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Transcript Regulation of the Recoded Archaeal α-l-Fucosidase In Vivo. Molecules 2021; 26:molecules26071861. [PMID: 33806142 PMCID: PMC8037382 DOI: 10.3390/molecules26071861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/22/2021] [Accepted: 03/19/2021] [Indexed: 11/17/2022] Open
Abstract
Genetic decoding is flexible, due to programmed deviation of the ribosomes from standard translational rules, globally termed "recoding". In Archaea, recoding has been unequivocally determined only for termination codon readthrough events that regulate the incorporation of the unusual amino acids selenocysteine and pyrrolysine, and for -1 programmed frameshifting that allow the expression of a fully functional α-l-fucosidase in the crenarchaeon Saccharolobus solfataricus, in which several functional interrupted genes have been identified. Increasing evidence suggests that the flexibility of the genetic code decoding could provide an evolutionary advantage in extreme conditions, therefore, the identification and study of interrupted genes in extremophilic Archaea could be important from an astrobiological point of view, providing new information on the origin and evolution of the genetic code and on the limits of life on Earth. In order to shed some light on the mechanism of programmed -1 frameshifting in Archaea, here we report, for the first time, on the analysis of the transcription of this recoded archaeal α-l-fucosidase and of its full-length mutant in different growth conditions in vivo. We found that only the wild type mRNA significantly increased in S. solfataricus after cold shock and in cells grown in minimal medium containing hydrolyzed xyloglucan as carbon source. Our results indicated that the increased level of fucA mRNA cannot be explained by transcript up-regulation alone. A different mechanism related to translation efficiency is discussed.
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Zhou T, Yao X, Wang J, Feng Y. Solution structure of an archaeal DUF61 family protein SSO0941 encoded by a gene in the operon of box C/D RNA protein complexes. J Struct Biol 2018. [PMID: 29526782 DOI: 10.1016/j.jsb.2018.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Domain of unknown function 61 (DUF61) family proteins widely exist in archaea and the genes of DUF61 proteins in crenarchaea are in an operon containing two genes of box C/D RNA protein complexes. Here we report the solution NMR structure of DUF61 family member protein SSO0941, from the hyperthermophilic archaeon Sulfolobus solfataricus. SSO0941 has a rigid core structure and flexible N- and C-terminal regions as well as a negatively-charged independent C-terminal helix. The core structure consists of N- and C-terminal subdomains, in which the C-terminal subdomain shows significant structural similarity with several nucleic acid binding proteins. The structure of SSO0941 is the first representative structure of DUF61 family proteins.
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Affiliation(s)
- Tao Zhou
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xingzhe Yao
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Jinfeng Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Yingang Feng
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China.
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Quehenberger J, Shen L, Albers SV, Siebers B, Spadiut O. Sulfolobus - A Potential Key Organism in Future Biotechnology. Front Microbiol 2017; 8:2474. [PMID: 29312184 PMCID: PMC5733018 DOI: 10.3389/fmicb.2017.02474] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 11/28/2017] [Indexed: 11/13/2022] Open
Abstract
Extremophilic organisms represent a potentially valuable resource for the development of novel bioprocesses. They can act as a source for stable enzymes and unique biomaterials. Extremophiles are capable of carrying out microbial processes and biotransformations under extremely hostile conditions. Extreme thermoacidophilic members of the well-characterized genus Sulfolobus are outstanding in their ability to thrive at both high temperatures and low pH. This review gives an overview of the biological system Sulfolobus including its central carbon metabolism and the development of tools for its genetic manipulation. We highlight findings of commercial relevance and focus on potential industrial applications. Finally, the current state of bioreactor cultivations is summarized and we discuss the use of Sulfolobus species in biorefinery applications.
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Affiliation(s)
- Julian Quehenberger
- Research Division Biochemical Engineering, Faculty of Technical Chemistry, Institute of Chemical, Environmental and Biological Engineering, Vienna University of Technology, Vienna, Austria
| | - Lu Shen
- Department of Molecular Enzyme Technology and Biochemistry, Faculty of Chemistry – Biofilm Centre, University of Duisburg-Essen, Essen, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II-Microbiology, Faculty of Biology, University of Freiburg, Freiburg im Breisgau, Germany
| | - Bettina Siebers
- Department of Molecular Enzyme Technology and Biochemistry, Faculty of Chemistry – Biofilm Centre, University of Duisburg-Essen, Essen, Germany
| | - Oliver Spadiut
- Research Division Biochemical Engineering, Faculty of Technical Chemistry, Institute of Chemical, Environmental and Biological Engineering, Vienna University of Technology, Vienna, Austria
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Kepplinger D, Takhar M, Sasaki M, Hollander Z, Smith D, McManus B, McMaster WR, Ng RT, Cohen Freue GV. PGCA: An algorithm to link protein groups created from MS/MS data. PLoS One 2017; 12:e0177569. [PMID: 28562641 PMCID: PMC5451011 DOI: 10.1371/journal.pone.0177569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 04/28/2017] [Indexed: 11/19/2022] Open
Abstract
The quantitation of proteins using shotgun proteomics has gained popularity in the last decades, simplifying sample handling procedures, removing extensive protein separation steps and achieving a relatively high throughput readout. The process starts with the digestion of the protein mixture into peptides, which are then separated by liquid chromatography and sequenced by tandem mass spectrometry (MS/MS). At the end of the workflow, recovering the identity of the proteins originally present in the sample is often a difficult and ambiguous process, because more than one protein identifier may match a set of peptides identified from the MS/MS spectra. To address this identification problem, many MS/MS data processing software tools combine all plausible protein identifiers matching a common set of peptides into a protein group. However, this solution introduces new challenges in studies with multiple experimental runs, which can be characterized by three main factors: i) protein groups' identifiers are local, i.e., they vary run to run, ii) the composition of each group may change across runs, and iii) the supporting evidence of proteins within each group may also change across runs. Since in general there is no conclusive evidence about the absence of proteins in the groups, protein groups need to be linked across different runs in subsequent statistical analyses. We propose an algorithm, called Protein Group Code Algorithm (PGCA), to link groups from multiple experimental runs by forming global protein groups from connected local groups. The algorithm is computationally inexpensive and enables the connection and analysis of lists of protein groups across runs needed in biomarkers studies. We illustrate the identification problem and the stability of the PGCA mapping using 65 iTRAQ experimental runs. Further, we use two biomarker studies to show how PGCA enables the discovery of relevant candidate protein group markers with similar but non-identical compositions in different runs.
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Affiliation(s)
- David Kepplinger
- Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mandeep Takhar
- NCE CECR PROOF Centre of Excellence, Vancouver, British Columbia, Canada
| | - Mayu Sasaki
- NCE CECR PROOF Centre of Excellence, Vancouver, British Columbia, Canada
| | | | - Derek Smith
- University of Victoria - Genome BC Proteomics Centre, Victoria, British Columbia, Canada
| | - Bruce McManus
- NCE CECR PROOF Centre of Excellence, Vancouver, British Columbia, Canada
| | - W. Robert McMaster
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Raymond T. Ng
- NCE CECR PROOF Centre of Excellence, Vancouver, British Columbia, Canada
- Department of Computer Science, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gabriela V. Cohen Freue
- Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
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Soo E, Rudrappa D, Blum P. Membrane Association and Catabolite Repression of the Sulfolobus solfataricus α-Amylase. Microorganisms 2015; 3:567-87. [PMID: 27682106 PMCID: PMC5023256 DOI: 10.3390/microorganisms3030567] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 08/10/2015] [Accepted: 09/11/2015] [Indexed: 11/16/2022] Open
Abstract
Sulfolobus solfataricus is a thermoacidophilic member of the archaea whose envelope consists of an ether-linked lipid monolayer surrounded by a protein S-layer. Protein translocation across this envelope must accommodate a steep proton gradient that is subject to temperature extremes. To better understand this process in vivo, studies were conducted on the S. solfataricus glycosyl hydrolyase family 57 α-Amylase (AmyA). Cell lines harboring site specific modifications of the amyA promoter and AmyA structural domains were created by gene replacement using markerless exchange and characterized by Western blot, enzyme assay and culture-based analysis. Fusion of amyA to the malAp promoter overcame amyAp-mediated regulatory responses to media composition including glucose and amino acid repression implicating action act at the level of transcription. Deletion of the AmyA Class II N-terminal signal peptide blocked protein secretion and intracellular protein accumulation. Deletion analysis of a conserved bipartite C-terminal motif consisting of a hydrophobic region followed by several charged residues indicated the charged residues played an essential role in membrane-association but not protein secretion. Mutants lacking the C-terminal bipartite motif exhibited reduced growth rates on starch as the sole carbon and energy source; therefore, association of AmyA with the membrane improves carbohydrate utilization. Widespread occurrence of this motif in other secreted proteins of S. solfataricus and of related Crenarchaeota suggests protein association with membranes is a general trait used by these organisms to influence external processes.
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Affiliation(s)
- Edith Soo
- School of Biological Sciences, University of Nebraska-Lincoln, 1901 Vine Street, Lincoln 68588, NE, USA.
| | - Deepak Rudrappa
- School of Biological Sciences, University of Nebraska-Lincoln, 1901 Vine Street, Lincoln 68588, NE, USA.
| | - Paul Blum
- School of Biological Sciences, University of Nebraska-Lincoln, 1901 Vine Street, Lincoln 68588, NE, USA.
