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Karlo J, Dhillon AK, Siddhanta S, Singh SP. Reverse stable isotope labelling with Raman spectroscopy for microbial proteomics. JOURNAL OF BIOPHOTONICS 2024; 17:e202300341. [PMID: 38010366 DOI: 10.1002/jbio.202300341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/26/2023] [Accepted: 11/01/2023] [Indexed: 11/29/2023]
Abstract
Global proteome changes in microbes affect the survival and overall production of commercially relevant metabolites through different bioprocesses. The existing methods to monitor proteome level changes are destructive in nature. Stable isotope probing (SIP) coupled with Raman spectroscopy is a relatively new approach for proteome analysis. However, applying this approach for monitoring changes in a large culture volume is not cost-effective. In this study, for the first time we are presenting a novel method of combining reverse SIP using 13 C-glucose and Deuterium to monitor the proteome changes through Raman spectroscopy. The findings of the study revealed visible changes (blue shifts) in proteome related peaks that can be used for monitoring proteome dynamics, that is, synthesis of nascent amino acids and its turnover with time in a non-destructive, cost-effective, and label-free manner.
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Affiliation(s)
- Jiro Karlo
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, India
| | | | - Soumik Siddhanta
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi, India
| | - Surya Pratap Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, India
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2
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Liese A, Eichstädt B, Lederer S, Schulz P, Oehlschläger J, Matschi S, Feijó JA, Schulze WX, Konrad KR, Romeis T. Imaging of plant calcium-sensor kinase conformation monitors real time calcium-dependent decoding in planta. THE PLANT CELL 2024; 36:276-297. [PMID: 37433056 PMCID: PMC11210078 DOI: 10.1093/plcell/koad196] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 06/14/2023] [Accepted: 07/10/2023] [Indexed: 07/13/2023]
Abstract
Changes in cytosolic calcium (Ca2+) concentration are among the earliest reactions to a multitude of stress cues. While a plethora of Ca2+-permeable channels may generate distinct Ca2+ signatures and contribute to response specificities, the mechanisms by which Ca2+ signatures are decoded are poorly understood. Here, we developed a genetically encoded Förster resonance energy transfer (FRET)-based reporter that visualizes the conformational changes in Ca2+-dependent protein kinases (CDPKs/CPKs). We focused on two CDPKs with distinct Ca2+-sensitivities, highly Ca2+-sensitive Arabidopsis (Arabidopsis thaliana) AtCPK21 and rather Ca2+-insensitive AtCPK23, to report conformational changes accompanying kinase activation. In tobacco (Nicotiana tabacum) pollen tubes, which naturally display coordinated spatial and temporal Ca2+ fluctuations, CPK21-FRET, but not CPK23-FRET, reported oscillatory emission ratio changes mirroring cytosolic Ca2+ changes, pointing to the isoform-specific Ca2+-sensitivity and reversibility of the conformational change. In Arabidopsis guard cells, CPK21-FRET-monitored conformational dynamics suggest that CPK21 serves as a decoder of signal-specific Ca2+ signatures in response to abscisic acid and the flagellin peptide flg22. Based on these data, CDPK-FRET is a powerful approach for tackling real-time live-cell Ca2+ decoding in a multitude of plant developmental and stress responses.
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Affiliation(s)
- Anja Liese
- Department for Biochemistry of Plant Interactions, Leibniz Institute of Plant Biochemistry, D-06120 Halle (Saale), Germany
- Dahlem Centre of Plant Sciences, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Bernadette Eichstädt
- Dahlem Centre of Plant Sciences, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Sarah Lederer
- Department for Biochemistry of Plant Interactions, Leibniz Institute of Plant Biochemistry, D-06120 Halle (Saale), Germany
| | - Philipp Schulz
- Dahlem Centre of Plant Sciences, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Jan Oehlschläger
- Department for Biochemistry of Plant Interactions, Leibniz Institute of Plant Biochemistry, D-06120 Halle (Saale), Germany
| | - Susanne Matschi
- Department for Biochemistry of Plant Interactions, Leibniz Institute of Plant Biochemistry, D-06120 Halle (Saale), Germany
| | - José A Feijó
- Department of Cell Biology & Molecular Genetics, University of Maryland, 2136 Bioscience Research Bldg, College Park, MD 20742-5815, USA
| | - Waltraud X Schulze
- Plant Systems Biology, Universität Hohenheim, D-70593 Stuttgart, Germany
| | - Kai R Konrad
- Julius-Von-Sachs Institute for Biosciences, Julius Maximilians Universität Würzburg, D-97082 Würzburg, Germany
| | - Tina Romeis
- Department for Biochemistry of Plant Interactions, Leibniz Institute of Plant Biochemistry, D-06120 Halle (Saale), Germany
- Dahlem Centre of Plant Sciences, Freie Universität Berlin, D-14195 Berlin, Germany
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Hocher A, Laursen SP, Radford P, Tyson J, Lambert C, Stevens KM, Montoya A, Shliaha PV, Picardeau M, Sockett RE, Luger K, Warnecke T. Histones with an unconventional DNA-binding mode in vitro are major chromatin constituents in the bacterium Bdellovibrio bacteriovorus. Nat Microbiol 2023; 8:2006-2019. [PMID: 37814071 PMCID: PMC10627809 DOI: 10.1038/s41564-023-01492-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 09/08/2023] [Indexed: 10/11/2023]
Abstract
Histone proteins bind DNA and organize the genomes of eukaryotes and most archaea, whereas bacteria rely on different nucleoid-associated proteins. Homology searches have detected putative histone-fold domains in a few bacteria, but whether these function like archaeal/eukaryotic histones is unknown. Here we report that histones are major chromatin components in the bacteria Bdellovibrio bacteriovorus and Leptospira interrogans. Patterns of sequence evolution suggest important roles for histones in additional bacterial clades. Crystal structures (<2.0 Å) of the B. bacteriovorus histone (Bd0055) dimer and the histone-DNA complex confirm conserved histone-fold topology but indicate a distinct DNA-binding mode. Unlike known histones in eukaryotes, archaea and viruses, Bd0055 binds DNA end-on, forming a sheath of dimers encasing straight DNA rather than wrapping DNA around their outer surface. Our results demonstrate that histones are present across the tree of life and highlight potential evolutionary innovation in how they associate with DNA.
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Affiliation(s)
- Antoine Hocher
- Medical Research Council London Institute of Medical Sciences, London, UK.
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK.
| | - Shawn P Laursen
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Paul Radford
- School of Life Sciences, Medical School, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - Jess Tyson
- School of Life Sciences, Medical School, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - Carey Lambert
- School of Life Sciences, Medical School, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - Kathryn M Stevens
- Medical Research Council London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Alex Montoya
- Medical Research Council London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Pavel V Shliaha
- Medical Research Council London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Mathieu Picardeau
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Biology of Spirochetes Unit, Paris, France
| | - R Elizabeth Sockett
- School of Life Sciences, Medical School, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - Karolin Luger
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Tobias Warnecke
- Medical Research Council London Institute of Medical Sciences, London, UK.
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK.
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Cao Q, Han M, Zhang Z, Yu C, Xu L, Shi T, Zheng P, Sun J. Novel 15N Metabolic Labeling-Based Large-Scale Absolute Quantitative Proteomics Method for Corynebacterium glutamicum. Anal Chem 2023; 95:4829-4833. [PMID: 36897266 DOI: 10.1021/acs.analchem.2c05524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
With fast growth, synthetic biology powers us with the capability to produce high commercial value products in an efficient resource/energy-consuming manner. Comprehensive knowledge of the protein regulatory network of a bacterial host chassis, e.g., the actual amount of the given proteins, is the key to building cell factories for certain target hyperproduction. Many talent methods have been introduced for absolute quantitative proteomics. However, for most cases, a set of reference peptides with isotopic labeling (e.g., SIL, AQUA, QconCAT) or a set of reference proteins (e.g., commercial UPS2 kit) needs to be prepared. The higher cost hinders these methods for large sample research. In this work, we proposed a novel metabolic labeling-based absolute quantification approach (termed nMAQ). The reference Corynebacterium glutamicum strain is metabolically labeled with 15N, and a set of endogenous anchor proteins of the reference proteome is quantified by chemically synthesized light (14N) peptides. The prequantified reference proteome was then utilized as an internal standard (IS) and spiked into the target (14N) samples. SWATH-MS analysis is performed to obtain the absolute expression levels of the proteins from the target cells. The cost for nMAQ is estimated to be less than 10 dollars per sample. We have benchmarked the quantitative performance of the novel method. We believe this method will help with the deep understanding of the intrinsic regulatory mechanism of C. glutamicum during bioengineering and will promote the process of building cell factories for synthetic biology.
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Affiliation(s)
- Qichen Cao
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Systems Biology Centre, Technical Support Core Facilities, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Manman Han
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Systems Biology Centre, Technical Support Core Facilities, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Zuoqing Zhang
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Systems Biology Centre, Technical Support Core Facilities, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Chang Yu
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Systems Biology Centre, Technical Support Core Facilities, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- College of Life Sciences, Nankai University, Tianjin 300350, China
| | - Lida Xu
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Systems Biology Centre, Technical Support Core Facilities, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Tuo Shi
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Ping Zheng
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Jibin Sun
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Systems Biology Centre, Technical Support Core Facilities, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
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Abstract
Microbes that can recycle one-carbon (C1) greenhouse gases into fuels and chemicals are vital for the biosustainability of future industries. Acetogens are the most efficient known microbes for fixing carbon oxides CO2 and CO. Understanding proteome allocation is important for metabolic engineering as it dictates metabolic fitness. Here, we use absolute proteomics to quantify intracellular concentrations for >1,000 proteins in the model acetogen Clostridium autoethanogenum grown autotrophically on three gas mixtures (CO, CO+H2, or CO+CO2+H2). We detect the prioritization of proteome allocation for C1 fixation and the significant expression of proteins involved in the production of acetate and ethanol as well as proteins with unclear functions. The data also revealed which isoenzymes are likely relevant in vivo for CO oxidation, H2 metabolism, and ethanol production. The integration of proteomic and metabolic flux data demonstrated that enzymes catalyze high fluxes with high concentrations and high in vivo catalytic rates. We show that flux adjustments were dominantly accompanied by changing enzyme catalytic rates rather than concentrations. IMPORTANCE Acetogen bacteria are important for maintaining biosustainability as they can recycle gaseous C1 waste feedstocks (e.g., industrial waste gases and syngas from gasified biomass or municipal solid waste) into fuels and chemicals. Notably, the acetogen Clostridium autoethanogenum is being used as a cell factory in industrial-scale gas fermentation. Here, we perform reliable absolute proteome quantification for the first time in an acetogen. This is important as our work advances both rational metabolic engineering of acetogen cell factories and accurate in silico reconstruction of their phenotypes. Furthermore, this absolute proteomics data set serves as a reference toward a better systems-level understanding of the ancient metabolism of acetogens.
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Going Micro in Leptospirosis Kidney Disease. Cells 2022; 11:cells11040698. [PMID: 35203344 PMCID: PMC8869946 DOI: 10.3390/cells11040698] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 02/13/2022] [Accepted: 02/14/2022] [Indexed: 02/05/2023] Open
Abstract
Leptospirosis is a zoonotic and waterborne disease worldwide. It is a neglected infectious disease caused by Leptospira spp., as well as a reemerging disease and global public health problem with respect to morbidity and mortality both in humans and animals. Leptospirosis emerges as a leading cause of acute febrile illness along with hepatorenal injury in many countries, including Thailand. While most affected persons are symptomatic in acute disease, which is always difficult to differentiate from other tropical diseases, there is growing evidence of subtle manifestations that cause unrecognized chronic symptoms. The kidney is one of the common organs affected by Leptospires. Although acute kidney injury in the spectrum of interstitial nephritis is a well-described characteristic in severe leptospirosis, chronic kidney disease from leptospirosis is widely discussed. Early recognition of severe leptospirosis leads to reduce morbidity and mortality. Thus, in this review, we highlight the spectrum of characteristics involved in leptospirosis kidney disease and the use of serologic and molecular methods, as well as the treatments of severe leptospirosis.
