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Kumar K, Kumari A, Durgesh K, Sevanthi AM, Sharma S, Singh NK, Gaikwad K. Identification of superior haplotypes for flowering time in pigeonpea through candidate gene-based association study of a diverse minicore collection. PLANT CELL REPORTS 2024; 43:156. [PMID: 38819495 DOI: 10.1007/s00299-024-03230-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 05/05/2024] [Indexed: 06/01/2024]
Abstract
KEY MESSAGE In current study candidate gene (261 genes) based association mapping on 144 pigeonpea accessions for flowering time and related traits and 29 MTAs producing eight superior haplotypes were identified. In the current study, we have conducted an association analysis for flowering-associated traits in a diverse pigeonpea mini-core collection comprising 144 accessions using the SNP data of 261 flowering-related genes. In total, 13,449 SNPs were detected in the current study, which ranged from 743 (ICP10228) to 1469 (ICP6668) among the individuals. The nucleotide diversity (0.28) and Watterson estimates (0.34) reflected substantial diversity, while Tajima's D (-0.70) indicated the abundance of rare alleles in the collection. A total of 29 marker trait associations (MTAs) were identified, among which 19 were unique to days to first flowering (DOF) and/or days to fifty percent flowering (DFF), 9 to plant height (PH), and 1 to determinate (Det) growth habit using 3 years of phenotypic data. Among these MTAs, six were common to DOF and/or DFF, and four were common to DOF/DFF along with the PH, reflecting their pleiotropic action. These 29 MTAs spanned 25 genes, among which 10 genes clustered in the protein-protein network analysis, indicating their concerted involvement in floral induction. Furthermore, we identified eight haplotypes, four of which regulate late flowering, while the remaining four regulate early flowering using the MTAs. Interestingly, haplotypes conferring late flowering (H001, H002, and H008) were found to be taller, while those involved in early flowering (H003) were shorter in height. The expression pattern of these genes, as inferred from the transcriptome data, also underpinned their involvement in floral induction. The haplotypes identified will be highly useful to the pigeonpea breeding community for haplotype-based breeding.
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Affiliation(s)
- Kuldeep Kumar
- ICAR-National Institute for Plant Biotechnology, Pusa, New Delhi, India
- ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, India
- The Graduate School, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India
| | - Anita Kumari
- Department of Botany, North Campus, University of Delhi, Delhi, New Delhi, India
| | - Kumar Durgesh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India
| | | | - Sandhya Sharma
- ICAR-National Institute for Plant Biotechnology, Pusa, New Delhi, India
| | | | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, Pusa, New Delhi, India.
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Han L, Shen B, Wu X, Zhang J, Wen YJ. Compressed variance component mixed model reveals epistasis associated with flowering in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2024; 14:1283642. [PMID: 38259933 PMCID: PMC10800901 DOI: 10.3389/fpls.2023.1283642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 12/15/2023] [Indexed: 01/24/2024]
Abstract
Introduction Epistasis is currently a topic of great interest in molecular and quantitative genetics. Arabidopsis thaliana, as a model organism, plays a crucial role in studying the fundamental biology of diverse plant species. However, there have been limited reports about identification of epistasis related to flowering in genome-wide association studies (GWAS). Therefore, it is of utmost importance to conduct epistasis in Arabidopsis. Method In this study, we employed Levene's test and compressed variance component mixed model in GWAS to detect quantitative trait nucleotides (QTNs) and QTN-by-QTN interactions (QQIs) for 11 flowering-related traits of 199 Arabidopsis accessions with 216,130 markers. Results Our analysis detected 89 QTNs and 130 pairs of QQIs. Around these loci, 34 known genes previously reported in Arabidopsis were confirmed to be associated with flowering-related traits, such as SPA4, which is involved in regulating photoperiodic flowering, and interacts with PAP1 and PAP2, affecting growth of Arabidopsis under light conditions. Then, we observed significant and differential expression of 35 genes in response to variations in temperature, photoperiod, and vernalization treatments out of unreported genes. Functional enrichment analysis revealed that 26 of these genes were associated with various biological processes. Finally, the haplotype and phenotypic difference analysis revealed 20 candidate genes exhibiting significant phenotypic variations across gene haplotypes, of which the candidate genes AT1G12990 and AT1G09950 around QQIs might have interaction effect to flowering time regulation in Arabidopsis. Discussion These findings may offer valuable insights for the identification and exploration of genes and gene-by-gene interactions associated with flowering-related traits in Arabidopsis, that may even provide valuable reference and guidance for the research of epistasis in other species.
