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Grismer TS, Karundasa SS, Shrestha R, Byun D, Ni W, Reyes AV, Xu SL. Workflow enhancement of TurboID-mediated proximity labeling for SPY signaling network mapping. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.17.580820. [PMID: 38405906 PMCID: PMC10888891 DOI: 10.1101/2024.02.17.580820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
TurboID-based proximity labeling coupled to mass spectrometry (PL-MS) has emerged as a powerful tool for mapping protein-protein interactions in both plant and animal systems. Despite advances in sensitivity, PL-MS studies can still suffer from false negatives, especially when dealing with low abundance bait proteins and their transient interactors. Protein-level enrichment for biotinylated proteins is well developed and popular, but direct detection of biotinylated proteins by peptide-level enrichment and the difference in results between direct and indirect detection remain underexplored. To address this gap, we compared and improved enrichment and data analysis methods using TurboID fused to SPY, a low-abundance O-fucose transferase, using an AAL-enriched SPY target library for cross-referencing. Our results showed that MyOne and M280 streptavidin beads significantly outperformed antibody beads for peptide-level enrichment, with M280 performing best. In addition, while a biotin concentration ≤ 50 μM is recommended for protein-level enrichment in plants, higher biotin concentrations can be used for peptide-level enrichment, allowing us to improve detection and data quality. FragPipe's MSFragger protein identification and quantification software outperformed Maxquant and Protein Prospector for SPY interactome enrichment due to its superior detection of biotinylated peptides. Our improved washing protocols for protein-level enrichment mitigated bead collapse issues, improving data quality, and reducing experimental time. We found that the two enrichment methods provided complementary results and identified a total of 160 SPY-TurboID-enriched interactors, including 60 previously identified in the AAL-enriched SPY target list and 100 additional novel interactors. SILIA quantitative proteomics comparing WT and spy-4 mutants showed that SPY affects the protein levels of some of the identified interactors, such as nucleoporin proteins. We expect that our improvement will extend beyond TurboID to benefit other PL systems and hold promise for broader applications in biological research.
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Affiliation(s)
- TaraBryn S Grismer
- Division of biosphere science and engineering, Carnegie Institution for Science, Stanford, California, USA
- Carnegie Mass Spectrometry Facility, Carnegie Institution for Science, Stanford, California, USA
| | - Sumudu S Karundasa
- Division of biosphere science and engineering, Carnegie Institution for Science, Stanford, California, USA
| | - Ruben Shrestha
- Division of biosphere science and engineering, Carnegie Institution for Science, Stanford, California, USA
| | - Danbi Byun
- Division of biosphere science and engineering, Carnegie Institution for Science, Stanford, California, USA
| | - Weimin Ni
- Division of biosphere science and engineering, Carnegie Institution for Science, Stanford, California, USA
| | - Andres V Reyes
- Division of biosphere science and engineering, Carnegie Institution for Science, Stanford, California, USA
- Carnegie Mass Spectrometry Facility, Carnegie Institution for Science, Stanford, California, USA
| | - Shou-Ling Xu
- Division of biosphere science and engineering, Carnegie Institution for Science, Stanford, California, USA
- Carnegie Mass Spectrometry Facility, Carnegie Institution for Science, Stanford, California, USA
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2
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Ma X, Feng L, Tao A, Zenda T, He Y, Zhang D, Duan H, Tao Y. Identification and validation of seed dormancy loci and candidate genes and construction of regulatory networks by WGCNA in maize introgression lines. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:259. [PMID: 38038768 DOI: 10.1007/s00122-023-04495-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/26/2023] [Indexed: 12/02/2023]
Abstract
KEY MESSAGE Seventeen PHS-QTLs and candidate genes were obtained, including eleven major loci, three under multiple environments and two with co-localization by the other mapping methods; The functions of three candidate genes were validated using mutants; nine target proteins and five networks were filtered by joint analysis of GWAS and WGCNA. Seed dormancy (SD) and pre-harvest sprouting (PHS) affect yield, as well as grain and hybrid quality in seed production. Therefore, identification of genetic and regulatory pathways underlying PHS and SD is key to gene function analysis, allelic variation mining and genetic improvement. In this study, 78,360 SNPs by SLAF-seq of 230 maize chromosome segment introgression lines (ILs), PHS under five environments were used to conduct GWAS (genome wide association study) (a threshold of 1/n), and seventeen unreported PHS QTLs were obtained, including eleven QTLs with PVE > 10% and three QTLs under multiple environments. Two QTL loci were co-located between the other two genetic mapping methods. Using differential gene expression analyses at two stages of grain development, gene functional analysis of Arabidopsis mutants, and gene functional analysis in the QTL region, seventeen PHS QTL-linked candidate genes were identified, and their five molecular regulatory networks constructed. Based on the Arabidopsis T-DNA mutations, three candidate genes were shown to regulate for SD and PHS. Meanwhile, using RNA-seq of grain development, the weighted correlation network analysis (WGCNA) was performed, deducing five regulatory pathways and target genes that regulate PHS and SD. Based on the conjoint analysis of GWAS and WGCNA, four pathways, nine target proteins and target genes were revealed, most of which regulate cell wall metabolism, cell proliferation and seed dehydration tolerance. This has important theoretical and practical significance for elucidating the genetic basis of maize PHS and SD, as well as mining of genetic resources and genetic improvement of traits.
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Affiliation(s)
- Xiaolin Ma
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
| | - Liqing Feng
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
| | - Anyan Tao
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
| | - Tinashe Zenda
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
| | - Yuan He
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
| | - Daxiao Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
| | - Huijun Duan
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China.
| | - Yongsheng Tao
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China.
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3
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Rahmati Ishka M, Julkowska M. Tapping into the plasticity of plant architecture for increased stress resilience. F1000Res 2023; 12:1257. [PMID: 38434638 PMCID: PMC10905174 DOI: 10.12688/f1000research.140649.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/24/2023] [Indexed: 03/05/2024] Open
Abstract
Plant architecture develops post-embryonically and emerges from a dialogue between the developmental signals and environmental cues. Length and branching of the vegetative and reproductive tissues were the focus of improvement of plant performance from the early days of plant breeding. Current breeding priorities are changing, as we need to prioritize plant productivity under increasingly challenging environmental conditions. While it has been widely recognized that plant architecture changes in response to the environment, its contribution to plant productivity in the changing climate remains to be fully explored. This review will summarize prior discoveries of genetic control of plant architecture traits and their effect on plant performance under environmental stress. We review new tools in phenotyping that will guide future discoveries of genes contributing to plant architecture, its plasticity, and its contributions to stress resilience. Subsequently, we provide a perspective into how integrating the study of new species, modern phenotyping techniques, and modeling can lead to discovering new genetic targets underlying the plasticity of plant architecture and stress resilience. Altogether, this review provides a new perspective on the plasticity of plant architecture and how it can be harnessed for increased performance under environmental stress.
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Bi Y, Shrestha R, Zhang Z, Hsu CC, Reyes AV, Karunadasa S, Baker PR, Maynard JC, Liu Y, Hakimi A, Lopez-Ferrer D, Hassan T, Chalkley RJ, Xu SL, Wang ZY. SPINDLY mediates O-fucosylation of hundreds of proteins and sugar-dependent growth in Arabidopsis. THE PLANT CELL 2023; 35:1318-1333. [PMID: 36739885 PMCID: PMC10118272 DOI: 10.1093/plcell/koad023] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 01/21/2023] [Indexed: 06/18/2023]
Abstract
The recent discovery of SPINDLY (SPY)-catalyzed protein O-fucosylation revealed a novel mechanism for regulating nucleocytoplasmic protein functions in plants. Genetic evidence indicates the important roles of SPY in diverse developmental and physiological processes. However, the upstream signal controlling SPY activity and the downstream substrate proteins O-fucosylated by SPY remain largely unknown. Here, we demonstrated that SPY mediates sugar-dependent growth in Arabidopsis (Arabidopsis thaliana). We further identified hundreds of O-fucosylated proteins using lectin affinity chromatography followed by mass spectrometry. All the O-fucosylation events quantified in our proteomic analyses were undetectable or dramatically decreased in the spy mutants, and thus likely catalyzed by SPY. The O-fucosylome includes mostly nuclear and cytosolic proteins. Many O-fucosylated proteins function in essential cellular processes, phytohormone signaling, and developmental programs, consistent with the genetic functions of SPY. The O-fucosylome also includes many proteins modified by O-linked N-acetylglucosamine (O-GlcNAc) and by phosphorylation downstream of the target of rapamycin (TOR) kinase, revealing the convergence of these nutrient signaling pathways on key regulatory functions such as post-transcriptional/translational regulation and phytohormone responses. Our study identified numerous targets of SPY/O-fucosylation and potential nodes of crosstalk among sugar/nutrient signaling pathways, enabling future dissection of the signaling network that mediates sugar regulation of plant growth and development.
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Affiliation(s)
| | | | | | - Chuan-Chih Hsu
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, USA
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan
| | - Andres V Reyes
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, USA
- Carnegie Mass Spectrometry Facility, Carnegie Institution for Science, Stanford, California 94305, USA
| | - Sumudu Karunadasa
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, USA
| | - Peter R Baker
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California 94143, USA
| | - Jason C Maynard
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California 94143, USA
| | - Yang Liu
- ThermoFisher Scientific, San Jose, California 95134, USA
| | | | | | - Tahmid Hassan
- ThermoFisher Scientific, Somerset, New Jersey 08873, USA
| | - Robert J Chalkley
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California 94143, USA
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Jiang H, Chen Y, Liu Y, Shang J, Sun X, Du J. Multifaceted roles of the ERECTA family in plant organ morphogenesis. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7208-7218. [PMID: 36056777 DOI: 10.1093/jxb/erac353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
Receptor-like kinases (RLKs) can participate in multiple signalling pathways and are considered one of the most critical components of the early events of intercellular signalling. As an RLK, the ERECTA family (ERf), which comprises ERECTA (ER), ERECTA-Like1 (ERL1), and ERECTA-Like2 (ERL2) in Arabidopsis, regulates multiple signalling pathways in plant growth and development. Despite its indispensability, detailed information on ERf-manipulated signalling pathways remains elusive. In this review, we attempt to summarize the essential roles of the ERf in plant organ morphogenesis, including shoot apical meristem, stem, and reproductive organ development.
