleus isolation combined with nanowell-based library preparation. Our method enables the transcriptome analysis of thousands of individual plant nuclei. It serves as an alternative to the use of protoplast isolation, which is currently a standard methodology for plant single-cell genomics, although it can be challenging for some plant tissues. We show the applicability of our nucleus isolation method by using different plant materials from different species. The potential of our single-nucleus RNA sequencing method is shown through the characterization of transcriptomes of seedlings and developing flowers from Arabidopsis thaliana. We evaluated the transcriptome dynamics during the early stages of anther development, identified stage-specific activities of transcription factors regulating this process, and predicted potential target genes of these transcription factors. Our nucleus isolation procedure can be applied in different plant species and tissues, thus expanding the toolkit for plant single-cell genomics experiments.
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Affiliation(s)
- Daniele Y Sunaga-Franze
- Genomics Platforms, Max Delbrück Center for Molecular Medicine in the Helmholtz Association/Berlin Institute of Health, Berlin, Germany
| | - Jose M Muino
- Systems Biology of Gene Regulation, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Caroline Braeuning
- Genomics Platforms, Max Delbrück Center for Molecular Medicine in the Helmholtz Association/Berlin Institute of Health, Berlin, Germany
| | - Xiaocai Xu
- Plant Cell and Molecular Biology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Minglei Zong
- 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
| | - Wenhao Yan
- Plant Cell and Molecular Biology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Cornelius Fischer
- Genomics Platforms, Max Delbrück Center for Molecular Medicine in the Helmholtz Association/Berlin Institute of Health, Berlin, Germany
| | - Ramon Vidal
- Genomics Platforms, Max Delbrück Center for Molecular Medicine in the Helmholtz Association/Berlin Institute of Health, Berlin, Germany
| | - Magdalena Kliem
- Genomics Platforms, Max Delbrück Center for Molecular Medicine in the Helmholtz Association/Berlin Institute of Health, Berlin, Germany
| | - Kerstin Kaufmann
- Plant Cell and Molecular Biology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sascha Sauer
- Genomics Platforms, Max Delbrück Center for Molecular Medicine in the Helmholtz Association/Berlin Institute of Health, Berlin, Germany
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19
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Sunaga-Franze DY, Muino JM, Braeuning C, Xu X, Zong M, Smaczniak C, Yan W, Fischer C, Vidal R, Kliem M, Kaufmann K, Sauer S. Single-nucleus RNA sequencing of plant tissues using a nanowell-based system. Plant J 2021; 108:859-869. [PMID: 34390289 DOI: 10.1101/2020.11.14.382812] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 07/16/2021] [Accepted: 08/02/2021] [Indexed: 05/22/2023]
Abstract
Single-cell genomics provides unprecedented potential for research on plant development and environmental responses. Here, we introduce a generic procedure for plant nucleus isolation combined with nanowell-based library preparation. Our method enables the transcriptome analysis of thousands of individual plant nuclei. It serves as an alternative to the use of protoplast isolation, which is currently a standard methodology for plant single-cell genomics, although it can be challenging for some plant tissues. We show the applicability of our nucleus isolation method by using different plant materials from different species. The potential of our single-nucleus RNA sequencing method is shown through the characterization of transcriptomes of seedlings and developing flowers from Arabidopsis thaliana. We evaluated the transcriptome dynamics during the early stages of anther development, identified stage-specific activities of transcription factors regulating this process, and predicted potential target genes of these transcription factors. Our nucleus isolation procedure can be applied in different plant species and tissues, thus expanding the toolkit for plant single-cell genomics experiments.
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Affiliation(s)
- Daniele Y Sunaga-Franze
- Genomics Platforms, Max Delbrück Center for Molecular Medicine in the Helmholtz Association/Berlin Institute of Health, Berlin, Germany
| | - Jose M Muino
- Systems Biology of Gene Regulation, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Caroline Braeuning
- Genomics Platforms, Max Delbrück Center for Molecular Medicine in the Helmholtz Association/Berlin Institute of Health, Berlin, Germany
| | - Xiaocai Xu
- Plant Cell and Molecular Biology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Minglei Zong
- 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
| | - Wenhao Yan
- Plant Cell and Molecular Biology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Cornelius Fischer
- Genomics Platforms, Max Delbrück Center for Molecular Medicine in the Helmholtz Association/Berlin Institute of Health, Berlin, Germany
| | - Ramon Vidal
- Genomics Platforms, Max Delbrück Center for Molecular Medicine in the Helmholtz Association/Berlin Institute of Health, Berlin, Germany
| | - Magdalena Kliem
- Genomics Platforms, Max Delbrück Center for Molecular Medicine in the Helmholtz Association/Berlin Institute of Health, Berlin, Germany
| | - Kerstin Kaufmann
- Plant Cell and Molecular Biology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sascha Sauer
- Genomics Platforms, Max Delbrück Center for Molecular Medicine in the Helmholtz Association/Berlin Institute of Health, Berlin, Germany
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20
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Lai X, Vega-Léon R, Hugouvieux V, Blanc-Mathieu R, van der Wal F, Lucas J, Silva CS, Jourdain A, Muino JM, Nanao MH, Immink R, Kaufmann K, Parcy F, Smaczniak C, Zubieta C. The intervening domain is required for DNA-binding and functional identity of plant MADS transcription factors. Nat Commun 2021; 12:4760. [PMID: 34362909 DOI: 10.1038/s41467-021-24978-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/14/2021] [Indexed: 02/06/2023] Open
Abstract
The MADS transcription factors (TF) are an ancient eukaryotic protein family. In plants, the family is divided into two main lineages. Here, we demonstrate that DNA binding in both lineages absolutely requires a short amino acid sequence C-terminal to the MADS domain (M domain) called the Intervening domain (I domain) that was previously defined only in type II lineage MADS. Structural elucidation of the MI domains from the floral regulator, SEPALLATA3 (SEP3), shows a conserved fold with the I domain acting to stabilise the M domain. Using the floral organ identity MADS TFs, SEP3, APETALA1 (AP1) and AGAMOUS (AG), domain swapping demonstrate that the I domain alters genome-wide DNA-binding specificity and dimerisation specificity. Introducing AG carrying the I domain of AP1 in the Arabidopsis ap1 mutant resulted in strong complementation and restoration of first and second whorl organs. Taken together, these data demonstrate that the I domain acts as an integral part of the DNA-binding domain and significantly contributes to the functional identity of the MADS TF. MADS transcription factors regulate multiple aspects of plant development. Here the authors show that the intervening I domain is conserved in both type I and type II plant MADS lineages and contributes to the functional identity of the protein by influencing both DNA binding activity and dimerisation specificity.