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Affiliation(s)
- Le Han
- College of Science, Nanjing Agricultural University, Nanjing, China
| | - Bolin Shen
- College of Science, Nanjing Agricultural University, Nanjing, China
| | - Xinyi Wu
- College of Science, Nanjing Agricultural University, Nanjing, China
| | - Jin Zhang
- College of Science, Nanjing Agricultural University, Nanjing, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China
| | - Yang-Jun Wen
- College of Science, Nanjing Agricultural University, Nanjing, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China
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Boanares D, Da-Silva CJ, Costa KJA, Filgueira JPPS, Salles MLOC, Neto LP, Gastauer M, Valadares R, Medeiros PS, Ramos SJ, Caldeira CF. Exogenous Nitric Oxide Alleviates Water Deficit and Increases the Seed Production of an Endemic Amazonian Canga Grass. Int J Mol Sci 2023; 24:16676. [PMID: 38068998 PMCID: PMC10706291 DOI: 10.3390/ijms242316676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/13/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
Open pit mining can cause loss in different ecosystems, including damage to habitats of rare and endemic species. Understanding the biology of these species is fundamental for their conservation, and to assist in decision-making. Sporobolus multiramosus is an annual grass endemic to the Amazon canga ecosystems, which comprise rocky outcrop vegetation covering one of the world's largest iron ore reserves. Here, we evaluated whether nitric oxide aids S. multiramosus in coping with water shortages and examined the physiological processes behind these adaptations. nitric oxide application improved the water status, photosynthetic efficiency, biomass production, and seed production and germination of S. multiramosus under water deficit conditions. These enhancements were accompanied by adjustments in leaf and root anatomy, including changes in stomata density and size and root endodermis thickness and vascular cylinder diameter. Proteomic analysis revealed that nitric oxide promoted the activation of several proteins involved in the response to environmental stress and flower and fruit development. Overall, the results suggest that exogenous nitric oxide has the potential to enhance the growth and productivity of S. multiramosus. Enhancements in seed productivity have significant implications for conservation initiatives and can be applied to seed production areas, particularly for the restoration of native ecosystems.
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Affiliation(s)
- Daniela Boanares
- Instituto Tecnológico Vale, Belém 66055-090, PA, Brazil; (D.B.); (K.J.A.C.); (J.P.P.S.F.); (M.L.O.C.S.); (M.G.); (R.V.); (P.S.M.); (S.J.R.)
| | - Cristiane J. Da-Silva
- Department of Horticulture Science, North Carolina State University, Raleigh, NC 27695-7609, USA;
| | - Keila Jamille Alves Costa
- Instituto Tecnológico Vale, Belém 66055-090, PA, Brazil; (D.B.); (K.J.A.C.); (J.P.P.S.F.); (M.L.O.C.S.); (M.G.); (R.V.); (P.S.M.); (S.J.R.)
| | | | | | - Luiz Palhares Neto
- Department of Biology, Universidade Estadual do Sudoeste da Bahia, Jequié 45083-900, BA, Brazil;
| | - Markus Gastauer
- Instituto Tecnológico Vale, Belém 66055-090, PA, Brazil; (D.B.); (K.J.A.C.); (J.P.P.S.F.); (M.L.O.C.S.); (M.G.); (R.V.); (P.S.M.); (S.J.R.)
| | - Rafael Valadares
- Instituto Tecnológico Vale, Belém 66055-090, PA, Brazil; (D.B.); (K.J.A.C.); (J.P.P.S.F.); (M.L.O.C.S.); (M.G.); (R.V.); (P.S.M.); (S.J.R.)
| | - Priscila Sanjuan Medeiros
- Instituto Tecnológico Vale, Belém 66055-090, PA, Brazil; (D.B.); (K.J.A.C.); (J.P.P.S.F.); (M.L.O.C.S.); (M.G.); (R.V.); (P.S.M.); (S.J.R.)
| | - Silvio Junio Ramos
- Instituto Tecnológico Vale, Belém 66055-090, PA, Brazil; (D.B.); (K.J.A.C.); (J.P.P.S.F.); (M.L.O.C.S.); (M.G.); (R.V.); (P.S.M.); (S.J.R.)
| | - Cecilio Frois Caldeira
- Instituto Tecnológico Vale, Belém 66055-090, PA, Brazil; (D.B.); (K.J.A.C.); (J.P.P.S.F.); (M.L.O.C.S.); (M.G.); (R.V.); (P.S.M.); (S.J.R.)
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Li S, Devi B, Allam G, Bhullar A, Murmu J, Li E, Hepworth SR. Regulation of secondary growth by poplar BLADE-ON-PETIOLE genes in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2023; 14:1244583. [PMID: 38034559 PMCID: PMC10682204 DOI: 10.3389/fpls.2023.1244583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/17/2023] [Indexed: 12/02/2023]
Abstract
BLADE-ON-PETIOLE (BOP) genes are essential regulators of vegetative and reproductive development in land plants. First characterized in Arabidopsis thaliana (Arabidopsis), members of this clade function as transcriptional co-activators by recruiting TGACG-motif binding (TGA) basic leucine zipper (bZIP) transcription factors. Highly expressed at organ boundaries, these genes are also expressed in vascular tissue and contribute to lignin biosynthesis during secondary growth. How these genes function in trees, which undergo extensive secondary growth to produce wood, remains unclear. Here, we investigate the functional conservation of BOP orthologs in Populus trichocarpa (poplar), a widely-used model for tree development. Within the poplar genome, we identified two BOP-like genes, PtrBPL1 and PtrBPL2, with abundant transcripts in stems. To assess their functions, we used heterologous assays in Arabidopsis plants. The promoters of PtrBPL1 and PtrBPL2, fused with a β-glucuronidase (GUS) reporter gene showed activity at organ boundaries and in secondary xylem and phloem. When introduced into Arabidopsis plants, PtrBPL1 and PtrBPL2 complemented leaf and flower patterning defects in bop1 bop2 mutants. Notably, Arabidopsis plants overexpressing PtrBPL1 and PtrBPL2 showed defects in stem elongation and the lignification of secondary tissues in the hypocotyl and stem. Finally, PtrBPL1 and PtrBPL2 formed complexes with TGA bZIP proteins in yeast. Collectively, our findings suggest that PtrBPL1 and PtrBPL2 are orthologs of Arabidopsis BOP1 and BOP2, potentially contributing to secondary growth regulation in poplar trees. This work provides a foundation for functional studies in trees.