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Affiliation(s)
- Hengke Jiang
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
- Research Center for Modern Agriculture of the Middle East, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Ministry of Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Yuhui Chen
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
- Research Center for Modern Agriculture of the Middle East, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Ministry of Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Yuhan Liu
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
- Research Center for Modern Agriculture of the Middle East, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Ministry of Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Jing Shang
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
- Research Center for Modern Agriculture of the Middle East, Sichuan Agricultural University, Chengdu 611130, China
| | - Xin Sun
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
- Research Center for Modern Agriculture of the Middle East, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Ministry of Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Junbo Du
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
- Research Center for Modern Agriculture of the Middle East, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Ministry of Agriculture, Sichuan Agricultural University, Chengdu 611130, China
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6
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Hauvermale AL, Cárdenas JJ, Bednarek SY, Steber CM. GA signaling expands: The plant UBX domain-containing protein 1 is a binding partner for the GA receptor. PLANT PHYSIOLOGY 2022; 190:2651-2670. [PMID: 36149293 PMCID: PMC9706445 DOI: 10.1093/plphys/kiac406] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 07/19/2022] [Indexed: 06/07/2023]
Abstract
The plant Ubiquitin Regulatory X (UBX) domain-containing protein 1 (PUX1) functions as a negative regulator of gibberellin (GA) signaling. GAs are plant hormones that stimulate seed germination, the transition to flowering, and cell elongation and division. Loss of Arabidopsis (Arabidopsis thaliana) PUX1 resulted in a "GA-overdose" phenotype including early flowering, increased stem and root elongation, and partial resistance to the GA-biosynthesis inhibitor paclobutrazol during seed germination and root elongation. Furthermore, GA application failed to stimulate further stem elongation or flowering onset suggesting that elongation and flowering response to GA had reached its maximum. GA hormone partially repressed PUX1 protein accumulation, and PUX1 showed a GA-independent interaction with the GA receptor GA-INSENSITIVE DWARF-1 (GID1). This suggests that PUX1 is GA regulated and/or regulates elements of the GA signaling pathway. Consistent with PUX1 function as a negative regulator of GA signaling, the pux1 mutant caused increased GID1 expression and decreased accumulation of the DELLA REPRESSOR OF GA1-3, RGA. PUX1 is a negative regulator of the hexameric AAA+ ATPase CDC48, a protein that functions in diverse cellular processes including unfolding proteins in preparation for proteasomal degradation, cell division, and expansion. PUX1 binding to GID1 required the UBX domain, a binding motif necessary for CDC48 interaction. Moreover, PUX1 overexpression in cell culture not only stimulated the disassembly of CDC48 hexamer but also resulted in co-fractionation of GID1, PUX1, and CDC48 subunits in velocity sedimentation assays. Based on our results, we propose that PUX1 and CDC48 are additional factors that need to be incorporated into our understanding of GA signaling.
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Affiliation(s)
- Amber L Hauvermale
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, USA
- Molecular Plant Sciences, Washington State University, Pullman, Washington, USA
| | - Jessica J Cárdenas
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Integrated Program in Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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7
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Zhu W, Yang C, Yong B, Wang Y, Li B, Gu Y, Wei S, An Z, Sun W, Qiu L, He C. An enhancing effect attributed to a nonsynonymous mutation in SOYBEAN SEED SIZE 1, a SPINDLY-like gene, is exploited in soybean domestication and improvement. THE NEW PHYTOLOGIST 2022; 236:1375-1392. [PMID: 36068955 DOI: 10.1111/nph.18461] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/12/2022] [Indexed: 05/26/2023]
Abstract
Soybean (Glycine max) was domesticated from its wild relative Glycine soja. One-hundred-seed weight is one of the most important domesticated traits determining soybean yield; however, its underlying genetic basis remains elusive. We characterized a soybean seed size 1 (sss1) mutant featuring large seeds compared to its wild-type background. Positional cloning revealed that the candidate gene GmSSS1 encoded a SPINDLY homolog and was co-located in a well-identified quantitative trait locus (QTL)-rich region on chromosome 19. Knocking out GmSSS1 resulted in small seeds, while overexpressing GmSSS1/Gmsss1 induced large seeds. Modulating GmSSS1/Gmsss1 in transgenic plants can positively influence cell expansion and cell division. Relative to GmSSS1, one mutation leading to an E to Q substitution at the 182nd residue in Gmsss1 conferred an enhancing effect on seed weight. GmSSS1 underwent diversification in wild-type and cultivated soybean, and the alleles encoding the Gmsss1-type substitution of 182nd -Q, which originated along the central and downstream parts of the Yellow River, were selected and expanded during soybean domestication and improvement. We cloned the causative gene for the sss1 mutant, which is linked with a seed weight QTL, identified an elite allele of this gene for increasing seed weight, and provided new insights into soybean domestication and breeding.
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Affiliation(s)
- Weiwei Zhu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
| | - Ce Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
| | - Bin Yong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
| | - Yan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
| | - Bingbing Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
| | - Yongzhe Gu
- National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Siming Wei
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
| | - Zhenghong An
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
| | - Wenkai Sun
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
| | - Lijuan Qiu
- National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chaoying He
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
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Bouré N, Peaucelle A, Goussot M, Adroher B, Soubigou-Taconnat L, Borrega N, Biot E, Tariq Z, Martin-Magniette ML, Pautot V, Laufs P, Arnaud N. A cell wall-associated gene network shapes leaf boundary domains. Development 2022; 149:275600. [DOI: 10.1242/dev.200359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 04/29/2022] [Indexed: 11/20/2022]
Abstract
ABSTRACT
Boundary domains delimit and organize organ growth throughout plant development almost relentlessly, building plant architecture and morphogenesis. Boundary domains display reduced growth and orchestrate development of adjacent tissues in a non-cell-autonomous manner. How these two functions are achieved remains elusive despite the identification of several boundary-specific genes. Here, we show using morphometrics at the organ and cellular levels that leaf boundary domain development requires SPINDLY (SPY), an O-fucosyltransferase, to act as cell growth repressor. Furthermore, we show that SPY acts redundantly with the CUP-SHAPED COTYLEDON transcription factors (CUC2 and CUC3), which are major determinants of boundaries development. Accordingly, at the molecular level CUC2 and SPY repress a common set of genes involved in cell wall loosening, providing a molecular framework for the growth repression associated with boundary domains. Atomic force microscopy confirmed that young leaf boundary domain cells have stiffer cell walls than marginal outgrowth. This differential cell wall stiffness was reduced in spy mutant plants. Taken together, our data reveal a concealed CUC2 cell wall-associated gene network linking tissue patterning with cell growth and mechanics.
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Affiliation(s)
- Nathalie Bouré
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB) 1 , 78000 Versailles , France
- Université Paris-Saclay 2 , 91405 Orsay , France
| | - Alexis Peaucelle
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB) 1 , 78000 Versailles , France
| | - Magali Goussot
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB) 1 , 78000 Versailles , France
| | - Bernard Adroher
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB) 1 , 78000 Versailles , France
| | - Ludivine Soubigou-Taconnat
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2) 3 , 91405 Orsay , France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2) 4 , 91405 Orsay , France
| | - Néro Borrega
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB) 1 , 78000 Versailles , France
| | - Eric Biot
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB) 1 , 78000 Versailles , France
| | - Zakia Tariq
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2) 3 , 91405 Orsay , France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2) 4 , 91405 Orsay , France
| | - Marie-Laure Martin-Magniette
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2) 3 , 91405 Orsay , France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2) 4 , 91405 Orsay , France
| | - Véronique Pautot
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB) 1 , 78000 Versailles , France
| | - Patrick Laufs
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB) 1 , 78000 Versailles , France
| | - Nicolas Arnaud
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB) 1 , 78000 Versailles , France
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9
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Basnet P, Um T, Roy NS, Cho WS, Park SC, Park KC, Choi IY. Identification and Characterization of Key Genes Responsible for Weedy and Cultivar Growth Types in Soybean. Front Genet 2022; 13:805347. [PMID: 35281824 PMCID: PMC8907156 DOI: 10.3389/fgene.2022.805347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/17/2022] [Indexed: 11/13/2022] Open
Abstract
In cultivated plants, shoot morphology is an important factor that influences crop economic value. However, the effects of gene expression patterns on shoot morphology are not clearly understood. In this study, the molecular mechanism behind shoot morphology (including leaf, stem, and node) was analyzed using RNA sequencing to compare weedy (creeper) and cultivar (stand) growth types obtained in F7 derived from a cross of wild and cultivated soybeans. A total of 12,513 (in leaves), 14,255 (in stems), and 11,850 (in nodes) differentially expressed genes were identified among weedy and cultivar soybeans. Comparative transcriptome and expression analyses revealed 22 phytohormone-responsive genes. We found that GIBBERELLIN 2-OXIDASE 8 (GA2ox), SPINDLY (SPY), FERONIA (FER), AUXIN RESPONSE FACTOR 8 (ARF8), CYTOKININ DEHYDROGENASE-1 (CKX1), and ARABIDOPSIS HISTIDINE KINASE-3 (AHK3), which are crucial phytohormone response genes, were mainly regulated in the shoot of weedy and cultivar types. These results indicate that interactions between phytohormone signaling genes regulate shoot morphology in weedy and cultivar growth type plants. Our study provides insights that are useful for breeding and improving crops to generate high-yield soybean varieties.
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Affiliation(s)
- Prakash Basnet
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, South Korea
| | - Taeyoung Um
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, South Korea
| | - Neha Samir Roy
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, South Korea
| | - Woo Suk Cho
- Department of Agricultural Biotechnology/National Academy of Agricultural Science, Rural Development Administration, Jeonju, South Korea
| | - Soo Chul Park
- Department of Agricultural Biotechnology/National Academy of Agricultural Science, Rural Development Administration, Jeonju, South Korea
| | - Kyong-Cheul Park
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, South Korea
| | - Ik-Young Choi
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, South Korea
- *Correspondence: Ik-Young Choi,
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Kim NS, Kim SJ, Jo JS, Lee JG, Lee SI, Kim DH, Kim JA. The BrGI Circadian Clock Gene Is Involved in the Regulation of Glucosinolates in Chinese Cabbage. Genes (Basel) 2021; 12:genes12111664. [PMID: 34828270 PMCID: PMC8621042 DOI: 10.3390/genes12111664] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 11/16/2022] Open
Abstract
Circadian clocks integrate environmental cues with endogenous signals to coordinate physiological outputs. Clock genes in plants are involved in many physiological and developmental processes, such as photosynthesis, stomata opening, stem elongation, light signaling, and floral induction. Many Brassicaceae family plants, including Chinese cabbage (Brassica rapa ssp. pekinensis), produce a unique glucosinolate (GSL) secondary metabolite, which enhances plant protection, facilitates the design of functional foods, and has potential medical applications (e.g., as antidiabetic and anticancer agents). The levels of GSLs change diurnally, suggesting a connection to the circadian clock system. We investigated whether circadian clock genes affect the biosynthesis of GSLs in Brassica rapa using RNAi-mediated suppressed transgenic Brassica rapa GIGENTEA homolog (BrGI knockdown; hereafter GK1) Chinese cabbage. GIGANTEA plays an important role in the plant circadian clock system and is related to various developmental and metabolic processes. Using a validated GK1 transgenic line, we performed RNA sequencing and high-performance liquid chromatography analyses. The transcript levels of many GSL pathway genes were significantly altered in GK1 transgenic plants. In addition, GSL contents were substantially reduced in GK1 transgenic plants. We report that the BrGI circadian clock gene is required for the biosynthesis of GSLs in Chinese cabbage plants.
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Affiliation(s)
- Nan Sun Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Science, Rural Development Administration, Jeonju 54874, Korea; (N.S.K.); (S.I.L.)
| | - Su Jeong Kim
- Department of Plant Science and Technology, Chung-Ang University, Anseong 17546, Korea;
| | - Jung Su Jo
- Department of Horticulture, College of Agriculture & Life Sciences, Jeonbuk National University, Jeonju 54896, Korea; (J.S.J.); (J.G.L.)
| | - Jun Gu Lee
- Department of Horticulture, College of Agriculture & Life Sciences, Jeonbuk National University, Jeonju 54896, Korea; (J.S.J.); (J.G.L.)
| | - Soo In Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Science, Rural Development Administration, Jeonju 54874, Korea; (N.S.K.); (S.I.L.)
| | - Dong Hwan Kim
- Department of Plant Science and Technology, Chung-Ang University, Anseong 17546, Korea;
- Correspondence: (D.H.K.); (J.A.K.); Tel.: +82-31-670-3260 (D.H.K.); +82-63-238-4619 (J.A.K.)
| | - Jin A. Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Science, Rural Development Administration, Jeonju 54874, Korea; (N.S.K.); (S.I.L.)
