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Chen M, Song Y, Feng X, Tang K, Jiao N, Tian J, Zhang Y. Genomic Characteristics and Potential Metabolic Adaptations of Hadal Trench Roseobacter and Alteromonas Bacteria Based on Single-Cell Genomics Analyses. Front Microbiol 2020; 11:1739. [PMID: 32793171 PMCID: PMC7393951 DOI: 10.3389/fmicb.2020.01739] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 07/03/2020] [Indexed: 11/30/2022] Open
Abstract
Heterotrophic bacteria such as those from the Roseobacter group and genus Alteromonas dominate the hadal zones of oceans; however, we know little about the genomic characteristics and potential metabolic adaptations of hadal trench-dwelling bacteria. Here, we report multiple single amplified genomes (SAGs) belonging to Roseobacter and Alteromonas, recovered from the hadal zone of the Mariana Trench. While phylogenetic analyses show that these hadal SAGs cluster with their surface relatives, an analysis of genomic recruitment indicates that they have higher relative abundances in the hadal zone of the Mariana Trench. Comparative genomic analyses between the hadal SAGs and reference genomes of closely related shallow-water relatives indicate that genes involved in the mobilome (prophages and transposons) are overrepresented among the unique genes of the hadal Roseobacter and Alteromonas SAGs; the functional proteins encoded by this category of genes also shows higher amino acid sequence variation than those encoded by other gene sets within the Roseobacter SAGs. We also found that genes involved in cell wall/membrane/envelope biogenesis, transcriptional regulation, and metal transport may be important for the adaptation of hadal Roseobacter and Alteromonas lineages. These results imply that the modification of cell surface-related proteins and transporters is the major direction of genomic evolution in Roseobacter and Alteromonas bacteria adapting to the hadal environment, and that prophages and transposons may be the key factors driving this process.
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Affiliation(s)
- Mingming Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Yu Song
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Xiaoyuan Feng
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Kai Tang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Jiwei Tian
- Physical Oceanography Laboratory, Ocean University of China, Qingdao, China
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
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Membrane Proteomics in Gram-Positive Bacteria: Two Complementary Approaches to Target the Hydrophobic Species of Proteins. Methods Mol Biol 2018; 1841:21-33. [PMID: 30259477 DOI: 10.1007/978-1-4939-8695-8_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
This protocol represents a detailed instruction how to prepare protein samples in order to raise mass spectrometry-based identification and quantification rates with respect to the challenging class of membrane proteins. This will increase comprehensiveness of global proteome studies on the one hand but could also be of interest for researchers targeting specific membrane proteins or membrane protein sequences on the other hand. The protocol is a composite of two parts, one focusing on the identification of protein sequences exterior to a cellular membrane (loops of integral membrane proteins, peripheral membrane proteins), and the other part targeting primarily protein domains spanning the lipid bilayer. The feasibility of the protocol, as it is described here, was originally shown for the gram-positive pathogenic bacterium Staphylococcus aureus but should be applicable to any kind of membrane protein.
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3
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Global analysis of bacterial membrane proteins and their modifications. Int J Med Microbiol 2015; 305:203-8. [DOI: 10.1016/j.ijmm.2014.12.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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Ternan NG, Jain S, Graham RLJ, McMullan G. Semiquantitative analysis of clinical heat stress in Clostridium difficile strain 630 using a GeLC/MS workflow with emPAI quantitation. PLoS One 2014; 9:e88960. [PMID: 24586458 PMCID: PMC3933415 DOI: 10.1371/journal.pone.0088960] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 01/16/2014] [Indexed: 12/11/2022] Open
Abstract
Clostridium difficile is considered to be the most frequent cause of infectious bacterial diarrhoea in hospitals worldwide yet its adaptive ability remains relatively uncharacterised. Here, we used GeLC/MS and the exponentially modified protein abundance index (emPAI) calculation to determine proteomic changes in response to a clinically relevant heat stress. Reproducibility between both biological and technical replicates was good, and a 37°C proteome of 224 proteins was complemented by a 41°C proteome of 202 proteins at a 1% false discovery rate. Overall, 236 C. difficile proteins were identified and functionally categorised, of which 178 were available for comparative purposes. A total of 65 proteins (37%) were modulated by 1.5-fold or more at 41°C compared to 37°C and we noted changes in the majority of proteins associated with amino acid metabolism, including upregulation of the reductive branch of the leucine fermentation pathway. Motility was reduced at 41°C as evidenced by a 2.7 fold decrease in the flagellar filament protein, FliC, and a global increase in proteins associated with detoxification and adaptation to atypical conditions was observed, concomitant with decreases in proteins mediating transcriptional elongation and the initiation of protein synthesis. Trigger factor was down regulated by almost 5-fold. We propose that under heat stress, titration of the GroESL and dnaJK/grpE chaperones by misfolded proteins will, in the absence of trigger factor, prevent nascent chains from emerging efficiently from the ribosome causing translational stalling and also an increase in secretion. The current work has thus allowed development of a heat stress model for the key cellular processes of protein folding and export.