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21
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Górska AM, Gouveia P, Borba AR, Zimmermann A, Serra TS, Carvalho P, Lourenço TF, Oliveira MM, Peterhänsel C, Saibo NJM. ZmOrphan94 Transcription Factor Downregulates ZmPEPC1 Gene Expression in Maize Bundle Sheath Cells. Front Plant Sci 2021; 12:559967. [PMID: 33897718 PMCID: PMC8062929 DOI: 10.3389/fpls.2021.559967] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
Spatial separation of the photosynthetic reactions is a key feature of C4 metabolism. In most C4 plants, this separation requires compartmentation of photosynthetic enzymes between mesophyll (M) and bundle sheath (BS) cells. The upstream region of the gene encoding the maize PHOSPHOENOLPYRUVATE CARBOXYLASE 1 (ZmPEPC1) has been shown sufficient to drive M-specific ZmPEPC1 gene expression. Although this region has been well characterized, to date, only few trans-factors involved in the ZmPEPC1 gene regulation were identified. Here, using a yeast one-hybrid approach, we have identified three novel maize transcription factors ZmHB87, ZmCPP8, and ZmOrphan94 as binding to the ZmPEPC1 upstream region. Bimolecular fluorescence complementation assays in maize M protoplasts unveiled that ZmOrphan94 forms homodimers and interacts with ZmCPP8 and with two other ZmPEPC1 regulators previously reported, ZmbHLH80 and ZmbHLH90. Trans-activation assays in maize M protoplasts unveiled that ZmHB87 does not have a clear transcriptional activity, whereas ZmCPP8 and ZmOrphan94 act as activator and repressor, respectively. Moreover, we observed that ZmOrphan94 reduces the trans-activation activity of both activators ZmCPP8 and ZmbHLH90. Using the electromobility shift assay, we showed that ZmOrphan94 binds to several cis-elements present in the ZmPEPC1 upstream region and one of these cis-elements overlaps with the ZmbHLH90 binding site. Gene expression analysis revealed that ZmOrphan94 is preferentially expressed in the BS cells, suggesting that ZmOrphan94 is part of a transcriptional regulatory network downregulating ZmPEPC1 transcript level in the BS cells. Based on both this and our previous work, we propose a model underpinning the importance of a regulatory mechanism within BS cells that contributes to the M-specific ZmPEPC1 gene expression.
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Affiliation(s)
- Alicja M. Górska
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - Paulo Gouveia
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - Ana Rita Borba
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - Anna Zimmermann
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
- Institut für Botanik, Leibniz Universität Hannover, Hannover, Germany
| | - Tânia S. Serra
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - Pedro Carvalho
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Tiago F. Lourenço
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - M. Margarida Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | | | - Nelson J. M. Saibo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
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22
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Kivivirta KI, Herbert D, Roessner C, de Folter S, Marsch-Martinez N, Becker A. Transcriptome analysis of gynoecium morphogenesis uncovers the chronology of gene regulatory network activity. Plant Physiol 2021; 185:1076-1090. [PMID: 33793890 PMCID: PMC8133673 DOI: 10.1093/plphys/kiaa090] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 12/04/2020] [Indexed: 05/12/2023]
Abstract
The gynoecium is the most complex organ formed by the flowering plants. It encloses the ovules, provides a surface for pollen contact and self-incompatibility reactions, allows pollen tube growth, and, post fertilization, develops into the fruit. Consequently, the regulation of gynoecium morphogenesis is complex and appropriate timing of this process in part determines reproductive success. However, little is known about the global control of gynoecium development, even though many regulatory genes have been characterized. Here, we characterized dynamic gene expression changes using laser-microdissected gynoecium tissue from four developmental stages in Arabidopsis. We provide a high-resolution map of global expression dynamics during gynoecium morphogenesis and link these to the gynoecium interactome. We reveal groups of genes acting together early and others acting late in morphogenesis. Clustering of co-expressed genes enables comparisons between the leaf, shoot apex, and gynoecium transcriptomes, allowing the dissection of common and distinct regulators. Furthermore, our results lead to the discovery of genes with putative transcription factor activity (B3LF1, -2, DOFLF1), which, when mutated, lead to impaired gynoecium expansion, illustrating that global transcriptome analyses reveal yet unknown developmental regulators. Our data show that genes encoding highly interacting proteins, such as SEPALLATA3, AGAMOUS, and TOPLESS, are expressed evenly during development but switch interactors over time, whereas stage-specific proteins tend to have fewer interactors. Our analysis connects specific transcriptional regulator activities, protein interactions, and underlying metabolic processes, contributing toward a dynamic network model for gynoecium development.