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Jia B, Liu J, Van Duyet L, Sun Y, Xuan YH, Cheong GW. Proteome profiling of heat, oxidative, and salt stress responses in Thermococcus kodakarensis KOD1. Front Microbiol 2015; 6:605. [PMID: 26150806 PMCID: PMC4473059 DOI: 10.3389/fmicb.2015.00605] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 06/02/2015] [Indexed: 01/18/2023] Open
Abstract
The thermophilic species, Thermococcus kodakarensis KOD1, a model microorganism for studying hyperthermophiles, has adapted to optimal growth under conditions of high temperature and salinity. However, the environmental conditions for the strain are not always stable, and this strain might face different stresses. In the present study, we compared the proteome response of T. kodakarensis to heat, oxidative, and salt stresses using two-dimensional electrophoresis, and protein spots were identified through MALDI-TOF/MS. Fifty-nine, forty-two, and twenty-nine spots were induced under heat, oxidative, and salt stresses, respectively. Among the up-regulated proteins, four proteins (a hypothetical protein, pyridoxal biosynthesis lyase, peroxiredoxin, and protein disulphide oxidoreductase) were associated with all three stresses. Gene ontology analysis showed that these proteins were primarily involved metabolic and cellular processes. The KEGG pathway analysis suggested that the main metabolic pathways involving these enzymes were related to carbohydrate metabolism, secondary metabolite synthesis, and amino acid biosynthesis. These data might enhance our understanding of the functions and molecular mechanisms of thermophilic Archaea for survival and adaptation in extreme environments.
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Affiliation(s)
- Baolei Jia
- Department of Life Science, Chung-Ang University, Seoul South Korea ; Division of Applied Life Sciences and Research Institute of Natural Science, Gyeongsang National University Jinju, South Korea
| | - Jinliang Liu
- College of Plant Sciences, Jilin University Changchun, China
| | - Le Van Duyet
- Division of Applied Life Sciences and Research Institute of Natural Science, Gyeongsang National University Jinju, South Korea
| | - Ying Sun
- College of Plant Sciences, Jilin University Changchun, China
| | - Yuan H Xuan
- College of Plant Protection, Shenyang Agricultural University Shenyang, China
| | - Gang-Won Cheong
- Division of Applied Life Sciences and Research Institute of Natural Science, Gyeongsang National University Jinju, South Korea
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Feng J, Wang J, Zhang Y, Du X, Xu Z, Wu Y, Tang W, Li M, Tang B, Tang XF. Proteomic analysis of the secretome of haloarchaeon Natrinema sp. J7-2. J Proteome Res 2014; 13:1248-58. [PMID: 24512091 DOI: 10.1021/pr400728x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although in silico predictions have revealed that haloarchaea can be distinguished from other organisms in that the Tat pathway is used more extensively than the Sec pathway for haloarchaeal protein secretion, only a few haloarchaeal-secreted proteins have been experimentally confirmed. Here, the culture supernatant and membrane fraction of the haloarchaeon Natrinema sp. J7-2 grown at 23% salt concentration were subjected to RPLC-ESI-MS/MS analysis. In total, 46 predicted Tat substrates, 14 predicted Sec substrates, and 3 class III signal peptide-bearing proteins were detected. Approximately 65% of the detected Tat substrates contain lipoboxes, emphasizing the role of the Tat pathway in haloarchaeal lipoprotein secretion. Most of the detected Tat substrates are extracellular substrate (solute)-binding proteins and redox proteins. Despite the small number of Sec substrates, two of them, a cell surface glycoprotein and a putative lipoprotein carrier protein, were identified to be high-abundance secreted proteins. While limited proteins were detected in the culture supernatant, most of the secreted proteins were found in the membrane fraction. The anchoring of secreted proteins to the cell surface via a lipobox or a PGF-CTERM seems to be an adaptation strategy of haloarchaea to handle the harsh extracellular environment. Additionally, ∼15% of the integral membrane proteins (IMPs) detected in the membrane fraction possess putative Sec signal peptides or signal anchors, implying that the Sec pathway is important for membrane insertion of IMPs. This is the first report to describe the experimental secretome of haloarchaea and provide new information for better understanding of haloarchaeal protein secretion patterns.
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Affiliation(s)
- Jie Feng
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University , Wuhan 430072, China
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Kort JC, Esser D, Pham TK, Noirel J, Wright PC, Siebers B. A cool tool for hot and sour Archaea: Proteomics of Sulfolobus solfataricus. Proteomics 2013; 13:2831-50. [DOI: 10.1002/pmic.201300088] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 04/23/2013] [Accepted: 05/03/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Julia Christin Kort
- Molecular Enzyme Technology and Biochemistry; Biofilm Centre, Faculty of Chemistry, University of Duisburg-Essen; Essen Germany
| | - Dominik Esser
- Molecular Enzyme Technology and Biochemistry; Biofilm Centre, Faculty of Chemistry, University of Duisburg-Essen; Essen Germany
| | - Trong Khoa Pham
- Department of Chemical and Biological Engineering; ChELSI Institute, The University of Sheffield; Sheffield UK
| | - Josselin Noirel
- Department of Chemical and Biological Engineering; ChELSI Institute, The University of Sheffield; Sheffield UK
| | - Phillip C. Wright
- Department of Chemical and Biological Engineering; ChELSI Institute, The University of Sheffield; Sheffield UK
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry; Biofilm Centre, Faculty of Chemistry, University of Duisburg-Essen; Essen Germany
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Reimann J, Esser D, Orell A, Amman F, Pham TK, Noirel J, Lindås AC, Bernander R, Wright PC, Siebers B, Albers SV. Archaeal signal transduction: impact of protein phosphatase deletions on cell size, motility, and energy metabolism in Sulfolobus acidocaldarius. Mol Cell Proteomics 2013; 12:3908-23. [PMID: 24078887 PMCID: PMC3861733 DOI: 10.1074/mcp.m113.027375] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In this study, the in vitro and in vivo functions of the only two identified protein phosphatases, Saci-PTP and Saci-PP2A, in the crenarchaeal model organism Sulfolobus acidocaldarius were investigated. Biochemical characterization revealed that Saci-PTP is a dual-specific phosphatase (against pSer/pThr and pTyr), whereas Saci-PP2A exhibited specific pSer/pThr activity and inhibition by okadaic acid. Deletion of saci_pp2a resulted in pronounced alterations in growth, cell shape and cell size, which could be partially complemented. Transcriptome analysis of the three strains (Δsaci_ptp, Δsaci_pp2a and the MW001 parental strain) revealed 155 genes that were differentially expressed in the deletion mutants, and showed significant changes in expression of genes encoding the archaella (archaeal motility structure), components of the respiratory chain and transcriptional regulators. Phosphoproteome studies revealed 801 unique phosphoproteins in total, with an increase in identified phosphopeptides in the deletion mutants. Proteins from most functional categories were affected by phosphorylation, including components of the motility system, the respiratory chain, and regulatory proteins. In the saci_pp2a deletion mutant the up-regulation at the transcript level, as well as the observed phosphorylation pattern, resembled starvation stress responses. Hypermotility was also observed in the saci_pp2a deletion mutant. The results highlight the importance of protein phosphorylation in regulating essential cellular processes in the crenarchaeon S. acidocaldarius.
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Affiliation(s)
- Julia Reimann
- Molecular Biology of Archaea, Max Planck Institute for terrestrial Microbiology, Karl-von-Frisch Straβe 10, 35043 Marburg, Germany
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Data Acquisition Strategy for Mass Spectrometers Applied to Bottom-up-Based Protein Identification. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2013. [DOI: 10.1016/s1872-2040(13)60742-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Cohen Freue GV, Meredith A, Smith D, Bergman A, Sasaki M, Lam KKY, Hollander Z, Opushneva N, Takhar M, Lin D, Wilson-McManus J, Balshaw R, Keown PA, Borchers CH, McManus B, Ng RT, McMaster WR. Computational biomarker pipeline from discovery to clinical implementation: plasma proteomic biomarkers for cardiac transplantation. PLoS Comput Biol 2013; 9:e1002963. [PMID: 23592955 PMCID: PMC3617196 DOI: 10.1371/journal.pcbi.1002963] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2012] [Accepted: 01/16/2013] [Indexed: 11/19/2022] Open
Abstract
Recent technical advances in the field of quantitative proteomics have stimulated a large number of biomarker discovery studies of various diseases, providing avenues for new treatments and diagnostics. However, inherent challenges have limited the successful translation of candidate biomarkers into clinical use, thus highlighting the need for a robust analytical methodology to transition from biomarker discovery to clinical implementation. We have developed an end-to-end computational proteomic pipeline for biomarkers studies. At the discovery stage, the pipeline emphasizes different aspects of experimental design, appropriate statistical methodologies, and quality assessment of results. At the validation stage, the pipeline focuses on the migration of the results to a platform appropriate for external validation, and the development of a classifier score based on corroborated protein biomarkers. At the last stage towards clinical implementation, the main aims are to develop and validate an assay suitable for clinical deployment, and to calibrate the biomarker classifier using the developed assay. The proposed pipeline was applied to a biomarker study in cardiac transplantation aimed at developing a minimally invasive clinical test to monitor acute rejection. Starting with an untargeted screening of the human plasma proteome, five candidate biomarker proteins were identified. Rejection-regulated proteins reflect cellular and humoral immune responses, acute phase inflammatory pathways, and lipid metabolism biological processes. A multiplex multiple reaction monitoring mass-spectrometry (MRM-MS) assay was developed for the five candidate biomarkers and validated by enzyme-linked immune-sorbent (ELISA) and immunonephelometric assays (INA). A classifier score based on corroborated proteins demonstrated that the developed MRM-MS assay provides an appropriate methodology for an external validation, which is still in progress. Plasma proteomic biomarkers of acute cardiac rejection may offer a relevant post-transplant monitoring tool to effectively guide clinical care. The proposed computational pipeline is highly applicable to a wide range of biomarker proteomic studies.
