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Dar SA, Ahmad I, Ahmed I, Kaur H, Khursheed S, Nisar K, Magray AR, Chishti MZ. Strategies for describing myxozoan pathogens, dreadful fish diseases in aquaculture. Microb Pathog 2024; 187:106512. [PMID: 38154451 DOI: 10.1016/j.micpath.2023.106512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 10/23/2023] [Accepted: 12/19/2023] [Indexed: 12/30/2023]
Abstract
Myxozoans are obligate endoparasites, cosmopolitan in distribution with both vertebrate and invertebrate hosts. Their myxospores consist of shell valves, polar capsules with coiled polar tubules that are extrudible, and infective amoeboid germs. Myxozoan parasites are most abundant, and due to their increasing number in recent years, they can pose an emerging threat to the fish industry worldwide. Hence, the immediate need is to devise a strategy to understand and detect parasites and parasitism. They may proliferate to different organs with the advancement of infection. This all warrants the development/devising of strategies and results of integrative studies in order to identify these dreadful parasites and resolve taxonomic issues. Different methods whether classical methods including gross morphology or advanced methods such as electron microscopy (SEM, TEM, STEM), Confocal laser scanning microscopy (CLSM), histopathological studies, site preference, host and tissue specificity, a molecular approach using new markers can be clubbed for identification because these parasites are hidden and are difficult to recognize. This group was earlier classified only on the basis of myxospores morphology, but due to the high structural variability of this group advanced methods and approaches have to be implied which can minimize the problems in assigning new species.
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Affiliation(s)
- Shoaib Ali Dar
- Centre of Research for Development, University of Kashmir, Srinagar, 190006, India
| | - Ishtiyaq Ahmad
- Fish Nutrition Research Laboratory, Department of Zoology, University of Kashmir, Srinagar, 190006, India.
| | - Imtiaz Ahmed
- Fish Nutrition Research Laboratory, Department of Zoology, University of Kashmir, Srinagar, 190006, India
| | - Harpreet Kaur
- Department of Zoology, Panjab University, Chandigarh, 160014, India
| | - Saba Khursheed
- Department of Zoology, School of Bioengineering & Biosciences, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Kamran Nisar
- Centre of Research for Development, University of Kashmir, Srinagar, 190006, India
| | - Aqib Rehman Magray
- Centre of Research for Development, University of Kashmir, Srinagar, 190006, India
| | - M Z Chishti
- Department of Zoology, Central University of Kashmir, 191131, India
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Dolui AK, Latha M, Vijayaraj P. Activity-based Protein Profiling of Serine Hydrolase Superfamily Enzymes. Bio Protoc 2022; 12:e4356. [PMID: 35434188 PMCID: PMC8983155 DOI: 10.21769/bioprotoc.4356] [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: 01/25/2022] [Revised: 10/15/2021] [Accepted: 01/25/2022] [Indexed: 12/29/2022] Open
Abstract
Activity-based protein profiling (ABPP) is a chemoproteomics platform to assess the functional state of enzymes in complex biological systems. Over the two decades, ABPP has emerged from a gel-based to gel-free platform, for in-depth proteome analysis with enhanced resolution, sensitivity for target detection, and discovery of small molecule inhibitors. The gel-free format of ABPP coupled with advanced mass spectrometry is highly sensitive and provides more comprehensive knowledge for the targeted enzyme family than the gel-based method. ABPP strategy is applied across microbe, plant, and animal models. It can be performed both in vitro and in vivo studies, and there is no limitation on sample origin. Here, we report an ultrasensitive, gel-free format of ABPP called active site peptide profiling. This protocol describes the identification of authentic functional proteins, by tagging their active sites in a native biological system. It is high throughput in nature and helps enrich even low abundance functional proteins. Since protein identification is virtually based on a single peptide, the identified peptide should be a unique peptide to identify its parent protein. It can be performed in a facile manner and offers to consolidate identification of protein targets as well as the site of probe modification. We have validated this approach using a fluorophosphonate (FP) serine hydrolase probe in the native proteome of the cereal crop Oryza sativa. Graphic abstract: Serine hydrolase active site peptide profiling.