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Affiliation(s)
- Nigel G. Ternan
- Northern Ireland Centre for Food and Health (NICHE), School of Biomedical Sciences, University of Ulster, Coleraine, Co. Londonderry, Northern Ireland, United Kingdom
- * E-mail:
| | - Shailesh Jain
- Northern Ireland Centre for Food and Health (NICHE), School of Biomedical Sciences, University of Ulster, Coleraine, Co. Londonderry, Northern Ireland, United Kingdom
| | - Robert L. J. Graham
- School of Medicine, University of Manchester, Manchester, Greater Manchester, United Kingdom
| | - Geoff McMullan
- Northern Ireland Centre for Food and Health (NICHE), School of Biomedical Sciences, University of Ulster, Coleraine, Co. Londonderry, Northern Ireland, United Kingdom
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Sun Z, Chen R, Cheng K, Liu H, Qin H, Ye M, Zou H. A new method for quantitative analysis of cell surface glycoproteome. Proteomics 2012; 12:3328-37. [DOI: 10.1002/pmic.201200150] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 07/10/2012] [Accepted: 09/10/2012] [Indexed: 12/22/2022]
Affiliation(s)
- Zhen Sun
- Key Laboratory of Separation Sciences for Analytical Chemistry; National Chromatographic R&A Center; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian China
| | - Rui Chen
- Key Laboratory of Separation Sciences for Analytical Chemistry; National Chromatographic R&A Center; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian China
| | - Kai Cheng
- Key Laboratory of Separation Sciences for Analytical Chemistry; National Chromatographic R&A Center; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian China
| | - Hongwei Liu
- Key Laboratory of Separation Sciences for Analytical Chemistry; National Chromatographic R&A Center; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian China
| | - Hongqiang Qin
- Key Laboratory of Separation Sciences for Analytical Chemistry; National Chromatographic R&A Center; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian China
| | - Mingliang Ye
- Key Laboratory of Separation Sciences for Analytical Chemistry; National Chromatographic R&A Center; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian China
| | - Hanfa Zou
- Key Laboratory of Separation Sciences for Analytical Chemistry; National Chromatographic R&A Center; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian China
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Jain S, Graham C, Graham RLJ, McMullan G, Ternan NG. Quantitative proteomic analysis of the heat stress response in Clostridium difficile strain 630. J Proteome Res 2011; 10:3880-90. [PMID: 21786815 DOI: 10.1021/pr200327t] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Clostridium difficile is a serious nosocomial pathogen whose prevalence worldwide is increasing. Postgenomic technologies can now be deployed to develop understanding of the evolution and diversity of this important human pathogen, yet little is known about the adaptive ability of C. difficile. We used iTRAQ labeling and 2D-LC-MS/MS driven proteomics to investigate the response of C. difficile 630 to a mild, but clinically relevant, heat stress. A statistically validated list of 447 proteins to which functional roles were assigned was generated, allowing reconstruction of central metabolic pathways including glycolysis, γ-aminobutyrate metabolism, and peptidoglycan biosynthesis. Some 49 proteins were significantly modulated under heat stress: classical heat shock proteins including GroEL, GroES, DnaK, Clp proteases, and HtpG were up-regulated in addition to several stress inducible rubrerythrins and proteins associated with protein modification, such as prolyl isomerases and proline racemase. The flagellar filament protein, FliC, was down-regulated, possibly as an energy conservation measure, as was the SecA1 preprotein translocase. The up-regulation of hydrogenases and various oxidoreductases suggests that electron flux across these pools of enzymes changes under heat stress. This work represents the first comparative proteomic analysis of the heat stress response in C. difficile strain 630, complementing the existing proteomics data sets and the single microarray comparative analysis of stress response. Thus we have a benchmark proteome for this pathogen, leading to a deeper understanding of its physiology and metabolism informed by the unique functional and adaptive processes used during a temperature upshift mimicking host pyrexia.