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Affiliation(s)
- Kimmo I Kivivirta
- Plant Development Group, Institute of Botany, Justus-Liebig-University, Heinrich-Buff-Ring 38, 35392 Gießen, Germany
| | - Denise Herbert
- Plant Development Group, Institute of Botany, Justus-Liebig-University, Heinrich-Buff-Ring 38, 35392 Gießen, Germany
| | - Clemens Roessner
- Plant Development Group, Institute of Botany, Justus-Liebig-University, Heinrich-Buff-Ring 38, 35392 Gießen, Germany
| | - Stefan de Folter
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Unidad de Genómica Avanzada (UGA-LANGEBIO), CP 36824 Irapuato, Mexico
| | | | - Annette Becker
- Plant Development Group, Institute of Botany, Justus-Liebig-University, Heinrich-Buff-Ring 38, 35392 Gießen, Germany
- Author for communication:
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23
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De Clercq I, Van de Velde J, Luo X, Liu L, Storme V, Van Bel M, Pottie R, Vaneechoutte D, Van Breusegem F, Vandepoele K. Integrative inference of transcriptional networks in Arabidopsis yields novel ROS signalling regulators. Nat Plants 2021; 7:500-513. [PMID: 33846597 DOI: 10.1038/s41477-021-00894-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 03/04/2021] [Indexed: 05/12/2023]
Abstract
Gene regulation is a dynamic process in which transcription factors (TFs) play an important role in controlling spatiotemporal gene expression. To enhance our global understanding of regulatory interactions in Arabidopsis thaliana, different regulatory input networks capturing complementary information about DNA motifs, open chromatin, TF-binding and expression-based regulatory interactions were combined using a supervised learning approach, resulting in an integrated gene regulatory network (iGRN) covering 1,491 TFs and 31,393 target genes (1.7 million interactions). This iGRN outperforms the different input networks to predict known regulatory interactions and has a similar performance to recover functional interactions compared to state-of-the-art experimental methods. The iGRN correctly inferred known functions for 681 TFs and predicted new gene functions for hundreds of unknown TFs. For regulators predicted to be involved in reactive oxygen species (ROS) stress regulation, we confirmed in total 75% of TFs with a function in ROS and/or physiological stress responses. This includes 13 ROS regulators, previously not connected to any ROS or stress function, that were experimentally validated in our ROS-specific phenotypic assays of loss- or gain-of-function lines. In conclusion, the presented iGRN offers a high-quality starting point to enhance our understanding of gene regulation in plants by integrating different experimental data types.
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Affiliation(s)
- Inge De Clercq
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
| | - Jan Van de Velde
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Xiaopeng Luo
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Li Liu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Veronique Storme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Michiel Van Bel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Robin Pottie
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Dries Vaneechoutte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium.
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24
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Schreiber KJ, Hassan JA, Lewis JD. Arabidopsis Abscisic Acid Repressor 1 is a susceptibility hub that interacts with multiple Pseudomonas syringae effectors. Plant J 2021; 105:1274-1292. [PMID: 33289145 DOI: 10.1111/tpj.15110] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 06/12/2023]
Abstract
Pathogens secrete effector proteins into host cells to suppress host immunity and promote pathogen virulence, although many features at the molecular interface of host-pathogen interactions remain to be characterized. In a yeast two-hybrid assay, we found that the Pseudomonas syringae effector HopZ1a interacts with the Arabidopsis transcriptional regulator Abscisic Acid Repressor 1 (ABR1). Further analysis revealed that ABR1 interacts with multiple P. syringae effectors, suggesting that it may be targeted as a susceptibility hub. Indeed, loss-of-function abr1 mutants exhibit reduced susceptibility to a number of P. syringae strains. The ABR1 protein comprises a conserved APETALA2 (AP2) domain flanked by long regions of predicted structural disorder. We verified the DNA-binding activity of the AP2 domain and demonstrated that the disordered domains act redundantly to enhance DNA binding and to facilitate transcriptional activation by ABR1. Finally, we compared gene expression profiles from wild-type and abr1 plants following inoculation with P. syringae, which suggested that the reduced susceptibility of abr1 mutants is due to the loss of a virulence target rather than an enhanced immune response. These data highlight ABR1 as a functionally important component at the host-pathogen interface.
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Affiliation(s)
- Karl J Schreiber
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Jana A Hassan
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Jennifer D Lewis
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
- United States Department of Agriculture, Plant Gene Expression Center, Albany, CA, USA
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25
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Käppel S, Eggeling R, Rümpler F, Groth M, Melzer R, Theißen G. DNA-binding properties of the MADS-domain transcription factor SEPALLATA3 and mutant variants characterized by SELEX-seq. Plant Mol Biol 2021; 105:543-557. [PMID: 33486697 PMCID: PMC7892521 DOI: 10.1007/s11103-020-01108-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 12/11/2020] [Indexed: 05/13/2023]
Abstract
We studied the DNA-binding profile of the MADS-domain transcription factor SEPALLATA3 and mutant variants by SELEX-seq. DNA-binding characteristics of SEPALLATA3 mutant proteins lead us to propose a novel DNA-binding mode. MIKC-type MADS-domain proteins, which function as essential transcription factors in plant development, bind as dimers to a 10-base-pair AT-rich motif termed CArG-box. However, this consensus motif cannot fully explain how the abundant family members in flowering plants can bind different target genes in specific ways. The aim of this study was to better understand the DNA-binding specificity of MADS-domain transcription factors. Also, we wanted to understand the role of a highly conserved arginine residue for binding specificity of the MADS-domain transcription factor family. Here, we studied the DNA-binding profile of the floral homeotic MADS-domain protein SEPALLATA3 by performing SELEX followed by high-throughput sequencing (SELEX-seq). We found a diverse set of bound sequences and could estimate the in vitro binding affinities of SEPALLATA3 to a huge number of different sequences. We found evidence for the preference of AT-rich motifs as flanking sequences. Whereas different CArG-boxes can act as SEPALLATA3 binding sites, our findings suggest that the preferred flanking motifs are almost always the same and thus mostly independent of the identity of the central CArG-box motif. Analysis of SEPALLATA3 proteins with a single amino acid substitution at position 3 of the DNA-binding MADS-domain further revealed that the conserved arginine residue, which has been shown to be involved in a shape readout mechanism, is especially important for the recognition of nucleotides at positions 3 and 8 of the CArG-box motif. This leads us to propose a novel DNA-binding mode for SEPALLATA3, which is different from that of other MADS-domain proteins known.