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Affiliation(s)
- Achintya Kumar Dolui
- Lipid and Nutrition Laboratory, Department of Lipid Science, Council of Scientific and Industrial Research-Central Food Technological Research Institute, Mysore, Karnataka 570020, India
,Academy of Scientific and Innovative Research, Ghaziabad 201002, Uttar Pradesh, India
| | - Mahadev Latha
- Lipid and Nutrition Laboratory, Department of Lipid Science, Council of Scientific and Industrial Research-Central Food Technological Research Institute, Mysore, Karnataka 570020, India
,Academy of Scientific and Innovative Research, Ghaziabad 201002, Uttar Pradesh, India
| | - Panneerselvam Vijayaraj
- Lipid and Nutrition Laboratory, Department of Lipid Science, Council of Scientific and Industrial Research-Central Food Technological Research Institute, Mysore, Karnataka 570020, India
,Academy of Scientific and Innovative Research, Ghaziabad 201002, Uttar Pradesh, India
,
*For correspondence:
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Dolui AK, Vijayakumar AK, Rajasekharan R, Vijayaraj P. Activity-based protein profiling of rice (Oryza sativa L.) bran serine hydrolases. Sci Rep 2020; 10:15191. [PMID: 32938958 PMCID: PMC7494864 DOI: 10.1038/s41598-020-72002-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 07/29/2020] [Indexed: 11/25/2022] Open
Abstract
Rice bran is an underutilized agricultural by-product with economic importance. The unique phytochemicals and fatty acid compositions of bran have been targeted for nutraceutical development. The endogenous lipases and hydrolases are responsible for the rapid deterioration of rice bran. Hence, we attempted to provide the first comprehensive profiling of active serine hydrolases (SHs) present in rice bran proteome by activity-based protein profiling (ABPP) strategy. The active site-directed fluorophosphonate probe (rhodamine and biotin-conjugated) was used for the detection and identification of active SHs. ABPP revealed 55 uncharacterized active-SHs and are representing five different known enzyme families. Based on motif and domain analyses, one of the uncharacterized and miss annotated SHs (Os12Ssp, storage protein) was selected for biochemical characterization by overexpressing in yeast. The purified recombinant protein authenticated the serine protease activity in time and protein-dependent studies. Os12Ssp exhibited the maximum activity at a pH between 7.0 and 8.0. The protease activity was inhibited by the covalent serine protease inhibitor, which suggests that the ABPP approach is indeed reliable than the sequence-based annotations. Collectively, the comprehensive knowledge generated from this study would be useful in expanding the current understanding of rice bran SHs and paves the way for better utilization/stabilization of rice bran.
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Affiliation(s)
- Achintya Kumar Dolui
- Lipid and Nutrition Laboratory, Department of Lipid Science, CSIR-Central Food Technological Research Institute, Mysuru, Karnataka, 570020, India
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India
| | - Arun Kumar Vijayakumar
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India
- CSIR-Central Food Technological Research Institute, Resource Centre Lucknow, Lucknow, 226018, India
| | - Ram Rajasekharan
- Lipid and Nutrition Laboratory, Department of Lipid Science, CSIR-Central Food Technological Research Institute, Mysuru, Karnataka, 570020, India
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India
- School of Life Sciences, Central University of Tamil Nadu, Tamil Nadu, Neelakudi, Thiruvarur, 610 005, India
| | - Panneerselvam Vijayaraj
- Lipid and Nutrition Laboratory, Department of Lipid Science, CSIR-Central Food Technological Research Institute, Mysuru, Karnataka, 570020, India.
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India.
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Identification of serum biomarkers for premature ovarian failure. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:219-226. [DOI: 10.1016/j.bbapap.2018.12.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/16/2018] [Accepted: 12/20/2018] [Indexed: 12/17/2022]
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Whidbey C, Sadler NC, Nair RN, Volk RF, DeLeon AJ, Bramer LM, Fansler SJ, Hansen JR, Shukla AK, Jansson JK, Thrall BD, Wright AT. A Probe-Enabled Approach for the Selective Isolation and Characterization of Functionally Active Subpopulations in the Gut Microbiome. J Am Chem Soc 2018; 141:42-47. [PMID: 30541282 DOI: 10.1021/jacs.8b09668] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Commensal microorganisms in the mammalian gut play important roles in host health and physiology, but a central challenge remains in achieving a detailed mechanistic understanding of specific microbial contributions to host biochemistry. New function-based approaches are needed that analyze gut microbial function at the molecular level by coupling detection and measurements of in situ biochemical activity with identification of the responsible microbes and enzymes. We developed a platform employing β-glucuronidase selective activity-based probes to detect, isolate, and identify microbial subpopulations in the gut responsible for this xenobiotic metabolism. We find that metabolic activity of gut microbiota can be plastic and that between individuals and during perturbation, phylogenetically disparate populations can provide β-glucuronidase activity. Our work links biochemical activity with molecular-scale resolution without relying on genomic inference.