- Correspondence: (D.H.K.); (J.A.K.); Tel.: +82-31-670-3260 (D.H.K.); +82-63-238-4619 (J.A.K.)
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11
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Liang L, Wang Q, Song Z, Wu Y, Liang Q, Wang Q, Yang J, Bi Y, Zhou W, Fan LM. O-fucosylation of CPN20 by SPINDLY Derepresses Abscisic Acid Signaling During Seed Germination and Seedling Development. FRONTIERS IN PLANT SCIENCE 2021; 12:724144. [PMID: 34712252 PMCID: PMC8545988 DOI: 10.3389/fpls.2021.724144] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 09/10/2021] [Indexed: 05/31/2023]
Abstract
SPINDLY is involved in some aspects of plant development. However, the nature of this protein as an O-fucosyltransferase was recently discovered. In this study, we show that SPINDLY (SPY) interacts with CPN20 in yeast two-hybrid and split-luc assays, and the interaction is promoted by ABA. CPN20 is a chloroplast-localized co-chaperonin that negatively regulates ABAR-mediated ABA signaling. By using Electron Transfer Dissociation-MS/MS analysis, two O-fucosylation sites, e.g., 116th and 119th threonines, were detected in ectopically expressed CPN20 in mammalian cells and in Arabidopsis. The O-fucosylation at both threonine residues was confirmed by in vitro peptide O-fucosylation assay. We further show that CPN20 accumulates in the chloroplast of spy mutants, suggesting that SPY negatively regulates CPN20 localization in the chloroplast. In vivo protein degradation assay along with CPN20 localization behavior suggest that import of CPN20 into the chloroplast is negatively regulated by SPY. Genetic analysis shows that ABA insensitive phenotypes of spy-3 in terms of seed germination and early seedling development are partially suppressed by the cpn20 mutation, suggesting that CPN20 acts downstream of SPY in this ABA signaling pathway and that there may exist other pathways in parallel with CPN20. Collectively, the above data support the notion that the O-fucosylation of CPN20 by SPY fine-tunes ABA signaling in Arabidopsis.
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Affiliation(s)
- Lin Liang
- State Key Laboratory for Plant Gene and Protein Research, School of Life Sciences, School of Advanced Agriculture Sciences, Peking University, Beijing, China
- PKU Core Facility of Mass Spectrometry, School of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Qi Wang
- State Key Laboratory for Plant Gene and Protein Research, School of Life Sciences, School of Advanced Agriculture Sciences, Peking University, Beijing, China
| | - Zihao Song
- State Key Laboratory for Plant Gene and Protein Research, School of Life Sciences, School of Advanced Agriculture Sciences, Peking University, Beijing, China
| | - Yaxin Wu
- State Key Laboratory for Plant Gene and Protein Research, School of Life Sciences, School of Advanced Agriculture Sciences, Peking University, Beijing, China
| | - Qing Liang
- State Key Laboratory for Plant Gene and Protein Research, School of Life Sciences, School of Advanced Agriculture Sciences, Peking University, Beijing, China
| | - Qingsong Wang
- State Key Laboratory for Plant Gene and Protein Research, School of Life Sciences, School of Advanced Agriculture Sciences, Peking University, Beijing, China
| | - Jinli Yang
- State Key Laboratory for Plant Gene and Protein Research, School of Life Sciences, School of Advanced Agriculture Sciences, Peking University, Beijing, China
| | - Ying Bi
- State Key Laboratory for Plant Gene and Protein Research, School of Life Sciences, School of Advanced Agriculture Sciences, Peking University, Beijing, China
| | - Wen Zhou
- PKU Core Facility of Mass Spectrometry, School of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Liu-Min Fan
- State Key Laboratory for Plant Gene and Protein Research, School of Life Sciences, School of Advanced Agriculture Sciences, Peking University, Beijing, China
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12
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Chen F, Li Y, Li X, Li W, Xu J, Cao H, Wang Z, Li Y, Soppe WJJ, Liu Y. Ectopic expression of the Arabidopsis florigen gene FLOWERING LOCUS T in seeds enhances seed dormancy via the GA and DOG1 pathways. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:909-924. [PMID: 34037275 DOI: 10.1111/tpj.15354] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 05/13/2021] [Indexed: 05/27/2023]
Abstract
Ectopic expression of specific genes in seeds could be a tool for molecular design of crops to alter seed dormancy and germination, thereby improving production. Here, a seed-specific vector, 12S-pLEELA, was applied to study the roles of genes in Arabidopsis seeds. Transgenic lines containing FLOWERING LOCUS T (FT) driven by the 12S promoter exhibited significantly increased seed dormancy and earlier flowering. Mutated FT(Y85H) and TERMINAL FLOWER1 (TFL1) transgenic lines also showed increased seed dormancy but without altered flowering time. FT(Y85H) and TFL1 caused weaker seed dormancy enhancement compared to FT. The FT and TFL1 transgenic lines showed hypersensitivity to paclobutrazol, but not to abscisic acid in seed germination. The levels of bioactive gibberellin 3 (GA3 ) and GA4 were significantly reduced, consistent with decreased expression of COPALYL DIPHOSPHATE SYNTHASE (CPS), KAURENE OXIDASE (KO), GIBBERELLIN 3-OXIDASE2 (GA3ox2), and GA20ox1 in p12S::FT lines. Exogenous GA4+7 could recover the germination ability of FT transgenic lines. These results revealed that FT regulates GA biosynthesis. A genetic analysis indicated that the GA signaling regulator SPINDLY (SPY) is epistatic to FT in GA-mediated seed germination. Furthermore, DELAY OF GERMINATION1 (DOG1) showed significantly higher transcript levels in p12S::FT lines. Seed dormancy analysis of dog1-2 spy-3 p12S::FT-2 indicated that the combination of SPY and DOG1 is epistatic to FT in the regulation of dormancy. Overall, we showed that ectopic expression of FT and TFL1 in seeds enhances dormancy through affecting GA and DOG1 pathways.
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Affiliation(s)
- Fengying Chen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yu Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoying Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Wenlong Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Science and Technology Daily, Beijing, China
| | - Jimei Xu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Hong Cao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Zhi Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yong Li
- Institute of Genetic Epidemiology, Medical Centre - University of Freiburg, Freiburg, Germany
| | | | - Yongxiu Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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13
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Li F, Hu Q, Chen F, Jiang JF. Transcriptome analysis reveals Vernalization is independent of cold acclimation in Arabidopsis. BMC Genomics 2021; 22:462. [PMID: 34154522 PMCID: PMC8218483 DOI: 10.1186/s12864-021-07763-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 05/31/2021] [Indexed: 01/08/2023] Open
Abstract
Background Through vernalization, plants achieve flowering competence by sensing prolonged cold exposure (constant exposure approximately 2-5 °C). During this process, plants initiate defense responses to endure cold conditions. Here, we conducted transcriptome analysis of Arabidopsis plants subjected to prolonged cold exposure (6 weeks) to explore the physiological dynamics of vernalization and uncover the relationship between vernalization and cold stress. Results Time-lag initiation of the two pathways and weighted gene co-expression network analysis (WGCNA) revealed that vernalization is independent of cold acclimation. Moreover, WGCNA revealed three major networks involving ethylene and jasmonic acid response, cold acclimation, and chromatin modification in response to prolonged cold exposure. Finally, throughout vernalization, the cold stress response is regulated via an alternative splicing-mediated mechanism. Conclusion These findings illustrate a comprehensive picture of cold stress- and vernalization-mediated global changes in Arabidopsis. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07763-3.
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Affiliation(s)
- Fei Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qian Hu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fadi Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jia Fu Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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14
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De Coninck T, Gistelinck K, Janse van Rensburg HC, Van den Ende W, Van Damme EJM. Sweet Modifications Modulate Plant Development. Biomolecules 2021; 11:756. [PMID: 34070047 PMCID: PMC8158104 DOI: 10.3390/biom11050756] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 04/28/2021] [Accepted: 05/12/2021] [Indexed: 02/07/2023] Open
Abstract
Plant development represents a continuous process in which the plant undergoes morphological, (epi)genetic and metabolic changes. Starting from pollination, seed maturation and germination, the plant continues to grow and develops specialized organs to survive, thrive and generate offspring. The development of plants and the interplay with its environment are highly linked to glycosylation of proteins and lipids as well as metabolism and signaling of sugars. Although the involvement of these protein modifications and sugars is well-studied, there is still a long road ahead to profoundly comprehend their nature, significance, importance for plant development and the interplay with stress responses. This review, approached from the plants' perspective, aims to focus on some key findings highlighting the importance of glycosylation and sugar signaling for plant development.
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Affiliation(s)
- Tibo De Coninck
- Laboratory of Glycobiology & Biochemistry, Department of Biotechnology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium; (T.D.C.); (K.G.)
| | - Koen Gistelinck
- Laboratory of Glycobiology & Biochemistry, Department of Biotechnology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium; (T.D.C.); (K.G.)
| | - Henry C. Janse van Rensburg
- Laboratory of Molecular Plant Biology, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium; (H.C.J.v.R.); (W.V.d.E.)
| | - Wim Van den Ende
- Laboratory of Molecular Plant Biology, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium; (H.C.J.v.R.); (W.V.d.E.)
| | - Els J. M. Van Damme
- Laboratory of Glycobiology & Biochemistry, Department of Biotechnology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium; (T.D.C.); (K.G.)
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15
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Arabidopsis ACINUS is O-glycosylated and regulates transcription and alternative splicing of regulators of reproductive transitions. Nat Commun 2021; 12:945. [PMID: 33574257 PMCID: PMC7878923 DOI: 10.1038/s41467-021-20929-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 12/17/2020] [Indexed: 01/30/2023] Open
Abstract
O-GlcNAc modification plays important roles in metabolic regulation of cellular status. Two homologs of O-GlcNAc transferase, SECRET AGENT (SEC) and SPINDLY (SPY), which have O-GlcNAc and O-fucosyl transferase activities, respectively, are essential in Arabidopsis but have largely unknown cellular targets. Here we show that AtACINUS is O-GlcNAcylated and O-fucosylated and mediates regulation of transcription, alternative splicing (AS), and developmental transitions. Knocking-out both AtACINUS and its distant paralog AtPININ causes severe growth defects including dwarfism, delayed seed germination and flowering, and abscisic acid (ABA) hypersensitivity. Transcriptomic and protein-DNA/RNA interaction analyses demonstrate that AtACINUS represses transcription of the flowering repressor FLC and mediates AS of ABH1 and HAB1, two negative regulators of ABA signaling. Proteomic analyses show AtACINUS's O-GlcNAcylation, O-fucosylation, and association with splicing factors, chromatin remodelers, and transcriptional regulators. Some AtACINUS/AtPININ-dependent AS events are altered in the sec and spy mutants, demonstrating a function of O-glycosylation in regulating alternative RNA splicing.
