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Castro C, Niknafs S, Gonzalez-Ortiz G, Tan X, Bedford MR, Roura E. Dietary xylo-oligosaccharides and arabinoxylans improved growth efficiency by reducing gut epithelial cell turnover in broiler chickens. J Anim Sci Biotechnol 2024; 15:35. [PMID: 38433214 PMCID: PMC10910751 DOI: 10.1186/s40104-024-00991-z] [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: 09/14/2023] [Accepted: 01/02/2024] [Indexed: 03/05/2024] Open
Abstract
BACKGROUND One of the main roles of the intestinal mucosa is to protect against environmental hazards. Supplementation of xylo-oligosaccharides (XOS) is known to selectively stimulate the growth of beneficial intestinal bacteria and improve gut health and function in chickens. XOS may have an impact on the integrity of the intestinal epithelia where cell turnover is critical to maintain the compatibility between the digestive and barrier functions. The aim of the study was to evaluate the effect of XOS and an arabinoxylan-rich fraction (AXRF) supplementation on gut function and epithelial integrity in broiler chickens. METHODS A total of 128 broiler chickens (Ross 308) were assigned into one of two different dietary treatments for a period of 42 d: 1) control diet consisting of a corn/soybean meal-based diet; or 2) a control diet supplemented with 0.5% XOS and 1% AXRF. Each treatment was randomly distributed across 8 pens (n = 8) with 8 chickens each. Feed intake and body weight were recorded weekly. On d 42, one male chicken per pen was selected based on average weight and euthanized, jejunum samples were collected for proteomics analysis. RESULTS Dietary XOS/AXRF supplementation improved feed efficiency (P < 0.05) from d 1 to 42 compared to the control group. Proteomic analysis was used to understand the mechanism of improved efficiency uncovering 346 differentially abundant proteins (DAP) (Padj < 0.00001) in supplemented chickens compared to the non-supplemented group. In the jejunum, the DAP translated into decreased ATP production indicating lower energy expenditure by the tissue (e.g., inhibition of glycolysis and tricarboxylic acid cycle pathways). In addition, DAP were associated with decreased epithelial cell differentiation, and migration by reducing the actin polymerization pathway. Putting the two main pathways together, XOS/AXRF supplementation may decrease around 19% the energy required for the maintenance of the gastrointestinal tract. CONCLUSIONS Dietary XOS/AXRF supplementation improved growth efficiency by reducing epithelial cell migration and differentiation (hence, turnover), actin polymerization, and consequently energy requirement for maintenance of the jejunum of broiler chickens.
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Affiliation(s)
- Carla Castro
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Shahram Niknafs
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | | | - Xinle Tan
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | | | - Eugeni Roura
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia.
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2
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White MEH, Sinn LR, Jones DM, de Folter J, Aulakh SK, Wang Z, Flynn HR, Krüger L, Tober-Lau P, Demichev V, Kurth F, Mülleder M, Blanchard V, Messner CB, Ralser M. Oxonium ion scanning mass spectrometry for large-scale plasma glycoproteomics. Nat Biomed Eng 2024; 8:233-247. [PMID: 37474612 DOI: 10.1038/s41551-023-01067-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 06/15/2023] [Indexed: 07/22/2023]
Abstract
Protein glycosylation, a complex and heterogeneous post-translational modification that is frequently dysregulated in disease, has been difficult to analyse at scale. Here we report a data-independent acquisition technique for the large-scale mass-spectrometric quantification of glycopeptides in plasma samples. The technique, which we named 'OxoScan-MS', identifies oxonium ions as glycopeptide fragments and exploits a sliding-quadrupole dimension to generate comprehensive and untargeted oxonium ion maps of precursor masses assigned to fragment ions from non-enriched plasma samples. By applying OxoScan-MS to quantify 1,002 glycopeptide features in the plasma glycoproteomes from patients with COVID-19 and healthy controls, we found that severe COVID-19 induces differential glycosylation in IgA, haptoglobin, transferrin and other disease-relevant plasma glycoproteins. OxoScan-MS may allow for the quantitative mapping of glycoproteomes at the scale of hundreds to thousands of samples.
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Affiliation(s)
- Matthew E H White
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Ludwig R Sinn
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - D Marc Jones
- Bioinformatics and Computational Biology Laboratory, The Francis Crick Institute, London, UK
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London, UK
| | - Joost de Folter
- Software Engineering and Artificial Intelligence Technology Platform, The Francis Crick Institute, London, UK
| | - Simran Kaur Aulakh
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Ziyue Wang
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Helen R Flynn
- Mass Spectrometry Proteomics Science Technology Platform, The Francis Crick Institute, London, UK
| | - Lynn Krüger
- Institute of Diagnostic Laboratory Medicine, Charité - Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Human Medicine, Medical School Berlin, Berlin, Germany
| | - Pinkus Tober-Lau
- Department of Infectious Diseases and Critical Care Medicine, Charité - Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Vadim Demichev
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Florian Kurth
- Department of Infectious Diseases and Critical Care Medicine, Charité - Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Michael Mülleder
- Core Facility High-throughput Mass Spectrometry, Charité - Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Véronique Blanchard
- Institute of Diagnostic Laboratory Medicine, Charité - Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Human Medicine, Medical School Berlin, Berlin, Germany
| | - Christoph B Messner
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.
- Precision Proteomic Center, Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland.
| | - Markus Ralser
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
- Max Planck Institute for Molecular Genetics, Berlin, Germany.
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3
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Kerr ED, Fox GP, Schulz BL. Proteomics and Metabolomics Reveal that an Abundant α-Glucosidase Drives Sorghum Fermentability for Beer Brewing. J Proteome Res 2023; 22:3596-3606. [PMID: 37821127 DOI: 10.1021/acs.jproteome.3c00436] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Sorghum (Sorghum bicolor), a grass native to Africa, is a popular alternative to barley for brewing beer. The importance of sorghum to beer brewing is increasing because it is a naturally gluten-free cereal, and climate change is expected to cause a reduction in the production of barley over the coming decades. However, there are challenges associated with the use of sorghum instead of barley in beer brewing. Here, we used proteomics and metabolomics to gain insights into the sorghum brewing process to advise processes for efficient beer production from sorghum. We found that during malting, sorghum synthesizes the amylases and proteases necessary for brewing. Proteomics revealed that mashing with sorghum malt required higher temperatures than barley malt for efficient protein solubilization. Both α- and β-amylase were considerably less abundant in sorghum wort than in barley wort, correlating with lower maltose concentrations in sorghum wort. However, metabolomics revealed higher glucose concentrations in sorghum wort than in barley wort, consistent with the presence of an abundant α-glucosidase detected by proteomics in sorghum malt. Our results indicate that sorghum can be a viable grain for industrial fermented beverage production, but that its use requires careful process optimization for efficient production of fermentable wort and high-quality beer.
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Affiliation(s)
- Edward D Kerr
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Glen P Fox
- Department of Food Science and Technology, University of California Davis, Davis, California 95616, United States
| | - Benjamin L Schulz
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
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4
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Kitata RB, Yang JC, Chen YJ. Advances in data-independent acquisition mass spectrometry towards comprehensive digital proteome landscape. MASS SPECTROMETRY REVIEWS 2023; 42:2324-2348. [PMID: 35645145 DOI: 10.1002/mas.21781] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 12/17/2021] [Accepted: 01/21/2022] [Indexed: 06/15/2023]
Abstract
The data-independent acquisition mass spectrometry (DIA-MS) has rapidly evolved as a powerful alternative for highly reproducible proteome profiling with a unique strength of generating permanent digital maps for retrospective analysis of biological systems. Recent advancements in data analysis software tools for the complex DIA-MS/MS spectra coupled to fast MS scanning speed and high mass accuracy have greatly expanded the sensitivity and coverage of DIA-based proteomics profiling. Here, we review the evolution of the DIA-MS techniques, from earlier proof-of-principle of parallel fragmentation of all-ions or ions in selected m/z range, the sequential window acquisition of all theoretical mass spectra (SWATH-MS) to latest innovations, recent development in computation algorithms for data informatics, and auxiliary tools and advanced instrumentation to enhance the performance of DIA-MS. We further summarize recent applications of DIA-MS and experimentally-derived as well as in silico spectra library resources for large-scale profiling to facilitate biomarker discovery and drug development in human diseases with emphasis on the proteomic profiling coverage. Toward next-generation DIA-MS for clinical proteomics, we outline the challenges in processing multi-dimensional DIA data set and large-scale clinical proteomics, and continuing need in higher profiling coverage and sensitivity.
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Affiliation(s)
| | - Jhih-Ci Yang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Sustainable Chemical Science and Technology, Taiwan International Graduate Program, Academia Sinica and National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Sustainable Chemical Science and Technology, Taiwan International Graduate Program, Academia Sinica and National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
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Yin H, Zhu J. Methods for quantification of glycopeptides by liquid separation and mass spectrometry. MASS SPECTROMETRY REVIEWS 2023; 42:887-917. [PMID: 35099083 PMCID: PMC9339036 DOI: 10.1002/mas.21771] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 11/14/2021] [Accepted: 01/13/2022] [Indexed: 05/05/2023]
Abstract
Recent advances in analytical techniques provide the opportunity to quantify even low-abundance glycopeptides derived from complex biological mixtures, allowing for the identification of glycosylation differences between healthy samples and those derived from disease states. Herein, we discuss the sample preparation procedures and the mass spectrometry (MS) strategies that have facilitated glycopeptide quantification, as well as the standards used for glycopeptide quantification. For sample preparation, various glycopeptide enrichment methods are summarized including the columns used for glycopeptide separation in liquid chromatography separation. For MS analysis strategies, MS1 level-based quantification and MS2 level-based quantification are described, either with or without labeling, where we have covered isotope labeling, TMT/iTRAQ labeling, data dependent acquisition, data independent acquisition, multiple reaction monitoring, and parallel reaction monitoring. The strengths and weaknesses of these methods are compared, particularly those associated with the figures of merit that are important for clinical biomarker studies and the pathological and functional studies of glycoproteins in various diseases. Possible future developments for glycopeptide quantification are discussed.
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Affiliation(s)
- Haidi Yin
- Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518132, China
- Correspondence to: Haidi Yin, Shenzhen Bay Laboratory, A1201, Shenzhen, Guangdong, 518132, China. Phone: 0755-26849276. , Jianhui Zhu, Department of Surgery, University of Michigan, 1150 West Medical Center Drive, Building MSRB1, Rm A500, Ann Arbor, MI 48109-0656, USA. Tel: 734-615-2567. Fax: 734-615-2088.
| | - Jianhui Zhu
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109, USA
- Correspondence to: Haidi Yin, Shenzhen Bay Laboratory, A1201, Shenzhen, Guangdong, 518132, China. Phone: 0755-26849276. , Jianhui Zhu, Department of Surgery, University of Michigan, 1150 West Medical Center Drive, Building MSRB1, Rm A500, Ann Arbor, MI 48109-0656, USA. Tel: 734-615-2567. Fax: 734-615-2088.
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Raza A, Schulz BL, Nouwens A, Naseem MN, Kamran M, Mantilla Valdivieso EF, Kerr ED, Constantinoiu C, Jonsson NN, James P, Tabor AE. Application of quantitative proteomics to discover biomarkers for tick resistance in cattle. Front Immunol 2023; 14:1091066. [PMID: 36793724 PMCID: PMC9924087 DOI: 10.3389/fimmu.2023.1091066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 01/04/2023] [Indexed: 01/31/2023] Open
Abstract
Introduction Breeding for tick resistance is a sustainable alternative to control cattle ticks due to widespread resistance to acaricidal drugs and the lack of a protective vaccine. The most accurate method used to characterise the phenotype for tick resistance in field studies is the standard tick count, but this is labour-intensive and can be hazardous to the operator. Efficient genetic selection requires reliable phenotyping or biomarker(s) for accurately identifying tick-resistant cattle. Although breed-specific genes associated with tick resistance have been identified, the mechanisms behind tick resistance have not yet been fully characterised. Methods This study applied quantitative proteomics to examine the differential abundance of serum and skin proteins using samples from naïve tick-resistant and -susceptible Brangus cattle at two-time points following tick exposure. The proteins were digested into peptides, followed by identification and quantification using sequential window acquisition of all theoretical fragment ion mass spectrometry. Results Resistant naïve cattle had a suite of proteins associated with immune response, blood coagulation and wound healing that were significantly (adjusted P < 10- 5) more abundant compared with susceptible naïve cattle. These proteins included complement factors (C3, C4, C4a), alpha-1-acid glycoprotein (AGP), beta-2-glycoprotein-1, keratins (KRT1 & KRT3) and fibrinogens (alpha & beta). The mass spectrometry findings were validated by identifying differences in the relative abundance of selected serum proteins with ELISA. The proteins showing a significantly different abundance in resistant cattle following early and prolonged tick exposures (compared to resistant naïve) were associated with immune response, blood coagulation, homeostasis, and wound healing. In contrast, susceptible cattle developed some of these responses only after prolonged tick exposure. Discussion Resistant cattle were able to transmigrate immune-response related proteins towards the tick bite sites, which may prevent tick feeding. Significantly differentially abundant proteins identified in this research in resistant naïve cattle may provide a rapid and efficient protective response to tick infestation. Physical barrier (skin integrity and wound healing) mechanisms and systemic immune responses were key contributors to resistance. Immune response-related proteins such as C4, C4a, AGP and CGN1 (naïve samples), CD14, GC and AGP (post-infestation) should be further investigated as potential biomarkers for tick resistance.