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Affiliation(s)
- Christopher Whidbey
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Natalie C Sadler
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Reji N Nair
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Regan F Volk
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Adrian J DeLeon
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Lisa M Bramer
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Sarah J Fansler
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Joshua R Hansen
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Anil K Shukla
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Janet K Jansson
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Brian D Thrall
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Aaron T Wright
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States.,The Gene and Linda Voiland School of Chemical Engineering and Bioengineering , Washington State University , Pullman , Washington 99163 , United States
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Genomics and Proteomics of Foodborne Microorganisms. Food Microbiol 2014. [DOI: 10.1128/9781555818463.ch39] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Thongboonkerd V. Proteomics in leptospirosis research: towards molecular diagnostics and vaccine development. Expert Rev Mol Diagn 2014; 8:53-61. [DOI: 10.1586/14737159.8.1.53] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Janvilisri T, Scaria J, Teng CH, McDonough SP, Gleed RD, Fubini SL, Zhang S, Akey B, Chang YF. Temporal differential proteomes of Clostridium difficile in the pig ileal-ligated loop model. PLoS One 2012; 7:e45608. [PMID: 23029131 PMCID: PMC3445491 DOI: 10.1371/journal.pone.0045608] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 08/23/2012] [Indexed: 12/29/2022] Open
Abstract
The impact of Clostridium difficile infection (CDI) on healthcare is becoming increasingly recognized as it represents a major cause of nosocomial diarrhea. A rising number of CDI cases and outbreaks have been reported worldwide. Here, we developed the pig ileal-ligated loop model for semi-quantitative analysis comparing temporal differential proteomes in C. difficile following in vivo incubation with in vitro growth using isobaric tags for relative and absolute quantification (iTRAQ). Proteins retrieved from the in vitro cultures and the loop contents after 4, 8, and 12 h in vivo incubation were subjected to in-solution digestion, iTRAQ labeling, two-dimensional liquid chromatography/tandem mass spectrometry and statistical analyses. From a total of 1152 distinct proteins identified in this study, 705 proteins were available for quantitative measures at all time points in both biological and technical replicates; 109 proteins were found to be differentially expressed. With analysis of clusters of orthologous group and protein-protein network interactions, we identified the proteins that might play roles in adaptive responses to the host environment, hence enhancing pathogenicity during CDI. This report represents the quantitative proteomic analysis of C. difficile that demonstrates time-dependent protein expression changes under conditions that mimic in vivo infection and identifies potential candidates for diagnostic or therapeutic measures.
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Affiliation(s)
- Tavan Janvilisri
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Joy Scaria
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Ching-Hao Teng
- Institute of Molecular Medicine, National Cheng Kung University Medical College, Tainan, Taiwan
| | - Sean P. McDonough
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Robin D. Gleed
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Susan L. Fubini
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Sheng Zhang
- Proteomics and Mass Spectrometry Core Facility, Cornell University, Ithaca, New York, United States of America
| | - Bruce Akey
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Yung-Fu Chang
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
- * E-mail:
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Two-dimensional gel electrophoresis in bacterial proteomics. Protein Cell 2012; 3:346-63. [PMID: 22610887 DOI: 10.1007/s13238-012-2034-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2012] [Accepted: 02/22/2012] [Indexed: 02/01/2023] Open
Abstract
Two-dimensional gel electrophoresis (2-DE) is a gel-based technique widely used for analyzing the protein composition of biological samples. It is capable of resolving complex mixtures containing more than a thousand protein components into individual protein spots through the coupling of two orthogonal biophysical separation techniques: isoelectric focusing (first dimension) and polyacrylamide gel electrophoresis (second dimension). 2-DE is ideally suited for analyzing the entire expressed protein complement of a bacterial cell: its proteome. Its relative simplicity and good reproducibility have led to 2-DE being widely used for exploring proteomics within a wide range of environmental and medically-relevant bacteria. Here we give a broad overview of the basic principles and historical development of gel-based proteomics, and how this powerful approach can be applied for studying bacterial biology and physiology. We highlight specific 2-DE applications that can be used to analyze when, where and how much proteins are expressed. The links between proteomics, genomics and mass spectrometry are discussed. We explore how proteomics involving tandem mass spectrometry can be used to analyze (post-translational) protein modifications or to identify proteins of unknown origin by de novo peptide sequencing. The use of proteome fractionation techniques and non-gel-based proteomic approaches are also discussed. We highlight how the analysis of proteins secreted by bacterial cells (secretomes or exoproteomes) can be used to study infection processes or the immune response. This review is aimed at non-specialists who wish to gain a concise, comprehensive and contemporary overview of the nature and applications of bacterial proteomics.
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Bermúdez-Crespo J, Balboa S, Alonso J, Romalde J. Two-dimensional proteome reference map of Vibrio tapetis, the aetiological agent of brown ring disease in clams. J Appl Microbiol 2012; 112:853-64. [DOI: 10.1111/j.1365-2672.2012.05271.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Seneviratne CJ, Wang Y, Jin L, Wong SSW, Herath TDK, Samaranayake LP. Unraveling the resistance of microbial biofilms: Has proteomics been helpful? Proteomics 2012; 12:651-65. [DOI: 10.1002/pmic.201100356] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 10/07/2011] [Accepted: 10/11/2011] [Indexed: 01/03/2023]
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Balboa S, Bermudez-Crespo J, Gianzo C, López JL, Romalde JL. Proteomics and multilocus sequence analysis confirm intraspecific variability of Vibrio tapetis. FEMS Microbiol Lett 2011; 324:80-7. [DOI: 10.1111/j.1574-6968.2011.02393.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Revised: 08/17/2011] [Accepted: 08/22/2011] [Indexed: 11/30/2022] Open
Affiliation(s)
| | - José Bermudez-Crespo
- Departamento de Genética CIBUS; Universidad de Santiago de Compostela; Santiago de Compostela; Spain
| | - Cristina Gianzo
- Departamento de Genética CIBUS; Universidad de Santiago de Compostela; Santiago de Compostela; Spain
| | - José L. López
- Departamento de Genética CIBUS; Universidad de Santiago de Compostela; Santiago de Compostela; Spain
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Chemical genetic screen identifies Toxoplasma DJ-1 as a regulator of parasite secretion, attachment, and invasion. Proc Natl Acad Sci U S A 2011; 108:10568-73. [PMID: 21670272 DOI: 10.1073/pnas.1105622108] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Toxoplasma gondii is a member of the phylum Apicomplexa that includes several important human pathogens, such as Cryptosporidium and Plasmodium falciparum, the causative agent of human malaria. It is an obligate intracellular parasite that can cause severe disease in congenitally infected neonates and immunocompromised individuals. Despite the importance of attachment and invasion to the success of the parasite, little is known about the underlying mechanisms that drive these processes. Here we describe a screen to identify small molecules that block the process of host cell invasion by the T. gondii parasite. We identified a small molecule that specifically and irreversibly blocks parasite attachment and subsequent invasion of host cells. Using tandem orthogonal proteolysis-activity-based protein profiling, we determined that this compound covalently modifies a single cysteine residue in a poorly characterized protein homologous to the human protein DJ-1. Mutation of this key cysteine residue in the native gene sequence resulted in parasites that were resistant to inhibition of host cell attachment and invasion by the compound. Further analysis of the invasion phenotype confirmed that modification of Cys127 on TgDJ-1 resulted in a block of microneme secretion and motility, even in the presence of direct stimulators of calcium release. Together, our results suggest that TgDJ-1 plays an important role that is likely downstream of the calcium flux required for microneme secretion, parasite motility, and subsequent invasion of host cells.