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Affiliation(s)
- Shailesh Jain
- School of Biomedical Sciences, University of Ulster, Cromore Road, Coleraine, Co Londonderry, North Ireland, United Kingdom
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Jagannadham MV, Abou-Eladab EF, Kulkarni HM. Identification of outer membrane proteins from an Antarctic bacterium Pseudomonas syringae Lz4W. Mol Cell Proteomics 2011; 10:M110.004549. [PMID: 21447709 DOI: 10.1074/mcp.m110.004549] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Subcellular fractionation of proteins is a preferred method of choice for detection and identification of proteins from complex mixtures such as bacterial cells. To characterize the membrane proteins of the Antarctic bacterium Pseudomonas syringae Lz4W, the membrane fractions were prepared using three different methods, namely Triton X-100 solubilization, sucrose density gradient, and carbonate extraction methods. The proteins were separated on one-dimensional polyacrylamide gels and analyzed using a combination of liquid chromatography-coupled electrospray ionization-MS. The membrane proteins that were prepared by carbonate extraction were separated on two-dimensional PAGE in different pI ranges using the detergent 2% amidosulfobetaine (ASB). The proteins were then subjected to matrix-assisted laser desorption ionization-time-of-flight/time-of-flight for analysis and identification. Because the genome sequence of P. syringae Lz4W is not known, the proteins were identified by using the relevant sequence databases of the Pseudomonas sp available at National Centre for Biotechnology Information (NCBI). The sequence identification of some tryptic peptides were validated by de novo sequencing and others by chemical modification and mass spectrometry. The peptide sequences of P. syringae Lz4W were then matched with the sequences of the peptides from different Pseudomonas sp. by similarity search of the proteins from different species using clustal W2 program. Thus by using a combination of the methods, we have been able to identify large number of proteins of this bacterial strain, which include most of the outer membrane proteins.
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Affiliation(s)
- M V Jagannadham
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Hyderabad, India.
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Comparative proteome analysis of alkaliphilic Bacillus sp. N16-5 grown on different carbon sources. SCIENCE CHINA-LIFE SCIENCES 2011; 54:90-100. [PMID: 21253875 DOI: 10.1007/s11427-010-4106-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Accepted: 04/26/2010] [Indexed: 10/18/2022]
Abstract
To determine the impact of carbohydrates on the metabolic pathway in alkaliphiles, proteomes were obtained from cultures containing different carbohydrates and were resolved on two-dimensional gel electrophoresis (2-DE). The proteomes were compared to determine differentially expressed proteins. A novel alkaliphilic bacterium (alkaliphilic Bacillus sp. N16-5 isolated from Wudunur Soda Lake, China) was isolated in media with five different carbon sources (glucose, mannose, galactose, arabinose, and xylose). Comparative proteome analysis identified 61 differentially expressed proteins, which were mainly involved in carbohydrate metabolism, amino acid transport, and metabolism, as well as energy production and conversion. The comparison was based on the draft genome sequence of strain N16-5. The abundance of enzymes involved in central metabolism was significantly changed when exposed to various carbohydrates. Notably, catabolite control protein A (CcpA) was up-regulated under all carbon sources compared with glucose. In addition, pentose exhibited a stronger effect than hexose in CcpA-mediated carbon catabolite repression. These results provided a fundamental understanding of carbohydrate metabolism in alkaliphiles.