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Affiliation(s)
- Ali Raza
- Queensland Alliance for Agriculture & Food Innovation, Centre for Animal Science, The University of Queensland, St Lucia, QLD, Australia
| | - Benjamin L Schulz
- The University of Queensland, School of Chemistry and Molecular Biosciences, St. Lucia, QLD, Australia
| | - Amanda Nouwens
- The University of Queensland, School of Chemistry and Molecular Biosciences, St. Lucia, QLD, Australia
| | - Muhammad Noman Naseem
- Queensland Alliance for Agriculture & Food Innovation, Centre for Animal Science, The University of Queensland, St Lucia, QLD, Australia
| | - Muhammad Kamran
- Queensland Alliance for Agriculture & Food Innovation, Centre for Animal Science, The University of Queensland, St Lucia, QLD, Australia
| | - Emily F Mantilla Valdivieso
- Queensland Alliance for Agriculture & Food Innovation, Centre for Animal Science, The University of Queensland, St Lucia, QLD, Australia
| | - Edward D Kerr
- The University of Queensland, School of Chemistry and Molecular Biosciences, St. Lucia, QLD, Australia
| | - Constantin Constantinoiu
- College of Public Health, Medical & Veterinary Sciences, James Cook University, Townsville, QLD, Australia
| | - Nicholas N Jonsson
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Peter James
- Queensland Alliance for Agriculture & Food Innovation, Centre for Animal Science, The University of Queensland, St Lucia, QLD, Australia
| | - Ala E Tabor
- Queensland Alliance for Agriculture & Food Innovation, Centre for Animal Science, The University of Queensland, St Lucia, QLD, Australia.,The University of Queensland, School of Chemistry and Molecular Biosciences, St. Lucia, QLD, Australia
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Massel K, Hintzsche J, Restall J, Kerr ED, Schulz BL, Godwin ID. CRISPR-knockout of β-kafirin in sorghum does not recapitulate the grain quality of natural mutants. PLANTA 2022; 257:8. [PMID: 36481955 DOI: 10.1007/s00425-022-04038-3] [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: 08/28/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
When gene editing was applied to knockout beta-kafirin, there was a compensatory increase of gamma-kafirin which does not occur in domesticated null varieties, so enhanced grain quality was not achieved. Sorghum bicolor is an important animal feedstock cereal crop throughout Australia and the southern United States, where its use as a food product is limited by issues with low calorific and nutritive value. Qualities such as reduced digestibility and low essential amino acid content are directly attributed to the kafirin grain storage proteins, the major components of protein bodies within the endosperm. Specifically, the β- and γ-kafirins have few protease cleavage sites and high levels of cysteine residues which lead to a highly cross-linked shell of intra- and inter-molecular disulphide linkages that encapsulate the more digestible α- and δ-kafirins in the core of the protein bodies. Naturally occurring β-kafirin mutants exist and are known to have improved grain quality, with enhanced protein contents and digestibility, traits which are often attributed to the lack of this cysteine-rich kafirin in the mature grain. However, when CRISPR/Cas9 editing was used to create β-kafirin knockout lines, there was no improvement to grain quality in the Tx430 background, although they did have unique protein composition and changes to protein body morphology in the vitreous endosperm. One explanation of the divergence in quality traits found the lines lacking β-kafirin are due to a drastic increase of γ-kafirin which was only found in the gene edited lines. This study highlights that in some germplasm, there is a level of redundancy between the peripheral kafirins, and that improvement of grain protein digestibility cannot be achieved by simply removing the β-kafirin protein in all genetic backgrounds.
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Affiliation(s)
- Karen Massel
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia.
| | - Jessica Hintzsche
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jemma Restall
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Edward D Kerr
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Benjamin L Schulz
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ian D Godwin
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
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Li HT, Kerr ED, Schulz BL, Gidley MJ, Dhital S. Pasting properties of high-amylose wheat in conventional and high-temperature Rapid Visco Analyzer: Molecular contribution of starch and gluten proteins. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2022.107840] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Nguyen LT, Lau LY, Fortes MRS. Proteomic Analysis of Hypothalamus and Pituitary Gland in Pre and Postpubertal Brahman Heifers. Front Genet 2022; 13:935433. [PMID: 35774501 PMCID: PMC9237413 DOI: 10.3389/fgene.2022.935433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 05/25/2022] [Indexed: 11/28/2022] Open
Abstract
The hypothalamus and the pituitary gland are directly involved in the complex systemic changes that drive the onset of puberty in cattle. Here, we applied integrated bioinformatics to elucidate the critical proteins underlying puberty and uncover potential molecular mechanisms from the hypothalamus and pituitary gland of prepubertal (n = 6) and postpubertal (n = 6) cattle. Proteomic analysis in the hypothalamus and pituitary gland revealed 275 and 186 differentially abundant (DA) proteins, respectively (adjusted p-value < 0.01). The proteome profiles found herein were integrated with previously acquired transcriptome profiles. These transcriptomic studies used the same tissues harvested from the same heifers at pre- and post-puberty. This comparison detected a small number of matched transcripts and protein changes at puberty in each tissue, suggesting the need for multiple omics analyses for interpreting complex biological systems. In the hypothalamus, upregulated DA proteins at post-puberty were enriched in pathways related to puberty, including GnRH, calcium and oxytocin signalling pathways, whereas downregulated proteins were observed in the estrogen signalling pathway, axon guidance and GABAergic synapse. Additionally, this study revealed that ribosomal pathway proteins in the pituitary were involved in the pubertal development of mammals. The reported molecules and derived protein-protein networks are a starting point for future experimental approaches that might dissect with more detail the role of each molecule to provide new insights into the mechanisms of puberty onset in cattle.
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Affiliation(s)
- Loan To Nguyen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia
- *Correspondence: Loan To Nguyen,
| | - Li Yieng Lau
- Agency of Science, Technology and Research, Singapore, Singapore
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Niknafs S, Fortes MRS, Cho S, Black JL, Roura E. Alanine-specific appetite in slow growing chickens is associated with impaired glucose transport and TCA cycle. BMC Genomics 2022; 23:393. [PMID: 35606689 PMCID: PMC9128104 DOI: 10.1186/s12864-022-08625-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 05/09/2022] [Indexed: 11/24/2022] Open
Abstract
Background The rate of protein accretion and growth affect amino acid requirements in young animals. Differences in amino acid metabolism contribute to individual variations in growth rate. This study aimed at determining how amino acid needs may change with growth rates in broiler chickens. Experiment 1 consisted of testing amino acid choices in two chicken groups with extreme growth rates (the slowest –SG- or fastest –FG- growing birds in a flock). Essential (EAA) (methionine, lysine and threonine) or non-essential (NEAA) (alanine, aspartic acid and asparagine) amino acids were added to a standard control feed (13.2 MJ/kg; 21.6% crude protein). The chickens were offered simultaneous access to the control feed and a feed supplemented with one of the two amino acid mixes added at 73% above standard dietary levels. Experiment 2 consisted of the selection of the bottom 5 SG and top 5 FG chickens from a flock of 580 to study differences in amino acid metabolism using the proventriculus representing gut sensing mechanism. In this experiment, transcriptomic, proteomic, and genomic analyses were used to compare the two groups of chickens. Results SG preferred NEAA, while they rejected EAA supplemented feeds (P < 0.05). However, FG rejected NEAA (P < 0.05), and they were indifferent to EAA supplemented feed (P > 0.05). Transcriptomic and proteomic analyses identified 909 differentially expressed genes and 146 differentially abundant proteins associated with differences in growth rate (P < 0.05). The integration of gene expression and protein abundance patterns showed the downregulation of sensing and transport of alanine and glucose associated with increased alanine catabolism to pyruvate in SG chickens. Conclusion Dietary preferences for NEAA in the SG group are associated with a potential cytosolic depletion of alanine following an upregulation of the catabolism into TCA cycle intermediates. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08625-2.
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Affiliation(s)
- Shahram Niknafs
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Marina R S Fortes
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Sungbo Cho
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - John L Black
- John L Black Consulting, Warrimoo, NSW, 2774, Australia
| | - Eugeni Roura
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia.
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Identification and characterisation of sPEPs in Cryptococcus neoformans. Fungal Genet Biol 2022; 160:103688. [PMID: 35339703 DOI: 10.1016/j.fgb.2022.103688] [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: 01/04/2022] [Revised: 03/02/2022] [Accepted: 03/21/2022] [Indexed: 11/24/2022]
Abstract
Short open reading frame (sORF)-encoded peptides (sPEPs) have been found across a wide range of genomic locations in a variety of species. To date, their identification, validation, and characterisation in the human fungal pathogen Cryptococcus neoformans has been limited due to a lack of standardised protocols. We have developed an enrichment process that enables sPEP detection within a protein sample from this polysaccharide-encapsulated yeast, and implemented proteogenomics to provide insights into the validity of predicted and hypothetical sORFs annotated in the C. neoformans genome. Novel sORFs were discovered within the 5' and 3' UTRs of known transcripts as well as in "non-coding" RNAs. One novel candidate, dubbed NPB1, that resided in an RNA annotated as "non-coding", was chosen for characterisation. Through the creation of both specific point mutations and a full deletion allele, the function of the new sPEP, Npb1, was shown to resemble that of the bacterial trans-translation protein SmpB.
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Fang P, Ji Y, Oellerich T, Urlaub H, Pan KT. Strategies for Proteome-Wide Quantification of Glycosylation Macro- and Micro-Heterogeneity. Int J Mol Sci 2022; 23:ijms23031609. [PMID: 35163546 PMCID: PMC8835892 DOI: 10.3390/ijms23031609] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 12/03/2022] Open
Abstract
Protein glycosylation governs key physiological and pathological processes in human cells. Aberrant glycosylation is thus closely associated with disease progression. Mass spectrometry (MS)-based glycoproteomics has emerged as an indispensable tool for investigating glycosylation changes in biological samples with high sensitivity. Following rapid improvements in methodologies for reliable intact glycopeptide identification, site-specific quantification of glycopeptide macro- and micro-heterogeneity at the proteome scale has become an urgent need for exploring glycosylation regulations. Here, we summarize recent advances in N- and O-linked glycoproteomic quantification strategies and discuss their limitations. We further describe a strategy to propagate MS data for multilayered glycopeptide quantification, enabling a more comprehensive examination of global and site-specific glycosylation changes. Altogether, we show how quantitative glycoproteomics methods explore glycosylation regulation in human diseases and promote the discovery of biomarkers and therapeutic targets.
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Affiliation(s)
- Pan Fang
- Department of Biochemistry and Molecular Biology, School of Biology & Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou 215123, China;
| | - Yanlong Ji
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany;
- Hematology/Oncology, Department of Medicine II, Johann Wolfgang Goethe University, 60590 Frankfurt am Main, Germany;
- Frankfurt Cancer Institute, Johann Wolfgang Goethe University, 60596 Frankfurt am Main, Germany
| | - Thomas Oellerich
- Hematology/Oncology, Department of Medicine II, Johann Wolfgang Goethe University, 60590 Frankfurt am Main, Germany;
- Frankfurt Cancer Institute, Johann Wolfgang Goethe University, 60596 Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany;
- Institute of Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany
- Correspondence: (H.U.); (K.-T.P.)
| | - Kuan-Ting Pan
- Hematology/Oncology, Department of Medicine II, Johann Wolfgang Goethe University, 60590 Frankfurt am Main, Germany;
- Frankfurt Cancer Institute, Johann Wolfgang Goethe University, 60596 Frankfurt am Main, Germany
- Correspondence: (H.U.); (K.-T.P.)
