1
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Qin S, Zhang Y, Tian Z. Quantitative N-glycoproteomics characterization of differential N-glycosylation in Sorghum bicolor under salinity stress. Biochem Biophys Res Commun 2024; 737:150509. [PMID: 39137587 DOI: 10.1016/j.bbrc.2024.150509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 07/24/2024] [Accepted: 08/05/2024] [Indexed: 08/15/2024]
Abstract
Salt stress is one of the significant environmental stresses that severely affect plant growth and development. Here, we report quantitative N-glycoproteomics characterization of differential N-glycosylation in Sorghum bicolor under low, median and high salinity stress. 21,621 intact N-glycopeptides coming from the combination of 127 N-glycan structures on 6574 N-glycosites from 5321 proteins were identified; differential N-glycosylation was observed for 682 N-glycoproteins which are mainly involved in the pathways of biosynthesis of secondary metabolites, biosynthesis of amino acids and several metabolic pathways. 41 N-glycan structures modifying on 338 N-glycopeptides from 122 glycoproteins were co-quantified and deregulated under at least one salt stress, including enzymes of energy production and carbohydrate metabolisms, cell wall organization related proteins, glycosyltransferases and so on. Intriguingly, with increasing salt concentration, there was an increase in the percentage of complex N-glycans on the altered N-glycopeptides. Furthermore, the observation of glycoproteins with distinct salt sensitivity is noteworthy, particularly the upregulated hyposensitive glycoproteins that predominantly undergo complex N-glycan modification. This is the first N-glycoproteome description of salt stress response at the intact N-glycopeptide level in sorghum and a further validation of data reported here would likely provide deeper insights into the stress physiology of this important crop plant.
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Affiliation(s)
- Shanshan Qin
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai, 200092, China
| | - Yumiao Zhang
- College of Biological and Environmental Engineering, Shandong University of Aeronautics, Binzhou, 256600, China
| | - Zhixin Tian
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai, 200092, China.
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2
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Yang J, Zhao Y, Wang X, Yang J, Tang K, Liu J. N-linked glycoproteome analysis reveals central glycosylated proteins involved in response to wheat yellow mosaic virus in wheat. Int J Biol Macromol 2023; 253:126818. [PMID: 37690635 DOI: 10.1016/j.ijbiomac.2023.126818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/12/2023]
Abstract
Glycosylation is an important proteins post-translational modification and is involved in protein folding, stability and enzymatic activity, which plays a crucial role in regulating protein function in plants. Here, we report for the first time on the changes of N-glycoproteome in wheat response to wheat yellow mosaic virus (WYMV) infection. Quantitative analyses of N-linked glycoproteome were performed in wheat without and with WYMV infection by ZIC-HILIC enrichment method combined with LC-MS/MS. Altogether 1160 N-glycopeptides and 971 N-glycosylated sites corresponding to 734 N-glycoproteins were identified, of which 64 N-glycopeptides and 64 N-glycosylated sites in 60 N-glycoproteins were significantly differentially expressed. Two conserved typical N-glycosylation motifs N-X-T and N-X-S and a nontypical motifs N-X-C were enriched in wheat. Gene Ontology analysis showed that most differentially expressed proteins were mainly enriched in metabolic process, catalytic activity and response to stress. Kyoto Encyclopedia of Genes and Genomes analysis indicated that two significantly changed glycoproteins were specifically related to plant-pathogen interaction. Furthermore, we found that over-expression of TaCERK reduced WYMV accumulation. Glycosylation site mutation further suggested that N-glycosylation of TaCERK could regulate wheat resistance to WYMV. This study provides a new insight for the regulation of protein N-glycosylation in defense response of plant.
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Affiliation(s)
- Jiaqian Yang
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass spectrometry and Clinical Application, School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, China; Zhenhai Institute of Mass Spectrometry, Ningbo 315211, China
| | - Yingjie Zhao
- State Key Laboratory for Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Xia Wang
- State Key Laboratory for Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jian Yang
- State Key Laboratory for Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Keqi Tang
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass spectrometry and Clinical Application, School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, China; Zhenhai Institute of Mass Spectrometry, Ningbo 315211, China.
| | - Jiaqian Liu
- State Key Laboratory for Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China.
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3
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Yu Y, Tang W, Lin W, Li W, Zhou X, Li Y, Chen R, Zheng R, Qin G, Cao W, Pérez-Henríquez P, Huang R, Ma J, Qiu Q, Xu Z, Zou A, Lin J, Jiang L, Xu T, Yang Z. ABLs and TMKs are co-receptors for extracellular auxin. Cell 2023; 186:5457-5471.e17. [PMID: 37979582 PMCID: PMC10827329 DOI: 10.1016/j.cell.2023.10.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 09/03/2023] [Accepted: 10/18/2023] [Indexed: 11/20/2023]
Abstract
Extracellular perception of auxin, an essential phytohormone in plants, has been debated for decades. Auxin-binding protein 1 (ABP1) physically interacts with quintessential transmembrane kinases (TMKs) and was proposed to act as an extracellular auxin receptor, but its role was disputed because abp1 knockout mutants lack obvious morphological phenotypes. Here, we identified two new auxin-binding proteins, ABL1 and ABL2, that are localized to the apoplast and directly interact with the extracellular domain of TMKs in an auxin-dependent manner. Furthermore, functionally redundant ABL1 and ABL2 genetically interact with TMKs and exhibit functions that overlap with those of ABP1 as well as being independent of ABP1. Importantly, the extracellular domain of TMK1 itself binds auxin and synergizes with either ABP1 or ABL1 in auxin binding. Thus, our findings discovered auxin receptors ABL1 and ABL2 having functions overlapping with but distinct from ABP1 and acting together with TMKs as co-receptors for extracellular auxin.
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Affiliation(s)
- Yongqiang Yu
- Haixia Institute of Science and Technology, School of Future Technology, and College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, P.R. China; Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, P.R. China
| | - Wenxin Tang
- Haixia Institute of Science and Technology, School of Future Technology, and College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, P.R. China
| | - Wenwei Lin
- Haixia Institute of Science and Technology, School of Future Technology, and College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, P.R. China
| | - Wei Li
- Haixia Institute of Science and Technology, School of Future Technology, and College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, P.R. China; College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, P.R. China
| | - Xiang Zhou
- Haixia Institute of Science and Technology, School of Future Technology, and College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, P.R. China; Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, Guangdong 518055, P.R. China; Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, P.R. China
| | - Ying Li
- Haixia Institute of Science and Technology, School of Future Technology, and College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, P.R. China
| | - Rong Chen
- Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, P.R. China
| | - Rui Zheng
- Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, P.R. China
| | - Guochen Qin
- Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, P.R. China; Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, P.R. China
| | - Wenhan Cao
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, P.R. China
| | - Patricio Pérez-Henríquez
- Institute of Integrative Genome Biology, and Department of Botany and Plant Sciences, University of California-Riverside, Riverside, CA 92507, USA
| | - Rongfeng Huang
- Haixia Institute of Science and Technology, School of Future Technology, and College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, P.R. China
| | - Jun Ma
- Haixia Institute of Science and Technology, School of Future Technology, and College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, P.R. China
| | - Qiqi Qiu
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, P.R. China
| | - Ziwei Xu
- Haixia Institute of Science and Technology, School of Future Technology, and College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, P.R. China
| | - Ailing Zou
- Haixia Institute of Science and Technology, School of Future Technology, and College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, P.R. China
| | - Juncheng Lin
- Haixia Institute of Science and Technology, School of Future Technology, and College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, P.R. China
| | - Liwen Jiang
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, P.R. China
| | - Tongda Xu
- Haixia Institute of Science and Technology, School of Future Technology, and College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, P.R. China; Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, P.R. China.
| | - Zhenbiao Yang
- Haixia Institute of Science and Technology, School of Future Technology, and College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, P.R. China; Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, Guangdong 518055, P.R. China; Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, P.R. China; Institute of Integrative Genome Biology, and Department of Botany and Plant Sciences, University of California-Riverside, Riverside, CA 92507, USA.
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4
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Jia X, Zhang H, Qin H, Li K, Liu X, Wang W, Ye M, Yin H. Protein O-GlcNAcylation impairment caused by N-acetylglucosamine phosphate mutase deficiency leads to growth variations in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:613-635. [PMID: 36799458 DOI: 10.1111/tpj.16156] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 02/06/2023] [Accepted: 02/13/2023] [Indexed: 05/10/2023]
Abstract
As an essential enzyme in the uridine diphosphate (UDP)-GlcNAc biosynthesis pathway, the significant role of N-acetylglucosamine phosphate mutase (AGM) remains unknown in plants. In the present study, a functional plant AGM (AtAGM) was identified from Arabidopsis thaliana. AtAGM catalyzes the isomerization of GlcNAc-1-P and GlcNAc-6-P, and has broad catalytic activity on different phosphohexoses. UDP-GlcNAc contents were significantly decreased in AtAGM T-DNA insertional mutants, which caused temperature-dependent growth defects in seedlings and vigorous growth in adult plants. Further analysis revealed that protein O-GlcNAcylation but not N-glycosylation was dramatically impaired in Atagm mutants due to UDP-GlcNAc shortage. Combined with the results from O-GlcNAcylation or N-glycosylation deficient mutants, and O-GlcNAcase inhibitor all suggested that protein O-GlcNAcylation impairment mainly leads to the phenotypic variations of Atagm plants. In conclusion, based on the essential role in UDP-GlcNAc biosynthesis, AtAGM is important for plant growth mainly via protein O-GlcNAcylation-level regulation.
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Affiliation(s)
- Xiaochen Jia
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023, Dalian, China
| | - Hongyan Zhang
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023, Dalian, China
| | - Hongqiang Qin
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Kuikui Li
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023, Dalian, China
| | - Xiaoyan Liu
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Wenxia Wang
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023, Dalian, China
| | - Mingliang Ye
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Heng Yin
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023, Dalian, China
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5
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Zhao X, Zeng L, Wang J, Shi Y, Zhang B, Liu Y, Pan Y, Li X. Quantitative N-Glycomic and N-Glycoproteomic Profiling of Peach [ Prunus persica (L.) Batsch] during Fruit Ripening. J Proteome Res 2023; 22:885-895. [PMID: 36725203 DOI: 10.1021/acs.jproteome.2c00662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Being part of the human diet, peach is an important fruit consumed worldwide. In the present study, a systematic first insight into the N-glycosylation of peach fruit during ripening was provided. First, N-glycome by reactive matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry indicated that 6 of 24 N-glycans of peach were differentially expressed. Second, a comparative N-glycoproteome was characterized via 18O-tagged N-glycosylation site labeling followed by nano-liquid chromatography-electrospray ionization-tandem mass spectrometry (nLC-ESI-MS/MS). Totally 1464 N-glycosites on 881 N-glycoproteins were identified, among which 291 N-glycosites on 237 N-glycoproteins were expressed differentially with a fold change value of 1.5 or 0.67. The enrichment analysis of GO and KEGG revealed that four pathways including other glycan degradation, phenylpropanoid biosynthesis, amino sugar and nucleotide sugar metabolism, and protein processing in endoplasmic reticulum were mainly enriched, in which several important N-glycoproteins with dynamic change during fruit ripening were further screened out. Our findings on a large scale for N-glycosylation analysis of peach fruit during ripening may provide new molecular insights for comprehending N-glycoprotein functions, which should be of great interest to both glycobiologists and analytical chemists.
