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Burock R, Cajic S, Hennig R, Buettner FFR, Reichl U, Rapp E. Reliable N-Glycan Analysis-Removal of Frequently Occurring Oligosaccharide Impurities by Enzymatic Degradation. Molecules 2023; 28:molecules28041843. [PMID: 36838829 PMCID: PMC9967028 DOI: 10.3390/molecules28041843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/08/2023] [Accepted: 02/10/2023] [Indexed: 02/18/2023] Open
Abstract
Glycosylation, especially N-glycosylation, is one of the most common protein modifications, with immense importance at the molecular, cellular, and organismal level. Thus, accurate and reliable N-glycan analysis is essential in many areas of pharmaceutical and food industry, medicine, and science. However, due to the complexity of the cellular glycosylation process, in-depth glycoanalysis is still a highly challenging endeavor. Contamination of samples with oligosaccharide impurities (OSIs), typically linear glucose homo-oligomers, can cause further complications. Due to their physicochemical similarity to N-glycans, OSIs produce potentially overlapping signals, which can remain unnoticed. If recognized, suspected OSI signals are usually excluded in data evaluation. However, in both cases, interpretation of results can be impaired. Alternatively, sample preparation can be repeated to include an OSI removal step from samples. However, this significantly increases sample amount, time, and effort necessary. To overcome these issues, we investigated the option to enzymatically degrade and thereby remove interfering OSIs as a final sample preparation step. Therefore, we screened ten commercially available enzymes concerning their potential to efficiently degrade maltodextrins and dextrans as most frequently found OSIs. Of these enzymes, only dextranase from Chaetomium erraticum and glucoamylase P from Hormoconis resinae enabled a degradation of OSIs within only 30 min that is free of side reactions with N-glycans. Finally, we applied the straightforward enzymatic degradation of OSIs to N-glycan samples derived from different standard glycoproteins and various stem cell lysates.
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Affiliation(s)
- Robert Burock
- MPI for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
- glyXera GmbH, Brenneckestraße 20, 39120 Magdeburg, Germany
| | - Samanta Cajic
- MPI for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
- glyXera GmbH, Brenneckestraße 20, 39120 Magdeburg, Germany
| | - René Hennig
- MPI for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
- glyXera GmbH, Brenneckestraße 20, 39120 Magdeburg, Germany
- Correspondence:
| | - Falk F. R. Buettner
- Institute of Clinical Biochemistry, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Udo Reichl
- MPI for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
- Bioprocess Engineering, Otto-von-Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - Erdmann Rapp
- MPI for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
- glyXera GmbH, Brenneckestraße 20, 39120 Magdeburg, Germany
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Cassarini M, Besaury L, Rémond C. Valorisation of wheat bran to produce natural pigments using selected microorganisms. J Biotechnol 2021; 339:81-92. [PMID: 34364925 DOI: 10.1016/j.jbiotec.2021.08.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 11/27/2022]
Abstract
Pigments are compounds with highly diverse structures and wide uses, which production is increasing worldwide. An eco-friendly method of bioproduction is to use the ability of some microorganisms to ferment on renewable carbon sources. Wheat bran (WB) is a cheap and abundant lignocellulosic co-product of low recalcitrance to biological conversion. Microbial candidates with theoretical ability to degrade WB were first preselected using specific databases. The microorganisms were Ashbya gossypii (producing riboflavin), Chitinophaga pinensis (producing flexirubin), Chromobacterium vaccinii (violacein) and Gordonia alkanivorans (carotenoids). Growth was shown for each on minimal salt medium supplemented with WB at 5 g.L-1. Activities of the main enzymes consuming WB were measured, showing leucine amino-peptidase (up to 8.45 IU. mL-1) and β-glucosidase activities (none to 6.44 IU. mL-1). This was coupled to a FTIR (Fourier Transform Infra-Red) study of the WB residues that showed main degradation of the WB protein fraction for C. pinensis, C. vaccinii and G. alkanivorans. Production of the pigments on WB was assessed for all the strains except Ashbya, with values of production reaching up to 1.47 mg.L-1. The polyphasic approach used in this study led to a proof of concept of pigment production from WB as a cheap carbon source.
