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Yeak KYC, Boekhorst J, Wels M, Abee T, Wells-Bennik MHJ. Prediction and validation of novel SigB regulon members in Bacillus subtilis and regulon structure comparison to Bacillales members. BMC Microbiol 2023; 23:17. [PMID: 36653740 PMCID: PMC9847131 DOI: 10.1186/s12866-022-02700-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 11/11/2022] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Sigma factor B (SigB) is the central regulator of the general stress response in Bacillus subtilis and regulates a group of genes in response to various stressors, known as the SigB regulon members. Genes that are directly regulated by SigB contain a promotor binding motif (PBM) with a previously identified consensus sequence. RESULTS In this study, refined SigB PBMs were derived and different spacer compositions and lengths (N12-N17) were taken into account. These were used to identify putative SigB-regulated genes in the B. subtilis genome, revealing 255 genes: 99 had been described in the literature and 156 genes were newly identified, increasing the number of SigB putative regulon members (with and without a SigB PBM) to > 500 in B. subtilis. The 255 genes were assigned to five categories (I-V) based on their similarity to the original SigB consensus sequences. The functionalities of selected representatives per category were assessed using promoter-reporter fusions in wt and ΔsigB mutants upon exposure to heat, ethanol, and salt stress. The activity of the PrsbV (I) positive control was induced upon exposure to all three stressors. PytoQ (II) showed SigB-dependent activity only upon exposure to ethanol, whereas PpucI (II) with a N17 spacer and PylaL (III) with a N16 spacer showed mild induction regardless of heat/ethanol/salt stress. PywzA (III) and PyaaI (IV) displayed ethanol-specific SigB-dependent activities despite a lower-level conserved - 10 binding motif. PgtaB (V) was SigB-induced under ethanol and salt stress while lacking a conserved - 10 binding region. The activities of PygaO and PykaA (III) did not show evident changes under the conditions tested despite having a SigB PBM that highly resembled the consensus. The identified extended SigB regulon candidates in B. subtilis are mainly involved in coping with stress but are also engaged in other cellular processes. Orthologs of SigB regulon candidates with SigB PBMs were identified in other Bacillales genomes, but not all showed a SigB PBM. Additionally, genes involved in the integration of stress signals to activate SigB were predicted in these genomes, indicating that SigB signaling and regulon genes are species-specific. CONCLUSION The entire SigB regulatory network is sophisticated and not yet fully understood even for the well-characterized organism B. subtilis 168. Knowledge and information gained in this study can be used in further SigB studies to uncover a complete picture of the role of SigB in B. subtilis and other species.
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Affiliation(s)
- Kah Yen Claire Yeak
- grid.419921.60000 0004 0588 7915NIZO, Ede, The Netherlands ,grid.4818.50000 0001 0791 5666Food Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Jos Boekhorst
- grid.419921.60000 0004 0588 7915NIZO, Ede, The Netherlands ,grid.4818.50000 0001 0791 5666Host Microbe Interactomics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Michiel Wels
- grid.419921.60000 0004 0588 7915NIZO, Ede, The Netherlands ,grid.426040.4Rijk Zwaan Breeding B.V, Fijnaart, The Netherlands
| | - Tjakko Abee
- grid.4818.50000 0001 0791 5666Food Microbiology, Wageningen University and Research, Wageningen, The Netherlands
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Proteomic Analysis of Normal Expression Differences Exist in Bacillus Subtilis 168 Cultivation. Curr Microbiol 2018; 75:803-810. [PMID: 29427007 DOI: 10.1007/s00284-018-1451-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 02/06/2018] [Indexed: 10/18/2022]
Abstract
Biological science discovery often involves comparing conditions to a normal state, but little is known about "normal." Therefore, we used proteomic strategy to compare data from replicate samples of Bacillus subtilis 168 which were grown under identical condition. The results show that 294 differentially expressed proteins were annotated in 88 Gene Ontology functional groups and enriched in 13 KEGG pathways. We assume that normal expression differences are associated with adaptation to diverse environments. Moreover, five proteins (CotY, ThiG, SspA, SspB, and SspE) and their related genes were identified as having significantly different expressions at translational and transcriptional levels. Most of them are related to stress resistance and germination, indicating that normal expression differences can be regarded as a rapid response mechanism for survival. However, unstable protein expression may cause some fermentative problems that were observed in histidine and sulfur metabolism pathways. Our study facilitates dissection of the influence of biological variance on cultivation safety and stability.
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Ruiz L, Hidalgo C, Blanco-Míguez A, Lourenço A, Sánchez B, Margolles A. Tackling probiotic and gut microbiota functionality through proteomics. J Proteomics 2016; 147:28-39. [DOI: 10.1016/j.jprot.2016.03.023] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 02/19/2016] [Accepted: 03/10/2016] [Indexed: 12/24/2022]
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4
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Maaß S, Becher D. Methods and applications of absolute protein quantification in microbial systems. J Proteomics 2016; 136:222-33. [PMID: 26825536 DOI: 10.1016/j.jprot.2016.01.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 01/05/2016] [Accepted: 01/21/2016] [Indexed: 02/05/2023]
Abstract
In the last years the scientific community faced an increased need to provide high-quality data on the concentration of single proteins within a cell. Especially against the background of the fast evolving field of systems biology this does not only apply for a few proteins but preferably for the whole proteome of the organism. Therefore there has been a rapid development from pure identification of proteins via characterization of changes between different conditions by relative protein quantification towards determination of absolute protein amounts for hundreds of protein species in a cell. This review aims for discussion of different small-scale and large-scale approaches for absolute protein quantification in bacterial cells to picture biological processes and explore life in deeper detail. The presented advantages and limitations of various methods may provide interested researchers help to appraise available methods, select the most appropriate technique and avoid common pitfalls during determination of protein concentration in a complex sample.
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Affiliation(s)
- Sandra Maaß
- Institute for Microbiology, Ernst Moritz Arndt Universität Greifswald, D-17487 Greifswald, Germany.
| | - Dörte Becher
- Institute for Microbiology, Ernst Moritz Arndt Universität Greifswald, D-17487 Greifswald, Germany
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5
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Pires VMR, Madeira MS, Dowle AA, Thomas J, Almeida AM, Prates JAM. Increased intramuscular fat induced by reduced dietary protein in finishing pigs: effects on the longissimus lumborum muscle proteome. MOLECULAR BIOSYSTEMS 2016; 12:2447-57. [DOI: 10.1039/c6mb00213g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Reduced protein diets affects the amounts of proteins related to fibre type and structure and energy.