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Affiliation(s)
- Xiaoyong Zhao
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou 310058, China
| | - Lin Zeng
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou 310058, China
| | - Jiaqi Wang
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou 310058, China
| | - Yanna Shi
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou 310058, China
| | - Bo Zhang
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou 310058, China
| | - Yaqin Liu
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Yuanjiang Pan
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Xian Li
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou 310058, China
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6
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San Clemente H, Jamet E. N-glycoproteins in Plant Cell Walls: A Survey. PLANTS (BASEL, SWITZERLAND) 2022; 11:3204. [PMID: 36501244 PMCID: PMC9738366 DOI: 10.3390/plants11233204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/16/2022] [Accepted: 11/20/2022] [Indexed: 06/17/2023]
Abstract
Cell walls are an extracellular compartment specific to plant cells, which are not found in animal cells. Their composition varies between cell types, plant species, and physiological states. They are composed of a great diversity of polymers, i.e., polysaccharides, proteins, and lignins. Cell wall proteins (CWPs) are major players involved in the plasticity of cell walls which support cell growth and differentiation, as well as adaptation to environmental changes. In order to reach the extracellular space, CWPs are transported through the secretory pathway where they may undergo post-translational modifications, including N-glycosylations on the Asn residues in specific motifs (Asn-X-Ser/Thr-X, with X≠Pro). This review aims at providing a survey of the present knowledge related to cell wall N-glycoproteins with (i) an overview of the experimental workflows, (ii) a selection of relevant articles dedicated to N-glycoproteomics, (iii) a description of the diversity of N-glycans, and (iv) a focus on the importance of N-glycans for CWP structure and/or function.
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Xu Y, Wang H, Sahu SK, Li L, Liang H, Günther G, Wong GKS, Melkonian B, Melkonian M, Liu H, Wang S. Chromosome-level genome of Pedinomonas minor (Chlorophyta) unveils adaptations to abiotic stress in a rapidly fluctuating environment. THE NEW PHYTOLOGIST 2022; 235:1409-1425. [PMID: 35560066 DOI: 10.1111/nph.18220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
The Pedinophyceae (Viridiplantae) comprise a class of small uniflagellate algae with a pivotal position in the phylogeny of the Chlorophyta as the sister group of the 'core chlorophytes'. We present a chromosome-level genome assembly of the freshwater type species of the class, Pedinomonas minor. We sequenced the genome using Pacbio, Illumina and Hi-C technologies, performed comparative analyses of genome and gene family evolution, and analyzed the transcriptome under various abiotic stresses. Although the genome is relatively small (55 Mb), it shares many traits with core chlorophytes including number of introns and protein-coding genes, messenger RNA (mRNA) lengths, and abundance of transposable elements. Pedinomonas minor is only bounded by the plasma membrane, thriving in temporary habitats that frequently dry out. Gene family innovations and expansions and transcriptomic responses to abiotic stresses have shed light on adaptations of P. minor to its fluctuating environment. Horizontal gene transfers from bacteria and fungi have possibly contributed to the evolution of some of these traits. We identified a putative endogenization site of a nucleocytoplasmic large DNA virus and hypothesized that endogenous viral elements donated foreign genes to the host genome, their spread enhanced by transposable elements, located at gene boundaries in several of the expanded gene families.
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Affiliation(s)
- Yan Xu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 10049, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Hongli Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 10049, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Linzhou Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Hongping Liang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 10049, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Gerd Günther
- Private Laboratory, Knittkuhler Str. 61, Düsseldorf, 40629, Germany
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
- Department of Medicine, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Barbara Melkonian
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Michael Melkonian
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Huan Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 10049, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Sibo Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
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8
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Liu Y, Cao D, Ma L, Jin X. Upregulation of protein N-glycosylation plays crucial roles in the response of Camellia sinensis leaves to fluoride. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 183:138-150. [PMID: 35597102 DOI: 10.1016/j.plaphy.2022.05.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 05/06/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
The tea plant (Camellia sinensis) is one of the three major beverage crops in the world with its leaves consumption as tea. However, it can hyperaccumulate fluoride with about 98% fluoride deposition in the leaves. Our previously studies found that cell wall proteins (CWPs) might play a central role in fluoride accumulation/detoxification in C. sinensis. CWP is known to be glycosylated, however the response of CWP N-glycosylation to fluoride remains unknown in C. sinensis. In this study, a comparative N-glycoproteomic analysis was performed through HILIC enrichment coupled with UPLC-MS/MS based on TMT-labeling approach in C. sinensis leaves. Totally, 237 N-glycoproteins containing 326 unique N-glycosites were identified. 73.4%, 18.6%, 6.3% and 1.7% of these proteins possess 1, 2, 3, and ≥4 modification site, respectively. 93.2% of these proteins were predicted to be localized in the secretory pathway and 78.9% of them were targeted to the cell wall and the plasma membrane. 133 differentially accumulated N-glycosites (DNGSs) on 100 N-glycoproteins (DNGPs) were detected and 85.0% of them exhibited upregulated expression after fluoride treatment. 78.0% DNGPs were extracellular DNGPs, which belonged to CWPs, and 53.0% of them were grouped into protein acting on cell wall polysaccharides, proteases and oxido-reductases, whereas the majority of the remaining DNGPs were mainly related to N-glycoprotein biosynthesis, trafficking and quality control. Our study shed new light on the N-glycoproteome study, and revealed that increased N-glycosylation abundance of CWPs might contribute to fluoride accumulation/detoxification in C. sinensis leave.
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Affiliation(s)
- Yanli Liu
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China.
| | - Dan Cao
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Linlong Ma
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Xiaofang Jin
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China.
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9
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Zhang J, Xia Y, Wang D, Du Y, Chen Y, Zhang C, Mao J, Wang M, She YM, Peng X, Liu L, Voglmeir J, He Z, Liu L, Li J. A Predominant Role of AtEDEM1 in Catalyzing a Rate-Limiting Demannosylation Step of an Arabidopsis Endoplasmic Reticulum-Associated Degradation Process. FRONTIERS IN PLANT SCIENCE 2022; 13:952246. [PMID: 35874007 PMCID: PMC9302962 DOI: 10.3389/fpls.2022.952246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
Endoplasmic reticulum-associated degradation (ERAD) is a key cellular process for degrading misfolded proteins. It was well known that an asparagine (N)-linked glycan containing a free α1,6-mannose residue is a critical ERAD signal created by Homologous to α-mannosidase 1 (Htm1) in yeast and ER-Degradation Enhancing α-Mannosidase-like proteins (EDEMs) in mammals. An earlier study suggested that two Arabidopsis homologs of Htm1/EDEMs function redundantly in generating such a conserved N-glycan signal. Here we report that the Arabidopsis irb1 (reversal of bri1) mutants accumulate brassinosteroid-insensitive 1-5 (bri1-5), an ER-retained mutant variant of the brassinosteroid receptor BRI1 and are defective in one of the Arabidopsis Htm1/EDEM homologs, AtEDEM1. We show that the wild-type AtEDEM1, but not its catalytically inactive mutant, rescues irb1-1. Importantly, an insertional mutation of the Arabidopsis Asparagine-Linked Glycosylation 3 (ALG3), which causes N-linked glycosylation with truncated glycans carrying a different free α1,6-mannose residue, completely nullifies the inhibitory effect of irb1-1 on bri1-5 ERAD. Interestingly, an insertional mutation in AtEDEM2, the other Htm1/EDEM homolog, has no detectable effect on bri1-5 ERAD; however, it enhances the inhibitory effect of irb1-1 on bri1-5 degradation. Moreover, AtEDEM2 transgenes rescued the irb1-1 mutation with lower efficacy than AtEDEM1. Simultaneous elimination of AtEDEM1 and AtEDEM2 completely blocks generation of α1,6-mannose-exposed N-glycans on bri1-5, while overexpression of either AtEDEM1 or AtEDEM2 stimulates bri1-5 ERAD and enhances the bri1-5 dwarfism. We concluded that, despite its functional redundancy with AtEDEM2, AtEDEM1 plays a predominant role in promoting bri1-5 degradation.
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Affiliation(s)
- Jianjun Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Yang Xia
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Dinghe Wang
- University of Chinese Academy of Sciences, Beijing, China
- The Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yamin Du
- Glycomics and Glycan Bioengineering Research Center, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yongwu Chen
- University of Chinese Academy of Sciences, Beijing, China
- The Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Congcong Zhang
- University of Chinese Academy of Sciences, Beijing, China
- The Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Juan Mao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Muyang Wang
- The Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yi-Min She
- The Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xinxiang Peng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Li Liu
- Glycomics and Glycan Bioengineering Research Center, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Josef Voglmeir
- Glycomics and Glycan Bioengineering Research Center, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Zuhua He
- The Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Linchuan Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Jianming Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
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10
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A conserved asparagine residue in the inner surface of BRI1 superhelix is essential for protein native conformation. Biochem Biophys Res Commun 2022; 615:49-55. [DOI: 10.1016/j.bbrc.2022.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/04/2022] [Indexed: 11/19/2022]
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11
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Protein glycosylation changes during systemic acquired resistance in Arabidopsis thaliana. Int J Biol Macromol 2022; 212:381-392. [PMID: 35623457 DOI: 10.1016/j.ijbiomac.2022.05.126] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 05/08/2022] [Accepted: 05/17/2022] [Indexed: 01/01/2023]
Abstract
N-glycosylation, an important post-translational modification of proteins in all eukaryotes, has been clearly shown to be involved in numerous diseases in mammalian systems. In contrast, little is known regarding the role of protein N-glycosylation in plant defensive responses to pathogen infection. We identified, for the first time, glycoproteins related to systemic acquired resistance (SAR) in an Arabidopsis thaliana model, using a glycoproteomics platform based on high-resolution mass spectrometry. 407 glycosylation sites corresponding to 378 glycopeptides and 273 unique glycoproteins were identified. 65 significantly changed glycoproteins with 80 N-glycosylation sites were detected in systemic leaves of SAR-induced plants, including numerous GDSL-like lipases, thioglucoside glucohydrolases, kinases, and glycosidases. Functional enrichment analysis revealed that significantly changed glycoproteins were involved mainly in N-glycan biosynthesis and degradation, phenylpropanoid biosynthesis, cutin and wax biosynthesis, and plant-pathogen interactions. Comparative analysis of glycoproteomics and proteomics data indicated that glycoproteomics analysis is an efficient method for screening proteins associated with SAR. The present findings clarify glycosylation status and sites of A. thaliana proteins, and will facilitate further research on roles of glycoproteins in SAR induction.