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13
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Cain JA, Dale AL, Cordwell SJ. Exploiting pglB Oligosaccharyltransferase-Positive and -Negative Campylobacter jejuni and a Multiprotease Digestion Strategy to Identify Novel Sites Modified by N-Linked Protein Glycosylation. J Proteome Res 2021; 20:4995-5009. [PMID: 34677046 DOI: 10.1021/acs.jproteome.1c00482] [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: 11/29/2022]
Abstract
Campylobacter jejuni is a bacterial pathogen encoding a unique N-linked glycosylation (pgl) system that mediates attachment of a heptasaccharide to N-sequon-containing membrane proteins by the PglB oligosaccharyltransferase (OST). Many targets of PglB are known, yet only a fraction of sequons are experimentally confirmed, and site occupancy remains elusive. We exploited pglB-positive (wild-type; WT) and -negative (ΔpglB) proteomes to identify potential glycosites. The nonglycosylated forms of known glycopeptides were typically increased in protein normalized abundance in ΔpglB relative to WT and restored by pglB reintroduction (ΔpglB::pglB). Sequon-containing peptide abundances were thus consistent with significant site occupancy in the presence of the OST. Peptides with novel sequons were either unaltered (likely not glycosylated) or showed abundance consistent with known glycopeptides. Topology analysis revealed that unaltered sequons often displayed cytoplasmic localization, despite originating from membrane proteins. Novel glycosites were confirmed using parallel multiprotease digestion, LC-MS/MS, and FAIMS-MS to define the glycoproteomes of WT and ΔpglB::pglB C. jejuni. We identified 142 glycosites, of which 32 were novel, and 83% of sites predicted by proteomics were validated. There are now 166 experimentally verified C. jejuni glycosites and evidence for occupancy or nonoccupancy of 31 additional sites. This study serves as a model for the use of OST-negative cells and proteomics for highlighting novel glycosites and determining occupancy in a range of organisms.
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Affiliation(s)
- Joel A Cain
- Charles Perkins Centre, The University of Sydney, Sydney 2006, Australia.,School of Life and Environmental Sciences, The University of Sydney, Sydney 2006, Australia
| | - Ashleigh L Dale
- Charles Perkins Centre, The University of Sydney, Sydney 2006, Australia.,School of Life and Environmental Sciences, The University of Sydney, Sydney 2006, Australia
| | - Stuart J Cordwell
- Charles Perkins Centre, The University of Sydney, Sydney 2006, Australia.,School of Life and Environmental Sciences, The University of Sydney, Sydney 2006, Australia.,Sydney Mass Spectrometry, The University of Sydney, Sydney 2006, Australia
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14
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Abstract
Mass spectrometry (MS) is a powerful technique for protein identification, quantification and characterization that is widely applied in biochemical studies, and which can provide data on the quantity, structural integrity and post-translational modifications of proteins. It is therefore a versatile and widely used analytic tool for quality control of biopharmaceuticals, especially in quantifying host-cell protein impurities, identifying post-translation modifications and structural characterization of biopharmaceutical proteins. Here, we summarize recent advances in MS-based analyses of these key quality attributes of the biopharmaceutical development and manufacturing processes.
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15
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Jenull S, Mair T, Tscherner M, Penninger P, Zwolanek F, Silao FGS, de San Vicente KM, Riedelberger M, Bandari NC, Shivarathri R, Petryshyn A, Chauhan N, Zacchi LF, -Landmann SL, Ljungdahl PO, Kuchler K. The histone chaperone HIR maintains chromatin states to control nitrogen assimilation and fungal virulence. Cell Rep 2021; 36:109406. [PMID: 34289370 PMCID: PMC8493472 DOI: 10.1016/j.celrep.2021.109406] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 03/10/2021] [Accepted: 06/24/2021] [Indexed: 12/13/2022] Open
Abstract
Adaptation to changing environments and immune evasion is pivotal for fitness of pathogens. Yet, the underlying mechanisms remain largely unknown. Adaptation is governed by dynamic transcriptional re-programming, which is tightly connected to chromatin architecture. Here, we report a pivotal role for the HIR histone chaperone complex in modulating virulence of the human fungal pathogen Candida albicans. Genetic ablation of HIR function alters chromatin accessibility linked to aberrant transcriptional responses to protein as nitrogen source. This accelerates metabolic adaptation and increases the release of extracellular proteases, which enables scavenging of alternative nitrogen sources. Furthermore, HIR controls fungal virulence, as HIR1 deletion leads to differential recognition by immune cells and hypervirulence in a mouse model of systemic infection. This work provides mechanistic insights into chromatin-coupled regulatory mechanisms that fine-tune pathogen gene expression and virulence. Furthermore, the data point toward the requirement of refined screening approaches to exploit chromatin modifications as antifungal strategies.
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Affiliation(s)
- Sabrina Jenull
- Department of Medical Biochemistry, Max Perutz Labs Vienna, Medical University of Vienna, Campus Vienna Biocenter, 1030 Vienna, Austria
| | - Theresia Mair
- Department of Medical Biochemistry, Max Perutz Labs Vienna, Medical University of Vienna, Campus Vienna Biocenter, 1030 Vienna, Austria
| | - Michael Tscherner
- Department of Medical Biochemistry, Max Perutz Labs Vienna, Medical University of Vienna, Campus Vienna Biocenter, 1030 Vienna, Austria
| | - Philipp Penninger
- Department of Medical Biochemistry, Max Perutz Labs Vienna, Medical University of Vienna, Campus Vienna Biocenter, 1030 Vienna, Austria
| | - Florian Zwolanek
- Department of Medical Biochemistry, Max Perutz Labs Vienna, Medical University of Vienna, Campus Vienna Biocenter, 1030 Vienna, Austria
| | - Fitz-Gerald S Silao
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden
| | - Kontxi Martinez de San Vicente
- Section of Immunology, Vetsuisse Faculty, University of Zürich, 8006 Zürich, Switzerland; Institute of Experimental Immunology, University of Zürich, 8057 Zürich, Switzerland
| | - Michael Riedelberger
- Department of Medical Biochemistry, Max Perutz Labs Vienna, Medical University of Vienna, Campus Vienna Biocenter, 1030 Vienna, Austria
| | - Naga C Bandari
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Raju Shivarathri
- Public Health Research Institute, Rutgers, The State University of New Jersey, Newark, NJ 07102, USA
| | - Andriy Petryshyn
- Department of Medical Biochemistry, Max Perutz Labs Vienna, Medical University of Vienna, Campus Vienna Biocenter, 1030 Vienna, Austria
| | - Neeraj Chauhan
- Public Health Research Institute, Rutgers, The State University of New Jersey, Newark, NJ 07102, USA; Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
| | - Lucia F Zacchi
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Salomé LeibundGut -Landmann
- Section of Immunology, Vetsuisse Faculty, University of Zürich, 8006 Zürich, Switzerland; Institute of Experimental Immunology, University of Zürich, 8057 Zürich, Switzerland
| | - Per O Ljungdahl
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden
| | - Karl Kuchler
- Department of Medical Biochemistry, Max Perutz Labs Vienna, Medical University of Vienna, Campus Vienna Biocenter, 1030 Vienna, Austria.
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16
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Zhuang A, Yap FYT, Borg DJ, McCarthy D, Fotheringham A, Leung S, Penfold SA, Sourris KC, Coughlan MT, Schulz BL, Forbes JM. The AGE receptor, OST48 drives podocyte foot process effacement and basement membrane expansion (alters structural composition). Endocrinol Diabetes Metab 2021; 4:e00278. [PMID: 34277994 PMCID: PMC8279619 DOI: 10.1002/edm2.278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 05/16/2021] [Accepted: 05/22/2021] [Indexed: 11/17/2022] Open
Abstract
AIMS The accumulation of advanced glycation end products is implicated in the development and progression of diabetic kidney disease. No study has examined whether stimulating advanced glycation clearance via receptor manipulation is reno-protective in diabetes. Podocytes, which are early contributors to diabetic kidney disease and could be a target for reno-protection. MATERIALS AND METHODS To examine the effects of increased podocyte oligosaccharyltransferase-48 on kidney function, glomerular sclerosis, tubulointerstitial fibrosis and proteome (PXD011434), we generated a mouse with increased oligosaccharyltransferase-48kDa subunit abundance in podocytes driven by the podocin promoter. RESULTS Despite increased urinary clearance of advanced glycation end products, we observed a decline in renal function, significant glomerular damage including glomerulosclerosis, collagen IV deposition, glomerular basement membrane thickening and foot process effacement and tubulointerstitial fibrosis. Analysis of isolated glomeruli identified enrichment in proteins associated with collagen deposition, endoplasmic reticulum stress and oxidative stress. Ultra-resolution microscopy of podocytes revealed denudation of foot processes where there was co-localization of oligosaccharyltransferase-48kDa subunit and advanced glycation end-products. CONCLUSIONS These studies indicate that increased podocyte expression of oligosaccharyltransferase-48 kDa subunit results in glomerular endoplasmic reticulum stress and a decline in kidney function.
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Affiliation(s)
- Aowen Zhuang
- Glycation and Diabetes ComplicationsMater Research Institute – The University of QueenslandTranslational Research InstituteWoolloongabbaQldAustralia
- Faculty of MedicineUniversity of QueenslandSt LuciaQldAustralia
- Baker Heart and Diabetes InstituteMelbourneVicAustralia
| | | | - Danielle J. Borg
- Glycation and Diabetes ComplicationsMater Research Institute – The University of QueenslandTranslational Research InstituteWoolloongabbaQldAustralia
| | - Domenica McCarthy
- Glycation and Diabetes ComplicationsMater Research Institute – The University of QueenslandTranslational Research InstituteWoolloongabbaQldAustralia
| | - Amelia Fotheringham
- Glycation and Diabetes ComplicationsMater Research Institute – The University of QueenslandTranslational Research InstituteWoolloongabbaQldAustralia
| | - Sherman Leung
- Glycation and Diabetes ComplicationsMater Research Institute – The University of QueenslandTranslational Research InstituteWoolloongabbaQldAustralia
| | | | - Karly C. Sourris
- Baker Heart and Diabetes InstituteMelbourneVicAustralia
- Department of DiabetesCentral Clinical SchoolMonash UniversityMelbourneVicAustralia
| | - Melinda T. Coughlan
- Baker Heart and Diabetes InstituteMelbourneVicAustralia
- Department of DiabetesCentral Clinical SchoolMonash UniversityMelbourneVicAustralia
| | - Benjamin L. Schulz
- School of Chemistry and Molecular BiosciencesUniversity of QueenslandSt LuciaQldAustralia
| | - Josephine M. Forbes
- Glycation and Diabetes ComplicationsMater Research Institute – The University of QueenslandTranslational Research InstituteWoolloongabbaQldAustralia
- Faculty of MedicineUniversity of QueenslandSt LuciaQldAustralia
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17
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Osama SK, Kerr ED, Yousif AM, Phung TK, Kelly AM, Fox GP, Schulz BL. Proteomics reveals commitment to germination in barley seeds is marked by loss of stress response proteins and mobilisation of nutrient reservoirs. J Proteomics 2021; 242:104221. [PMID: 33866056 DOI: 10.1016/j.jprot.2021.104221] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 02/06/2023]
Abstract
Germination is a critical process in the reproduction and propagation of flowering plants, and is also the key stage of industrial grain malting. Germination commences when seeds are steeped in water, followed by degradation of the endosperm cell walls, enzymatic digestion of starch and proteins to provide nutrients for the growing plant, and emergence of the radicle from the seed. Dormancy is a state where seeds fail to germinate upon steeping, but which prevents inappropriate premature germination of the seeds before harvest from the field. This can result in inefficiencies in industrial malting. We used Sequential Window Acquisition of all THeoretical ions Mass Spectrometry (SWATH-MS) proteomics to measure changes in the barley seed proteome throughout germination. We found a large number of proteins involved in desiccation tolerance and germination inhibition rapidly decreased in abundance after imbibition. This was followed by a decrease in proteins involved in lipid, protein and nutrient reservoir storage, consistent with induction and activation of systems for nutrient mobilisation to provide nutrients to the growing embryo. Dormant seeds that failed to germinate showed substantial biochemical activity distinct from that of seeds undergoing germination, with differences in sulfur metabolic enzymes, endogenous alpha-amylase/trypsin inhibitors, and histone proteins. We verified our findings with analysis of germinating barley seeds from two commercial malting facilities, demonstrating that key features of the dynamic proteome of germinating barley seeds were conserved between laboratory and industrial scales. The results provide a more detailed understanding of the changes in the barley proteome during germination and give possible target proteins for testing or to inform selective breeding to enhance germination or control dormancy. SIGNIFICANCE: Germination is critical to the reproduction and propagation of flowering plants, and in industrial malting. Dormancy, where seeds fail to germinate upon steeping, can result in inefficiencies in industrial malting. Our DIA/SWATH-MS proteomics analyses identified key changes during germination, including an initial loss of proteins involved in desiccation tolerance and germination inhibition, followed by decreases in lipid, protein and nutrient reservoir storage. These changes were consistent between laboratory and industrial malting scales, and therefore demonstrate the utility of laboratory-scale barley germination as a model system for industrial malt house processes. We also showed that dormant seeds that failed to germinate showed substantial biochemical activity distinct from that of seeds undergoing germination, consistent with dormancy being an actively regulated state. Our results provide a more detailed understanding of the changes in the barley proteome during germination and give possible target proteins for testing or to inform selective breeding to enhance germination or control dormancy.