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Franz A, Coscia F, Shen C, Charaoui L, Mann M, Sander C. Molecular response to PARP1 inhibition in ovarian cancer cells as determined by mass spectrometry based proteomics. J Ovarian Res 2021; 14:140. [PMID: 34686201 PMCID: PMC8539835 DOI: 10.1186/s13048-021-00886-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 09/27/2021] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Poly (ADP)-ribose polymerase (PARP) inhibitors have entered routine clinical practice for the treatment of high-grade serous ovarian cancer (HGSOC), yet the molecular mechanisms underlying treatment response to PARP1 inhibition (PARP1i) are not fully understood. METHODS Here, we used unbiased mass spectrometry based proteomics with data-driven protein network analysis to systematically characterize how HGSOC cells respond to PARP1i treatment. RESULTS We found that PARP1i leads to pronounced proteomic changes in a diverse set of cellular processes in HGSOC cancer cells, consistent with transcript changes in an independent perturbation dataset. We interpret decreases in the levels of the pro-proliferative transcription factors SP1 and β-catenin and in growth factor signaling as reflecting the anti-proliferative effect of PARP1i; and the strong activation of pro-survival processes NF-κB signaling and lipid metabolism as PARPi-induced adaptive resistance mechanisms. Based on these observations, we nominate several protein targets for therapeutic inhibition in combination with PARP1i. When tested experimentally, the combination of PARPi with an inhibitor of fatty acid synthase (TVB-2640) has a 3-fold synergistic effect and is therefore of particular pre-clinical interest. CONCLUSION Our study improves the current understanding of PARP1 function, highlights the potential that the anti-tumor efficacy of PARP1i may not only rely on DNA damage repair mechanisms and informs on the rational design of PARP1i combination therapies in ovarian cancer.
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Affiliation(s)
- Alexandra Franz
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
| | - Fabian Coscia
- Proteomics Program, NNF Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Ciyue Shen
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Lea Charaoui
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Matthias Mann
- Proteomics Program, NNF Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Chris Sander
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
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Fukunaga T, Tanaka N, Furumoto T, Nakakita S, Ohashi T, Higuchi Y, Maekawa H, Takegawa K. Substrate specificities of α1,2- and α1,3-galactosyltransferases and characterization of Gmh1p and Otg1p in Schizosaccharomyces pombe. Glycobiology 2021; 31:1037-1045. [PMID: 33909078 DOI: 10.1093/glycob/cwab028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/29/2021] [Accepted: 03/31/2021] [Indexed: 12/26/2022] Open
Abstract
In the fission yeast Schizosaccharomyces pombe, α1,2- and α1,3-linked D-galactose (Gal) residues are transferred to N- and O-linked oligosaccharides of glycoproteins by galactosyltransferases. Although the galactomannans are important for cell-cell communication in S. pombe (e.g., in non-sexual aggregation), the mechanisms underlying galactosylation in cells remain unclear. S. pombe has 10 galactosyltransferase-related genes: seven belonging to glycosyltransferase (GT) family 34 and three belonging GT family 8. Disruption of all 10 α-galactosyltransferases (strain Δ10GalT) has been shown to result in a complete lack of α-Gal residues. Here, we have investigated the function and substrate specificities of galactosyltransferases in S pombe by using strains expressing single α-galactosyltransferases in the Δ10GalT background. High-performance liquid chromatography (HPLC) analysis of pyridylaminated O-linked oligosaccharides showed that two GT family 34 α1,2-galactosyltransferases (Gma12p and Gmh6p) and two GT family 8 α1,3-galactosyltransferases (Otg2p and Otg3p) are involved in galactosylation of O-linked oligosaccharide. Moreover, 1H-NMR of N-glycans revealed that three GT family 34 α1,2-galactosyltransferases (Gmh1p, Gmh2p, and Gmh3p) are required for galactosylation of N-linked oligosaccharides. Furthermore, HPLC and lectin-blot analysis revealed that Otg1p showed α1,3-galactosyltransferase activity under conditions of co-expression with Gmh6p, indicating that α-1,2-linked galactose is required for the galactosylation activity of Otg1p in S. pombe. In conclusion, eight galactosyltransferases have been shown to have activity in S. pombe with different substrate specificities. These findings will be useful for genetically tailoring the galactosylation of both N- and O- glycans in fission yeast.
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Affiliation(s)
- Takamasa Fukunaga
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Naotaka Tanaka
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Kagawa, Japan
| | - Toshio Furumoto
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Kagawa, Japan
| | - Shinichi Nakakita
- Department of Endocrinology; Department of Immunology and Immunopathology, Faculty of Medicine, Kagawa University, Kagawa, Japan; and Life Science Research Center, Kagawa University, Kagawa, Japan
| | - Takao Ohashi
- Faculty of Science and Engineering Department of Life Science, Setsunan University, Osaka, Japan
| | - Yujiro Higuchi
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Hiromi Maekawa
- Centre for Promotion of International Education and Research, Faculty of Agriculture, Kyushu university, Fukuoka, Japan
| | - Kaoru Takegawa
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
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Saha-Shah A, Esmaeili M, Sidoli S, Hwang H, Yang J, Klein PS, Garcia BA. Single Cell Proteomics by Data-Independent Acquisition To Study Embryonic Asymmetry in Xenopus laevis. Anal Chem 2019; 91:8891-8899. [PMID: 31194517 PMCID: PMC6688503 DOI: 10.1021/acs.analchem.9b00327] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Techniques that allow single cell analysis are gaining widespread attention, and most of these studies utilize genomics-based approaches. While nanofluidic technologies have enabled mass spectrometric analysis of single cells, these measurements have been limited to metabolomics and lipidomic studies. Single cell proteomics has the potential to improve our understanding of intercellular heterogeneity. However, this approach has faced challenges including limited sample availability, as well as a requirement of highly sensitive methods for sample collection, cleanup, and detection. We present a technique to overcome these limitations by combining a micropipette (pulled glass capillary) based sample collection strategy with offline sample preparation and nanoLC-MS/MS to analyze proteins through a bottom-up proteomic strategy. This study explores two types of proteomics data acquisition strategies namely data-dependent (DDA) and data-independent acquisition (DIA). Results from the study indicate DIA to be more sensitive enabling analysis of >1600 proteins from ∼130 μm Xenopus laevis embryonic cells containing <6 nL of cytoplasm. The method was found to be robust in obtaining reproducible protein quantifications from single cells spanning the 1-128-cell stages of development. Furthermore, we used micropipette sampling to study intercellular heterogeneity within cells in a single embryo and investigated embryonic asymmetry along both animal-vegetal and dorsal-ventral axes during early stages of development. Investigation of the animal-vegetal axis led to discovery of various asymmetrically distributed proteins along the animal-vegetal axis. We have further compared the hits found from our proteomic data sets with other studies and validated a few hits using an orthogonal imaging technique. This study forms the first report of vegetal enrichment of the germ plasm associated protein DDX4/VASA in Xenopus embyos. Overall, the method and data presented here holds promise to enable important leads in developmental biology.
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Affiliation(s)
- Anumita Saha-Shah
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Melody Esmaeili
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Simone Sidoli
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Hyojeong Hwang
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, 2001 South Lincoln Avenue, 3411 Veterinary Medicine Basic Sciences Building, Urbana, IL 61802, USA
| | - Jing Yang
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, 2001 South Lincoln Avenue, 3411 Veterinary Medicine Basic Sciences Building, Urbana, IL 61802, USA
| | - Peter S. Klein
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine (Hematology-Oncology), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Benjamin A. Garcia
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
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10
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Zhao J, Zhang H, Qin B, Nikolay R, He QY, Spahn CMT, Zhang G. Multifaceted Stoichiometry Control of Bacterial Operons Revealed by Deep Proteome Quantification. Front Genet 2019; 10:473. [PMID: 31178895 PMCID: PMC6544118 DOI: 10.3389/fgene.2019.00473] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 05/01/2019] [Indexed: 12/03/2022] Open
Abstract
More than half of the protein-coding genes in bacteria are organized in polycistronic operons composed of two or more genes. It remains under debate whether the operon organization maintains the stoichiometric expression of the genes within an operon. In this study, we performed a label-free data-independent acquisition hyper reaction monitoring mass-spectrometry (HRM-MS) experiment to quantify the Escherichia coli proteome in exponential phase and quantified 93.6% of the cytosolic proteins, covering 67.9% and 56.0% of the translating polycistronic operons in BW25113 and MG1655 strains, respectively. We found that the translational regulation contributes largely to the proteome complexity: the shorter operons tend to be more tightly controlled for stoichiometry than longer operons; the operons which mainly code for complexes is more tightly controlled for stoichiometry than the operons which mainly code for metabolic pathways. The gene interval (distance between adjacent genes in one operon) may serve as a regulatory factor for stoichiometry. The catalytic efficiency might be a driving force for differential expression of enzymes encoded in one operon. These results illustrated the multifaceted nature of the operon regulation: the operon unified transcriptional level and gene-specific translational level. This multi-level regulation benefits the host by optimizing the efficiency of the productivity of metabolic pathways and maintenance of different types of protein complexes.
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Affiliation(s)
- Jing Zhao
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan University, Guangzhou, China
| | - Hong Zhang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan University, Guangzhou, China
| | - Bo Qin
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Rainer Nikolay
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Qing-Yu He
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan University, Guangzhou, China
| | - Christian M T Spahn
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Gong Zhang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan University, Guangzhou, China
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Gerlitz M, Knopp M, Kapust N, Xavier JC, Martin WF. Elusive data underlying debate at the prokaryote-eukaryote divide. Biol Direct 2018; 13:21. [PMID: 31196150 PMCID: PMC6888934 DOI: 10.1186/s13062-018-0221-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 08/16/2018] [Indexed: 12/11/2022] Open
Abstract
Background The origin of eukaryotic cells was an important transition in evolution. The factors underlying the origin and evolutionary success of the eukaryote lineage are still discussed. One camp argues that mitochondria were essential for eukaryote origin because of the unique configuration of internalized bioenergetic membranes that they conferred to the common ancestor of all known eukaryotic lineages. A recent paper by Lynch and Marinov concluded that mitochondria were energetically irrelevant to eukaryote origin, a conclusion based on analyses of previously published numbers of various molecules and ribosomes per cell and cell volumes as a presumed proxy for the role of mitochondria in evolution. Their numbers were purportedly extracted from the literature. Results We have examined the numbers upon which the recent study was based. We report that for a sample of 80 numbers that were purportedly extracted from the literature and that underlie key inferences of the recent study, more than 50% of the values do not exist in the cited papers to which the numbers are attributed. The published result cannot be independently reproduced. Other numbers that the recent study reports differ inexplicably from those in the literature to which they are ascribed. We list the discrepancies between the recently published numbers and the purported literature sources of those numbers in a head to head manner so that the discrepancies are readily evident, although the source of error underlying the discrepancies remains obscure. Conclusion The data purportedly supporting the view that mitochondria had no impact upon eukaryotic evolution data exhibits notable irregularities. The paper in question evokes the impression that the published numbers are of up to seven significant digit accuracy, when in fact more than half the numbers are nowhere to be found in the literature to which they are attributed. Though the reasons for the discrepancies are unknown, it is important to air these issues, lest the prominent paper in question become a point source of a snowballing error through the literature or become interpreted as a form of evidence that mitochondria were irrelevant to eukaryote evolution. Reviewers This article was reviewed by Eric Bapteste, Jianzhi Zhang and Martin Lercher.