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16
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Sun TP. Novel nucleocytoplasmic protein O-fucosylation by SPINDLY regulates diverse developmental processes in plants. Curr Opin Struct Biol 2021; 68:113-121. [PMID: 33476897 DOI: 10.1016/j.sbi.2020.12.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/23/2020] [Accepted: 12/29/2020] [Indexed: 12/17/2022]
Abstract
In metazoans, protein O-fucosylation of Ser/Thr residues was only found in secreted or cell surface proteins, and this post-translational modification is catalyzed by ER-localized protein O-fucosyltransferases (POFUTs) in the GT65 family. Recently, a novel nucleocytoplasmic POFUT, SPINDLY (SPY), was identified in the reference plant Arabidopsis thaliana to modify nuclear transcription regulators DELLAs, revealing a new regulatory mechanism for gene expression. The paralog of AtSPY, SECRET AGENT (SEC), is an O-link-N-acetylglucosamine (GlcNAc) transferase (OGT), which O-GlcNAcylates Ser/Thr residues of target proteins. Both AtSPY and AtSEC are tetratricopeptide repeat-domain-containing glycosyltransferases in the GT41 family. The discovery that AtSPY is a POFUT clarified decades of miss-classification of AtSPY as an OGT. SPY and SEC play pleiotropic roles in plant development, and the interactions between SPY and SEC are complex. SPY-like genes are conserved in diverse organisms, except in fungi and metazoans, suggesting that O-fucosylation is a common mechanism in modulating intracellular protein functions.
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Affiliation(s)
- Tai-Ping Sun
- Department of Biology, Duke University, Durham, NC 27708, USA.
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17
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Brandoli C, Petri C, Egea-Cortines M, Weiss J. Gigantea: Uncovering New Functions in Flower Development. Genes (Basel) 2020; 11:genes11101142. [PMID: 32998354 PMCID: PMC7600796 DOI: 10.3390/genes11101142] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/19/2020] [Accepted: 09/22/2020] [Indexed: 11/16/2022] Open
Abstract
GIGANTEA (GI) is a gene involved in multiple biological functions, which have been analysed and are partially conserved in a series of mono- and dicotyledonous plant species. The identified biological functions include control over the circadian rhythm, light signalling, cold tolerance, hormone signalling and photoperiodic flowering. The latter function is a central role of GI, as it involves a multitude of pathways, both dependent and independent of the gene CONSTANS(CO), as well as on the basis of interaction with miRNA. The complexity of the gene function of GI increases due to the existence of paralogs showing changes in genome structure as well as incidences of sub- and neofunctionalization. We present an updated report of the biological function of GI, integrating late insights into its role in floral initiation, flower development and volatile flower production.
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Affiliation(s)
- Claudio Brandoli
- Genética Molecular, Instituto de Biotecnología Vegetal, Edificio I+D+I, Plaza del Hospital s/n, Universidad Politécnica de Cartagena, 30202 Cartagena, Spain; (C.B.); (M.E.-C.)
| | - Cesar Petri
- Instituto de Hortofruticultura Subtropical y Mediterránea-UMA-CSIC, Departamento de Fruticultura Subtropical y Mediterránea, 29750 Algarrobo-costa, Málaga, Spain;
| | - Marcos Egea-Cortines
- Genética Molecular, Instituto de Biotecnología Vegetal, Edificio I+D+I, Plaza del Hospital s/n, Universidad Politécnica de Cartagena, 30202 Cartagena, Spain; (C.B.); (M.E.-C.)
| | - Julia Weiss
- Genética Molecular, Instituto de Biotecnología Vegetal, Edificio I+D+I, Plaza del Hospital s/n, Universidad Politécnica de Cartagena, 30202 Cartagena, Spain; (C.B.); (M.E.-C.)
- Correspondence: ; Tel.: +34-868-071-078
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18
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Wang Y, He Y, Su C, Zentella R, Sun TP, Wang L. Nuclear Localized O-Fucosyltransferase SPY Facilitates PRR5 Proteolysis to Fine-Tune the Pace of Arabidopsis Circadian Clock. MOLECULAR PLANT 2020; 13:446-458. [PMID: 31899321 PMCID: PMC7058189 DOI: 10.1016/j.molp.2019.12.013] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/25/2019] [Accepted: 12/28/2019] [Indexed: 05/07/2023]
Abstract
Post-translational modifications play essential roles in finely modulating eukaryotic circadian clock systems. In plants, the effects of O-glycosylation on the circadian clock and the underlying mechanisms remain largely unknown. The O-fucosyltransferase SPINDLY (SPY) and the O-GlcNAc transferase SECRET AGENT (SEC) are two prominent O-glycosylation enzymes in higher plants, with both overlapped and unique functions in plant growth and development. Unlike the critical role of O-GlcNAc in regulating the animal circadian clock, here we report that nuclear-localized SPY, but not SEC, specifically modulates the pace of the Arabidopsis circadian clock. By identifying the interactome of SPY, we identified PSEUDO-RESPONSE REGULATOR 5 (PRR5), one of the core circadian clock components, as a new SPY-interacting protein. PRR5 can be O-fucosylated by SPY in planta, while point mutation in the catalytic domain of SPY abolishes the O-fucosylation of PRR5. The protein abundance of PRR5 is strongly increased in spy mutants, while the degradation rate of PRR5 is much reduced, suggesting that PRR5 proteolysis is promoted by SPY-mediated O-fucosylation. Moreover, multiple lines of genetic evidence indicate that PRR5 is a major downstream target of SPY to specifically mediate its modulation of the circadian clock. Collectively, our findings provide novel insights into the specific role of the O-fucosyltransferase activity of SPY in modulating the circadian clock and implicate that O-glycosylation might play an evolutionarily conserved role in modulating the circadian clock system, via O-GlcNAcylation in mammals, but via O-fucosylation in higher plants.
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Affiliation(s)
- Yan Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuqing He
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chen Su
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Tai-Ping Sun
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Lei Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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19
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Yan Z, Shi H, Liu Y, Jing M, Han Y. KHZ1 and KHZ2, novel members of the autonomous pathway, repress the splicing efficiency of FLC pre-mRNA in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:1375-1386. [PMID: 31701139 PMCID: PMC7031081 DOI: 10.1093/jxb/erz499] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 11/06/2019] [Indexed: 05/03/2023]
Abstract
As one of the most important events during the life cycle of flowering plants, the floral transition is of crucial importance for plant propagation and requires the precise coordination of multiple endogenous and external signals. There have been at least four flowering pathways (i.e. photoperiod, vernalization, gibberellin, and autonomous) identified in Arabidopsis. We previously reported that two Arabidopsis RNA-binding proteins, KHZ1 and KHZ2, redundantly promote flowering. However, the underlying mechanism was unclear. Here, we found that the double mutant khz1 khz2 flowered late under both long-day and short-day conditions, but responded to vernalization and gibberellin treatments. The late-flowering phenotype was almost completely rescued by mutating FLOWERING LOCUS C (FLC) and fully rescued by overexpressing FLOWERING LOCUS T (FT). Additional experiments demonstrated that the KHZs could form homodimers or interact to form heterodimers, localized to nuclear dots, and repressed the splicing efficiency of FLC pre-mRNA. Together, these data indicate that the KHZs could promote flowering via the autonomous pathway by repressing the splicing efficiency of FLC pre-mRNA.
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Affiliation(s)
- Zongyun Yan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Huiying Shi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yanan Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Meng Jing
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yuzhen Han
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
- Correspondence:
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20
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Cao H, Han Y, Li J, Ding M, Li Y, Li X, Chen F, Soppe WJ, Liu Y. Arabidopsis thaliana SEED DORMANCY 4-LIKE regulates dormancy and germination by mediating the gibberellin pathway. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:919-933. [PMID: 31641755 DOI: 10.1093/jxb/erz471] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 10/10/2019] [Indexed: 06/10/2023]
Abstract
The molecular mechanisms underlying seed dormancy and germination are not fully understood. Here, we show that Arabidopsis thaliana SEED DORMANCY 4-LIKE (AtSdr4L) is a novel specific regulator of dormancy and germination. AtSdr4L encodes a protein with an unknown biochemical function that is localized in the nucleus and is expressed specifically in seeds. Loss of function of AtSdr4L results in increased seed dormancy. The germination of freshly harvested seeds of the Atsdr4l mutant is insensitive to gibberellin (GA). After-ripened mutant seeds are hypersensitive to the GA biosynthesis-inhibitor paclobutrazol but show unaltered sensitivity to abscisic acid. Several GA biosynthesis genes and GA-regulated cell wall remodeling genes are down-regulated in the mutant in both dormant and after-ripened seeds. These results suggest that the Atsdr4l mutation causes both decreased GA biosynthesis and reduced responses. In addition, a genetic analysis indicated that AtSdr4L is epistatic to DELAY OF GERMINATION1 (DOG1) for dormancy and acts upstream of RGA-LIKE 2 (RGL2) in the GA pathway. We propose that AtSdr4L regulates seed dormancy and germination by mediating both the DOG1 and GA pathways.
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Affiliation(s)
- Hong Cao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yi Han
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Shandong Provincial Center of Forest Tree Germplasm Resources, Jinan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jingyi Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Meng Ding
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yu Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoying Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fengying Chen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Wim Jj Soppe
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Yongxiu Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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Tameshige T, Ikematsu S, Torii KU, Uchida N. Stem development through vascular tissues: EPFL-ERECTA family signaling that bounces in and out of phloem. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:45-53. [PMID: 27965367 PMCID: PMC5854166 DOI: 10.1093/jxb/erw447] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/10/2016] [Indexed: 05/19/2023]
Abstract
Plant cells communicate with each other using a variety of signaling molecules. Recent studies have revealed that various types of secreted peptides, as well as phytohormones known since long ago, mediate cell-cell communication in diverse contexts of plant life. These peptides affect cellular activities, such as proliferation and cell fate decisions, through their perception by cell surface receptors located on the plasma membrane of target cells. ERECTA (ER), an Arabidopsis thaliana receptor kinase gene, was first identified as a stem growth regulator, and since then an increasing number of studies have shown that ER is involved in a wide range of developmental and physiological processes. In particular, molecular functions of ER have been extensively studied in stomatal patterning. Furthermore, the importance of ER signaling in vascular tissues of inflorescence stems, especially in phloem cells, has recently been highlighted. In this review article, first we briefly summarize the history of ER research including studies on stomatal development, then introduce ER functions in vascular tissues, and discuss its interactions with phytohormones and other receptor kinase signaling pathways. Future questions and challenges will also be addressed.
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Affiliation(s)
- Toshiaki Tameshige
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Shuka Ikematsu
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Keiko U Torii
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
- Department of Biology, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Naoyuki Uchida
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
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22
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Cui H, Kong D, Wei P, Hao Y, Torii KU, Lee JS, Li J. SPINDLY, ERECTA, and its ligand STOMAGEN have a role in redox-mediated cortex proliferation in the Arabidopsis root. MOLECULAR PLANT 2014; 7:1727-39. [PMID: 25267734 PMCID: PMC4261839 DOI: 10.1093/mp/ssu106] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Reactive oxygen species (ROS) are harmful to all living organisms and therefore they must be removed to ensure normal growth and development. ROS are also signaling molecules, but so far little is known about the mechanisms of ROS perception and developmental response in plants. We here report that hydrogen peroxide induces cortex proliferation in the Arabidopsis root and that SPINDLY (SPY), an O-linked glucosamine acetyltransferase, regulates cortex proliferation by maintaining cellular redox homeostasis. We also found that mutation in the leucine-rich receptor kinase ERECTA and its putative peptide ligand STOMAGEN block the effect of hydrogen peroxide on root cortex proliferation. However, ERECTA and STOMAGEN are expressed in the vascular tissue, whereas extra cortex cells are produced from the endodermis, suggesting the involvement of intercellular signaling. SPY appears to act downstream of ERECTA, because the spy mutation still caused cortex proliferation in the erecta mutant background. We therefore have not only gained insight into the mechanism by which SPY regulates root development but also uncovered a novel pathway for ROS signaling in plants. The importance of redox-mediated cortex proliferation as a protective mechanism against oxidative stress is also discussed.