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Affiliation(s)
- Gabriela V. Cohen Freue
- NCE CECR Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
- Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Anna Meredith
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Derek Smith
- University of Victoria Genome BC Proteomics Centre, Victoria, British Columbia, Canada
| | - Axel Bergman
- Immunity and Infection Research Centre, Vancouver, British Columbia, Canada
| | - Mayu Sasaki
- Immunity and Infection Research Centre, Vancouver, British Columbia, Canada
| | - Karen K. Y. Lam
- NCE CECR Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Zsuzsanna Hollander
- NCE CECR Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nina Opushneva
- NCE CECR Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
| | - Mandeep Takhar
- NCE CECR Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
| | - David Lin
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Janet Wilson-McManus
- NCE CECR Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert Balshaw
- NCE CECR Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
- Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Paul A. Keown
- NCE CECR Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Immunology Laboratory, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Christoph H. Borchers
- University of Victoria Genome BC Proteomics Centre, Victoria, British Columbia, Canada
| | - Bruce McManus
- NCE CECR Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- UBC James Hogg Research Centre, Vancouver, British Columbia, Canada
| | - Raymond T. Ng
- NCE CECR Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
- Department of Computer Science, University of British Columbia, Vancouver, British Columbia, Canada
| | - W. Robert McMaster
- NCE CECR Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
- Immunity and Infection Research Centre, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
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Szabo Z, Pohlschroder M. Diversity and subcellular distribution of archaeal secreted proteins. Front Microbiol 2012; 3:207. [PMID: 22783239 PMCID: PMC3387779 DOI: 10.3389/fmicb.2012.00207] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 05/21/2012] [Indexed: 12/12/2022] Open
Abstract
Secreted proteins make up a significant percentage of a prokaryotic proteome and play critical roles in important cellular processes such as polymer degradation, nutrient uptake, signal transduction, cell wall biosynthesis, and motility. The majority of archaeal proteins are believed to be secreted either in an unfolded conformation via the universally conserved Sec pathway or in a folded conformation via the Twin arginine transport (Tat) pathway. Extensive in vivo and in silico analyses of N-terminal signal peptides that target proteins to these pathways have led to the development of computational tools that not only predict Sec and Tat substrates with high accuracy but also provide information about signal peptide processing and targeting. Predictions therefore include indications as to whether a substrate is a soluble secreted protein, a membrane or cell wall anchored protein, or a surface structure subunit, and whether it is targeted for post-translational modification such as glycosylation or the addition of a lipid. The use of these in silico tools, in combination with biochemical and genetic analyses of transport pathways and their substrates, has resulted in improved predictions of the subcellular localization of archaeal secreted proteins, allowing for a more accurate annotation of archaeal proteomes, and has led to the identification of potential adaptations to extreme environments, as well as phyla-specific pathways among the archaea. A more comprehensive understanding of the transport pathways used and post-translational modifications of secreted archaeal proteins will also facilitate the identification and heterologous expression of commercially valuable archaeal enzymes.
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Pereira SB, Ow SY, Barrios-Llerena ME, Wright PC, Moradas-Ferreira P, Tamagnini P. iTRAQ-based quantitative proteomic analysis of Gloeothece sp. PCC 6909: Comparison with its sheathless mutant and adaptations to nitrate deficiency and sulfur limitation. J Proteomics 2011; 75:270-83. [DOI: 10.1016/j.jprot.2011.09.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Revised: 07/25/2011] [Accepted: 09/09/2011] [Indexed: 11/25/2022]
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14
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Bewley MA, Pham TK, Marriott HM, Noirel J, Chu HP, Ow SY, Ryazanov AG, Read RC, Whyte MKB, Chain B, Wright PC, Dockrell DH. Proteomic evaluation and validation of cathepsin D regulated proteins in macrophages exposed to Streptococcus pneumoniae. Mol Cell Proteomics 2011; 10:M111.008193. [PMID: 21474794 PMCID: PMC3108842 DOI: 10.1074/mcp.m111.008193] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Revised: 04/01/2011] [Indexed: 11/23/2022] Open
Abstract
Macrophages are central effectors of innate immune responses to bacteria. We have investigated how activation of the abundant macrophage lysosomal protease, cathepsin D, regulates the macrophage proteome during killing of Streptococcus pneumoniae. Using the cathepsin D inhibitor pepstatin A, we demonstrate that cathepsin D differentially regulates multiple targets out of 679 proteins identified and quantified by eight-plex isobaric tag for relative and absolute quantitation. Our statistical analysis identified 18 differentially expressed proteins that passed all paired t-tests (α = 0.05). This dataset was enriched for proteins regulating the mitochondrial pathway of apoptosis or inhibiting competing death programs. Five proteins were selected for further analysis. Western blotting, followed by pharmacological inhibition or genetic manipulation of cathepsin D, verified cathepsin D-dependent regulation of these proteins, after exposure to S. pneumoniae. Superoxide dismutase-2 up-regulation was temporally related to increased reactive oxygen species generation. Gelsolin, a known regulator of mitochondrial outer membrane permeabilization, was down-regulated in association with cytochrome c release from mitochondria. Eukaryotic elongation factor (eEF2), a regulator of protein translation, was also down-regulated by cathepsin D. Using absence of the negative regulator of eEF2, eEF2 kinase, we confirm that eEF2 function is required to maintain expression of the anti-apoptotic protein Mcl-1, delaying macrophage apoptosis and confirm using a murine model that maintaining eEF2 function is associated with impaired macrophage apoptosis-associated killing of Streptococcus pneumoniae. These findings demonstrate that cathepsin D regulates multiple proteins controlling the mitochondrial pathway of macrophage apoptosis or competing death processes, facilitating intracellular bacterial killing.
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Affiliation(s)
| | - Trong K. Pham
- §ChELSI Institute, Department of Chemical and Processing Engineering, University of Sheffield, Sheffield, UK
| | | | - Josselin Noirel
- §ChELSI Institute, Department of Chemical and Processing Engineering, University of Sheffield, Sheffield, UK
| | - Hseuh-Ping Chu
- ‖Department of Pharmacology University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, New Jersey, USA
| | - Saw Y. Ow
- §ChELSI Institute, Department of Chemical and Processing Engineering, University of Sheffield, Sheffield, UK
| | - Alexey G. Ryazanov
- ‖Department of Pharmacology University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, New Jersey, USA
| | - Robert C. Read
- From the ‡Medical School
- ‡‡Sheffield Teaching Hospitals and
| | | | - Benny Chain
- ¶Division of Infection and Immunity, University College London, London, UK
| | - Phillip C. Wright
- §ChELSI Institute, Department of Chemical and Processing Engineering, University of Sheffield, Sheffield, UK
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16
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Shaping the archaeal cell envelope. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2010; 2010:608243. [PMID: 20671907 PMCID: PMC2910488 DOI: 10.1155/2010/608243] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Accepted: 05/29/2010] [Indexed: 12/12/2022]
Abstract
Although archaea have a similar cellular organization as other prokaryotes, the lipid composition of their membranes and their cell surface is unique. Here we discuss recent developments in our understanding of the archaeal protein secretion mechanisms, the assembly of macromolecular cell surface structures, and the release of S-layer-coated vesicles from the archaeal membrane.
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17
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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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18
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Pham TK, Sierocinski P, van der Oost J, Wright PC. Quantitative proteomic analysis of Sulfolobus solfataricus membrane proteins. J Proteome Res 2010; 9:1165-72. [PMID: 19954172 DOI: 10.1021/pr9007688] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A quantitative proteomic analysis of the membrane of the archaeon Sulfolobus solfataricus P2 using iTRAQ was successfully demonstrated in this technical note. The estimated number of membrane proteins of this organism is 883 (predicted based on Gravy score), corresponding to 30% of the total number of proteins. Using a modified iTRAQ protocol for membrane protein analysis, of the 284 proteins detected, 246 proteins were identified as membrane proteins, while using an original iTRAQ protocol, 147 proteins were detected with only 133 proteins being identified as membrane proteins. Furthermore, 97.2% of proteins identified in the modified protocol contained more than 2 distinct peptides compared to the original workflow. The successful application of this modified protocol offers a potential technique for quantitatively analyzing membrane-associated proteomes of organisms in the archaeal kingdom. The combination of 3 different iTRAQ experiments resulted in the detection of 395 proteins (>or=2 distinct peptides) of which 373 had predicted membrane properties. Approximately 20% of the quantified proteins were observed to exhibit >or=1.5-fold differential expression at temperatures well below the optimum for growth.
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Affiliation(s)
- Trong Khoa Pham
- ChELSI Institute, Biological and Environmental Systems Group, Department of Chemical and Process Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
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19
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Ellen AF, Albers SV, Driessen AJM. Comparative study of the extracellular proteome of Sulfolobus species reveals limited secretion. Extremophiles 2009; 14:87-98. [PMID: 19957093 PMCID: PMC2797410 DOI: 10.1007/s00792-009-0290-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2009] [Accepted: 11/10/2009] [Indexed: 01/01/2023]
Abstract
Although a large number of potentially secreted proteins can be predicted on the basis of genomic distribution of signal sequence-bearing proteins, protein secretion in Archaea has barely been studied. A proteomic inventory and comparison of the growth medium proteins in three hyperthermoacidophiles, i.e., Sulfolobus solfataricus, S. acidocaldarius and S. tokodaii, indicates that only few proteins are freely secreted into the growth medium and that the majority originates from cell envelope bound forms. In S. acidocaldarius both cell-associated and secreted alpha-amylase activities are detected. Inactivation of the amyA gene resulted in a complete loss of activity, suggesting that the same protein is responsible for the a-amylase activity at both locations. It is concluded that protein secretion in Sulfolobus is a limited process, and it is suggested that the S-layer may act as a barrier for the free diffusion of folded proteins into the medium.
