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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: 0.3] [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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2
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Absorption, translocation, and effects of Bt Cry1Ac peptides from transgenic cotton to the intercrops and soil functional bacteria. Sci Rep 2020; 10:17294. [PMID: 33057018 PMCID: PMC7557920 DOI: 10.1038/s41598-020-73375-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 08/11/2020] [Indexed: 11/08/2022] Open
Abstract
Insecticidal proteins encoded by the truncated genes from Bacillus thuringiensis (Bt) in transgenic crops are released into soil mainly through root exudate and crop residues. In the present study, Bt Cry1Ac protein was hydrolyzed by pronase that was secreted by the soil bacterium Streptomyces griseus. Six peptides were identified as the products of enzymatic hydrolysis by nano liquid chromatography tandem mass spectrometry (LC-MS/MS). One of the six peptides was labeled with radioactive isotope iodine-125 and then purified. The 125I-peptide solution was irrigated to the rhizosphere soil of watermelon seedlings (Citrullus lanatus L.) and wheat seedlings (Triticum aestivum L.), which the two crops usually intercrop with cotton in China. Detection of radioactivity in both plant tissues within one hour proved adsorption, uptake and translocation of the peptide into watermelon and wheat seedlings. Three of the identified peptides were sprayed onto the seedling leaves of watermelon, wheat and maize (Zea mays L.) in the field or the growth chamber. No significant effects on plant growth were observed. These peptides also did not affect growth of organic phosphate-dissolving, nitrogen-fixing, and potassium-dissolving bacteria in the culture. This study provides a new view of GMO risk assessment methodology.
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Yates ND, Dowsett MR, Bentley P, Dickenson-Fogg JA, Pratt A, Blanford CF, Fascione MA, Parkin A. Aldehyde-Mediated Protein-to-Surface Tethering via Controlled Diazonium Electrode Functionalization Using Protected Hydroxylamines. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:5654-5664. [PMID: 31721585 DOI: 10.1021/acs.langmuir.9b01254] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We report a diazonium electro-grafting method for the covalent modification of conducting surfaces with aldehyde-reactive hydroxylamine functionalities that facilitate the wiring of redox-active (bio)molecules to electrode surfaces. Hydroxylamine near-monolayer formation is achieved via a phthalimide-protection and hydrazine-deprotection strategy that overcomes the multilayer formation that typically complicates diazonium surface modification. This surface modification strategy is characterized using electrochemistry (electrochemical impedance spectroscopy and cyclic voltammetry), X-ray photoelectron spectroscopy, and quartz crystal microbalance with dissipation monitoring. Thus-modified glassy carbon, boron-doped diamond, and gold surfaces are all shown to ligate to small molecule aldehydes, yielding surface coverages of 150-170, 40, and 100 pmol cm-2, respectively. Bioconjugation is demonstrated via the coupling of a dilute (50 μM) solution of periodate-oxidized horseradish peroxidase enzyme to a functionalized gold surface under biocompatible conditions (H2O solvent, pH 4.5, 25 °C).