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Affiliation(s)
- V. M. R. Pires
- CIISA
- Faculdade de Medicina Veterinária
- Universidade de Lisboa
- Avenida da Universidade Técnica
- 1300-477 Lisbon
| | - M. S. Madeira
- CIISA
- Faculdade de Medicina Veterinária
- Universidade de Lisboa
- Avenida da Universidade Técnica
- 1300-477 Lisbon
| | - A. A. Dowle
- Centre of Excellence in Mass Spectrometry
- University of York
- York
- UK
| | - J. Thomas
- Centre of Excellence in Mass Spectrometry
- University of York
- York
- UK
| | - A. M. Almeida
- CIISA
- Faculdade de Medicina Veterinária
- Universidade de Lisboa
- Avenida da Universidade Técnica
- 1300-477 Lisbon
| | - J. A. M. Prates
- CIISA
- Faculdade de Medicina Veterinária
- Universidade de Lisboa
- Avenida da Universidade Técnica
- 1300-477 Lisbon
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6
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Proteomics discovery of radioresistant cancer biomarkers for radiotherapy. Cancer Lett 2015; 369:289-97. [DOI: 10.1016/j.canlet.2015.09.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 09/08/2015] [Accepted: 09/23/2015] [Indexed: 12/28/2022]
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7
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Lee B, Tachon S, Eigenheer RA, Phinney BS, Marco ML. Lactobacillus casei Low-Temperature, Dairy-Associated Proteome Promotes Persistence in the Mammalian Digestive Tract. J Proteome Res 2015; 14:3136-47. [DOI: 10.1021/acs.jproteome.5b00387] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bokyung Lee
- Department of Food Science & Technology, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Sybille Tachon
- Department of Food Science & Technology, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Richard A. Eigenheer
- Proteomics
Core Facility, Genome Center, University of California, 451 East
Health Sciences Drive, Davis, California 95616, United States
| | - Brett S. Phinney
- Proteomics
Core Facility, Genome Center, University of California, 451 East
Health Sciences Drive, Davis, California 95616, United States
| | - Maria L. Marco
- Department of Food Science & Technology, University of California, One Shields Avenue, Davis, California 95616, United States
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Wendler S, Otto A, Ortseifen V, Bonn F, Neshat A, Schneiker-Bekel S, Walter F, Wolf T, Zemke T, Wehmeier UF, Hecker M, Kalinowski J, Becher D, Pühler A. Comprehensive proteome analysis of Actinoplanes sp. SE50/110 highlighting the location of proteins encoded by the acarbose and the pyochelin biosynthesis gene cluster. J Proteomics 2015; 125:1-16. [DOI: 10.1016/j.jprot.2015.04.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 04/02/2015] [Accepted: 04/12/2015] [Indexed: 01/05/2023]
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Voigt B, Albrecht D, Sievers S, Becher D, Bongaerts J, Evers S, Schweder T, Maurer KH, Hecker M. High-resolution proteome maps of Bacillus licheniformis
cells growing in minimal medium. Proteomics 2015; 15:2629-33. [DOI: 10.1002/pmic.201400504] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 02/09/2015] [Accepted: 04/09/2015] [Indexed: 12/30/2022]
Affiliation(s)
- Birgit Voigt
- Institute for Microbiology; Ernst-Moritz-Arndt-University; Greifswald Germany
| | - Dirk Albrecht
- Institute for Microbiology; Ernst-Moritz-Arndt-University; Greifswald Germany
| | - Susanne Sievers
- Institute for Microbiology; Ernst-Moritz-Arndt-University; Greifswald Germany
| | - Dörte Becher
- Institute for Microbiology; Ernst-Moritz-Arndt-University; Greifswald Germany
| | - Johannes Bongaerts
- Department of Chemistry and Biotechnology; Aachen University of Applied Sciences; Jülich Germany
| | | | - Thomas Schweder
- Institute of Pharmacy; Ernst-Moritz-Arndt-University; Greifswald Germany
| | | | - Michael Hecker
- Institute for Microbiology; Ernst-Moritz-Arndt-University; Greifswald Germany
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10
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Reddy PJ, Sinha S, Ray S, Sathe GJ, Chatterjee A, Prasad TSK, Dhali S, Srikanth R, Panda D, Srivastava S. Comprehensive analysis of temporal alterations in cellular proteome of Bacillus subtilis under curcumin treatment. PLoS One 2015; 10:e0120620. [PMID: 25874956 PMCID: PMC4397091 DOI: 10.1371/journal.pone.0120620] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 02/05/2015] [Indexed: 11/18/2022] Open
Abstract
Curcumin is a natural dietary compound with antimicrobial activity against various gram positive and negative bacteria. This study aims to investigate the proteome level alterations in Bacillus subtilis due to curcumin treatment and identification of its molecular/cellular targets to understand the mechanism of action. We have performed a comprehensive proteomic analysis of B. subtilis AH75 strain at different time intervals of curcumin treatment (20, 60 and 120 min after the drug exposure, three replicates) to compare the protein expression profiles using two complementary quantitative proteomic techniques, 2D-DIGE and iTRAQ. To the best of our knowledge, this is the first comprehensive longitudinal investigation describing the effect of curcumin treatment on B. subtilis proteome. The proteomics analysis revealed several interesting targets such UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1, putative septation protein SpoVG and ATP-dependent Clp protease proteolytic subunit. Further, in silico pathway analysis using DAVID and KOBAS has revealed modulation of pathways related to the fatty acid metabolism and cell wall synthesis, which are crucial for cell viability. Our findings revealed that curcumin treatment lead to inhibition of the cell wall and fatty acid synthesis in addition to differential expression of many crucial proteins involved in modulation of bacterial metabolism. Findings obtained from proteomics analysis were further validated using 5-cyano-2,3-ditolyl tetrazolium chloride (CTC) assay for respiratory activity, resazurin assay for metabolic activity and membrane integrity assay by potassium and inorganic phosphate leakage measurement. The gene expression analysis of selected cell wall biosynthesis enzymes has strengthened the proteomics findings and indicated the major effect of curcumin on cell division.
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Affiliation(s)
- Panga Jaipal Reddy
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Sneha Sinha
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Sandipan Ray
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Gajanan J. Sathe
- Institute of Bioinformatics, International Tech Park, Whitefield, Bangalore, India
- Manipal University, Madhav Nagar,Manipal, India
| | - Aditi Chatterjee
- Institute of Bioinformatics, International Tech Park, Whitefield, Bangalore, India
- Manipal University, Madhav Nagar,Manipal, India
| | - T. S. Keshava Prasad
- Institute of Bioinformatics, International Tech Park, Whitefield, Bangalore, India
| | - Snigdha Dhali
- Proteomics Laboratory, National Centre for Cell Science, Ganeshkhind, Pune, Maharashtra, India
| | - Rapole Srikanth
- Proteomics Laboratory, National Centre for Cell Science, Ganeshkhind, Pune, Maharashtra, India
| | - Dulal Panda
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
- * E-mail:
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11
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A comprehensive proteomic analysis of totarol induced alterations in Bacillus subtilis by multipronged quantitative proteomics. J Proteomics 2015; 114:247-62. [DOI: 10.1016/j.jprot.2014.10.025] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 09/28/2014] [Accepted: 10/20/2014] [Indexed: 12/25/2022]
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12
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Otto A, Becher D, Schmidt F. Quantitative proteomics in the field of microbiology. Proteomics 2014; 14:547-65. [PMID: 24376008 DOI: 10.1002/pmic.201300403] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Revised: 11/15/2013] [Accepted: 12/06/2013] [Indexed: 12/11/2022]
Abstract
Quantitative proteomics has become an indispensable analytical tool for microbial research. Modern microbial proteomics covers a wide range of topics in basic and applied research from in vitro characterization of single organisms to unravel the physiological implications of stress/starvation to description of the proteome content of a cell at a given time. With the techniques available, ranging from classical gel-based procedures to modern MS-based quantitative techniques, including metabolic and chemical labeling, as well as label-free techniques, quantitative proteomics is today highly successful in sophisticated settings of high complexity such as host-pathogen interactions, mixed microbial communities, and microbial metaproteomics. In this review, we will focus on the vast range of techniques practically applied in current research with an introduction of the workflows used for quantitative comparisons, a description of the advantages/disadvantages of the various methods, reference to hallmark publications and presentation of applications in current microbial research.