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Gandy MN, Debowski AW, Stubbs KA. A general method for affinity-based proteomic profiling of exo-α-glycosidases. Chem Commun (Camb) 2011; 47:5037-9. [PMID: 21431156 DOI: 10.1039/c1cc10308c] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Synthesis of iminosugar-based affinity-based proteomics probes for use in probing exo-α-glycosidase activity.
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Affiliation(s)
- Michael N Gandy
- Chemistry M313, School of Biomedical, Biomolecular and Chemical Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA Australia6009
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Wessels HJCT, Gloerich J, van der Biezen E, Jetten MSM, Kartal B. Liquid chromatography-mass spectrometry-based proteomics of Nitrosomonas. Methods Enzymol 2011; 486:465-82. [PMID: 21185449 DOI: 10.1016/b978-0-12-381294-0.00021-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
During the last century, the research on aerobic ammonium-oxidizing bacteria (AOB) lead to many exciting physiological and biochemical discoveries. Nevertheless the molecular biology of AOB is not well understood. The availability of the genome sequences of several Nitrosomonas species opened up new possiblities to use state of the art transcriptomic and proteomic tools to study AOB. With the currect technology, thousands of proteins can be analyzed in several hours of measurement and translated proteins can be detected at femtomole and attomole concentrations. Moreover, it is possible to use mass spectrometry-based proteomics approach to analyze the expression, subcellular localization, posttranslational modifications, and interactions of translated proteins. In this chapter, we describe our LC-MS/MS methodology and quality control strategy to study the protein complement of Nitrosomonas eutropha C91.
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Affiliation(s)
- Hans J C T Wessels
- Nijmegen Centre for Mitochondrial Disorders, Department of Laboratory Medicine, Nijmegen Proteomics Facility, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
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Abstract
Toxoplasma gondii is a ubiquitous, Apicomplexan parasite that, in humans, can cause several clinical syndromes, including encephalitis, chorioretinitis and congenital infection. T. gondii was described a little over 100 years ago in the tissues of the gundi (Ctenodoactylus gundi). There are a large number of applicable experimental techniques available for this pathogen and it has become a model organism for the study of intracellular pathogens. With the completion of the genomes for a type I (GT-1), type II (ME49) and type III (VEG) strains, proteomic studies on this organism have been greatly facilitated. Several subcellular proteomic studies have been completed on this pathogen. These studies have helped elucidate specialized invasion organelles and their composition, as well as proteins associated with the cytoskeleton. Global proteomic studies are leading to improved strategies for genome annotation in this organism and an improved understanding of protein regulation in this pathogen. Web-based resources, such as EPIC-DB and ToxoDB, provide proteomic data and support for studies on T. gondii. This review will summarize the current status of proteomic research on T. gondii.
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Affiliation(s)
- Louis M Weiss
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Forchheimer 504, 1300 Morris Park Avenue, Bronx, NY 10461, USA.
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Stubbs KA, Vocadlo DJ. Affinity-Based Proteomics Probes; Tools for Studying Carbohydrate-Processing Enzymes. Aust J Chem 2009. [DOI: 10.1071/ch09140] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
As more information becomes available through the efforts of high-throughput screens, there is increasing pressure on the three main ‘omic’ fields, genomics, proteomics, and metabolomics, to organize this material into useful libraries that enable further understanding of biological systems. Proteomics especially is faced with two highly challenging tasks. The first is assigning the activity of thousands of putative proteins, the existence of which has been suggested by genomics studies. The second is to serve as a link between genomics and metabolomics by demonstrating which enzymes play roles in specific metabolic pathways. Underscoring these challenges in one area are the thousands of putative carbohydrate-processing enzymes that have been bioinformatically identified, mostly in prokaryotes, but that have unknown or unverified activities. Using two brief examples, we illustrate how biochemical pathways within bacteria that involve carbohydrate-processing enzymes present interesting potential antimicrobial targets, offering a clear motivation for gaining a functional understanding of biological proteomes. One method for studying proteomes that has been developed recently is to use synthetic compounds termed activity-based proteomics probes. Activity-based proteomic profiling using such probes facilitates rapid identification of enzyme activities within proteomes and assignment of function to putative enzymes. Here we discuss the general design principles for these probes with particular reference to carbohydrate-processing enzymes and give an example of using such a probe for the profiling of a bacterial proteome.
