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Long Y, Zeng J, Liu X, Wang Z, Tong Q, Zhou R, Liu X. Transcriptomic and metabolomic profiling reveals molecular regulatory network involved in flower development and phenotypic changes in two Lonicera macranthoides varieties. 3 Biotech 2024; 14:174. [PMID: 38855147 PMCID: PMC11153451 DOI: 10.1007/s13205-024-04019-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 05/26/2024] [Indexed: 06/11/2024] Open
Abstract
Due to the medicinal importance of the flowers of Xianglei type (XL) Lonicera macranthoides, it is important to understand the molecular mechanisms that underlie their development. In this study, we elucidated the transcriptomic and metabolomic mechanisms that underlie the flower development mechanism of two L. macranthoides varieties. In this study, 3435 common differentially expressed unigenes (DEGs) and 1138 metabolites were identified. These common DEGs were mainly enriched in plant hormone signal transduction pathways. Metabolomic analysis showed that amino acids were the main metabolites of differential accumulation in wild-type (WT) L. macranthoides, whereas in XL, they were flavonoids and phenylalanine metabolites. Genes and transcription factors (TFs), such as MYB340, histone deacetylase 1 (HDT1), small auxin-up RNA 32 (SAUR32), auxin response factor 6 (ARF6), PIN-LIKES 7 (PILS7), and WRKY6, likely drive metabolite accumulation. Plant hormone signals, especially auxin signals, and various TFs induce downstream flower organ recognition genes, resulting in a differentiation of the two L. macranthoides varieties in terms of their developmental trajectories. In addition, photoperiodic, autonomous, and plant hormone pathways jointly regulated the L. macranthoides corolla opening. SAUR32, Arabidopsis response regulator 9 (ARR9), Gibberellin receptor (GID1B), and Constans-like 10 (COL10) were closely related to the unfolding of the L. macranthoides corolla. These findings offer valuable understanding of the flower growth process of L. macranthoides and the excellent XL phenotypes at the molecular level. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-04019-1.
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Affiliation(s)
- YuQing Long
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208 Hunan Province China
- Key Laboratory of Germplasm Resources and Standardized Planting of Hunan Large-Scale Genuine Medicinal Materials, Changsha, 410208 Hunan Province China
| | - Juan Zeng
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208 Hunan Province China
- Key Laboratory of Germplasm Resources and Standardized Planting of Hunan Large-Scale Genuine Medicinal Materials, Changsha, 410208 Hunan Province China
| | - XiaoRong Liu
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208 Hunan Province China
- Key Laboratory of Germplasm Resources and Standardized Planting of Hunan Large-Scale Genuine Medicinal Materials, Changsha, 410208 Hunan Province China
| | - ZhiHui Wang
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208 Hunan Province China
- Key Laboratory of Germplasm Resources and Standardized Planting of Hunan Large-Scale Genuine Medicinal Materials, Changsha, 410208 Hunan Province China
| | - QiaoZhen Tong
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208 Hunan Province China
- Key Laboratory of Germplasm Resources and Standardized Planting of Hunan Large-Scale Genuine Medicinal Materials, Changsha, 410208 Hunan Province China
- Key Laboratory of Modern Research of TCM, Education Department of Hunan Province, Changsha, 410208 Hunan Province China
| | - RiBao Zhou
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208 Hunan Province China
- Key Laboratory of Germplasm Resources and Standardized Planting of Hunan Large-Scale Genuine Medicinal Materials, Changsha, 410208 Hunan Province China
- Key Laboratory of Modern Research of TCM, Education Department of Hunan Province, Changsha, 410208 Hunan Province China
| | - XiangDan Liu
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208 Hunan Province China
- Key Laboratory of Germplasm Resources and Standardized Planting of Hunan Large-Scale Genuine Medicinal Materials, Changsha, 410208 Hunan Province China
- Key Laboratory of Modern Research of TCM, Education Department of Hunan Province, Changsha, 410208 Hunan Province China
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Jiang G, Koppolu R, Rutten T, Hensel G, Lundqvist U, Tandron Moya YA, Huang Y, Rajaraman J, Poursarebani N, von Wirén N, Kumlehn J, Mascher M, Schnurbusch T. Non-cell-autonomous signaling associated with barley ALOG1 specifies spikelet meristem determinacy. Curr Biol 2024; 34:2344-2358.e5. [PMID: 38781954 DOI: 10.1016/j.cub.2024.04.083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 03/18/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024]
Abstract