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Affiliation(s)
- Andreas Otto
- Institute for Microbiology, Ernst Moritz Arndt University Greifswald, Germany
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13
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Maaβ S, Wachlin G, Bernhardt J, Eymann C, Fromion V, Riedel K, Becher D, Hecker M. Highly precise quantification of protein molecules per cell during stress and starvation responses in Bacillus subtilis. Mol Cell Proteomics 2014; 13:2260-76. [PMID: 24878497 PMCID: PMC4159648 DOI: 10.1074/mcp.m113.035741] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 05/02/2014] [Indexed: 11/06/2022] Open
Abstract
Systems biology based on high quality absolute quantification data, which are mandatory for the simulation of biological processes, successively becomes important for life sciences. We provide protein concentrations on the level of molecules per cell for more than 700 cytosolic proteins of the Gram-positive model bacterium Bacillus subtilis during adaptation to changing growth conditions. As glucose starvation and heat stress are typical challenges in B. subtilis' natural environment and induce both, specific and general stress and starvation proteins, these conditions were selected as models for starvation and stress responses. Analyzing samples from numerous time points along the bacterial growth curve yielded reliable and physiologically relevant data suitable for modeling of cellular regulation under altered growth conditions. The analysis of the adaptational processes based on protein molecules per cell revealed stress-specific modulation of general adaptive responses in terms of protein amount and proteome composition. Furthermore, analysis of protein repartition during glucose starvation showed that biomass seems to be redistributed from proteins involved in amino acid biosynthesis to enzymes of the central carbon metabolism. In contrast, during heat stress most resources of the cell, namely those from amino acid synthetic pathways, are used to increase the amount of chaperones and proteases. Analysis of dynamical aspects of protein synthesis during heat stress adaptation revealed, that these proteins make up almost 30% of the protein mass accumulated during early phases of this stress.
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Affiliation(s)
- Sandra Maaβ
- From the ‡Institute for Microbiology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany
| | - Gerhild Wachlin
- From the ‡Institute for Microbiology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany
| | - Jörg Bernhardt
- From the ‡Institute for Microbiology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany
| | - Christine Eymann
- From the ‡Institute for Microbiology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany
| | - Vincent Fromion
- §INRA, Mathématique Informatique et Génome UR1077, 78350 Jouy-en-Josas, France
| | - Katharina Riedel
- From the ‡Institute for Microbiology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany
| | - Dörte Becher
- From the ‡Institute for Microbiology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany;
| | - Michael Hecker
- From the ‡Institute for Microbiology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany
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14
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You J, Willcox MD, Madigan MC, Wasinger V, Schiller B, Walsh BJ, Graham PH, Kearsley JH, Li Y. Tear fluid protein biomarkers. Adv Clin Chem 2014; 62:151-96. [PMID: 24772667 DOI: 10.1016/b978-0-12-800096-0.00004-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The tear film covers and protects the ocular surface. It contains various molecules including a large variety of proteins. The protein composition of the tear fluid can change with respect to various local and systemic diseases. Prior to the advent of the proteomic era, tear protein analysis was limited to a few analytical techniques, the most common of which was immunoelectrophoresis, an approach dependent on antibody availability. Using proteomics, hundreds of tear proteins could potentially be identified and subsequently studied. Although detection of low-abundance proteins in the complex tear proteome remains a challenge, advances in sample fractionation and mass spectrometry have greatly enhanced our ability to detect these proteins. With increasing proteomic applications, tears show great potential as biomarkers in the development of clinical assays for various human diseases. In this chapter, we discuss the structure and functions of the tear film and methods for its collection. We also summarize potential tear protein biomarkers identified using proteomic techniques for both ocular and systemic diseases. Finally, modern proteomic techniques for tear biomarker research and future challenges are explored.
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Oliveira BM, Coorssen JR, Martins-de-Souza D. 2DE: the phoenix of proteomics. J Proteomics 2014; 104:140-50. [PMID: 24704856 DOI: 10.1016/j.jprot.2014.03.035] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 03/21/2014] [Accepted: 03/24/2014] [Indexed: 12/22/2022]
Abstract
UNLABELLED Given the rapid developments in mass spectrometry (MS) in terms of sensitivity, mass accuracy, and throughput, some have suggested that two-dimensional gel electrophoresis (2DE) may no longer be a method of choice for proteomic analyses. However, as recognition of issues with these newer shotgun-MS approaches grows, there is a fresh and growing regard for the maturity of 2DE-MS as a genuine top-down analytical approach, particularly as it resolves thousands of intact protein species in a single run, enabling the simultaneous analysis of total protein complement, including isoforms and post-translational modifications. Given the strengths of both, it is most appropriate to view these as complementary or at least parallel approaches: as proteins encompass a myriad of physico-chemical properties, and the real aim is to explore proteomes as deeply as possible, all available resolving strategies must be considered in terms of the complexity encountered. It is time to critically and constructively focus on the optimization and integration of existing techniques rather than simplistically suggesting that one should replace the other. Our intention here is thus to present an overview of protein resolving techniques, focusing on milestones associated with 2DE, including pros, cons, advances and variations, in particular relative to shotgun proteomic approaches. BIOLOGICAL SIGNIFICANCE Proteomic researchers recognize the importance of 2DE in the history of proteomics. But the latest developments in mass spectrometry-based techniques have led some researchers to retire 2DE in their labs. However, we argue here that 2DE-MS is a genuine top-down analytical approach. The significance of this discussion is to make proteomic researchers aware of the importance of this technique in a proteomic pipeline. This article is part of a Special Issue entitled: Environmental and structural proteomics.
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Affiliation(s)
- Bruno M Oliveira
- Catarinense Federal Institute, Videira Campus, Videira, SC, Brazil
| | - Jens R Coorssen
- Dept. of Molecular Physiology, School of Medicine, University of Western Sydney, Australia; UWS Molecular Medicine Research Group, University of Western Sydney, Australia.
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry, Institute of Biology, State University of Campinas (UNICAMP), Campinas, Sao Paulo, Brazil; Laboratory of Neuroscience (LIM-27), Department and Institute of Psychiatry, Faculty of Medicine, University of São Paulo, Brazil; Dept. of Psychiatry and Psychotherapy, Ludwig Maximilians University (LMU), Munich, Germany.
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Antelmann H, Hecker M, Zuber P. Proteomic signatures uncover thiol-specific electrophile resistance mechanisms inBacillus subtilis. Expert Rev Proteomics 2014; 5:77-90. [DOI: 10.1586/14789450.5.1.77] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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17
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Beretov J, Wasinger VC, Graham PH, Millar EK, Kearsley JH, Li Y. Proteomics for breast cancer urine biomarkers. Adv Clin Chem 2014; 63:123-67. [PMID: 24783353 DOI: 10.1016/b978-0-12-800094-6.00004-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Although the survival of breast cancer (BC) patients has increased over the last two decades due to improved screening programs and postoperative adjuvant systemic therapies, many patients die from metastatic relapse. Current biomarkers used in the clinic are not useful for the early detection of BC, or monitoring its progression, and have limited value in predicting response to treatment. The development of proteomic techniques has sparked new searches for novel protein markers for many diseases including BC. Proteomic techniques allow for a high-throughput analysis of samples with the visualization and quantification of thousands of potential protein and peptide markers. Human urine is one of the most interesting and useful biofluids for routine testing and provides an excellent resource for the discovery of novel biomarkers, with the advantage over tissue biopsy samples due to the ease and less invasive nature of collection. In this review, we summarize the results from studies where urine was used as a source for BC biomarker research and discuss urine sample preparation, its advantage, challenges, and limitation. We focus on the gel-based proteomic approaches as well as the recent development of quantitative techniques in BC urine biomarker detection. Finally, the future use of modern proteomic techniques in BC biomarker identification will be discussed.
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Miller I, Serchi T, Murk AJ, Gutleb AC. The added value of proteomics for toxicological studies. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART B, CRITICAL REVIEWS 2014; 17:225-246. [PMID: 24828453 DOI: 10.1080/10937404.2014.904730] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Proteomics has the potential to elucidate complex patterns of toxic action attributed to its unique holistic a posteriori approach. In the case of toxic compounds for which the mechanism of action is not completely understood, a proteomic approach may provide valuable mechanistic insight. This review provides an overview of currently available proteomic techniques, including examples of their application in toxicological in vivo and in vitro studies. Future perspectives for a wider application of state-of-the-art proteomic techniques in the field of toxicology are discussed. The examples concern experiments with dioxins, polychlorinated biphenyls, and polybrominated diphenyl ethers as model compounds, as they exhibit a plethora of sublethal effects, of which some mechanisms were revealed via successful proteomic studies. Generally, this review shows the added value of including proteomics in a modern tool box for toxicological studies.