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Jain S, Graham RL, McMullan G, Ternan NG. Proteomic analysis of the insoluble subproteome of Clostridium difficile strain 630. FEMS Microbiol Lett 2010; 312:151-9. [DOI: 10.1111/j.1574-6968.2010.02111.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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11
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Daher Z, Recorbet G, Valot B, Robert F, Balliau T, Potin S, Schoefs B, Dumas-Gaudot E. Proteomic analysis of Medicago truncatula root plastids. Proteomics 2010; 10:2123-37. [DOI: 10.1002/pmic.200900345] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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12
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Rupp S. An approach to characterize the membrane proteome of Candida albicans. Future Microbiol 2010; 5:147-51. [DOI: 10.2217/fmb.10.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Evaluation of: Cabezon V, Llama-Palacios A, Nombela C, Monteoliva L, Gil C: Analysis of Candida albicans plasma membrane proteome. Proteomics 9, 4770–4786 (2009). The opportunistic human fungal pathogen Candida albicans causes a wide variety of infections, including deep systemic infection. The C. albicans plasma membrane is an important interface in the host–pathogen relationship. Plasma membrane proteins mediate a variety of functions, including sensing and signaling to the external environment, in which the glycosylphosphatidylinositol (GPI)-anchored membrane proteins play a crucial role. A subproteomic approach to obtain a global picture of the protein composition of the C. albicans plasma membrane was developed, and different strategies were tested in order to extract the largest number of yeast plasma membrane proteins and GPI-anchored membrane proteins. These methods involved protoplast generation, mechanical disruption, ultracentrifugation in sucrose gradients and Na2CO3 treatments. To isolate GPI-anchored proteins two additional steps were performed: two-phase separation and phosphatidylinositol-phospholipase C treatment. After liquid chromatography tandem mass spectrometry analysis using both a MALDI-TOF/TOF and a linear ion trap quadrupole, a total of 214 membrane proteins were identified, including 41 already described as plasma membrane proteins, 20 plasma membrane-associated proteins and 22 proteins with unknown membrane localization. Bioinformatic analysis revealed that this set of C. albicans membrane proteins is highly enriched in proteins involved in biopolymer biosynthesis or transport processes. Furthermore, following phosphatidylinositol-phospholipase C treatment, 12 GPI-anchored membrane proteins were released and identified; most of them are associated with cell wall glucan synthesis and maintenance or are virulence factors, such as phospholipases or aspartyl proteinases.
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Affiliation(s)
- Steffen Rupp
- Fraunhofer Institute for Interfacial Engineering, Nobelstr. 12, 70569 Stuttgart, Germany
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Burg DW, Lauro FM, Williams TJ, Raftery MJ, Guilhaus M, Cavicchioli R. Analyzing the Hydrophobic Proteome of the Antarctic Archaeon Methanococcoides burtonii Using Differential Solubility Fractionation. J Proteome Res 2009; 9:664-76. [DOI: 10.1021/pr9007865] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dominic W. Burg
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, NSW, Australia and Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, 2052, NSW, Australia
| | - Federico M. Lauro
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, NSW, Australia and Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, 2052, NSW, Australia
| | - Timothy J. Williams
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, NSW, Australia and Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, 2052, NSW, Australia
| | - Mark J. Raftery
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, NSW, Australia and Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, 2052, NSW, Australia
| | - Michael Guilhaus
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, NSW, Australia and Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, 2052, NSW, Australia
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, NSW, Australia and Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, 2052, NSW, Australia