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Affiliation(s)
- Sarah K Osama
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Toowoomba, Qld 4350, Australia
| | - Edward D Kerr
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia 4072, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane 4072, Australia
| | - Adel M Yousif
- Tasmanian Institute of Agriculture, College of Science and Engineering, University of Tasmania, Sandy Bay Campus, TAS, 7005, Australia
| | - Toan K Phung
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia 4072, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane 4072, Australia
| | - Alison M Kelly
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Toowoomba, Qld 4350, Australia; Department of Agriculture and Fisheries, Leslie Research Facility, Toowoomba, Qld 4350, Australia
| | - Glen P Fox
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Toowoomba, Qld 4350, Australia; Department of Food Science and Technology, University of California Davis, CA 95616, USA.
| | - Benjamin L Schulz
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia 4072, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane 4072, Australia.
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18
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Raza A, Schulz BL, Nouwens A, Jackson LA, Piper EK, James P, Jonsson NN, Tabor AE. Serum proteomes of Santa Gertrudis cattle before and after infestation with Rhipicephalus australis ticks. Parasite Immunol 2021; 43:e12836. [PMID: 33843060 DOI: 10.1111/pim.12836] [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: 12/15/2020] [Revised: 03/05/2021] [Accepted: 03/08/2021] [Indexed: 01/22/2023]
Abstract
Previous studies have applied genomics and transcriptomics to identify immune and genetic markers as key indicator traits for cattle tick susceptibility/resistance; however, results differed between breeds, and there is lack of information on the use of host proteomics. Serum samples from Santa Gertrudis cattle (naïve and phenotyped over 105 days as tick-resistant [TR] or tick-susceptible [TS]) were used to conduct differential abundance analyses of protein profiles. Serum proteins were digested into peptides followed by identification and quantification using sequential window acquisition of all instances of theoretical fragment ion mass spectrometry. Before tick infestation, abundance of 28 proteins differed significantly (adjusted P < 10-5 ) between TR and TS. These differences were also observed following tick infestation (TR vs TS) with a further eight differentially abundant proteins in TR cattle, suggesting possible roles in adaptive responses. The intragroup comparisons (TS-0 vs TS and TR-0 vs TR) showed that tick infestation elicited quite similar responses in both groups of cattle, but with relatively stronger responses in TR cattle. Many of the significantly differentially abundant proteins in TR Santa Gertrudis cattle (before and after tick infestation) were associated with immune responses including complement factors, chemotaxis for immune cells and acute-phase responses.
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Affiliation(s)
- Ali Raza
- Centre for Animal Science, Queensland Alliance for Agriculture & Food Innovation, University of Queensland, St Lucia, Qld, Australia
| | - Benjamin L Schulz
- School of Chemistry and Molecular Bioscience, University of Queensland, Brisbane, Qld, Australia
| | - Amanda Nouwens
- School of Chemistry and Molecular Bioscience, University of Queensland, Brisbane, Qld, Australia
| | - Lousie A Jackson
- Biosecurity Sciences Laboratory, Department of Agriculture and Fisheries, Brisbane, Qld, Australia
| | - Emily K Piper
- Global Genetics Laboratory Operations and Customer Support, Kalamazoo, MI, USA
| | - Peter James
- Centre for Animal Science, Queensland Alliance for Agriculture & Food Innovation, University of Queensland, St Lucia, Qld, Australia
| | - Nicholas N Jonsson
- The University of Glasgow, Institute of Biodiversity, Animal Health and Comparative Medicine, Glasgow, UK
| | - Ala E Tabor
- Centre for Animal Science, Queensland Alliance for Agriculture & Food Innovation, University of Queensland, St Lucia, Qld, Australia.,School of Chemistry and Molecular Bioscience, University of Queensland, Brisbane, Qld, Australia
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19
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Coagulation factor IX analysis in bioreactor cell culture supernatant predicts quality of the purified product. Commun Biol 2021; 4:390. [PMID: 33758337 PMCID: PMC7988164 DOI: 10.1038/s42003-021-01903-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 02/18/2021] [Indexed: 02/07/2023] Open
Abstract
Coagulation factor IX (FIX) is a complex post-translationally modified human serum glycoprotein and high-value biopharmaceutical. The quality of recombinant FIX (rFIX), especially complete γ-carboxylation, is critical for rFIX clinical efficacy. Bioreactor operating conditions can impact rFIX production and post-translational modifications (PTMs). With the goal of optimizing rFIX production, we developed a suite of Data Independent Acquisition Mass Spectrometry (DIA-MS) proteomics methods and used these to investigate rFIX yield, γ-carboxylation, other PTMs, and host cell proteins during bioreactor culture and after purification. We detail the dynamics of site-specific PTM occupancy and structure on rFIX during production, which correlated with the efficiency of purification and the quality of the purified product. We identified new PTMs in rFIX near the GLA domain which could impact rFIX GLA-dependent purification and function. Our workflows are applicable to other biologics and expression systems, and should aid in the optimization and quality control of upstream and downstream bioprocesses.
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20
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Ye Z, Vakhrushev SY. The Role of Data-Independent Acquisition for Glycoproteomics. Mol Cell Proteomics 2021; 20:100042. [PMID: 33372048 PMCID: PMC8724878 DOI: 10.1074/mcp.r120.002204] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 12/26/2020] [Accepted: 12/28/2020] [Indexed: 12/13/2022] Open
Abstract
Data-independent acquisition (DIA) is now an emerging method in bottom–up proteomics and capable of achieving deep proteome coverage and accurate label-free quantification. However, for post-translational modifications, such as glycosylation, DIA methodology is still in the early stage of development. The full characterization of glycoproteins requires site-specific glycan identification as well as subsequent quantification of glycan structures at each site. The tremendous complexity of glycosylation represents a significant analytical challenge in glycoproteomics. This review focuses on the development and perspectives of DIA methodology for N- and O-linked glycoproteomics and posits that DIA-based glycoproteomics could be a method of choice to address some of the challenging aspects of glycoproteomics. First, the current challenges in glycoproteomics and the basic principles of DIA are briefly introduced. DIA-based glycoproteomics is then summarized and described into four aspects based on the actual samples. Finally, we discussed the important challenges and future perspectives in the field. We believe that DIA can significantly facilitate glycoproteomic studies and contribute to the development of future advanced tools and approaches in the field of glycoproteomics. Protein glycosylation and challenges in glycoproteomics. Data-independent acquisition for deglycosylated and intact N-linked glycopeptides. Unbiased screening of oxonium ions from all glycopeptide precursors. Glyco–data-independent acquisition on mucin-type O-glycopeptides.
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Affiliation(s)
- Zilu Ye
- Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen N, Denmark
| | - Sergey Y Vakhrushev
- Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen N, Denmark.
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21
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Starch granular protein of high-amylose wheat gives innate resistance to amylolysis. Food Chem 2020; 330:127328. [DOI: 10.1016/j.foodchem.2020.127328] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 06/02/2020] [Accepted: 06/10/2020] [Indexed: 12/12/2022]
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22
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Cipollo JF, Parsons LM. Glycomics and glycoproteomics of viruses: Mass spectrometry applications and insights toward structure-function relationships. MASS SPECTROMETRY REVIEWS 2020; 39:371-409. [PMID: 32350911 PMCID: PMC7318305 DOI: 10.1002/mas.21629] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 04/01/2020] [Accepted: 04/05/2020] [Indexed: 05/21/2023]
Abstract
The advancement of viral glycomics has paralleled that of the mass spectrometry glycomics toolbox. In some regard the glycoproteins studied have provided the impetus for this advancement. Viral proteins are often highly glycosylated, especially those targeted by the host immune system. Glycosylation tends to be dynamic over time as viruses propagate in host populations leading to increased number of and/or "movement" of glycosylation sites in response to the immune system and other pressures. This relationship can lead to highly glycosylated, difficult to analyze glycoproteins that challenge the capabilities of modern mass spectrometry. In this review, we briefly discuss five general areas where glycosylation is important in the viral niche and how mass spectrometry has been used to reveal key information regarding structure-function relationships between viral glycoproteins and host cells. We describe the recent past and current glycomics toolbox used in these analyses and give examples of how the requirement to analyze these complex glycoproteins has provided the incentive for some advances seen in glycomics mass spectrometry. A general overview of viral glycomics, special cases, mass spectrometry methods and work-flows, informatics and complementary chemical techniques currently used are discussed. © 2020 The Authors. Mass Spectrometry Reviews published by John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- John F. Cipollo
- Center for Biologics Evaluation and Research, Food and Drug AdministrationSilver SpringMaryland
| | - Lisa M. Parsons
- Center for Biologics Evaluation and Research, Food and Drug AdministrationSilver SpringMaryland
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23
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Development of a Rapid Method to Assess Beer Foamability Based on Relative Protein Content Using RoboBEER and Machine Learning Modeling. BEVERAGES 2020. [DOI: 10.3390/beverages6020028] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Foam-related parameters are associated with beer quality and dependent, among others, on the protein content. This study aimed to develop a machine learning (ML) model to predict the pattern and presence of 54 proteins. Triplicates of 24 beer samples were analyzed through proteomics. Furthermore, samples were analyzed using the RoboBEER to evaluate 15 physical parameters (color, foam, and bubbles), and a portable near-infrared (NIR) device. Proteins were grouped according to their molecular weight (MW), and a matrix was developed to assess only the significant correlations (p < 0.05) with the physical parameters. Two ML models were developed using the NIR (Model 1), and RoboBEER (Model 2) data as inputs to predict the relative quantification of 54 proteins. Proteins in the 0–20 kDa group were negatively correlated with the maximum volume of foam (MaxVol; r = −0.57) and total lifetime of foam (TLTF; r = −0.58), while those within 20–40 kDa had a positive correlation with MaxVol (r = 0.47) and TLTF (r = 0.47). Model 1 was not as accurate (testing r = 0.68; overall r = 0.89) as Model 2 (testing r = 0.90; overall r = 0.93), which may serve as a reliable and affordable method to incorporate the relative quantification of important proteins to explain beer quality.
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24
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Knopf JD, Landscheidt N, Pegg CL, Schulz BL, Kühnle N, Chao CW, Huck S, Lemberg MK. Intramembrane protease RHBDL4 cleaves oligosaccharyltransferase subunits to target them for ER-associated degradation. J Cell Sci 2020; 133:jcs243790. [PMID: 32005703 DOI: 10.1242/jcs.243790] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 01/21/2020] [Indexed: 08/31/2023] Open
Abstract
The endoplasmic reticulum (ER)-resident intramembrane rhomboid protease RHBDL4 generates metastable protein fragments and together with the ER-associated degradation (ERAD) machinery provides a clearance mechanism for aberrant and surplus proteins. However, the endogenous substrate spectrum and with that the role of RHBDL4 in physiological ERAD is mainly unknown. Here, we use a substrate trapping approach in combination with quantitative proteomics to identify physiological RHBDL4 substrates. This revealed oligosaccharyltransferase (OST) complex subunits such as the catalytic active subunit STT3A as substrates for the RHBDL4-dependent ERAD pathway. RHBDL4-catalysed cleavage inactivates OST subunits by triggering dislocation into the cytoplasm and subsequent proteasomal degradation. RHBDL4 thereby controls the abundance and activity of OST, suggesting a novel link between the ERAD machinery and glycosylation tuning.