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Affiliation(s)
- Marie Gerlitz
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Michael Knopp
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Nils Kapust
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Joana C Xavier
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - William F Martin
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany.
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12
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Nascimento Filho EG, Vieira ML, Teixeira AF, Santos JC, Fernandes LGV, Passalia FJ, Daroz BB, Rossini A, Kochi LT, Cavenague MF, Pimenta DC, Nascimento ALTO. Proteomics as a tool to understand Leptospira physiology and virulence: Recent advances, challenges and clinical implications. J Proteomics 2018; 180:80-87. [PMID: 29501847 DOI: 10.1016/j.jprot.2018.02.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 02/14/2018] [Accepted: 02/22/2018] [Indexed: 01/24/2023]
Affiliation(s)
- Edson G Nascimento Filho
- Laboratório Especial de Desenvolvimento de Vacinas, Instituto Butantan, Avenida Vital Brazil, 1500, 05503-900 Sao Paulo, SP, Brazil
| | - Monica L Vieira
- Laboratório Especial de Desenvolvimento de Vacinas, Instituto Butantan, Avenida Vital Brazil, 1500, 05503-900 Sao Paulo, SP, Brazil
| | - Aline F Teixeira
- Laboratório Especial de Desenvolvimento de Vacinas, Instituto Butantan, Avenida Vital Brazil, 1500, 05503-900 Sao Paulo, SP, Brazil
| | - Jademilson C Santos
- Laboratório Especial de Desenvolvimento de Vacinas, Instituto Butantan, Avenida Vital Brazil, 1500, 05503-900 Sao Paulo, SP, Brazil
| | - Luis G V Fernandes
- Laboratório Especial de Desenvolvimento de Vacinas, Instituto Butantan, Avenida Vital Brazil, 1500, 05503-900 Sao Paulo, SP, Brazil
| | - Felipe J Passalia
- Laboratório Especial de Desenvolvimento de Vacinas, Instituto Butantan, Avenida Vital Brazil, 1500, 05503-900 Sao Paulo, SP, Brazil; Programa de Pos-Graduação Interunidades em Biotecnologia, Instituto de Ciências Biomédicas, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Brenda B Daroz
- Laboratório Especial de Desenvolvimento de Vacinas, Instituto Butantan, Avenida Vital Brazil, 1500, 05503-900 Sao Paulo, SP, Brazil; Programa de Pos-Graduação Interunidades em Biotecnologia, Instituto de Ciências Biomédicas, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Amanda Rossini
- Laboratório Especial de Desenvolvimento de Vacinas, Instituto Butantan, Avenida Vital Brazil, 1500, 05503-900 Sao Paulo, SP, Brazil; Programa de Pos-Graduação Interunidades em Biotecnologia, Instituto de Ciências Biomédicas, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Leandro T Kochi
- Laboratório Especial de Desenvolvimento de Vacinas, Instituto Butantan, Avenida Vital Brazil, 1500, 05503-900 Sao Paulo, SP, Brazil; Programa de Pos-Graduação Interunidades em Biotecnologia, Instituto de Ciências Biomédicas, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Maria F Cavenague
- Laboratório Especial de Desenvolvimento de Vacinas, Instituto Butantan, Avenida Vital Brazil, 1500, 05503-900 Sao Paulo, SP, Brazil; Programa de Pos-Graduação Interunidades em Biotecnologia, Instituto de Ciências Biomédicas, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Daniel C Pimenta
- Laboratório de Bioquímica e Biofísica, Instituto Butantan, Avenida Vital Brazil, 1500, 05503-900 Sao Paulo, SP, Brazil
| | - Ana L T O Nascimento
- Laboratório Especial de Desenvolvimento de Vacinas, Instituto Butantan, Avenida Vital Brazil, 1500, 05503-900 Sao Paulo, SP, Brazil.
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13
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Manes NP, Nita-Lazar A. Application of targeted mass spectrometry in bottom-up proteomics for systems biology research. J Proteomics 2018; 189:75-90. [PMID: 29452276 DOI: 10.1016/j.jprot.2018.02.008] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 01/25/2018] [Accepted: 02/07/2018] [Indexed: 02/08/2023]
Abstract
The enormous diversity of proteoforms produces tremendous complexity within cellular proteomes, facilitates intricate networks of molecular interactions, and constitutes a formidable analytical challenge for biomedical researchers. Currently, quantitative whole-proteome profiling often relies on non-targeted liquid chromatography-mass spectrometry (LC-MS), which samples proteoforms broadly, but can suffer from lower accuracy, sensitivity, and reproducibility compared with targeted LC-MS. Recent advances in bottom-up proteomics using targeted LC-MS have enabled previously unachievable identification and quantification of target proteins and posttranslational modifications within complex samples. Consequently, targeted LC-MS is rapidly advancing biomedical research, especially systems biology research in diverse areas that include proteogenomics, interactomics, kinomics, and biological pathway modeling. With the recent development of targeted LC-MS assays for nearly the entire human proteome, targeted LC-MS is positioned to enable quantitative proteomic profiling of unprecedented quality and accessibility to support fundamental and clinical research. Here we review recent applications of bottom-up proteomics using targeted LC-MS for systems biology research. SIGNIFICANCE: Advances in targeted proteomics are rapidly advancing systems biology research. Recent applications include systems-level investigations focused on posttranslational modifications (such as phosphoproteomics), protein conformation, protein-protein interaction, kinomics, proteogenomics, and metabolic and signaling pathways. Notably, absolute quantification of metabolic and signaling pathway proteins has enabled accurate pathway modeling and engineering. Integration of targeted proteomics with other technologies, such as RNA-seq, has facilitated diverse research such as the identification of hundreds of "missing" human proteins (genes and transcripts that appear to encode proteins but direct experimental evidence was lacking).
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Affiliation(s)
- Nathan P Manes
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Aleksandra Nita-Lazar
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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14
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The binding landscape of a partially-selective isopeptidase inhibitor with potent pro-death activity, based on the bis(arylidene)cyclohexanone scaffold. Cell Death Dis 2018; 9:184. [PMID: 29416018 PMCID: PMC5833369 DOI: 10.1038/s41419-017-0259-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 12/07/2017] [Accepted: 12/22/2017] [Indexed: 01/19/2023]
Abstract
Diaryldienone derivatives with accessible β-carbons show strong anti-neoplastic properties, related to their ability to make covalent adducts with free thiols by Michael addition, and low toxicity in vivo. Accumulation of poly-ubiquitylated proteins, activation of the unfolded protein response (UPR) and induction of cell death are universal hallmarks of their activities. These compounds have been characterized as inhibitors of isopeptidases, a family of cysteine-proteases, which de-conjugate ubiquitin and ubiquitin-like proteins from their targets. However, it is unclear whether they can also react with additional proteins. In this work, we utilized the biotin-conjugated diaryldienone-derivative named 2c, as a bait to purify novel cellular targets of these small molecules. Proteomic analyses have unveiled that, in addition to isopeptidases, these inhibitors can form stable covalent adducts with different intracellular proteins, thus potentially impacting on multiple functions of the cells, from cytoskeletal organization to metabolism. These widespread activities can explain the ability of diaryldienone derivatives to efficiently trigger different cell death pathways.
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15
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Kalule JB, Fortuin S, Calder B, Robberts L, Keddy KH, Nel AJM, Garnett S, Nicol M, Warner DF, Soares NC, Blackburn JM. Proteomic comparison of three clinical diarrhoeagenic drug-resistant Escherichia coli isolates grown on CHROMagar™STEC media. J Proteomics 2017; 180:25-35. [PMID: 28887208 DOI: 10.1016/j.jprot.2017.09.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 08/21/2017] [Accepted: 09/02/2017] [Indexed: 02/06/2023]
Abstract
Shiga-toxin-producing Escherichia coli (STEC) and enteropathogenic Escherichia coli (EPEC) are key diarrhoea-causing foodborne pathogens. We used proteomics to characterize the virulence and antimicrobial resistance protein profiles of three clinical pathogenic E. coli isolates (two EPEC [one resistant to ciprofloxacin] and one STEC) cultured on CHROMagar™STEC solid media after minimal laboratory passage. We identified 4767 unique peptides from 1630 protein group across all three clinical E. coli strains. Label-free proteomic analysis allowed the identification of virulence and drug resistance proteins that were unique to each of the clinical isolates compared in this study. The B subunit of Shiga toxin, ToxB, was uniquely detected in the STEC strain while several other virulence factors including SheA, OmpF, OmpC and OmpX were significantly more abundant in the STEC strain. The ciprofloxacin resistant EPEC isolate possessed reduced levels of key virulence proteins compared to the ciprofloxacin susceptible EPEC and STEC strains. Parallel reaction monitoring assays validated the presence of biologically relevant proteins across biologically-replicated cultures. Propagation of clinical isolates on a relevant solid medium followed by mass spectrometry analysis represents a convenient means to quantify virulence factors and drug resistance determinants that might otherwise be lost through extensive in vitro passage in enteropathogenic bacteria. SIGNIFICANCE Through the use of quantitative proteomics, we have characterized the virulence and antimicrobial resistance attributes of three clinically isolated, pathogenic E. coli strains cultured on solid media. Our results provide new, quantitative data on the expressed proteomes of these tellurite-resistant, diarrhoeagenic E. coli strains and reveal a subset of antimicrobial resistance and virulence proteins that are differentially abundant between these clinical strains. Our quantitative proteomics-based approach should thus have applicability in microbiological diagnostic labs for the identification of pathogenic/drug resistant E. coli in the future.
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Affiliation(s)
- John Bosco Kalule
- Division of Medical Microbiology, Department of Pathology, University of Cape Town, South Africa
| | - Suereta Fortuin
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Bridget Calder
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Lourens Robberts
- Division of Medical Microbiology, Department of Pathology, University of Cape Town, South Africa
| | - Karen H Keddy
- Bacteriology Division, Centre for Enteric Diseases, National Institute for Communicable Diseases, Sandringham, Johannesburg, South Africa; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Andrew J M Nel
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Shaun Garnett
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Mark Nicol
- Division of Medical Microbiology, Department of Pathology, University of Cape Town, South Africa; Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, South Africa
| | - Digby F Warner
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, South Africa; MRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research, Division of Medical Microbiology, Department of Pathology, University of Cape Town, South Africa
| | - Nelson C Soares
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa.
| | - Jonathan M Blackburn
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa; Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, South Africa.