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Affiliation(s)
- Hongchang Cui
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA
| | - Danyu Kong
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA
| | - Pengcheng Wei
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA Present address: Biotechnical Group, Institute of Rice Research, Anhui Agricultural Academy of Science, 40#, Nongke South Road, Hefei, Anhui, 230031, China
| | - Yueling Hao
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA
| | - Keiko U Torii
- Howard Hughes Medical Institute, Department of Biology, University of Washington, Seattle, WA 98195-1800, USA
| | - Jin Suk Lee
- Howard Hughes Medical Institute, Department of Biology, University of Washington, Seattle, WA 98195-1800, USA
| | - Jie Li
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA
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Putarjunan A, Rodermel S. gigantea suppresses immutans variegation by interactions with cytokinin and gibberellin signaling pathways. PLANT PHYSIOLOGY 2014; 166:2115-32. [PMID: 25349324 PMCID: PMC4256849 DOI: 10.1104/pp.114.250647] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 10/15/2014] [Indexed: 05/08/2023]
Abstract
The immutans (im) variegation mutant of Arabidopsis (Arabidopsis thaliana) is an ideal model to gain insight into factors that control chloroplast biogenesis. im defines the gene for PTOX, a plastoquinol terminal oxidase that participates in the control of thylakoid redox. Here, we report that the im defect can be suppressed during the late stages of plant development by gigantea (gi2), which defines the gene for GI, a central component of the circadian clock that plays a poorly understood role in diverse plant developmental processes. imgi2 mutants are late flowering and display other well-known phenotypes associated with gi2, such as starch accumulation and resistance to oxidative stress. We show that the restoration of chloroplast biogenesis in imgi2 is caused by a development-specific derepression of cytokinin signaling that involves cross talk with signaling pathways mediated by gibberellin (GA) and SPINDLY (SPY), a GA response inhibitor. Suppression of the plastid defect in imgi2 is likely caused by a relaxation of excitation pressures in developing plastids by factors contributed by gi2, including enhanced rates of photosynthesis and increased resistance to oxidative stress. Interestingly, the suppression phenotype of imgi can be mimicked by crossing im with the starch accumulation mutant, starch excess1 (sex1), perhaps because sex1 utilizes pathways similar to gi. We conclude that our studies provide a direct genetic linkage between GI and chloroplast biogenesis, and we construct a model of interactions between signaling pathways mediated by gi, GA, SPY, cytokinins, and sex1 that are required for chloroplast biogenesis.
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Affiliation(s)
- Aarthi Putarjunan
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011
| | - Steve Rodermel
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011
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24
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Hauvermale AL, Ariizumi T, Steber CM. Gibberellin signaling: a theme and variations on DELLA repression. PLANT PHYSIOLOGY 2012; 160:83-92. [PMID: 22843665 PMCID: PMC3440232 DOI: 10.1104/pp.112.200956] [Citation(s) in RCA: 156] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 07/24/2012] [Indexed: 05/17/2023]
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25
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Stamm P, Verma V, Ramamoorthy R, Kumar PP. Manipulation of plant architecture to enhance lignocellulosic biomass. AOB PLANTS 2012; 2012:pls026. [PMID: 23071897 PMCID: PMC3471074 DOI: 10.1093/aobpla/pls026] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 07/03/2012] [Accepted: 08/19/2012] [Indexed: 05/18/2023]
Abstract
BACKGROUND Biofuels hold the promise to replace an appreciable proportion of fossil fuels. Not only do they emit significantly lower amounts of greenhouse gases, they are much closer to being 'carbon neutral', since the source plants utilize carbon dioxide for their growth. In particular, second-generation lignocellulosic biofuels from agricultural wastes and non-food crops such as switchgrass promise sustainability and avoid diverting food crops to fuel. Currently, available lignocellulosic biomass could yield sufficient bioethanol to replace ∼10 % of worldwide petroleum use. Increasing the biomass used for biofuel production and the yield of bioethanol will thus help meet global energy demands while significantly reducing greenhouse gas emissions. SCOPE We discuss the advantages of various biotechnological approaches to improve crops and highlight the contribution of genomics and functional genomics in this field. Current knowledge concerning plant hormones and their intermediates involved in the regulation of plant architecture is presented with a special focus on gibberellins and cytokinins, and their signalling intermediates. We highlight the potential of information gained from model plants such as Arabidopsis thaliana and rice (Oryza sativa) to accelerate improvement of fuel crops.
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Affiliation(s)
- Petra Stamm
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore117543
| | - Vivek Verma
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore117543
| | - Rengasamy Ramamoorthy
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore117543
| | - Prakash P. Kumar
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore117543
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore117604
- Corresponding author's e-mail address:
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26
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Qin F, Kodaira KS, Maruyama K, Mizoi J, Tran LSP, Fujita Y, Morimoto K, Shinozaki K, Yamaguchi-Shinozaki K. SPINDLY, a negative regulator of gibberellic acid signaling, is involved in the plant abiotic stress response. PLANT PHYSIOLOGY 2011; 157:1900-13. [PMID: 22013217 PMCID: PMC3327212 DOI: 10.1104/pp.111.187302] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Accepted: 10/17/2011] [Indexed: 05/18/2023]
Abstract
The SPINDLY (SPY) gene was first identified as a negative regulator of plant gibberellic acid (GA) signaling because mutation of this gene phenocopies plants treated with an overdose of bioactive GA and results in insensitivity to a GA inhibitor during seed germination. The SPY gene encodes an O-linked N-acetylglucosamine transferase that can modify the target protein and modulate the protein activity in cells. In this study, we describe the strong salt and drought tolerance phenotypes of Arabidopsis (Arabidopsis thaliana) spy-1 and spy-3 mutants in addition to their GA-related phenotypes. SPY gene expression was found to be drought stress inducible and slightly responsive to salt stress. Transcriptome analysis of spy-3 revealed that many GA-responsive genes were up-regulated, which could explain the GA-overdosed phenotype of spy-3. Some stress-inducible genes were found to be up-regulated in spy-3, such as genes encoding late embryogenesis abundant proteins, Responsive to Dehydration20, and AREB1-like transcription factor, which may confer stress tolerance on spy-3. CKX3, a cytokinin (CK) catabolism gene, was up-regulated in spy-3; this up-regulation indicates that the mutant possesses reduced CK signaling, which is consistent with a positive role for SPY in CK signaling. Moreover, overexpression of SPY in transgenics (SPY overexpressing [SPY-OX]) impaired plant drought stress tolerance, opposite to the phenotype of spy. The expression levels of several genes, such as DREB1E/DDF1 and SNH1/WIN1, were decreased in SPY-OX but increased in spy-3. Taken together, these data indicate that SPY plays a negative role in plant abiotic stress tolerance, probably by integrating environmental stress signals via GA and CK cross talk.
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27
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Srikanth A, Schmid M. Regulation of flowering time: all roads lead to Rome. Cell Mol Life Sci 2011; 68:2013-37. [PMID: 21611891 PMCID: PMC11115107 DOI: 10.1007/s00018-011-0673-y] [Citation(s) in RCA: 527] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Revised: 02/08/2011] [Accepted: 03/17/2011] [Indexed: 01/01/2023]
Abstract
Plants undergo a major physiological change as they transition from vegetative growth to reproductive development. This transition is a result of responses to various endogenous and exogenous signals that later integrate to result in flowering. Five genetically defined pathways have been identified that control flowering. The vernalization pathway refers to the acceleration of flowering on exposure to a long period of cold. The photoperiod pathway refers to regulation of flowering in response to day length and quality of light perceived. The gibberellin pathway refers to the requirement of gibberellic acid for normal flowering patterns. The autonomous pathway refers to endogenous regulators that are independent of the photoperiod and gibberellin pathways. Most recently, an endogenous pathway that adds plant age to the control of flowering time has been described. The molecular mechanisms of these pathways have been studied extensively in Arabidopsis thaliana and several other flowering plants.
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Affiliation(s)
- Anusha Srikanth
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 37-39/VI, 72076 Tübingen, Germany
| | - Markus Schmid
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 37-39/VI, 72076 Tübingen, Germany
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28
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Srikanth A, Schmid M. Regulation of flowering time: all roads lead to Rome. Cell Mol Life Sci 2011; 68:2013-2037. [PMID: 21611891 DOI: 10.1007/s00018-011-0673-y/figures/3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Revised: 02/08/2011] [Accepted: 03/17/2011] [Indexed: 05/26/2023]
Abstract
Plants undergo a major physiological change as they transition from vegetative growth to reproductive development. This transition is a result of responses to various endogenous and exogenous signals that later integrate to result in flowering. Five genetically defined pathways have been identified that control flowering. The vernalization pathway refers to the acceleration of flowering on exposure to a long period of cold. The photoperiod pathway refers to regulation of flowering in response to day length and quality of light perceived. The gibberellin pathway refers to the requirement of gibberellic acid for normal flowering patterns. The autonomous pathway refers to endogenous regulators that are independent of the photoperiod and gibberellin pathways. Most recently, an endogenous pathway that adds plant age to the control of flowering time has been described. The molecular mechanisms of these pathways have been studied extensively in Arabidopsis thaliana and several other flowering plants.
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Affiliation(s)
- Anusha Srikanth
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 37-39/VI, Tübingen, Germany
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29
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Stamm P, Kumar PP. The phytohormone signal network regulating elongation growth during shade avoidance. JOURNAL OF EXPERIMENTAL BOTANY 2010; 61:2889-2903. [PMID: 20501746 DOI: 10.1093/jxb/erq147] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
In contrast to animals, plants maintain highly plastic growth and development throughout their life, which enables them to adapt to environmental fluctuations. Phytohormones coordinately regulate these adaptations by integrating environmental inputs into a complex signalling network. In this review, the focus is on the rapid elongation that occurs in response to canopy shading or submergence, and current knowledge and recent advances in deciphering the network of phytohormone signalling that regulates this response are explored. The review concentrates on the involvement of the phytohormones auxins, gibberellins, cytokinins, and ethylene. Despite the occurrence of considerable gaps in current understanding of the underlying molecular mechanisms, it was possible to identify a network of phytohormone signalling intermediates at multiple levels that regulates elongation growth in response to canopy shade or submergence. Based on the observations that there are spatial and temporal differences in the interactions of phytohormones, the importance of more integrative approaches for future studies is highlighted.
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Affiliation(s)
- Petra Stamm
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 117543
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30
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van Zanten M, Snoek LB, van Eck-Stouten E, Proveniers MCG, Torii KU, Voesenek LACJ, Millenaar FF, Peeters AJM. ERECTA controls low light intensity-induced differential petiole growth independent of phytochrome B and cryptochrome 2 action in Arabidopsis thaliana. PLANT SIGNALING & BEHAVIOR 2010; 5:284-6. [PMID: 20037477 PMCID: PMC2881279 DOI: 10.4161/psb.5.3.10706] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Plants can respond quickly and profoundly to changes in their environment. Several species, including Arabidopsis thaliana, are capable of differential petiole growth driven upward leaf movement (hyponastic growth) to escape from detrimental environmental conditions. Recently, we demonstrated that the leucine-rich repeat receptor-like Ser/Thr kinase gene ERECTA, explains a major effect Quantitative Trait Locus (QTL) for ethylene-induced hyponastic growth in Arabidopsis. Here, we demonstrate that ERECTA controls the hyponastic growth response to low light intensity treatment in a genetic background dependent manner. Moreover, we show that ERECTA affects low light-induced hyponastic growth independent of Phytochrome B and Cryptochrome 2 signaling, despite that these photoreceptors are positive regulators of low light-induced hyponastic growth.