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Affiliation(s)
- Nicholas D Yates
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, United Kingdom
| | - Mark R Dowsett
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, United Kingdom
| | - Phillip Bentley
- Department of Physics, University of York, Heslington, York, YO10 5DD, United Kingdom
| | - Jack A Dickenson-Fogg
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, United Kingdom
| | - Andrew Pratt
- Department of Physics, University of York, Heslington, York, YO10 5DD, United Kingdom
| | - Christopher F Blanford
- School of Materials, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Martin A Fascione
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, United Kingdom
| | - Alison Parkin
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, United Kingdom
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N-glycans in Toxicodendron vernicifluum lacquer laccase. Carbohydr Res 2019; 474:57-66. [PMID: 30738956 DOI: 10.1016/j.carres.2018.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 12/02/2018] [Accepted: 12/03/2018] [Indexed: 11/24/2022]
Abstract
The N-glycans in Toxicodendron vernicifluum (Rhus vernicifera) lacquer laccase was elucidated for the first time through a combination of enzymatic digestion and subsequent mass spectrometry measurements using LC-MS/MS and MALDI-TOF MS. Lacquer laccase was isolated from a Japanese lacquer acetone powder from consecutive Sephadex C-50 and DEAE A-50 column chromatography. Trypsin and chymotrypsin digestions of the lacquer laccase resulted in a mixture of peptides and N-glycopeptides, which were treated with peptide-N-glycosidases and then Nα-(aminooxyacetyl)tryptophanylarginine methyl ester (aoWR) to give the aoWR-labelled N-glycans. The MS measurements revealed that GlcNAc4Hex5Fuc3Xyl1 N-glycan was attached at 12 N-glycosylation sites (Asn 5, 14, 180, 194, 233, 274, 284, 347, 364, 381, 398, and 519), GlcNAc3Hex4Fuc2Xyl1 N-glycan at two sites (Asn 124 and 454), and GlcNAc3Hex6Fuc1Xyl1 N-glycan at one site (Asn 28). A database search (Mascot search) of the peptides also suggested the presence of N-glycans at the 15 potential N-glycosylation sites (Asn-X-Ser/Thr).
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Fu B, Baker MR, Li QX. Effect of N-Linked Glycosylation of Recombinant Windmill Palm Tree Peroxidase on Its Activity and Stability. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:4414-4421. [PMID: 29648454 DOI: 10.1021/acs.jafc.8b00234] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Plant secretory peroxidases are valuable commercial enzymes. The windmill palm tree Trachycarpus fortunei produces one of the most stable and fastest peroxidases (WPTP) characterized to date; however, an economical source is needed. Pichia pastoris has been used as an expression system for WPTP and other peroxidases. However, yeast and plants synthesize different types of N-linked glycan structures and may differ the level of glycosylation at each site. Such non-native glycosylation can have unwanted consequences. Glycosylation site N256 was under-glycosylated in the wild-type (1.5%) compared to the native enzyme (55%); therefore, we mutated WPTP to promote glycosylation at this site (WPTP E254G). Glycosylation increased four-fold, as measured by liquid chromatography-tandem mass spectrometry. The mutation did not change the substrate specificity and optimal pH- and thermo-stability ranges, but it increased the catalytic activity 2-3-fold. In comparison with wild-type WPTP, WPTP E254G showed a shift of the most stable pH from 7 to 9, making it suitable for applications under alkaline conditions.
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Affiliation(s)
- Bo Fu
- Department of Molecular Biosciences and Bioengineering , University of Hawaii at Manoa , Honolulu , Hawaii 96822 , United States
| | - Margaret R Baker
- Department of Molecular Biosciences and Bioengineering , University of Hawaii at Manoa , Honolulu , Hawaii 96822 , United States
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering , University of Hawaii at Manoa , Honolulu , Hawaii 96822 , United States
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Baker MR, Ching T, Tabb DL, Li QX. Characterization of Plant Glycoproteins: Analysis of Plant Glycopeptide Mass Spectrometry Data with plantGlycoMS, a Package in the R Statistical Computing Environment. Methods Mol Biol 2018; 1789:205-220. [PMID: 29916082 DOI: 10.1007/978-1-4939-7856-4_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
plantGlycoMS is a set of tools, implemented in R, which is used to assess and validate glycopeptide spectrum matches (gPSMs). Validity of gPSMs is based on characteristic fragmentation patterns of glycopeptides (gPSMvalidator), adherence of the glycan moiety to the known N-glycan biosynthesis pathway in plants (pGlycoFilter), and elution of the glycopeptide within the observed retention time window of other glycopeptides sharing the same peptide backbone (rt.Restrict). plantGlycoMS also contains a tool for relative quantitation of glycoforms based on selected ion chromatograms of glycopeptide ion precursors in the mass spectrometry level 1 data (glycoRQ). This protocol walks the user through this workflow with example mass spectrometry data obtained for a plant glycoprotein.
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Affiliation(s)
- Margaret R Baker
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Travers Ching
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, USA
| | - David L Tabb
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, SA MRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical TB Research, Stellenbosch University, Cape Town, South Africa
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, USA.