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Affiliation(s)
- Albert F Ellen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
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20
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Liu N, Chan W, Lee KC, Cai Z. A method to enhance a1 ions and application for peptide sequencing and protein identification. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:1214-1223. [PMID: 19299168 DOI: 10.1016/j.jasms.2009.02.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2008] [Revised: 02/10/2009] [Accepted: 02/10/2009] [Indexed: 05/27/2023]
Abstract
A simple and effective method was developed for peptide sequencing and protein identification through the determination of its N-terminal residue. The method of N-terminal carbamidomethylation with iodoacetamide could specifically and remarkably enhance the intensity of a(1) ions in the tandem mass spectra of the peptide derivatives without significantly altering their fragmentation pattern, thus allowing determination of their N-terminal residues. The effectiveness and specificity of the method was demonstrated by confirming and extending sequence interpretation of several model peptides and proteins. The developed method was then applied in the LC-MS/MS analysis of the tryptic digests of myoglobin and a whole protein extract from rat heart tissues. The results from database searches were well validated with the enhancement of a(1) ions in tandem mass spectra and the specificity of protein identification was obtained when the information of N-terminal residues was included in the database search.
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Affiliation(s)
- Ning Liu
- Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China
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21
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22
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Palmieri G, Catara G, Saviano M, Langella E, Gogliettino M, Rossi M. First Archaeal PEPB-Serine Protease Inhibitor from Sulfolobus solfataricus with Noncanonical Amino Acid Sequence in the Reactive-Site Loop. J Proteome Res 2009; 8:327-34. [PMID: 19118453 DOI: 10.1021/pr800587t] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The specific inhibition of serine proteinases, which are crucial switches in many important physiological processes, is of great value both for basic research and for therapeutic applications. In this study, we report the molecular cloning of the sso0767 gene from Sulfolobus solfataricus, and the functional characterization of its product, SsCEI, which represents the first archaeal phosphatidylethanolamine-binding protein (PEBP)-serine proteinase inhibitor, reported to date. SsCEI is a monomer protein with a molecular mass of 19.0 kDa and a pI of 6.7, which is able to inhibit the serine proteases alpha-chymotrypsin and elastase with K(i) values of 0.08 and 0.1 microM, respectively. Moreover SsCEI is extremely resistant to both thermal inactivation and proteolytic attack suggesting compact folding of the protein. Within the I51 family, the archaeal inhibitor shows strong similarity to the human and murine members. The three-dimensional model of SsCEI revealed a general beta-fold and the presence of an anion-binding pocket, the hallmark of the PEBP family. Moreover SsCEI binds the cognate proteases according to a common, substrate-like standard mechanism. Point mutation experiments supported the prediction of the protease-binding site located on the surface at the C- terminal region of the protein. Interestingly, searches based on preidentified structural reactive loop motifs revealed the occurrence of a sequence (T123-N130) that is not represented in all serine-protease inhibitor families. This unique motif may provide new insights into both the inhibitor/protease binding mode and the specific biological functions of SsCEI within the PEBP family.
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Affiliation(s)
- Gianna Palmieri
- Istituto di Biochimica delle Proteine, Via P. Castellino 111, 80131 Napoli, Italy
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23
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Kwon SO, Kang SG, Park SH, Kim YH, Choi JS, Lee JH, Kim SI. Proteomic characterization of the sulfur-reducing hyperthermophilic archaeon Thermococcus onnurineus NA1 by 2-DE/MS-MS. Extremophiles 2009; 13:379-87. [PMID: 19132287 DOI: 10.1007/s00792-008-0220-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2008] [Accepted: 12/09/2008] [Indexed: 11/28/2022]
Abstract
Thermococcus onnurineus NA1, a sulfur-reducing hyperthermophilic archaeon, was isolated from a deep-sea hydrothermal vent area in Papua New Guinea. The strain requires elemental sulfur as a terminal electron acceptor for heterotrophic growth on peptides, amino acids and sugars. Recently, genome sequencing of Thermococcus onnurineus NA1 was completed. In this study, 2-DE/MS-MS analysis of the cytosolic proteome was performed to elucidate the metabolic characterization of Thermococcus onnurineus NA1 at the protein level. Among the 1,136 visualized protein spots, 110 proteins were identified. Enzymes related to metabolic pathways of amino acids utilization, glycolysis, pyruvate conversion, ATP synthesis, and protein synthesis were identified as abundant proteins, highlighting the fact that these are major metabolic pathways in Thermococcus onnurineus NA1. Interestingly, multiple spots of phosphoenolpyruvate synthetase and elongation factor Tu were found on 2D gels generated by truncation at the N-terminus, implicating the cellular regulatory mechanism of this key enzyme by protease degradation. In addition to the proteins involved in metabolic systems, we also identified various proteases and stress-related proteins. The proteomic characterization of abundantly induced proteins using 2-DE/MS-MS enables a better understanding of Thermococcus onnurineus NA1 metabolism.
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Affiliation(s)
- Sang Oh Kwon
- Korea Basic Science Institute, Daejeon 305-333, South Korea
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24
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Bagos PG, Tsirigos KD, Plessas SK, Liakopoulos TD, Hamodrakas SJ. Prediction of signal peptides in archaea. Protein Eng Des Sel 2008; 22:27-35. [PMID: 18988691 DOI: 10.1093/protein/gzn064] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Computational prediction of signal peptides (SPs) and their cleavage sites is of great importance in computational biology; however, currently there is no available method capable of predicting reliably the SPs of archaea, due to the limited amount of experimentally verified proteins with SPs. We performed an extensive literature search in order to identify archaeal proteins having experimentally verified SP and managed to find 69 such proteins, the largest number ever reported. A detailed analysis of these sequences revealed some unique features of the SPs of archaea, such as the unique amino acid composition of the hydrophobic region with a higher than expected occurrence of isoleucine, and a cleavage site resembling more the sequences of gram-positives with almost equal amounts of alanine and valine at the position-3 before the cleavage site and a dominant alanine at position-1, followed in abundance by serine and glycine. Using these proteins as a training set, we trained a hidden Markov model method that predicts the presence of the SPs and their cleavage sites and also discriminates such proteins from cytoplasmic and transmembrane ones. The method performs satisfactorily, yielding a 35-fold cross-validation procedure, a sensitivity of 100% and specificity 98.41% with the Matthews' correlation coefficient being equal to 0.964. This particular method is currently the only available method for the prediction of secretory SPs in archaea, and performs consistently and significantly better compared with other available predictors that were trained on sequences of eukaryotic or bacterial origin. Searching 48 completely sequenced archaeal genomes we identified 9437 putative SPs. The method, PRED-SIGNAL, and the results are freely available for academic users at http://bioinformatics.biol.uoa.gr/PRED-SIGNAL/ and we anticipate that it will be a valuable tool for the computational analysis of archaeal genomes.
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Affiliation(s)
- P G Bagos
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Athens 15701, Greece.
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25
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Kirkland PA, Humbard MA, Daniels CJ, Maupin-Furlow JA. Shotgun proteomics of the haloarchaeon Haloferax volcanii. J Proteome Res 2008; 7:5033-9. [PMID: 18816081 DOI: 10.1021/pr800517a] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Haloferax volcanii, an extreme halophile originally isolated from the Dead Sea, is used worldwide as a model organism for furthering our understanding of archaeal cell physiology. In this study, a combination of approaches was used to identify a total of 1296 proteins, representing 32% of the theoretical proteome of this haloarchaeon. This included separation of (phospho)proteins/peptides by 2-dimensional gel electrophoresis (2-D), immobilized metal affinity chromatography (IMAC), metal oxide affinity chromatography (MOAC), and Multidimensional Protein Identification Technology (MudPIT) including strong cation exchange (SCX) chromatography coupled with reversed phase (RP) HPLC. Proteins were identified by tandem mass spectrometry (MS/MS) using nanoelectrospray ionization hybrid quadrupole time-of-flight (QSTAR XL Hybrid LC/MS/MS System) and quadrupole ion trap (Thermo LCQ Deca). Results indicate that a SCX RP HPLC fractionation coupled with MS/MS provides the best high-throughput workflow for overall protein identification.