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Affiliation(s)
- Julia D Knopf
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Nina Landscheidt
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Cassandra L Pegg
- School of Chemistry and Molecular Biosciences, ARC Training Centre for Biopharmaceutical Innovation, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Benjamin L Schulz
- School of Chemistry and Molecular Biosciences, ARC Training Centre for Biopharmaceutical Innovation, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Nathalie Kühnle
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Chao-Wei Chao
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Simon Huck
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Marius K Lemberg
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
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25
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Zacchi LF, Recinos DR, Otte E, Aitken C, Hunt T, Sandford V, Lee YY, Schulz BL, Howard CB. S-Trap Eliminates Cell Culture Media Polymeric Surfactants for Effective Proteomic Analysis of Mammalian Cell Bioreactor Supernatants. J Proteome Res 2020; 19:2149-2158. [DOI: 10.1021/acs.jproteome.0c00106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lucia F. Zacchi
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Dinora Roche Recinos
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Queensland 4072, Australia
- CSL Limited, Parkville, Victoria 3052, Australia
| | - Ellen Otte
- CSL Limited, Parkville, Victoria 3052, Australia
| | | | - Tony Hunt
- CSL Limited, Parkville, Victoria 3052, Australia
| | | | - Yih Yean Lee
- CSL Limited, Parkville, Victoria 3052, Australia
| | - Benjamin L. Schulz
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Queensland 4072, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Christopher B. Howard
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Queensland 4072, Australia
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Zhou C, Schulz BL. Glycopeptide variable window SWATH for improved data independent acquisition glycoprotein analysis. Anal Biochem 2020; 597:113667. [PMID: 32119847 DOI: 10.1016/j.ab.2020.113667] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 02/24/2020] [Accepted: 02/26/2020] [Indexed: 01/06/2023]
Abstract
N-glycosylation plays an essential role in regulating protein folding and function in eukaryotic cells. Sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH) has proven useful as a data independent acquisition (DIA) MS method for analysis of glycoproteins and their glycan modifications. By separating the entire m/z range into consecutive isolation windows, DIA-MS allows comprehensive MS data acquisition and high-sensitivity detection of molecules of interest. Variable width DIA windows allow optimal analyte measurement, as peptide ions are not evenly distributed across the full m/z range. However, the m/z distribution of glycopeptides is different to that of unmodified peptides because of their large glycan structures. Here, we improved the performance of DIA glycoproteomics by using variable width windows optimized for glycopeptides. This method allocates narrow windows at m/z ranges rich in glycopeptides, improving analytical specificity and performance. We show that related glycoforms must fall in separate windows to allow accurate glycopeptide measurement. We demonstrate the utility of the method by comparing the cell wall glycoproteomes of wild-type and N-glycan biosynthesis deficient yeast and showing improved measurement of glycopeptides with different glycan structures. Our results highlight the importance of appropriately optimized DIA methods for measurement of post-translationally modified peptides.
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Affiliation(s)
- Chun Zhou
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, 4072, Queensland, Australia
| | - Benjamin L Schulz
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, 4072, Queensland, Australia; Australian Infectious Disease Research Centre, The University of Queensland, St Lucia, 4072, Queensland, Australia; Centre for Biopharmaceutical Innovation, Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, St Lucia, 4072, Queensland, Australia.
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Midorikawa R, Takakura D, Morise J, Wakazono Y, Kawasaki N, Oka S, Takamiya K. Monitoring the glycosylation of α-amino-3-hydroxy-5-methyl-4-isoxazole-propionate-type glutamate receptors using specific antibodies reveals a novel regulatory mechanism of N-glycosylation occupancy by molecular chaperones in mice. J Neurochem 2020; 153:567-585. [PMID: 31958346 DOI: 10.1111/jnc.14964] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 01/11/2020] [Accepted: 01/13/2020] [Indexed: 01/11/2023]
Abstract
In the mammalian nervous system, protein N-glycosylation plays an important role in neuronal physiology. In this study, we performed a comprehensive N-glycosylation analysis of mouse GluA1, one of the major subunits of α-amino-3-hydroxy-5-methyl-4-isoxazole-propionate type glutamate receptor, which possesses six potential N-glycosylation sites in the N-terminal domain. By mass spectrometry-based analysis, we identified the N-glycoforms and semiquantitatively determined the site-specific N-glycosylation occupancy of GluA1. In addition, only the N401-glycosylation site demonstrated incomplete N-glycosylation occupancy. Therefore, we generated a peptide antibody that specifically detects the N401-glycan-free form to precisely quantify N401-glycosylation occupancy. Using this antibody, we clarified that N401 occupancy varies between cell types and increases in an age-dependent manner in mouse forebrains. To address the regulatory mechanism of N401-glycosylation, binding proteins of GluA1 around the N401 site were screened. HSP70 family proteins, including Bip, were identified as candidates. Bip has been known as a molecular chaperone that plays a key role in protein folding in the ER (endoplasmic reticulum). To examine the involvement of Bip in N401-glycosylation, the effect of Bip over-expression on N401 occupancy was evaluated in HEK293T cells, and the results demonstrated Bip increases the N401 glycan-free form by mediating selective prolongation of its protein half-life. Taken together, we propose that the N401-glycosite of GluA1 receives a unique control of modification, and we also propose a novel N-glycosylation occupancy regulatory mechanism by Bip that might be associated with α-amino-3-hydroxy-5-methyl-4-isoxazole-propionate receptors function in the brain.
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Affiliation(s)
- Ryosuke Midorikawa
- Department of Neuroscience, University of Miyazaki Faculty of Medicine, Miyazaki, Japan
| | - Daisuke Takakura
- Project for Utilizing Glycans in the Development of Innovative Drug Discovery Technologies, Shinanomachi Research Park, Keio University School of Medicine, Tokyo, Japan
| | - Jyoji Morise
- Department of Biological Chemistry, Human Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshihiko Wakazono
- Department of Neuroscience, University of Miyazaki Faculty of Medicine, Miyazaki, Japan
| | - Nana Kawasaki
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Shogo Oka
- Department of Biological Chemistry, Human Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kogo Takamiya
- Department of Neuroscience, University of Miyazaki Faculty of Medicine, Miyazaki, Japan
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28
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Abstract
Nontypeable Haemophilus influenzae (NTHi) is a leading cause of respiratory tract infections worldwide and continues to be a global health burden. Adhesion and colonization of host cells are crucial steps in bacterial pathogenesis, and in many strains of NTHi, the interaction with the host is mediated by the high molecular weight adhesins HMW1A and HMW2A. These adhesins are N-glycoproteins that are modified by cytoplasmic glycosyltransferases HMW1C and HMW2C. Phase variation in the number of short sequence repeats in the promoters of hmw1A and hmw2A directly affects their expression. Here, we report the presence of similar variable repeat elements in the promoters of hmw1C and hmw2C in diverse NTHi isolates. In an ex vivo assay, we systematically altered the substrate and glycosyltransferase expression and showed that both of these factors quantitatively affected the site-specific efficiency of glycosylation on HMW-A. This represents a novel mechanism through which phase variation can generate diversity in the quantitative extent of site-specific post-translational modifications on antigenic surface proteins. Glycosylation occupancy was incomplete at many sites, variable between sites, and generally lower close to the C-terminus of HMW-A. We investigated the causes of this variability. As HMW-C glycosylates HMW-A in the cytoplasm, we tested how secretion affected glycosylation on HMW-A and showed that retaining HMW-A in the cytoplasm indeed increased glycosylation occupancy across the full length of the protein. Site-directed mutagenesis showed that HMW-C had no inherent preference for glycosylating asparagines in NxS or NxT sequons. This work provides key insights into factors contributing to the heterogenous modifications of NTHi HMW-A adhesins, expands knowledge of NTHi population diversity and pathogenic capability, and is relevant to vaccine design for NTHi and related pathogens.
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Tahir MS, Nguyen LT, Schulz BL, Boe-Hansen GA, Thomas MG, Moore SS, Lau LY, Fortes MRS. Proteomics Recapitulates Ovarian Proteins Relevant to Puberty and Fertility in Brahman Heifers ( Bos indicus L.). Genes (Basel) 2019; 10:E923. [PMID: 31726744 PMCID: PMC6895798 DOI: 10.3390/genes10110923] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 11/06/2019] [Indexed: 12/16/2022] Open
Abstract
High fertility and early puberty in Bos indicus heifers are desirable and genetically correlated traits in beef production. The hypothalamus-pituitary-ovarian (HPO) axis synthesizes steroid hormones, which contribute to the shift from the pre-pubertal state into the post-pubertal state and influence subsequent fertility. Understanding variations in abundance of proteins that govern steroid synthesis and ovarian signaling pathways remains crucial to understanding puberty and fertility. We used whole ovaries of six pre-pubertal and six post-pubertal Brahman heifers to conduct differential abundance analyses of protein profiles between the two physiological states. Extracted proteins were digested into peptides followed by identification and quantification with massspectrometry (MS) by sequential window acquisition of all instances of theoretical fragment ion mass spectrometry (SWATH-MS). MS and statistical analysis identified 566 significantly differentially abundant (DA) proteins (adjusted p < 0.05), which were then analyzed for gene ontology and pathway enrichment. Our data indicated an up-regulation of steroidogenic proteins contributing to progesterone synthesis at luteal phase post-puberty. Proteins related to progesterone signaling, TGF-β, retinoic acid, extracellular matrix, cytoskeleton, and pleiotrophin signaling were DA in this study. The DA proteins probably relate to the formation and function of the corpus luteum, which is only present after ovulation, post-puberty. Some DA proteins might also be related to granulosa cells signaling, which regulates oocyte maturation or arrest in ovaries prior to ovulation. Ten DA proteins were coded by genes previously associated with reproductive traits according to the animal quantitative trait loci (QTL) database. In conclusion, the DA proteins and their pathways were related to ovarian activity in Bos indicus cattle. The genes that code for these proteins may explain some known QTLs and could be targeted in future genetic studies.
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Affiliation(s)
- Muhammad S. Tahir
- School of Chemistry and Molecular Bioscience, University of Queensland, Brisbane 4072, Queensland, Australia; (M.S.T.); (B.L.S.); (L.Y.L.)
| | - Loan T. Nguyen
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Queensland, Australia; (L.T.N.); (S.S.M.)
| | - Benjamin L. Schulz
- School of Chemistry and Molecular Bioscience, University of Queensland, Brisbane 4072, Queensland, Australia; (M.S.T.); (B.L.S.); (L.Y.L.)
| | - Gry A. Boe-Hansen
- School of Veterinary Sciences, University of Queensland, Brisbane 4343, Queensland, Australia;
| | - Milton G. Thomas
- Department of Animal Science, Colorado State University, Fort Collins, CO 80523, USA;
| | - Stephen S. Moore
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Queensland, Australia; (L.T.N.); (S.S.M.)
| | - Li Yieng Lau
- School of Chemistry and Molecular Bioscience, University of Queensland, Brisbane 4072, Queensland, Australia; (M.S.T.); (B.L.S.); (L.Y.L.)
| | - Marina R. S. Fortes
- School of Chemistry and Molecular Bioscience, University of Queensland, Brisbane 4072, Queensland, Australia; (M.S.T.); (B.L.S.); (L.Y.L.)
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30
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Zhuang A, Yap FYT, McCarthy D, Leung C, Sourris KC, Penfold SA, Thallas-Bonke V, Coughlan MT, Schulz BL, Forbes JM. Globally elevating the AGE clearance receptor, OST48, does not protect against the development of diabetic kidney disease, despite improving insulin secretion. Sci Rep 2019; 9:13664. [PMID: 31541173 PMCID: PMC6754370 DOI: 10.1038/s41598-019-50221-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 09/09/2019] [Indexed: 01/08/2023] Open
Abstract
The accumulation of advanced glycation end products (AGEs) have been implicated in the development and progression of diabetic kidney disease (DKD). There has been interest in investigating the potential of AGE clearance receptors, such as oligosaccharyltransferase-48 kDa subunit (OST48) to prevent the detrimental effects of excess AGE accumulation seen in the diabetic kidney. Here the objective of the study was to increase the expression of OST48 to examine if this slowed the development of DKD by facilitating the clearance of AGEs. Groups of 8-week-old heterozygous knock-in male mice (n = 9-12/group) over-expressing the gene encoding for OST48, dolichyl-diphosphooligosaccharide-protein glycosyltransferase (DDOST+/-) and litter mate controls were randomised to either (i) no diabetes or (ii) diabetes induced via multiple low-dose streptozotocin and followed for 24 weeks. By the study end, global over expression of OST48 increased glomerular OST48. This facilitated greater renal excretion of AGEs but did not affect circulating or renal AGE concentrations. Diabetes resulted in kidney damage including lower glomerular filtration rate, albuminuria, glomerulosclerosis and tubulointerstitial fibrosis. In diabetic mice, tubulointerstitial fibrosis was further exacerbated by global increases in OST48. There was significantly insulin effectiveness, increased acute insulin secretion, fasting insulin concentrations and AUCinsulin observed during glucose tolerance testing in diabetic mice with global elevations in OST48 when compared to diabetic wild-type littermates. Overall, this study suggested that despite facilitating urinary-renal AGE clearance, there were no benefits observed on kidney functional and structural parameters in diabetes afforded by globally increasing OST48 expression. However, the improvements in insulin secretion seen in diabetic mice with global over-expression of OST48 and their dissociation from effects on kidney function warrant future investigation.
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Affiliation(s)
- Aowen Zhuang
- Glycation and Diabetes Complications, Mater Research Institute, The University of Queensland, Translational Research Institute, Woolloongabba, Australia.,School of Medicine, University of Queensland, St Lucia, Australia
| | - Felicia Y T Yap
- Baker IDI Heart and Diabetes Institute, Melbourne, Australia.,Department of Immunology, Central and Eastern Clinical School, AMREP Precinct, Monash University, Melbourne, Australia
| | - Domenica McCarthy
- Glycation and Diabetes Complications, Mater Research Institute, The University of Queensland, Translational Research Institute, Woolloongabba, Australia
| | - Chris Leung
- Department of Medicine, University of Melbourne, Austin Hospital, Heidelberg, Australia
| | - Karly C Sourris
- Baker IDI Heart and Diabetes Institute, Melbourne, Australia
| | - Sally A Penfold
- Baker IDI Heart and Diabetes Institute, Melbourne, Australia
| | | | | | - Benjamin L Schulz
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Australia
| | - Josephine M Forbes
- Glycation and Diabetes Complications, Mater Research Institute, The University of Queensland, Translational Research Institute, Woolloongabba, Australia. .,School of Medicine, University of Queensland, St Lucia, Australia. .,Mater Clinical School, University of Queensland, St Lucia, Australia.
