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Larrouy-Maumus G, Gilleron M, Skovierová H, Zuberogoitia S, Brennan PJ, Puzo G, Jackson M, Nigou J. A glycomic approach reveals a new mycobacterial polysaccharide. Glycobiology 2015; 25:1163-71. [PMID: 26261090 DOI: 10.1093/glycob/cwv061] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 08/05/2015] [Indexed: 12/26/2022] Open
Abstract
Mycobacterium tuberculosis lipoarabinomannan (LAM) and biosynthetically related lipoglycans and glycans play an important role in host-pathogen interactions. Therefore, the elucidation of the complete biosynthetic pathways of these important molecules is expected to afford novel therapeutic targets. The characterization of biosynthetic enzymes and transporters involved in the formation and localization of these complex macromolecules in the bacterial cell envelope largely relies on genetic manipulation of mycobacteria and subsequent analyses of lipoglycan structural alterations. However, lipoglycans are present in relatively low amounts. Their purification to homogeneity remains tedious and time-consuming. To overcome these issues and to reduce the biomass and time required for lipoglycan purification, we report here the development of a methodology to efficiently purify lipoglycans by sodium deoxycholate-polyacrylamide gel electrophoresis. This faster purification method can be applied on a small amount of mycobacterial cells biomass (10-50 mg), resulting in tens of micrograms of purified lipoglycans. This amount of purified products was found to be sufficient to undertake structural analyses of lipoglycans and glycans carbohydrate domains by a combination of highly sensitive analytical procedures, involving cryoprobe NMR analysis of intact macromolecules and chemical degradations monitored by gas chromatography and capillary electrophoresis. This glycomic approach was successfully applied to the purification and structural characterization of a newly identified polysaccharide, structurally related to LAM, in the model fast-growing species Mycobacterium smegmatis.
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Affiliation(s)
- Gérald Larrouy-Maumus
- CNRS, Institut de Pharmacologie et de Biologie Structurale (IPBS), UMR 5089 CNRS/Université Paul Sabatier, 205 route de Narbonne, BP 64182, F-31077 Toulouse Cedex 4, France Université de Toulouse, Université Paul Sabatier, IPBS, F-31077 Toulouse, France
| | - Martine Gilleron
- CNRS, Institut de Pharmacologie et de Biologie Structurale (IPBS), UMR 5089 CNRS/Université Paul Sabatier, 205 route de Narbonne, BP 64182, F-31077 Toulouse Cedex 4, France Université de Toulouse, Université Paul Sabatier, IPBS, F-31077 Toulouse, France
| | - Henrieta Skovierová
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523-1682, USA
| | - Sophie Zuberogoitia
- CNRS, Institut de Pharmacologie et de Biologie Structurale (IPBS), UMR 5089 CNRS/Université Paul Sabatier, 205 route de Narbonne, BP 64182, F-31077 Toulouse Cedex 4, France Université de Toulouse, Université Paul Sabatier, IPBS, F-31077 Toulouse, France
| | - Patrick J Brennan
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523-1682, USA
| | - Germain Puzo
- CNRS, Institut de Pharmacologie et de Biologie Structurale (IPBS), UMR 5089 CNRS/Université Paul Sabatier, 205 route de Narbonne, BP 64182, F-31077 Toulouse Cedex 4, France Université de Toulouse, Université Paul Sabatier, IPBS, F-31077 Toulouse, France
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523-1682, USA
| | - Jérôme Nigou
- CNRS, Institut de Pharmacologie et de Biologie Structurale (IPBS), UMR 5089 CNRS/Université Paul Sabatier, 205 route de Narbonne, BP 64182, F-31077 Toulouse Cedex 4, France Université de Toulouse, Université Paul Sabatier, IPBS, F-31077 Toulouse, France
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LIANG XU, WANG JINGRONG, WONG KAMWAIV, HSIAO WENLUAN, ZHOU HUA, JIANG ZHIHONG, KAM KINTINGR, LIU LIANG. Optimization of 2-dimensional gel electrophoresis for proteomic studies of solid tumor tissue samples. Mol Med Rep 2013; 9:626-32. [DOI: 10.3892/mmr.2013.1815] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 09/16/2013] [Indexed: 11/05/2022] Open
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Seelert H, Krause F. Preparative isolation of protein complexes and other bioparticles by elution from polyacrylamide gels. Electrophoresis 2008; 29:2617-36. [PMID: 18494038 DOI: 10.1002/elps.200800061] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Due to its unmatched resolution, gel electrophoresis is an indispensable tool for the analysis of diverse biomolecules. By adaptation of the electrophoretic conditions, even fragile protein complexes as parts of intracellular networks migrate through the gel matrix under sustainment of their integrity. If the thickness of such native gels is significantly increased compared to the analytical version, also high sample loads can be processed. However, the cage-like network obstructs an in-depth analysis for deciphering structure and function of protein complexes and other species. Consequently, the biomolecules have to be removed from the gel matrix into solution. Several approaches summarized in this review tackle this problem. While passive elution relies on diffusion processes, electroelution employs an electric field to force biomolecules out of the gel. An alternative procedure requires a special electrophoresis setup, the continuous elution device. In this apparatus, molecules migrate in the electric field until they leave the gel and were collected in a buffer stream. Successful isolation of diverse protein complexes like photosystems, ATP-dependent enzymes or active respiratory supercomplexes and some other bioparticles demonstrates the versatility of preparative electrophoresis. After liberating particles out of the gel cage, numerous applications are feasible. They include elucidation of the individual components up to high resolution structures of protein complexes. Therefore, preparative electrophoresis can complement standard purification methods and is in some cases superior to them.