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12
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Kajiura H, Hiwasa-Tanase K, Ezura H, Fujiyama K. Effect of fruit maturation on N-glycosylation of plant-derived native and recombinant miraculin. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 178:70-79. [PMID: 35276597 DOI: 10.1016/j.plaphy.2022.02.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/26/2022] [Accepted: 02/27/2022] [Indexed: 06/14/2023]
Abstract
Miracle fruit, Synsepalum dulcificum, produces a unique taste-modifying protein, miraculin (MIR), which has an attractive potential for commercial application as a novel low-calorie sweetener. To establish a stable supply system for MIR, a previous study established a platform for recombinant MIR (rMIR) production in tomato plants and demonstrated that native miraculin from miracle fruit (nMIR) and rMIR were almost identical in their protein modifications with N-glycan. However, neither N-glycosylation nor the influence of fruit maturation on the structural changes of N-glycan have been fully characterized in detail. Here, with a focus on N-glycosylation and the contribution of fruit maturation to N-glycan, we reanalyzed the N-glycosylation of the natural maturation stages of nMIR and rMIR, and then compared the N-glycan structures on MIRs prepared from the fruit at two different maturation stages. The detailed peptide mapping and N-glycosylation analysis of MIRs provided evidence that MIRs have variants, which were derived mainly from the differences in the N-glycan structure in nMIR and the N-glycosylation in rMIR and not from the cleavage of the peptide backbone. N-Glycan analysis of MIRs from the maturation stage of fruits demonstrated that N-glycan structures were similar among nMIRs and rMIRs at every maturation stage. These results indicated that the heterogeneously expressed rMIRs had the same characteristics in post-translational modifications, especially N-glycosylation and N-glycan structures, throughout the maturation stages. This study demonstrated the potential of recombinant protein expressed in tomato plants and paves the way for the commercial use of rMIR.
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Affiliation(s)
- Hiroyuki Kajiura
- International Center for Biotechnology, Osaka University, 2-1 Yamada-oka, Suita-shi, Osaka, 565, Japan; Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, 2-1 Yamada-oka, Suita-shi, Osaka, 565-0871, Japan.
| | - Kyoko Hiwasa-Tanase
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan; Tsukuba-Plant Innovation Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Hiroshi Ezura
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan; Tsukuba-Plant Innovation Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Kazuhito Fujiyama
- International Center for Biotechnology, Osaka University, 2-1 Yamada-oka, Suita-shi, Osaka, 565, Japan; Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, 2-1 Yamada-oka, Suita-shi, Osaka, 565-0871, Japan; Osaka University Cooperative Research Station in Southeast Asia (OU:CRS), Faculty of Science, Mahidol University, Bangkok, Thailand
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13
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Qin S, Qin S, Tian Z. Comprehensive site- and structure-specific characterization of N-glycosylation in model plant Arabidopsis using mass-spectrometry-based N-glycoproteomics. J Chromatogr B Analyt Technol Biomed Life Sci 2022; 1198:123234. [DOI: 10.1016/j.jchromb.2022.123234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 03/12/2022] [Accepted: 03/28/2022] [Indexed: 02/05/2023]
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14
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Plasma membrane N-glycoproteome analysis of wheat seedling leaves under drought stress. Int J Biol Macromol 2021; 193:1541-1550. [PMID: 34740685 DOI: 10.1016/j.ijbiomac.2021.10.217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/12/2021] [Accepted: 10/29/2021] [Indexed: 01/23/2023]
Abstract
Protein glycosylation is one of the ubiquitous post-translational modifications in eukaryotic cells, which play important roles in plant growth and adverse response. In this study, we performed the first comprehensive wheat plasma membrane N-glycoproteome analysis under drought stress via glycopeptide HILIC enrichment and LC-MS/MS identification. In total, 414 glycosylated sites corresponding to 407 glycopeptides and 312 unique glycoproteins were identified, of which 173 plasma membrane glycoproteins with 215 N-glycosylation sites were significantly regulated by drought stress. Functional enrichment analysis reveals that the significantly regulated N-glycosylation proteins were particularly related to protein kinase activity involved in the reception and transduction of extracellular signal and plant cell wall remolding. The motifs and sequence structures analysis showed that the significantly regulated N-glycosylation sites were concentrated within [NxT] motif, and 79.5% of them were located on the random coil that is always on the protein surface and flexible regions, which could facilitate protein glycosylated modification and enhance protein structural stability via reducing protein flexibility. PNGase F enzyme digestion and glycosylation site mutation further indicated that N-glycosylated modification could increase protein stability. Therefore, N-glycosylated modification is involved in plant adaptation to drought stress by improving the stability of cell wall remodeling related plasma membrane proteins.
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15
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Liu C, Niu G, Li X, Zhang H, Chen H, Hou D, Lan P, Hong Z. Comparative Label-Free Quantitative Proteomics Analysis Reveals the Essential Roles of N-Glycans in Salt Tolerance by Modulating Protein Abundance in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2021; 12:646425. [PMID: 34276718 PMCID: PMC8283305 DOI: 10.3389/fpls.2021.646425] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 06/02/2021] [Indexed: 06/01/2023]
Abstract
Many pieces of evidence show that the adaptive response of plants to salt stress requires the maturation of N-glycan on associated proteins. However, it is still little known about the salt-responsive glycoproteins that function in this process. In the present study, we identified salt-responsive glycoproteins in wild-type (WT) Arabidopsis and two mutants defective in N-glycan maturation, mns1 mns2 and cgl1. A total of 97 proteins with abundance changes of >1.5- or <0.67-fold were identified against salt stress by label-free liquid chromatography coupled mass spectrometry (LC-MS/MS) quantitative analyses. A comparison of differentially abundant glycoproteins (DAGs) indicated the substrate preferences regulated by MNS1/MNS2 and CGL1. In addition, the DAGs in mns1 mns2 hardly form functional regulatory networks in STRING analysis. Comparably, the regulatory network in cgl1 was visible and shared overlapping with that in WT. Such difference may supply the evidence to partially explain the lower salt sensitivity of mutant cgl1 than mns1 mns2. We further confirmed that two N-glycosylation clients, peroxidases PRX32 and PRX34, were involved in the salt stress response since the double mutants showed enhanced salt sensitivity. Together, our study provided proteomic evidence that N-glycans are crucial for modulating stress-responsive protein levels, and several novel glycoproteins responsible for salt stress tolerance in Arabidopsis were listed. Data are available via ProteomeXchange with identifier PXD006893.
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Affiliation(s)
- Chuanfa Liu
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, China
- Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Guanting Niu
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, China
| | - Xiaowen Li
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, China
| | - Huchen Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, China
| | - Huawei Chen
- Research Center for Proteome Analysis, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Dongxia Hou
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, China
| | - Ping Lan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences (CAS), Nanjing, China
| | - Zhi Hong
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, China
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16
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Leschevin M, Ismael M, Quero A, San Clemente H, Roulard R, Bassard S, Marcelo P, Pageau K, Jamet E, Rayon C. Physiological and Biochemical Traits of Two Major Arabidopsis Accessions, Col-0 and Ws, Under Salinity. FRONTIERS IN PLANT SCIENCE 2021; 12:639154. [PMID: 34234793 PMCID: PMC8256802 DOI: 10.3389/fpls.2021.639154] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 04/20/2021] [Indexed: 06/01/2023]
Abstract
Salinity affects plant growth and development as shown with the glycophyte model plant, Arabidopsis thaliana (Arabidopsis). Two Arabidopsis accessions, Wassilewskija (Ws) and Columbia (Col-0), are widely used to generate mutants available from various Arabidopsis seed resources. However, these two ecotypes are known to be salt-sensitive with different degrees of tolerance. In our study, 3-week-old Col-0 and Ws plants were treated with and without 150 mM NaCl for 48, 72, or 96 h, and several physiological and biochemical traits were characterized on shoots to identify any specific traits in their tolerance to salinity. Before salt treatment was carried out, a different phenotype was observed between Col-0 and Ws, whose main inflorescence stem became elongated in contrast to Col-0, which only displayed rosette leaves. Our results showed that Col-0 and Ws were both affected by salt stress with limited growth associated with a reduction in nutrient uptake, a degradation of photosynthetic pigments, an increase in protein degradation, as well as showing changes in carbohydrate metabolism and cell wall composition. These traits were often more pronounced in Col-0 and occurred usually earlier than in Ws. Tandem Mass Tags quantitative proteomics data correlated well with the physiological and biochemical results. The Col-0 response to salt stress was specifically characterized by a greater accumulation of osmoprotectants such as anthocyanin, galactinol, and raffinose; a lower reactive oxygen detoxification capacity; and a transient reduction in galacturonic acid content. Pectin degradation was associated with an overaccumulation of the wall-associated kinase 1, WAK1, which plays a role in cell wall integrity (CWI) upon salt stress exposure. Under control conditions, Ws produced more antioxidant enzymes than Col-0. Fewer specific changes occurred in Ws in response to salt stress apart from a higher number of different fascilin-like arabinogalactan proteins and a greater abundance of expansin-like proteins, which could participate in CWI. Altogether, these data indicate that Col-0 and Ws trigger similar mechanisms to cope with salt stress, and specific changes are more likely related to the developmental stage than to their respective genetic background.
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Affiliation(s)
- Maïté Leschevin
- UMR INRAE 1158 BioEcoAgro, BIOlogie des Plantes et Innovation, Université de Picardie Jules Verne, Amiens, France
| | - Marwa Ismael
- UMR INRAE 1158 BioEcoAgro, BIOlogie des Plantes et Innovation, Université de Picardie Jules Verne, Amiens, France
| | - Anthony Quero
- UMR INRAE 1158 BioEcoAgro, BIOlogie des Plantes et Innovation, Université de Picardie Jules Verne, Amiens, France
| | | | - Romain Roulard
- UMR INRAE 1158 BioEcoAgro, BIOlogie des Plantes et Innovation, Université de Picardie Jules Verne, Amiens, France
| | - Solène Bassard
- UMR INRAE 1158 BioEcoAgro, BIOlogie des Plantes et Innovation, Université de Picardie Jules Verne, Amiens, France
| | - Paulo Marcelo
- Plateforme d’Ingénierie Cellulaire & Analyses des Protéines ICAP Université de Picardie Jules Verne, Amiens, France
| | - Karine Pageau
- UMR INRAE 1158 BioEcoAgro, BIOlogie des Plantes et Innovation, Université de Picardie Jules Verne, Amiens, France
| | - Elisabeth Jamet
- LRSV, Université de Toulouse, CNRS, UPS, Auzeville-Tolosane, France
| | - Catherine Rayon
- UMR INRAE 1158 BioEcoAgro, BIOlogie des Plantes et Innovation, Université de Picardie Jules Verne, Amiens, France
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17
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Meng X, Li L, Wang X. An integrated strategy for the construction of a species-specific glycan library for mass spectrometry-based intact glycopeptide analyses. Talanta 2021; 234:122626. [PMID: 34364435 DOI: 10.1016/j.talanta.2021.122626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 11/15/2022]
Abstract
Mass spectrometry (MS)-based strategies and related software tools using glycan mass lists have greatly facilitated the analysis of intact glycopeptides. Most glycan mass lists are derived from normal glycans of mammals and contain limited monosaccharides, which has significantly hindered high throughput studies of unusual glycosylation events observed in other species. In this work, an integrated strategy was developed for the construction of a species-specific glycan mass list from glycan structure databases and published papers. We developed a computational tool called LibGlycan, which could process the different formats of glycans. Then, the software tool generated a glycan library that contained the monoisotope mass, average mass, isotope distribution, and glycan mass list for input into Byonic software. This strategy was applied to analyze the N-glycosylation of rice roots and O-glycosylation of Acinetobacter baumannii ATCC17978, leading to the identification of 296 and 145 intact glycopeptides respectively. Combined, these results show that this strategy is a robust computational approach for the determination of glycan diversity within different complex biological systems.