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Affiliation(s)
- P Aaron Kirkland
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611-0700, USA
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26
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Ning ZB, Li QR, Dai J, Li RX, Shieh CH, Zeng R. Fractionation of Complex Protein Mixture by Virtual Three-Dimensional Liquid Chromatography Based on Combined pH and Salt Steps. J Proteome Res 2008; 7:4525-37. [DOI: 10.1021/pr800318j] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Zhi-Bin Ning
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Qing-Run Li
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jie Dai
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Rong-Xia Li
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Chia-Hui Shieh
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Rong Zeng
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Science, Chinese Academy of Sciences, Shanghai, 200031, China
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27
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Berkner S, Lipps G. Genetic tools for Sulfolobus spp.: vectors and first applications. Arch Microbiol 2008; 190:217-30. [PMID: 18542925 DOI: 10.1007/s00203-008-0392-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2008] [Revised: 05/14/2008] [Accepted: 05/19/2008] [Indexed: 10/22/2022]
Abstract
Sulfolobus species belong to the best-studied archaeal organisms but have lacked powerful genetic methods. Recently, there has been considerable progress in the field of Sulfolobus genetics. Urgently needed basic genetic tools, such as targeted gene knockout techniques and shuttle vectors are being developed at an increasing pace. For S. solfataricus knockout systems as well as different shuttle vectors are available. For the genetically more stable S. acidocaldarius shuttle vectors have been recently developed. In this review we summarize the currently available genetic tools and methods for the genus Sulfolobus. Different transformation protocols are discussed, as well as all so far developed knockout systems and Sulfolobus-Escherichia coli shuttle vectors are summarized. Special emphasis is put on the important vector components, i.e., selectable markers and Sulfolobus replicons. Additionally, the information gathered on different Sulfolobus strains with respect to their use as recipient strains is reviewed. The advantages and disadvantages of the different systems are discussed and aims for further improvement of genetic systems are identified.
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Affiliation(s)
- Silvia Berkner
- Department of Biochemistry, University of Bayreuth, Universitätsstr. 30, 95447 Bayreuth, Germany
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28
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Wang N, Li L. Exploring the precursor ion exclusion feature of liquid chromatography-electrospray ionization quadrupole time-of-flight mass spectrometry for improving protein identification in shotgun proteome analysis. Anal Chem 2008; 80:4696-710. [PMID: 18479145 DOI: 10.1021/ac800260w] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In shotgun proteome analysis by liquid chromatography-tandem mass spectrometry (LC-MS/MS), not all coeluting peptides at a given retention time are subjected to MS/MS due to the limitation of spectral acquisition speed of a mass spectrometer. In this work, precursor ion exclusion (PIE) in an electrospray ionization (ESI) quadrupole time-of-flight (QTOF) mass spectrometer was explored as a means of mitigating the undersampling problem. This strategy is based on running replicates of the sample where the precursor ions detected in the initial run(s) are excluded for MS/MS in the subsequent run. Four PIE methods as well as running replicates without PIE were investigated and compared for their effectiveness in identifying peptides and proteins. In the analysis of an MCF-7 breast cancer cell lysate digest by three replicate 2 h gradient LC-ESI runs, the first PIE method used a list of precursor ions detected in the initial run(s) for exclusion and identified a total of 572 proteins from the three runs combined with an average of 3.59 peptides matched to a protein. The second PIE method involved in the generation of a list of m/ z values of precursor ions along with their retention time information from the initial run(s), followed by entering these ions with retention times into the ion exclusion program of the QTOF control software for exclusion at a predefined retention time window (i.e., +/-150 s). In comparison to the first PIE method, this method reduced the possibility of excluding different peptide ions of the same m/ z (within a mass tolerance window) eluted at different retention windows. A total of 657 proteins were identified with an average of 3.75 peptides matched to a protein. The third PIE method studied relied on the exclusion of the precursor ions of peptides identified through database search of the MS/MS spectra generated in the initial run(s). This selective PIE method identified a total of 681 proteins with an average of 3.68 peptides matched to a protein. The final PIE method investigated involves the expansion of the selective PIE list by including nonidentifiable peptide ions found in the database search. This complete PIE method identified a total of 726 proteins with an average of 3.66 peptides per protein. In the case of three replicate runs without PIE, a total of 460 proteins were identified with an average of 3.51 peptides matched to a protein. Thus, the use of an optimal PIE strategy significantly increased the number of proteins identified from replicate runs (i.e., 726 vs 460 or a 58% increase). It is further demonstrated that this PIE strategy also improves protein identification efficiency in the analysis of a yeast whole cell lysate digesta less complex proteome digest. A total of 533 proteins identified from five replicate runs with complete PIE, compared to 353 proteins identified from the five replicate runs without PIE, representing a 51% increase in the number of proteins identified.
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Affiliation(s)
- Nan Wang
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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29
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Assiddiq BF, Snijders APL, Chong PK, Wright PC, Dickman MJ. Identification and Characterization of Sulfolobus solfataricus P2 Proteome Using Multidimensional Liquid Phase Protein Separations. J Proteome Res 2008; 7:2253-61. [DOI: 10.1021/pr7006472] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Bobby F. Assiddiq
- Biological and Environmental Systems Group, Department of Chemical and Process Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Ambrosius P. L. Snijders
- Biological and Environmental Systems Group, Department of Chemical and Process Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Poh Kuan Chong
- Biological and Environmental Systems Group, Department of Chemical and Process Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Phillip C. Wright
- Biological and Environmental Systems Group, Department of Chemical and Process Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Mark. J. Dickman
- Biological and Environmental Systems Group, Department of Chemical and Process Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
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30
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Chong PK, Burja AM, Radianingtyas H, Fazeli A, Wright PC. Proteome and transcriptional analysis of ethanol-grown Sulfolobus solfataricus P2 reveals ADH2, a potential alcohol dehydrogenase. J Proteome Res 2007; 6:3985-94. [PMID: 17824633 DOI: 10.1021/pr070232y] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sulfolobus solfataricus P2 was shown to survive on ethanol at various concentrations (0.08-3.97% w/v) as the sole carbon source. The highest ethanol consumption rate was 15.1 mg/L/hr (via GC-MS analysis) in cultures grown on 0.79% w/v ethanol. In vivo metabolic labeling, using 13C universally labeled ethanol, provided evidence for both ethanol uptake and metabolic utilization. Results obtained from isobaric mass tag-facilitated shotgun proteomics (iTRAQ) indicate that on average, 21 and 31% of the 284 proteins identified (with > or = 2 MS/MS) are increased and decreased expression in ethanol cultures compared to glucose control cultures. Preliminary analysis shows >2-fold increase of the zinc-dependent alcohol dehydrogenase, ADH-10 (SSO2536), and the putative ADH-2 (SSO0764) in both translational and transcriptional data (using quantitative RT-PCR), suggesting both proteins are integral to ethanol metabolism. Evidence that ethanol was catabolised into central metabolism via acetyl-CoA intermediates was further indicated by another >2-fold increase in protein expression levels of various acetyl-CoA synthetases. The decreased expression (>2-fold) of isocitrate dehydrogenase at the protein level suggests that the ethanol grown cultures shifted toward the glyoxylate cycle. Subsequently, the activity of ADH-2 was confirmed by overexpression in Escherichia coli, with the resultant purified in vitro enzyme exhibiting an activity that increased with temperature up to 95 degrees C, and giving a specific activity of 1.05 U/mg.
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Affiliation(s)
- Poh Kuan Chong
- Biological and Environmental Systems Group, Department of Chemical and Process Engineering, University of Sheffield, Mappin Street, Sheffield S1 3JD, United Kingdom
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31
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Pereira-Medrano AG, Sterling A, Snijders APL, Reardon KF, Wright PC. A systematic evaluation of chip-based nanoelectrospray parameters for rapid identification of proteins from a complex mixture. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2007; 18:1714-25. [PMID: 17689093 DOI: 10.1016/j.jasms.2007.06.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2006] [Revised: 06/15/2007] [Accepted: 06/22/2007] [Indexed: 05/16/2023]
Abstract
HPLC-MS/MS is widely used for protein identification from gel spots and shotgun fractions. Although HPLC has well recognized benefits, this type of sample infusion also has some undesirable attributes: relatively low sample throughput, potential sample-to-sample carryover, time-varying sample composition, and no option for longer sample infusion for longer MS analyses. An automated chip-based ESI device (CB-ESI) has the potential to overcome these limitations. This report describes a systematic evaluation of the information-dependant acquisition (IDA) and sample preparation protocols for rapid protein identification from a complex mixture using a CB-ESI source compared with HPLC-ESI (gradient and isocratic elutions). Cytochrome c and a six-protein mixture (11-117 kDa) were used to develop an IDA protocol for rapid protein identification and to evaluate the effects of sample preparation protocols. MS (1-10 s) and MS/MS (1-60 s) scan times, sample concentration (50-500 fmol/microL), and ZipTipC(18) cleanup were evaluated. Based on MOWSE scores, protein coverage, experimental run time, number of identified proteins, and reproducibility, a 12.5 min experiment (22 cycles, each with one 3 s MS and eight 10 s MS/MS scans) was determined to be the optimal IDA protocol for CB-ESI. This work flow yielded up to 220% greater peptide coverage compared with gradient HPLC-ESI and provided protein identifications with up to a 2-fold higher throughput rate than either HPLC-ESI approach, whilst employing half the amount of sample over the same time frame. The results from this study support the use of CB-ESI as a rapid alternative to the identification of protein mixtures.