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Affiliation(s)
- Sandra Käppel
- Matthias Schleiden Institute/Genetics, Friedrich Schiller University Jena, Philosophenweg 12, 07743, Jena, Germany
| | - Ralf Eggeling
- Department of Computer Science, University of Helsinki, Pietari Kalmin katu 5, 00014, Helsinki, Finland
- Methods in Medical Informatics, Department of Computer Science, University of Tübingen, Sand 14, 72076, Tübingen, Germany
- Institute for Biomedical Informatics, University of Tübingen, Tübingen, Germany
| | - Florian Rümpler
- Matthias Schleiden Institute/Genetics, Friedrich Schiller University Jena, Philosophenweg 12, 07743, Jena, Germany
| | - Marco Groth
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Core Facility DNA Sequencing, Beutenbergstraße 11, 07745, Jena, Germany
| | - Rainer Melzer
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Günter Theißen
- Matthias Schleiden Institute/Genetics, Friedrich Schiller University Jena, Philosophenweg 12, 07743, Jena, Germany.
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26
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Lai X, Stigliani A, Lucas J, Hugouvieux V, Parcy F, Zubieta C. Genome-wide binding of SEPALLATA3 and AGAMOUS complexes determined by sequential DNA-affinity purification sequencing. Nucleic Acids Res 2020; 48:9637-9648. [PMID: 32890394 PMCID: PMC7515736 DOI: 10.1093/nar/gkaa729] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 08/17/2020] [Accepted: 08/24/2020] [Indexed: 01/18/2023] Open
Abstract
The MADS transcription factors (TF), SEPALLATA3 (SEP3) and AGAMOUS (AG) are required for floral organ identity and floral meristem determinacy. While dimerization is obligatory for DNA binding, SEP3 and SEP3–AG also form tetrameric complexes. How homo and hetero-dimerization and tetramerization of MADS TFs affect genome-wide DNA-binding and gene regulation is not known. Using sequential DNA affinity purification sequencing (seq-DAP-seq), we determined genome-wide binding of SEP3 homomeric and SEP3–AG heteromeric complexes, including SEP3Δtet-AG, a complex with a SEP3 splice variant, SEP3Δtet, which is largely dimeric and SEP3–AG tetramer. SEP3 and SEP3–AG share numerous bound regions, however each complex bound unique sites, demonstrating that protein identity plays a role in DNA-binding. SEP3–AG and SEP3Δtet-AG share a similar genome-wide binding pattern; however the tetrameric form could access new sites and demonstrated a global increase in DNA-binding affinity. Tetramerization exhibited significant cooperative binding with preferential distances between two sites, allowing efficient binding to regions that are poorly recognized by dimeric SEP3Δtet-AG. By intersecting seq-DAP-seq with ChIP-seq and expression data, we identified unique target genes bound either in SEP3–AG seq-DAP-seq or in SEP3/AG ChIP-seq. Seq-DAP-seq is a versatile genome-wide technique and complements in vivo methods to identify putative direct regulatory targets.
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Affiliation(s)
- Xuelei Lai
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble-Alpes, CNRS, CEA, INRAE, IRIG-DBSCI, 38000 Grenoble, France
| | - Arnaud Stigliani
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble-Alpes, CNRS, CEA, INRAE, IRIG-DBSCI, 38000 Grenoble, France.,Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, DK-2200, Denmark.,Department of Biology, University of Copenhagen, Copenhagen, DK-2200 Denmark
| | - Jérémy Lucas
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble-Alpes, CNRS, CEA, INRAE, IRIG-DBSCI, 38000 Grenoble, France
| | - Véronique Hugouvieux
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble-Alpes, CNRS, CEA, INRAE, IRIG-DBSCI, 38000 Grenoble, France
| | - François Parcy
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble-Alpes, CNRS, CEA, INRAE, IRIG-DBSCI, 38000 Grenoble, France
| | - Chloe Zubieta
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble-Alpes, CNRS, CEA, INRAE, IRIG-DBSCI, 38000 Grenoble, France
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27
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Abstract
The adaptation of plants to unstable environments relies on their ability to sense their surroundings and to generate and transmit corresponding signals to different parts of the plant to evoke changes necessary for optimizing growth and defense. Plants, like animals, contain a huge repertoire of intra- and intercellular signals, including organic and inorganic molecules. The occurrence of neurotransmitter-like signaling molecules in plants has been an intriguing field of research. Among these, γ-aminobutyric acid (GABA) was discovered in plants over half a century ago, and studies of its roles as a primary metabolite have been well documented, particularly in the context of stress responses. In contrast, evidence of the potential mechanism by which GABA acts as a signaling molecule in plants has only recently been reported. In spite of this breakthrough, the roles of GABA as a signaling molecule in plants have yet to be established and several aspects of the complexity of the GABA signaling system remain obscure. This review summarizes the uncertainties in GABA signaling in plants and suggests research directions and technologies that would help in answering unsolved questions.
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Affiliation(s)
- Hillel Fromm
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
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28
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Lai X, Chahtane H, Martin-Arevalillo R, Zubieta C, Parcy F. Contrasted evolutionary trajectories of plant transcription factors. Curr Opin Plant Biol 2020; 54:101-107. [PMID: 32417720 DOI: 10.1016/j.pbi.2020.03.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 01/14/2020] [Accepted: 03/04/2020] [Indexed: 05/28/2023]
Abstract
Because of their prominent roles in plant development, transcription factors (TF) play central roles as drivers of innovation in the evolution of the green lineage (viridiplantae). The advent of massive sequencing combined with comparative genetics/genomics allows a rigorous investigation of how TF families have contributed to plant diversification from charophyte algae to bryophytes to angiosperms. Here, we review recent progress on TF family reconstruction and the identification of distantly related TFs present throughout the evolutionary timeline from algae to angiosperms. These data provide examples of contrasting evolutionary trajectories of TF families and illustrate how conserved TFs adopt diverse roles over the course of evolution.