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Affiliation(s)
- Xianbin Meng
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry and Biology, Beijing University of Technology, Beijing, 100124, China
| | - Lijie Li
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry and Biology, Beijing University of Technology, Beijing, 100124, China
| | - Xiayan Wang
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry and Biology, Beijing University of Technology, Beijing, 100124, China.
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18
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Leschevin M, Marcelo P, Ismael M, San-Clemente H, Jamet E, Rayon C, Pageau K. A Tandem Mass Tags (TMTs) labeling approach highlights differences between the shoot proteome of two Arabidopsis thaliana ecotypes, Col-0 and Ws. Proteomics 2021; 21:e2000293. [PMID: 33891803 DOI: 10.1002/pmic.202000293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/10/2021] [Accepted: 04/07/2021] [Indexed: 12/13/2022]
Abstract
Arabidopsis has become a powerful model to study morphogenesis, plant growth, development but also plant response to environmental conditions. Over 1000 Arabidopsis genomes are available and show natural genetic variations. Among them, the main reference accessions Wassilewskija (Ws) and Columbia (Col-0), originally growing at contrasted altitudes and temperatures, are widely studied, but data contributing to their molecular phenotyping are still scarce. A global quantitative proteomics approach using isobaric stable isotope labeling (Tandem Mass Tags, TMT) was performed on Ws and Col-0. Plants have been hydroponically grown at 16 h/8 h (light/dark cycle) at 23°C day/19°C night for three weeks. A TMT labeling of the proteins extracted from their shoots has been performed and showed a differential pattern of protein abundance between them. These results have allowed identifying several proteins families possibly involved in the differential responses observed for Ws and Col-0 during plant development and upon environmental changes. In particular, Ws and Col-0 mainly differ in photosynthesis, cell wall-related proteins, plant defense/stress, ROS scavenging enzymes/redox homeostasis and DNA/RNA binding/transcription/translation/protein folding.
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Affiliation(s)
- Maïté Leschevin
- UMRT 1158 BioEcoAgro, BIOlogie des Plantes et Innovation (BIOPI), Université de Picardie Jules Verne, Amiens, France
| | - Paulo Marcelo
- Plateforme d'Ingénierie Cellulaire & Analyses des Protéines ICAP, FR CNRS 3085 ICP, Université de Picardie Jules Verne, Amiens, France
| | - Marwa Ismael
- UMRT 1158 BioEcoAgro, BIOlogie des Plantes et Innovation (BIOPI), Université de Picardie Jules Verne, Amiens, France
| | | | - Elisabeth Jamet
- LRSV, Université de Toulouse, CNRS, UPS, Auzeville-Tolosane, France
| | - Catherine Rayon
- UMRT 1158 BioEcoAgro, BIOlogie des Plantes et Innovation (BIOPI), Université de Picardie Jules Verne, Amiens, France
| | - Karine Pageau
- UMRT 1158 BioEcoAgro, BIOlogie des Plantes et Innovation (BIOPI), Université de Picardie Jules Verne, Amiens, France
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19
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Dou L, Sun Y, Li S, Ge C, Shen Q, Li H, Wang W, Mao J, Xiao G, Pang C. Transcriptomic analyses show that 24-epibrassinolide (EBR) promotes cold tolerance in cotton seedlings. PLoS One 2021; 16:e0245070. [PMID: 33524020 PMCID: PMC7850480 DOI: 10.1371/journal.pone.0245070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 12/21/2020] [Indexed: 11/19/2022] Open
Abstract
In plants, brassinosteroids (BRs) are a class of steroidal hormones that are involved in numerous physiological responses. However, the function of BRs in cold tolerance in cotton has not been explored. In this study, cotton seedlings were treated with five concentrations (0, 0.05, 0.1, 0.2, 0.5 and 1.0 mg/L) of 24-Epibrassinolide (EBR) at 4°C. We measured the electrolyte leakage, malondialdehyde (MDA) content, proline content, and net photosynthesis rate (Pn) of the seedlings, which showed that EBR treatment increased cold tolerance in cotton in a dose-dependent manner, and that 0.2 mg/L is an optimum concentration for enhancing cold tolerance. The function of EBR in cotton cotyledons was investigated in the control 0 mg/L (Cold+water) and 0.2 mg/L (Cold+EBR) treatments using RNA-Seq. A total of 4,001 differentially expressed genes (DEGs), including 2,591 up-regulated genes and 1,409 down-regulated genes were identified. Gene Ontology (GO) and biochemical pathway enrichment analyses showed that EBR is involved in the genetic information process, secondary metabolism, and also inhibits abscisic acid (ABA) and ethylene (ETH) signal transduction. In this study, physiological experiments showed that EBR can increase cold tolerance in cotton seedlings, and the comprehensive RNA-seq data shed light on the mechanisms through which EBR increases cold tolerance in cotton seedlings.
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Affiliation(s)
- Lingling Dou
- School of Chemistry and Chemical Engineering, Xianyang Normal University, Xianyang, Shaanxi, China
| | - Yaru Sun
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, Henan, China
| | - Shuye Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Changwei Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Qian Shen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Huaizhu Li
- School of Chemistry and Chemical Engineering, Xianyang Normal University, Xianyang, Shaanxi, China
| | - Wenbo Wang
- School of Chemistry and Chemical Engineering, Xianyang Normal University, Xianyang, Shaanxi, China
| | - Jiayi Mao
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Guanghui Xiao
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
- * E-mail: (GX); (CP)
| | - Chaoyou Pang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
- * E-mail: (GX); (CP)
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20
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Jiao Q, Chen T, Niu G, Zhang H, Zhou C, Hong Z. N-glycosylation is involved in stomatal development by modulating the release of active abscisic acid and auxin in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5865-5879. [PMID: 32649744 DOI: 10.1093/jxb/eraa321] [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: 03/12/2020] [Accepted: 07/09/2020] [Indexed: 05/11/2023]
Abstract
Asparagine-linked glycosylation (N-glycosylation) is one of the most important protein modifications in eukaryotes, affecting the folding, transport, and function of a wide range of proteins. However, little is known about the roles of N-glycosylation in the development of stomata in plants. In the present study, we provide evidence that the Arabidopsis stt3a-2 mutant, defective in oligosaccharyltransferase catalytic subunit STT3, has a greater transpirational water loss and weaker drought avoidance, accompanied by aberrant stomatal distribution. Through physiological, biochemical, and genetic analyses, we found that the abnormal stomatal density of stt3a-2 was partially attributed to low endogenous abscisic acid (ABA) and auxin (IAA) content. Exogenous application of ABA or IAA could partially rescue the mutant's salt-sensitive and abnormal stomatal phenotype. Further analyses revealed that the decrease of IAA or ABA in stt3a-2 seedlings was associated with the underglycosylation of β-glucosidase (AtBG1), catalysing the conversion of conjugated ABA/IAA to active hormone. Our results provide strong evidence that N-glycosylation is involved in stomatal development and participates in abiotic stress tolerance by modulating the release of active plant hormones.
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Affiliation(s)
- Qingsong Jiao
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, China
| | - Tianshu Chen
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, China
| | - Guanting Niu
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, China
| | - Huchen Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, China
| | - ChangFang Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, China
| | - Zhi Hong
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, China
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21
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Na 2CO 3-responsive Photosynthetic and ROS Scavenging Mechanisms in Chloroplasts of Alkaligrass Revealed by Phosphoproteomics. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 18:271-288. [PMID: 32683046 PMCID: PMC7801222 DOI: 10.1016/j.gpb.2018.10.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 09/08/2018] [Accepted: 10/23/2018] [Indexed: 12/27/2022]
Abstract
Alkali-salinity exerts severe osmotic, ionic, and high-pH stresses to plants. To understand the alkali-salinity responsive mechanisms underlying photosynthetic modulation and reactive oxygen species (ROS) homeostasis, physiological and diverse quantitative proteomics analyses of alkaligrass (Puccinellia tenuiflora) under Na2CO3 stress were conducted. In addition, Western blot, real-time PCR, and transgenic techniques were applied to validate the proteomic results and test the functions of the Na2CO3-responsive proteins. A total of 104 and 102 Na2CO3-responsive proteins were identified in leaves and chloroplasts, respectively. In addition, 84 Na2CO3-responsive phosphoproteins were identified, including 56 new phosphorylation sites in 56 phosphoproteins from chloroplasts, which are crucial for the regulation of photosynthesis, ion transport, signal transduction, and energy homeostasis. A full-length PtFBA encoding an alkaligrass chloroplastic fructose-bisphosphate aldolase (FBA) was overexpressed in wild-type cells of cyanobacterium Synechocystis sp. Strain PCC 6803, leading to enhanced Na2CO3 tolerance. All these results indicate that thermal dissipation, state transition, cyclic electron transport, photorespiration, repair of photosystem (PS) II, PSI activity, and ROS homeostasis were altered in response to Na2CO3 stress, which help to improve our understanding of the Na2CO3-responsive mechanisms in halophytes.
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22
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Jozefowicz AM, Döll S, Mock HP. Proteomic Approaches to Identify Proteins Responsive to Cold Stress. Methods Mol Biol 2020; 2156:161-170. [PMID: 32607981 DOI: 10.1007/978-1-0716-0660-5_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Changing environmental conditions greatly affect the accumulation of many proteins; therefore, the analysis of alterations in the proteome is essential to understand the plant response to abiotic stress. Proteomics provides a platform for the identification and quantification of plant proteins responsive to cold stress and taking part in cold acclimation. Here, we describe the preparation of proteins for LC-MS measurement to monitor the changes of protein patterns during cold treatment in Arabidopsis thaliana. In our protocol, proteins are precipitated using TCA/acetone, quantified with 2D Quant Kit and digested with trypsin using a filter-based method and analyzed using an LC-MS approach. The acquired results can be further applied for label-free protein quantification.
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Affiliation(s)
- Anna M Jozefowicz
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland, Germany
| | - Stefanie Döll
- Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale), Germany.,Molecular Interaction Ecology, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena- Leipzig, Leipzig, Germany
| | - Hans-Peter Mock
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland, Germany.