Inflorescence architecture and crop productivity are often tightly coupled in our major cereal crops. However, the underlying genetic mechanisms controlling cereal inflorescence development remain poorly understood. Here, we identified recessive alleles of barley (Hordeum vulgare L.) HvALOG1 (Arabidopsis thaliana LSH1 and Oryza G1) that produce non-canonical extra spikelets and fused glumes abaxially to the central spikelet from the upper-mid portion until the tip of the inflorescence. Notably, we found that HvALOG1 exhibits a boundary-specific expression pattern that specifically excludes reproductive meristems, implying the involvement of previously proposed localized signaling centers for branch regulation. Importantly, during early spikelet formation, non-cell-autonomous signals associated with HvALOG1 expression may specify spikelet meristem determinacy, while boundary formation of floret organs appears to be coordinated in a cell-autonomous manner. Moreover, barley ALOG family members synergistically modulate inflorescence morphology, with HvALOG1 predominantly governing meristem maintenance and floral organ development. We further propose that spatiotemporal redundancies of expressed HvALOG members specifically in the basal inflorescence may be accountable for proper patterning of spikelet formation in mutant plants. Our research offers new perspectives on regulatory signaling roles of ALOG transcription factors during the development of reproductive meristems in cereal inflorescences.
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Affiliation(s)
- Guojing Jiang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, Germany
| | - Ravi Koppolu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, Germany
| | - Twan Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, Germany
| | - Goetz Hensel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, Germany
| | | | - Yudelsy Antonia Tandron Moya
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, Germany
| | - Yongyu Huang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, Germany
| | - Jeyaraman Rajaraman
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, Germany
| | - Naser Poursarebani
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, Germany
| | - Nicolaus von Wirén
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, Germany
| | - Jochen Kumlehn
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, Germany
| | - Thorsten Schnurbusch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, Germany; Faculty of Natural Sciences III, Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany.
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Rodas AL, Roque E, Hamza R, Gómez-Mena C, Beltrán JP, Cañas LA. SUPERMAN strikes again in legumes. FRONTIERS IN PLANT SCIENCE 2023; 14:1120342. [PMID: 36794219 PMCID: PMC9923009 DOI: 10.3389/fpls.2023.1120342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
The SUPERMAN (SUP) gene was described in Arabidopsis thaliana over 30 years ago. SUP was classified as a cadastral gene required to maintain the boundaries between reproductive organs, thus controlling stamen and carpel number in flowers. We summarize the information on the characterization of SUP orthologs in plant species other than Arabidopsis, focusing on the findings for the MtSUP, the ortholog in the legume Medicago truncatula. M. truncatula has been widely used as a model system to study the distinctive developmental traits of this family of plants, such as the existence of compound inflorescence and complex floral development. MtSUP participates in the complex genetic network controlling these developmental processes in legumes, sharing conserved functions with SUP. However, transcriptional divergence between SUP and MtSUP provided context-specific novel functions for a SUPERMAN ortholog in a legume species. MtSUP controls the number of flowers per inflorescence and the number of petals, stamens and carpels regulating the determinacy of ephemeral meristems that are unique in legumes. Results obtained in M. truncatula provided new insights to the knowledge of compound inflorescence and flower development in legumes. Since legumes are valuable crop species worldwide, with high nutritional value and important roles in sustainable agriculture and food security, new information on the genetic control of their compound inflorescence and floral development could be used for plant breeding.
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Chahtane H, Lai X, Tichtinsky G, Rieu P, Arnoux-Courseaux M, Cancé C, Marondedze C, Parcy F. Flower Development in Arabidopsis. Methods Mol Biol 2023; 2686:3-38. [PMID: 37540352 DOI: 10.1007/978-1-0716-3299-4_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Like in other angiosperms, the development of flowers in Arabidopsis starts right after the floral transition, when the shoot apical meristem (SAM) stops producing leaves and makes flowers instead. On the flanks of the SAM emerge the flower meristems (FM) that will soon differentiate into the four main floral organs, sepals, petals, stamens, and pistil, stereotypically arranged in concentric whorls. Each phase of flower development-floral transition, floral bud initiation, and floral organ development-is under the control of specific gene networks. In this chapter, we describe these different phases and the gene regulatory networks involved, from the floral transition to the floral termination.