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Affiliation(s)
- Xuelei Lai
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000 Grenoble, France
| | - Hicham Chahtane
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000 Grenoble, France
| | - Raquel Martin-Arevalillo
- Laboratoire de Reproduction et de Développement des Plantes, INRAE, CNRS, ENS de Lyon, UCB Lyon 1, Université de Lyon, France
| | - Chloe Zubieta
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000 Grenoble, France
| | - François Parcy
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000 Grenoble, France.
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29
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Batista RA, Moreno-Romero J, Qiu Y, van Boven J, Santos-González J, Figueiredo DD, Köhler C. The MADS-box transcription factor PHERES1 controls imprinting in the endosperm by binding to domesticated transposons. eLife 2019; 8:50541. [PMID: 31789592 PMCID: PMC6914339 DOI: 10.7554/elife.50541] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 11/30/2019] [Indexed: 12/31/2022] Open
Abstract
MADS-box transcription factors (TFs) are ubiquitous in eukaryotic organisms and play major roles during plant development. Nevertheless, their function in seed development remains largely unknown. Here, we show that the imprinted Arabidopsis thaliana MADS-box TF PHERES1 (PHE1) is a master regulator of paternally expressed imprinted genes, as well as of non-imprinted key regulators of endosperm development. PHE1 binding sites show distinct epigenetic modifications on maternal and paternal alleles, correlating with parental-specific transcriptional activity. Importantly, we show that the CArG-box-like DNA-binding motifs that are bound by PHE1 have been distributed by RC/Helitron transposable elements. Our data provide an example of the molecular domestication of these elements which, by distributing PHE1 binding sites throughout the genome, have facilitated the recruitment of crucial endosperm regulators into a single transcriptional network.
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Affiliation(s)
- Rita A Batista
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jordi Moreno-Romero
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Yichun Qiu
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Joram van Boven
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Juan Santos-González
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Duarte D Figueiredo
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Claudia Köhler
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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30
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Kulkarni SR, Vandepoele K. Inference of plant gene regulatory networks using data-driven methods: A practical overview. Biochim Biophys Acta Gene Regul Mech 2020; 1863:194447. [PMID: 31678628 DOI: 10.1016/j.bbagrm.2019.194447] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 10/08/2019] [Accepted: 10/31/2019] [Indexed: 11/20/2022]
Abstract
Transcriptional regulation is a complex and dynamic process that plays a vital role in plant growth and development. A key component in the regulation of genes is transcription factors (TFs), which coordinate the transcriptional control of gene activity. A gene regulatory network (GRN) is a collection of regulatory interactions between TFs and their target genes. The accurate delineation of GRNs offers a significant contribution to our understanding about how plant cells are organized and function, and how individual genes are regulated in various conditions, organs or cell types. During the past decade, important progress has been made in the identification of GRNs using experimental and computational approaches. However, a detailed overview of available platforms supporting the analysis of GRNs in plants is missing. Here, we review current databases, platforms and tools that perform data-driven analyses of gene regulation in Arabidopsis. The platforms are categorized into two sections, 1) promoter motif analysis tools that use motif mapping approaches to find TF motifs in the regulatory sequences of genes of interest and 2) network analysis tools that identify potential regulators for a set of input genes using a range of data types in order to generate GRNs. We discuss the diverse datasets integrated and highlight the strengths and caveats of different platforms. Finally, we shed light on the limitations of the above approaches and discuss future perspectives, including the need for integrative approaches to unravel complex GRNs in plants.
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31
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Lai X, Daher H, Galien A, Hugouvieux V, Zubieta C. Structural Basis for Plant MADS Transcription Factor Oligomerization. Comput Struct Biotechnol J 2019; 17:946-953. [PMID: 31360333 PMCID: PMC6639411 DOI: 10.1016/j.csbj.2019.06.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 06/06/2019] [Accepted: 06/11/2019] [Indexed: 10/26/2022] Open
Abstract
MADS transcription factors (TFs) are DNA binding proteins found in almost all eukaryotes that play essential roles in diverse biological processes. While present in animals and fungi as a small TF family, the family has dramatically expanded in plants over the course of evolution, with the model flowering plant, Arabidopsis thaliana, possessing over 100 type I and type II MADS TFs. All MADS TFs contain a core and highly conserved DNA binding domain called the MADS or M domain. Plant MADS TFs have diversified this domain with plant-specific auxiliary domains. Plant type I MADS TFs have a highly diverse and largely unstructured Carboxy-terminal (C domain), whereas type II MADS have added oligomerization domains, called Intervening (I domain) and Keratin-like (K domain), in addition to the C domain. In this mini review, we describe the overall structure of the type II "MIKC" type MADS TFs in plants, with a focus on the K domain, a critical oligomerization module. We summarize the determining factors for oligomerization and provide mechanistic insights on how secondary structural elements are required for oligomerization capability and specificity. Using MADS TFs that are involved in flower organ specification as an example, we provide case studies and homology modeling of MADS TFs complex formation. Finally, we highlight outstanding questions in the field.
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Affiliation(s)
- Xuelei Lai
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, Univ. Grenoble Alpes, CEA, INRA, IRIG, Grenoble, France
| | - Hussein Daher
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, Univ. Grenoble Alpes, CEA, INRA, IRIG, Grenoble, France
| | - Antonin Galien
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, Univ. Grenoble Alpes, CEA, INRA, IRIG, Grenoble, France
| | - Veronique Hugouvieux
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, Univ. Grenoble Alpes, CEA, INRA, IRIG, Grenoble, France
| | - Chloe Zubieta
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, Univ. Grenoble Alpes, CEA, INRA, IRIG, Grenoble, France
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32
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Lai X, Stigliani A, Vachon G, Carles C, Smaczniak C, Zubieta C, Kaufmann K, Parcy F. Building Transcription Factor Binding Site Models to Understand Gene Regulation in Plants. Mol Plant 2019; 12:743-763. [PMID: 30447332 DOI: 10.1016/j.molp.2018.10.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/20/2018] [Accepted: 10/30/2018] [Indexed: 06/09/2023]
Abstract
Transcription factors (TFs) are key cellular components that control gene expression. They recognize specific DNA sequences, the TF binding sites (TFBSs), and thus are targeted to specific regions of the genome where they can recruit transcriptional co-factors and/or chromatin regulators to fine-tune spatiotemporal gene regulation. Therefore, the identification of TFBSs in genomic sequences and their subsequent quantitative modeling is of crucial importance for understanding and predicting gene expression. Here, we review how TFBSs can be determined experimentally, how the TFBS models can be constructed in silico, and how they can be optimized by taking into account features such as position interdependence within TFBSs, DNA shape, and/or by introducing state-of-the-art computational algorithms such as deep learning methods. In addition, we discuss the integration of context variables into the TFBS modeling, including nucleosome positioning, chromatin states, methylation patterns, 3D genome architectures, and TF cooperative binding, in order to better predict TF binding under cellular contexts. Finally, we explore the possibilities of combining the optimized TFBS model with technological advances, such as targeted TFBS perturbation by CRISPR, to better understand gene regulation, evolution, and plant diversity.