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Affiliation(s)
- Ana Gabriela Pereira-Medrano
- Biological and Environmental Systems Group, Department of Chemical and Process Engineering, University of Sheffield, Sheffield, United Kingdom
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32
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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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33
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Salzano AM, Febbraio F, Farias T, Cetrangolo GP, Nucci R, Scaloni A, Manco G. Redox stress proteins are involved in adaptation response of the hyperthermoacidophilic archaeon Sulfolobus solfataricus to nickel challenge. Microb Cell Fact 2007; 6:25. [PMID: 17692131 PMCID: PMC1995220 DOI: 10.1186/1475-2859-6-25] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2007] [Accepted: 08/12/2007] [Indexed: 11/21/2022] Open
Abstract
Background Exposure to nickel (Ni) and its chemical derivatives has been associated with severe health effects in human. On the contrary, poor knowledge has been acquired on target physiological processes or molecular mechanisms of this metal in model organisms, including Bacteria and Archaea. In this study, we describe an analysis focused at identifying proteins involved in the recovery of the archaeon Sulfolobus solfataricus strain MT4 from Ni-induced stress. Results To this purpose, Sulfolobus solfataricus was grown in the presence of the highest nickel sulphate concentration still allowing cells to survive; crude extracts from treated and untreated cells were compared at the proteome level by using a bi-dimensional chromatography approach. We identified several proteins specifically repressed or induced as result of Ni treatment. Observed up-regulated proteins were largely endowed with the ability to trigger recovery from oxidative and osmotic stress in other biological systems. It is noteworthy that most of the proteins induced following Ni treatment perform similar functions and a few have eukaryal homologue counterparts. Conclusion These findings suggest a series of preferential gene expression pathways activated in adaptation response to metal challenge.
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Affiliation(s)
- Anna M Salzano
- Laboratorio di Proteomica e Spettrometria di Massa, ISPAAM, Consiglio Nazionale delle Ricerche, 80147 Napoli, Italy
| | - Ferdinando Febbraio
- Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Tiziana Farias
- Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Giovanni P Cetrangolo
- Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Roberto Nucci
- Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Andrea Scaloni
- Laboratorio di Proteomica e Spettrometria di Massa, ISPAAM, Consiglio Nazionale delle Ricerche, 80147 Napoli, Italy
| | - Giuseppe Manco
- Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, Via Pietro Castellino 111, 80131 Naples, Italy
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Fiorentino G, Ronca R, Cannio R, Rossi M, Bartolucci S. MarR-like transcriptional regulator involved in detoxification of aromatic compounds in Sulfolobus solfataricus. J Bacteriol 2007; 189:7351-60. [PMID: 17675388 PMCID: PMC2168448 DOI: 10.1128/jb.00885-07] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
A DNA binding protein, BldR, was identified in the crenarchaeon Sulfolobus solfataricus as a protein 5- to 10-fold more abundant in cells grown in the presence of toxic aldehydes; it binds to regulatory sequences located upstream of an alcohol dehydrogenase gene (Sso2536). BldR is homologous to bacterial representatives of the MarR (multiple antibiotic resistance) family of transcriptional regulators that mediate response to multiple environmental stresses. Transcriptional analysis revealed that the bldR gene was transcribed in a bicistronic unit composed of the genes encoding the transcriptional regulator (Sso1352) and a putative multidrug transporter (Sso1351) upstream. By homology to bacterial counterparts, the bicistron was named the mar-like operon. The level of mar-like operon expression was found to be increased at least 10-fold in response to chemical stress by aromatic aldehydes. Under the same growth conditions, similar enhanced in vivo levels of Sso2536 gene transcript were also measured. The gene encoding BldR was expressed in E. coli, and the recombinant protein was purified to homogeneity. DNA binding assays demonstrated that the protein is indeed a transcription factor able to recognize site specifically both the Sso2536 and mar-like promoters at sites containing palindromic consensus sequences. Benzaldehyde, the substrate of ADH(Ss), stimulates DNA binding of BldR at both promoters. The role of BldR in the auto-activation as well as in the regulation of the Sso2536 gene, together with results of increased operon and gene expression under conditions of exposure to aromatic aldehydes, indicates a novel coordinate regulatory mechanism in cell defense against stress by aromatic compounds.
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Affiliation(s)
- Gabriella Fiorentino
- Dipartimento di Biologia Strutturale e Funzionale, Università degli Studi di Napoli Federico II, Complesso Universitario Monte S Angelo, Via Cinthia, 80126, Napoli, Italy.
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Salzano AM, Arena S, Renzone G, D'Ambrosio C, Rullo R, Bruschi M, Ledda L, Maglione G, Candiano G, Ferrara L, Scaloni A. A widespread picture of theStreptococcus thermophilus proteome by cell lysate fractionation and gel-based/gel-free approaches. Proteomics 2007; 7:1420-33. [PMID: 17407180 DOI: 10.1002/pmic.200601030] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Among the group of lactic acid bacteria, Streptococcus thermophilus has found a wide application in industrial processes used for the manufacture of dairy products. Taking advantage of different proteome extraction and subfractionation protocols, bacterial cytosolic and membrane proteins were isolated and resolved by independent gel-free and gel-based separation procedures. Whole cytosolic fraction and its acid, basic and low molecular mass protein components were separated by different resolutive 2-DE and tricine 1-DE gels and identified by MALDI-TOF PMF and/or microLC-ESI-IT-MS/MS. Membrane proteins were resolved by 2-DE and SDS-PAGE gels and similarly identified by PMF and TMS analysis. In parallel, whole extract was trypsinized and resulting peptides were identified by shotgun 2-D LC-ESI-IT-MS/MS analysis. Using this combined approach, expression products corresponding to 458 different genes were identified, which cover almost a third of the predicted vegetative proteome. Relative protein concentration and hydrophobicity affected protein detection. Broad recognition was obtained for enzymes involved in carbohydrate, fatty acid, amino acid and nucleotide metabolism, replication, transcription, translation, cell wall synthesis, as well as for proteins affecting bacterial functions important for industrial applications, i.e. milk sugar import and exopolysaccharide biosynthesis. By providing detailed reference electrophoretic/chromatographic maps to be used in future comparative proteomic investigations on bacteria grown under various experimental conditions or on different bacterial strains, our results will favour dedicated studies on S. thermophilus metabolism and its regulation or on detection of biomarkers for selection of optimal strains for industrial applications.
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Affiliation(s)
- Anna Maria Salzano
- Proteomics and Mass Spectrometry Laboratory, Istituto per il Sistema Produzione Animale in Ambiente Mediterraneo, National Research Council, Naples, Italy
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Gan CS, Chong PK, Pham TK, Wright PC. Technical, experimental, and biological variations in isobaric tags for relative and absolute quantitation (iTRAQ). J Proteome Res 2007; 6:821-7. [PMID: 17269738 DOI: 10.1021/pr060474i] [Citation(s) in RCA: 341] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We assess the reliability of isobaric-tags for relative and absolute quantitation (iTRAQ), based on different types of replicate analyses taking into account technical, experimental, and biological variations. In total, 10 iTRAQ experiments were analyzed across three domains of life involving Saccharomyces cerevisiae KAY446, Sulfolobus solfataricus P2, and Synechocystis sp. PCC 6803. The coverage of protein expression of iTRAQ analysis increases as the variation tolerance increases. In brief, a cutoff point at +/-50% variation (+/-0.50) would yield 88% coverage in quantification based on an analysis of biological replicates. Technical replicate analysis produces a higher coverage level of 95% at a lower cutoff point of +/-30% variation. Experimental or iTRAQ variations exhibit similar behavior as biological variations, which suggest that most of the measurable deviations come from biological variations. These findings underline the importance of replicate analysis as a validation tool and benchmarking technique in protein expression analysis.
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Affiliation(s)
- Chee Sian Gan
- Biological and Environmental Systems Group, Department of Chemical and Process Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, United Kingdom
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Chong PK, Burja AM, Radianingtyas H, Fazeli A, Wright PC. Translational and transcriptional analysis of Sulfolobus solfataricus P2 to provide insights into alcohol and ketone utilisation. Proteomics 2007; 7:424-35. [PMID: 17211831 DOI: 10.1002/pmic.200600746] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The potential of Sulfolobus solfataricus P2 for alcohol or ketone bioconversion was explored in this study. S. solfataricus was grown in different concentrations (0.1-0.8% w/v) of alcohols or ketones (ethanol, iso-propanol, n-propanol, acetone, phenol and hexanol) in the presence of 0.4% w/v glucose. Consequently, the addition of these alcohols or ketones into the growth media had an inhibitory effect on biomass production, whereby lag times increased and specific growth rates decreased when compared to a glucose control. Complete glucose utilisation was observed in all cultures, although slower rates of glucose consumption were observed in experimental cultures (average of 14.9 mg/L/h compared to 18.9 mg/L/h in the control). On the other hand, incomplete solvent utilisation was observed, with the highest solvent consumption being approximately 51% of the initial concentration in acetone cultures. Translational responses of S. solfataricus towards these alcohols or ketones were then investigated using the isobaric tags for relative and absolute quantitation (iTRAQ) technique. The majority (>80%) of proteins identified and quantified showed no discernable changes in regulation compared to the control. These results, along with those obtained from transcriptional analysis of key genes involved within this catabolic process using quantitative RT-PCR and metabolite analysis, demonstrate successful alcohol or ketone conversion in S. solfataricus.
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Affiliation(s)
- Poh Kuan Chong
- Biological and Environmental Systems Group, Department of Chemical and Process Engineering, University of Sheffield, Sheffield, UK
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Chong PK, Burja AM, Radianingtyas H, Fazeli A, Wright PC. Proteome analysis of Sulfolobus solfataricus P2 propanol metabolism. J Proteome Res 2007; 6:1430-9. [PMID: 17315908 DOI: 10.1021/pr060575g] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sulfolobus solfataricus P2 is able to metabolize n-propanol as the sole carbon source. An average n-propanol consumption rate of 9.7 and 3.3 mg/L/hr was detected using GC-MS analysis from S. solfataricus cultures grown in 0.40 and 0.16% w/v n-propanol, respectively. The detection of propionaldehyde, the key intermediate of n-propanol degradation, produced at a rate of 1.3 and 1.0 mg/L/hr in 0.40 and 0.16% w/v n-propanol cultures, further validated the ability of S. solfataricus to utilize n-propanol. The translational and transcriptional responses of S. solfataricus grown on n-propanol versus glucose were also investigated using quantitative RT-PCR and iTRAQ approaches. Approximately 257 proteins with > or =2 MS/MS spectra were identified and quantified via iTRAQ. The global quantitative proteome overview obtained showed significant up-regulation of acetyl-CoA synthetases, propionyl-CoA carboxylase, and methylmalonyl-CoA mutase enzymes. This led to the proposition that the propionyl-CoA formed from n-propanol degradation is catabolised into the citrate cycle (central metabolism) via succinyl-CoA intermediates. In contrast, evidence obtained from these analysis approaches and in vivo stable isotope labeling experiments, suggests that S. solfataricus is only capable of converting isopropyl alcohol to acetone (and vice versa) but lacks the ability to further metabolize these compounds.