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Affiliation(s)
- Hicham Chahtane
- CNRS, Université Grenoble Alpes, CEA, INRAE, IRIG, BIG-LPCV, Grenoble, France
- Institut de Recherche Pierre Fabre, Green Mission Pierre Fabre, Conservatoire Botanique Pierre Fabre, Soual, France
| | - Xuelei Lai
- CNRS, Université Grenoble Alpes, CEA, INRAE, IRIG, BIG-LPCV, Grenoble, France
- Huazhong Agricultural University, National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Wuhan, China
| | | | - Philippe Rieu
- CNRS, Université Grenoble Alpes, CEA, INRAE, IRIG, BIG-LPCV, Grenoble, France
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | | | - Coralie Cancé
- CNRS, Université Grenoble Alpes, CEA, INRAE, IRIG, BIG-LPCV, Grenoble, France
| | - Claudius Marondedze
- CNRS, Université Grenoble Alpes, CEA, INRAE, IRIG, BIG-LPCV, Grenoble, France
- Department of Biochemistry, Faculty of Medicine, Midlands State University, Senga, Gweru, Zimbabwe
| | - François Parcy
- CNRS, Université Grenoble Alpes, CEA, INRAE, IRIG, BIG-LPCV, Grenoble, France.
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Bačovský V, Čegan R, Tihlaříková E, Neděla V, Hudzieczek V, Smrža L, Janíček T, Beneš V, Hobza R. Chemical genetics in Silene latifolia elucidate regulatory pathways involved in gynoecium development. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2354-2368. [PMID: 35045170 DOI: 10.1093/jxb/erab538] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
Dioecious plants possess diverse sex determination systems and unique mechanisms of reproductive organ development; however, little is known about how sex-linked genes shape the expression of regulatory cascades that lead to developmental differences between sexes. In Silene latifolia, a dioecious plant with stable dimorphism in floral traits, early experiments suggested that female-regulator genes act on the factors that determine the boundaries of the flower whorls. To identify these regulators, we sequenced the transcriptome of male flowers with fully developed gynoecia, induced by rapid demethylation in the parental generation. Eight candidates were found to have a positive role in gynoecium promotion, floral organ size, and whorl boundary, and affect the expression of class B MADS-box flower genes. To complement our transcriptome analysis, we closely examined the floral organs in their native state using field emission environmental scanning electron microscopy, and examined the differences between females and androhermaphrodites in their placenta and ovule organization. Our results reveal the regulatory pathways potentially involved in sex-specific flower development in the classical model of dioecy, S. latifolia. These pathways include previously hypothesized and unknown female-regulator genes that act on the factors that determine the flower boundaries, and a negative regulator of anther development, SUPERMAN-like (SlSUP).
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Affiliation(s)
- Václav Bačovský
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Radim Čegan
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Eva Tihlaříková
- Environmental Electron Microscopy Group, Institute of Scientific Instruments of the Czech Academy of Sciences, Kralovopolska 147, 612 64 Brno, Czech Republic
| | - Vilém Neděla
- Environmental Electron Microscopy Group, Institute of Scientific Instruments of the Czech Academy of Sciences, Kralovopolska 147, 612 64 Brno, Czech Republic
| | - Vojtěch Hudzieczek
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Lubomír Smrža
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Tomáš Janíček
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Vladimír Beneš
- EMBL Genomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, D-69117 Heidelberg, Germany
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
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Xu W, Zhu W, Yang L, Liang W, Li H, Yang L, Chen M, Luo Z, Huang G, Duan L, Dreni L, Zhang D. SMALL REPRODUCTIVE ORGANS, a SUPERMAN-like transcription factor, regulates stamen and pistil growth in rice. THE NEW PHYTOLOGIST 2022; 233:1701-1718. [PMID: 34761379 DOI: 10.1111/nph.17849] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 10/28/2021] [Indexed: 06/13/2023]
Abstract
Organ size is determined mainly by cell division and cell expansion. Several genetic factors regulating development of plant lateral organs have been characterized, but those involved in determining reproductive organ size and separation in rice (Oryza sativa) remain unknown. We have isolated the rice gene SMALL REPRODUCTIVE ORGANS (SRO) encoding a nucleus-localized Cys2His2 (C2 H2 ) zinc finger protein orthologous to Arabidopsis transcription factor (TF) SUPERMAN (SUP). Combined developmental, genetic, histological and transcriptomic analyses were used to determine the function of SRO in regulating reproductive organ size. SRO affects genes involved in cell division, cell expansion and phytohormone signalling in the rice flower. SRO is specifically expressed in the first stages of stamen filament development to regulate their correct formation and separation. In addition, SRO noncell-autonomously regulates the size and functionality of male and female reproductive organs. The B-class MADS-box gene OsMADS16/SPW1 is epistatic to SRO, whereas SRO regulates reproductive organ specification and floral meristem determinacy synergistically with C-class genes OsMADS3 and OsMADS58. These findings provide insights into how an evolutionarily conserved TF has a pivotal role in reproductive organ development in core eudicots and monocots, through partially conserved expression, function and regulatory network.