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Affiliation(s)
- Xuelei Lai
- CNRS, Univ. Grenoble Alpes, CEA, INRA, BIG-LPCV, 38000 Grenoble, France.
| | - Arnaud Stigliani
- CNRS, Univ. Grenoble Alpes, CEA, INRA, BIG-LPCV, 38000 Grenoble, France
| | - Gilles Vachon
- CNRS, Univ. Grenoble Alpes, CEA, INRA, BIG-LPCV, 38000 Grenoble, France
| | - Cristel Carles
- CNRS, Univ. Grenoble Alpes, CEA, INRA, BIG-LPCV, 38000 Grenoble, France
| | - Cezary Smaczniak
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Chloe Zubieta
- CNRS, Univ. Grenoble Alpes, CEA, INRA, BIG-LPCV, 38000 Grenoble, France
| | - Kerstin Kaufmann
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - François Parcy
- CNRS, Univ. Grenoble Alpes, CEA, INRA, BIG-LPCV, 38000 Grenoble, France.
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Zúñiga-Mayo VM, Gómez-Felipe A, Herrera-Ubaldo H, de Folter S. Gynoecium development: networks in Arabidopsis and beyond. J Exp Bot 2019; 70:1447-1460. [PMID: 30715461 DOI: 10.1093/jxb/erz026] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 01/14/2019] [Indexed: 05/27/2023]
Abstract
Life has always found a way to preserve itself. One strategy that has been developed for this purpose is sexual reproduction. In land plants, the gynoecium is considered to be at the top of evolutionary innovation, since it has been a key factor in the success of the angiosperms. The gynoecium is composed of carpels with different tissues that need to develop and differentiate in the correct way. In order to control and guide gynoecium development, plants have adapted elements of pre-existing gene regulatory networks (GRNs) but new ones have also evolved. The GRNs can interact with internal factors (e.g. hormones and other metabolites) and external factors (e.g. mechanical signals and temperature) at different levels, giving robustness and flexibility to gynoecium development. Here, we review recent findings regarding the role of cytokinin-auxin crosstalk and the genes that connect these hormonal pathways during early gynoecium development. We also discuss some examples of internal and external factors that can modify GRNs. Finally, we make a journey through the flowering plant lineage to determine how conserved are these GRNs that regulate gynoecium and fruit development.
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Affiliation(s)
- Victor M Zúñiga-Mayo
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Guanajuato, México
| | - Andrea Gómez-Felipe
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Guanajuato, México
| | - Humberto Herrera-Ubaldo
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Guanajuato, México
| | - Stefan de Folter
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Guanajuato, México
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de Bruijn S, Zhao T, Muiño JM, Schranz EM, Angenent GC, Kaufmann K. PISTILLATA paralogs in Tarenaya hassleriana have diverged in interaction specificity. BMC Plant Biol 2018; 18:368. [PMID: 30577806 PMCID: PMC6303913 DOI: 10.1186/s12870-018-1574-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 11/26/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND Floral organs are specified by MADS-domain transcription factors that act in a combinatorial manner, as summarized in the (A)BCE model. However, this evolutionarily conserved model is in contrast to a remarkable amount of morphological diversity in flowers. One of the mechanisms suggested to contribute to this diversity is duplication of floral MADS-domain transcription factors. Although gene duplication is often followed by loss of one of the copies, sometimes both copies are retained. If both copies are retained they will initially be redundant, providing freedom for one of the paralogs to change function. Here, we examine the evolutionary fate and functional consequences of a transposition event at the base of the Brassicales that resulted in the duplication of the floral regulator PISTILLATA (PI), using Tarenaya hassleriana (Cleomaceae) as a model system. RESULTS The transposition of a genomic region containing a PI gene led to two paralogs which are located at different positions in the genome. The original PI copy is syntenic in position with most angiosperms, whereas the transposed copy is syntenic with the PI genes in Brassicaceae. The two PI paralogs of T. hassleriana have very similar expression patterns. However, they may have diverged in function, as only one of these PI proteins was able to act heterologously in the first whorl of A. thaliana flowers. We also observed differences in protein complex formation between the two paralogs, and the two paralogs exhibit subtle differences in DNA-binding specificity. Sequence analysis indicates that most of the protein sequence divergence between the two T. hassleriana paralogs emerged in a common ancestor of the Cleomaceae and the Brassicaceae. CONCLUSIONS We found that the PI paralogs in T. hassleriana have similar expression patterns, but may have diverged at the level of protein function. Data suggest that most protein sequence divergence occurred rapidly, prior to the origin of the Brassicaceae and Cleomaceae. It is tempting to speculate that the interaction specificities of the Brassicaceae-specific PI proteins are different compared to the PI found in other angiosperms. This could lead to PI regulating partly different genes in the Brassicaceae, and ultimately might result in change floral in morphology.