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16
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Nally JE, Grassmann AA, Planchon S, Sergeant K, Renaut J, Seshu J, McBride AJ, Caimano MJ. Pathogenic Leptospires Modulate Protein Expression and Post-translational Modifications in Response to Mammalian Host Signals. Front Cell Infect Microbiol 2017; 7:362. [PMID: 28848720 PMCID: PMC5553009 DOI: 10.3389/fcimb.2017.00362] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 07/26/2017] [Indexed: 12/24/2022] Open
Abstract
Pathogenic species of Leptospira cause leptospirosis, a bacterial zoonotic disease with a global distribution affecting over one million people annually. Reservoir hosts of leptospirosis, including rodents, dogs, and cattle, exhibit little to no signs of disease but shed large numbers of organisms in their urine. Transmission occurs when mucosal surfaces or abraded skin come into contact with infected urine or urine-contaminated water or soil. Whilst little is known about how Leptospira adapt to and persist within a reservoir host, in vitro studies suggest that leptospires alter their transcriptomic and proteomic profiles in response to environmental signals encountered during mammalian infection. We applied the dialysis membrane chamber (DMC) peritoneal implant model to compare the whole cell proteome of in vivo derived leptospires with that of leptospires cultivated in vitro at 30°C and 37°C by 2-dimensional difference in-gel electrophoresis (2-D DIGE). Of 1,735 protein spots aligned across 9 2-D DIGE gels, 202 protein spots were differentially expressed (p < 0.05, fold change >1.25 or < −1.25) across all three conditions. Differentially expressed proteins were excised for identification by mass spectrometry. Data are available via ProteomeXchange with identifier PXD006995. The greatest differences were detected when DMC-cultivated leptospires were compared with IV30- or IV37-cultivated leptospires, including the increased expression of multiple isoforms of Loa22, a known virulence factor. Unexpectedly, 20 protein isoforms of LipL32 and 7 isoforms of LipL41 were uniformly identified by DIGE as differentially expressed, suggesting that unique post-translational modifications (PTMs) are operative in response to mammalian host conditions. To test this hypothesis, a rat model of persistent renal colonization was used to isolate leptospires directly from the urine of experimentally infected rats. Comparison of urinary derived leptospires to IV30 leptospires by 2-D immunoblotting confirmed that modification of proteins with trimethyllysine and acetyllysine occurs to a different degree in response to mammalian host signals encountered during persistent renal colonization. These results provide novel insights into differential protein and PTMs present in response to mammalian host signals which can be used to further define the unique equilibrium that exists between pathogenic leptospires and their reservoir host of infection.
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Affiliation(s)
- Jarlath E Nally
- Infectious Bacterial Diseases Research, National Animal Disease Center, United States Department of Agriculture, Agricultural Research ServiceAmes, IA, United States
| | - Andre A Grassmann
- Biotechnology Unit, Technological Development Center, Federal University of PelotasPelotas, Brazil.,Departments of Medicine, Pediatrics, and Molecular Biology and Biophysics, University of Connecticut Health CenterFarmington, CT, United States
| | - Sébastien Planchon
- Environmental Research and Innovation Department, Luxembourg Institute of Science and TechnologyBelvaux, Luxembourg
| | - Kjell Sergeant
- Environmental Research and Innovation Department, Luxembourg Institute of Science and TechnologyBelvaux, Luxembourg
| | - Jenny Renaut
- Environmental Research and Innovation Department, Luxembourg Institute of Science and TechnologyBelvaux, Luxembourg
| | - Janakiram Seshu
- Department of Biology, University of Texas San AntoniaSan Antonia, TX, United States
| | - Alan J McBride
- Biotechnology Unit, Technological Development Center, Federal University of PelotasPelotas, Brazil.,Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Ministry of HealthSalvador, Brazil
| | - Melissa J Caimano
- Departments of Medicine, Pediatrics, and Molecular Biology and Biophysics, University of Connecticut Health CenterFarmington, CT, United States
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17
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Lynch M, Marinov GK. Membranes, energetics, and evolution across the prokaryote-eukaryote divide. eLife 2017; 6:20437. [PMID: 28300533 PMCID: PMC5354521 DOI: 10.7554/elife.20437] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Accepted: 01/17/2017] [Indexed: 12/19/2022] Open
Abstract
The evolution of the eukaryotic cell marked a profound moment in Earth’s history, with most of the visible biota coming to rely on intracellular membrane-bound organelles. It has been suggested that this evolutionary transition was critically dependent on the movement of ATP synthesis from the cell surface to mitochondrial membranes and the resultant boost to the energetic capacity of eukaryotic cells. However, contrary to this hypothesis, numerous lines of evidence suggest that eukaryotes are no more bioenergetically efficient than prokaryotes. Thus, although the origin of the mitochondrion was a key event in evolutionary history, there is no reason to think membrane bioenergetics played a direct, causal role in the transition from prokaryotes to eukaryotes and the subsequent explosive diversification of cellular and organismal complexity. Over time, life on Earth has evolved into three large groups: archaea, bacteria, and eukaryotes. The most familiar forms of life – such as fungi, plants and animals – all belong to the eukaryotes. Bacteria and archaea are simpler, single-celled organisms and are collectively referred to as prokaryotes. The hallmark feature that distinguishes eukaryotes from prokaryotes is that eukaryotic cells contain compartments called organelles that are surrounded by membranes. Each organelle supports different activities in the cell. Mitochondria, for example, are organelles that provide eukaryotes with most of their energy by producing energy-rich molecules called ATP. Prokaryotes lack mitochondria and instead produce their ATP on their cell surface membrane. Some researchers have suggested that mitochondria might actually be one of the reasons that eukaryotic cells are typically larger than prokaryotes and more varied in their shape and structure. The thinking is that producing ATP on dedicated membranes inside the cell, rather than on the cell surface, boosted the amount of energy available to eukaryotic cells and allowed them to diversify more. However, other researchers are not convinced by this view. Moreover, some recent evidence suggested that eukaryotes are no more efficient in producing energy than prokaryotes. Lynch and Marinov have now used computational and comparative analysis to compare the energy efficiency of different organisms including prokaryotes and eukaryotes grown under defined conditions. To do the comparison, the results were scaled based on cell volume and the total surface area deployed in energy production. From their findings, Lynch and Marinov concluded that mitochondria did not enhance how much energy eukaryotes could produce per unit of cell volume in any substantial way. Although the origin of mitochondria was certainly a key event in evolutionary history, it is unlikely to have been responsible for the diversity and complexity of today’s life forms.
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Affiliation(s)
- Michael Lynch
- Department of Biology, Indiana University, Bloomington, United States
| | - Georgi K Marinov
- Department of Biology, Indiana University, Bloomington, United States
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18
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Liu Y, Beyer A, Aebersold R. On the Dependency of Cellular Protein Levels on mRNA Abundance. Cell 2016; 165:535-50. [PMID: 27104977 DOI: 10.1016/j.cell.2016.03.014] [Citation(s) in RCA: 1798] [Impact Index Per Article: 224.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Indexed: 12/30/2022]
Abstract
The question of how genomic information is expressed to determine phenotypes is of central importance for basic and translational life science research and has been studied by transcriptomic and proteomic profiling. Here, we review the relationship between protein and mRNA levels under various scenarios, such as steady state, long-term state changes, and short-term adaptation, demonstrating the complexity of gene expression regulation, especially during dynamic transitions. The spatial and temporal variations of mRNAs, as well as the local availability of resources for protein biosynthesis, strongly influence the relationship between protein levels and their coding transcripts. We further discuss the buffering of mRNA fluctuations at the level of protein concentrations. We conclude that transcript levels by themselves are not sufficient to predict protein levels in many scenarios and to thus explain genotype-phenotype relationships and that high-quality data quantifying different levels of gene expression are indispensable for the complete understanding of biological processes.
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Affiliation(s)
- Yansheng Liu
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Andreas Beyer
- Cellular Networks and Systems Biology, University of Cologne, CECAD, Joseph-Stelzmann-Strasse 26, Cologne 50931, Germany.
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland; Faculty of Science, University of Zurich, 8057 Zurich, Switzerland.
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19
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Hsiao JJ, Smits MM, Ng BH, Lee J, Wright ME. Discovery Proteomics Identifies a Molecular Link between the Coatomer Protein Complex I and Androgen Receptor-dependent Transcription. J Biol Chem 2016; 291:18818-42. [PMID: 27365400 PMCID: PMC5009256 DOI: 10.1074/jbc.m116.732313] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Indexed: 12/18/2022] Open
Abstract
Aberrant androgen receptor (AR)-dependent transcription is a hallmark of human prostate cancers. At the molecular level, ligand-mediated AR activation is coordinated through spatial and temporal protein-protein interactions involving AR-interacting proteins, which we designate the “AR-interactome.” Despite many years of research, the ligand-sensitive protein complexes involved in ligand-mediated AR activation in prostate tumor cells have not been clearly defined. Here, we describe the development, characterization, and utilization of a novel human LNCaP prostate tumor cell line, N-AR, which stably expresses wild-type AR tagged at its N terminus with the streptavidin-binding peptide epitope (streptavidin-binding peptide-tagged wild-type androgen receptor; SBP-AR). A bioanalytical workflow involving streptavidin chromatography and label-free quantitative mass spectrometry was used to identify SBP-AR and associated ligand-sensitive cytosolic proteins/protein complexes linked to AR activation in prostate tumor cells. Functional studies verified that ligand-sensitive proteins identified in the proteomic screen encoded modulators of AR-mediated transcription, suggesting that these novel proteins were putative SBP-AR-interacting proteins in N-AR cells. This was supported by biochemical associations between recombinant SBP-AR and the ligand-sensitive coatomer protein complex I (COPI) retrograde trafficking complex in vitro. Extensive biochemical and molecular experiments showed that the COPI retrograde complex regulates ligand-mediated AR transcriptional activation, which correlated with the mobilization of the Golgi-localized ARA160 coactivator to the nuclear compartment of prostate tumor cells. Collectively, this study provides a bioanalytical strategy to validate the AR-interactome and define novel AR-interacting proteins involved in ligand-mediated AR activation in prostate tumor cells. Moreover, we describe a cellular system to study how compartment-specific AR-interacting proteins influence AR activation and contribute to aberrant AR-dependent transcription that underlies the majority of human prostate cancers.
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Affiliation(s)
- Jordy J Hsiao
- From the Department of Molecular Physiology and Biophysics, Carver College of Medicine, Iowa City, Iowa 52242
| | - Melinda M Smits
- From the Department of Molecular Physiology and Biophysics, Carver College of Medicine, Iowa City, Iowa 52242
| | - Brandon H Ng
- From the Department of Molecular Physiology and Biophysics, Carver College of Medicine, Iowa City, Iowa 52242
| | - Jinhee Lee
- From the Department of Molecular Physiology and Biophysics, Carver College of Medicine, Iowa City, Iowa 52242
| | - Michael E Wright
- From the Department of Molecular Physiology and Biophysics, Carver College of Medicine, Iowa City, Iowa 52242
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20
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Armengaud J. Next-generation proteomics faces new challenges in environmental biotechnology. Curr Opin Biotechnol 2016; 38:174-82. [DOI: 10.1016/j.copbio.2016.02.025] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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Schons-Fonseca L, da Silva JB, Milanez JS, Domingos RH, Smith JL, Nakaya HI, Grossman AD, Ho PL, da Costa RMA. Analysis of LexA binding sites and transcriptomics in response to genotoxic stress in Leptospira interrogans. Nucleic Acids Res 2016; 44:1179-91. [PMID: 26762976 PMCID: PMC4756842 DOI: 10.1093/nar/gkv1536] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 12/15/2015] [Accepted: 12/25/2015] [Indexed: 11/13/2022] Open
Abstract
We determined the effects of DNA damage caused by ultraviolet radiation on gene expression in Leptospira interrogans using DNA microarrays. These data were integrated with DNA binding in vivo of LexA1, a regulator of the DNA damage response, assessed by chromatin immunoprecipitation and massively parallel DNA sequencing (ChIP-seq). In response to DNA damage, Leptospira induced expression of genes involved in DNA metabolism, in mobile genetic elements and defective prophages. The DNA repair genes involved in removal of photo-damage (e.g. nucleotide excision repair uvrABC, recombinases recBCD and resolvases ruvABC) were not induced. Genes involved in various metabolic pathways were down regulated, including genes involved in cell growth, RNA metabolism and the tricarboxylic acid cycle. From ChIP-seq data, we observed 24 LexA1 binding sites located throughout chromosome 1 and one binding site in chromosome 2. Expression of many, but not all, genes near those sites was increased following DNA damage. Binding sites were found as far as 550 bp upstream from the start codon, or 1 kb into the coding sequence. Our findings indicate that there is a shift in gene expression following DNA damage that represses genes involved in cell growth and virulence, and induces genes involved in mutagenesis and recombination.