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Affiliation(s)
- Wei Xu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wanwan Zhu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Liu Yang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wanqi Liang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hui Li
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, 200032, China
| | - Li Yang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Mingjiao Chen
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhijing Luo
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Guoqiang Huang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lei Duan
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ludovico Dreni
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
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Cucinotta M, Cavalleri A, Chandler JW, Colombo L. Auxin and Flower Development: A Blossoming Field. Cold Spring Harb Perspect Biol 2021; 13:a039974. [PMID: 33355218 PMCID: PMC7849340 DOI: 10.1101/cshperspect.a039974] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The establishment of the species-specific floral organ body plan involves many coordinated spatiotemporal processes, which include the perception of positional information that specifies floral meristem and floral organ founder cells, coordinated organ outgrowth coupled with the generation and maintenance of inter-organ and inter-whorl boundaries, and the termination of meristem activity. Auxin is integrated within the gene regulatory networks that control these processes and plays instructive roles at the level of tissue-specific biosynthesis and polar transport to generate local maxima, perception, and signaling. Key features of auxin function in several floral contexts include cell nonautonomy, interaction with cytokinin gradients, and the central role of MONOPTEROS and ETTIN to regulate canonical and noncanonical auxin response pathways, respectively. Arabidopsis flowers are not representative of the enormous angiosperm floral diversity; therefore, comparative studies are required to understand how auxin underlies these developmental differences. It will be of great interest to compare the conservation of auxin pathways among flowering plants and to discuss the evolutionary role of auxin in floral development.
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Affiliation(s)
- Mara Cucinotta
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milan, Italy
| | - Alex Cavalleri
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milan, Italy
| | | | - Lucia Colombo
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milan, Italy
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Min Y, Kramer EM. Transcriptome profiling and weighted gene co-expression network analysis of early floral development in Aquilegia coerulea. Sci Rep 2020; 10:19637. [PMID: 33184405 PMCID: PMC7665038 DOI: 10.1038/s41598-020-76750-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 10/29/2020] [Indexed: 11/08/2022] Open
Abstract
The earliest phases of floral development include a number of crucial processes that lay the foundation for the subsequent morphogenesis of floral organs and success in reproduction. Currently, key transcriptional changes during this developmental window have been characterized in the model species Arabidopsis thaliana, but little is known about how transcriptional dynamics change over the course of these developmental processes in other plant systems. Here, we have conducted the first in-depth transcriptome profiling of early floral development in Aquilegia at four finely dissected developmental stages, with eight biological replicates per stage. Using differential gene expression analysis and weighted gene co-expression network analysis, we identified both crucial genes whose expression changes mark the transitions between developmental stages and hub genes in co-expression modules. Our results support the potential functional conservation of key genes in early floral development that have been identified in other systems, but also reveal a number of previously unknown or overlooked loci that are worthy of further investigation. In addition, our results highlight not only the dynamics of transcriptional regulation during early floral development, but also the potential involvement of the complex, essential networks of small RNA and post-translational regulation to these developmental stages.
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Affiliation(s)
- Ya Min
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave., Cambridge, MA, USA
| | - Elena M Kramer
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave., Cambridge, MA, USA.