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Affiliation(s)
- I Miller
- a Institute for Medical Biochemistry, Department for Biomedical Sciences , University of Veterinary Medicine Vienna , Vienna , Austria
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Differential Proteomic Analysis of Acute Contusive Spinal Cord Injury in Rats Using iTRAQ Reagent Labeling and LC–MS/MS. Neurochem Res 2013; 38:2247-55. [DOI: 10.1007/s11064-013-1132-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 07/18/2013] [Accepted: 08/10/2013] [Indexed: 11/25/2022]
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Tanca A, Biosa G, Pagnozzi D, Addis MF, Uzzau S. Comparison of detergent-based sample preparation workflows for LTQ-Orbitrap analysis of the Escherichia coli proteome. Proteomics 2013; 13:2597-607. [PMID: 23784971 DOI: 10.1002/pmic.201200478] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 04/09/2013] [Accepted: 05/28/2013] [Indexed: 11/06/2022]
Abstract
This work presents a comparative evaluation of several detergent-based sample preparation workflows for the MS-based analysis of bacterial proteomes, performed using the model organism Escherichia coli. Initially, RapiGest- and SDS-based buffers were compared for their protein extraction efficiency and quality of the MS data generated. As a result, SDS performed best in terms of total protein yields and overall number of MS identifications, mainly due to a higher efficiency in extracting high molecular weight (MW) and membrane proteins, while RapiGest led to an enrichment in periplasmic and fimbrial proteins. Then, SDS extracts underwent five different MS sample preparation workflows, including: detergent removal by spin columns followed by in-solution digestion (SC), protein precipitation followed by in-solution digestion in ammonium bicarbonate or urea buffer, filter-aided sample preparation (FASP), and 1DE separation followed by in-gel digestion. On the whole, about 1000 proteins were identified upon LC-MS/MS analysis of all preparations (>1100 with the SC workflow), with FASP producing more identified peptides and a higher mean sequence coverage. Each protocol exhibited specific behaviors in terms of MW, hydrophobicity, and subcellular localization distribution of the identified proteins; a comparative assessment of the different outputs is presented.
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Affiliation(s)
- Alessandro Tanca
- Porto Conte Ricerche, Tramariglio, Alghero, Italy; Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
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Voigt B, Hieu CX, Hempel K, Becher D, Schlüter R, Teeling H, Glöckner FO, Amann R, Hecker M, Schweder T. Cell surface proteome of the marine planctomycete Rhodopirellula baltica. Proteomics 2012; 12:1781-91. [PMID: 22623273 DOI: 10.1002/pmic.201100512] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The surface proteome (surfaceome) of the marine planctomycete Rhodopirellula baltica SH1(T) was studied using a biotinylation and a proteinase K approach combined with SDS-PAGE and mass spectrometry. 52 of the proteins identified in both approaches could be assigned to the group of potential surface proteins. Among them are some high molecular weight proteins, potentially involved in cell-cell attachment, that contain domains shown before to be typical for surface proteins like cadherin/dockerin domains, a bacterial adhesion domain or the fasciclin domain. The identification of proteins with enzymatic functions in the R. baltica surfaceome provides further clues for the suggestion that some degradative enzymes may be anchored onto the cell surface. YTV proteins, which have been earlier supposed to be components of the proteinaceous cell wall of R. baltica, were detected in the surface proteome. Additionally, 8 proteins with a novel protein structure combining a conserved type IV pilin/N-methylation domain and a planctomycete-typical DUF1559 domain were identified.
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Affiliation(s)
- Birgit Voigt
- Institute for Microbiology, Ernst-Moritz-Arndt-University, Greifswald, Germany
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22
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Yu Y, Xie L, Gunawardena HP, Khatun J, Maier C, Spitzer W, Leerkes M, Giddings MC, Chen X. GOFAST: an integrated approach for efficient and comprehensive membrane proteome analysis. Anal Chem 2012; 84:9008-14. [PMID: 23030679 DOI: 10.1021/ac300134e] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Membrane proteomics, the large-scale analysis of membrane proteins, is often constrained by the difficulties of achieving fully resolvable separation and resistance to proteolysis, both of which could lead to low recovery and low identification rates of membrane proteins. Here, we introduce a novel integrated approach, GELFrEE Optimized FASP Technology (GOFAST) for large-scale and comprehensive membrane proteins analysis. Using an array of sample preparation techniques including gel-eluted liquid fraction entrapment electrophoresis (GELFrEE), filter-aided sample preparation (FASP), and microwave-assisted on-filter enzymatic digestion, we identified 2 090 proteins from the membrane fraction of a leukemia cell line (K562). Of these, 37% are annotated as membrane proteins according to gene ontology analysis, resulting in the largest membrane proteome of leukemia cells reported to date. Our approach combines the advantages of GELFrEE high-loading capacity, gel-free separation, efficient depletion of detergents, and microwave-assisted on-filter digestion, minimizing sample losses and maximizing MS-detectable sequence coverage of individual proteins. In addition, this approach also shows great potential for the identification of alternative splicing products.
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Affiliation(s)
- Yanbao Yu
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, North Carolina 27599, United States
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Gesslbauer B, Poljak A, Handwerker C, Schüler W, Schwendenwein D, Weber C, Lundberg U, Meinke A, Kungl AJ. Comparative membrane proteome analysis of three Borrelia species. Proteomics 2012; 12:845-58. [PMID: 22539435 DOI: 10.1002/pmic.201100211] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The versatility of the surface of Borrelia, the causative agent of Lyme borreliosis, is very important in host-pathogen interactions allowing bacteria to survive in ticks and to persist in a mammalian environment. To identify the surface proteome of Borrelia, we have performed a large comparative proteomic analysis on the three most important pathogenic Borrelia species, namely B. burgdorferi (strain B31), B. afzelii (strain K78), and B. garinii (strain PBi). Isolation of membrane proteins was performed by using three different approaches: (i) a detergent-based fractionation of outer membrane proteins; (ii) a trypsin-based partial shedding of outer cell surface proteins; (iii) biotinylation of membrane proteins and preparation of the biotin-labelled fraction using streptavidin. Proteins derived from the detergent-based fractionation were further sub-fractionated by heparin affinity chromatography since heparin-like molecules play an important role for microbial entry into human cells. All isolated proteins were analysed using either a gel-based liquid chromatography (LC)-MS/MS technique or by two-dimensional (2D)-LC-MS/MS resulting in the identification of 286 unique proteins. Ninety seven of these were found in all three Borrelia species, representing potential targets for a broad coverage vaccine for the prevention of Lyme borreliosis caused by the different Borrelia species.
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Kailasa SK, Wu HF. Dispersive liquid–liquid microextraction using functionalized Mg(OH)2 NPs with oleic acid as hydrophobic affinity probes for the analysis of hydrophobic proteins in bacteria by MALDI MS. Analyst 2012; 137:4490-6. [DOI: 10.1039/c2an35788g] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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25
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Rogers RS, Dharsee M, Ackloo S, Sivak JM, Flanagan JG. Proteomics analyses of human optic nerve head astrocytes following biomechanical strain. Mol Cell Proteomics 2011; 11:M111.012302. [PMID: 22126795 DOI: 10.1074/mcp.m111.012302] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
We investigate the role of glial cell activation in the human optic nerve caused by raised intraocular pressure, and their potential role in the development of glaucomatous optic neuropathy. To do this we present a proteomics study of the response of cultured, optic nerve head astrocytes to biomechanical strain, the magnitude and mode of strain based on previously published quantitative models. In this case, astrocytes were subjected to 3 and 12% stretches for either 2 h or 24 h. Proteomic methods included nano-liquid chromatography, tandem mass spectrometry, and iTRAQ labeling. Using controls for both stretch and time, a six-plex iTRAQ liquid chromatography- tandem MS (LC/MS/MS) experiment yielded 573 proteins discovered at a 95% confidence limit. The pathways included transforming growth factor β1, tumor necrosis factor, caspase 3, and tumor protein p53, which have all been implicated in the activation of astrocytes and are believed to play a role in the development of glaucomatous optic neuropathy. Confirmation of the iTRAQ analysis was performed by Western blotting of various proteins of interest including ANXA 4, GOLGA2, and αB-Crystallin.