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Affiliation(s)
- Martijn van Zanten
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Utrecht, the Netherlands.
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31
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Singh DP, Filardo FF, Storey R, Jermakow AM, Yamaguchi S, Swain SM. Overexpression of a gibberellin inactivation gene alters seed development, KNOX gene expression, and plant development in Arabidopsis. PHYSIOLOGIA PLANTARUM 2010; 138:74-90. [PMID: 19825007 DOI: 10.1111/j.1399-3054.2009.01289.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We have examined the role of gibberellins (GAs) in plant development by expression of the pea GA 2-oxidase2 (PsGA2ox2) cDNA, which encodes a GA inactivating enzyme, under the control of the MEDEA (MEA) promoter. Expression of MEA:PsGA2ox2 in Arabidopsis caused seed abortion, demonstrating that active GAs in the endosperm are essential for normal seed development. MEA:PsGA2ox2 plants had reduced ovule number per ovary and exhibited defects in phyllotaxy and leaf morphology which were partly suppressed by GA treatment. The leaf architecture and phyllotaxy defects of MEA:PsGA2ox2 plants were also restored by sly1-d which reduces DELLA protein stability to increase GA response. MEA:PsGA2ox2 seedlings had increased expression of the KNOTTED1-like homeobox (KNOX) genes, BP, KNAT2 and KNAT6, which are known to control plant architecture. The expression of KNOX genes is also altered in wild-type plants treated with GA. These results support the conclusion that GAs can suppress the effects of elevated KNOX gene expression, and raise the possibility that localized changes in GA levels caused by PsGA2ox2 alter the expression of KNOX genes to modify plant architecture.
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32
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Zhou X, Cooke P, Li L. Eukaryotic release factor 1-2 affects Arabidopsis responses to glucose and phytohormones during germination and early seedling development. JOURNAL OF EXPERIMENTAL BOTANY 2009; 61:357-67. [PMID: 19939886 PMCID: PMC2803205 DOI: 10.1093/jxb/erp308] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2009] [Revised: 09/22/2009] [Accepted: 10/01/2009] [Indexed: 05/20/2023]
Abstract
Germination and early seedling development are coordinately regulated by glucose and phytohormones such as ABA, GA, and ethylene. However, the molecules that affect plant responses to glucose and phytohormones remain to be fully elucidated. Eukaryotic release factor 1 (eRF1) is responsible for the recognition of the stop codons in mRNAs during protein synthesis. Accumulating evidence indicates that eRF1 functions in other processes in addition to translation termination. The physiological role of eRF1-2, a member of the eRF1 family, in Arabidopsis was examined here. The eRF1-2 gene was found to be specifically induced by glucose. Arabidopsis plants overexpressing eRF1-2 were hypersensitive to glucose during germination and early seedling development. Such hypersensitivity to glucose was accompanied by a dramatic reduction of the expression of glucose-regulated genes, chlorophyll a/b binding protein and plastocyanin. The hypersensitive response was not due to the enhanced accumulation of ABA. In addition, the eRF1-2 overexpressing plants showed increased sensitivity to paclobutrazol, an inhibitor of GA biosynthesis, and exogenous GA restored their normal growth. By contrast, the loss-of-function erf1-2 mutant exhibited resistance to paclobutrazol, suggesting that eRF1-2 may exert a negative effect on the GA signalling pathway. Collectively, these data provide evidence in support of a novel role of eRF1-2 in affecting glucose and phytohormone responses in modulating plant growth and development.
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Affiliation(s)
- Xiangjun Zhou
- Robert W Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Peter Cooke
- Microscopic Imaging, Eastern Regional Research Center, 600 E. Mermaid Lane, Wyndmoor, PA 19038, USA
| | - Li Li
- Robert W Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853, USA
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33
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Feng H, Xu WZ, Lin HH, Chong K. Transcriptional regulation of wheat VER2 promoter in rice in response to abscisic acid, jasmonate, and light. J Genet Genomics 2009; 36:371-7. [PMID: 19539247 DOI: 10.1016/s1673-8527(08)60126-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2008] [Revised: 02/26/2009] [Accepted: 03/02/2009] [Indexed: 10/20/2022]
Abstract
VER2 is a key gene associated with vernalization process in winter wheat. The expression of VER2 can be induced by low temperature treatment. To further understand how the expression of this gene is mediated by various external and internal factors, different lengths of the VER2 promoter region have been transcriptionally fused with a reporter gene, green fluorescence protein (GFP), and transformed into the model plant, rice (Oryza sativa L.). Using confocal and Western blot analyses, we determined several possible response elements in the promoter region, which could sense ABA, JA, and other environmental cues.
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Affiliation(s)
- Hong Feng
- College of Life Science, Sichuan University, Chendu, China
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34
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Wolters H, Jürgens G. Survival of the flexible: hormonal growth control and adaptation in plant development. Nat Rev Genet 2009; 10:305-17. [PMID: 19360022 DOI: 10.1038/nrg2558] [Citation(s) in RCA: 292] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Plant development is subject to hormonal growth control and adapts to environmental cues such as light or stress. Recently, significant progress has been made in elucidating hormone synthesis, signalling and degradation pathways, and in resolving spatial and temporal aspects of hormone responses. Here we review how hormones control maintenance of stem cell systems, influence developmental transitions of stem cell daughters and define developmental compartments in Arabidopsis thaliana. We also discuss how environmental cues change plant growth by modulating hormone levels and response. Future analysis of hormone crosstalk and of hormone action at both single cell and organ levels will substantially improve our understanding of how plant development adapts to changes in intrinsic and environmental conditions.
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Affiliation(s)
- Hanno Wolters
- ZMBP, Entwicklungsgenetik, Universität Tübingen, Auf der Morgenstelle 3, 72076 Tübingen, Germany
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35
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Maymon I, Greenboim-Wainberg Y, Sagiv S, Kieber JJ, Moshelion M, Olszewski N, Weiss D. Cytosolic activity of SPINDLY implies the existence of a DELLA-independent gibberellin-response pathway. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 58:979-88. [PMID: 19228341 DOI: 10.1111/j.1365-313x.2009.03840.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Specific plant developmental processes are modulated by cross-talk between gibberellin (GA)- and cytokinin-response pathways. Coordination of the two pathways involves the O-linked N-acetylglucosamine transferase SPINDLY (SPY) that suppresses GA signaling and promotes cytokinin responses in Arabidopsis. Although SPY is a nucleocytoplasmic protein, its site of action and targets are unknown. Several studies have suggested that SPY acts in the nucleus, where it modifies nuclear components such as the DELLA proteins to regulate signaling networks. Using chimeric GFP-SPY fused to a nuclear-export signal or to a glucocorticoid receptor, we show that cytosolic SPY promotes cytokinin responses and suppresses GA signaling. In contrast, nuclear-localized GFP-SPY failed to complement the spy mutation. To examine whether modulation of cytokinin activity by GA and spy is mediated by the nuclear DELLA proteins, cytokinin responses were studied in double and quadruple della mutants lacking the activities of REPRESSOR OF GA1-3 (RGA) and GA-INSENSITIVE (GAI) or RGA, GAI, RGA Like1 (RGL1) and RGL2. Unlike spy, the della mutants were cytokinin-sensitive. Moreover, when GA was applied to a cytokinin-treated quadruple della mutant it was able to suppress various cytokinin responses. These results suggest that cytosolic SPY and GA regulate cytokinin responses via a DELLA-independent pathway(s).
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Affiliation(s)
- Inbar Maymon
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agricultural, Food and Environmental Quality Sciences, The Hebrew University of Jerusalem, PO Box 12, Rehovot 76100, Israel
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36
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O-GlcNAc modifications regulate cell survival and epiboly during zebrafish development. BMC DEVELOPMENTAL BIOLOGY 2009; 9:28. [PMID: 19383152 PMCID: PMC2680843 DOI: 10.1186/1471-213x-9-28] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2008] [Accepted: 04/21/2009] [Indexed: 12/27/2022]
Abstract
Background The post-translational addition of the monosaccharide O-linked β-N-acetylglucosamine (O-GlcNAc) regulates the activity of a wide variety of nuclear and cytoplasmic proteins. The enzymes O-GlcNAc Transferase (Ogt) and O-GlcNAcase (Oga) catalyze, respectively, the attachment and removal of O-GlcNAc to target proteins. In adult mice, Ogt and Oga attenuate the response to insulin by modifying several components of the signal transduction pathway. Complete loss of ogt function, however, is lethal to mouse embryonic stem cells, suggesting that the enzyme has additional, unstudied roles in development. We have utilized zebrafish as a model to determine role of O-GlcNAc modifications in development. Zebrafish has two ogt genes, encoding six different enzymatic isoforms that are expressed maternally and zygotically. Results We manipulated O-GlcNAc levels in zebrafish embryos by overexpressing zebrafish ogt, human oga or by injecting morpholinos against ogt transcripts. Each of these treatments results in embryos with shortened body axes and reduced brains at 24 hpf. The embryos had 23% fewer cells than controls, and displayed increased rates of cell death as early as the mid-gastrula stages. An extensive marker analysis indicates that derivatives of three germ layers are reduced to variable extents, and the embryos are severely disorganized after gastrulation. Overexpression of Ogt and Oga delayed epiboly and caused a severe disorganization of the microtubule and actin based cytoskeleton in the extra-embryonic yolk syncytial layer (YSL). The cytoskeletal defects resemble those previously reported for embryos lacking function of the Pou5f1/Oct4 transcription factor spiel ohne grenzen. Consistent with this, Pou5f1/Oct4 is modified by O-GlcNAc in human embryonic stem cells. Conclusion We conclude that O-GlcNAc modifications control the activity of proteins that regulate apoptosis and epiboly movements, but do not seem to regulate germ layer specification. O-GlcNAc modifies the transcription factor Spiel ohne grenzen/Pou5f1 and may regulate its activity.
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van Zanten M, Snoek LB, Proveniers MCG, Peeters AJM. The many functions of ERECTA. TRENDS IN PLANT SCIENCE 2009; 14:214-8. [PMID: 19303350 DOI: 10.1016/j.tplants.2009.01.010] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2008] [Revised: 01/12/2009] [Accepted: 01/22/2009] [Indexed: 05/19/2023]
Abstract
The Arabidopsis thaliana accession Landsberg erecta contains an induced mutation in the leucine-rich repeat receptor-like Ser/Thr kinase gene ERECTA. Landsberg erecta is commonly used as a genetic background in mutant screens and in natural variation studies. Therefore, the erecta mutation is present in many loss-of-function mutants and recombinant inbred lines. Information on how the absence of functional ERECTA affects the interpretation of obtained phenotypic results is scattered. In this report we inventoried ERECTA functions and highlight ERECTA as a pleiotropic regulator of developmental and physiological processes, as well as a modulator of responses to environmental stimuli.