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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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Wang Q, Han H, Xue Y, Qian Z, Meng B, Peng F, Wang Z, Tong W, Zhou C, Wang Q, Guo Y, Li G, Liu S, Ma Y. Exploring membrane and cytoplasm proteomic responses of Alkalimonas amylolytica N10 to different external pHs with combination strategy of de novo peptide sequencing. Proteomics 2009; 9:1254-73. [PMID: 19253282 DOI: 10.1002/pmic.200800244] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Identification of differentially proteomic responses to external pHs would pave an access for understanding of survival mechanisms of bacteria living at extreme pH environment. We cultured Alkalimonas amylolytica N10 (N10), a novel alkaliphilic bacterium found in Lake Chahannor, in media with three different pHs and extracted the correspondent membrane and cytoplasm proteins for proteomic analysis through 2-DE. The differential 2-DE spots corresponding to the altered pHs were delivered to MALDI TOF/TOF MS for protein identification. Since the genomic data of strain N10 was unavailable, we encountered a problem at low rate of protein identification with 18.1%. We employed, therefore, a combined strategy of de novo sequencing to analyze MS/MS signals generated from MALDI TOF/TOF MS. A significantly improved rate of protein identification was thus achieved at over than 70.0%. Furthermore, we extensively investigated the expression of these pH-dependent N10 genes using Western blot and real-time PCR. The conclusions drawn from immunoblot and mRNA measurements were mostly in agreement with the proteomic observations. We conducted the bioinformatic analysis to all the pH-dependent N10 proteins and found that some membrane proteins participated in iron transport were differentially expressed as external pH elevated and most of differential proteins with increased or bell-shape mode of pH-dependence were involved in bioenergetic process and metabolism of carbohydrates, fatty acid, amino acids, and nucleotides. Our data thus provide a functional profile of the pH-responsive proteins in alkaliphiles, leading to elucidation of alkaliphilic-adaptive mechanism.
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Affiliation(s)
- Quanhui Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
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Abstract
About one quarter to one third of all bacterial genes encode proteins of the inner or outer bacterial membrane. These proteins perform essential physiological functions, such as the import or export of metabolites, the homeostasis of metal ions, the extrusion of toxic substances or antibiotics, and the generation or conversion of energy. The last years have witnessed completion of a plethora of whole-genome sequences of bacteria important for biotechnology or medicine, which is the foundation for proteome and other functional genome analyses. In this review, we discuss the challenges in membrane proteome analysis, starting from sample preparation and leading to MS-data analysis and quantification. The current state of available proteomics technologies as well as their advantages and disadvantages will be described with a focus on shotgun proteomics. Then, we will briefly introduce the most abundant proteins and protein families present in bacterial membranes before bacterial membrane proteomics studies of the last years will be presented. It will be shown how these works enlarged our knowledge about the physiological adaptations that take place in bacteria during fine chemical production, bioremediation, protein overexpression, and during infections. Furthermore, several examples from literature demonstrate the suitability of membrane proteomics for the identification of antigens and different pathogenic strains, as well as the elucidation of membrane protein structure and function.
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Affiliation(s)
- Ansgar Poetsch
- Lehrstuhl für Biochemie der Pflanzen, Ruhr Universität Bochum, Bochum, Germany.
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Liu T, Martin AM, Sinai AP, Lynn BC. Three-layer sandwich gel electrophoresis: a method of salt removal and protein concentration in proteome analysis. J Proteome Res 2008; 7:4256-65. [PMID: 18795766 DOI: 10.1021/pr800182b] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sample preparation plays a critical role in successful proteomic applications. Features of electrospray mass spectrometry impose limits on the types of buffers, detergents and other reagents that can be used in sample preparation. Unfortunately, many of these mass spectrometry incompatible reagents significantly enhance protein recoveries from complex matrices. This problem prompted our search for a better cleanup protocol. Our data suggest that the Three-layer Sandwich Gel Electrophoresis (TSGE) protocol can solve this problem and provide near quantitative recovery of extremely low concentration proteins from harsh solutions, a feature not available from other cleanup protocols. The hallmark of the TSGE protocol is the combination of the properties of agarose gels (that serve as the matrix to immobilize the proteins of interest) with low- and high-percentage polyacrylamide gels (that serve as the concentration and sealing layers, respectively). By electrophoretically driving the proteins of interest from the agarose matrix into the concentration layer, the TSGE protocol simultaneously concentrates the sample in the concentration layer and provides an environment amenable to downstream buffer exchange and proteolytic digestion. In combination with 2D-LC-MS/MS, the TSGE protocol was evaluated in the analysis of a whole cell extract from the protozoan parasite Toxoplasma gondii. Comparison of our experimental proteomic results with in silico predictions from gene data indicated that TSGE did not bias the protein identification.