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Affiliation(s)
- Luciane Schons-Fonseca
- Centro de Biotecnologia, Instituto Butantan, São Paulo, São Paulo 05503-900, Brazil Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo 05508-000, Brazil Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, MA 02139, USA
| | - Josefa B da Silva
- Centro de Biotecnologia, Instituto Butantan, São Paulo, São Paulo 05503-900, Brazil
| | - Juliana S Milanez
- Centro de Biotecnologia, Instituto Butantan, São Paulo, São Paulo 05503-900, Brazil Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, São Paulo 05508-000, Brazil
| | - Renan H Domingos
- Centro de Biotecnologia, Instituto Butantan, São Paulo, São Paulo 05503-900, Brazil
| | - Janet L Smith
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, MA 02139, USA
| | - Helder I Nakaya
- Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, São Paulo 05508-000, Brazil
| | - Alan D Grossman
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, MA 02139, USA
| | - Paulo L Ho
- Centro de Biotecnologia, Instituto Butantan, São Paulo, São Paulo 05503-900, Brazil
| | - Renata M A da Costa
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, São Paulo 09210580, Brazil
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22
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Maaß S, Becher D. Methods and applications of absolute protein quantification in microbial systems. J Proteomics 2016; 136:222-33. [PMID: 26825536 DOI: 10.1016/j.jprot.2016.01.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 01/05/2016] [Accepted: 01/21/2016] [Indexed: 02/05/2023]
Abstract
In the last years the scientific community faced an increased need to provide high-quality data on the concentration of single proteins within a cell. Especially against the background of the fast evolving field of systems biology this does not only apply for a few proteins but preferably for the whole proteome of the organism. Therefore there has been a rapid development from pure identification of proteins via characterization of changes between different conditions by relative protein quantification towards determination of absolute protein amounts for hundreds of protein species in a cell. This review aims for discussion of different small-scale and large-scale approaches for absolute protein quantification in bacterial cells to picture biological processes and explore life in deeper detail. The presented advantages and limitations of various methods may provide interested researchers help to appraise available methods, select the most appropriate technique and avoid common pitfalls during determination of protein concentration in a complex sample.
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Affiliation(s)
- Sandra Maaß
- Institute for Microbiology, Ernst Moritz Arndt Universität Greifswald, D-17487 Greifswald, Germany.
| | - Dörte Becher
- Institute for Microbiology, Ernst Moritz Arndt Universität Greifswald, D-17487 Greifswald, Germany
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23
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Schmidt A, Kochanowski K, Vedelaar S, Ahrné E, Volkmer B, Callipo L, Knoops K, Bauer M, Aebersold R, Heinemann M. The quantitative and condition-dependent Escherichia coli proteome. Nat Biotechnol 2015; 34:104-10. [PMID: 26641532 PMCID: PMC4888949 DOI: 10.1038/nbt.3418] [Citation(s) in RCA: 484] [Impact Index Per Article: 53.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 10/28/2015] [Indexed: 12/26/2022]
Abstract
Measuring precise concentrations of proteins can provide insights into biological processes. Here, we use efficient protein extraction and sample fractionation and state-of-the-art quantitative mass spectrometry techniques to generate a comprehensive, condition-dependent protein abundance map of Escherichia coli. We measure cellular protein concentrations for 55% of predicted E. coli genes (>2300 proteins) under 22 different experimental conditions and identify methylation and N-terminal protein acetylations previously not known to be prevalent in bacteria. We uncover system-wide proteome allocation, expression regulation, and post-translational adaptations. These data provide a valuable resource for the systems biology and broader E. coli research communities.
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Affiliation(s)
| | - Karl Kochanowski
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Silke Vedelaar
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Erik Ahrné
- Biozentrum, University of Basel, Basel, Switzerland
| | - Benjamin Volkmer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Luciano Callipo
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Kèvin Knoops
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Manuel Bauer
- Biozentrum, University of Basel, Basel, Switzerland
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Matthias Heinemann
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
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24
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Jamdhade MD, Pawar H, Chavan S, Sathe G, Umasankar PK, Mahale KN, Dixit T, Madugundu AK, Prasad TSK, Gowda H, Pandey A, Patole MS. Comprehensive proteomics analysis of glycosomes from Leishmania donovani. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2015; 19:157-70. [PMID: 25748437 DOI: 10.1089/omi.2014.0163] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Leishmania donovani is a kinetoplastid protozoan that causes a severe and fatal disease kala-azar, or visceral leishmaniasis. L. donovani infects human host after the phlebotomine sandfly takes a blood meal and resides within the phagolysosome of infected macrophages. Previous studies on host-parasite interactions have not focused on Leishmania organelles and the role that they play in the survival of this parasite within macrophages. Leishmania possess glycosomes that are unique and specialized subcellular microbody organelles. Glycosomes are known to harbor most peroxisomal enzymes and, in addition, they also possess nine glycolytic enzymes. In the present study, we have carried out proteomic profiling using high resolution mass spectrometry of a sucrose density gradient-enriched glycosomal fraction isolated from L. donovani promastigotes. This study resulted in the identification of 4022 unique peptides, leading to the identification of 1355 unique proteins from a preparation enriched in L. donovani glycosomes. Based on protein annotation, 566 (41.8%) were identified as hypothetical proteins with no known function. A majority of the identified proteins are involved in metabolic processes such as carbohydrate, lipid, and nucleic acid metabolism. Our present proteomic analysis is the most comprehensive study to date to map the proteome of L. donovani glycosomes.
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25
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Säll A, Sjöholm K, Waldemarson S, Happonen L, Karlsson C, Persson H, Malmström J. Development of Phage-Based Antibody Fragment Reagents for Affinity Enrichment of Bacterial Immunoglobulin G Binding Proteins. J Proteome Res 2015; 14:4704-13. [PMID: 26452057 DOI: 10.1021/acs.jproteome.5b00585] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Disease and death caused by bacterial infections are global health problems. Effective bacterial strategies are required to promote survival and proliferation within a human host, and it is important to explore how this adaption occurs. However, the detection and quantification of bacterial virulence factors in complex biological samples are technically demanding challenges. These can be addressed by combining targeted affinity enrichment of antibodies with the sensitivity of liquid chromatography-selected reaction monitoring mass spectrometry (LC-SRM MS). However, many virulence factors have evolved properties that make specific detection by conventional antibodies difficult. We here present an antibody format that is particularly well suited for detection and analysis of immunoglobulin G (IgG)-binding virulence factors. As proof of concept, we have generated single chain fragment variable (scFv) antibodies that specifically target the IgG-binding surface proteins M1 and H of Streptococcus pyogenes. The binding ability of the developed scFv is demonstrated against both recombinant soluble protein M1 and H as well as the intact surface proteins on a wild-type S. pyogenes strain. Additionally, the capacity of the developed scFv antibodies to enrich their target proteins from both simple and complex backgrounds, thereby allowing for detection and quantification with LC-SRM MS, was demonstrated. We have established a workflow that allows for affinity enrichment of bacterial virulence factors.
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Affiliation(s)
- Anna Säll
- Department of Immunotechnology, Lund University , Medicon Village (House 406), SE 223 81, Lund, Sweden
| | - Kristoffer Sjöholm
- Department of Immunotechnology, Lund University , Medicon Village (House 406), SE 223 81, Lund, Sweden
| | - Sofia Waldemarson
- Department of Immunotechnology, Lund University , Medicon Village (House 406), SE 223 81, Lund, Sweden
| | - Lotta Happonen
- Division of Infection Medicine, Department of Clinical Sciences, Lund University , SE 221 00, Lund, Sweden
| | - Christofer Karlsson
- Division of Infection Medicine, Department of Clinical Sciences, Lund University , SE 221 00, Lund, Sweden
| | - Helena Persson
- Department of Immunotechnology, Lund University , Medicon Village (House 406), SE 223 81, Lund, Sweden.,Science for Life Laboratory, Royal Institute of Technology , 17121 Stockholm, Sweden
| | - Johan Malmström
- Division of Infection Medicine, Department of Clinical Sciences, Lund University , SE 221 00, Lund, Sweden
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26
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Glatter T, Ahrné E, Schmidt A. Comparison of Different Sample Preparation Protocols Reveals Lysis Buffer-Specific Extraction Biases in Gram-Negative Bacteria and Human Cells. J Proteome Res 2015; 14:4472-85. [PMID: 26412744 DOI: 10.1021/acs.jproteome.5b00654] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We evaluated different in-solution and FASP-based sample preparation strategies for absolute protein quantification. Label-free quantification (LFQ) was employed to compare different sample preparation strategies in the bacterium Pseudomonas aeruginosa and human embryonic kidney cells (HEK), and organismal-specific differences in general performance and enrichment of specific protein classes were noted. The original FASP protocol globally enriched for most proteins in the bacterial sample, whereas the sodium deoxycholate in-solution strategy was more efficient with HEK cells. Although detergents were found to be highly suited for global proteome analysis, higher intensities were obtained for high-abundant nucleic acid-associated protein complexes, like the ribosome and histone proteins, using guanidine hydrochloride. Importantly, we show for the first time that the observable total proteome mass of a sample strongly depends on the sample preparation protocol, with some protocols resulting in a significant underestimation of protein mass due to incomplete protein extraction of biased protein groups. Furthermore, we demonstrate that some of the observed abundance biases can be overcome by incorporating a nuclease treatment step or, alternatively, a correction factor for complementary sample preparation approaches.
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Affiliation(s)
- Timo Glatter
- Proteomics Core Facility, Biozentrum, University of Basel , 4056 Basel, Switzerland
| | - Erik Ahrné
- Proteomics Core Facility, Biozentrum, University of Basel , 4056 Basel, Switzerland
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum, University of Basel , 4056 Basel, Switzerland
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27
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Kreibich S, Hardt WD. Experimental approaches to phenotypic diversity in infection. Curr Opin Microbiol 2015; 27:25-36. [PMID: 26143306 DOI: 10.1016/j.mib.2015.06.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Revised: 06/03/2015] [Accepted: 06/06/2015] [Indexed: 12/16/2022]
Abstract
Microbial infections are burdening human health, even after the advent of antibiotics, vaccines and hygiene. Thus, infection biology has aimed at the molecular understanding of the pathogen-host interaction. This has revealed key virulence factors, host cell signaling pathways and immune responses. However, our understanding of the infection process is still incomplete. Recent evidence suggests that phenotypic diversity can have important consequences for the infection process. Diversity arises from the formation of distinct subpopulations of pathogen cells (with distinct virulence factor expression patterns) and host cells (with distinct response capacities). For technical reasons, such phenotypic diversity has often been overlooked. We are highlighting several striking examples and discuss the experimental approaches available for analyzing the different subpopulations. Single cell reporters and approaches from systems biology do hold much promise.