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Affiliation(s)
- Holger Seelert
- Department of Chemistry, Physical Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany.
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Vâlcu CM, Schlink K. Reduction of proteins during sample preparation and two-dimensional gel electrophoresis of woody plant samples. Proteomics 2006; 6:1599-605. [PMID: 16456882 DOI: 10.1002/pmic.200500314] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Protein extraction procedure and the reducing agent content (DTT, dithioerythritol, tributyl phosphine and tris (2-carboxyethyl) phosphine (TCEP)) of the sample and rehydration buffers were optimised for European beech leaves and roots and Norway spruce needles. Optimal extraction was achieved with 100 mM DTT for leaves and needles and a mixture of 2 mM TCEP and 50 mM DTT for roots. Performing IEF in buffers containing hydroxyethyldisulphide significantly enhanced the quality of separation for all proteins except for acidic root proteins, which were optimally focused in the same buffer as extracted.
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Affiliation(s)
- Cristina-Maria Vâlcu
- Section of Forest Genetics, Technische Universität München, Freising-Weihenstephan, Germany.
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Abstract
Due to their unique capability to attack lignified biopolymers, extracellular enzymes of white-rot fungi enjoy an increasing interest in various fields of white biotechnology. The edible fungus Pleurotus sapidus was selected as a model organism for the analysis of the secretome by means of 2-DE. For enzyme production, the fungus was grown in submerged cultures either on peanut shells or on glass wool as a carrier material. Identification of the secreted enzymes was performed by tryptic digestion, ESI-MS/MS ab initio sequencing, and homology searches against public databases. The spectrum of secreted enzymes comprised various types of hydrolases and lignolytic enzymes of the manganese peroxidase/versatile peroxidase family. While peptidases were secreted mainly by the cultures grown on peanut shells, versatile peroxidase type enzymes dominated in the cultures grown on glass wool.
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Affiliation(s)
- Holger Zorn
- Zentrum Angewandte Chemie, Institut für Lebensmittelchemie der Universität Hannover, Wunstorfer Strasse 14, D-30453 Hannover, Germany.
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Herbert B, Galvani M, Hamdan M, Olivieri E, MacCarthy J, Pedersen S, Righetti PG. Reduction and alkylation of proteins in preparation of two-dimensional map analysis: why, when, and how? Electrophoresis 2001; 22:2046-57. [PMID: 11465505 DOI: 10.1002/1522-2683(200106)22:10<2046::aid-elps2046>3.0.co;2-c] [Citation(s) in RCA: 189] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The standard procedure adopted up to the present in proteome analysis calls for just reduction prior to the isoelectric focusing/immobilized pH gradient (IEF/IPG) step, followed by a second reduction/alkylation step in between the first and second dimension, in preparation for the sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) step. This protocol is far from being optimal. It is here demonstrated, by matrix assisted laser desorption/ionization-time of flight (MALDI-TOF)-mass spectrometry, that failure to reduce and alkylate proteins prior to any electrophoretic step (including the first dimension) results in a large number of spurious spots in the alkaline pH region, due to "scrambled" disulfide bridges among like and unlike chains. This series of artefactual spots comprises not only dimers, but an impressive series of oligomers (up to nonamers) in the case of simple polypeptides such as the human alpha- and beta-globin chains, which possess only one (alpha-) or two (beta-) -SH groups. As a result, misplaced spots are to be found in the resulting two-dimensional (2-D) map, if performed with the wrong protocol. The number of such artefactual spots can be impressively large. In the case of analysis of complex samples, such as human plasma, it is additionally shown that failure to alkylate proteins results in a substantial loss of spots in the alkaline gel region, possibly due to the fact that these proteins, at their pI, regenerate their disulfide bridges with concomitant formation of macroaggregates which become entangled with and trapped within the polyacrylamide gel fibers. This strongly quenches their transfer in the subsequent SDS-PAGE step.