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Affiliation(s)
- Ronan S Rogers
- Institute of Medical Science, University of Toronto, Toronto, Canada.
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26
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Ang CS, Binos S, Knight MI, Moate PJ, Cocks BG, McDonagh MB. Global Survey of the Bovine Salivary Proteome: Integrating Multidimensional Prefractionation, Targeted, and Glycocapture Strategies. J Proteome Res 2011; 10:5059-69. [DOI: 10.1021/pr200516d] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Ching-Seng Ang
- Biosciences Research Division, ‡Dairy Futures Cooperative Research Centre, and §Future Farming Research Division, Department of Primary Industries, 1 Park Drive, Bundoora, Victoria, Australia
| | - Steve Binos
- Biosciences Research Division, ‡Dairy Futures Cooperative Research Centre, and §Future Farming Research Division, Department of Primary Industries, 1 Park Drive, Bundoora, Victoria, Australia
| | - Matthew I Knight
- Biosciences Research Division, ‡Dairy Futures Cooperative Research Centre, and §Future Farming Research Division, Department of Primary Industries, 1 Park Drive, Bundoora, Victoria, Australia
| | - Peter J Moate
- Biosciences Research Division, ‡Dairy Futures Cooperative Research Centre, and §Future Farming Research Division, Department of Primary Industries, 1 Park Drive, Bundoora, Victoria, Australia
| | - Benjamin G Cocks
- Biosciences Research Division, ‡Dairy Futures Cooperative Research Centre, and §Future Farming Research Division, Department of Primary Industries, 1 Park Drive, Bundoora, Victoria, Australia
| | - Matthew B McDonagh
- Biosciences Research Division, ‡Dairy Futures Cooperative Research Centre, and §Future Farming Research Division, Department of Primary Industries, 1 Park Drive, Bundoora, Victoria, Australia
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Ramírez-Boo M, Núnez E, Jorge I, Navarro P, Fernandes LT, Segalés J, Garrido JJ, Vázquez J, Moreno Á. Quantitative proteomics by 2-DE, 16O/18O labelling and linear ion trap mass spectrometry analysis of lymph nodes from piglets inoculated by porcine circovirus type 2. Proteomics 2011; 11:3452-69. [DOI: 10.1002/pmic.201000610] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Revised: 05/18/2011] [Accepted: 05/30/2011] [Indexed: 12/13/2022]
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From the genome sequence to the protein inventory of Bacillus subtilis. Proteomics 2011; 11:2971-80. [DOI: 10.1002/pmic.201100090] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Revised: 04/07/2011] [Accepted: 04/20/2011] [Indexed: 12/12/2022]
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Chiapello M, Daghino S, Martino E, Perotto S. Cellular response of Fusarium oxysporum to crocidolite asbestos as revealed by a combined proteomic approach. J Proteome Res 2010; 9:3923-31. [PMID: 20578744 DOI: 10.1021/pr100133d] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Cellular mechanisms of asbestos toxicity rely, at least in part, on the chemical composition of these minerals. Iron ions are directly involved in the accepted mechanism of fiber toxicity because they constitute active centers where release of free radicals and reactive oxygen species takes place. Although no current technology is available for the remediation of asbestos polluted sites, the soil fungus Fusarium oxysporum was found to be very effective in iron extraction from crocidolite asbestos in vitro, and to cause a significant reduction in asbestos surface reactivity and oxidative damage to naked DNA. As little information is available on the molecular mechanisms of the fungus-asbestos interactions, a combined proteomic approach that used 2-DE, shotgun and quantitative iTRAQ proteomics was used to investigate the fungal metabolic activities in the presence of crocidolite, an iron-rich type of asbestos. Although global proteomic analyses did not show significant changes in the protein expression pattern of F. oxysporum when exposed to asbestos fibers, some proteins specifically regulated by asbestos suggest up-regulation of metabolic pathways involved in protection from oxidative stress. When compared with the response to crocidolite observed by other authors in human lung epithelial cells, that unlike fungi can internalize the asbestos fibres, a significant difference was the regulation of the pentose phosphate pathway.
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Affiliation(s)
- Marco Chiapello
- Department of Plant Biology, University of Torino, and Institute for Plant Protection CNR, v.le Mattioli 25, Torino, Italy
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30
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Ang CS, Phung J, Nice EC. The discovery and validation of colorectal cancer biomarkers. Biomed Chromatogr 2010; 25:82-99. [PMID: 21058408 DOI: 10.1002/bmc.1528] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Accepted: 08/23/2010] [Indexed: 12/27/2022]
Abstract
Colorectal cancer is currently the third most common malignancy in the world. Patients have excellent prognosis following surgical resection if their tumour is still localized at diagnosis. By contrast, once the tumour has started to metastasize, prognosis is much poorer. Accurate early detection can therefore significantly reduce the mortality from this disease. However, current tests either lack the required sensitivity and selectivity or are costly and invasive. Improved biomarkers, or panels of biomarkers, are therefore urgently required. We have addressed current screening strategies and potential protein biomarkers that have been proposed. The role of both discovery and hypothesis-driven proteomics approaches for biomarker discovery and validation is discussed. Using such approaches we show how multiple reaction monitoring (MRM) can be successfully developed and used for quantitative multiplexed analysis of potential faecal biomarkers.