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23
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Chen T, Zhang H, Niu G, Zhang S, Hong Z. Multiple N-glycans cooperate in balancing misfolded BRI1 secretion and ER retention. PLANT MOLECULAR BIOLOGY 2020; 103:581-596. [PMID: 32409993 DOI: 10.1007/s11103-020-01012-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 05/04/2020] [Indexed: 06/11/2023]
Abstract
N-glycans play a protective or monitoring role according to the folding state of associated protein or the distance from structural defects. Asparagine-linked (Asn/N-) glycosylation is one of the most prevalent and complex protein modifications and the associated N-glycans play crucial roles on protein folding and secretion. The studies have shown that many glycoproteins hold multiple N-glycans, yet little is known about the redundancy of N-glycans on a protein. In this study, we used BRI1 to decipher the roles of N-glycans on protein secretion and function. We found that all 14 potential N-glycosylation sites on BRI1 were occupied with oligosaccharides. The elimination of single N-glycan had no obvious effect on BRI1 secretion or function except N154-glycan, which resulted in the retention of BRI1 in the endoplasmic reticulum (ER), similar to the loss of multiple highly conserved N-glycans. To misfolded bri1, the absence of N-glycans next to local structural defects enhanced the ER retention and the artificial addition of N-glycan could help the misfolded bri1-GFPs exiting from the ER, indicating that the N-glycans might serve as steric hindrance to protect the structure defects from ER recognition. We also found that the retention of misfolded bri1-9 by lectins and chaperones in the ER relied on the presence of multiple N-glycans distal to the local defects. Our findings revealed that the N-glycans might play a protective or monitoring role according to the folding state of associated protein or the distance from structural defects.
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Affiliation(s)
- Tianshu Chen
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210046, Jiangsu, China
| | - Huchen Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210046, Jiangsu, China
| | - Guanting Niu
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210046, Jiangsu, China
| | - Shuo Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210046, Jiangsu, China
| | - Zhi Hong
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210046, Jiangsu, China.
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24
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Song W, Tang F, Cai W, Zhang Q, Zhou F, Ning M, Tian H, Shan C. iTRAQ-based quantitative proteomics analysis of cantaloupe (Cucumis melo var. saccharinus) after cold storage. BMC Genomics 2020; 21:390. [PMID: 32493266 PMCID: PMC7268308 DOI: 10.1186/s12864-020-06797-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 05/26/2020] [Indexed: 12/25/2022] Open
Abstract
Background Cantaloupe is susceptible to cold stress when it is stored at low temperatures, resulting in the loss of edible and commercial quality. To ascertain the molecular mechanisms of low temperatures resistance in cantaloupe, a cold-sensitive cultivar, Golden Empress-308 (GE) and a cold-tolerant cultivar, Jia Shi-310 (JS), were selected in parallel for iTRAQ quantitative proteomic analysis. Results The two kinds of commercial cultivars were exposed to a temperature of 0.5 °C for 0, 12 and 24 days. We found that the cold-sensitive cultivar (GE) suffered more severe damage as the length of the cold treatment increased. Proteomic analysis of both cultivars indicated that the number of differentially expressed proteins (DEPs) changed remarkably during the chilly treatment. JS expressed cold-responsive proteins more rapidly and mobilized more groups of proteins than GE. Furthermore, metabolic analysis revealed that more amino acids were up-regulated in JS during the early phases of low temperatures stress. The DEPs we found were mainly related to carbohydrate and energy metabolism, structural proteins, reactive oxygen species scavenging, amino acids metabolism and signal transduction. The consequences of phenotype assays, metabolic analysis and q-PCR validation confirm the findings of the iTRAQ analysis. Conclusion We found that the prompt response and mobilization of proteins in JS allowed it to maintain a higher level of cold tolerance than GE, and that the slower cold responses in GE may be a vital reason for the severe chilling injury commonly found in this cultivar. The candidate proteins we identified will form the basis of future studies and may improve our understanding of the mechanisms of cold tolerance in cantaloupe.
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Affiliation(s)
- Wen Song
- College of Food, Shihezi University, Xinjiang, 832000, China
| | - Fengxian Tang
- College of Food, Shihezi University, Xinjiang, 832000, China
| | - Wenchao Cai
- College of Food, Shihezi University, Xinjiang, 832000, China
| | - Qin Zhang
- College of Food, Shihezi University, Xinjiang, 832000, China
| | - Fake Zhou
- College of Food, Shihezi University, Xinjiang, 832000, China
| | - Ming Ning
- College of Food, Shihezi University, Xinjiang, 832000, China
| | - Huan Tian
- College of Food, Shihezi University, Xinjiang, 832000, China
| | - Chunhui Shan
- College of Food, Shihezi University, Xinjiang, 832000, China.
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25
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Ramirez-Rodriguez EA, Heazlewood JL. Enrichment of N-Linked Glycopeptides and Their Identification by Complementary Fragmentation Techniques. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2020; 2139:225-240. [PMID: 32462590 DOI: 10.1007/978-1-0716-0528-8_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
N-linked glycans are a ubiquitous posttranslational modification and are essential for correct protein folding in the endoplasmic reticulum of plants. However, this likely represents a narrow functional role for the diverse array of glycan structures currently associated with N-glycoproteins in plants. The identification of N-linked glycosylation sites and their structural characterization by mass spectrometry remains challenging due to their size, relative abundance, structural heterogeneity, and polarity. Current proteomic workflows are not optimized for the enrichment, identification and characterization of N-glycopeptides. Here we describe a detailed analytical procedure employing hydrophilic interaction chromatography enrichment, high-resolution tandem mass spectrometry employing complementary fragmentation techniques (higher-energy collisional dissociation and electron-transfer dissociation) and a data analytics workflow to produce an unbiased high confidence N-glycopeptide profile from plant samples.
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Affiliation(s)
| | - Joshua L Heazlewood
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia.
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26
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Hashimoto T, Mustafa G, Nishiuchi T, Komatsu S. Comparative Analysis of the Effect of Inorganic and Organic Chemicals with Silver Nanoparticles on Soybean under Flooding Stress. Int J Mol Sci 2020; 21:E1300. [PMID: 32075105 PMCID: PMC7072913 DOI: 10.3390/ijms21041300] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/03/2020] [Accepted: 02/11/2020] [Indexed: 12/13/2022] Open
Abstract
Extensive utilization of silver nanoparticles (NPs) in agricultural products results in their interaction with other chemicals in the environment. To study the combined effects of silver NPs with nicotinic acid and potassium nitrate (KNO3), a gel-free/label-free proteomic technique was used. Root length/weight and hypocotyl length/weight of soybean were enhanced by silver NPs mixed with nicotinic acid and KNO3. Out of a total 6340 identified proteins, 351 proteins were significantly changed, out of which 247 and 104 proteins increased and decreased, respectively. Differentially changed proteins were predominantly associated with protein degradation and synthesis according to the functional categorization. Protein-degradation-related proteins mainly consisted of the proteasome degradation pathway. The cell death was significantly higher in the root tips of soybean under the combined treatment compared to flooding stress. Accumulation of calnexin/calreticulin and glycoproteins was significantly increased under flooding with silver NPs, nicotinic acid, and KNO3. Growth of soybean seedlings with silver NPs, nicotinic acid, and KNO3 was improved under flooding stress. These results suggest that the combined mixture of silver NPs, nicotinic acid, and KNO3 causes positive effects on soybean seedling by regulating the protein quality control for the mis-folded proteins in the endoplasmic reticulum. Therefore, it might improve the growth of soybean under flooding stress.
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Affiliation(s)
- Takuya Hashimoto
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan; (T.H.); (G.M.)
| | - Ghazala Mustafa
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan; (T.H.); (G.M.)
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Takumi Nishiuchi
- Institute for Gene Research, Kanazawa University, Kanazawa 920-8640, Japan;
| | - Setsuko Komatsu
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan; (T.H.); (G.M.)
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27
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Duran Garzon C, Lequart M, Rautengarten C, Bassard S, Sellier-Richard H, Baldet P, Heazlewood JL, Gibon Y, Domon JM, Giauffret C, Rayon C. Regulation of carbon metabolism in two maize sister lines contrasted for chilling tolerance. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:356-369. [PMID: 31557299 DOI: 10.1093/jxb/erz421] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 09/16/2019] [Indexed: 05/16/2023]
Abstract
Maize can grow in cool temperate climates but is often exposed to spring chilling temperatures that can affect early seedling growth. Here, we used two sister double-haploid lines displaying a contrasted tolerance to chilling to identify major determinants of long-term chilling tolerance. The chilling-sensitive (CS) and the chilling-tolerant (CT) lines were grown at 14 °C day/10 °C night for 60 d. CS plants displayed a strong reduction in growth and aerial biomass compared with CT plants. Photosynthetic efficiency was affected with an increase in energy dissipation in both lines. Chilling tolerance in CT plants was associated with higher chlorophyll content, glucose-6-phosphate dehydrogenase activity, and higher sucrose to starch ratio. Few changes in cell wall composition were observed in both genotypes. There was no obvious correlation between nucleotide sugar content and cell wall polysaccharide composition. Our findings suggest that the central starch-sucrose metabolism is one major determinant of the response to low temperature, and its modulation accounts for the ability of CT plants to cope with low temperature. This modulation seemed to be linked to a strong alteration in the biosynthesis of nucleotide sugars that, at a high level, could reflect the remobilization of carbon in response to chilling.