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Affiliation(s)
- Saskia Kreibich
- Institute of Microbiology, ETH Zürich, CH-8093 Zürich, Switzerland
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28
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Schuller S, Sergeant K, Renaut J, Callanan JJ, Scaife C, Nally JE. Comparative proteomic analysis of lung tissue from guinea pigs with leptospiral pulmonary haemorrhage syndrome (LPHS) reveals a decrease in abundance of host proteins involved in cytoskeletal and cellular organization. J Proteomics 2015; 122:55-72. [PMID: 25818725 DOI: 10.1016/j.jprot.2015.03.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 02/20/2015] [Accepted: 03/08/2015] [Indexed: 12/17/2022]
Abstract
UNLABELLED Leptospiral pulmonary haemorrhage syndrome (LPHS) is a particularly severe form of leptospirosis. LPHS is increasingly recognized in both humans and animals and is characterized by rapidly progressive intra-alveolar haemorrhage leading to high mortality. The pathogenic mechanisms of LPHS are poorly understood which hampers the application of effective treatment regimes. In this study a 2-D guinea pig proteome lung map was created and used to investigate the pathogenic mechanisms of LPHS. Comparison of lung proteomes from infected and non-infected guinea pigs via differential in-gel electrophoresis revealed highly significant differences in abundance of proteins contained in 130 spots. Acute phase proteins were the largest functional group amongst proteins with increased abundance in LPHS lung tissue, and likely reflect a local and/or systemic host response to infection. The observed decrease in abundance of proteins involved in cytoskeletal and cellular organization in LPHS lung tissue further suggests that infection with pathogenic Leptospira induces changes in the abundance of host proteins involved in cellular architecture and adhesion contributing to the dramatically increased alveolar septal wall permeability seen in LPHS. BIOLOGICAL SIGNIFICANCE The recent completion of the complete genome sequence of the guinea pig (Cavia porcellus) provides innovative opportunities to apply proteomic technologies to an important animal model of disease. In this study, the comparative proteomic analysis of lung tissue from experimentally infected guinea pigs with leptospiral pulmonary haemorrhage syndrome (LPHS) revealed a decrease in abundance of proteins involved in cellular architecture and adhesion, suggesting that loss or down-regulation of cytoskeletal and adhesion molecules plays an important role in the pathogenesis of LPHS. A publically available guinea pig lung proteome map was constructed to facilitate future pulmonary proteomics in this species.
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Affiliation(s)
- Simone Schuller
- University College Dublin, School of Veterinary Medicine, Belfield, Dublin 4, Ireland; Vetsuisse Faculty University of Bern, Länggassstrasse 128, 3012 Bern, Switzerland.
| | - Kjell Sergeant
- Luxembourg Institute of Science and Technology, Environmental Research and Innovation" (ERIN) department, 41, rue du Brill, 4422 Belvaux, Luxembourg
| | - Jenny Renaut
- Luxembourg Institute of Science and Technology, Environmental Research and Innovation" (ERIN) department, 41, rue du Brill, 4422 Belvaux, Luxembourg
| | - John J Callanan
- University College Dublin, School of Veterinary Medicine, Belfield, Dublin 4, Ireland; Conway Institute for Biomolecular & Biomedical Research, Belfield, Dublin 4, Ireland; Ross University School of Veterinary Medicine, St Kitts and Nevis, West Indies
| | - Caitriona Scaife
- Conway Institute for Biomolecular & Biomedical Research, Belfield, Dublin 4, Ireland
| | - Jarlath E Nally
- University College Dublin, School of Veterinary Medicine, Belfield, Dublin 4, Ireland; Conway Institute for Biomolecular & Biomedical Research, Belfield, Dublin 4, Ireland; Bacterial Diseases of Livestock Research Unit, National Animal Disease Center, Agricultural Research Service, Department of Agriculture, Ames, IA 50010, USA
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29
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Hui S, Silverman JM, Chen SS, Erickson DW, Basan M, Wang J, Hwa T, Williamson JR. Quantitative proteomic analysis reveals a simple strategy of global resource allocation in bacteria. Mol Syst Biol 2015; 11:784. [PMID: 25678603 PMCID: PMC4358657 DOI: 10.15252/msb.20145697] [Citation(s) in RCA: 201] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
A central aim of cell biology was to understand the strategy of gene expression in response to the environment. Here, we study gene expression response to metabolic challenges in exponentially growing Escherichia coli using mass spectrometry. Despite enormous complexity in the details of the underlying regulatory network, we find that the proteome partitions into several coarse-grained sectors, with each sector's total mass abundance exhibiting positive or negative linear relations with the growth rate. The growth rate-dependent components of the proteome fractions comprise about half of the proteome by mass, and their mutual dependencies can be characterized by a simple flux model involving only two effective parameters. The success and apparent generality of this model arises from tight coordination between proteome partition and metabolism, suggesting a principle for resource allocation in proteome economy of the cell. This strategy of global gene regulation should serve as a basis for future studies on gene expression and constructing synthetic biological circuits. Coarse graining may be an effective approach to derive predictive phenomenological models for other ‘omics’ studies.
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Affiliation(s)
- Sheng Hui
- Department of Physics, University of California at San Diego, La Jolla, CA, USA
| | - Josh M Silverman
- Department of Integrative Structural and Computational Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Stephen S Chen
- Department of Integrative Structural and Computational Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - David W Erickson
- Department of Physics, University of California at San Diego, La Jolla, CA, USA
| | - Markus Basan
- Department of Physics, University of California at San Diego, La Jolla, CA, USA
| | - Jilong Wang
- Department of Physics, University of California at San Diego, La Jolla, CA, USA
| | - Terence Hwa
- Department of Physics, University of California at San Diego, La Jolla, CA, USA Section of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA, USA
| | - James R Williamson
- Department of Integrative Structural and Computational Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
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30
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Valgepea K, Peebo K, Adamberg K, Vilu R. Lean-proteome strains - next step in metabolic engineering. Front Bioeng Biotechnol 2015; 3:11. [PMID: 25705616 PMCID: PMC4319490 DOI: 10.3389/fbioe.2015.00011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Accepted: 01/22/2015] [Indexed: 12/18/2022] Open
Affiliation(s)
- Kaspar Valgepea
- Competence Center of Food and Fermentation Technologies , Tallinn , Estonia
| | - Karl Peebo
- Competence Center of Food and Fermentation Technologies , Tallinn , Estonia ; Department of Chemistry, Tallinn University of Technology , Tallinn , Estonia
| | - Kaarel Adamberg
- Competence Center of Food and Fermentation Technologies , Tallinn , Estonia ; Department of Food Processing, Tallinn University of Technology , Tallinn , Estonia
| | - Raivo Vilu
- Competence Center of Food and Fermentation Technologies , Tallinn , Estonia ; Department of Chemistry, Tallinn University of Technology , Tallinn , Estonia
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31
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Abstract
Mass spectrometry has been widely applied in characterization and quantification of proteins from complex biological samples. Because the numbers of absolute amounts of proteins are needed in construction of mathematical models for molecular systems of various biological phenotypes and phenomena, a number of quantitative proteomic methods have been adopted to measure absolute quantities of proteins using mass spectrometry. The liquid chromatography-tandem mass spectrometry (LC-MS/MS) coupled with internal peptide standards, i.e., the stable isotope-coded peptide dilution series, which was originated from the field of analytical chemistry, becomes a widely applied method in absolute quantitative proteomics research. This approach provides more and more absolute protein quantitation results of high confidence. As quantitative study of posttranslational modification (PTM) that modulates the biological activity of proteins is crucial for biological science and each isoform may contribute a unique biological function, degradation, and/or subcellular location, the absolute quantitation of protein PTM isoforms has become more relevant to its biological significance. In order to obtain the absolute cellular amount of a PTM isoform of a protein accurately, impacts of protein fractionation, protein enrichment, and proteolytic digestion yield should be taken into consideration and those effects before differentially stable isotope-coded PTM peptide standards are spiked into sample peptides have to be corrected. Assisted with stable isotope-labeled peptide standards, the absolute quantitation of isoforms of posttranslationally modified protein (AQUIP) method takes all these factors into account and determines the absolute amount of a protein PTM isoform from the absolute amount of the protein of interest and the PTM occupancy at the site of the protein. The absolute amount of the protein of interest is inferred by quantifying both the absolute amounts of a few PTM-site-independent peptides in the total cellular protein and their peptide yields. The PTM occupancy determination is achieved by measuring the absolute amounts of both PTM and non-PTM peptides from the highly purified protein sample expressed in transgenic organisms or directly isolated from an organism using affinity purification. The absolute amount of each PTM isoform in the total cellular protein extract is finally calculated from these two variables. Following this approach, the ion intensities given by mass spectrometers are used to calculated the peptide amounts, from which the amounts of protein isoforms are then deduced. In this chapter, we describe the principles underlying the experimental design and procedures used in AQUIP method. This quantitation method basically employs stable isotope-labeled peptide standards and affinity purification from a tagged recombinant protein of interest. Other quantitation strategies and purification techniques related to this method are also discussed.
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Affiliation(s)
- Zhu Yang
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China,
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32
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Bauer M, Ahrné E, Baron AP, Glatter T, Fava LL, Santamaria A, Nigg EA, Schmidt A. Evaluation of Data-Dependent and -Independent Mass Spectrometric Workflows for Sensitive Quantification of Proteins and Phosphorylation Sites. J Proteome Res 2014; 13:5973-88. [DOI: 10.1021/pr500860c] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Manuel Bauer
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Erik Ahrné
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Anna P. Baron
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Timo Glatter
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Luca L. Fava
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Anna Santamaria
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Erich A. Nigg
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Alexander Schmidt
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
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33
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Maaβ S, Wachlin G, Bernhardt J, Eymann C, Fromion V, Riedel K, Becher D, Hecker M. Highly precise quantification of protein molecules per cell during stress and starvation responses in Bacillus subtilis. Mol Cell Proteomics 2014; 13:2260-76. [PMID: 24878497 PMCID: PMC4159648 DOI: 10.1074/mcp.m113.035741] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 05/02/2014] [Indexed: 11/06/2022] Open
Abstract
Systems biology based on high quality absolute quantification data, which are mandatory for the simulation of biological processes, successively becomes important for life sciences. We provide protein concentrations on the level of molecules per cell for more than 700 cytosolic proteins of the Gram-positive model bacterium Bacillus subtilis during adaptation to changing growth conditions. As glucose starvation and heat stress are typical challenges in B. subtilis' natural environment and induce both, specific and general stress and starvation proteins, these conditions were selected as models for starvation and stress responses. Analyzing samples from numerous time points along the bacterial growth curve yielded reliable and physiologically relevant data suitable for modeling of cellular regulation under altered growth conditions. The analysis of the adaptational processes based on protein molecules per cell revealed stress-specific modulation of general adaptive responses in terms of protein amount and proteome composition. Furthermore, analysis of protein repartition during glucose starvation showed that biomass seems to be redistributed from proteins involved in amino acid biosynthesis to enzymes of the central carbon metabolism. In contrast, during heat stress most resources of the cell, namely those from amino acid synthetic pathways, are used to increase the amount of chaperones and proteases. Analysis of dynamical aspects of protein synthesis during heat stress adaptation revealed, that these proteins make up almost 30% of the protein mass accumulated during early phases of this stress.