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31
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Kerr ED, Caboche CH, Schulz BL. Posttranslational Modifications Drive Protein Stability to Control the Dynamic Beer Brewing Proteome. Mol Cell Proteomics 2019; 18:1721-1731. [PMID: 31186289 PMCID: PMC6731079 DOI: 10.1074/mcp.ra119.001526] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/03/2019] [Indexed: 12/20/2022] Open
Abstract
Mashing is a key step in beer brewing in which starch and proteins are solubilized from malted barley in a hot water extraction and digested to oligomaltose and free amino nitrogen. We used SWATH-MS to measure the abundance and site-specific modifications of proteins throughout a small-scale pale ale mash. Proteins extracted from the malt at low temperatures early in the mash decreased precipitously in abundance at higher temperatures late in the mash due to temperature/time-induced unfolding and aggregation. We validated these observations using experimental manipulation of time and temperature parameters in a microscale pale ale mash. Correlation analysis of temperature/time-dependent abundance showed that sequence and structure were the main features that controlled protein abundance profiles. Partial proteolysis by barley proteases was common early in the mash. The resulting proteolytically clipped proteins were particularly sensitive and were preferentially lost at high temperatures late in the mash, while intact proteins remained soluble. The beer brewing proteome is therefore driven by the interplay between protein solubilization and proteolysis, which are in turn determined by barley variety, growth conditions, and brewing process parameters.
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Affiliation(s)
- Edward D Kerr
- ‡School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia 4072, Queensland, Australia.; §Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane 4072, Australia
| | - Christopher H Caboche
- ‡School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia 4072, Queensland, Australia.; §Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane 4072, Australia
| | - Benjamin L Schulz
- ‡School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia 4072, Queensland, Australia.; §Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane 4072, Australia.; ¶Centre for Biopharmaceutical Innovation, Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, St. Lucia 4072, Queensland, Australia.
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32
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Ivleva VB, Cooper JW, Arnold FJ, Lei QP. Overcoming Challenges in Structural Characterization of HIV-1 Envelope Glycoprotein by LC-MS/MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1663-1678. [PMID: 31111416 PMCID: PMC7476438 DOI: 10.1007/s13361-019-02225-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 04/05/2019] [Accepted: 04/10/2019] [Indexed: 05/30/2023]
Abstract
Characterization of HIV Env glycoprotein with 28 glycosylation sites is the essential step of structure-based vaccine design programs. A comprehensive LC-MS/MS peptide mapping analysis was applied to assess the primary sequence, glycosylation profiles, and glycosite occupancy of Env to ensure the adequate mimicking of the native immunogen. Another structural feature was reported, related to its cleaved subunits within the trimeric assembly. We bring attention to the importance of thorough inspection of the results generated by the informatics tools which are currently available for the biopharmaceutical characterization. The complexity of Env translates into a vast amount of data with occasional information gaps that could not possibly be filled by means of the automatic data analysis. A series of data validation steps was applied, followed by the illustrations on how the high-quality results may be misinterpreted. It was shown that the glycan sites can only be characterized to a certain limit, and that any claim of full structural characterization of this molecule beyond these limits should be treated with caution. Following the result verification, the percent glycan occupancy was reported for 25 N-glycan sites, including 3 critical antibody-recognition sites. The exact glycan profiles were provided for 20 individual sites, whereas only the glycosylation type could be deduced for 5 sites, dictated by their location within Env sequence. The distribution of the unprocessed high mannose-type glycans correlated with the expected "mannose patch." Experimental procedure optimization and a workflow for glycan characterization with a focus on stringent data testing are presented in the current study.
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Affiliation(s)
- Vera B Ivleva
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9 West Watkins Mill Rd., Gaithersburg, MD, 20878, USA
| | - Jonathan W Cooper
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9 West Watkins Mill Rd., Gaithersburg, MD, 20878, USA
| | - Frank J Arnold
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9 West Watkins Mill Rd., Gaithersburg, MD, 20878, USA
| | - Q Paula Lei
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9 West Watkins Mill Rd., Gaithersburg, MD, 20878, USA.
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33
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Kerr ED, Phung TK, Caboche CH, Fox GP, Platz GJ, Schulz BL. The intrinsic and regulated proteomes of barley seeds in response to fungal infection. Anal Biochem 2019; 580:30-35. [PMID: 31181183 DOI: 10.1016/j.ab.2019.06.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/03/2019] [Accepted: 06/03/2019] [Indexed: 01/14/2023]
Abstract
Barley is an important cereal grain used for beer brewing, animal feed, and human food consumption. Fungal disease can impact barley production, as it causes substantial yield loss and lowers seed quality. We used sequential window acquisition of all theoretical ions mass spectrometry (SWATH-MS) to measure and quantify the relative abundance of proteins within seeds of different barley varieties under various fungal pathogen burdens (ProteomeXchange Datasets PXD011303 and PXD014093). Fungal burden in the leaves and stems of barley resulted in changes to the seed proteome. However, these changes were minimal and showed substantial variation among barley samples infected with different pathogens. The limited effect of intrinsic disease resistance on the seed proteome is consistent with the main mediators of disease resistance being present in the leaves and stems of the plant. The seeds of barley varieties accredited for use as malt had higher levels of proteins associated with starch synthesis and beer quality. The proteomic workflows developed and implemented here have potential application in quality control, breeding and processing of barley, and other agricultural products.
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Affiliation(s)
- Edward D Kerr
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, 4072, Queensland, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, 4072, Australia
| | - Toan K Phung
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, 4072, Queensland, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, 4072, Australia
| | - Christopher H Caboche
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, 4072, Queensland, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, 4072, Australia
| | - Glen P Fox
- Centre for Nutrition and Food Sciences, Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, 4072, Queensland, Australia
| | - Greg J Platz
- Department of Agriculture & Fisheries, Hermitage Research Facility, Warwick, 4370, Queensland, Australia
| | - Benjamin L Schulz
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, 4072, Queensland, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, 4072, Australia; Centre for Biopharmaceutical Innovation, Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, St Lucia, 4072, Queensland, Australia.
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Enculescu C, Kerr ED, Yeo KYB, Schenk G, Fortes MRS, Schulz BL. Proteomics Reveals Profound Metabolic Changes in the Alcohol Use Disorder Brain. ACS Chem Neurosci 2019; 10:2364-2373. [PMID: 30807102 DOI: 10.1021/acschemneuro.8b00660] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Changes in brain metabolism are a hallmark of alcohol use disorder (AUD). Determining how AUD changes the brain proteome is critical for understanding the effects of alcohol consumption on biochemical processes in the brain. We used data-independent acquisition mass spectrometry proteomics to study differences in the abundance of proteins associated with AUD in prefrontal lobe and motor cortex from autopsy brain. AUD had a substantial effect on the overall brain proteome exceeding the inherent differences between brain regions. Proteins associated with glycolysis, trafficking, the cytoskeleton, and excitotoxicity were altered in abundance in AUD. We observed extensive changes in the abundance of key metabolic enzymes, consistent with a switch from glucose to acetate utilization in the AUD brain. We propose that metabolic adaptations allowing efficient acetate utilization contribute to ethanol dependence in AUD.
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Affiliation(s)
- Charmaine Enculescu
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Australia
| | - Edward D. Kerr
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Australia
| | - K. Y. Benjamin Yeo
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Australia
| | - Marina R. S. Fortes
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Australia
| | - Benjamin L. Schulz
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Australia
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Zou W, Schulz BL, Tan X, Sissons M, Warren FJ, Gidley MJ, Gilbert RG. The role of thermostable proteinaceous α-amylase inhibitors in slowing starch digestion in pasta. Food Hydrocoll 2019. [DOI: 10.1016/j.foodhyd.2018.12.023] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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36
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Liu G, Gilding EK, Kerr ED, Schulz BL, Tabet B, Hamaker BR, Godwin ID. Increasing protein content and digestibility in sorghum grain with a synthetic biology approach. J Cereal Sci 2019. [DOI: 10.1016/j.jcs.2018.11.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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37
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Abstract
Flocculation is one of the most important characteristics of brewing yeast as it allows for the easy and cheap removal of cells after fermentation. The genes responsible for both the Flo1 and NewFlo flocculation phenotypes are well characterized. However, the relationship between Flo protein abundance and flocculation efficiency is poorly understood. In this present study, we used mass spectrometry proteomics to compare the cell wall and whole cell proteomes of commercial yeast strains with diverse flocculation behaviors. We found that the relative abundance of Flo1/5 or Flo10 in the cell wall was correlated with the ability of these yeast strains to flocculate. Analysis of whole cell proteomes identified differences in the proteomes of yeast strains and identified the potential for high metabolic diversity. Characterization of the cell wall and whole cell proteomes during fermentation showed high levels of Flo10 in cells that settled early during fermentation. Our data reveal the diversity of the cell wall and global proteomes of brewing yeast, highlighting the potential biochemical diversity present in yeast that can be utilized in the production of fermented beverages.
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Fortes MRS, Zacchi LF, Nguyen LT, Raidan F, Weller MMDCA, Choo JJY, Reverter A, Rego JPA, Boe-Hansen GB, Porto-Neto LR, Lehnert SA, Cánovas A, Schulz BL, Islas-Trejo A, Medrano JF, Thomas MG, Moore SS. Pre- and post-puberty expression of genes and proteins in the uterus of Bos indicus heifers: the luteal phase effect post-puberty. Anim Genet 2018; 49:539-549. [PMID: 30192028 DOI: 10.1111/age.12721] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2018] [Indexed: 12/17/2022]
Abstract
Progesterone signaling and uterine function are crucial in terms of pregnancy establishment. To investigate how the uterine tissue and its secretion changes in relation to puberty, we sampled tissue and uterine fluid from six pre- and six post-pubertal Brahman heifers. Post-pubertal heifers were sampled in the luteal phase. Gene expression of the uterine tissue was investigated with RNA-sequencing, whereas the uterine fluid was used for protein profiling with mass spectrometry. A total of 4034 genes were differentially expressed (DE) at a nominal P-value of 0.05, and 26 genes were significantly DE after Bonferroni correction (P < 3.1 × 10-6 ). We also identified 79 proteins (out of 230 proteins) that were DE (P < 1 × 10-5 ) in the uterine fluid. When we compared proteomics and transcriptome results, four DE proteins were identified as being encoded by DE genes: OVGP1, GRP, CAP1 and HBA. Except for CAP1, the other three had lower expression post-puberty. The function of these four genes hypothetically related to preparation of the uterus for a potential pregnancy is discussed in the context of puberty. All DE genes and proteins were also used in pathway and ontology enrichment analyses to investigate overall function. The DE genes were enriched for terms related to ribosomal activity. Transcription factors that were deemed key regulators of DE genes are also reported. Transcription factors ZNF567, ZNF775, RELA, PIAS2, LHX4, SOX2, MEF2C, ZNF354C, HMG20A, TCF7L2, ZNF420, HIC1, GTF3A and two novel genes had the highest regulatory impact factor scores. These data can help to understand how puberty influences uterine function.