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Su S, Lei Y, Zhou X, Suzuki T, Xiao W, Higashiyama T. A BLADE-ON-PETIOLE orthologue regulates corolla differentiation in the proximal region in Torenia fournieri. Nat Commun 2023; 14:4763. [PMID: 37553331 PMCID: PMC10409793 DOI: 10.1038/s41467-023-40399-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 07/26/2023] [Indexed: 08/10/2023] Open
Abstract
The three-dimensional shape of a flower is integrated by morphogenesis along different axes. Differentiation along the petal proximodistal axis is tightly linked to the specification of pollinators; however, it is still unclear how a petal patterns this axis. The corolla of Torenia fournieri exhibits strong differentiation along the proximodistal axis, and we previously found a proximal regulator, TfALOG3, controlling corolla neck differentiation. Here, we report another gene, TfBOP2, which is predominantly expressed in the proximal region of the corolla. TfBOP2 mutants have shorter proximal corolla tubes and longer distal lobe, demonstrating its function as a proximal regulator. Arabidopsis BOPs mutant shows similar defects, favouring a shared role of BOPs homologues. Genetic analysis demonstrates the interaction between TfBOP2 and TfALOG3, and we further found that TfALOG3 physically interacts with TfBOP2 and can recruit TfBOP2 to the nuclear region. Our study favours a hypothetical shared BOP-ALOG complex that is recruited to regulate corolla differentiation in the proximal region axis of T. fournieri.
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Affiliation(s)
- Shihao Su
- School of Agriculture, Sun Yat-sen University, 518107, Shenzhen, China.
| | - Yawen Lei
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, 510316, Guangzhou, Guangdong, China
| | - Xuan Zhou
- School of Agriculture, Sun Yat-sen University, 518107, Shenzhen, China
| | - Takamasa Suzuki
- College of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, 487-8501, Japan
| | - Wei Xiao
- MBP-Center for Plant Molecular Biology, University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Tetsuya Higashiyama
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
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Dolde U, Muzzopappa F, Delesalle C, Neveu J, Erdel F, Vert G. LEAFY homeostasis is regulated via ubiquitin-dependent degradation and sequestration in cytoplasmic condensates. iScience 2023; 26:106880. [PMID: 37260753 PMCID: PMC10227421 DOI: 10.1016/j.isci.2023.106880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 04/06/2023] [Accepted: 05/11/2023] [Indexed: 06/02/2023] Open
Abstract
The transcription factor LEAFY (LFY) plays crucial roles in flower development by activating floral homeotic genes. Activation of LFY targets requires the combined action of LFY and the E3 ubiquitin ligase UFO, although the precise underlying mechanism remains unclear. Here, we show that LFY accumulates in biomolecular condensates within the cytoplasm, while recombinant LFY forms condensates with similar properties in vitro. UFO interacts with LFY within these condensates and marks it for degradation. LFY levels in the nucleus are buffered against changes in total LFY levels induced by proteasome inhibition, UFO overexpression, or mutation of lysine residues in a disordered region of LFY. Perturbation of cytoplasmic LFY condensates by 1,6-hexanediol treatment induces the relocalization of LFY to the nucleus and the subsequent activation of the LFY target AP3 in flowers. Our data suggest that nucleocytoplasmic partitioning, condensation, and ubiquitin-dependent degradation regulate LFY levels in the nucleus to control its activity.
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Affiliation(s)
- Ulla Dolde
- Plant Science Research Laboratory (LRSV), UMR5546 CNRS/University of Toulouse/Toulouse-INP, 24 chemin de Borde Rouge, 31320 Auzeville Tolosane, France
| | - Fernando Muzzopappa
- Center for Integrative Biology (CBI), Molecular, Cellular and Developmental Biology UMR5077 CNRS/University of Toulouse, 169 Avenue Marianne Grunberg-Manago, 31062 Toulouse Cedex, France
| | - Charlotte Delesalle
- Plant Science Research Laboratory (LRSV), UMR5546 CNRS/University of Toulouse/Toulouse-INP, 24 chemin de Borde Rouge, 31320 Auzeville Tolosane, France
| | - Julie Neveu
- Plant Science Research Laboratory (LRSV), UMR5546 CNRS/University of Toulouse/Toulouse-INP, 24 chemin de Borde Rouge, 31320 Auzeville Tolosane, France
| | - Fabian Erdel
- Center for Integrative Biology (CBI), Molecular, Cellular and Developmental Biology UMR5077 CNRS/University of Toulouse, 169 Avenue Marianne Grunberg-Manago, 31062 Toulouse Cedex, France
| | - Grégory Vert
- Plant Science Research Laboratory (LRSV), UMR5546 CNRS/University of Toulouse/Toulouse-INP, 24 chemin de Borde Rouge, 31320 Auzeville Tolosane, France
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7
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Rieu P, Turchi L, Thévenon E, Zarkadas E, Nanao M, Chahtane H, Tichtinsky G, Lucas J, Blanc-Mathieu R, Zubieta C, Schoehn G, Parcy F. The F-box protein UFO controls flower development by redirecting the master transcription factor LEAFY to new cis-elements. NATURE PLANTS 2023; 9:315-329. [PMID: 36732360 DOI: 10.1038/s41477-022-01336-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 12/20/2022] [Indexed: 06/18/2023]
Abstract
In angiosperms, flower development requires the combined action of the transcription factor LEAFY (LFY) and the ubiquitin ligase adaptor F-box protein, UNUSUAL FLORAL ORGANS (UFO), but the molecular mechanism underlying this synergy has remained unknown. Here we show in transient assays and stable transgenic plants that the connection to ubiquitination pathways suggested by the UFO F-box domain is mostly dispensable. On the basis of biochemical and genome-wide studies, we establish that UFO instead acts by forming an active transcriptional complex with LFY at newly discovered regulatory elements. Structural characterization of the LFY-UFO-DNA complex by cryo-electron microscopy further demonstrates that UFO performs this function by directly interacting with both LFY and DNA. Finally, we propose that this complex might have a deep evolutionary origin, largely predating flowering plants. This work reveals a unique mechanism of an F-box protein directly modulating the DNA binding specificity of a master transcription factor.