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Affiliation(s)
- Catalina Duran Garzon
- EA3900-BIOPI, Biologie des Plantes et Innovation, Université de Picardie Jules Verne, Amiens, France
| | - Michelle Lequart
- EA3900-BIOPI, Biologie des Plantes et Innovation, Université de Picardie Jules Verne, Amiens, France
| | | | - Solène Bassard
- EA3900-BIOPI, Biologie des Plantes et Innovation, Université de Picardie Jules Verne, Amiens, France
| | - Hélène Sellier-Richard
- Unité Expérimentale Grandes Cultures Innovation et Environnement, INRA-Estrées-Mons, Péronne, France
| | - Pierre Baldet
- UMR1332, Biologie du Fruit et Pathologie, Bordeaux Métabolome, INRA, Université de Bordeaux, Villenave d'Ornon, France
| | - Joshua L Heazlewood
- School of BioSciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Yves Gibon
- UMR1332, Biologie du Fruit et Pathologie, Bordeaux Métabolome, INRA, Université de Bordeaux, Villenave d'Ornon, France
| | - Jean-Marc Domon
- EA3900-BIOPI, Biologie des Plantes et Innovation, Université de Picardie Jules Verne, Amiens, France
| | | | - Catherine Rayon
- EA3900-BIOPI, Biologie des Plantes et Innovation, Université de Picardie Jules Verne, Amiens, France
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28
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Donczo B, Kiraly G, Guttman A. Effect of the elapsed time between sampling and formalin fixation on the
N
‐glycosylation profile of mouse tissue specimens. Electrophoresis 2019; 40:3057-3061. [DOI: 10.1002/elps.201900109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 07/22/2019] [Accepted: 09/13/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Boglarka Donczo
- Horváth Csaba Laboratory of Bioseparation Sciences, Research Center for Molecular Medicine, Faculty of MedicineUniversity of Debrecen Debrecen Hungary
| | - Gabor Kiraly
- Department of Biotechnology and MicrobiologyUniversity of Debrecen Hungary
| | - Andras Guttman
- Horváth Csaba Laboratory of Bioseparation Sciences, Research Center for Molecular Medicine, Faculty of MedicineUniversity of Debrecen Debrecen Hungary
- MTA‐PE Translational Glycomics Research Group, Research Institute for Biomolecular and Chemical EngineeringUniversity of Pannonia Veszprem Hungary
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Tjondro HC, Loke I, Chatterjee S, Thaysen-Andersen M. Human protein paucimannosylation: cues from the eukaryotic kingdoms. Biol Rev Camb Philos Soc 2019; 94:2068-2100. [PMID: 31410980 DOI: 10.1111/brv.12548] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 07/10/2019] [Accepted: 07/17/2019] [Indexed: 12/11/2022]
Abstract
Paucimannosidic proteins (PMPs) are bioactive glycoproteins carrying truncated α- or β-mannosyl-terminating asparagine (N)-linked glycans widely reported across the eukaryotic domain. Our understanding of human PMPs remains limited, despite findings documenting their existence and association with human disease glycobiology. This review comprehensively surveys the structures, biosynthetic routes and functions of PMPs across the eukaryotic kingdoms with the aim of synthesising an improved understanding on the role of protein paucimannosylation in human health and diseases. Convincing biochemical, glycoanalytical and biological data detail a vast structural heterogeneity and fascinating tissue- and subcellular-specific expression of PMPs within invertebrates and plants, often comprising multi-α1,3/6-fucosylation and β1,2-xylosylation amongst other glycan modifications and non-glycan substitutions e.g. O-methylation. Vertebrates and protists express less-heterogeneous PMPs typically only comprising variable core fucosylation of bi- and trimannosylchitobiose core glycans. In particular, the Manα1,6Manβ1,4GlcNAc(α1,6Fuc)β1,4GlcNAcβAsn glycan (M2F) decorates various human neutrophil proteins reportedly displaying bioactivity and structural integrity demonstrating that they are not degradation products. Less-truncated paucimannosidic glycans (e.g. M3F) are characteristic glycosylation features of proteins expressed by human cancer and stem cells. Concertedly, these observations suggest the involvement of human PMPs in processes related to innate immunity, tumorigenesis and cellular differentiation. The absence of human PMPs in diverse bodily fluids studied under many (patho)physiological conditions suggests extravascular residence and points to localised functions of PMPs in peripheral tissues. Absence of PMPs in Fungi indicates that paucimannosylation is common, but not universally conserved, in eukaryotes. Relative to human PMPs, the expression of PMPs in plants, invertebrates and protists is more tissue-wide and constitutive yet, similar to their human counterparts, PMP expression remains regulated by the physiology of the producing organism and PMPs evidently serve essential functions in development, cell-cell communication and host-pathogen/symbiont interactions. In most PMP-producing organisms, including humans, the N-acetyl-β-hexosaminidase isoenzymes and linkage-specific α-mannosidases are glycoside hydrolases critical for generating PMPs via N-acetylglucosaminyltransferase I (GnT-I)-dependent and GnT-I-independent truncation pathways. However, the identity and structure of many species-specific PMPs in eukaryotes, their biosynthetic routes, strong tissue- and development-specific expression, and diverse functions are still elusive. Deep exploration of these PMP features involving, for example, the characterisation of endogenous PMP-recognising lectins across a variety of healthy and N-acetyl-β-hexosaminidase-deficient human tissue types and identification of microbial adhesins reactive to human PMPs, are amongst the many tasks required for enhanced insight into the glycobiology of human PMPs. In conclusion, the literature supports the notion that PMPs are significant, yet still heavily under-studied biomolecules in human glycobiology that serve essential functions and create structural heterogeneity not dissimilar to other human N-glycoprotein types. Human PMPs should therefore be recognised as bioactive glycoproteins that are distinctly different from the canonical N-glycoprotein classes and which warrant a more dedicated focus in glycobiological research.
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Affiliation(s)
- Harry C Tjondro
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, 2109, Australia
| | - Ian Loke
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, 2109, Australia.,Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Sayantani Chatterjee
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, 2109, Australia
| | - Morten Thaysen-Andersen
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, 2109, Australia
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Li Y, Wang X, Ban Q, Zhu X, Jiang C, Wei C, Bennetzen JL. Comparative transcriptomic analysis reveals gene expression associated with cold adaptation in the tea plant Camellia sinensis. BMC Genomics 2019; 20:624. [PMID: 31366321 PMCID: PMC6670155 DOI: 10.1186/s12864-019-5988-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 07/22/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Low temperature restricts the planting range of all crops, but cold acclimation induces adaption to cold stress in many plants. Camellia sinensis, a perennial evergreen tree that is the source of tea, is mainly grown in warm areas. Camellia sinensis var. sinensis (CSS) has greater cold tolerance than Camellia sinensis var. assamica (CSA). To gain deep insight into the molecular mechanisms underlying cold adaptation, we investigated the physiological responses and transcriptome profiles by RNA-Seq in two tea varieties, cold resistant SCZ (classified as CSS) and cold susceptible YH9 (classified as CSA), during cold acclimation. RESULTS Under freezing stress, lower relative electrical conductivity and higher chlorophyll fluorescence (Fv/Fm) values were detected in SCZ than in YH9 when subjected to freezing acclimation. During cold treatment, 6072 and 7749 DEGs were observed for SCZ and YH9, respectively. A total of 978 DEGs were common for both SCZ and YH9 during the entire cold acclimation process. DEGs were enriched in pathways of photosynthesis, hormone signal transduction, and transcriptional regulation of plant-pathogen interactions. Further analyses indicated that decreased expression of Lhca2 and higher expression of SnRK2.8 are correlated with cold tolerance in SCZ. CONCLUSIONS Compared with CSA, CSS was significantly more resistant to freezing after cold acclimation, and this increased resistance was associated with an earlier expression of cold-induced genes. Because the greater transcriptional differentiation during cold acclimation in SCZ may contribute to its greater cold tolerance, our studies identify specific genes involved in photoinhibition, ABA signal conduction, and plant immunity that should be studied for understanding the processes involved in cold tolerance. Marker-assisted breeding focused on the allelic variation at these loci provides an avenue for the possible generation of CSA cultivars that have CSS-level cold tolerance.
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Affiliation(s)
- Yeyun Li
- State Key Laboratory of Tea Plant Biology and Utilization/International Joint Laboratory on Tea Chemistry and Health Effects, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036 Anhui People’s Republic of China
| | - Xuewen Wang
- State Key Laboratory of Tea Plant Biology and Utilization/International Joint Laboratory on Tea Chemistry and Health Effects, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036 Anhui People’s Republic of China
- Department of Genetics, University of Georgia, Athens, USA
| | - Qiuyan Ban
- State Key Laboratory of Tea Plant Biology and Utilization/International Joint Laboratory on Tea Chemistry and Health Effects, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036 Anhui People’s Republic of China
| | - Xiangxiang Zhu
- State Key Laboratory of Tea Plant Biology and Utilization/International Joint Laboratory on Tea Chemistry and Health Effects, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036 Anhui People’s Republic of China
| | - Changjun Jiang
- State Key Laboratory of Tea Plant Biology and Utilization/International Joint Laboratory on Tea Chemistry and Health Effects, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036 Anhui People’s Republic of China
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization/International Joint Laboratory on Tea Chemistry and Health Effects, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036 Anhui People’s Republic of China
| | - Jeffrey L. Bennetzen
- State Key Laboratory of Tea Plant Biology and Utilization/International Joint Laboratory on Tea Chemistry and Health Effects, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036 Anhui People’s Republic of China
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31
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Millar AH, Heazlewood JL, Giglione C, Holdsworth MJ, Bachmair A, Schulze WX. The Scope, Functions, and Dynamics of Posttranslational Protein Modifications. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:119-151. [PMID: 30786234 DOI: 10.1146/annurev-arplant-050718-100211] [Citation(s) in RCA: 140] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Assessing posttranslational modification (PTM) patterns within protein molecules and reading their functional implications present grand challenges for plant biology. We combine four perspectives on PTMs and their roles by considering five classes of PTMs as examples of the broader context of PTMs. These include modifications of the N terminus, glycosylation, phosphorylation, oxidation, and N-terminal and protein modifiers linked to protein degradation. We consider the spatial distribution of PTMs, the subcellular distribution of modifying enzymes, and their targets throughout the cell, and we outline the complexity of compartmentation in understanding of PTM function. We also consider PTMs temporally in the context of the lifetime of a protein molecule and the need for different PTMs for assembly, localization, function, and degradation. Finally, we consider the combined action of PTMs on the same proteins, their interactions, and the challenge ahead of integrating PTMs into an understanding of protein function in plants.
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Affiliation(s)
- A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia;
| | - Joshua L Heazlewood
- School of BioSciences, University of Melbourne, Melbourne, Victoria 3010, Australia;
| | - Carmela Giglione
- Institute for Integrative Biology of the Cell, CNRS UMR9198, F-91198 Gif-sur-Yvette Cedex, France;
| | - Michael J Holdsworth
- School of Biosciences, University of Nottingham, Loughborough LE12 5RD, United Kingdom;
| | - Andreas Bachmair
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria;
| | - Waltraud X Schulze
- Systembiologie der Pflanze, Universität Hohenheim, 70599 Stuttgart, Germany;
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32
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Yu J, Zhang Y, Liu J, Wang L, Liu P, Yin Z, Guo S, Ma J, Lu Z, Wang T, She Y, Miao Y, Ma L, Chen S, Li Y, Dai S. Proteomic discovery of H 2O 2 response in roots and functional characterization of PutGLP gene from alkaligrass. PLANTA 2018; 248:1079-1099. [PMID: 30039231 DOI: 10.1007/s00425-018-2940-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 06/13/2018] [Indexed: 06/08/2023]
Abstract
Hydrogen peroxide-responsive pathways in roots of alkaligrass analyzed by proteomic studies and PutGLP enhance the plant tolerance to saline-, alkali- and cadmium-induced oxidative stresses. Oxidative stress adaptation is critical for plants in response to various stress environments. The halophyte alkaligrass (Puccinellia tenuiflora) is an outstanding pasture with strong tolerance to salt and alkali stresses. In this study, iTRAQ- and 2DE-based proteomics approaches, as well as qRT-PCR and molecular genetics, were employed to investigate H2O2-responsive mechanisms in alkaligrass roots. The evaluation of membrane integrity and reactive oxygen species (ROS)-scavenging systems, as well as abundance patterns of H2O2-responsive proteins/genes indicated that Ca2+-mediated kinase signaling pathways, ROS homeostasis, osmotic modulation, and transcriptional regulation were pivotal for oxidative adaptation in alkaligrass roots. Overexpressing a P. tenuiflora germin-like protein (PutGLP) gene in Arabidopsis seedlings revealed that the apoplastic PutGLP with activities of oxalate oxidase and superoxide dismutase was predominantly expressed in roots and played important roles in ROS scavenging in response to salinity-, alkali-, and CdCl2-induced oxidative stresses. The results provide insights into the fine-tuned redox-responsive networks in halophyte roots.