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Affiliation(s)
- Martijn van Zanten
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
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Benková E, Hejátko J. Hormone interactions at the root apical meristem. PLANT MOLECULAR BIOLOGY 2009; 69:383-96. [PMID: 18807199 DOI: 10.1007/s11103-008-9393-6] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2008] [Accepted: 08/27/2008] [Indexed: 05/18/2023]
Abstract
Plants exhibit an amazing developmental flexibility. Plant embryogenesis results in the establishment of a simple apical-basal axis represented by apical shoot and basal root meristems. Later, during postembryonic growth, shaping of the plant body continues by the formation and activation of numerous adjacent meristems that give rise to lateral shoot branches, leaves, flowers, or lateral roots. This developmental plasticity reflects an important feature of the plant's life strategy based on the rapid reaction to different environmental stimuli, such as temperature fluctuations, availability of nutrients, light or water and response resulting in modulation of developmental programs. Plant hormones are important endogenous factors for the integration of these environmental inputs and regulation of plant development. After a period of studies focused primarily on single hormonal pathways that enabled us to understand the hormone perception and signal transduction mechanisms, it became obvious that the developmental output mediated by a single hormonal pathway is largely modified through a whole network of interactions with other hormonal pathways. In this review, we will summarize recent knowledge on hormonal networks that regulate the development and growth of root with focus on the hormonal interactions that shape the root apical meristem.
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Affiliation(s)
- Eva Benková
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Gent University, Technologiepark 927, 9052 Gent, Belgium.
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Kilcoyne M, Shah M, Gerlach JQ, Bhavanandan V, Nagaraj V, Smith AD, Fujiyama K, Sommer U, Costello CE, Olszewski N, Joshi L. O-glycosylation of protein subpopulations in alcohol-extracted rice proteins. JOURNAL OF PLANT PHYSIOLOGY 2009; 166:219-232. [PMID: 18639953 DOI: 10.1016/j.jplph.2008.05.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2008] [Revised: 05/22/2008] [Accepted: 05/22/2008] [Indexed: 05/26/2023]
Abstract
Mucin-type O-glycosylation has been well characterized in mammalian systems but not in plants. In this study, the purified alcohol-soluble, non-reduced protein (prolamin) fraction from rice seed was investigated for the occurrence of O-linked oligosaccharides. As storage prolamins are unlikely to be O-glycosylated, any O-glycosylation found was likely to belong to co-extracted proteins, whether because of association with the protein body or solubility. SDS-PAGE and MS analyses revealed 14 and 16kDa protein families in fractions that bound to the lectins peanut agglutinin (PNA), Vicia villosa lectin (VVL) and Jacalin, indicative of the presence of O-linked saccharides. Enzymatic cleavage, fluorescent labeling and high-performance liquid chromatography (HPLC) analysis demonstrated a peak consistent with Gal-beta-(1-->3)-GalNAc, with similar MS/MS fragmentation. Additionally, upon chemical analysis, a GlcNAc-containing O-linked carbohydrate moiety was discovered. Protein blotting with anti-O-GlcNAc antibody (clone CTD110.6) was positive in a subpopulation of the 14kDa alcohol-soluble protein fraction, but a hot capping experiment was negative. Therefore, the GlcNAc residue in this case is unlikely to be terminal. Additionally, a positive reaction with CTD110.6mAb cannot be taken as absolute proof of O-GlcNAc modification and further confirmatory experiments should be employed. We hypothesize that O-glycosylation may contribute to protein functionality or regulation. Further investigation is required to identify the specific proteins with these modifications. This 'reverse' approach could lead to the identification of proteins involved in mRNA targeting, signaling, translation, anchoring or maintenance of translational quiescence and may be applied to germinating rice seed extracts for further elucidation of protein function and regulation.
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Affiliation(s)
- Michelle Kilcoyne
- Center for Glycosciences and Technology, Biodesign Institute at Arizona State University, 1001 S McAllister Avenue, Tempe, AZ 85287, USA
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Filardo F, Robertson M, Singh DP, Parish RW, Swain SM. Functional analysis of HvSPY, a negative regulator of GA response, in barley aleurone cells and Arabidopsis. PLANTA 2009; 229:523-537. [PMID: 19011896 DOI: 10.1007/s00425-008-0843-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2008] [Accepted: 10/10/2008] [Indexed: 05/27/2023]
Abstract
SPINDLY (SPY) is an important regulator of plant development, and consists of an N-half tetratricopeptide repeat (TPR) domain containing 10 TPR motifs and a C-half catalytic domain, similar to O-GlcNAc transferase (OGT) of animals. The best characterised role of SPY is a negative regulator of GA signalling, and all known spy alleles have been isolated based on increased GA response. Of the eight alleles that directly affect the TPR domain, all alter TPRs 6, 8 and/or 9. To test the hypothesis that a subset of TPRs, including 6, 8 and 9, are both essential and sufficient for the regulation of GA response, we overexpressed the full-length barley (Hordeum vulgare L.) SPY protein (HvSPY) and several deletion mutants in barley aleurone cells and in Arabidopsis wild type (WT) and spy-4 plants. Transient assays in barley aleurone cells, that also express endogenous HvSPY, demonstrated that introduced HvSPY and HvTPR inhibited GA(3)-induced alpha-amylase expression. With the exception of HvSPYDelta1-5, the other deletion proteins were partially active in the barley assay, including HvSPYDelta6-9 which lacks TPRs 6, 8 and 9. In Arabidopsis, analysis of seed germination under a range of conditions revealed that 35S:HvSPY increased seed dormancy. Hvspy-2, which lacks parts of the eighth and ninth TPRs, was able to partially complement all aspects of the spy-4 phenotype. In the presence of AtSPY, 35S:HvTPR caused some phenotypes consistent with a decrease in GA signalling, including increased seed sensitivity to paclobutrazol and delayed flowering. These plants also possessed distorted leaf morphology and altered epidermal cell shape. Thus, despite genetic analysis demonstrating that TPRs 6, 8 and 9 are required for regulation of GA signalling, our results suggest that these TPRs are neither absolutely essential nor sufficient for SPY activity.
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Ariizumi T, Murase K, Sun TP, Steber CM. Proteolysis-independent downregulation of DELLA repression in Arabidopsis by the gibberellin receptor GIBBERELLIN INSENSITIVE DWARF1. THE PLANT CELL 2008; 20:2447-59. [PMID: 18827182 PMCID: PMC2570730 DOI: 10.1105/tpc.108.058487] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2008] [Revised: 07/24/2008] [Accepted: 09/11/2008] [Indexed: 05/19/2023]
Abstract
This article presents evidence that DELLA repression of gibberellin (GA) signaling is relieved both by proteolysis-dependent and -independent pathways in Arabidopsis thaliana. DELLA proteins are negative regulators of GA responses, including seed germination, stem elongation, and fertility. GA stimulates GA responses by causing DELLA repressor degradation via the ubiquitin-proteasome pathway. DELLA degradation requires GA biosynthesis, three functionally redundant GA receptors GIBBERELLIN INSENSITIVE DWARF1 (GID1a, b, and c), and the SLEEPY1 (SLY1) F-box subunit of an SCF E3 ubiquitin ligase. The sly1 mutants accumulate more DELLA proteins but display less severe dwarf and germination phenotypes than the GA biosynthesis mutant ga1-3 or the gid1abc triple mutant. Interestingly, GID1 overexpression rescued the sly1 dwarf and infertility phenotypes without decreasing the accumulation of the DELLA protein REPRESSOR OF ga1-3. GID1 rescue of sly1 mutants was dependent on the level of GID1 protein, GA, and the presence of a functional DELLA motif. Since DELLA shows increasing interaction with GID1 with increasing GA levels, it appears that GA-bound GID1 can block DELLA repressor activity by direct protein-protein interaction with the DELLA domain. Thus, a SLY1-independent mechanism for GA signaling may function without DELLA degradation.
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Affiliation(s)
- Tohru Ariizumi
- Department of Crop and Soil Science, Washington State University, Pullman, Washington 99164-6420, USA
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42
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Toh S, Imamura A, Watanabe A, Nakabayashi K, Okamoto M, Jikumaru Y, Hanada A, Aso Y, Ishiyama K, Tamura N, Iuchi S, Kobayashi M, Yamaguchi S, Kamiya Y, Nambara E, Kawakami N. High temperature-induced abscisic acid biosynthesis and its role in the inhibition of gibberellin action in Arabidopsis seeds. PLANT PHYSIOLOGY 2008; 146:1368-85. [PMID: 18162586 PMCID: PMC2259091 DOI: 10.1104/pp.107.113738] [Citation(s) in RCA: 239] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Suppression of seed germination at supraoptimal high temperature (thermoinhibiton) during summer is crucial for Arabidopsis (Arabidopsis thaliana) to establish vegetative and reproductive growth in appropriate seasons. Abscisic acid (ABA) and gibberellins (GAs) are well known to be involved in germination control, but it remains unknown how these hormone actions (metabolism and responsiveness) are altered at high temperature. Here, we show that ABA levels in imbibed seeds are elevated at high temperature and that this increase is correlated with up-regulation of the zeaxanthin epoxidase gene ABA1/ZEP and three 9-cis-epoxycarotenoid dioxygenase genes, NCED2, NCED5, and NCED9. Reverse-genetic studies show that NCED9 plays a major and NCED5 and NCED2 play relatively minor roles in high temperature-induced ABA synthesis and germination inhibition. We also show that bioactive GAs stay at low levels at high temperature, presumably through suppression of GA 20-oxidase genes, GA20ox1, GA20ox2, and GA20ox3, and GA 3-oxidase genes, GA3ox1 and GA3ox2. Thermoinhibition-tolerant germination of loss-of-function mutants of GA negative regulators, SPINDLY (SPY) and RGL2, suggests that repression of GA signaling is required for thermoinibition. Interestingly, ABA-deficient aba2-2 mutant seeds show significant expression of GA synthesis genes and repression of SPY expression even at high temperature. In addition, the thermoinhibition-resistant germination phenotype of aba2-1 seeds is suppressed by a GA biosynthesis inhibitor, paclobutrazol. We conclude that high temperature stimulates ABA synthesis and represses GA synthesis and signaling through the action of ABA in Arabidopsis seeds.
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Affiliation(s)
- Shigeo Toh
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
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Sun TP. Gibberellin metabolism, perception and signaling pathways in Arabidopsis. THE ARABIDOPSIS BOOK 2008; 6:e0103. [PMID: 22303234 PMCID: PMC3243332 DOI: 10.1199/tab.0103] [Citation(s) in RCA: 146] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Bioactive gibberellins (GAs) are diterpene phytohormones that modulate growth and development throughout the whole life cycle of the plant. Arabidopsis genes encoding most GA biosynthesis and catabolism enzymes, as well as GA receptors (GIBBERELLIN INSENSITIVE DWARF1, GID1) and early GA signaling components have been identified. Expression studies on the GA biosynthesis genes are beginning to reveal the potential sites of GA biosynthesis during plant development. Biochemical and genetic analyses demonstrate that GA de-represses its signaling pathway by binding to GID1s, which induce degradation of GA signaling repressors (DELLAs) via an ubiquitin-proteasome pathway. To modulate plant growth and development, the GA pathway is also regulated by endogenous signals (other hormones) and environmental cues (such as light, temperature and salt stress). In many cases, these internal and external cues directly affect GA metabolism and bioactive GA levels, and indirectly alter DELLA accumulation and GA responses. Importantly, direct negative interaction between DELLA and PIF3 and PIF4 (2 phytochrome interacting transcription factors) appears to integrate the effects of light and GA on hypocotyl elongation.