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Affiliation(s)
- Philippe Rieu
- Laboratoire Physiologie Cellulaire et Végétale, IRIG-DBSCI-LPCV, Université Grenoble Alpes, CEA, CNRS, INRAE, Grenoble, France
| | - Laura Turchi
- Laboratoire Physiologie Cellulaire et Végétale, IRIG-DBSCI-LPCV, Université Grenoble Alpes, CEA, CNRS, INRAE, Grenoble, France
- Translational Innovation in Medicine and Complexity, Université Grenoble Alpes, CNRS, Grenoble, France
| | - Emmanuel Thévenon
- Laboratoire Physiologie Cellulaire et Végétale, IRIG-DBSCI-LPCV, Université Grenoble Alpes, CEA, CNRS, INRAE, Grenoble, France
| | - Eleftherios Zarkadas
- IBS, Université Grenoble Alpes, CNRS, CEA, Grenoble, France
- EMBL, ISBG, Université Grenoble Alpes, CNRS, CEA, Grenoble, France
| | - Max Nanao
- Structural Biology Group, European Synchrotron Radiation Facility, Grenoble, France
| | - Hicham Chahtane
- Laboratoire Physiologie Cellulaire et Végétale, IRIG-DBSCI-LPCV, Université Grenoble Alpes, CEA, CNRS, INRAE, Grenoble, France
- Green Mission Pierre Fabre, Conservatoire Botanique Pierre Fabre, Institut de Recherche Pierre Fabre, Soual, France
| | - Gabrielle Tichtinsky
- Laboratoire Physiologie Cellulaire et Végétale, IRIG-DBSCI-LPCV, Université Grenoble Alpes, CEA, CNRS, INRAE, Grenoble, France
| | - Jérémy Lucas
- Laboratoire Physiologie Cellulaire et Végétale, IRIG-DBSCI-LPCV, Université Grenoble Alpes, CEA, CNRS, INRAE, Grenoble, France
| | - Romain Blanc-Mathieu
- Laboratoire Physiologie Cellulaire et Végétale, IRIG-DBSCI-LPCV, Université Grenoble Alpes, CEA, CNRS, INRAE, Grenoble, France
| | - Chloe Zubieta
- Laboratoire Physiologie Cellulaire et Végétale, IRIG-DBSCI-LPCV, Université Grenoble Alpes, CEA, CNRS, INRAE, Grenoble, France
| | - Guy Schoehn
- IBS, Université Grenoble Alpes, CNRS, CEA, Grenoble, France
| | - François Parcy
- Laboratoire Physiologie Cellulaire et Végétale, IRIG-DBSCI-LPCV, Université Grenoble Alpes, CEA, CNRS, INRAE, Grenoble, France.
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Overexpression of Liriodenron WOX5 in Arabidopsis Leads to Ectopic Flower Formation and Altered Root Morphology. Int J Mol Sci 2023; 24:ijms24020906. [PMID: 36674428 PMCID: PMC9860802 DOI: 10.3390/ijms24020906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/23/2022] [Accepted: 12/26/2022] [Indexed: 01/06/2023] Open
Abstract
Roots are essential for plant growth, and studies on root-related genes, exemplified by WUSCHEL-RELATED HOMEOBOX5 (WOX5), have mainly concentrated on model organisms with less emphasis on the function of these genes in woody plants. Here, we report that overexpression of the WOX5 gene from Liriodendron hybrid (LhWOX5) in Arabidopsis leads to significant morphological changes in both the aerial and subterranean organs. In the Arabidopsis aerial parts, overexpression of LhWOX5 results in the production of ectopic floral meristems and leaves, possibly via the ectopic activation of CLV3 and LFY. In addition, in the Arabidopsis root, overexpression of LhWOX5 alters root apical meristem morphology, leading to a curled and shortened primary root. Importantly, these abnormal phenotypes in the aerial and subterranean organs caused by constitutive ectopic expression of LhWOX5 mimic the observed phenotypes when overexpressing AtWUS and AtWOX5 in Arabidopsis, respectively. Taken together, we propose that the LhWOX5 gene, originating from the Magnoliaceae plant Liriodendron, is a functional homolog of the AtWUS gene from Arabidopsis, while showing the highest degree of sequence similarity with its ortholog, AtWOX5. Our study provides insight into the potential role of LhWOX5 in the development of both the shoot and root.