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Bugert J. Hightech im Dienste der Infektiologie. LEXIKON DER INFEKTIONSKRANKHEITEN DES MENSCHEN 2009. [PMCID: PMC7121986 DOI: 10.1007/978-3-540-39026-8_471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Tafelmeyer P, Laurent C, Lenormand P, Rousselle JC, Marsollier L, Reysset G, Zhang R, Sickmann A, Stinear TP, Namane A, Cole ST. Comprehensive proteome analysis of Mycobacterium ulcerans and quantitative comparison of mycolactone biosynthesis. Proteomics 2008; 8:3124-38. [PMID: 18615429 DOI: 10.1002/pmic.200701018] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Mycobacterium ulcerans is the causative agent of Buruli ulcer, a rapidly emerging human disease in which mycolactone, a cytotoxic and immunosuppressive macrocyclic polyketide, is responsible for massive skin destruction. The genome sequencing of M. ulcerans has recently been accomplished (http://genolist.pasteur.fr/BuruList/) enabling the first proteome study of this important human pathogen. Here, we present a comprehensive proteome analysis of different subcellular fractions and culture supernatant of in vitro grown M. ulcerans. By a combination of gel-based and gel-free techniques for protein and peptide separation with subsequent analysis by MS, we identified 1074 different proteins, corresponding to 25% of the protein-coding DNA sequence. Interestingly, new information was obtained about central metabolism and lipid biosynthesis, and as many as 192 conserved hypothetical proteins were found. Comparative analysis of the wild-type strain and an isogenic mycolactone-deficient mutant, by 2-DE and iTRAQ labeling of the cytoplasmic fraction, revealed differences in the expression profiles of proteins involved in lipid metabolism and information pathways, as well as stress responses.
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Abstract
In this chapter, we outline the tools and techniques available to study the process of host cell invasion by apicomplexan parasites and we provide specific examples of how these methods have been used to further our understanding of apicomplexan invasive mechanisms. Throughout the chapter we focus our discussion on Toxoplasmagondii, because T. gondii is the most experimentally accessible model organism for studying apicomplexan invasion (discussed further in the section, "Toxoplasma as a Model Apicomplexan") and more is known about invasion in T. gondii than in any other apicomplexan.
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Paulick MG, Bogyo M. Application of activity-based probes to the study of enzymes involved in cancer progression. Curr Opin Genet Dev 2008; 18:97-106. [PMID: 18294838 DOI: 10.1016/j.gde.2007.12.001] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2007] [Accepted: 12/19/2007] [Indexed: 01/07/2023]
Abstract
Many tumor cells have elevated levels of hydrolytic and proteolytic enzymes, presumably to aid in key processes such as angiogenesis, cancer cell invasion, and metastasis. Functional roles of enzymes in cancer progression are difficult to study using traditional genomic and proteomic methods because the activities of these enzymes are often regulated by post-translational mechanisms. Thus, methods that allow for the direct monitoring of enzyme activity in a physiologically relevant environment are required to better understand the roles of specific players in the complex process of tumorigenesis. This review highlights advances in the field of activity-based proteomics, which uses small molecules known as activity-based probes (ABPs) that covalently bind to the catalytic site of target enzymes. We discuss the application of ABPs to cancer biology, especially to the discovery of tumor biomarkers, the screening of enzyme inhibitors, and the imaging of enzymes implicated in cancer.
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Affiliation(s)
- Margot G Paulick
- Department of Pathology, Stanford University, Stanford, CA 94305-5324, USA
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23
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Kumari S, Kumar A, Samant M, Sundar S, Singh N, Dube A. Proteomic approaches for discovery of new targets for vaccine and therapeutics against visceral leishmaniasis. Proteomics Clin Appl 2008; 2:372-86. [PMID: 21136840 DOI: 10.1002/prca.200780017] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2007] [Indexed: 11/06/2022]
Abstract
Visceral leishmaniasis (VL) is the most devastating type caused by Leishmania donovani, Leishmania infantum, and Leishmania chagasi. The therapeutic mainstay is still based on the antiquated pentavalent antimonial against which resistance is now increasing. Unfortunately, due to the digenetic life cycle of parasite, there is significant antigenic diversity. There is an urgent need to develop novel drug/vaccine targets against VL for which the primary goal should be to identify and characterize the structural and functional proteins. Proteomics, being widely employed in the study of Leishmania seems to be a suitable strategy as the availability of annotated sequenced genome of Leishmania major has opened the door for dissection of both protein expression/regulation and function. Advances in clinical proteomic technologies have enable to enhance our mechanistic understanding of virulence/pathogenicity/host-pathogen interactions, drug resistance thereby defining novel therapeutic/vaccine targets. Expression proteomics exploits the differential expression of leishmanial proteins as biomarkers for application towards early diagnosis. Further using immunoproteomics efforts were also focused on evaluating responses to define parasite T-cell epitopes as vaccine/diagnostic targets. This review has highlighted some of the relevant developments in the rapidly emerging field of leishmanial proteomics and focus on its future applications in drug and vaccine discovery against VL.