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Affiliation(s)
- Mathieu Cassarini
- Université de Reims Champagne Ardenne, INRAE, FARE, UMR A 614, Chaire AFERE, 51097, Reims, France.
| | - Ludovic Besaury
- Université de Reims Champagne Ardenne, INRAE, FARE, UMR A 614, Chaire AFERE, 51097, Reims, France.
| | - Caroline Rémond
- Université de Reims Champagne Ardenne, INRAE, FARE, UMR A 614, Chaire AFERE, 51097, Reims, France.
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Harvey DJ. NEGATIVE ION MASS SPECTROMETRY FOR THE ANALYSIS OF N-LINKED GLYCANS. MASS SPECTROMETRY REVIEWS 2020; 39:586-679. [PMID: 32329121 DOI: 10.1002/mas.21622] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 12/13/2019] [Accepted: 12/22/2019] [Indexed: 05/03/2023]
Abstract
N-glycans from glycoproteins are complex, branched structures whose structural determination presents many analytical problems. Mass spectrometry, usually conducted in positive ion mode, often requires extensive sample manipulation, usually by derivatization such as permethylation, to provide the necessary structure-revealing fragment ions. The newer but, so far, lesser used negative ion techniques, on the contrary, provide a wealth of structural information not present in positive ion spectra that greatly simplify the analysis of these compounds and can usually be conducted without the need for derivatization. This review describes the use of negative ion mass spectrometry for the structural analysis of N-linked glycans and emphasises the many advantages that can be gained by this mode of operation. Biosynthesis and structures of the compounds are described followed by methods for release of the glycans from the protein. Methods for ionization are discussed with emphasis on matrix-assisted laser desorption/ionization (MALDI) and methods for producing negative ions from neutral compounds. Acidic glycans naturally give deprotonated species under most ionization conditions. Fragmentation of negative ions is discussed next with particular reference to those ions that are diagnostic for specific features such as the branching topology of the glycans and substitution positions of moieties such as fucose and sulfate, features that are often difficult to identify easily by conventional techniques such as positive ion fragmentation and exoglycosidase digestions. The advantages of negative over positive ions for this structural work are emphasised with an example of a series of glycans where all other methods failed to produce a structure. Fragmentation of derivatized glycans is discussed next, both with respect to derivatives at the reducing terminus of the molecules, and to methods for neutralization of the acidic groups on sialic acids to both stabilize them for MALDI analysis and to produce the diagnostic fragments seen with the neutral glycans. The use of ion mobility, combined with conventional mass spectrometry is described with emphasis on its use to extract clean glycan spectra both before and after fragmentation, to separate isomers and its use to extract additional information from separated fragment ions. A section on applications follows with examples of the identification of novel structures from lower organisms and tables listing the use of negative ions for structural identification of specific glycoproteins, glycans from viruses and uses in the biopharmaceutical industry and in medicine. The review concludes with a summary of the advantages and disadvantages of the technique. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom
- Centre for Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Life Sciences Building 85, Highfield Campus, Southampton, SO17 1BJ, United Kingdom
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Xie C, Gong W, Zhu Z, Zhou Y, Yan L, Hu Z, Ai L, Peng Y. Mapping the Secretome and Its N-Linked Glycosylation of Pleurotus eryngii and Pleurotus ostreatus Grown on Hemp Stalks. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:5486-5495. [PMID: 31012315 DOI: 10.1021/acs.jafc.9b00061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Our previous research showed that Pleurotus eryngii and Pleurotus ostreatus were effective fungi for pretreatment of industrial hemp stalks to improve enzymatic saccharification. The secretomes of these two fungi were analyzed to search for the effective enzyme cocktails degrading hemp lignin during the pretreatment process. In total, 169 and 155 proteins were identified in Pleurotus eryngii and Pleurotus ostreatus, respectively, and 50% of the proteins involved in lignocellulose degradation were CAZymes. Because most of the extracellular proteins secreted by fungi are glycosylated proteins, the N-linked glycosylation of enzymes could be mapped. In total, 27 and 24 N-glycosylated peptides were detected in Pleurotus eryngii and Pleurotus ostreatus secretomes, respectively. N-Glycosylated peptides of laccase, GH92, exoglucanase, phenol oxidase, α-galactosidase, carboxylic ester hydrolase, and pectin lyase were identified. Deglycosylation could decrease enzymatic saccharification of hemp stalks. The activities of laccase, α-galactosidase, and phenol oxidase and the thermal stability of laccase were reduced after deglycosylation.