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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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Liu S, Magne K, Zhou J, Laude J, Dalmais M, Le Signor C, Bendahmane A, Thompson R, Couzigou JM, Ratet P. The transcriptional co-regulators NBCL1 and NBCL2 redundantly coordinate aerial organ development and root nodule identity in legumes. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:194-213. [PMID: 36197099 DOI: 10.1093/jxb/erac389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Medicago truncatula NODULE ROOT1 (MtNOOT1) and Pisum sativum COCHLEATA1 (PsCOCH1) are orthologous genes belonging to the NOOT-BOP-COCH-LIKE (NBCL) gene family which encodes key transcriptional co-regulators of plant development. In Mtnoot1 and Pscoch1 mutants, the development of stipules, flowers, and symbiotic nodules is altered. MtNOOT2 and PsCOCH2 represent the single paralogues of MtNOOT1 and PsCOCH1, respectively. In M. truncatula, MtNOOT1 and MtNOOT2 are both required for the establishment and maintenance of symbiotic nodule identity. In legumes, the role of NBCL2 in above-ground development is not known. To better understand the roles of NBCL genes in legumes, we used M. truncatula and P. sativum nbcl mutants, isolated a knockout mutant for the PsCOCH2 locus and generated Pscoch1coch2 double mutants in P. sativum. Our work shows that single Mtnoot2 and Pscoch2 mutants develop wild-type stipules, flowers, and symbiotic nodules. However, the number of flowers was increased and the pods and seeds were smaller compared to the wild type. Furthermore, in comparison to the corresponding nbcl1 single mutants, both the M. truncatula and P. sativum nbcl double mutants show a drastic alteration in stipule, inflorescence, flower, and nodule development. Remarkably, in both M. truncatula and P. sativum nbcl double mutants, stipules are transformed into a range of aberrant leaf-like structures.
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Affiliation(s)
- Shengbin Liu
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, 91190, Gif sur Yvette, France
| | - Kévin Magne
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, 91190, Gif sur Yvette, France
| | - Jing Zhou
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, 31320, Auzeville Tolosane, France
| | - Juliette Laude
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, 91190, Gif sur Yvette, France
| | - Marion Dalmais
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, 91190, Gif sur Yvette, France
| | - Christine Le Signor
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique (INRAE), Université Bourgogne Franche-Comté, 21000, Dijon, France
| | - Abdelhafid Bendahmane
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, 91190, Gif sur Yvette, France
| | - Richard Thompson
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique (INRAE), Université Bourgogne Franche-Comté, 21000, Dijon, France
| | - Jean-Malo Couzigou
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, 31320, Auzeville Tolosane, France
| | - Pascal Ratet
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, 91190, Gif sur Yvette, France
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11
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Zhang J, Wang X, Han L, Zhang J, Xie Y, Li J, Wang ZY, Wen J, Mysore KS, Zhou C. The formation of stipule requires the coordinated actions of the legume orthologs of Arabidopsis BLADE-ON-PETIOLE and LEAFY. THE NEW PHYTOLOGIST 2022; 236:1512-1528. [PMID: 36031740 DOI: 10.1111/nph.18445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 08/06/2022] [Indexed: 06/15/2023]
Abstract
Stipule morphology is a classical botanical key character used in plant identification. Stipules are considerably diverse in size, function and architecture, such as leaf-like stipules, spines or tendrils. However, the molecular mechanism that regulates stipule identity remains largely unknown. We isolated mutants with abnormal stipules. The mutated gene encodes the NODULE ROOT1 (MtNOOT1), which is the ortholog of BLADE-ON-PETIOLE (BOP) in Medicago truncatula. We also obtained mutants of MtNOOT2, the homolog of MtNOOT1, but they do not show obvious defects in stipules. The mtnoot1 mtnoot2 double mutant shows a higher proportion of transformation from stipules to leaflet-like stipules than the single mutants, suggesting that they redundantly determine stipule identity. Further investigations show that MtNOOTs control stipule initiation together with SINGLE LEAFLET1 (SGL1), which functions in development of lateral leaflets. Increasing SGL1 activity in mtnoot1 mtnoot2 is sufficient for the transformation of stipules to leaves. Moreover, MtNOOTs inhibit SGL1 expression during stipule development, which is probably conserved in legume species. Our study proposes a genetic regulatory model for stipule development, specifically with regard to the MtNOOTs-SGL1 module, which functions in two phases of stipule development, first in the control of stipule initiation and second in stipule patterning.
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Affiliation(s)
- Juanjuan Zhang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Xiao Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Lu Han
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Jing Zhang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Yangyang Xie
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Jie Li
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Zeng-Yu Wang
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jiangqi Wen
- Institute for Agricultural Biosciences, Oklahoma State University, 3210 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Kirankumar S Mysore
- Institute for Agricultural Biosciences, Oklahoma State University, 3210 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Chuanen Zhou
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
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12
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Gao X, Li X, Chen C, Wang C, Fu Y, Zheng Z, Shi M, Hao X, Zhao L, Qiu M, Kai G, Zhou W. Mining of the CULLIN E3 ubiquitin ligase genes in the whole genome of Salvia miltiorrhiza. Curr Res Food Sci 2022; 5:1760-1768. [PMID: 36268136 PMCID: PMC9576582 DOI: 10.1016/j.crfs.2022.10.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/01/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022] Open
Abstract
CULLIN (CUL) proteins are E3 ubiquitin ligases that are involved in a wide variety of biological processes as well as in response to stress in plants. In Salvia miltiorrhiza, CUL genes have not been characterized and its role in plant development, stress response and secondary metabolite synthesis have not been studied. In this study, genome-wide analyses were performed to identify and to predict the structure and function of CUL of S. miltiorrhiza. Eight CUL genes were identified from the genome of S. miltiorrhiza. The CUL genes were clustered into four subgroups according to phylogenetic relationships. The CUL domain was highly conserved across the family of CUL genes. Analysis of cis-acting elements suggested that CUL genes might play important roles in a variety of biological processes, including abscission reaction acid (ABA) processing. To investigate this hypothesis, we treated hairy roots of S. miltiorrhiza with ABA. The expression of CUL genes varied obviously after ABA treatment. Co-expression network results indicated that three CUL genes might be involved in the biosynthesis of phenolic acid or tanshinone. In summary, the mining of the CUL genes in the whole genome of S. miltiorrhiza contribute novel information to the understanding of the CUL genes and its functional roles in plant secondary metabolites, growth and development.