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Affiliation(s)
- Ting Liu
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, USA
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Wolff S, Hahne H, Hecker M, Becher D. Complementary analysis of the vegetative membrane proteome of the human pathogen Staphylococcus aureus. Mol Cell Proteomics 2008; 7:1460-8. [PMID: 18460691 DOI: 10.1074/mcp.m700554-mcp200] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The Gram-positive bacterium Staphylococcus aureus is a serious human pathogen causing a wide variety of diseases, and its increasing resistance toward all available antibiotics makes its further investigation absolutely essential. We examined the membrane proteome of exponentially growing cells of S. aureus COL because this subproteome plays a major role in the virulence of the bacterium in its host. In general, an analysis of membrane proteins is impeded by their hydrophobic nature as well as by a high abundance of many cytosolic proteins. The implementation of three different technologies, one-dimensional gel-LC, two-dimensional LC, and a membrane shaving approach combined with MS/MS analyses, enabled an identification of 271 integral and 86 peripheral membrane proteins from exponentially growing cells. In particular, the latter approach that combined membrane shaving with a subsequent chymotrypsin digest of integral membrane domains of proteins greatly facilitated the detection of hydrophobic peptides derived from membrane-spanning segments (713 peptides, 60% of all peptides) and therefore yielded almost exclusively highly hydrophobic integral membrane proteins (96.7%). A comparison of the various methods disclosed the one-dimensional gel-LC and the shaving approach to be highly complementary techniques. A combination of them will reveal a most comprehensive view on membrane proteomes.
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Affiliation(s)
- Susanne Wolff
- Institute for Microbiology, Ernst Moritz Arndt University, D-17489 Greifswald, Germany
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Graham RLJ, Graham C, McMullan G. Microbial proteomics: a mass spectrometry primer for biologists. Microb Cell Fact 2007; 6:26. [PMID: 17697372 PMCID: PMC1971468 DOI: 10.1186/1475-2859-6-26] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2007] [Accepted: 08/15/2007] [Indexed: 11/29/2022] Open
Abstract
It is now more than 10 years since the publication of the first microbial genome sequence and science is now moving towards a post genomic era with transcriptomics and proteomics offering insights into cellular processes and function. The ability to assess the entire protein network of a cell at a given spatial or temporal point will have a profound effect upon microbial science as the function of proteins is inextricably linked to phenotype. Whilst such a situation is still beyond current technologies rapid advances in mass spectrometry, bioinformatics and protein separation technologies have produced a step change in our current proteomic capabilities. Subsequently a small, but steadily growing, number of groups are taking advantage of this cutting edge technology to discover more about the physiology and metabolism of microorganisms. From this research it will be possible to move towards a systems biology understanding of a microorganism. Where upon researchers can build a comprehensive cellular map for each microorganism that links an accurately annotated genome sequence to gene expression data, at a transcriptomic and proteomic level.In order for microbiologists to embrace the potential that proteomics offers, an understanding of a variety of analytical tools is required. The aim of this review is to provide a basic overview of mass spectrometry (MS) and its application to protein identification. In addition we will describe how the protein complexity of microbial samples can be reduced by gel-based and gel-free methodologies prior to analysis by MS. Finally in order to illustrate the power of microbial proteomics a case study of its current application within the Bacilliaceae is given together with a description of the emerging discipline of metaproteomics.
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Affiliation(s)
- Robert LJ Graham
- School of Biomedical Sciences, University of Ulster, Coleraine, County Londonderry, BT52 1SA, UK
| | - Ciaren Graham
- School of Biomedical Sciences, University of Ulster, Coleraine, County Londonderry, BT52 1SA, UK
| | - Geoff McMullan
- School of Biomedical Sciences, University of Ulster, Coleraine, County Londonderry, BT52 1SA, UK
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Affiliation(s)
- Anna E Speers
- Department of Pharmacology, University of Colorado School of Medicine, P.O. Box 6511, MS 8303, Aurora, Colorado 80045, USA
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