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High-Throughput Sequencing and Expression Analysis Suggest the Involvement of Pseudomonas putida RA-Responsive microRNAs in Growth and Development of Arabidopsis. Int J Mol Sci 2020; 21:ijms21155468. [PMID: 32751751 PMCID: PMC7432263 DOI: 10.3390/ijms21155468] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/18/2020] [Accepted: 07/21/2020] [Indexed: 01/11/2023] Open
Abstract
Beneficial soil microorganisms largely comprise of plant growth-promoting rhizobacteria (PGPR), which adhere to plant roots and facilitate their growth and development. Pseudomonas putida (RA) strain MTCC5279 is one such PGPR that exhibits several characteristics of plant growth promotion, such as P-solubilization, and siderophores and IAA production. Plant–PGPR interactions are very complex phenomena, and essentially modulate the expression of numerous genes, consequently leading to changes in the physiological, biochemical, cellular and molecular responses of plants. Therefore, in order to understand the molecular bases of plant–PGPR interactions, we carried out the identification of microRNAs from the roots of Arabidopsis upon P. putida RA-inoculation, and analyses of their expression. MicroRNAs (miRNAs) are 20- to 24-nt non-coding small RNAs known to regulate the expression of their target genes. Small RNA sequencing led to the identification of 293 known and 67 putative novel miRNAs, from the control and RA-inoculated libraries. Among these, 15 known miRNAs showed differential expression upon RA-inoculation in comparison to the control, and their expressions were corroborated by stem-loop quantitative real-time PCR. Overall, 28,746 and 6931 mRNAs were expected to be the targets of the known and putative novel miRNAs, respectively, which take part in numerous biological, cellular and molecular processes. An inverse correlation between the expression of RA-responsive miRNAs and their target genes also strengthened the crucial role of RA in developmental regulation. Our results offer insights into the understanding of the RA-mediated modulation of miRNAs and their targets in Arabidopsis, and pave the way for the further exploitation and characterization of candidate RA-responsive miRNA(s) for various crop improvement strategies directed towards plant sustainable growth and development.
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10
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Lyu T, Cao J. Cys₂/His₂ Zinc-Finger Proteins in Transcriptional Regulation of Flower Development. Int J Mol Sci 2018; 19:E2589. [PMID: 30200325 PMCID: PMC6164605 DOI: 10.3390/ijms19092589] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 08/28/2018] [Accepted: 08/29/2018] [Indexed: 11/17/2022] Open
Abstract
Flower development is the core of higher-plant ontogenesis and is controlled by complex gene regulatory networks. Cys₂/His₂ zinc-finger proteins (C2H2-ZFPs) constitute one of the largest transcription factor families and are highly involved in transcriptional regulation of flowering induction, floral organ morphogenesis, and pollen and pistil maturation. Nevertheless, the molecular mechanism of C2H2-ZFPs has been gradually revealed only in recent years. During flowering induction, C2H2-ZFPs can modify the chromatin of FLOWERING LOCUS C, thereby providing additional insights into the quantification of transcriptional regulation caused by chromatin regulation. C2H2-ZFPs are involved in cell division and proliferation in floral organ development and are associated with hormonal regulation, thereby revealing how a flower is partitioned into four developmentally distinct whorls. The studies reviewed in this work integrate the information from the endogenous, hormonal, and environmental regulation of flower development. The structure of C2H2-ZFPs determines their function as transcriptional regulators. The findings indicate that C2H2-ZFPs play a crucial role in flower development. In this review, we summarize the current understanding of the structure, expression, and function of C2H2-ZFPs and discuss their molecular mechanism in flower development.
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Affiliation(s)
- Tianqi Lyu
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China.
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China.
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China.
| | - Jiashu Cao
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China.
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China.
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China.
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Woźniak NJ, Sicard A. Evolvability of flower geometry: Convergence in pollinator-driven morphological evolution of flowers. Semin Cell Dev Biol 2018; 79:3-15. [DOI: 10.1016/j.semcdb.2017.09.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 09/18/2017] [Accepted: 09/19/2017] [Indexed: 01/01/2023]
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Yu H, Huang T. Correction: Yu, H.; et al. Molecular Mechanisms of Floral Boundary Formation in Arabidopsis. Int. J. Mol. Sci. 2016, 17, 317. Int J Mol Sci 2018; 19:E1845. [PMID: 29932148 PMCID: PMC6073951 DOI: 10.3390/ijms19071845] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 06/22/2018] [Indexed: 01/18/2023] Open
Abstract
The authors wish to make the following correction to their paper [1].[...].
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Affiliation(s)
- Hongyang Yu
- College of Life Sciences and Oceanography, Shenzhen University, 3688 Nanhai Ave., Shenzhen 518060, China.
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, 3688 Nanhai Ave., Shenzhen 518060, China.
| | - Tengbo Huang
- College of Life Sciences and Oceanography, Shenzhen University, 3688 Nanhai Ave., Shenzhen 518060, China.