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Affiliation(s)
- Suzanne de Bruijn
- Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Bioscience, Wageningen Plant Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Tao Zhao
- Biosystematics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Jose M. Muiño
- Institute for Biology, Systems Biology of Gene Regulation, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Eric M. Schranz
- Biosystematics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Gerco C. Angenent
- Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Bioscience, Wageningen Plant Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Kerstin Kaufmann
- Institute for Biology, Plant Cell and Molecular Biology, Humboldt-Universität zu Berlin, Philippstraße 13, 10115 Berlin, Germany
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Chen D, Yan W, Fu LY, Kaufmann K. Architecture of gene regulatory networks controlling flower development in Arabidopsis thaliana. Nat Commun 2018; 9:4534. [PMID: 30382087 PMCID: PMC6208445 DOI: 10.1038/s41467-018-06772-3] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 09/26/2018] [Indexed: 11/29/2022] Open
Abstract
Floral homeotic transcription factors (TFs) act in a combinatorial manner to specify the organ identities in the flower. However, the architecture and the function of the gene regulatory network (GRN) controlling floral organ specification is still poorly understood. In particular, the interconnections of homeotic TFs, microRNAs (miRNAs) and other factors controlling organ initiation and growth have not been studied systematically so far. Here, using a combination of genome-wide TF binding, mRNA and miRNA expression data, we reconstruct the dynamic GRN controlling floral meristem development and organ differentiation. We identify prevalent feed-forward loops (FFLs) mediated by floral homeotic TFs and miRNAs that regulate common targets. Experimental validation of a coherent FFL shows that petal size is controlled by the SEPALLATA3-regulated miR319/TCP4 module. We further show that combinatorial DNA-binding of homeotic factors and selected other TFs is predictive of organ-specific patterns of gene expression. Our results provide a valuable resource for studying molecular regulatory processes underlying floral organ specification in plants. Homeotic transcription factors and miRNAs promote floral organ specification. Here Chen et al. reconstruct gene regulatory networks in Arabidopsis flowers and find evidence for feed forward loops between transcription factors, miRNAs and their targets that determine organ-specific gene expression.
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Affiliation(s)
- Dijun Chen
- Institute for Biology, Plant Cell and Molecular Biology, Humboldt-Universität zu Berlin, 10115, Berlin, Germany.
| | - Wenhao Yan
- Institute for Biology, Plant Cell and Molecular Biology, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| | - Liang-Yu Fu
- Institute for Biology, Plant Cell and Molecular Biology, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| | - Kerstin Kaufmann
- Institute for Biology, Plant Cell and Molecular Biology, Humboldt-Universität zu Berlin, 10115, Berlin, Germany.
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Chen D, Fu LY, Hu D, Klukas C, Chen M, Kaufmann K. The HTPmod Shiny application enables modeling and visualization of large-scale biological data. Commun Biol 2018; 1:89. [PMID: 30271970 PMCID: PMC6123733 DOI: 10.1038/s42003-018-0091-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 06/03/2018] [Indexed: 01/20/2023] Open
Abstract
The wave of high-throughput technologies in genomics and phenomics are enabling data to be generated on an unprecedented scale and at a reasonable cost. Exploring the large-scale data sets generated by these technologies to derive biological insights requires efficient bioinformatic tools. Here we introduce an interactive, open-source web application (HTPmod) for high-throughput biological data modeling and visualization. HTPmod is implemented with the Shiny framework by integrating the computational power and professional visualization of R and including various machine-learning approaches. We demonstrate that HTPmod can be used for modeling and visualizing large-scale, high-dimensional data sets (such as multiple omics data) under a broad context. By reinvestigating example data sets from recent studies, we find not only that HTPmod can reproduce results from the original studies in a straightforward fashion and within a reasonable time, but also that novel insights may be gained from fast reinvestigation of existing data by HTPmod. Dijun Chen et al. present HTPmod, a Shiny web application for modeling and visualization of large-scale genomic and phenomic datasets. The authors show that HTPmod can quickly reproduce analyses of high-throughput biological datasets and produce publication-quality figures.
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Affiliation(s)
- Dijun Chen
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, Berlin, 10115, Germany. .,Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Gatersleben, 06466, Germany.
| | - Liang-Yu Fu
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, Berlin, 10115, Germany
| | - Dahui Hu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Christian Klukas
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Gatersleben, 06466, Germany.,Digitalization in Research & Development (ROM), BASF SE, Ludwigshafen am Rhein, 67056, Germany
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Kerstin Kaufmann
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, Berlin, 10115, Germany.
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Käppel S, Melzer R, Rümpler F, Gafert C, Theißen G. The floral homeotic protein SEPALLATA3 recognizes target DNA sequences by shape readout involving a conserved arginine residue in the MADS-domain. Plant J 2018; 95:341-357. [PMID: 29744943 DOI: 10.1111/tpj.13954] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/17/2018] [Accepted: 04/23/2018] [Indexed: 05/05/2023]
Abstract
SEPALLATA3 of Arabidopsis thaliana is a MADS-domain transcription factor (TF) and a key regulator of flower development. MADS-domain proteins bind to sequences termed 'CArG-boxes' [consensus 5'-CC(A/T)6 GG-3']. Because only a fraction of the CArG-boxes in the Arabidopsis genome are bound by SEPALLATA3, more elaborate principles have to be discovered to better understand which features turn CArG-boxes into genuine recognition sites. Here, we investigate to what extent the shape of the DNA is involved in a 'shape readout' that contributes to the binding of SEPALLATA3. We determined in vitro binding affinities of SEPALLATA3 to DNA probes that all contain the CArG-box motif, but differ in their predicted DNA shape. We found that binding affinity correlates well with a narrow minor groove of the DNA. Substitution of canonical bases with non-standard bases supports the hypothesis of minor groove shape readout by SEPALLATA3. Analysis of mutant SEPALLATA3 proteins further revealed that a highly conserved arginine residue, which is expected to contact the DNA minor groove, contributes significantly to the shape readout. Our studies show that the specific recognition of cis-regulatory elements by a plant MADS-domain TF, and by inference probably also of other TFs of this type, heavily depends on shape readout mechanisms.