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Affiliation(s)
- Poh Kuan Chong
- Biological and Environmental Systems Group, Department of Chemical and Process Engineering, University of Sheffield, Mappin Street, Sheffield S1 3JD, UK
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Graham RLJ, Pollock CE, O'Loughlin SN, Ternan NG, Weatherly DB, Jackson PJ, Tarleton RL, McMullan G. Multidimensional proteomic analysis of the soluble subproteome of the emerging nosocomial pathogen Ochrobactrum anthropi. J Proteome Res 2007; 5:3145-53. [PMID: 17081066 DOI: 10.1021/pr060293g] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report the first large-scale gel-free proteomic analysis of the soluble subproteome of the emerging pathogen Ochrobactrum anthropi. Utilizing our robust offline multidimensional protein identification protocol, a total of 57 280 peptides were initially identified utilizing automated MS/MS analysis software. We describe our investigation of the heuristic protein validation tool PROVALT and demonstrate its ability to increase the speed and accuracy of the curation process of large-scale proteomic datasets. PROVALT reduced our peptide list to 8517 identified peptides and further manual curation of these peptides led to a final list of 984 uniquely identified peptides that resulted in the positive identification of 249 proteins. These identified proteins were functionally classified and physiochemically characterized. A variety of typical "housekeeping" functions identified within the proteome included nucleic acid, amino and fatty acid anabolism and catabolism, glycolysis, TCA cycle, and pyruvate and selenoamino acid metabolism. In addition, a number of potential virulence factors of relevance to both plant and human disease were identified.
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Affiliation(s)
- Robert Leslie James Graham
- School of Biomedical Sciences, University of Ulster, Coleraine, County Londonderry, BT52 1SA, United Kingdom.
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Savidor A, Donahoo RS, Hurtado-Gonzales O, Verberkmoes NC, Shah MB, Lamour KH, McDonald WH. Expressed peptide tags: an additional layer of data for genome annotation. J Proteome Res 2007; 5:3048-58. [PMID: 17081056 DOI: 10.1021/pr060134x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
While genome sequencing is becoming ever more routine, genome annotation remains a challenging process. Identification of the coding sequences within the genomic milieu presents a tremendous challenge, especially for eukaryotes with their complex gene architectures. Here, we present a method to assist the annotation process through the use of proteomic data and bioinformatics. Mass spectra of digested protein preparations of the organism of interest were acquired and searched against a protein database created by a six-frame translation of the genome. The identified peptides were mapped back to the genome, compared to the current annotation, and then categorized as supporting or extending the current genome annotation. We named the classified peptides Expressed Peptide Tags (EPTs). The well-annotated bacterium Rhodopseudomonas palustris was used as a control for the method and showed a high degree of correlation between EPT mapping and the current annotation, with 86% of the EPTs confirming existing gene calls and less than 1% of the EPTs expanding on the current annotation. The eukaryotic plant pathogens Phytophthora ramorum and Phytophthora sojae, whose genomes have been recently sequenced and are much less well-annotated, were also subjected to this method. A series of algorithmic steps were taken to increase the confidence of EPT identification for these organisms, including generation of smaller subdatabases to be searched against, and definition of EPT criteria that accommodates the more complex eukaryotic gene architecture. As expected, the analysis of the Phytophthora species showed less correlation between EPT mapping and their current annotation. While approximately 76% of Phytophthora EPTs supported the current annotation, a portion of them (7.7% and 12.9% for P. ramorum and P. sojae, respectively) suggested modification to current gene calls or identified novel genes that were missed by the current genome annotation of these organisms.
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Affiliation(s)
- Alon Savidor
- Graduate School of Genome Science and Technology, University of Tennessee-Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
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41
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Graham RLJ, Pollock CE, O'Loughlin SN, Ternan NG, Weatherly DB, Tarleton RL, McMullan G. Multidimensional analysis of the insoluble sub-proteome ofOceanobacillus iheyensis HTE831, an alkaliphilic and halotolerant deep-sea bacterium isolated from the Iheya ridge. Proteomics 2007; 7:82-91. [PMID: 17146838 DOI: 10.1002/pmic.200600665] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We report the first proteomic analysis of the insoluble sub-proteome of the alkaliphilic and halotolerant deep-sea bacterium Oceanobacillus iheyensis HTE831. A multidimensional gel-based and gel-free analysis was utilised and a total of 4352 peptides were initially identified by automated MS/MS identification software. Automated curation of this list using PROVALT reduced our peptide list to 467 uniquely identified peptides that resulted in the positive identification of 153 proteins. These identified proteins were functionally classified and physiochemically characterised. Of 26 proteins identified as hypothetical conserved, we have assigned function to all but four. A total of 41 proteins were predicted to possess signal peptides. In silico investigation of these proteins allowed us to identify three of the five bacterial classes of signal peptide, namely: (i) twin-arginine translocation; (ii) Sec-type and (iii) lipoprotein transport. Our proteomic strategy has also allowed us to identify, at neutral pH, a number of proteins described previously as belonging to two putative transport systems believed to be of importance in the alkaliphilic adaptation of O. iheyensis HTE831.
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Affiliation(s)
- Robert L J Graham
- School of Biomedical Sciences, University of Ulster, Coleraine, County Londonderry, UK.
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Prosinecki V, Botelho HM, Francese S, Mastrobuoni G, Moneti G, Urich T, Kletzin A, Gomes CM. A proteomic approach toward the selection of proteins with enhanced intrinsic conformational stability. J Proteome Res 2006; 5:2720-6. [PMID: 17022643 DOI: 10.1021/pr0602491] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A detailed understanding of the molecular basis of protein folding and stability determinants partly relies on the study of proteins with enhanced conformational stability properties, such as those from thermophilic organisms. In this study, we set up a methodology aiming at identifying the subset of cytosolic hyperstable proteins using Sulfurispharea sp., a hyperthermophilic archaeon, able to grow between 70 and 97 degrees C, as a model organism. We have thermally and chemically perturbed the cytosolic proteome as a function of time (up to 96 h incubation at 90 degrees C), and proceeded with analysis of the remaining proteins by combining one- and two-dimensional gel electrophoresis, liquid chromatography fractionation, and protein identification by N-terminal sequencing and mass spectrometry methods. In total, 14 proteins with enhanced stabilities which are involved in key cellular processes such as detoxification, nucleic acid processing, and energy metabolism were identified including a superoxide dismutase, a peroxiredoxin, and a ferredoxin. We demonstrate that these proteins are biologically active after extensive thermal treatment of the proteome. The relevance of these and other targets is discussed in terms of the organism's ecology. This work thus illustrates an experimental approach aimed at mining a proteome for hyperstable proteins, a valuable tool for target selection in protein stability and structural studies.
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Affiliation(s)
- Vesna Prosinecki
- Instituto Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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Graham RLJ, O'Loughlin SN, Pollock CE, Ternan NG, Weatherly DB, Jackson PJ, Tarleton RL, McMullan G. A combined shotgun and multidimensional proteomic analysis of the insoluble subproteome of the obligate thermophile, Geobacillus thermoleovorans T80. J Proteome Res 2006; 5:2465-73. [PMID: 16944960 DOI: 10.1021/pr0602444] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To further our understanding of the biology of the thermophilic bacterium Geobacillus thermoleovorans T80, we now report the first proteomic analysis of the insoluble subproteome of this isolate. A combination of both shotgun and multidimensional methodologies were utilized, and a total of 8628 peptides was initially identified by automated MS/MS identification software. Curation of these peptides led to a final list of 184 positive protein identifications. The proteins from this insoluble subproteome were functionally classified, and physiochemical characterization was carried out. Of 15 hypothetical conserved proteins identified, we have assigned function to all but four. A total of 31 proteins were predicted to possess signal peptides. In silico investigation of these proteins allowed us to identify four of the five bacterial classes of signal peptide, namely, (i) twin-arginine translocation; (ii) Sec-type; (iii) lipoprotein, and (iv) ABC transport. In addition, a number of proteins were identified that are known to be involved in the transport of compatible solutes, known to be important in microbial stress responses.
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Affiliation(s)
- Robert Leslie James Graham
- School of Biomedical Sciences, University of Ulster, Coleraine, County Londonderry BT52 1SA, United Kingdom.