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Wen B, Baker MR, Zhao H, Cui Z, Li QX. Expression and Characterization of Windmill Palm Tree (Trachycarpus fortunei) Peroxidase by Pichia pastoris. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:4676-4682. [PMID: 28523913 DOI: 10.1021/acs.jafc.7b00318] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Currently, commercial plant peroxidases are all native and are isolated from plants such as horseradish and soybean. No recombinant plant peroxidase products have been available on the commercial market. The gene encoding peroxidase was cloned from windmill palm tree leaves. The codon-optimized gene was transformed into Pichia pastoris for expression. The recombinant windmill palm tree peroxidase (rWPTP) expressed by P. pastoris showed high stability under pH 2-10 and temperatures up to 70 °C to many metallic salts and organic solvents. The substrate specificity of WPTP was determined, and among the substrates tested, 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) was most suitable for WPTP. The Michaelis constants with the substrates H2O2 and ABTS were 4.6 × 10-4 and 1.6 × 10-4 M, respectively. The rWPTP expressed in P. pastoris may be a suitable enzyme for the biosynthesis of polymers because of its high stability and activity under acidic conditions.
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Affiliation(s)
- Boting Wen
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa , Honolulu, Hawaii 96822, United States
- College of Agronomy and Biotechnology, China Agricultural University , Beijing, China
| | - Margaret R Baker
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa , Honolulu, Hawaii 96822, United States
| | - Hongwei Zhao
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa , Honolulu, Hawaii 96822, United States
| | - Zongjun Cui
- College of Agronomy and Biotechnology, China Agricultural University , Beijing, China
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa , Honolulu, Hawaii 96822, United States
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Largy E, Cantais F, Van Vyncht G, Beck A, Delobel A. Orthogonal liquid chromatography-mass spectrometry methods for the comprehensive characterization of therapeutic glycoproteins, from released glycans to intact protein level. J Chromatogr A 2017; 1498:128-146. [PMID: 28372839 DOI: 10.1016/j.chroma.2017.02.072] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 01/04/2017] [Accepted: 02/28/2017] [Indexed: 01/16/2023]
Abstract
Proteins are increasingly used as therapeutics. Their characterization is challenging due to their size and inherent heterogeneity notably caused by post-translational modifications, among which glycosylation is probably the most prominent. The glycosylation profile of therapeutic proteins must therefore be thoroughly analyzed. Here, we illustrate how the use of a combination of various cutting-edge LC or LC/MS(/MS) methods, and operating at different levels of analysis allows the comprehensive characterization of both the N- and O-glycosylations of therapeutic proteins without the need for other approaches (capillary electrophoresis, MALDI-TOF). This workflow does not call for the use of highly specialized/custom hardware and software nor an extensive knowledge of glycan analysis. Most notably, we present the point of view of a contract research organization, with the constraints associated to the work in a regulated environment (GxP). Two salient points of this work are i) the use of mixed-mode chromatography as a fast and straightforward mean of profiling N-glycans sialylation as well as an orthogonal method to separate N-glycans co-eluting in the HILIC mode; and ii) the use of widepore HILIC/MS to analyze challenging N/O-glycosylation profiles at both the peptide and subunit levels. A particular attention was given to the sample preparations in terms of duration, specificity, versatility, and robustness, as well as the ease of data processing.
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Affiliation(s)
- Eric Largy
- Quality Assistance sa, Technoparc de Thudinie 2, 6536, Donstiennes, Belgium
| | - Fabrice Cantais
- Quality Assistance sa, Technoparc de Thudinie 2, 6536, Donstiennes, Belgium
| | - Géry Van Vyncht
- Quality Assistance sa, Technoparc de Thudinie 2, 6536, Donstiennes, Belgium
| | - Alain Beck
- Centre d'Immunologie Pierre Fabre (CIPF), 5 Av. Napoléon III, BP 60497, 74164, Saint-Julien-en-Genevois, France
| | - Arnaud Delobel
- Quality Assistance sa, Technoparc de Thudinie 2, 6536, Donstiennes, Belgium.