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Affiliation(s)
- Xiankui Gao
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 311402, PR China
| | - Xiujuan Li
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 311402, PR China
| | - Chengan Chen
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 311402, PR China
| | - Can Wang
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 311402, PR China
| | - Yuqi Fu
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 311402, PR China
| | - ZiZhen Zheng
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 311402, PR China
| | - Min Shi
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 311402, PR China
| | - Xiaolong Hao
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 311402, PR China
| | - Limei Zhao
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 311402, PR China
| | - Minghua Qiu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, PR China
| | - Guoyin Kai
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 311402, PR China,Corresponding author. School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Gaoke Road, Fuyang district, Hangzhou, Zhejiang, 311402, PR China.
| | - Wei Zhou
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 311402, PR China,Corresponding author. School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Gaoke Road, Fuyang district, Hangzhou, Zhejiang, 311402, PR China.
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13
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Varshney V, Majee M. Emerging roles of the ubiquitin-proteasome pathway in enhancing crop yield by optimizing seed agronomic traits. PLANT CELL REPORTS 2022; 41:1805-1826. [PMID: 35678849 DOI: 10.1007/s00299-022-02884-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
Ubiquitin-proteasome pathway has the potential to modulate crop productivity by influencing agronomic traits. Being sessile, the plant often uses the ubiquitin-proteasome pathway to maintain the stability of different regulatory proteins to survive in an ever-changing environment. The ubiquitin system influences plant reproduction, growth, development, responses to the environment, and processes that control critical agronomic traits. E3 ligases are the major players in this pathway, and they are responsible for recognizing and tagging the targets/substrates. Plants have a variety of E3 ubiquitin ligases, whose functions have been studied extensively, ranging from plant growth to defense strategies. Here we summarize three agronomic traits influenced by ubiquitination: seed size and weight, seed germination, and accessory plant agronomic traits particularly panicle architecture, tillering in rice, and tassels branch number in maize. This review article highlights some recent progress on how the ubiquitin system influences the stability/modification of proteins that determine seed agronomic properties like size, weight, germination and filling, and ultimately agricultural productivity and quality. Further research into the molecular basis of the aforementioned processes might lead to the identification of genes that could be modified or selected for crop development. Likewise, we also propose advances and future perspectives in this regard.
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Affiliation(s)
- Vishal Varshney
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Manoj Majee
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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14
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Smalley S, Hellmann H. Review: Exploring possible approaches using ubiquitylation and sumoylation pathways in modifying plant stress tolerance. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 319:111275. [PMID: 35487671 DOI: 10.1016/j.plantsci.2022.111275] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 06/14/2023]
Abstract
Ubiquitin and similar proteins, such as SUMO, are utilized by plants to modify target proteins to rapidly change their stability and activity in cells. This review will provide an overview of these crucial protein interactions with a focus on ubiquitylation and sumoylation in plants and how they contribute to stress tolerance. The work will also explore possibilities to use these highly conserved pathways for novel approaches to generate more robust crop plants better fit to cope with abiotic and biotic stress situations.
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Affiliation(s)
- Samuel Smalley
- Washington State University, Pullman, WA 99164, United States
| | - Hanjo Hellmann
- Washington State University, Pullman, WA 99164, United States.
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15
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(De)Activation (Ir)Reversibly or Degradation: Dynamics of Post-Translational Protein Modifications in Plants. Life (Basel) 2022; 12:life12020324. [PMID: 35207610 PMCID: PMC8874572 DOI: 10.3390/life12020324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/11/2022] [Accepted: 02/16/2022] [Indexed: 11/22/2022] Open
Abstract
The increasing dynamic functions of post-translational modifications (PTMs) within protein molecules present outstanding challenges for plant biology even at this present day. Protein PTMs are among the first and fastest plant responses to changes in the environment, indicating that the mechanisms and dynamics of PTMs are an essential area of plant biology. Besides being key players in signaling, PTMs play vital roles in gene expression, gene, and protein localization, protein stability and interactions, as well as enzyme kinetics. In this review, we take a broader but concise approach to capture the current state of events in the field of plant PTMs. We discuss protein modifications including citrullination, glycosylation, phosphorylation, oxidation and disulfide bridges, N-terminal, SUMOylation, and ubiquitination. Further, we outline the complexity of studying PTMs in relation to compartmentalization and function. We conclude by challenging the proteomics community to engage in holistic approaches towards identification and characterizing multiple PTMs on the same protein, their interaction, and mechanism of regulation to bring a deeper understanding of protein function and regulation in plants.