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Aucelli T, Contursi P, Girfoglio M, Rossi M, Cannio R. A spreadable, non-integrative and high copy number shuttle vector for Sulfolobus solfataricus based on the genetic element pSSVx from Sulfolobus islandicus. Nucleic Acids Res 2006; 34:e114. [PMID: 16971457 PMCID: PMC1635272 DOI: 10.1093/nar/gkl615] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The pSSVx genetic element from Sulfolobus islandicus REY15/4 is a hybrid between a plasmid and a fusellovirus, able to be maintained in non-integrative form and to spread when the helper SSV2 virus is present in the cells. In this work, the satellite virus was engineered to obtain an Escherichia coli-Sulfolobus solfataricus shuttle vector for gene transfer and expression in S.solfataricus by fusing site-specifically the pSSVx chromosome with an E.coli plasmid replicon and the ampicillin resistance gene. The pSSVx-based vector was proven functional like the parental virus, namely it was able to spread efficiently through infected S.solfataricus cells. Moreover, the hybrid plasmid stably transformed S.solfataricus and propagated with no rearrangement, recombination or integration into the host chromosome. The high copy number of the artificial genetic element was found comparable with that calculated for the wild-type pSSVx in the new host cells, with no need of genetic markers for vector maintenance in the cells and for transfomant enrichment. The newly constructed vector was also shown to be an efficient cloning vehicle for the expression of passenger genes in S.solfataricus. In fact, a derivative plasmid carrying an expression cassette of the lacS gene encoding the beta-glycosidase from S.solfataricus under the control of the Sulfolobus chaperonine (thermosome tf55) heat shock promoter was also able to drive the expression of a functional enzyme. Complementation of the beta-galactosidase deficiency in a deletion mutant strain of S.solfataricus demonstrated that lacS gene was an efficient marker for selection of single transformants on solid minimal lactose medium.
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Affiliation(s)
- Tiziana Aucelli
- Dipartimento di Biologia Strutturale e Funzionale, Università degli Studi di Napoli Federico IIVia Cinthia, 80126 Napoli, Italy
| | - Patrizia Contursi
- Dipartimento di Biologia Strutturale e Funzionale, Università degli Studi di Napoli Federico IIVia Cinthia, 80126 Napoli, Italy
| | | | | | - Raffaele Cannio
- To whom correspondence should be addressed at Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, Via Pietro Castellino 111, 80131, Naples, Italy. Tel: +39 081 613 2285; Fax: +39 081 613 2248;
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Samyn B, Sergeant K, Memmi S, Debyser G, Devreese B, Van Beeumen J. MALDI-TOF/TOFde novo sequence analysis of 2-D PAGE-separated proteins fromHalorhodospira halophila, a bacterium with unsequenced genome. Electrophoresis 2006; 27:2702-11. [PMID: 16739227 DOI: 10.1002/elps.200500959] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Because protein identifications rely on matches with sequence databases, high-throughput proteomics is currently largely restricted to those species for which comprehensive sequence databases are available. The identification of proteins derived from organisms with unsequenced genomes mainly depends on homology searching. Here, we report the use of a simplified, gel-based, chemical derivatization strategy for de novo sequence analysis using a MALDI-TOF/TOF mass spectrometer. This approach allows the determination of de novo peptide sequences of up to 20 amino acid residues in length. The protocol was applied on a proteomic study of 2-D PAGE-separated proteins from Halorhodospira halophila, an extremophilic eubacterium with yet unsequenced genome. Using three different homology-based search algorithms, we were able to identify more than 30 proteins from this organism using subpicomole quantities of protein.
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Affiliation(s)
- Bart Samyn
- Department of Biochemistry, Physiology and Microbiology, Laboratory of Protein Biochemistry and Protein Engineering, Ghent University, Gent, Belgium.
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Barry RC, Young MJ, Stedman KM, Dratz EA. Proteomic mapping of the hyperthermophilic and acidophilic archaeonSulfolobus solfataricus P2. Electrophoresis 2006; 27:2970-83. [PMID: 16721906 DOI: 10.1002/elps.200500851] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A proteomic map of Sulfolobus solfataricus P2, an archaeon that grows optimally at 80 degrees C and pH 3.2, was developed using high-resolution 2-DE and peptide mass fingerprinting. A total of 867 protein spots (659 aqueous Tris-soluble spots and 208 aqueous Tris-insoluble) were mapped over IPG 3-10, 4-7, and 6-11, with second-dimensional gels made of 8-18% polyacrylamide. Three hundred and twenty-four different gene products were represented by the 867 spots, with 274 gene products being identified in the Tris-soluble fractions and 100 gene products in the Tris-insoluble portion. Fifty gene products were found on gels from both fractions. Additionally, an average of 1.50 +/- 0.12 isoforms/protein was identified. This mapping study confirmed the expression of proteins involved in numerous metabolic, transport, energy production, nucleic acid replication, translation, and transcription pathways. Of particular interest, phosphoenolpyruvate carboxykinase (SSO2537) was detected even though the pathway for gluconeogenesis is unknown for this archaeon. Tris-soluble fractions contained many cytosolic proteins while Tris-insoluble fractions contained many membrane-associated proteins, including ABC transporters and an ATP synthase. This study provides an optimized 2-DE approach for investigating the biochemical pathways and post-translational modifications employed by Sulfolobus to survive in its extreme environment.
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Affiliation(s)
- Richard C Barry
- Biological Monitoring and Modeling, Pacific NW National Laboratory, Richland, WA, USA
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Graham RLJ, Pollock CE, Ternan NG, McMullan G. Top-down proteomic analysis of the soluble sub-proteome of the obligate thermophile, Geobacillus thermoleovorans T80: insights into its cellular processes. J Proteome Res 2006; 5:822-8. [PMID: 16602689 DOI: 10.1021/pr0504642] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report the first analysis of the soluble sub-proteome of the obligate thermophile, Geobacillus thermoleovorans T80, utilizing a robust multidimensional protein identification protocol. A total of 1,336 proteins were initially identified utilizing automated MS/MS identification software. Intensive manual curation resulted in a final list containing a total of 294 unique proteins. Physiochemical characterization and functional classification of the soluble sub-proteome was carried out. The strategy has allowed us to gain an insight into the cellular processes of this obligate thermophile, identifying a variety of proteins known to play a role in stress response. Included within these were a number of sigma factors such as sigma(A) that initiate transcription of the heat shock operons controlled by the HrcA-CIRCE complex within gram positive bacteria. In addition, it has enabled us to assign a degree of functionality to 29 out of 36 gene products detected in this study that were hitherto described as being only hypothetical conserved proteins.
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Affiliation(s)
- Robert Leslie James Graham
- School of Biomedical Sciences, University of Ulster, Coleraine, County Londonderry, BT52 1SA, United Kingdom.
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Barrios-Llerena ME, Chong PK, Gan CS, Snijders APL, Reardon KF, Wright PC. Shotgun proteomics of cyanobacteria—applications of experimental and data-mining techniques. Brief Funct Genomics 2006; 5:121-32. [PMID: 16772275 DOI: 10.1093/bfgp/ell021] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Cyanobacteria are photosynthetic bacteria notable for their ability to produce hydrogen and a variety of interesting secondary metabolites. As a result of the growing number of completed cyanobacterial genome projects, the development of post-genomics analysis for this important group has been accelerating. DNA microarrays and classical two-dimensional gel electrophoresis (2DE) were the first technologies applied in such analyses. In many other systems, ‘shotgun’ proteomics employing multi-dimensional liquid chromatography and tandem mass spectrometry has proven to be a powerful tool. However, this approach has been relatively under-utilized in cyanobacteria. This study assesses progress in cyanobacterial shotgun proteomics to date, and adds a new perspective by developing a protocol for the shotgun proteomic analysis of the filamentous cyanobacterium Anabaena variabilis ATCC 29413, a model for N2 fixation. Using approaches for enhanced protein extraction, 646 proteins were identified, which is more than double the previous results obtained using 2DE. Notably, the improved extraction method and shotgun approach resulted in a significantly higher representation of basic and hydrophobic proteins. The use of protein bioinformatics tools to further mine these shotgun data is illustrated through the application of PSORTb for localization, the grand average hydropathy (GRAVY) index for hydrophobicity, LipoP for lipoproteins and the exponentially modified protein abundance index (emPAI) for abundance. The results are compared with the most well-studied cyanobacterium, Synechocystis sp. PCC 6803. Some general issues in shotgun proteome identification and quantification are then addressed.
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Chong PK, Gan CS, Pham TK, Wright PC. Isobaric Tags for Relative and Absolute Quantitation (iTRAQ) Reproducibility: Implication of Multiple Injections. J Proteome Res 2006; 5:1232-40. [PMID: 16674113 DOI: 10.1021/pr060018u] [Citation(s) in RCA: 165] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We analyzed 10 isobaric tags for relative and absolute quantitation (iTRAQ) experiments using three different model organisms across the domains of life: Saccharomyces cerevisiae KAY446, Sulfolobussolfataricus P2, and Synechocystis sp. PCC6803. A double database search strategy was employed to minimize the rate of false positives to less than 3% for all organisms. The reliability of proteins with single-peptide identification was also assessed using the search strategy, coupled with multiple analyses of samples into LC-MS/MS. The outcomes of the three LC-MS/MS analyses provided higher proteome coverage with an average increment in total proteins identified of 6%, 33%, and 50% found in S. cerevisiae, S. solfataricus, and Synechocystis sp., respectively. The iTRAQ quantification values were found to be highly reproducible across the injections, with an average coefficient of variation (CV) of 0.09 (scattering from 0.14 to 0.04) calculated based on log mean average ratio for all three organisms. Hence, we recommend multiple analyses of iTRAQ samples for greater proteome coverage and precise quantification.
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Affiliation(s)
- Poh Kuan Chong
- Biological and Environmental Systems Group, Department of Chemical and Process Engineering, University of Sheffield, Mappin Street, Sheffield S1 3JD, United Kingdom
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