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Affiliation(s)
- Sandra Käppel
- Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, D-07743, Jena, Germany
| | - Rainer Melzer
- Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, D-07743, Jena, Germany
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Florian Rümpler
- Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, D-07743, Jena, Germany
| | - Christian Gafert
- Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, D-07743, Jena, Germany
| | - Günter Theißen
- Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, D-07743, Jena, Germany
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Borba AR, Serra TS, Górska A, Gouveia P, Cordeiro AM, Reyna-Llorens I, Kneřová J, Barros PM, Abreu IA, Oliveira MM, Hibberd JM, Saibo NJM. Synergistic Binding of bHLH Transcription Factors to the Promoter of the Maize NADP-ME Gene Used in C4 Photosynthesis Is Based on an Ancient Code Found in the Ancestral C3 State. Mol Biol Evol 2018; 35:1690-1705. [PMID: 29659975 PMCID: PMC5995220 DOI: 10.1093/molbev/msy060] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
C4 photosynthesis has evolved repeatedly from the ancestral C3 state to generate a carbon concentrating mechanism that increases photosynthetic efficiency. This specialized form of photosynthesis is particularly common in the PACMAD clade of grasses, and is used by many of the world's most productive crops. The C4 cycle is accomplished through cell-type-specific accumulation of enzymes but cis-elements and transcription factors controlling C4 photosynthesis remain largely unknown. Using the NADP-Malic Enzyme (NADP-ME) gene as a model we tested whether mechanisms impacting on transcription in C4 plants evolved from ancestral components found in C3 species. Two basic Helix-Loop-Helix (bHLH) transcription factors, ZmbHLH128 and ZmbHLH129, were shown to bind the C4NADP-ME promoter from maize. These proteins form heterodimers and ZmbHLH129 impairs trans-activation by ZmbHLH128. Electrophoretic mobility shift assays indicate that a pair of cis-elements separated by a seven base pair spacer synergistically bind either ZmbHLH128 or ZmbHLH129. This pair of cis-elements is found in both C3 and C4 Panicoid grass species of the PACMAD clade. Our analysis is consistent with this cis-element pair originating from a single motif present in the ancestral C3 state. We conclude that C4 photosynthesis has co-opted an ancient C3 regulatory code built on G-box recognition by bHLH to regulate the NADP-ME gene. More broadly, our findings also contribute to the understanding of gene regulatory networks controlling C4 photosynthesis.
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Affiliation(s)
- Ana Rita Borba
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - Tânia S Serra
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - Alicja Górska
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - Paulo Gouveia
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - André M Cordeiro
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - Ivan Reyna-Llorens
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Jana Kneřová
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Pedro M Barros
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Isabel A Abreu
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - Maria Margarida Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Nelson J M Saibo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
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Abstract
This article comments on: Rümpler F, Theißen G, Melzer R. 2018. A conserved leucine zipper-like motif accounts for strong tetramerization capabilities of SEPALLATA-like MADS-domain transcription factors. Journal of Experimental Botany 69, 1943–1954.
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Affiliation(s)
- Veronique Hugouvieux
- Laboratoire de Physiologie Cellulaire & Végétale, CEA, Univ. Grenoble Alpes, CNRS, INRA, BIG, Grenoble, France
| | - Chloe Zubieta
- Laboratoire de Physiologie Cellulaire & Végétale, CEA, Univ. Grenoble Alpes, CNRS, INRA, BIG, Grenoble, France
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Schilling S, Pan S, Kennedy A, Melzer R. MADS-box genes and crop domestication: the jack of all traits. J Exp Bot 2018; 69:1447-1469. [PMID: 29474735 DOI: 10.1093/jxb/erx479] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 01/10/2018] [Indexed: 05/25/2023]
Abstract
MADS-box genes are key regulators of virtually every aspect of plant reproductive development. They play especially prominent roles in flowering time control, inflorescence architecture, floral organ identity determination, and seed development. The developmental and evolutionary importance of MADS-box genes is widely acknowledged. However, their role during flowering plant domestication is less well recognized. Here, we provide an overview illustrating that MADS-box genes have been important targets of selection during crop domestication and improvement. Numerous examples from a diversity of crop plants show that various developmental processes have been shaped by allelic variations in MADS-box genes. We propose that new genomic and genome editing resources provide an excellent starting point for further harnessing the potential of MADS-box genes to improve a variety of reproductive traits in crops. We also suggest that the biophysics of MADS-domain protein-protein and protein-DNA interactions, which is becoming increasingly well characterized, makes them especially suited to exploit coding sequence variations for targeted breeding approaches.
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Affiliation(s)
- Susanne Schilling
- School of Biology and Environmental Science, University College Dublin, Irel
| | - Sirui Pan
- School of Biology and Environmental Science, University College Dublin, Irel
| | - Alice Kennedy
- School of Biology and Environmental Science, University College Dublin, Irel
| | - Rainer Melzer
- School of Biology and Environmental Science, University College Dublin, Irel
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Abstract
Transcription factors that trigger major developmental decisions in plants and animals are termed "master regulators". Such master regulators are classically seen as acting on the top of a regulatory hierarchy that determines a complete developmental program, and they usually encode transcription factors. Here, we introduce master regulators of flowering time and flower development as examples to show how analysis of molecular interactions and gene-regulatory networks in plants has changed our view on the molecular mechanisms by which these factors control developmental processes. A picture has emerged that emphasizes a complex combinatorial interplay in determining cell-type transcriptional programs, and a high level of feedback control. The expression of master regulators themselves is usually regulated by multiple factors integrating environmental and endogenous spatiotemporal cues. Master regulatory transcription factors regulate gene expression by different mechanisms, including modifications in chromatin status in the bound regions. A poorly understood phenomenon is how developmental master regulators exert functions in different cell- and organ types. This is especially relevant for those factors that have important functions in several developmental processes.
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Ó'Maoiléidigh DS. Intrafamily Protein Interactions Contribute to DNA Localization. Plant Cell 2017; 29:2076-2077. [PMID: 28912347 PMCID: PMC5635982 DOI: 10.1105/tpc.17.00735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
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