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Affiliation(s)
- Chunliang Xie
- Institute of Bast Fiber Crops , Chinese Academy of Agricultural Sciences , Changsha 410205 , China
| | - Wenbing Gong
- Institute of Bast Fiber Crops , Chinese Academy of Agricultural Sciences , Changsha 410205 , China
| | - Zuohua Zhu
- Institute of Bast Fiber Crops , Chinese Academy of Agricultural Sciences , Changsha 410205 , China
| | - Yingjun Zhou
- Institute of Bast Fiber Crops , Chinese Academy of Agricultural Sciences , Changsha 410205 , China
| | - Li Yan
- Institute of Bast Fiber Crops , Chinese Academy of Agricultural Sciences , Changsha 410205 , China
| | - Zhenxiu Hu
- Institute of Bast Fiber Crops , Chinese Academy of Agricultural Sciences , Changsha 410205 , China
| | - Lianzhong Ai
- Institute of Bast Fiber Crops , Chinese Academy of Agricultural Sciences , Changsha 410205 , China
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering , University of Shanghai for Science and Technology , Shanghai 200093 , China
| | - Yuande Peng
- Institute of Bast Fiber Crops , Chinese Academy of Agricultural Sciences , Changsha 410205 , China
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2013-2014. MASS SPECTROMETRY REVIEWS 2018; 37:353-491. [PMID: 29687922 DOI: 10.1002/mas.21530] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 11/29/2016] [Indexed: 06/08/2023]
Abstract
This review is the eighth update of the original article published in 1999 on the application of Matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2014. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, and arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly- saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Much of this material is presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. © 2018 Wiley Periodicals, Inc. Mass Spec Rev 37:353-491, 2018.
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Affiliation(s)
- David J Harvey
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom
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Su X, Rehman L, Guo H, Li X, Cheng H. The oligosaccharyl transferase subunit STT3 mediates fungal development and is required for virulence in Verticillium dahliae. Curr Genet 2017; 64:235-246. [DOI: 10.1007/s00294-017-0729-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 07/23/2017] [Accepted: 07/31/2017] [Indexed: 12/20/2022]
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Aguiar TQ, Silva R, Domingues L. New biotechnological applications for Ashbya gossypii: Challenges and perspectives. Bioengineered 2016; 8:309-315. [PMID: 27791453 DOI: 10.1080/21655979.2016.1234543] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The filamentous fungus Ashbya gossypii has long been considered a paradigm of the White Biotechnology in what concerns riboflavin production. Its industrial relevance led to the development of a significant molecular and in silico modeling toolbox for its manipulation. This, together with the increasing knowledge of its genome and metabolism has helped designing effective metabolic engineering strategies for optimizing riboflavin production, but also for developing new A. gossypii strains for novel biotechnological applications, such as production of recombinant proteins, single cell oils (SCOs), and flavour compounds. With the recent availability of its genome-scale metabolic model, the exploration of the full biotechnological potential of A. gossypii is now in the spotlight. Here, we will discuss some of the challenges that these emerging A. gossypii applications still need to overcome to become economically attractive and will present future perspectives for these and other possible biotechnological applications for A. gossypii.