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Affiliation(s)
- Sandra Maaβ
- From the ‡Institute for Microbiology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany
| | - Gerhild Wachlin
- From the ‡Institute for Microbiology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany
| | - Jörg Bernhardt
- From the ‡Institute for Microbiology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany
| | - Christine Eymann
- From the ‡Institute for Microbiology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany
| | - Vincent Fromion
- §INRA, Mathématique Informatique et Génome UR1077, 78350 Jouy-en-Josas, France
| | - Katharina Riedel
- From the ‡Institute for Microbiology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany
| | - Dörte Becher
- From the ‡Institute for Microbiology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany;
| | - Michael Hecker
- From the ‡Institute for Microbiology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany
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34
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Breker M, Schuldiner M. The emergence of proteome-wide technologies: systematic analysis of proteins comes of age. Nat Rev Mol Cell Biol 2014; 15:453-64. [PMID: 24938631 DOI: 10.1038/nrm3821] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
During the lifetime of a cell proteins can change their localization, alter their abundance and undergo modifications, all of which cannot be assayed by tracking mRNAs alone. Methods to study proteomes directly are coming of age, thereby opening new perspectives on the role of post-translational regulation in stabilizing the cellular milieu. Proteomics has undergone a revolution, and novel technologies for the systematic analysis of proteins have emerged. These methods can expand our ability to acquire information from single proteins to proteomes, from static to dynamic measures and from the population level to the level of single cells. Such approaches promise that proteomes will soon be studied at a similar level of dynamic resolution as has been the norm for transcriptomes.
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Affiliation(s)
- Michal Breker
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
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35
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Characterisation of the Proteome of Leptospira interrogans Serovar Canicola as a Resource for the Identification of Common Serovar Immunogenic Proteins. INTERNATIONAL JOURNAL OF PROTEOMICS 2014; 2014:572901. [PMID: 24987528 PMCID: PMC4058600 DOI: 10.1155/2014/572901] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Revised: 04/24/2014] [Accepted: 04/24/2014] [Indexed: 11/18/2022]
Abstract
Over 230 serovars of Leptospira interrogans have been identified; however few have been completely characterised. The aim of this study was to characterise the proteome of serovar Canicola and to compare this against the serovars of Copenhageni and Pomona. 2D-LC/MS analysis identified 1653 Leptospira proteins in serovar Canicola; 60 of these proteins were common to Copenhageni and Pomona, 16 of which are known to be immunogenic. This study provides the first reported proteome for serovar Canicola and suggests that proteomic comparison of different serovars could be used as a tool for identification of novel target molecules for vaccine development.
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36
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Spatial proteomic and phospho-proteomic organization in three prototypical cell migration modes. Proteome Sci 2014; 12:23. [PMID: 24987309 PMCID: PMC4077045 DOI: 10.1186/1477-5956-12-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 04/25/2014] [Indexed: 01/01/2023] Open
Abstract
Background Tight spatio-temporal signaling of cytoskeletal and adhesion dynamics is required for localized membrane protrusion that drives directed cell migration. Different ensembles of proteins are therefore likely to get recruited and phosphorylated in membrane protrusions in response to specific cues. Results Here, we use an assay that allows to biochemically purify extending protrusions of cells migrating in response to three prototypical receptors: integrins, recepor tyrosine kinases and G-coupled protein receptors. Using quantitative proteomics and phospho-proteomics approaches, we provide evidence for the existence of cue-specific, spatially distinct protein networks in the different cell migration modes. Conclusions The integrated analysis of the large-scale experimental data with protein information from databases allows us to understand some emergent properties of spatial regulation of signaling during cell migration. This provides the cell migration community with a large-scale view of the distribution of proteins and phospho-proteins regulating directed cell migration.
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Valgepea K, Adamberg K, Seiman A, Vilu R. Escherichia coli achieves faster growth by increasing catalytic and translation rates of proteins. MOLECULAR BIOSYSTEMS 2014; 9:2344-58. [PMID: 23824091 DOI: 10.1039/c3mb70119k] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Regulation levels of the gene expression cascade controlling protein levels and metabolic fluxes for cells to achieve faster growth have not been elaborated in acceptable detail. Furthermore, there is need for specific growth rate (μ) dependent absolute quantitative transcriptome and proteome data to understand the molecular relationships for enabling cells to modify μ. We address these questions, for the first time, by presenting regulatory strategies for more efficient metabolism of Escherichia coli at higher μ by statistical covariance analysis of genome-wide intracellular mRNA and protein concentrations coupled to metabolic flux analysis in the steady state range of μ = 0.11-0.49 h(-1). Our analyses show dominating post-transcriptional control of protein abundances and post-translational control of flux rates. On average, E. coli achieved five-times faster growth through 3.7-fold increase of apparent catalytic rates of enzymes (kapp) and 2.5-fold increased translation rates, demonstrating the relevance of post-translational regulation for increasing flux throughput. Interestingly, pathways carrying the highest flux showed both high protein abundance and kapp values. Furthermore, co-regulation analysis of enzymatic capacities revealed tightly coupled regulatory dependencies of protein synthesis and RNA precursor synthesis, substrate utilization, biosynthetic and energy generation pathways carrying the highest flux. We also observed metabolic pathway and COG specific protein and metabolic flux control levels, protein expression costs and genome-wide principles for translation efficiency and transcription unit polarity. This work contributes to the much needed quantitative understanding of coordinated gene expression regulation and metabolic flux control. Our findings will also advance modeling and metabolic engineering of industrial strains.
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Affiliation(s)
- Kaspar Valgepea
- Tallinn University of Technology, Department of Chemistry, Akadeemia tee 15, 12618 Tallinn, Estonia.
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38
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Sjöholm K, Karlsson C, Linder A, Malmström J. A comprehensive analysis of the Streptococcus pyogenes and human plasma protein interaction network. MOLECULAR BIOSYSTEMS 2014; 10:1698-708. [PMID: 24525632 DOI: 10.1039/c3mb70555b] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Streptococcus pyogenes is a major human bacterial pathogen responsible for severe and invasive disease associated with high mortality rates. The bacterium interacts with several human blood plasma proteins and clarifying these interactions and their biological consequences will help to explain the progression from mild to severe infections. In this study, we used a combination of mass spectrometry (MS) based techniques to comprehensively quantify the components of the S. pyogenes-plasma protein interaction network. From an initial list of 181 interacting human plasma proteins defined using liquid chromatography (LC)-MS/MS analysis we further subdivided the interacting protein list using selected reaction monitoring (SRM) depending on the level of enrichment and protein concentration on the bacterial surface. The combination of MS methods revealed several previously characterized interactions between the S. pyogenes surface and human plasma along with many more, so far uncharacterised, possible plasma protein interactions with S. pyogenes. In follow-up experiments, the combination of MS techniques was applied to study differences in protein binding to a S. pyogenes wild type strain and an isogenic mutant lacking several important virulence factors, and a unique pair of invasive and non-invasive S. pyogenes isolates from the same patient. Comparing the plasma protein-binding properties of the wild type and the mutant and the invasive and non-invasive S. pyogenes bacteria revealed considerable differences, underlining the significance of these protein interactions. The results also demonstrate the power of the developed mass spectrometry method to investigate host-microbial relationships with a large proteomics depth and high quantitative accuracy.
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Affiliation(s)
- Kristoffer Sjöholm
- Department of Immunotechnology, Faculty of Engineering, Lund University, Sweden
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39
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Jüschke C, Dohnal I, Pichler P, Harzer H, Swart R, Ammerer G, Mechtler K, Knoblich JA. Transcriptome and proteome quantification of a tumor model provides novel insights into post-transcriptional gene regulation. Genome Biol 2013; 14:r133. [PMID: 24289286 PMCID: PMC4053992 DOI: 10.1186/gb-2013-14-11-r133] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 11/30/2013] [Indexed: 11/25/2022] Open
Abstract
Background Genome‐wide transcriptome analyses have given systems‐level insights into gene regulatory networks. Due to the limited depth of quantitative proteomics, however, our understanding of post‐transcriptional gene regulation and its effects on protein‐complex stoichiometry are lagging behind. Results Here, we employ deep sequencing and the isobaric tag for relative and absolute quantification (iTRAQ) technology to determine transcript and protein expression changes of a Drosophila brain tumor model at near genome‐wide resolution. In total, we quantify more than 6,200 tissue‐specific proteins, corresponding to about 70% of all transcribed protein‐coding genes. Using our integrated data set, we demonstrate that post‐transcriptional gene regulation varies considerably with biological function and is surprisingly high for genes regulating transcription. We combine our quantitative data with protein‐protein interaction data and show that post‐transcriptional mechanisms significantly enhance co‐regulation of protein‐complex subunits beyond transcriptional co‐regulation. Interestingly, our results suggest that only about 11% of the annotated Drosophila protein complexes are co‐regulated in the brain. Finally, we refine the composition of some of these core protein complexes by analyzing the co‐regulation of potential subunits. Conclusions Our comprehensive transcriptome and proteome data provide a valuable resource for quantitative biology and offer novel insights into understanding post‐transcriptional gene regulation in a tumor model.
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Schubert OT, Mouritsen J, Ludwig C, Röst HL, Rosenberger G, Arthur PK, Claassen M, Campbell DS, Sun Z, Farrah T, Gengenbacher M, Maiolica A, Kaufmann SHE, Moritz RL, Aebersold R. The Mtb proteome library: a resource of assays to quantify the complete proteome of Mycobacterium tuberculosis. Cell Host Microbe 2013; 13:602-612. [PMID: 23684311 DOI: 10.1016/j.chom.2013.04.008] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 03/27/2013] [Accepted: 04/15/2013] [Indexed: 12/18/2022]
Abstract
Research advancing our understanding of Mycobacterium tuberculosis (Mtb) biology and complex host-Mtb interactions requires consistent and precise quantitative measurements of Mtb proteins. We describe the generation and validation of a compendium of assays to quantify 97% of the 4,012 annotated Mtb proteins by the targeted mass spectrometric method selected reaction monitoring (SRM). Furthermore, we estimate the absolute abundance for 55% of all Mtb proteins, revealing a dynamic range within the Mtb proteome of over four orders of magnitude, and identify previously unannotated proteins. As an example of the assay library utility, we monitored the entire Mtb dormancy survival regulon (DosR), which is linked to anaerobic survival and Mtb persistence, and show its dynamic protein-level regulation during hypoxia. In conclusion, we present a publicly available research resource that supports the sensitive, precise, and reproducible quantification of virtually any Mtb protein by a robust and widely accessible mass spectrometric method.
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Affiliation(s)
- Olga T Schubert
- Institute of Molecular Systems Biology, ETH Zurich, Zurich CH-8093, Switzerland; Systems Biology Graduate School, Zurich, CH-8057, Switzerland
| | - Jeppe Mouritsen
- Institute of Molecular Systems Biology, ETH Zurich, Zurich CH-8093, Switzerland; Molecular Life Sciences Graduate School, Zurich, CH-8093, Switzerland
| | - Christina Ludwig
- Institute of Molecular Systems Biology, ETH Zurich, Zurich CH-8093, Switzerland
| | - Hannes L Röst
- Institute of Molecular Systems Biology, ETH Zurich, Zurich CH-8093, Switzerland; Systems Biology Graduate School, Zurich, CH-8057, Switzerland
| | - George Rosenberger
- Institute of Molecular Systems Biology, ETH Zurich, Zurich CH-8093, Switzerland; Systems Biology Graduate School, Zurich, CH-8057, Switzerland
| | - Patrick K Arthur
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Manfred Claassen
- Institute of Molecular Systems Biology, ETH Zurich, Zurich CH-8093, Switzerland
| | | | - Zhi Sun
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Terry Farrah
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Martin Gengenbacher
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin D-10117, Germany
| | - Alessio Maiolica
- Institute of Molecular Systems Biology, ETH Zurich, Zurich CH-8093, Switzerland
| | - Stefan H E Kaufmann
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin D-10117, Germany
| | | | - Ruedi Aebersold
- Institute of Molecular Systems Biology, ETH Zurich, Zurich CH-8093, Switzerland; Faculty of Science, University of Zurich, Zurich CH-8057, Switzerland.