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Affiliation(s)
- Tai-Ping Sun
- Department of Biology, Duke University, Durham, NC 27708
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Abstract
Here we summarize progress in identification of three classes of genes useful for control of plant architecture: those affecting hormone metabolism and signaling; transcription and other regulatory factors; and the cell cycle. We focus on strong modifiers of stature and form that may be useful for directed modification of plant architecture, rather than the detailed mechanisms of gene action. Gibberellin (GA) metabolic and response genes are particularly attractive targets for manipulation because many act in a dose-dependent manner; similar phenotypic effects can be readily achieved in heterologous species; and induced pleiotropic effects--such as on nitrogen assimilation, photosynthesis, and lateral root production--are usually positive with respect to crop performance. Genes encoding transcription factors represent strong candidates for manipulation of plant architecture. For example, AINTEGUMENTA, ARGOS (auxin-regulated gene controlling organ size), and growth-regulating factors (GRFs) are strong modifiers of leaf and/or flower size. Plants overexpressing these genes had increased organ size and did not display negative pleiotropic effects in glasshouse environments. TCP-domain genes such as CINCINNATA, and the associated regulatory miRNAs such as miRJAW, may provide useful means to modulate leaf curvature and other foliage properties. There are considerable opportunities for comparative and translational genomics in nonmodel plant systems.
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Affiliation(s)
- Victor B Busov
- Michigan Technological University, School of Forest Research and Environmental Science, 101 Noblet Hall, 1400 Townsend Drive, Houghton, MI 49931, USA
| | - Amy M Brunner
- Virginia Polytechnic Institute and State University, Department of Forestry, 304 Cheatham Hall (0324), Blacksburg, VA 24061, USA
| | - Steven H Strauss
- Oregon State University, Department of Forest Science, Corvallis, OR 97331-5752, USA
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Tan FC, Swain SM. Functional characterization of AP3, SOC1 and WUS homologues from citrus (Citrus sinensis). PHYSIOLOGIA PLANTARUM 2007; 131:481-95. [PMID: 18251886 DOI: 10.1111/j.1399-3054.2007.00971.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Flowering and flower formation are defining features of angiosperms and the control of these developmental processes involves a common repertoire of genes which are shared among different species of flowering plants. These genes were first identified using various homeotic and flowering time mutants of Arabidopsis and snapdragon, and homologous genes have subsequently been isolated from a wide range of different plant species based on the conservation of protein sequence and function. Using degenerate reverse-transcriptase polymerase chain reaction, we have isolated one APETALA3-like (CitMADS8) and two SOC1 (SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1)-like (CsSL1 and CsSL2) homologues from sweet orange (Citrus sinensis L.). Although the translated amino acid sequence of CitMADS8 shares many similarities with other higher plant APETALA3 proteins, CitMADS8 fails to complement the floral organ identity defects of the Arabidopsis ap3-3 mutant. By contrast, the two citrus SOC1-like genes, particularly CsSL1, are able to shorten the time taken to flower in the Arabidopsis wild-type ecotypes Columbia and C24, and functionally complement the late flowering phenotype of the soc1 mutant, essentially performing the endogenous function of Arabidopsis SOC1. Once flowering has commenced, interactions between specific flowering genes and a gene required for meristem maintenance, WUSCHEL, ensure that the Arabidopsis flower is a determinate structure with four whorls. We have isolated a citrus WUSCHEL homologue (CsWUS) that is capable of restoring most of the meristem function to the shoots and flowers of the Arabidopsis wus-1 mutant, implying that CsWUS is the functional equivalent of Arabidopsis WUSCHEL.
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Affiliation(s)
- Fui-Ching Tan
- CSIRO Plant Industry, Private Mail Bag, Merbein, Victoria 3505, Australia
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Silverstone AL, Tseng TS, Swain SM, Dill A, Jeong SY, Olszewski NE, Sun TP. Functional analysis of SPINDLY in gibberellin signaling in Arabidopsis. PLANT PHYSIOLOGY 2007; 143:987-1000. [PMID: 17142481 PMCID: PMC1803720 DOI: 10.1104/pp.106.091025] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The Arabidopsis (Arabidopsis thaliana) SPINDLY (SPY) protein negatively regulates the gibberellin (GA) signaling pathway. SPY is an O-linked N-acetylglucosamine (GlcNAc) transferase (OGT) with a protein-protein interaction domain consisting of 10 tetratricopeptide repeats (TPR). OGTs add a GlcNAc monosaccharide to serine/threonine residues of nuclear and cytosolic proteins. Determination of the molecular defects in 14 new spy alleles reveals that these mutations cluster in three TPRs and the C-terminal catalytic region. Phenotypic characterization of 12 spy alleles indicates that TPRs 6, 8, and 9 and the catalytic domain are crucial for GA-regulated stem elongation, floral induction, and fertility. TPRs 8 and 9 and the catalytic region are also important for modulating trichome morphology and inflorescence phyllotaxy. Consistent with a role for SPY in embryo development, several alleles affect seedling cotyledon number. These results suggest that three of the TPRs and the OGT activity in SPY are required for its function in GA signal transduction. We also examined the effect of spy mutations on another negative regulator of GA signaling, REPRESSOR OF ga1-3 (RGA). The DELLA motif in RGA is essential for GA-induced proteolysis of RGA, and deletion of this motif (as in rga-delta17) causes a GA-insensitive dwarf phenotype. Here, we demonstrate that spy partially suppresses the rga-delta17 phenotype but does not reduce rga-delta17 or RGA protein levels or alter RGA nuclear localization. We propose that SPY may function as a negative regulator of GA response by increasing the activity of RGA, and presumably other DELLA proteins, by GlcNAc modification.
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Affiliation(s)
- Aron L Silverstone
- Department of Biology, Duke University, Durham, North Carolina 27708, USA
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Shimada A, Ueguchi-Tanaka M, Sakamoto T, Fujioka S, Takatsuto S, Yoshida S, Sazuka T, Ashikari M, Matsuoka M. The rice SPINDLY gene functions as a negative regulator of gibberellin signaling by controlling the suppressive function of the DELLA protein, SLR1, and modulating brassinosteroid synthesis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2006; 48:390-402. [PMID: 17052323 DOI: 10.1111/j.1365-313x.2006.02875.x] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
SPINDLY (SPY) encodes an O-linked N-acetylglucosamine transferase that is considered to be a negative regulator of gibberellin (GA) signaling through an unknown mechanism. To understand the function of SPY in GA signaling in rice, we isolated a rice SPINDLY homolog (OsSPY) and produced knockdown transgenic plants in which OsSPY expression was reduced by introducing its antisense or RNAi construct. In knockdown plants, the enhanced elongation of lower internodes was correlated with decreased levels of OsSPY expression, similar to the spindly phenotype of Arabidopsis spy mutants, suggesting that OsSPY also functions as a negative factor in GA signaling in rice. The suppressive function of OsSPY in GA signaling was supported by the findings that the dwarfism was partially rescued and OsGA20ox2 (GA20 oxidase) expression was reduced in GA-deficient and GA-insensitive mutants by the knockdown of OsSPY function. The suppression of OsSPY function in a GA-insensitive mutant, gid2, also caused an increase in the phosphorylation of a rice DELLA protein, SLR1, but did not change the amount of SLR1. This indicates that the function of OsSPY in GA signaling is not via changes in the amount or stability of SLR1, but probably involves control of the suppressive function of SLR1. In addition to the GA-related phenotypes, OsSPY antisense and RNAi plants showed increased lamina joint bending, which is a brassinosteroid-related phenotype, indicating that OsSPY may play roles both in GA signaling and in the brassinosteroid pathway.
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Affiliation(s)
- Asako Shimada
- Bioscience and Biotechnology Center, Nagoya University, Chikusa, Nagoya, Aichi 464-8601, Japan
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Scott CL, Hartweck LM, de Jesús Pérez J, Chen D, García JA, Olszewski NE. SECRET AGENT, an Arabidopsis thaliana O-GlcNAc transferase, modifies the Plum pox virus capsid protein. FEBS Lett 2006; 580:5829-35. [PMID: 17027982 DOI: 10.1016/j.febslet.2006.09.046] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2006] [Revised: 09/15/2006] [Accepted: 09/15/2006] [Indexed: 12/01/2022]
Abstract
The capsid protein of Plum pox virus (PPV-CP) is modified with O-linked GlcNAc (O-GlcNAc). While Arabidopsis has two O-GlcNAc transferases, SECRET AGENT (SEC) and SPINDLY (SPY), previous work suggests that SEC modifies PPV-CP and that the modification plays a role in the infection process. Here, we show that when co-expressed in Escherichia coli SEC modifies PPV-CP. Deletion mapping and site-directed mutagenesis identified three threonine and a serine located near the N-terminus of PPV-CP that are modified by SEC. Two of these threonines have recently been shown to be modified in virus from plants suggesting that SEC has the same specificity in plants and E. coli.
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Affiliation(s)
- Cheryl L Scott
- Department of Plant Biology, University of Minnesota, 1445 Gortner Avenue, 250 Biological Sciences Center, St. Paul, MN 55108, USA
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Lefebvre T, Guinez C, Dehennaut V, Beseme-Dekeyser O, Morelle W, Michalski JC. Does O-GlcNAc play a role in neurodegenerative diseases? Expert Rev Proteomics 2006; 2:265-75. [PMID: 15892570 DOI: 10.1586/14789450.2.2.265] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
There are several lines of evidence that the modification of proteins by cytosolic- and nuclear-specific O-linked N-acetylglucosamine (O-GlcNAc) glycosylation is closely related to neuropathologies, particularly Alzheimer's disease. Several neuronal proteins have been identified as being modified with O-GlcNAc; these proteins could form part of the inclusion bodies found, for example, in the most frequently observed neurologic disorder (i.e., Alzheimer's disease; Tau protein and beta-amyloid peptide are the well known aggregated proteins). O-GlcNAc proteins are also implicated in synaptosomal transport (e.g., synapsins and clathrin-assembly proteins). Inclusion bodies are partly characterized by a deficiency in the ubiquitin-proteasome system, avoiding the degradation of aggregated proteins. From this perspective, it appears interesting that substrate proteins could be protected against proteasomal degradation by being covalently modified with single N-acetylglucosamine on serine or threonine, and that the proteasome itself is modified and regulated by O-GlcNAc (in this case the turnover of neuronal proteins correlates with extracellular glucose). Interestingly, glucose uptake and metabolism are impaired in neuronal disorders, and this phenomenon is linked to increased phosphorylation. In view of the existence of the dynamic interplay between O-GlcNAc and phosphorylation, it is tempting to draw a parallel between the use of glucose, O-GlcNAc glycosylation and phosphorylation. Lastly, the two enzymes responsible for O-GlcNAc dynamism (i.e., O-GlcNAc transferase and glucosaminidase) are both enriched in the brain and genes that encode the two enzymes are located in two regions that are found to be frequently mutated in neurologic disorders. The data presented in this review strongly suggest that O-GlcNAc could play an active role in neurodegenerative diseases.
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Affiliation(s)
- Tony Lefebvre
- UMR 8576, Centre National de la Recherche Scientifique , Laboratoire de Chimie-Biologique, Bâtiment C9, 59655 Villeneuve d'Ascq, France.
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Abstract
Life occurs in an ever-changing environment. Some of the most striking and predictable changes are the daily rhythms of light and temperature. To cope with these rhythmic changes, plants use an endogenous circadian clock to adjust their growth and physiology to anticipate daily environmental changes. Most studies of circadian functions in plants have been performed under continuous conditions. However, in the natural environment, diurnal outputs result from complex interactions of endogenous circadian rhythms and external cues. Accumulated studies using the hypocotyl as a model for plant growth have shown that both light signalling and circadian clock mutants have growth defects, suggesting strong interactions between hypocotyl elongation, light signalling and the circadian clock. Here, we review evidence suggesting that light, plant hormones and the circadian clock all interact to control diurnal patterns of plant growth.
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Affiliation(s)
- Kazunari Nozue
- Section of Plant Biology, College of Biological Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
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