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Affiliation(s)
- Shraddha Kumari
- Division of Parasitology, Central Drug Research Institute, Lucknow, Uttar Pradesh, India
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24
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Stubbs KA, Scaffidi A, Debowski AW, Mark BL, Stick RV, Vocadlo DJ. Synthesis and Use of Mechanism-Based Protein-Profiling Probes for Retaining β-d-Glucosaminidases Facilitate Identification ofPseudomonas aeruginosaNagZ. J Am Chem Soc 2008; 130:327-35. [DOI: 10.1021/ja0763605] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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25
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Virus analysis by electrophoresis on a microfluidic chip. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 860:173-9. [DOI: 10.1016/j.jchromb.2007.10.026] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2007] [Revised: 10/16/2007] [Accepted: 10/17/2007] [Indexed: 12/24/2022]
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26
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Bernardini G, Braconi D, Santucci A. The analysis of Neisseria meningitidis proteomes: Reference maps and their applications. Proteomics 2007; 7:2933-46. [PMID: 17628027 DOI: 10.1002/pmic.200700094] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Neisseria meningitidis is an encapsulated Gram-negative bacterium responsible for significant morbidity and mortality worldwide. The availability of meningococcal genome sequences in combination with the rapid growth of proteomic techniques and other high-throughput methods, provided new approaches to the analysis of bacterial system biology. This review considers the meningococcal reference maps so far published as a starting point aimed to elucidate bacterial physiology and pathogenicity, paying particular attention to proteins with potential vaccine and diagnostic applications.
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Affiliation(s)
- Giulia Bernardini
- Dipartimento di Biologia Molecolare, via Fiorentina 1, Università degli Studi di Siena, Siena, Italy
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27
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Sakata T, Winzeler EA. Genomics, systems biology and drug development for infectious diseases. MOLECULAR BIOSYSTEMS 2007; 3:841-8. [PMID: 18000561 DOI: 10.1039/b703924g] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Although a variety of drugs are available for many infectious diseases that predominantly affect the developing world reasons remain for continuing to search for new chemotherapeutics. First, the development of microbial resistance has made some of the most effective and inexpensive drug regimes unreliable and dangerous to use on severely ill patients. Second, many existing antimicrobial drugs show toxicity or are too expensive for countries where the per capita income is in the order of hundreds of dollars per year. In recognition of this, new publicly and privately financed drug discovery efforts have been established to identify and develop new therapies for diseases such as tuberculosis, malaria and AIDS. This in turn, has intensified the need for tools to facilitate drug identification for those microbes whose molecular biology is poorly understood, or which are difficult to grow in the laboratory. While much has been written about how functional genomics can be used to find novel protein targets for chemotherapeutics this review will concentrate on how genome-wide, systems biology approaches may be used following whole organism, cell-based screening to understand the mechanism of drug action or to identify biological targets of small molecules. Here we focus on protozoan parasites, however, many of the approaches can be applied to pathogenic bacteria or parasitic helminths, insects or disease-causing fungi.
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Affiliation(s)
- Tomoyo Sakata
- The Genomics Institute of the Novartis Research Foundation, 10660 John Jay Hopkins Dr., San Diego, CA 92121, USA
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28
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Affiliation(s)
- Michael J Evans
- The Skaggs Institute for Chemical Biology and Departments of Cell Biology and Chemistry, The Scripps Research Institute, La Jolla, California 92037, USA
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29
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Wang N, Mackenzie L, De Souza AG, Zhong H, Goss G, Li L. Proteome profile of cytosolic component of zebrafish liver generated by LC-ESI MS/MS combined with trypsin digestion and microwave-assisted acid hydrolysis. J Proteome Res 2007; 6:263-72. [PMID: 17203970 DOI: 10.1021/pr060367o] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The zebrafish genome has recently been sequenced and annotated allowing for high-throughput proteomic analysis. Here, we report for the first time a proteomic subset of zebrafish liver, an important organ for metabolizing toxins. Using a newly developed analytical procedure, we have identified 1204 proteins from the cytosolic component of a zebrafish liver tissue sample. Our methods involve cell-compartment fractionation of liver tissue samples, four levels of protein digestion, and off-line two-dimensional liquid chromatography (2-D LC) separations of resultant peptides. Proteins are identified using an electrospray ionization quadrupole time-of-flight tandem mass spectrometer (ESI-QTOF MS/MS), which provides high-resolution and high-accuracy mass measurement of peptide ions and their fragment ions. We demonstrate that greater proteome coverage can be achieved by combining the results obtained from four methods of protein digestion: three tryptic digests (one in buffer, one in methanol, and another in SDS), and a microwave-assisted acid hydrolysate of the protein extracts. Identified proteins--which included several groups of established protein biomarkers--were functionally classified. We discuss the functions and implications of these biomarkers within the context of zebrafish toxicology.