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Affiliation(s)
- Tatiana Q Aguiar
- a CEB - Centre of Biological Engineering , University of Minho , Braga , Portugal
| | - Rui Silva
- a CEB - Centre of Biological Engineering , University of Minho , Braga , Portugal
| | - Lucília Domingues
- a CEB - Centre of Biological Engineering , University of Minho , Braga , Portugal
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Aguiar TQ, Silva R, Domingues L. Ashbya gossypii beyond industrial riboflavin production: A historical perspective and emerging biotechnological applications. Biotechnol Adv 2015; 33:1774-86. [DOI: 10.1016/j.biotechadv.2015.10.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 09/28/2015] [Accepted: 10/04/2015] [Indexed: 10/22/2022]
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Gomes D, Aguiar TQ, Dias O, Ferreira EC, Domingues L, Rocha I. Genome-wide metabolic re-annotation of Ashbya gossypii: new insights into its metabolism through a comparative analysis with Saccharomyces cerevisiae and Kluyveromyces lactis. BMC Genomics 2014; 15:810. [PMID: 25253284 PMCID: PMC4190384 DOI: 10.1186/1471-2164-15-810] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 08/15/2014] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Ashbya gossypii is an industrially relevant microorganism traditionally used for riboflavin production. Despite the high gene homology and gene order conservation comparatively with Saccharomyces cerevisiae, it presents a lower level of genomic complexity. Its type of growth, placing it among filamentous fungi, questions how close it really is from the budding yeast, namely in terms of metabolism, therefore raising the need for an extensive and thorough study of its entire metabolism. This work reports the first manual enzymatic genome-wide re-annotation of A. gossypii as well as the first annotation of membrane transport proteins. RESULTS After applying a developed enzymatic re-annotation pipeline, 847 genes were assigned with metabolic functions. Comparatively to KEGG's annotation, these data corrected the function for 14% of the common genes and increased the information for 52 genes, either completing existing partial EC numbers or adding new ones. Furthermore, 22 unreported enzymatic functions were found, corresponding to a significant increase in the knowledge of the metabolism of this organism. The information retrieved from the metabolic re-annotation and transport annotation was used for a comprehensive analysis of A. gossypii's metabolism in comparison to the one of S. cerevisiae (post-WGD - whole genome duplication) and Kluyveromyces lactis (pre-WGD), suggesting some relevant differences in several parts of their metabolism, with the majority being found for the metabolism of purines, pyrimidines, nitrogen and lipids. A considerable number of enzymes were found exclusively in A. gossypii comparatively with K. lactis (90) and S. cerevisiae (13). In a similar way, 176 and 123 enzymatic functions were absent on A. gossypii comparatively to K. lactis and S. cerevisiae, respectively, confirming some of the well-known phenotypes of this organism. CONCLUSIONS This high quality metabolic re-annotation, together with the first membrane transporters annotation and the metabolic comparative analysis, represents a new important tool for the study and better understanding of A. gossypii's metabolism.
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Affiliation(s)
- Daniel Gomes
- CEB - Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Tatiana Q Aguiar
- CEB - Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Oscar Dias
- CEB - Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Eugénio C Ferreira
- CEB - Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Lucília Domingues
- CEB - Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Isabel Rocha
- CEB - Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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Aguiar TQ, Dinis C, Magalhães F, Oliveira C, Wiebe MG, Penttilä M, Domingues L. Molecular and Functional Characterization of an Invertase Secreted by Ashbya gossypii. Mol Biotechnol 2014; 56:524-34. [DOI: 10.1007/s12033-013-9726-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Magalhães F, Aguiar TQ, Oliveira C, Domingues L. High-level expression ofAspergillus nigerβ-galactosidase inAshbya gossypii. Biotechnol Prog 2014; 30:261-68. [DOI: 10.1002/btpr.1844] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Frederico Magalhães
- IBB-Ins. for Biotechnology and Bioengineering; Centre of Biological Engineering, Universidade do Minho; Campus de Gualtar 4710-057 Braga Portugal
| | - Tatiana Q. Aguiar
- IBB-Ins. for Biotechnology and Bioengineering; Centre of Biological Engineering, Universidade do Minho; Campus de Gualtar 4710-057 Braga Portugal
| | - Carla Oliveira
- IBB-Ins. for Biotechnology and Bioengineering; Centre of Biological Engineering, Universidade do Minho; Campus de Gualtar 4710-057 Braga Portugal
| | - Lucília Domingues
- IBB-Ins. for Biotechnology and Bioengineering; Centre of Biological Engineering, Universidade do Minho; Campus de Gualtar 4710-057 Braga Portugal
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