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Ying J, Zhao J, Hou Y, Wang Y, Qiu J, Li Z, Tong X, Shi Z, Zhu J, Zhang J. Mapping the N-linked glycosites of rice (Oryza sativa L.) germinating embryos. PLoS One 2017; 12:e0173853. [PMID: 28328971 PMCID: PMC5362090 DOI: 10.1371/journal.pone.0173853] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 02/28/2017] [Indexed: 11/19/2022] Open
Abstract
Germination is a key event in the angiosperm life cycle. N-glycosylation of proteins is one of the most common post-translational modifications, and has been recognized to be an important regulator of the proteome of the germinating embryo. Here, we report the first N-linked glycosites mapping of rice embryos during germination by using a hydrophilic interaction chromatography (HILIC) glycopeptides enrichment strategy associated with high accuracy mass spectrometry identification. A total of 242 glycosites from 191 unique proteins was discovered. Inspection of the motifs and sequence structures involved suggested that all the glycosites were concentrated within [NxS/T] motif, while 82.3% of them were in a coil structure. N-glycosylation preferentially occurred on proteins with glycoside hydrolase activities, which were significantly enriched in the starch and sucrose metabolism pathway, suggesting that N-glycosylation is involved in embryo germination by regulating carbohydrate metabolism. Notably, protein-protein interaction analysis revealed a network with several Brassinosteroids signaling proteins, including XIAO and other BR-responsive proteins, implying that glycosylation-mediated Brassinosteroids signaling may be a key mechanism regulating rice embryo germination. In summary, this study expanded our knowledge of protein glycosylation in rice, and provided novel insight into the PTM regulation in rice seed germination.
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Affiliation(s)
- Jiezheng Ying
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, P.R. China
| | - Juan Zhao
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, P.R. China
| | - Yuxuan Hou
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, P.R. China
| | - Yifeng Wang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, P.R. China
| | - Jiehua Qiu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, P.R. China
| | - Zhiyong Li
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, P.R. China
| | - Xiaohong Tong
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, P.R. China
| | | | - Jun Zhu
- Jingjie PTM-Biolabs, Hangzhou, P.R. China
| | - Jian Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, P.R. China
- * E-mail:
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Hashiguchi A, Komatsu S. Impact of Post-Translational Modifications of Crop Proteins under Abiotic Stress. Proteomes 2016; 4:proteomes4040042. [PMID: 28248251 PMCID: PMC5260974 DOI: 10.3390/proteomes4040042] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Revised: 11/30/2016] [Accepted: 12/16/2016] [Indexed: 12/15/2022] Open
Abstract
The efficiency of stress-induced adaptive responses of plants depends on intricate coordination of multiple signal transduction pathways that act coordinately or, in some cases, antagonistically. Protein post-translational modifications (PTMs) can regulate protein activity and localization as well as protein-protein interactions in numerous cellular processes, thus leading to elaborate regulation of plant responses to various external stimuli. Understanding responses of crop plants under field conditions is crucial to design novel stress-tolerant cultivars that maintain robust homeostasis even under extreme conditions. In this review, proteomic studies of PTMs in crops are summarized. Although the research on the roles of crop PTMs in regulating stress response mechanisms is still in its early stage, several novel insights have been retrieved so far. This review covers techniques for detection of PTMs in plants, representative PTMs in plants under abiotic stress, and how PTMs control functions of representative proteins. In addition, because PTMs under abiotic stresses are well described in soybeans under submergence, recent findings in PTMs of soybean proteins under flooding stress are introduced. This review provides information on advances in PTM study in relation to plant adaptations to abiotic stresses, underlining the importance of PTM study to ensure adequate agricultural production in the future.
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Affiliation(s)
- Akiko Hashiguchi
- Faculty of Medicine, University of Tsukuba, Tsukuba 305-8577, Japan.
| | - Setsuko Komatsu
- National Institute of Crop Science, NARO, Tsukuba 305-8518, Japan.
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