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Affiliation(s)
- Nan Wang
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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30
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Cañas B, Piñeiro C, Calvo E, López-Ferrer D, Gallardo JM. Trends in sample preparation for classical and second generation proteomics. J Chromatogr A 2007; 1153:235-58. [PMID: 17276441 DOI: 10.1016/j.chroma.2007.01.045] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2006] [Revised: 12/18/2006] [Accepted: 01/12/2007] [Indexed: 11/16/2022]
Abstract
Sample preparation is a fundamental step in the proteomics workflow. However, it is not easy to find compiled information updating this subject. In this paper, the strategies and protocols for protein extraction and identification, following either classical or second generation proteomics methodologies, are reviewed. Procedures for: tissue disruption, cell lysis, sample pre-fractionation, protein separation by 2-DE, protein digestion, mass spectrometry analysis, multidimensional peptide separations and quantification of protein expression level are described.
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Affiliation(s)
- Benito Cañas
- Dept. Química Analítica, Facultad de CC, Químicas, UCM, Av.Complutense s/n, Madrid 28040, Spain.
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31
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Kelly RT, Page JS, Tang K, Smith RD. Array of Chemically Etched Fused-Silica Emitters for Improving the Sensitivity and Quantitation of Electrospray Ionization Mass Spectrometry. Anal Chem 2007; 79:4192-8. [PMID: 17472340 DOI: 10.1021/ac062417e] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An array of emitters has been developed for increasing the sensitivity of electrospray ionization mass spectrometry (ESI-MS). The linear array consists of 19 chemically etched fused-silica capillaries arranged with 500 microm (center-to-center) spacing. The multiemitter device has a low dead volume to facilitate coupling to capillary liquid chromatography (LC) separations. The high aspect ratio of the emitters enables operation at flow rates as low as 20 nL/min/emitter, effectively extending the benefits of nanoelectrospray to higher flow rate analyses. To accommodate the larger ion current produced by the emitter array, a multicapillary inlet to the mass spectrometer was also constructed. The inlet, which matched the dimensions of the emitter array, preserved ion transmission efficiency. Standard reserpine solutions of varying concentration were electrosprayed at 1 microL/min using the multiemitter/multi-inlet combination, and the results were compared to those from a standard, single-emitter configuration. A 9-fold sensitivity enhancement was observed for the multiemitter relative to the single emitter. A bovine serum albumin tryptic digest was also analyzed, and a sensitivity increase ranging from 2.4- to 12.3-fold for the detected tryptic peptides resulted; the varying response was attributed to reduced ion suppression under the nanoESI conditions afforded by the emitter array. An equimolar mixture of leucine enkephalin and maltopentaose was studied to verify that ion suppression is indeed reduced for the multiplexed ESI (multi-ESI) array relative to a single emitter over a range of flow rates.
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Affiliation(s)
- Ryan T Kelly
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA
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32
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Kustos I, Kocsis B, Kilár F. Bacterial outer membrane protein analysis by electrophoresis and microchip technology. Expert Rev Proteomics 2007; 4:91-106. [PMID: 17288518 DOI: 10.1586/14789450.4.1.91] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Outer membrane proteins are indispensable components of bacterial cells and participate in several relevant functions of the microorganisms. Changes in the outer membrane protein composition might alter antibiotic sensitivity and pathogenicity. Furthermore, the effects of various factors on outer membrane protein expression, such as antibiotic treatment, mutation, changes in the environment, lipopolysaccharide modification and biofilm formation, have been analyzed. Traditionally, the outer membrane protein profile determination was performed by sodium dodecyl sulfate polyacrylamide gel electrophoresis. Converting this technique to capillary electrophoresis format resulted in faster separation, lower sample consumption and automation. Coupling capillary electrophoresis with mass spectrometry enabled the fast identification of bacterial proteins, while immediate quantitative analysis permitted the determination of up- and downregulation of certain outer membrane proteins. Adapting capillary electrophoresis to microchip format ensured a further ten- to 100-fold decrease in separation time. Application of different separation techniques combined with various sensitive detector systems has ensured further opportunities in the field of high-throughput bacterial protein analysis. This review provides an overview using selected examples of outer membrane proteins and the development and application of the electrophoretic and microchip technologies for the analysis of these proteins.
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Affiliation(s)
- Ildikó Kustos
- University of Pécs, Department of Medical Microbiology & Immunology, Faculty of Medicine, Pécs, Hungary.