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16
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Liu S, Magne K, Daniel S, Sibout R, Ratet P. Brachypodium distachyon UNICULME4 and LAXATUM-A are redundantly required for development. PLANT PHYSIOLOGY 2022; 188:363-381. [PMID: 34662405 PMCID: PMC8774750 DOI: 10.1093/plphys/kiab456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
In cultivated grasses, tillering, leaf, and inflorescence architecture, as well as abscission ability, are major agronomical traits. In barley (Hordeum vulgare), maize (Zea mays), rice (Oryza sativa), and brachypodium (Brachypodium distachyon), NOOT-BOP-COCH-LIKE (NBCL) genes are essential regulators of vegetative and reproductive development. Grass species usually possess 2-4 NBCL copies and until now a single study in O. sativa showed that the disruption of all NBCL genes strongly altered O. sativa leaf development. To improve our understanding of the role of NBCL genes in grasses, we extended the study of the two NBCL paralogs BdUNICULME4 (CUL4) and BdLAXATUM-A (LAXA) in the nondomesticated grass B. distachyon. For this, we applied reversed genetics and generated original B. distachyon single and double nbcl mutants by clustered regularly interspaced short palindromic repeats - CRISPR associated protein 9 (CRISPR-Cas9) approaches and genetic crossing between nbcl targeting induced local lesions in genomes (TILLING) mutants. Through the study of original single laxa CRISPR-Cas9 null alleles, we validated functions previously proposed for LAXA in tillering, leaf patterning, inflorescence, and flower development and also unveiled roles for these genes in seed yield. Furthermore, the characterization of cul4laxa double mutants revealed essential functions for nbcl genes in B. distachyon development, especially in the regulation of tillering, stem cell elongation and secondary cell wall composition as well as for the transition toward the reproductive phase. Our results also highlight recurrent antagonist interactions between NBCLs occurring in multiple aspects of B. distachyon development.
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Affiliation(s)
- Shengbin Liu
- Université Paris-Saclay, INRAE, CNRS, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay 91405, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Orsay 91405, France
| | - Kévin Magne
- Université Paris-Saclay, INRAE, CNRS, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay 91405, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Orsay 91405, France
| | - Sylviane Daniel
- UR1268 BIA (Biopolymères Interactions Assemblages), INRAE, Nantes 44300, France
| | - Richard Sibout
- UR1268 BIA (Biopolymères Interactions Assemblages), INRAE, Nantes 44300, France
| | - Pascal Ratet
- Université Paris-Saclay, INRAE, CNRS, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay 91405, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Orsay 91405, France
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17
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Klocko AL, Goddard AL, Jacobson JR, Magnuson AC, Strauss SH. RNAi Suppression of LEAFY Gives Stable Floral Sterility, and Reduced Growth Rate and Leaf Size, in Field-Grown Poplars. PLANTS 2021; 10:plants10081594. [PMID: 34451639 PMCID: PMC8398303 DOI: 10.3390/plants10081594] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/23/2021] [Accepted: 07/30/2021] [Indexed: 11/29/2022]
Abstract
The central floral development gene LEAFY (LFY), whose mutation leads to striking changes in flowering and often sterility, is commonly expressed in non-floral structures; however, its role in vegetative development is poorly understood. Sterility associated with suppression of LFY expression is an attractive means for mitigating gene flow by both seeds and pollen in vegetatively propagated forest trees, but the consequences of its suppression for tree form and wood production are unclear. To study the vegetative effects of RNAi suppression of LFY, we created a randomized, multiple-year field study with 30–40 trees (ramets) in each of two sterile gene insertion events, three transgenic control events, and a wild-type control population. We found that floral knock-down phenotypes were stable across years and propagation cycles, but that several leaf morphology and productivity traits were statistically and often substantially different in sterile vs. normal flowering RNAi-LFY trees. Though trees with suppressed LEAFY expression looked visibly normal, they appear to have reduced growth and altered leaf traits. LFY appears to have a significant role in vegetative meristem development, and evaluation of vegetative impacts from LFY suppression would be prudent prior to large-scale use for genetic containment.
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Affiliation(s)
- Amy L. Klocko
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA;
| | - Amanda L. Goddard
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97331, USA; (A.L.G.); (J.R.J.); (A.C.M.)
| | - Jeremy R. Jacobson
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97331, USA; (A.L.G.); (J.R.J.); (A.C.M.)
| | - Anna C. Magnuson
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97331, USA; (A.L.G.); (J.R.J.); (A.C.M.)
| | - Steven H. Strauss
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97331, USA; (A.L.G.); (J.R.J.); (A.C.M.)
- Correspondence:
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18
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Ban Z, Estelle M. CUL3 E3 ligases in plant development and environmental response. NATURE PLANTS 2021; 7:6-16. [PMID: 33452490 PMCID: PMC8932378 DOI: 10.1038/s41477-020-00833-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 12/08/2020] [Indexed: 05/19/2023]
Abstract
Thirty years of research have revealed the fundamental role of the ubiquitin-proteasome system in diverse aspects of cellular regulation in eukaryotes. The ubiquitin-protein ligases or E3s are central to the ubiquitin-proteasome system since they determine the specificity of ubiquitylation. The cullin-RING ligases (CRLs) constitute one large class of E3s that can be subdivided based on the cullin isoform and the substrate adapter. SCF complexes, composed of CUL1 and the SKP1/F-box protein substrate adapter, are perhaps the best characterized in plants. More recently, accumulating evidence has demonstrated the essential roles of CRL3 E3s, consisting of a CUL3 protein and a BTB/POZ substrate adaptor. In this Review, we describe the variety of CRL3s functioning in plants and the wide range of processes that they regulate. Furthermore, we illustrate how different classes of E3s may cooperate to regulate specific pathways or processes.
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Affiliation(s)
- Zhaonan Ban
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA
| | - Mark Estelle
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA.