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Affiliation(s)
- B Herbert
- Proteome Systems, North Ryde, Sydney, NSW, Australia
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Galvani M, Hamdan M, Herbert B, Righetti PG. Alkylation kinetics of proteins in preparation for two-dimensional maps: a matrix assisted laser desorption/ionization-mass spectrometry investigation. Electrophoresis 2001; 22:2058-65. [PMID: 11465506 DOI: 10.1002/1522-2683(200106)22:10<2058::aid-elps2058>3.0.co;2-z] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
All existing protocols for protein separation by two-dimensional (2-D) gel electrophoresis require the full reduction, denaturation, and alkylation as a precondition for an efficient and meaningful separation of such proteins. Existing literature provides a strong evidence to suggest that full reduction and denaturation can be achieved in a relatively short time; the same thing, however, can not be said for the alkylation process, which the present study shows that more than 6 h are required for a complete alkylation. We have used matrix assisted laser desorption/ionisation-time of flight-mass spectrometry (MALDI-TOF-MS) to monitor protein alkylation by iodoacetamide over the period 0-24 h at pH 9. The present, fast and specific MS method provided clear indication on the extent and speed of alkylation which reached approximately 70% in the first 2 min, yet the remaining 30% resisted complete alkylation up to 6 h. The use of sodium dodecyl sulfate (SDS) during the alkylation step resulted in a strong quenching of this reaction, whereas 2% 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS) exerted a much reduced inhibition. The implications of the present measurements on 2-D gel analysis in particular and proteomics in general are discussed.
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Affiliation(s)
- M Galvani
- University of Verona, Department of Agricultural and Industrial Biotechnologies, Verona, Italy.
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Hamdan M, Galvani M, Righetti PG. Monitoring 2-D gel-induced modifications of proteins by MALDI-TOF mass spectrometry. MASS SPECTROMETRY REVIEWS 2001; 20:121-141. [PMID: 11746345 DOI: 10.1002/mas.10000] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In addition to more than 200 endogenously produced post-translational modifications, a detailed analysis of 2-D gel-separated proteins must also consider other modifications that a protein can experience during various steps of its separation. This review describes the use of matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry to investigate some of these modifications, which can originate during sample preparation and/or during the separation phase. The analyses described were mostly conducted at pH 9-9.5, and yielded reliable information on stable adduct formation that involved protein-bound amino acids and a number of gel components, including acrylamide derivatives, gel cross-linkers, and Immobiline chemicals. The -SH group of Cys was found to be the prime target of such adducts; however, longer reaction times revealed the involvement of the epsilon-NH2 of Lys. The same analysis revealed that the failure to achieve full reduction/alkylation prior to any electrophoretic step could result in protein-protein interaction, which could lead to a number of spurious spots in the final 2-D map. The implications of these modifications on the MS analysis in particular and on proteome research in general are discussed.
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Affiliation(s)
- M Hamdan
- GlaxoSmithKline Group, Medicines Research Center, via Fleming 4, Verona, Italy.
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Hamdan M, Bordini E, Galvani M, Righetti PG. Protein alkylation by acrylamide, its N-substituted derivatives and cross-linkers and its relevance to proteomics: a matrix assisted laser desorption/ionization-time of flight-mass spectrometry study. Electrophoresis 2001; 22:1633-44. [PMID: 11425219 DOI: 10.1002/1522-2683(200105)22:9<1633::aid-elps1633>3.0.co;2-c] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The present review highlights some important alkylation pathways of proteins, as measured by matrix assisted laser desorption/ionization-time of flight (MALDI-TOF)-mass spectrometric analysis, engendered by acrylamide and a number of its derivatives, including N-substituted acrylamides, cross-linkers and Immobilines (the acrylamido weak acids and bases used to create immobilized pH gradients). The present data are of relevance in two-dimensional maps and proteome analysis. It is shown that acrylamide can alkylate the -SH group of proteins even when engaged in disulfide bridges. An order of reactivity is obtained for a series of cross-linkers, which are shown to have an extremely reacting double bond, with the second one almost unreactive, originating "pendant, unreacted ends", which can subtract proteins migrating in a gel by covalently affixing them to it. An analogous reactivity scale is constructed also for the Immobiline chemicals, whose reactivity is shown to be linearly dependent on the pK values, the least reacting species being the acidic compounds. When analyzing real-life samples by two-dimensional (2-D) maps, like milk powders, a number of modifications can be detected by MALDI-TOF mass spectra of eluted spots, including variable phosphorylation sites (up to nine) and lactosyl moieties. If, for eluting such spots, formic acid is used, MALDI-TOF mass spectrometry (MS) reveals an incredible number of formylation sites, on Ser and Thr residues.
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Affiliation(s)
- M Hamdan
- GlaxoSmithKline Group, Medicine Research Centre, Verona, Italy
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