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Affiliation(s)
- M R S Fortes
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - L F Zacchi
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - L T Nguyen
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia.,Faculty of Biotechnology, Vietnam National University of Agriculture, Gialam, Hanoi, Vietnam
| | - F Raidan
- Animal Science Department, Universidade Federal de Viçosa, Vicosa, Minas Gerais, 36570-900, Brazil
| | - M M D C A Weller
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, Brisbane, QLD 4072, Australia
| | - J J Y Choo
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - A Reverter
- Animal Science Department, Universidade Federal de Viçosa, Vicosa, Minas Gerais, 36570-900, Brazil
| | - J P A Rego
- Instituto Federal de Educação, Ciência e Tecnologia do Ceara, Fortaleza, Ceará, 62930-000, Brazil
| | - G B Boe-Hansen
- School of Veterinary Sciences, The University of Queensland, Gatton, QLD 4343, Australia
| | - L R Porto-Neto
- Animal Science Department, Universidade Federal de Viçosa, Vicosa, Minas Gerais, 36570-900, Brazil
| | - S A Lehnert
- Animal Science Department, Universidade Federal de Viçosa, Vicosa, Minas Gerais, 36570-900, Brazil
| | - A Cánovas
- Department of Animal Biosciences, Centre of Genetic Improvement for Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - B L Schulz
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - A Islas-Trejo
- Department of Animal Science, University of California Davis, Davis, CA, 95616, USA
| | - J F Medrano
- Department of Animal Science, University of California Davis, Davis, CA, 95616, USA
| | - M G Thomas
- Department of Animal Science, Colorado State University, Fort Collins, CO, 80523, USA
| | - S S Moore
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
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39
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Tan X, Sullivan MA, Nada SS, Deng B, Schulz BL, Gilbert RG. Proteomic Investigation of the Binding Agent between Liver Glycogen β Particles. ACS OMEGA 2018; 3:3640-3645. [PMID: 30023874 PMCID: PMC6045358 DOI: 10.1021/acsomega.8b00119] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 03/22/2018] [Indexed: 06/08/2023]
Abstract
Glycogen is a highly branched glucose polymer which plays an important role in glucose storage and the maintenance of blood sugar homeostasis. The dimeric protein glycogenin can self-glucosylate to act as a primer for glycogen synthesis, eventually resulting in small (∼20 nm diameter) glycogen β particles with a dimer of glycogenin at their core. In the liver, glycogen is also found in the form of α particles: large bound composites of many β particles. Here, we provide evidence using qualitative and quantitative proteomics and size-exclusion chromatography from healthy rat, mouse, and human liver glycogen that glycogenin is the binding agent linking β particles together into α particles.
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Affiliation(s)
- Xinle Tan
- Joint
International Research Laboratory of Agriculture and Agri-Product
Safety, College of Agriculture, Yangzhou
University, Yangzhou 225009, Jiangsu Province, China
- School of Chemistry and Molecular
Biosciences and Centre for Nutrition and Food Sciences,
Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland 4072, Australia
- Tongji
School of Pharmacy and Department of Pharmacy, Union Hospital, Tongji Medical
College, Huazhong University of Science
and Technology, Wuhan, Hubei 430030, China
| | - Mitchell A. Sullivan
- Glycation
and Diabetes, Mater Research Institute, Translational Research Institute, The University of Queensland, Brisbane, Queensland 4102, Australia
| | - Sharif S. Nada
- School of Chemistry and Molecular
Biosciences and Centre for Nutrition and Food Sciences,
Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Bin Deng
- Tongji
School of Pharmacy and Department of Pharmacy, Union Hospital, Tongji Medical
College, Huazhong University of Science
and Technology, Wuhan, Hubei 430030, China
| | - Benjamin L. Schulz
- School of Chemistry and Molecular
Biosciences and Centre for Nutrition and Food Sciences,
Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Robert G. Gilbert
- Joint
International Research Laboratory of Agriculture and Agri-Product
Safety, College of Agriculture, Yangzhou
University, Yangzhou 225009, Jiangsu Province, China
- School of Chemistry and Molecular
Biosciences and Centre for Nutrition and Food Sciences,
Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland 4072, Australia
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40
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Ruhaak LR, Xu G, Li Q, Goonatilleke E, Lebrilla CB. Mass Spectrometry Approaches to Glycomic and Glycoproteomic Analyses. Chem Rev 2018; 118:7886-7930. [PMID: 29553244 DOI: 10.1021/acs.chemrev.7b00732] [Citation(s) in RCA: 253] [Impact Index Per Article: 42.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Glycomic and glycoproteomic analyses involve the characterization of oligosaccharides (glycans) conjugated to proteins. Glycans are produced through a complicated nontemplate driven process involving the competition of enzymes that extend the nascent chain. The large diversity of structures, the variations in polarity of the individual saccharide residues, and the poor ionization efficiencies of glycans all conspire to make the analysis arguably much more difficult than any other biopolymer. Furthermore, the large number of glycoforms associated with a specific protein site makes it more difficult to characterize than any post-translational modification. Nonetheless, there have been significant progress, and advanced separation and mass spectrometry methods have been at its center and the main reason for the progress. While glycomic and glycoproteomic analyses are still typically available only through highly specialized laboratories, new software and workflow is making it more accessible. This review focuses on the role of mass spectrometry and separation methods in advancing glycomic and glycoproteomic analyses. It describes the current state of the field and progress toward making it more available to the larger scientific community.
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Affiliation(s)
- L Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine , Leiden University Medical Center , 2333 ZA Leiden , The Netherlands
| | - Gege Xu
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Qiongyu Li
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Elisha Goonatilleke
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Carlito B Lebrilla
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States.,Department of Biochemistry and Molecular Medicine , University of California, Davis , Davis , California 95616 , United States.,Foods for Health Institute , University of California, Davis , Davis , California 95616 , United States
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41
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Schulz BL, Phung TK, Bruschi M, Janusz A, Stewart J, Meehan J, Healy P, Nouwens AS, Fox GP, Vickers CE. Process Proteomics of Beer Reveals a Dynamic Proteome with Extensive Modifications. J Proteome Res 2018; 17:1647-1653. [PMID: 29457908 DOI: 10.1021/acs.jproteome.7b00907] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Modern beer production is a complex industrial process. However, some of its biochemical details remain unclear. Using mass spectrometry proteomics, we have performed a global untargeted analysis of the proteins present across time during nanoscale beer production. Samples included sweet wort produced by a high temperature infusion mash, hopped wort, and bright beer. This analysis identified over 200 unique proteins from barley and yeast, emphasizing the complexity of the process and product. We then used data independent SWATH-MS to quantitatively compare the relative abundance of these proteins throughout the process. This identified large and significant changes in the proteome at each process step. These changes described enrichment of proteins by their biophysical properties, and identified the appearance of dominant yeast proteins during fermentation. Altered levels of malt modification also quantitatively changed the proteomes throughout the process. Detailed inspection of the proteomic data revealed that many proteins were modified by protease digestion, glycation, or oxidation during the processing steps. This work demonstrates the opportunities offered by modern mass spectrometry proteomics in understanding the ancient process of beer production.
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Affiliation(s)
- Benjamin L Schulz
- School of Chemistry and Molecular Biosciences , The University of Queensland , Brisbane , Queensland 4072 , Australia.,ARC Training Centre for Biopharmaceutical Innovation, Australian Institute of Bioengineering and Nanotechnology , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Toan K Phung
- School of Chemistry and Molecular Biosciences , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Michele Bruschi
- Australian Institute of Bioengineering and Nanotechnology , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | | | - Jeff Stewart
- Lion , Sydney , New South Wales 2127 , Australia
| | - John Meehan
- Lion , Brisbane , Queensland 4064 , Australia
| | - Peter Healy
- Lion , Brisbane , Queensland 4064 , Australia
| | - Amanda S Nouwens
- School of Chemistry and Molecular Biosciences , The University of Queensland , Brisbane , Queensland 4072 , Australia.,Australian Institute of Bioengineering and Nanotechnology , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Glen P Fox
- Queensland Alliance for Agriculture and Food Innovation , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Claudia E Vickers
- Australian Institute of Bioengineering and Nanotechnology , The University of Queensland , Brisbane , Queensland 4072 , Australia
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42
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Poljak K, Breitling J, Gauss R, Rugarabamu G, Pellanda M, Aebi M. Analysis of substrate specificity of Trypanosoma brucei oligosaccharyltransferases (OSTs) by functional expression of domain-swapped chimeras in yeast. J Biol Chem 2017; 292:20342-20352. [PMID: 29042445 DOI: 10.1074/jbc.m117.811133] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 10/11/2017] [Indexed: 11/06/2022] Open
Abstract
N-Linked protein glycosylation is an essential and highly conserved post-translational modification in eukaryotes. The transfer of a glycan from a lipid-linked oligosaccharide (LLO) donor to the asparagine residue of a nascent polypeptide chain is catalyzed by an oligosaccharyltransferase (OST) in the lumen of the endoplasmic reticulum (ER). Trypanosoma brucei encodes three paralogue single-protein OSTs called TbSTT3A, TbSTT3B, and TbSTT3C that can functionally complement the Saccharomyces cerevisiae OST, making it an ideal experimental system to study the fundamental properties of OST activity. We characterized the LLO and polypeptide specificity of all three TbOST isoforms and their chimeric forms in the heterologous expression host S. cerevisiae where we were able to apply yeast genetic tools and newly developed glycoproteomics methods. We demonstrated that TbSTT3A accepted LLO substrates ranging from Man5GlcNAc2 to Man7GlcNAc2 In contrast, TbSTT3B required more complex precursors ranging from Man6GlcNAc2 to Glc3Man9GlcNAc2 structures, and TbSTT3C did not display any LLO preference. Sequence differences between the isoforms cluster in three distinct regions. We have swapped the individual regions between different OST proteins and identified region 2 to influence the specificity toward the LLO and region 1 to influence polypeptide substrate specificity. These results provide a basis to further investigate the molecular mechanisms and contribution of single amino acids in OST interaction with its substrates.
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Affiliation(s)
- Kristina Poljak
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - Jörg Breitling
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - Robert Gauss
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - George Rugarabamu
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - Mauro Pellanda
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - Markus Aebi
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland.
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43
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Lin CH, Krisp C, Packer NH, Molloy MP. Development of a data independent acquisition mass spectrometry workflow to enable glycopeptide analysis without predefined glycan compositional knowledge. J Proteomics 2017; 172:68-75. [PMID: 29069609 DOI: 10.1016/j.jprot.2017.10.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 10/16/2017] [Accepted: 10/20/2017] [Indexed: 01/16/2023]
Abstract
Glycoproteomics investigates glycan moieties in a site specific manner to reveal the functional roles of protein glycosylation. Identification of glycopeptides from data-dependent acquisition (DDA) relies on high quality MS/MS spectra of glycopeptide precursors and often requires manual validation to ensure confident assignments. In this study, we investigated pseudo-MRM (MRM-HR) and data-independent acquisition (DIA) as alternative acquisition strategies for glycopeptide analysis. These approaches allow data acquisition over the full MS/MS scan range allowing data re-analysis post-acquisition, without data re-acquisition. The advantage of MRM-HR over DDA for N-glycopeptide detection was demonstrated from targeted analysis of bovine fetuin where all three N-glycosylation sites were detected, which was not the case with DDA. To overcome the duty cycle limitation of MRM-HR acquisition needed for analysis of complex samples such as plasma we trialed DIA. This allowed development of a targeted DIA method to identify N-glycopeptides without pre-defined knowledge of the glycan composition, thus providing the potential to identify N-glycopeptides with unexpected structures. This workflow was demonstrated by detection of 59 N-glycosylation sites from 41 glycoproteins from a HILIC enriched human plasma tryptic digest. 21 glycoforms of IgG1 glycopeptides were identified including two truncated structures that are rarely reported. SIGNIFICANCE We developed a data-independent mass spectrometry workflow to identify specific glycopeptides from complex biological mixtures. The novelty is that this approach does not require glycan composition to be pre-defined, thereby allowing glycopeptides carrying unexpected glycans to be identified. This is demonstrated through the analysis of immunoglobulins in human plasma where we detected two IgG1 glycoforms that are rarely observed.
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Affiliation(s)
- Chi-Hung Lin
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney 2109, Australia; Australian Proteome Analysis Facility, Macquarie University, Sydney 2109, Australia
| | - Christoph Krisp
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney 2109, Australia; Australian Proteome Analysis Facility, Macquarie University, Sydney 2109, Australia
| | - Nicolle H Packer
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney 2109, Australia
| | - Mark P Molloy
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney 2109, Australia; Australian Proteome Analysis Facility, Macquarie University, Sydney 2109, Australia.
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44
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Poljak K, Selevsek N, Ngwa E, Grossmann J, Losfeld ME, Aebi M. Quantitative Profiling of N-linked Glycosylation Machinery in Yeast Saccharomyces cerevisiae. Mol Cell Proteomics 2017; 17:18-30. [PMID: 28993419 DOI: 10.1074/mcp.ra117.000096] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Indexed: 11/06/2022] Open
Abstract
Asparagine-linked glycosylation is a common posttranslational protein modification regulating the structure, stability and function of many proteins. The N-linked glycosylation machinery involves enzymes responsible for the assembly of the lipid-linked oligosaccharide (LLO), which is then transferred to the asparagine residues on the polypeptides by the enzyme oligosaccharyltransferase (OST). A major goal in the study of protein glycosylation is to establish quantitative methods for the analysis of site-specific extent of glycosylation. We developed a sensitive approach to examine glycosylation site occupancy in Saccharomyces cerevisiae by coupling stable isotope labeling (SILAC) approach to parallel reaction monitoring (PRM) mass spectrometry (MS). We combined the method with genetic tools and validated the approach with the identification of novel glycosylation sites dependent on the Ost3p and Ost6p regulatory subunits of OST. Based on the observations that alternations in LLO substrate structure and OST subunits activity differentially alter the systemic output of OST, we conclude that sequon recognition is a direct property of the catalytic subunit Stt3p, auxiliary subunits such as Ost3p and Ost6p extend the OST substrate range by modulating interfering pathways such as protein folding. In addition, our proteomics approach revealed a novel regulatory network that connects isoprenoid lipid biosynthesis and LLO substrate assembly.