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González-Carranza ZH, Zhang X, Peters JL, Boltz V, Szecsi J, Bendahmane M, Roberts JA. HAWAIIAN SKIRT controls size and floral organ number by modulating CUC1 and CUC2 expression. PLoS One 2017; 12:e0185106. [PMID: 28934292 PMCID: PMC5608315 DOI: 10.1371/journal.pone.0185106] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 09/06/2017] [Indexed: 12/02/2022] Open
Abstract
The Arabidopsis thaliana F-box gene HAWAIIAN SKIRT (HWS) affects organ growth and the timing of floral organ abscission. The loss-of-function hws-1 mutant exhibits fused sepals and increased organ size. To understand the molecular mechanisms of HWS during plant development, we mutagenized hws-1 seeds with ethylmethylsulphonate (EMS) and screened for mutations suppressing hws-1 associated phenotypes. We isolated the shs1/hws-1 (suppressor of hws-1) mutant in which hws-1 sepal fusion phenotype was suppressed. The shs1/hws-1 mutant carries a G→A nucleotide substitution in the MIR164 binding site of CUP-SHAPED COTYLEDON 1 (CUC1) mRNA. CUC1 and CUP-SHAPED COTYLEDON 2 (CUC2) transcript levels were altered in shs1, renamed cuc1-1D, and in hws-1 mutant. Genetic interaction analyses using single, double and triple mutants of cuc1-1D, cuc2-1D (a CUC2 mutant similar to cuc1-1D), and hws-1, demonstrate that HWS, CUC1 and CUC2 act together to control floral organ number. Loss of function of HWS is associated with larger petal size due to alterations in cell proliferation and mitotic growth, a role shared with the CUC1 gene.
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Affiliation(s)
- Zinnia H. González-Carranza
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom
| | - Xuebin Zhang
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom
| | - Janny L. Peters
- Department of Molecular Plant Physiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Veronique Boltz
- Laboratoire Reproduction et Développement des Plantes, Univesité de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Judit Szecsi
- Laboratoire Reproduction et Développement des Plantes, Univesité de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Mohammed Bendahmane
- Laboratoire Reproduction et Développement des Plantes, Univesité de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Jeremy A. Roberts
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom
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Espinosa-Ruiz A, Martínez C, de Lucas M, Fàbregas N, Bosch N, Caño-Delgado AI, Prat S. TOPLESS mediates brassinosteroid control of shoot boundaries and root meristem development in Arabidopsis thaliana. Development 2017; 144:1619-1628. [PMID: 28320734 DOI: 10.1242/dev.143214] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 02/27/2017] [Indexed: 01/07/2023]
Abstract
The transcription factor BRI1-EMS-SUPRESSOR 1 (BES1) is a master regulator of brassinosteroid (BR)-regulated gene expression. BES1 together with BRASSINAZOLE-RESISTANT 1 (BZR1) drive activated or repressed expression of several genes, and have a prominent role in negative regulation of BR synthesis. Here, we report that BES1 interaction with TOPLESS (TPL), via its ERF-associated amphiphilic repression (EAR) motif, is essential for BES1-mediated control of organ boundary formation in the shoot apical meristem and the regulation of quiescent center (QC) cell division in roots. We show that TPL binds via BES1 to the promoters of the CUC3 and BRAVO targets and suppresses their expression. Ectopic expression of TPL leads to similar organ boundary defects and alterations in QC cell division rate to the bes1-d mutation, while bes1-d defects are suppressed by the dominant interfering protein encoded by tpl-1, with these effects respectively correlating with changes in CUC3 and BRAVO expression. Together, our data unveil a pivotal role of the co-repressor TPL in the shoot and root meristems, which relies on its interaction with BES1 and regulation of BES1 target gene expression.
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Affiliation(s)
- Ana Espinosa-Ruiz
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología-CSIC, Darwin 3, Madrid E-28049, Spain
| | - Cristina Martínez
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología-CSIC, Darwin 3, Madrid E-28049, Spain
| | - Miguel de Lucas
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología-CSIC, Darwin 3, Madrid E-28049, Spain
| | - Norma Fàbregas
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Barcelona E-08193, Spain
| | - Nadja Bosch
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Barcelona E-08193, Spain
| | - Ana I Caño-Delgado
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Barcelona E-08193, Spain
| | - Salomé Prat
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología-CSIC, Darwin 3, Madrid E-28049, Spain
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