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Affiliation(s)
- Juanjuan Yu
- Alkali Soil Natural Environmental Science Center, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin, 150040, China
- Development Centre of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Yongxue Zhang
- Alkali Soil Natural Environmental Science Center, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin, 150040, China
- Development Centre of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Junming Liu
- Alkali Soil Natural Environmental Science Center, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin, 150040, China
| | - Lin Wang
- Alkali Soil Natural Environmental Science Center, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin, 150040, China
| | - Panpan Liu
- Alkali Soil Natural Environmental Science Center, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin, 150040, China
| | - Zepeng Yin
- Alkali Soil Natural Environmental Science Center, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin, 150040, China
| | - Siyi Guo
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng, 455000, China
| | - Jun Ma
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Zhuang Lu
- Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Tai Wang
- Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yimin She
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Yuchen Miao
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng, 455000, China
| | - Ling Ma
- Alkali Soil Natural Environmental Science Center, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin, 150040, China
| | - Sixue Chen
- Department of Biology, Genetics Institute, Plant Molecular and Cellular Program, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, 32610, USA
| | - Ying Li
- Alkali Soil Natural Environmental Science Center, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin, 150040, China.
| | - Shaojun Dai
- Alkali Soil Natural Environmental Science Center, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin, 150040, China.
- Development Centre of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China.
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McKown AD, Klápště J, Guy RD, El-Kassaby YA, Mansfield SD. Ecological genomics of variation in bud-break phenology and mechanisms of response to climate warming in Populus trichocarpa. THE NEW PHYTOLOGIST 2018; 220:300-316. [PMID: 29963703 DOI: 10.1111/nph.15273] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 05/14/2018] [Indexed: 05/10/2023]
Abstract
Spring bud-break phenology is a critical adaptive feature common to temperate perennial woody plants. Understanding the molecular underpinnings of variation in bud-break is important for elucidating adaptive evolution and predicting outcomes relating to climate change. Field and controlled growth chamber tests were used to assess population-wide patterns in bud-break from wild-sourced black cottonwood (Populus trichocarpa) genotypes. We conducted a genome-wide association study (GWAS) with single nucleotide polymorphisms (SNPs) derived from whole genome sequencing to test for loci underlying variation in bud-break. Bud-break had a quadratic relationship with latitude, where southern- and northern-most provenances generally broke bud earlier than those from central parts of the species' range. Reduced winter chilling increased population-wide variation in bud-break, whereas greater chilling decreased variation. GWAS uncovered 16 loci associated with bud-break. Phenotypic changes connected with allelic variation were replicated in an independent set of P. trichocarpa trees. Despite phenotypic similarities, genetic profiles between southern- and northern-most genotypes were dissimilar based on our GWAS-identified SNPs. We propose that the GWAS-identified loci underpin the geographical pattern in P. trichocarpa and that variation in bud-break reflects different selection for winter chilling and heat sum accumulation, both of which can be affected by climate warming.
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Affiliation(s)
- Athena D McKown
- Department of Forest and Conservation Sciences, Faculty of Forestry, Forest Sciences Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Jaroslav Klápště
- Department of Dendrology and Forest Tree Breeding, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, 165 21, Czech Republic
- Scion (New Zealand Forest Research Institute Ltd), Whakarewarewa, Rotorua, 3046, New Zealand
| | - Robert D Guy
- Department of Forest and Conservation Sciences, Faculty of Forestry, Forest Sciences Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, Forest Sciences Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Shawn D Mansfield
- Department of Wood Science, Faculty of Forestry, Forest Sciences Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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Jeong IS, Lee S, Bonkhofer F, Tolley J, Fukudome A, Nagashima Y, May K, Rips S, Lee SY, Gallois P, Russell WK, Jung HS, von Schaewen A, Koiwa H. Purification and characterization of Arabidopsis thaliana oligosaccharyltransferase complexes from the native host: a protein super-expression system for structural studies. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 94:131-145. [PMID: 29385647 DOI: 10.1111/tpj.13847] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 12/31/2017] [Accepted: 01/15/2018] [Indexed: 05/18/2023]
Abstract
The oligosaccharyltransferase (OT) complex catalyzes N-glycosylation of nascent secretory polypeptides in the lumen of the endoplasmic reticulum. Despite their importance, little is known about the structure and function of plant OT complexes, mainly due to lack of efficient recombinant protein production systems suitable for studies on large plant protein complexes. Here, we purified Arabidopsis OT complexes using the tandem affinity-tagged OT subunit STAUROSPORINE AND TEMPERATURE SENSITIVE3a (STT3a) expressed by an Arabidopsis protein super-expression platform. Mass-spectrometry analysis of the purified complexes identified three essential OT subunits, OLIGOSACCHARYLTRANSFERASE1 (OST1), HAPLESS6 (HAP6), DEFECTIVE GLYCOSYLATION1 (DGL1), and a number of ribosomal subunits. Transmission-electron microscopy showed that STT3a becomes incorporated into OT-ribosome super-complexes formed in vivo, demonstrating that this expression/purification platform is suitable for analysis of large protein complexes. Pairwise in planta interaction analyses of individual OT subunits demonstrated that all subunits identified in animal OT complexes are conserved in Arabidopsis and physically interact with STT3a. Genetic analysis of newly established OT subunit mutants for OST1 and DEFENDER AGAINST APOTOTIC DEATH (DAD) family genes revealed that OST1 and DAD1/2 subunits are essential for the plant life cycle. However, mutations in these individual isoforms produced much milder growth/underglycosylation phenotypes than previously reported for mutations in DGL1, OST3/6 and STT3a.
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Affiliation(s)
- In Sil Jeong
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA
- Department of Biomedical Engineering College of Creative Convergence Engineering, Catholic Kwandong University, Gangneung, Gangwon-do, 25601, South Korea
| | - Sangmin Lee
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, Chuncheon, Gangwon-do, 24341, South Korea
| | - Florian Bonkhofer
- Molekulare Physiologie der Pflanzen, Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Schlossplatz 7, D-48149, Münster, Germany
| | - Jordan Tolley
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Akihito Fukudome
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Yukihiro Nagashima
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Kimberly May
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Stephan Rips
- Molekulare Physiologie der Pflanzen, Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Schlossplatz 7, D-48149, Münster, Germany
| | - Sang Y Lee
- Division of Applied Life Science and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, South Korea
| | - Patrick Gallois
- Faculty of Biology, Medicine and Health, University of Manchester, Oxford Rd, Manchester, M13 9PT, UK
| | - William K Russell
- Department of Biochemistry and Molecular Biology, University of Texas-Medical Branch, Oxford Rd, Galveston, TX, 77555, USA
| | - Hyun Suk Jung
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, Chuncheon, Gangwon-do, 24341, South Korea
| | - Antje von Schaewen
- Molekulare Physiologie der Pflanzen, Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Schlossplatz 7, D-48149, Münster, Germany
| | - Hisashi Koiwa
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA
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Zhao Q, Chen W, Bian J, Xie H, Li Y, Xu C, Ma J, Guo S, Chen J, Cai X, Wang X, Wang Q, She Y, Chen S, Zhou Z, Dai S. Proteomics and Phosphoproteomics of Heat Stress-Responsive Mechanisms in Spinach. FRONTIERS IN PLANT SCIENCE 2018; 9:800. [PMID: 29997633 PMCID: PMC6029058 DOI: 10.3389/fpls.2018.00800] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 05/24/2018] [Indexed: 05/02/2023]
Abstract
Elevated temperatures limit plant growth and reproduction and pose a growing threat to agriculture. Plant heat stress response is highly conserved and fine-tuned in multiple pathways. Spinach (Spinacia oleracea L.) is a cold tolerant but heat sensitive green leafy vegetable. In this study, heat adaptation mechanisms in a spinach sibling inbred heat-tolerant line Sp75 were investigated using physiological, proteomic, and phosphoproteomic approaches. The abundance patterns of 911 heat stress-responsive proteins, and phosphorylation level changes of 45 phosphoproteins indicated heat-induced calcium-mediated signaling, ROS homeostasis, endomembrane trafficking, and cross-membrane transport pathways, as well as more than 15 transcription regulation factors. Although photosynthesis was inhibited, diverse primary and secondary metabolic pathways were employed for defense against heat stress, such as glycolysis, pentose phosphate pathway, amino acid metabolism, fatty acid metabolism, nucleotide metabolism, vitamin metabolism, and isoprenoid biosynthesis. These data constitute a heat stress-responsive metabolic atlas in spinach, which will springboard further investigations into the sophisticated molecular mechanisms of plant heat adaptation and inform spinach molecular breeding initiatives.
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Affiliation(s)
- Qi Zhao
- Development Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
- Key Laboratory of Forest Plant Ecology, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, China
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Wenxin Chen
- Development Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
| | - Jiayi Bian
- Development Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
| | - Hao Xie
- Key Laboratory of Forest Plant Ecology, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, China
| | - Ying Li
- Key Laboratory of Forest Plant Ecology, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, China
| | - Chenxi Xu
- Development Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
| | - Jun Ma
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, China
| | - Siyi Guo
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng, China
| | - Jiaying Chen
- Development Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
| | - Xiaofeng Cai
- Development Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
| | - Xiaoli Wang
- Development Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
| | - Quanhua Wang
- Development Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
| | - Yimin She
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, China
| | - Sixue Chen
- Development Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
- Plant Molecular and Cellular Biology Program, Department of Biology, Genetics Institute, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, United States
| | - Zhiqiang Zhou
- Key Laboratory of Forest Plant Ecology, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, China
- *Correspondence: Shaojun Dai, Zhiqiang Zhou,
| | - Shaojun Dai
- Development Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
- Key Laboratory of Forest Plant Ecology, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, China
- *Correspondence: Shaojun Dai, Zhiqiang Zhou,
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36
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Zeng W, Ford KL, Bacic A, Heazlewood JL. N-linked Glycan Micro-heterogeneity in Glycoproteins of Arabidopsis. Mol Cell Proteomics 2017; 17:413-421. [PMID: 29237727 DOI: 10.1074/mcp.ra117.000165] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 11/21/2017] [Indexed: 01/01/2023] Open
Abstract
N-glycosylation is one of the most common protein post-translational modifications in eukaryotes and has a relatively conserved core structure between fungi, animals and plants. In plants, the biosynthesis of N-glycans has been extensively studied with all the major biosynthetic enzymes characterized. However, few studies have applied advanced mass spectrometry to profile intact plant N-glycopeptides. In this study, we use hydrophilic enrichment, high-resolution tandem mass spectrometry with complementary and triggered fragmentation to profile Arabidopsis N-glycopeptides from microsomal membranes of aerial tissues. A total of 492 N-glycosites were identified from 324 Arabidopsis proteins with extensive N-glycan structural heterogeneity revealed through 1110 N-glycopeptides. To demonstrate the precision of the approach, we also profiled N-glycopeptides from the mutant (xylt) of β-1,2-xylosyltransferase, an enzyme in the N-glycan biosynthetic pathway. This analysis represents the most comprehensive and unbiased collection of Arabidopsis N-glycopeptides revealing an unsurpassed level of detail on the micro-heterogeneity present in N-glycoproteins of Arabidopsis. Data are available via ProteomeXchange with identifier PXD006270.