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19
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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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20
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Zavaliev R, Mohan R, Chen T, Dong X. Formation of NPR1 Condensates Promotes Cell Survival during the Plant Immune Response. Cell 2020; 182:1093-1108.e18. [PMID: 32810437 DOI: 10.1016/j.cell.2020.07.016] [Citation(s) in RCA: 154] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 04/20/2020] [Accepted: 07/13/2020] [Indexed: 01/07/2023]
Abstract
In plants, pathogen effector-triggered immunity (ETI) often leads to programmed cell death, which is restricted by NPR1, an activator of systemic acquired resistance. However, the biochemical activities of NPR1 enabling it to promote defense and restrict cell death remain unclear. Here we show that NPR1 promotes cell survival by targeting substrates for ubiquitination and degradation through formation of salicylic acid-induced NPR1 condensates (SINCs). SINCs are enriched with stress response proteins, including nucleotide-binding leucine-rich repeat immune receptors, oxidative and DNA damage response proteins, and protein quality control machineries. Transition of NPR1 into condensates is required for formation of the NPR1-Cullin 3 E3 ligase complex to ubiquitinate SINC-localized substrates, such as EDS1 and specific WRKY transcription factors, and promote cell survival during ETI. Our analysis of SINCs suggests that NPR1 is centrally integrated into the cell death or survival decisions in plant immunity by modulating multiple stress-responsive processes in this quasi-organelle.
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Affiliation(s)
- Raul Zavaliev
- Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA; Department of Biology, Duke University, Durham, NC 27708, USA
| | | | - Tianyuan Chen
- Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA; Department of Biology, Duke University, Durham, NC 27708, USA
| | - Xinnian Dong
- Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA; Department of Biology, Duke University, Durham, NC 27708, USA.
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21
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He L, Lei Y, Li X, Peng Q, Liu W, Jiao K, Su S, Hu Z, Shen Z, Luo D. SYMMETRIC PETALS 1 Encodes an ALOG Domain Protein that Controls Floral Organ Internal Asymmetry in Pea ( Pisum sativum L.). Int J Mol Sci 2020; 21:E4060. [PMID: 32517095 PMCID: PMC7313044 DOI: 10.3390/ijms21114060] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 05/31/2020] [Accepted: 06/03/2020] [Indexed: 11/16/2022] Open
Abstract
In contrast to typical radially symmetrical flowers, zygomorphic flowers, such as those produced by pea (Pisum sativum L.), have bilateral symmetry, manifesting dorsoventral (DV) and organ internal (IN) asymmetry. However, the molecular mechanism controlling IN asymmetry remains largely unclear. Here, we used a comparative mapping approach to clone SYMMETRIC PETALS 1 (SYP1), which encodes a key regulator of floral organ internal asymmetry. Phylogenetic analysis showed that SYP1 is an ortholog of Arabidopsis thaliana LIGHT-DEPENDENT SHORT HYPOCOTYL 3 (LSH3), an ALOG (Arabidopsis LSH1 and Oryza G1) family transcription factor. Genetic analysis and physical interaction assays showed that COCHLEATA (COCH, Arabidopsis BLADE-ON-PETIOLE ortholog), a known regulator of compound leaf and nodule identity in pea, is involved in organ internal asymmetry and interacts with SYP1. COCH and SYP1 had similar expression patterns and COCH and SYP1 target to the nucleus. Furthermore, our results suggested that COCH represses the 26S proteasome-mediated degradation of SYP1 and regulates its abundance. Our study suggested that the COCH-SYP1 module plays a pivotal role in floral organ internal asymmetry development in legumes.
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Affiliation(s)
- Liang He
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (L.H.); (Y.L.); (Q.P.); (W.L.); (K.J.); (S.S.); (D.L.)
| | - Yawen Lei
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (L.H.); (Y.L.); (Q.P.); (W.L.); (K.J.); (S.S.); (D.L.)
| | - Xin Li
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China;
| | - Qincheng Peng
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (L.H.); (Y.L.); (Q.P.); (W.L.); (K.J.); (S.S.); (D.L.)
| | - Wei Liu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (L.H.); (Y.L.); (Q.P.); (W.L.); (K.J.); (S.S.); (D.L.)
| | - Keyuan Jiao
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (L.H.); (Y.L.); (Q.P.); (W.L.); (K.J.); (S.S.); (D.L.)
| | - Shihao Su
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (L.H.); (Y.L.); (Q.P.); (W.L.); (K.J.); (S.S.); (D.L.)
| | - Zhubing Hu
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng 475004, China;
| | - Zhenguo Shen
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China;
| | - Da Luo
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (L.H.); (Y.L.); (Q.P.); (W.L.); (K.J.); (S.S.); (D.L.)
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Zhu Y, Wagner D. Plant Inflorescence Architecture: The Formation, Activity, and Fate of Axillary Meristems. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a034652. [PMID: 31308142 DOI: 10.1101/cshperspect.a034652] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The above-ground plant body in different plant species can have very distinct forms or architectures that arise by recurrent redeployment of a finite set of building blocks-leaves with axillary meristems, stems or branches, and flowers. The unique architectures of plant inflorescences in different plant families and species, on which this review focuses, determine the reproductive success and yield of wild and cultivated plants. Major contributors to the inflorescence architecture are the activity and developmental trajectories adopted by axillary meristems, which determine the degree of branching and the number of flowers formed. Recent advances in genetic and molecular analyses in diverse flowering plants have uncovered both common regulatory principles and unique players and/or regulatory interactions that underlie inflorescence architecture. Modulating activity of these regulators has already led to yield increases in the field. Additional insight into the underlying regulatory interactions and principles will not only uncover how their rewiring resulted in altered plant form, but will also enhance efforts at optimizing plant architecture in desirable ways in crop species.
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Affiliation(s)
- Yang Zhu
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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