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Affiliation(s)
- Ching-Seng Ang
- Ludwig Institute for Cancer Research, Melbourne Tumour Biology Branch, Melbourne, Australia
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31
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Engelen K, Sifrim A, Van de Plas B, Laukens K, Arckens L, Marchal K. Alternative Experimental Design with an Applied Normalization Scheme Can Improve Statistical Power in 2D-DIGE Experiments. J Proteome Res 2010; 9:4919-26. [DOI: 10.1021/pr100010u] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kristof Engelen
- Department of Microbial and Molecular Systems, Katholieke Universiteit Leuven, Kasteelpark Arenberg 20, 3001 Leuven, Belgium, Research group of Neuroplasticity and Neuroproteomics, Katholieke Universiteit Leuven, Naamsestraat 59, 3000 Leuven, Belgium, and Intelligent Systems Laboratory, University of Antwerp, Middelheimlaan 1 B, 2020 Antwerp, Belgium
| | - Alejandro Sifrim
- Department of Microbial and Molecular Systems, Katholieke Universiteit Leuven, Kasteelpark Arenberg 20, 3001 Leuven, Belgium, Research group of Neuroplasticity and Neuroproteomics, Katholieke Universiteit Leuven, Naamsestraat 59, 3000 Leuven, Belgium, and Intelligent Systems Laboratory, University of Antwerp, Middelheimlaan 1 B, 2020 Antwerp, Belgium
| | - Babs Van de Plas
- Department of Microbial and Molecular Systems, Katholieke Universiteit Leuven, Kasteelpark Arenberg 20, 3001 Leuven, Belgium, Research group of Neuroplasticity and Neuroproteomics, Katholieke Universiteit Leuven, Naamsestraat 59, 3000 Leuven, Belgium, and Intelligent Systems Laboratory, University of Antwerp, Middelheimlaan 1 B, 2020 Antwerp, Belgium
| | - Kris Laukens
- Department of Microbial and Molecular Systems, Katholieke Universiteit Leuven, Kasteelpark Arenberg 20, 3001 Leuven, Belgium, Research group of Neuroplasticity and Neuroproteomics, Katholieke Universiteit Leuven, Naamsestraat 59, 3000 Leuven, Belgium, and Intelligent Systems Laboratory, University of Antwerp, Middelheimlaan 1 B, 2020 Antwerp, Belgium
| | - Lutgarde Arckens
- Department of Microbial and Molecular Systems, Katholieke Universiteit Leuven, Kasteelpark Arenberg 20, 3001 Leuven, Belgium, Research group of Neuroplasticity and Neuroproteomics, Katholieke Universiteit Leuven, Naamsestraat 59, 3000 Leuven, Belgium, and Intelligent Systems Laboratory, University of Antwerp, Middelheimlaan 1 B, 2020 Antwerp, Belgium
| | - Kathleen Marchal
- Department of Microbial and Molecular Systems, Katholieke Universiteit Leuven, Kasteelpark Arenberg 20, 3001 Leuven, Belgium, Research group of Neuroplasticity and Neuroproteomics, Katholieke Universiteit Leuven, Naamsestraat 59, 3000 Leuven, Belgium, and Intelligent Systems Laboratory, University of Antwerp, Middelheimlaan 1 B, 2020 Antwerp, Belgium
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Soufi B, Kumar C, Gnad F, Mann M, Mijakovic I, Macek B. Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) Applied to Quantitative Proteomics of Bacillus subtilis. J Proteome Res 2010; 9:3638-46. [DOI: 10.1021/pr100150w] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Boumediene Soufi
- Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany, Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark, Micalis, AgroParisTech-INRA, Domaine de Vilvert, 78352 Jouy-en-Josas, France, and Proteome Center Tuebingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Chanchal Kumar
- Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany, Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark, Micalis, AgroParisTech-INRA, Domaine de Vilvert, 78352 Jouy-en-Josas, France, and Proteome Center Tuebingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Florian Gnad
- Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany, Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark, Micalis, AgroParisTech-INRA, Domaine de Vilvert, 78352 Jouy-en-Josas, France, and Proteome Center Tuebingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Matthias Mann
- Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany, Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark, Micalis, AgroParisTech-INRA, Domaine de Vilvert, 78352 Jouy-en-Josas, France, and Proteome Center Tuebingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Ivan Mijakovic
- Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany, Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark, Micalis, AgroParisTech-INRA, Domaine de Vilvert, 78352 Jouy-en-Josas, France, and Proteome Center Tuebingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Boris Macek
- Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany, Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark, Micalis, AgroParisTech-INRA, Domaine de Vilvert, 78352 Jouy-en-Josas, France, and Proteome Center Tuebingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
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Dumpala PR, Gülsoy N, Lawrence ML, Karsi A. Proteomic analysis of the fish pathogen Flavobacterium columnare. Proteome Sci 2010; 8:26. [PMID: 20525376 PMCID: PMC2890538 DOI: 10.1186/1477-5956-8-26] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Accepted: 06/04/2010] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Flavobacterium columnare causes columnaris disease in cultured and wild fish populations worldwide. Columnaris is the second most prevalent bacterial disease of commercial channel catfish industry in the United States. Despite its economic importance, little is known about the expressed proteins and virulence mechanisms of F. columnare. Here, we report the first high throughput proteomic analysis of F. columnare using 2-D LC ESI MS/MS and 2-DE MALDI TOF/TOF MS. RESULTS Proteins identified in this study and predicted from the draft F. columnare genome were clustered into functional groups using clusters of orthologous groups (COGs), and their subcellular locations were predicted. Possible functional relations among the identified proteins were determined using pathway analysis. The total number of unique F. columnare proteins identified using both 2-D LC and 2-DE approaches was 621, of which 10.95% (68) were identified by both methods, while 77.29% (480) and 11.76% (73) were unique in 2-D LC and 2-DE, respectively. COG groupings and subcellular localizations were similar between our data set and proteins predicted from the whole genome. Twenty eight pathways were significantly represented in our dataset (P < 0.05). CONCLUSION Results from this study provide experimental evidence for many proteins that were predicted from the F. columnare genome annotation, and they should accelerate functional and comparative studies aimed at understanding virulence mechanisms of this important pathogen.
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Affiliation(s)
- Pradeep R Dumpala
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762-6100, USA
| | - Nagihan Gülsoy
- Department of Biology, Faculty of Art and Science, Marmara University, Göztepe, İstanbul 34722, Turkey
| | - Mark L Lawrence
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762-6100, USA
| | - Attila Karsi
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762-6100, USA
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Matallana-Surget S, Leroy B, Wattiez R. Shotgun proteomics: concept, key points and data mining. Expert Rev Proteomics 2010; 7:5-7. [PMID: 20121468 DOI: 10.1586/epr.09.101] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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35
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Karp NA, Huber W, Sadowski PG, Charles PD, Hester SV, Lilley KS. Addressing accuracy and precision issues in iTRAQ quantitation. Mol Cell Proteomics 2010; 9:1885-97. [PMID: 20382981 DOI: 10.1074/mcp.m900628-mcp200] [Citation(s) in RCA: 403] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
iTRAQ (isobaric tags for relative or absolute quantitation) is a mass spectrometry technology that allows quantitative comparison of protein abundance by measuring peak intensities of reporter ions released from iTRAQ-tagged peptides by fragmentation during MS/MS. However, current data analysis techniques for iTRAQ struggle to report reliable relative protein abundance estimates and suffer with problems of precision and accuracy. The precision of the data is affected by variance heterogeneity: low signal data have higher relative variability; however, low abundance peptides dominate data sets. Accuracy is compromised as ratios are compressed toward 1, leading to underestimation of the ratio. This study investigated both issues and proposed a methodology that combines the peptide measurements to give a robust protein estimate even when the data for the protein are sparse or at low intensity. Our data indicated that ratio compression arises from contamination during precursor ion selection, which occurs at a consistent proportion within an experiment and thus results in a linear relationship between expected and observed ratios. We proposed that a correction factor can be calculated from spiked proteins at known ratios. Then we demonstrated that variance heterogeneity is present in iTRAQ data sets irrespective of the analytical packages, LC-MS/MS instrumentation, and iTRAQ labeling kit (4-plex or 8-plex) used. We proposed using an additive-multiplicative error model for peak intensities in MS/MS quantitation and demonstrated that a variance-stabilizing normalization is able to address the error structure and stabilize the variance across the entire intensity range. The resulting uniform variance structure simplifies the downstream analysis. Heterogeneity of variance consistent with an additive-multiplicative model has been reported in other MS-based quantitation including fields outside of proteomics; consequently the variance-stabilizing normalization methodology has the potential to increase the capabilities of MS in quantitation across diverse areas of biology and chemistry.
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Affiliation(s)
- Natasha A Karp
- European Bioinformatics Institute, European Molecular Biology Laboratory Outstation, Hinxton, UK
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36
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Delmotte N, Ahrens CH, Knief C, Qeli E, Koch M, Fischer HM, Vorholt JA, Hennecke H, Pessi G. An integrated proteomics and transcriptomics reference data set provides new insights into the Bradyrhizobium japonicum bacteroid metabolism in soybean root nodules. Proteomics 2010; 10:1391-400. [PMID: 20104621 DOI: 10.1002/pmic.200900710] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2009] [Accepted: 12/03/2009] [Indexed: 11/07/2022]
Abstract
Bradyrhizobium japonicum, a gram-negative soil bacterium that establishes an N(2)-fixing symbiosis with its legume host soybean (Glycine max), has been used as a symbiosis model system. Using a sensitive geLC-MS/MS proteomics approach, we report the identification of 2315 B. japonicum strain USDA110 proteins (27.8% of the theoretical proteome) that are expressed 21 days post infection in symbiosis with soybean cultivated in growth chambers, substantially expanding the previously known symbiosis proteome. Integration of transcriptomics data generated under the same conditions (2780 expressed genes) allowed us to compile a comprehensive expression profile of B. japonicum during soybean symbiosis, which comprises 3587 genes/proteins (43% of the predicted B. japonicum genes/proteins). Analysis of this data set revealed both the biases and the complementarity of these global profiling technologies. A functional classification and pathway analysis showed that most of the proteins involved in carbon and nitrogen metabolism are expressed, including a complete set of tricarboxylic acid cycle enzymes, several gluconeogenesis and pentose phosphate pathway enzymes, as well as several proteins that were previously not considered to be present during symbiosis. Congruent results were obtained for B. japonicum bacteroids harvested from soybeans grown under field conditions.