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Affiliation(s)
- Wei Zeng
- From the ‡ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia.,§Sino-Australia Plant Cell Wall Research Centre, State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, China
| | - Kristina L Ford
- From the ‡ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Antony Bacic
- From the ‡ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Joshua L Heazlewood
- From the ‡ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia; .,¶Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94702
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37
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Bu TT, Shen J, Chao Q, Shen Z, Yan Z, Zheng HY, Wang BC. Dynamic N-glycoproteome analysis of maize seedling leaves during de-etiolation using Concanavalin A lectin affinity chromatography and a nano-LC-MS/MS-based iTRAQ approach. PLANT CELL REPORTS 2017; 36:1943-1958. [PMID: 28942497 DOI: 10.1007/s00299-017-2209-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 09/12/2017] [Indexed: 06/07/2023]
Abstract
The identification of N -glycosylated proteins with information about changes in the level of N -glycosylation during de-etiolation provides a database that will aid further research on plant N -glycosylation and de-etiolation. N-glycosylation is one of the most prominent and abundant protein post-translational modifications in all eukaryotes and in plants it plays important roles in development, stress tolerance and immune responses. Because light-induced de-etiolation is one of the most dramatic developmental processes known in plants, seedlings undergoing de-etiolation are an excellent model for investigating dynamic proteomic profiles. Here, we present a comprehensive, quantitative N-glycoproteomic profile of maize seedlings undergoing 12 h of de-etiolation obtained using Concanavalin A (Con A) lectin affinity chromatography enrichment coupled with a nano-LC-MS/MS-based iTRAQ approach. In total, 1084 unique N-glycopeptides carrying 909 N-glycosylation sites and corresponding to 609 proteins were identified and quantified, including 186 N-glycosylation sites from 162 proteins that were significantly regulated over the course of the 12 h de-etiolation period. Based on hierarchical clustering analysis, the significantly regulated N-glycopeptides were divided into seven clusters that showed different N-glycosylation patterns during de-etiolation. We found no obvious difference in the enriched MapMan bincode categories for each cluster, and these clustered significantly regulated N-glycoproteins (SRNPs) are enriched in miscellaneous, protein, cell wall and signaling, indicating that although the N-glycosylation regulation patterns of these SRNPs might differ, they are involved in similar biological processes. Overall, this study represents the first large-scale quantitative N-glycoproteome of the model C4 plant, maize, which is one of the most important cereal and biofuel crops. Our results greatly expand the maize N-glycoproteomic database and also shed light on the potential roles of N-glycosylation modification during the greening of maize leaves.
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Affiliation(s)
- Tian-Tian Bu
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jie Shen
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Qing Chao
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Zhuo Shen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Zhen Yan
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hai-Yan Zheng
- Center for Advanced Biotechnology and Medicine, Robert-Wood Johnson Medical School-Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Bai-Chen Wang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
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38
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She YM, Farnsworth A, Li X, Cyr TD. Topological N-glycosylation and site-specific N-glycan sulfation of influenza proteins in the highly expressed H1N1 candidate vaccines. Sci Rep 2017; 7:10232. [PMID: 28860626 PMCID: PMC5579265 DOI: 10.1038/s41598-017-10714-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 08/14/2017] [Indexed: 01/20/2023] Open
Abstract
The outbreak of a pandemic influenza H1N1 in 2009 required the rapid generation of high-yielding vaccines against the A/California/7/2009 virus, which were achieved by either addition or deletion of a glycosylation site in the influenza proteins hemagglutinin and neuraminidase. In this report, we have systematically evaluated the glycan composition, structural distribution and topology of glycosylation for two high-yield candidate reassortant vaccines (NIBRG-121xp and NYMC-X181A) by combining various enzymatic digestions with high performance liquid chromatography and multiple-stage mass spectrometry. Proteomic data analyses of the full-length protein sequences determined 9 N-glycosylation sites of hemagglutinin, and defined 6 N-glycosylation sites and the glycan structures of low abundance neuraminidase, which were occupied by high-mannose, hybrid and complex-type N-glycans. A total of ~300 glycopeptides were analyzed and manually validated by tandem mass spectrometry. The specific N-glycan structure and topological location of these N-glycans are highly correlated to the spatial protein structure and the residential ligand binding. Interestingly, sulfation, fucosylation and bisecting N-acetylglucosamine of N-glycans were also reliably identified at the specific glycosylation sites of the two influenza proteins that may serve a crucial role in regulating the protein structure and increasing the protein abundance of the influenza virus reassortants.
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Affiliation(s)
- Yi-Min She
- Centre for Biologics Evaluation, Biologics and Genetic Therapies Directorate, Health Canada, Ottawa, Ontario, K1A 0K9, Canada
| | - Aaron Farnsworth
- Centre for Biologics Evaluation, Biologics and Genetic Therapies Directorate, Health Canada, Ottawa, Ontario, K1A 0K9, Canada
| | - Xuguang Li
- Centre for Biologics Evaluation, Biologics and Genetic Therapies Directorate, Health Canada, Ottawa, Ontario, K1A 0K9, Canada
| | - Terry D Cyr
- Centre for Biologics Evaluation, Biologics and Genetic Therapies Directorate, Health Canada, Ottawa, Ontario, K1A 0K9, Canada.
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Liu R, Fang L, Yang T, Zhang X, Hu J, Zhang H, Han W, Hua Z, Hao J, Zong X. Marker-trait association analysis of frost tolerance of 672 worldwide pea (Pisum sativum L.) collections. Sci Rep 2017; 7:5919. [PMID: 28724947 PMCID: PMC5517424 DOI: 10.1038/s41598-017-06222-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 06/08/2017] [Indexed: 12/18/2022] Open
Abstract
Frost stress is one of the major abiotic stresses causing seedling death and yield reduction in winter pea. To improve the frost tolerance of pea, field evaluation of frost tolerance was conducted on 672 diverse pea accessions at three locations in Northern China in three growing seasons from 2013 to 2016 and marker-trait association analysis of frost tolerance were performed with 267 informative SSR markers in this study. Sixteen accessions were identified as the most winter-hardy for their ability to survive in all nine field experiments with a mean survival rate of 0.57, ranging from 0.41 to 0.75. Population structure analysis revealed a structured population of two sub-populations plus some admixtures in the 672 accessions. Association analysis detected seven markers that repeatedly had associations with frost tolerance in at least two different environments with two different statistical models. One of the markers is the functional marker EST1109 on LG VI which was predicted to co-localize with a gene involved in the metabolism of glycoproteins in response to chilling stress and may provide a novel mechanism of frost tolerance in pea. These winter-hardy germplasms and frost tolerance associated markers will play a vital role in marker-assisted breeding for winter-hardy pea cultivar.
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Affiliation(s)
- Rong Liu
- Center for Crop Germplasm Resources/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Li Fang
- Center for Crop Germplasm Resources/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Tao Yang
- Center for Crop Germplasm Resources/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaoyan Zhang
- Qingdao Academy of Agricultural Sciences, Qingdao, 266100, Shandong, China
| | - Jinguo Hu
- USDA, Agricultural Research Service, Western Regional Plant Introduction Station, Washington State University, Pullman, WA, 99164, USA
| | - Hongyan Zhang
- Center for Crop Germplasm Resources/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wenliang Han
- Binzhou Academy of Agricultural Sciences, Binzhou, 256600, Shandong, China
| | - Zeke Hua
- Laiyang Agricultural Extension Center, Laiyang, 265200, Shandong, China
| | - Junjie Hao
- Qingdao Academy of Agricultural Sciences, Qingdao, 266100, Shandong, China
| | - Xuxiao Zong
- Center for Crop Germplasm Resources/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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40
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Qin G, Ma J, Chen X, Chu Z, She YM. Methylated-antibody affinity purification to improve proteomic identification of plant RNA polymerase Pol V complex and the interacting proteins. Sci Rep 2017; 7:42943. [PMID: 28224978 PMCID: PMC5320500 DOI: 10.1038/srep42943] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 01/17/2017] [Indexed: 11/09/2022] Open
Abstract
Affinity purification followed by enzymatic digestion and mass spectrometry has been widely utilized for the sensitive detection of interacting proteins and protein complexes in various organisms. In plants, the method is technically challenging due to the low abundance proteins, non-specific binding and difficulties of eluting interacting proteins from antibody beads. In this report, we describe a strategy to modify antibodies by reductive methylation of lysines without affecting their binding properties, followed by on-bead digestion of bound proteins with endoproteinase Lys-C. By this method, the antibody remains intact and does not interfere with the downstream identification of interacting proteins. Non-specific binding proteins were excluded using 14N/15N-metabolic labeling of wild-type and the transgenic plant counterparts. The method was employed to identify 12 co-immunoprecipitated protein subunits in Pol V complex and to discover 17 potential interacting protein targets in Arabidopsis. Our results demonstrated that the modification of antibodies by reductive dimethylation can improve the reliability and sensitivity of identifying low-abundance proteins through on-bead digestion and mass spectrometry. We also show that coupling this technique with chemical crosslinking enables in-depth characterization of endogenous protein complexes and the protein-protein interaction networks including mapping the surface topology and post-translational modifications of interacting proteins.
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Affiliation(s)
- Guochen Qin
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 3888 Chenhua Road, Shanghai 201602, P. R. China
| | - Jun Ma
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 3888 Chenhua Road, Shanghai 201602, P. R. China
| | - Xiaomei Chen
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 3888 Chenhua Road, Shanghai 201602, P. R. China
| | - Zhaoqing Chu
- Shanghai Chenshan Plant Science Research Center and Shanghai Chenshan Botanic Garden, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 3888 Chenhua Road, Shanghai 201602, P. R. China
| | - Yi-Min She
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 3888 Chenhua Road, Shanghai 201602, P. R. China.,Centre for Biologics Evaluation, Biologics and Genetic Therapies Directorate, Health Canada, Ottawa, Ontario, K1A 0K9, Canada
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41
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Sougrakpam Y, Deswal R. Hippophae rhamnoides N-glycoproteome analysis: a small step towards sea buckthorn proteome mining. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2016; 22:473-484. [PMID: 27924120 PMCID: PMC5120047 DOI: 10.1007/s12298-016-0390-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 10/13/2016] [Accepted: 10/14/2016] [Indexed: 05/09/2023]
Abstract
Hippophae rhamnoides is a hardy shrub capable of growing under extreme environmental conditions namely, high salt, drought and cold. Its ability to grow under extreme conditions and its wide application in pharmaceutical and nutraceutical industry calls for its in-depth analysis. N-glycoproteome mining by con A affinity chromatography from seedling was attempted. The glycoproteome was resolved on first and second dimension gel electrophoresis. A total of 48 spots were detected and 10 non-redundant proteins were identified by MALDI-TOF/TOF. Arabidopsis thaliana protein disulfide isomerase-like 1-4 (ATPDIL1-4) electron transporter, protein disulphide isomerase, calreticulin 1 (CRT1), glycosyl hydrolase family 38 (GH 38) protein, phantastica, maturase k, Arabidopsis trithorax related protein 6 (ATXR 6), cysteine protease inhibitor were identified out of which ATXR 6, phantastica and putative ATPDIL1-4 electron transporter are novel glycoproteins. Calcium binding protein CRT1 was validated for its calcium binding by stains all staining. GO analysis showed involvement of GH 38 and ATXR 6 in glycan and lysine degradation pathways. This is to our knowledge the first report of glycoproteome analysis for any Elaeagnaceae member.
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Affiliation(s)
- Yaiphabi Sougrakpam
- Molecular Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, New Delhi, India
| | - Renu Deswal
- Molecular Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, New Delhi, India
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