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33
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Katayama H, Oda Y. Chemical proteomics for drug discovery based on compound-immobilized affinity chromatography. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 855:21-7. [PMID: 17241823 DOI: 10.1016/j.jchromb.2006.12.047] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2006] [Revised: 12/19/2006] [Accepted: 12/30/2006] [Indexed: 10/23/2022]
Abstract
Chemical proteomics is an effective approach to focused proteomics, having the potential to find specific interactors in moderate-scale comprehensive analysis. Unlike chemical genetics, chemical proteomics directly and comprehensively identifies proteins that bind specifically to candidate compounds by means of affinity chromatographic purification using the immobilized candidate, combined with mass spectrometric identification of interacting proteins. This is an effective approach for discovering unknown protein functions, identifying the molecular mechanisms of drug action, and obtaining information for optimization of lead compounds. However, immobilized-small molecule affinity chromatography always suffers from the problem of non-specific binders. Although several approaches were reported to reduce non-specific binding proteins, these are mainly focused on the use of low-binding-affinity beads or insertion of a spacer between the bead and the compound. Stable isotope labeling strategies have proven particularly advantageous for the discrimination of true interactors from many non-specific binders, including carrier proteins, such as serum albumin, and are expected to be valuable for drug discovery.
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Affiliation(s)
- Hiroyuki Katayama
- Eisai Co., Ltd., Laboratory of Seed Finding Technology, Tsukuba, Ibaraki, Japan
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34
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Suen G, Arshinoff BI, Taylor RG, Welch RD. Practical Applications of Bacterial Functional Genomics. Biotechnol Genet Eng Rev 2007; 24:213-42. [DOI: 10.1080/02648725.2007.10648101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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35
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Ratcliffe SJ, Yi T, Khandekar SS. Synthesis and characterization of 5'-p-fluorosulfonylbenzoyl-2' (or 3')-(biotinyl)adenosine as an activity-based probe for protein kinases. ACTA ACUST UNITED AC 2006; 12:126-32. [PMID: 17166825 DOI: 10.1177/1087057106296685] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Most of the kinase inhibitors that are approved for therapeutic uses or that are undergoing clinical trials are directed toward the adenosine triphosphate (ATP) binding site of protein kinases. 5'-Fluorosulfonylbenzoyl 5'-adenosine (FSBA) is an activitybased probe (ABP) that covalently modifies a conserved lysine present in the nucleotide binding site of most kinases. Here the authors describe synthesis of FSBA derivatives, 2'-biotinyl-FSBA and 3'-biotinyl-FSBA as kinase ABPs, and delineate a Western blot method to screen and validate ATP competitive protein kinase inhibitors using biotinyl-FSBA as a nonselective activity-based probe for protein kinases.
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36
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Hochholdinger F, Sauer M, Dembinsky D, Hoecker N, Muthreich N, Saleem M, Liu Y. Proteomic dissection of plant development. Proteomics 2006; 6:4076-83. [PMID: 16786485 DOI: 10.1002/pmic.200500851] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Plant development is controlled by complex endogenous genetic programs and responses to environmental cues. Proteome analyses have recently been introduced to plant biology to identify proteins instrumental in these developmental processes. To date most plant proteome studies have been employed to generate reference maps of the most abundant soluble proteins of plant organs at a defined developmental stage. However, proteomics is now also utilized for genetic studies comparing the proteomes of different plant genotypes, for physiological studies analyzing the influences of exogenous signals on a particular plant organ, and developmental studies investigating proteome changes during development. Technical advances are now beginning to allow a proteomic dissection of individual cell types, thus greatly increasing the information revealed by proteome analyses.
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Affiliation(s)
- Frank Hochholdinger
- ZMBP, Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany.
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37
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Abstract
The lethal species of malaria parasite, Plasmodium falciparum, continues to exact a huge toll of mortality and morbidity, particularly in sub-Saharan Africa. Completion of the genome sequence of this organism and advances in proteomics and mass spectrometry have opened up unprecedented opportunities for understanding the complex biology of this parasite and how it responds to drug challenge and other interventions. This review describes recent progress that has been made in applying proteomics technology to this important pathogen and provides a look forward to likely future developments.
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Affiliation(s)
- Paul F G Sims
- University of Manchester, Faculty of Life Sciences, Jackson's Mill, PO Box 88, Manchester, M60 1QD, UK.
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38
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Stubbs KA, Vocadlo DJ. Functional Proteomic Profiling of Glycan‐Processing Enzymes. Methods Enzymol 2006; 415:253-68. [PMID: 17116479 DOI: 10.1016/s0076-6879(06)15016-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Glycoconjugates play critical roles in regulating cellular and organismal functions. Consequently, defining the relative levels of these glycoconjugates under varied physiological conditions is important. Thus identifying and understanding the regulation of the enzymes that process these glycoconjugates are essential steps in understanding the role of this "glycocode" in development and disease. Activity-based affinity reagents are useful tools for probing these enzymes and should facilitate the unraveling of proteomes. One advantage of activity-based affinity probes is that they can simultaneously reveal multiple enzymes having similar activities. These probes can also be used to enrich proteomes of interest, thereby facilitating identification and cloning of new carbohydrate-processing enzymes. Here we review the current state of activity-based affinity probes for profiling carbohydrate-processing enzymes, focusing on successes and limitations, general design features, and a specific example describing profiling of exoglycosidases from cell lysates.
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Affiliation(s)
- Keith A Stubbs
- Department of Chemistry, Simon Frasier University, Burnaby, British Columbia, Canada
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