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37
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Shao C, Liu Y, Ruan H, Li Y, Wang H, Kohl F, Goropashnaya AV, Fedorov VB, Zeng R, Barnes BM, Yan J. Shotgun proteomics analysis of hibernating arctic ground squirrels. Mol Cell Proteomics 2009; 9:313-26. [PMID: 19955082 DOI: 10.1074/mcp.m900260-mcp200] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mammalian hibernation involves complex mechanisms of metabolic reprogramming and tissue protection. Previous gene expression studies of hibernation have mainly focused on changes at the mRNA level. Large scale proteomics studies on hibernation have lagged behind largely because of the lack of an adequate protein database specific for hibernating species. We constructed a ground squirrel protein database for protein identification and used a label-free shotgun proteomics approach to analyze protein expression throughout the torpor-arousal cycle during hibernation in arctic ground squirrels (Urocitellus parryii). We identified more than 3,000 unique proteins from livers of arctic ground squirrels. Among them, 517 proteins showed significant differential expression comparing animals sampled after at least 8 days of continuous torpor (late torpid), within 5 h of a spontaneous arousal episode (early aroused), and 1-2 months after hibernation had ended (non-hibernating). Consistent with changes at the mRNA level shown in a previous study on the same tissue samples, proteins involved in glycolysis and fatty acid synthesis were significantly underexpressed at the protein level in both late torpid and early aroused animals compared with non-hibernating animals, whereas proteins involved in fatty acid catabolism were significantly overexpressed. On the other hand, when we compared late torpid and early aroused animals, there were discrepancies between mRNA and protein levels for a large number of genes. Proteins involved in protein translation and degradation, mRNA processing, and oxidative phosphorylation were significantly overexpressed in early aroused animals compared with late torpid animals, whereas no significant changes at the mRNA levels between these stages had been observed. Our results suggest that there is substantial post-transcriptional regulation of proteins during torpor-arousal cycles of hibernation.
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Affiliation(s)
- Chunxuan Shao
- Chinese Academy of Sciences-German Max Planck Society(CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes of Biological Sciences,320 Yue Yang Road, Shanghai 200031, China
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38
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Zhang W, Li F, Nie L. Integrating multiple 'omics' analysis for microbial biology: application and methodologies. MICROBIOLOGY-SGM 2009; 156:287-301. [PMID: 19910409 DOI: 10.1099/mic.0.034793-0] [Citation(s) in RCA: 356] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Recent advances in various 'omics' technologies enable quantitative monitoring of the abundance of various biological molecules in a high-throughput manner, and thus allow determination of their variation between different biological states on a genomic scale. Several popular 'omics' platforms that have been used in microbial systems biology include transcriptomics, which measures mRNA transcript levels; proteomics, which quantifies protein abundance; metabolomics, which determines abundance of small cellular metabolites; interactomics, which resolves the whole set of molecular interactions in cells; and fluxomics, which establishes dynamic changes of molecules within a cell over time. However, no single 'omics' analysis can fully unravel the complexities of fundamental microbial biology. Therefore, integration of multiple layers of information, the multi-'omics' approach, is required to acquire a precise picture of living micro-organisms. In spite of this being a challenging task, some attempts have been made recently to integrate heterogeneous 'omics' datasets in various microbial systems and the results have demonstrated that the multi-'omics' approach is a powerful tool for understanding the functional principles and dynamics of total cellular systems. This article reviews some basic concepts of various experimental 'omics' approaches, recent application of the integrated 'omics' for exploring metabolic and regulatory mechanisms in microbes, and advances in computational and statistical methodologies associated with integrated 'omics' analyses. Online databases and bioinformatic infrastructure available for integrated 'omics' analyses are also briefly discussed.
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Affiliation(s)
- Weiwen Zhang
- Center for Ecogenomics, Biodesign Institute, Arizona State University, Tempe, AZ 85287-6501, USA
| | - Feng Li
- Division of Biometrics II, Office of Biometrics/OTS/CDER/FDA, Silver Spring, MD 20993-0002, USA
| | - Lei Nie
- Division of Biometrics IV, Office of Biometrics/OTS/CDER/FDA, Silver Spring, MD 20993-0002, USA
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39
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Bacterial pleckstrin homology domains: a prokaryotic origin for the PH domain. J Mol Biol 2009; 396:31-46. [PMID: 19913036 PMCID: PMC2817789 DOI: 10.1016/j.jmb.2009.11.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2009] [Revised: 11/03/2009] [Accepted: 11/04/2009] [Indexed: 11/23/2022]
Abstract
Pleckstrin homology (PH) domains have been identified only in eukaryotic proteins to date. We have determined crystal structures for three members of an uncharacterized protein family (Pfam PF08000), which provide compelling evidence for the existence of PH-like domains in bacteria (PHb). The first two structures contain a single PHb domain that forms a dome-shaped, oligomeric ring with C(5) symmetry. The third structure has an additional helical hairpin attached at the C-terminus and forms a similar but much larger ring with C(12) symmetry. Thus, both molecular assemblies exhibit rare, higher-order, cyclic symmetry but preserve a similar arrangement of their PHb domains, which gives rise to a conserved hydrophilic surface at the intersection of the beta-strands of adjacent protomers that likely mediates protein-protein interactions. As a result of these structures, additional families of PHb domains were identified, suggesting that PH domains are much more widespread than originally anticipated. Thus, rather than being a eukaryotic innovation, the PH domain superfamily appears to have existed before prokaryotes and eukaryotes diverged.
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40
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Hakimov HA, Walters S, Wright TC, Meidinger RG, Verschoor CP, Gadish M, Chiu DKY, Strömvik MV, Forsberg CW, Golovan SP. Application of iTRAQ to catalogue the skeletal muscle proteome in pigs and assessment of effects of gender and diet dephytinization. Proteomics 2009; 9:4000-16. [DOI: 10.1002/pmic.200900049] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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41
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Werner JJ, Ptak AC, Rahm BG, Zhang S, Richardson RE. Absolute quantification of Dehalococcoides proteins: enzyme bioindicators of chlorinated ethene dehalorespiration. Environ Microbiol 2009; 11:2687-97. [PMID: 19650881 DOI: 10.1111/j.1462-2920.2009.01996.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The quantification of trace proteins in complex environmental samples and mixed microbial communities would be a valuable monitoring tool in countless applications, including the bioremediation of groundwater contaminated with chlorinated solvents. Measuring the concentrations of specific proteins provides unique information about the activity and physiological state of organisms in a sample. We developed sensitive (< 5 fmol), selective bioindicator assays for the absolute quantification of select proteins used by Dehalococcoides spp. when reducing carbon atoms in the common pollutants trichloroethene (TCE) and tetrachloroethene (PCE). From complex whole-sample digests of two different dechlorinating mixed communities, we monitored the chromatographic peaks of selected tryptic peptides chosen to represent 19 specific Dehalococcoides proteins. This was accomplished using multiple-reaction monitoring (MRM) assays using nano-liquid chromatography-tandem mass spectrometry (nLC-MS/MS), which provided the selectivity, sensitivity and reproducibility required to quantify Dehalococcoides proteins in complex samples. We observed reproducible peak areas (average CV = 0.14 over 4 days, n = 3) and linear responses in standard curves (n = 5, R(2) > 0.98) using synthetic peptide standards spiked into a background matrix of sediment peptides. We detected and quantified TCE reductive dehalogenase (TceA) at 7.6 +/- 1.7 x 10(3) proteins cell(-1) in the KB1 bioaugmentation culture, previously thought to be lacking TceA. Fragmentation data from MS/MS shotgun proteomics experiments were helpful in developing the MRM targets. Similar shotgun proteomics data are emerging in labs around the world for many environmentally relevant microbial proteins, and these data are a valuable resource for the future development of MRM assays. We expect targeted peptide quantification in environmental samples to be a useful tool in environmental monitoring.