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Affiliation(s)
- Kristina Poljak
- From the ‡Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - Nathalie Selevsek
- §Functional Genomics Center Zurich, UZH/ETH Zurich, CH-8057 Zurich, Switzerland
| | - Elsy Ngwa
- From the ‡Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - Jonas Grossmann
- §Functional Genomics Center Zurich, UZH/ETH Zurich, CH-8057 Zurich, Switzerland
| | - Marie Estelle Losfeld
- From the ‡Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - Markus Aebi
- From the ‡Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland;
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45
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Zhang X, Walsh T, Atherton JJ, Kostner K, Schulz B, Punyadeera C. Identification and Validation of a Salivary Protein Panel to Detect Heart Failure Early. Am J Cancer Res 2017; 7:4350-4358. [PMID: 29158831 PMCID: PMC5695135 DOI: 10.7150/thno.21727] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 08/24/2017] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Over 26 million people suffer from heart failure (HF) globally. Current diagnosis of HF relies on clinical evaluation, blood assays and imaging techniques. Our aim is to develop a diagnostic assay to detect HF in at risk individuals within the community using human saliva as a medium, potentially leading to a simple, safe early warning system. METHODS Saliva samples were collected from healthy controls (n=36) and HF patients (n=75). Salivary proteome profiles were analysed by Sequential Window Acquisition of All Theoretical fragment ion spectra - Mass Spectrometry (SWATH-MS). A total of 738 proteins were quantified and 177 proteins demonstrated significant differences between HF patients and healthy controls. Candidate biomarkers were chosen based on their abundance and difference between the two cohorts. A multi-protein panel was developed using logistic regression analysis. The diagnostic performance of the multi-protein panel was assessed using receiver operative characteristic curves. The candidate proteins were further confirmed, using western blot analysis, and validated technically, using an independent biological cohort. RESULTS A group of six proteins were chosen in the discovery phase as potential candidates based on their differences in the abundance between the two cohorts. During the validation phase, two of the proteins were not detected with western blotting and as such were removed. The final panel consists of four proteins with sensitivity of 83.3%, specificity of 62.5% with an area under ROC curve of 0.78 in discriminating healthy controls from NYHA class I/II HF patients, and was validated in a second independent cohort study. CONCLUSION Analysis of salivary proteome using SWATH-MS revealed novel HF-specific protein candidates yielding high diagnostic performance. A multi-centre longitudinal clinical trial will be the next step before clinical implementation of this panel.
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46
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Zhuang A, Yap FY, Bruce C, Leung C, Plan MR, Sullivan MA, Herath C, McCarthy D, Sourris KC, Kantharidis P, Coughlan MT, Febbraio MA, Hodson MP, Watt MJ, Angus P, Schulz BL, Forbes JM. Increased liver AGEs induce hepatic injury mediated through an OST48 pathway. Sci Rep 2017; 7:12292. [PMID: 28947796 PMCID: PMC5612946 DOI: 10.1038/s41598-017-12548-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 09/11/2017] [Indexed: 12/13/2022] Open
Abstract
The protein oligosaccharyltransferase-48 (OST48) is integral to protein N-glycosylation in the endoplasmic reticulum (ER) but is also postulated to act as a membrane localised clearance receptor for advanced glycation end-products (AGE). Hepatic ER stress and AGE accumulation are each implicated in liver injury. Hence the objective of this study was to increase the expression of OST48 and examine the effects on hepatic function and structure. Groups of 8 week old male mice (n = 10-12/group) over-expressing the gene for OST48, dolichyl-diphosphooligosaccharide-protein glycosyltransferase (DDOST+/-), were followed for 24 weeks, while randomised to diets either low or high in AGE content. By week 24 of the study, either increasing OST48 expression or consumption of high AGE diet impaired liver function and modestly increased hepatic fibrosis, but their combination significantly exacerbated liver injury in the absence of steatosis. DDOST+/- mice had increased both portal delivery and accumulation of hepatic AGEs leading to central adiposity, insulin secretory defects, shifted fuel usage to fatty and ketoacids, as well as hepatic glycogen accumulation causing hepatomegaly along with hepatic ER and oxidative stress. This study revealed a novel role of the OST48 and AGE axis in hepatic injury through ER stress, changes in fuel utilisation and glucose intolerance.
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Affiliation(s)
- Aowen Zhuang
- Glycation and Diabetes, Mater Research Institute - The University of Queensland, Translational Research Institute, Woolloongabba, Australia
- School of Medicine, University of Queensland, St Lucia, Australia
| | - Felicia Yt Yap
- Diabetic Complications Group, Baker IDI Heart and Diabetes Institute, Melbourne, Australia
- Department of Immunology and Medicine, Central and Eastern Clinical School, AMREP Precinct, Monash University, Clayton, Australia
| | - Clinton Bruce
- Institute for Physical Activity and Nutrition (IPAN), Deakin University, Burwood, Australia
| | - Chris Leung
- Department of Medicine, University of Melbourne, Austin Hospital, Heidelberg, Australia
| | - Manuel R Plan
- Metabolomics Australia, Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, Australia
| | - Mitchell A Sullivan
- Centre for Nutrition and Food Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, Australia
| | - Chandana Herath
- Department of Medicine, University of Melbourne, Austin Hospital, Heidelberg, Australia
| | - Domenica McCarthy
- Glycation and Diabetes, Mater Research Institute - The University of Queensland, Translational Research Institute, Woolloongabba, Australia
| | - Karly C Sourris
- Diabetic Complications Group, Baker IDI Heart and Diabetes Institute, Melbourne, Australia
- Department of Immunology and Medicine, Central and Eastern Clinical School, AMREP Precinct, Monash University, Clayton, Australia
| | - Phillip Kantharidis
- Diabetic Complications Group, Baker IDI Heart and Diabetes Institute, Melbourne, Australia
| | - Melinda T Coughlan
- Diabetic Complications Group, Baker IDI Heart and Diabetes Institute, Melbourne, Australia
- Department of Immunology and Medicine, Central and Eastern Clinical School, AMREP Precinct, Monash University, Clayton, Australia
| | - Mark A Febbraio
- Diabetic Complications Group, Baker IDI Heart and Diabetes Institute, Melbourne, Australia
| | - Mark P Hodson
- Metabolomics Australia, Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, Australia
- School of Pharmacy, University of Queensland, Woolloongabba, Australia
| | - Matthew J Watt
- Biomedicine Discovery Program and the Department of Physiology, Monash University, Clayton, Australia
| | - Peter Angus
- Department of Medicine, University of Melbourne, Austin Hospital, Heidelberg, Australia
| | - Benjamin L Schulz
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Australia
| | - Josephine M Forbes
- Glycation and Diabetes, Mater Research Institute - The University of Queensland, Translational Research Institute, Woolloongabba, Australia.
- Department of Medicine, University of Melbourne, Austin Hospital, Heidelberg, Australia.
- Mater Clinical School, University of Queensland, St Lucia, Australia.
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47
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Yang X, Wang Z, Guo L, Zhu Z, Zhang Y. Proteome-Wide Analysis of N-Glycosylation Stoichiometry Using SWATH Technology. J Proteome Res 2017; 16:3830-3840. [DOI: 10.1021/acs.jproteome.7b00480] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Xiangyun Yang
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiyuan Wang
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lin Guo
- University of Chinese Academy of Sciences, Beijing 100049, China
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48
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Liu T, Shang S, Li W, Qin X, Sun L, Zhang S, Liu Y. Assessment of Hepatocellular Carcinoma Metastasis Glycobiomarkers Using Advanced Quantitative N-glycoproteome Analysis. Front Physiol 2017; 8:472. [PMID: 28736531 PMCID: PMC5500640 DOI: 10.3389/fphys.2017.00472] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 06/21/2017] [Indexed: 12/27/2022] Open
Abstract
Hepatocelluar carcinoma (HCC) is one of the most common malignant tumors with high incidence of metastasis. Glycosylation is involved in fundamental molecular and cell biology process occurring in cancer including metastasis formation. In this study, lectin microarray, lectin blotting, lectin affinity chromatography and tandem 18O stable isotope labeling coupled with liquid chromatography-mass spectrometer (LC-MS) analysis were applied to quantify the changes in N-glycosite occupancy for HCC metastasis serum. Firstly, lectin microarray was used to screen glycoforms and Phaseolus vulgaris Leucoagglutinin (PHA-L) reactive structure (β1,6-GlcNAc branched N-glycan) was found to be increased significantly in HCC patients with metastasis compared with those with non-metastasis. Then, PHA-L affinity glycoproteins were enriched followed by N-glycosite occupancy measurement with strategy of tandem 18O stable isotope labeling. 11 glycoproteins with significantly changed N-glycosite occupancy were identified, they were associated with cell migration, invasion and adhesion through p38 mitogen-activated protein kinase signaling pathway and nuclear factor kappa B signaling pathway. Quantification of N-glycosite occupancy for PHA-L reactive glycoproteins could help to discover important glycoproteins of potential clinically significance in terms of HCC etiology. Also, understanding of N-glycosite occupancy alterations will aid the characterization of molecular mechanism of HCC metastasis as well as establishment of novel glycobiomarkers.
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Affiliation(s)
- Tianhua Liu
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan UniversityShanghai, China.,Institutes of Biomedical Sciences, Fudan UniversityShanghai, China
| | - Shuxin Shang
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical UniversityNanning, China
| | - Wei Li
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan UniversityShanghai, China.,Institutes of Biomedical Sciences, Fudan UniversityShanghai, China
| | - Xue Qin
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical UniversityNanning, China
| | - Lu Sun
- Institutes of Biomedical Sciences, Fudan UniversityShanghai, China
| | - Shu Zhang
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan UniversityShanghai, China
| | - Yinkun Liu
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan UniversityShanghai, China.,Institutes of Biomedical Sciences, Fudan UniversityShanghai, China
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49
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Hu H, Khatri K, Zaia J. Algorithms and design strategies towards automated glycoproteomics analysis. MASS SPECTROMETRY REVIEWS 2017; 36:475-498. [PMID: 26728195 PMCID: PMC4931994 DOI: 10.1002/mas.21487] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 11/30/2015] [Indexed: 05/09/2023]
Abstract
Glycoproteomics involves the study of glycosylation events on protein sequences ranging from purified proteins to whole proteome scales. Understanding these complex post-translational modification (PTM) events requires elucidation of the glycan moieties (monosaccharide sequences and glycosidic linkages between residues), protein sequences, as well as site-specific attachment of glycan moieties onto protein sequences, in a spatial and temporal manner in a variety of biological contexts. Compared with proteomics, bioinformatics for glycoproteomics is immature and many researchers still rely on tedious manual interpretation of glycoproteomics data. As sample preparation protocols and analysis techniques have matured, the number of publications on glycoproteomics and bioinformatics has increased substantially; however, the lack of consensus on tool development and code reuse limits the dissemination of bioinformatics tools because it requires significant effort to migrate a computational tool tailored for one method design to alternative methods. This review discusses algorithms and methods in glycoproteomics, and refers to the general proteomics field for potential solutions. It also introduces general strategies for tool integration and pipeline construction in order to better serve the glycoproteomics community. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:475-498, 2017.
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Affiliation(s)
- Han Hu
- Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, Massachusetts 02118, USA
| | - Kshitij Khatri
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, Massachusetts 02118, USA
| | - Joseph Zaia
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, Massachusetts 02118, USA
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Quantification of N-glycosylation site occupancy status based on labeling/label-free strategies with LC-MS/MS. Talanta 2017; 170:509-513. [PMID: 28501204 DOI: 10.1016/j.talanta.2017.04.053] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 04/18/2017] [Accepted: 04/21/2017] [Indexed: 12/30/2022]
Abstract
Protein N-glycosylation plays important roles in physiological and pathological processes. Characterizing the site-specific N-glycosylation including N-glycan macroheterogeneity (glycosylation site occupancy) and microheterogeneity (site-specific glycan structure) is important for understanding of glycoprotein biosynthesis and function. N-Glycan macroheterogeneity is a physiological property of glycoprotein and the technical obstacles have restricted research into the regulation and functions of this heterogeneity. Quantification of N-glycosylation site occupancy would uncover the critical role of macroheterogeneity in a variety of biological properties. Liquid chromatography (LC)- mass spectrometry (MS)-based quantification is emerging as a powerful tool for glycosylation characterization. This review summarizes the labeling and label-free quantitative MS approaches for quantifying N-glycosylation site occupancy, including its quantification for target glycoproteins in recent years.
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