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Affiliation(s)
- Jeffrey J Werner
- School of Civil and Environmental Engineering, Cornell University, Hollister Hall, Ithaca, NY 14853, USA
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42
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Carranza P, Hartmann I, Lehner A, Stephan R, Gehrig P, Grossmann J, Barkow-Oesterreicher S, Roschitzki B, Eberl L, Riedel K. Proteomic profiling of Cronobacter turicensis
3032, a food-borne opportunistic pathogen. Proteomics 2009; 9:3564-79. [DOI: 10.1002/pmic.200900016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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43
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Bogaerts A, Baggerman G, Vierstraete E, Schoofs L, Verleyen P. The hemolymph proteome of the honeybee: Gel-based or gel-free? Proteomics 2009; 9:3201-8. [DOI: 10.1002/pmic.200800604] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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44
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Zhao C, Guo XJ, Shi ZH, Wang FQ, Huang XY, Huo R, Zhu H, Wang XR, Liu JY, Zhou ZM, Sha JH. Role of translation by mitochondrial-type ribosomes during sperm capacitation: an analysis based on a proteomic approach. Proteomics 2009; 9:1385-99. [PMID: 19253287 DOI: 10.1002/pmic.200800353] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Mammalian spermatozoa contain a complex population of mRNAs, some of which have been demonstrated to be translated de novo by mitochondrial-type ribosomes using D-chloramphenicol (CP), a specific inhibitor of mitochondrial translation. However, little is known about the functions of these mRNAs in mature sperm. In the present study, differential proteomic approaches were applied to study sperm protein profiles translated by mitochondrial-type ribosomes using the inhibitor CP and 44 proteins were identified with lower expression in CP-treated sperm in comparison to capacitated sperm (ratio >or= 1.5, p<0.05). Results of Western blot and real-time PCR suggest that four proteins were translated by mitochondrial-type ribosomes. Bioinformatics analysis indicated that 26 of 44 proteins were involved in some critical processes correlated to sperm-egg interaction event. In addition, Mups, whose functions in reproduction have never been studied, were chosen for further study. Our results showed that Mups proteins were localized to the acrosome and flagellum of precapacitated sperm, and were also expressed in the equatorial segment of capacitated sperm. The depletion of Mups using neutralizing antibodies significantly inhibited capacitation in a dose-dependent manner, subsequently inhibited acrosome reaction and sperm-egg fusion. In summary, mitochondrial translation during capacitation can store proteins beneficial for sperm-egg interaction.
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Affiliation(s)
- Chun Zhao
- Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, PR China
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45
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Gagnaire V, Jardin J, Jan G, Lortal S. Invited review: Proteomics of milk and bacteria used in fermented dairy products: From qualitative to quantitative advances. J Dairy Sci 2009; 92:811-25. [DOI: 10.3168/jds.2008-1476] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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46
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47
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Shui W, Gilmore SA, Sheu L, Liu J, Keasling JD, Bertozzi CR. Quantitative proteomic profiling of host-pathogen interactions: the macrophage response to Mycobacterium tuberculosis lipids. J Proteome Res 2009; 8:282-9. [PMID: 19053526 DOI: 10.1021/pr800422e] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Mycobacterium tuberculosis (M. tuberculosis) is an intracellular pathogen possessing a complex mixture of cell wall lipids that are thought to modulate the activities of host macrophages. In this study, we employed two state-of-the-art quantitative proteomic approaches, metabolic labeling SILAC and chemical isobaric tagging iTRAQ, to study changes in macrophage protein expression in response to exposure to M. tuberculosis lipids. From a total of 1286 proteins identified, 463 were discovered by both isotope-labeling strategies at a high consistency, and the rest of proteins were detected by only one of the two approaches. Upon exposure to mycobacterial cell wall lipids, 166 macrophage proteins showed differential expression. These included proteins involved in the immune response, oxidation and reduction, and vesicle transport, as well as other cellular processes. The response of the macrophage proteome to M. tuberculosis lipids reflects the cell's innate defense mechanisms as well as lipid-induced processes that may benefit the pathogen.
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Affiliation(s)
- Wenqing Shui
- Department of Chemistry, University of California, Berkeley, California 94720, USA
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48
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Hahne H, Wolff S, Hecker M, Becher D. From complementarity to comprehensiveness--targeting the membrane proteome of growing Bacillus subtilis by divergent approaches. Proteomics 2009; 8:4123-36. [PMID: 18763711 DOI: 10.1002/pmic.200800258] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The analysis of integral membrane proteins (IMPs) with mass spectrometry-centered technologies has undergone great progress during the past few years, allowing for the analysis of several hundreds of IMPs. In this study, we investigated three promising shotgun approaches for the identification of IMPs of the model organism Bacillus subtilis. One comprises a classical membrane preparation procedure with carbonate and high-ionic-strength buffers, followed by SDS-PAGE and LC-MS/MS analysis. The two others are based on enzymatic trimming of the crude membrane fraction either with trypsin or proteinase K and subsequent gel-free analysis. As a result, we observed the highest degree of complementarity between the gel-based and the proteinase K approach, since the first exclusively addresses soluble loops and domains of IMPs and gave rise to 8709 unique peptides, whereas the latter contributed 1180 unique peptide identifications from otherwise inaccessible transmembrane helices (TMHs). All three methods contribute significant numbers (381, 284, and 276, respectively) to the total of 527 IMP identifications from the membrane fraction of exponentially growing B. subtilis cells, thus representing approximately 69% of all transcribed IMPs.
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Affiliation(s)
- Hannes Hahne
- Institute for Microbiology, Ernst-Moritz-Arndt-University, Greifswald, Germany
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49
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Abstract
The degree of protein diversity and dynamic range within organisms means that even the simplest proteome cannot be captured by any single extraction and separation step. New techniques have focused on major protein classes often under-represented in proteome analysis; low abundance, membrane, and alkaline proteins. The last decade has seen considerable technology development in fractionation tools aimed at complexity reduction in many forms. The key outcome of complexity reduction is that each fraction, or sub-proteome, can be studied in more detail, and proteins which would have remained undetected in a total extract are present in sufficient quantities. However, the tools available are fractionations, not amplifications, and like all mining for rare and difficult items, a large amount of starting material is often required. The key shortcomings of many proteome analysis techniques are now well documented. With this knowledge, the best modern proteomics 'platform' involves combining multiple protein extractions, gel and chromatographic separations, and multiple MS analysis methods.
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Affiliation(s)
- Ben Herbert
- Department of Medical and Molecular Biosciences, University of Technology, Sydney, 15 Broadway, Ultimo, Sydney, NSW 2007, Australia
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50
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Nie L, Wu G, Zhang W. Statistical Application and Challenges in Global Gel-Free Proteomic Analysis by Mass Spectrometry. Crit Rev Biotechnol 2008; 28:297-307. [DOI: 10.1080/07388550802543158] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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