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Schmutz C, Ahrné E, Kasper CA, Tschon T, Sorg I, Dreier RF, Schmidt A, Arrieumerlou C. Systems-level overview of host protein phosphorylation during Shigella flexneri infection revealed by phosphoproteomics. Mol Cell Proteomics 2013; 12:2952-68. [PMID: 23828894 PMCID: PMC3790303 DOI: 10.1074/mcp.m113.029918] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 06/14/2013] [Indexed: 01/01/2023] Open
Abstract
The enteroinvasive bacterium Shigella flexneri invades the intestinal epithelium of humans. During infection, several injected effector proteins promote bacterial internalization, and interfere with multiple host cell responses. To obtain a systems-level overview of host signaling during infection, we analyzed the global dynamics of protein phosphorylation by liquid chromatography-tandem MS and identified several hundred of proteins undergoing a phosphorylation change during the first hours of infection. Functional bioinformatic analysis revealed that they were mostly related to the cytoskeleton, transcription, signal transduction, and cell cycle. Fuzzy c-means clustering identified six temporal profiles of phosphorylation and a functional module composed of ATM-phosphorylated proteins related to genotoxic stress. Pathway enrichment analysis defined mTOR as the most overrepresented pathway. We showed that mTOR complex 1 and 2 were required for S6 kinase and AKT activation, respectively. Comparison with a published phosphoproteome of Salmonella typhimurium-infected cells revealed a large subset of coregulated phosphoproteins. Finally, we showed that S. flexneri effector OspF affected the phosphorylation of several hundred proteins, thereby demonstrating the wide-reaching impact of a single bacterial effector on the host signaling network.
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Affiliation(s)
- Christoph Schmutz
- From the ‡Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Erik Ahrné
- From the ‡Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Christoph A. Kasper
- From the ‡Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Therese Tschon
- From the ‡Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Isabel Sorg
- From the ‡Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Roland F. Dreier
- From the ‡Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Alexander Schmidt
- From the ‡Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Cécile Arrieumerlou
- From the ‡Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
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42
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Ferreira AM, Bislev SL, Bendixen E, Almeida AM. The mammary gland in domestic ruminants: a systems biology perspective. J Proteomics 2013; 94:110-23. [PMID: 24076120 DOI: 10.1016/j.jprot.2013.09.012] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 09/04/2013] [Accepted: 09/17/2013] [Indexed: 11/16/2022]
Abstract
UNLABELLED Milk and dairy products are central elements in the human diet. It is estimated that 108kg of milk per year are consumed per person worldwide. Therefore, dairy production represents a relevant fraction of the economies of many countries, being cattle, sheep, goat, water buffalo, and other ruminants the main species used worldwide. An adequate management of dairy farming cannot be achieved without the knowledge on the biological mechanisms behind lactation in ruminants. Thus, understanding the morphology, development and regulation of the mammary gland in health, disease and production is crucial. Presently, innovative and high-throughput technologies such as genomics, transcriptomics, proteomics and metabolomics allow a much broader and detailed knowledge on such issues. Additionally, the application of a systems biology approach to animal science is vastly growing, as new advances in one field of specialization or animal species lead to new lines of research in other areas or/and are expanded to other species. This article addresses how modern research approaches may help us understand long-known issues in mammary development, lactation biology and dairy production. BIOLOGICAL SIGNIFICANCE Dairy production depends upon the knowledge of the morphology and regulation of the mammary gland and lactation. High-throughput technologies allow a much broader and detailed knowledge on the biology of the mammary gland. This paper reviews the major contributions that genomics, transcriptomics, metabolomics and proteomics approaches have provided to understand the regulation of the mammary gland in health, disease and production. In the context of mammary gland "omics"-based research, the integration of results using a Systems Biology Approach is of key importance.
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Affiliation(s)
- Ana M Ferreira
- Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Universidade de Évora, Évora, Portugal; BCV Laboratory, Instituto de Tecnologia Química e Biológica/Universidade Nova de Lisboa (ITQB/UNL), Oeiras, Portugal
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43
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Milo R. What is the total number of protein molecules per cell volume? A call to rethink some published values. Bioessays 2013; 35:1050-5. [PMID: 24114984 PMCID: PMC3910158 DOI: 10.1002/bies.201300066] [Citation(s) in RCA: 355] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Novel methods such as mass-spectrometry enable a view of the proteomes of cells in unprecedented detail. Recently, these efforts have culminated in quantitative measurements of the number of copies per cell for most expressed proteins in organisms ranging from bacteria to mammalian cells. Here, we estimate the expected total number of proteins per unit of cell volume using known parameters related to the composition of cells such as the fraction of cell mass that is protein, and the average protein length. Using simple arguments, we estimate a range of 2–4 million proteins per cubic micron (i.e. 1 fL) in bacteria, yeast, and mammalian cells. Interestingly, we find that measured values that are reported for fission yeast and mammalian cells are often about 3–10 times lower. We discuss this apparent discrepancy and how to use the estimate as benchmark to recalibrate proteome-wide quantitative censuses or to revisit assumptions about cell composition. We estimate the expected total number of proteins per unit cell volume as 2–4 million proteins per cubic micron. Some reported values for fission yeast and mammalian cells using mass spectrometry are 3–10 times lower than these estimates. We discuss this apparent discrepancy and how to recalibrate proteome-wide quantitative censuses.
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Affiliation(s)
- Ron Milo
- Department of Plant Sciences, Weizmann Institute of Science, Israel
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44
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Role for cis-acting RNA sequences in the temperature-dependent expression of the multiadhesive lig proteins in Leptospira interrogans. J Bacteriol 2013; 195:5092-101. [PMID: 24013626 DOI: 10.1128/jb.00663-13] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The spirochete Leptospira interrogans causes a systemic infection that provokes a febrile illness. The putative lipoproteins LigA and LigB promote adhesion of Leptospira to host proteins, interfere with coagulation, and capture complement regulators. In this study, we demonstrate that the expression level of the LigA and LigB proteins was substantially higher when L. interrogans proliferated at 37°C instead of the standard culture temperature of 30°C. The RNA comprising the 175-nucleotide 5' untranslated region (UTR) and first six lig codons, whose sequence is identical in ligA and ligB, is predicted to fold into two distinct stem-loop structures separated by a single-stranded region. The ribosome-binding site is partially sequestered in double-stranded RNA within the second structure. Toeprint analysis revealed that in vitro formation of a 30S-tRNA(fMet)-mRNA ternary complex was inhibited unless a 5' deletion mutation disrupted the second stem-loop structure. To determine whether the lig sequence could mediate temperature-regulated gene expression in vivo, the 5' UTR and the first six codons were inserted between the Escherichia coli l-arabinose promoter and bgaB (β-galactosidase from Bacillus stearothermophilus) to create a translational fusion. The lig fragment successfully conferred thermoregulation upon the β-galactosidase reporter in E. coli. The second stem-loop structure was sufficient to confer thermoregulation on the reporter, while sequences further upstream in the 5' UTR slightly diminished expression at each temperature tested. Finally, the expression level of β-galactosidase was significantly higher when point mutations predicted to disrupt base pairs in the second structure were introduced into the stem. Compensatory mutations that maintained base pairing of the stem without restoring the wild-type sequence reinstated the inhibitory effect of the 5' UTR on expression. These results indicate that ligA and ligB expression is limited by double-stranded RNA that occludes the ribosome-binding site. At elevated temperatures, the ribosome-binding site is exposed to promote translation initiation.
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45
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Finka A, Goloubinoff P. Proteomic data from human cell cultures refine mechanisms of chaperone-mediated protein homeostasis. Cell Stress Chaperones 2013; 18:591-605. [PMID: 23430704 PMCID: PMC3745260 DOI: 10.1007/s12192-013-0413-3] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 02/06/2013] [Accepted: 02/07/2013] [Indexed: 10/27/2022] Open
Abstract
In the crowded environment of human cells, folding of nascent polypeptides and refolding of stress-unfolded proteins is error prone. Accumulation of cytotoxic misfolded and aggregated species may cause cell death, tissue loss, degenerative conformational diseases, and aging. Nevertheless, young cells effectively express a network of molecular chaperones and folding enzymes, termed here "the chaperome," which can prevent formation of potentially harmful misfolded protein conformers and use the energy of adenosine triphosphate (ATP) to rehabilitate already formed toxic aggregates into native functional proteins. In an attempt to extend knowledge of chaperome mechanisms in cellular proteostasis, we performed a meta-analysis of human chaperome using high-throughput proteomic data from 11 immortalized human cell lines. Chaperome polypeptides were about 10% of total protein mass of human cells, half of which were Hsp90s and Hsp70s. Knowledge of cellular concentrations and ratios among chaperome polypeptides provided a novel basis to understand mechanisms by which the Hsp60, Hsp70, Hsp90, and small heat shock proteins (HSPs), in collaboration with cochaperones and folding enzymes, assist de novo protein folding, import polypeptides into organelles, unfold stress-destabilized toxic conformers, and control the conformal activity of native proteins in the crowded environment of the cell. Proteomic data also provided means to distinguish between stable components of chaperone core machineries and dynamic regulatory cochaperones.
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Affiliation(s)
- Andrija Finka
- Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Pierre Goloubinoff
- Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland
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46
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Ahrné E, Molzahn L, Glatter T, Schmidt A. Critical assessment of proteome-wide label-free absolute abundance estimation strategies. Proteomics 2013; 13:2567-78. [PMID: 23794183 DOI: 10.1002/pmic.201300135] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 05/27/2013] [Accepted: 06/17/2013] [Indexed: 11/06/2022]
Abstract
There is a great interest in reliable ways to obtain absolute protein abundances at a proteome-wide scale. To this end, label-free LC-MS/MS quantification methods have been proposed where all identified proteins are assigned an estimated abundance. Several variants of this quantification approach have been presented, based on either the number of spectral counts per protein or MS1 peak intensities. Equipped with several datasets representing real biological environments, containing a high number of accurately quantified reference proteins, we evaluate five popular low-cost and easily implemented quantification methods (Absolute Protein Expression, Exponentially Modified Protein Abundance Index, Intensity-Based Absolute Quantification Index, Top3, and MeanInt). Our results demonstrate considerably improved abundance estimates upon implementing accurately quantified reference proteins; that is, using spiked in stable isotope labeled standard peptides or a standard protein mix, to generate a properly calibrated quantification model. We show that only the Top3 method is directly proportional to protein abundance over the full quantification range and is the preferred method in the absence of reference protein measurements. Additionally, we demonstrate that spectral count based quantification methods are associated with higher errors than MS1 peak intensity based methods. Furthermore, we investigate the impact of miscleaved, modified, and shared peptides as well as protein size and the number of employed reference proteins on quantification accuracy.
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Affiliation(s)
- Erik Ahrné
- Proteomics Core Facility, Biozentrum, University of Basel, Basel, Switzerland
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47
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Omasits U, Quebatte M, Stekhoven DJ, Fortes C, Roschitzki B, Robinson MD, Dehio C, Ahrens CH. Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome. Genome Res 2013; 23:1916-27. [PMID: 23878158 PMCID: PMC3814891 DOI: 10.1101/gr.151035.112] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Prokaryotes, due to their moderate complexity, are particularly amenable to the comprehensive identification of the protein repertoire expressed under different conditions. We applied a generic strategy to identify a complete expressed prokaryotic proteome, which is based on the analysis of RNA and proteins extracted from matched samples. Saturated transcriptome profiling by RNA-seq provided an endpoint estimate of the protein-coding genes expressed under two conditions which mimic the interaction of Bartonella henselae with its mammalian host. Directed shotgun proteomics experiments were carried out on four subcellular fractions. By specifically targeting proteins which are short, basic, low abundant, and membrane localized, we could eliminate their initial underrepresentation compared to the estimated endpoint. A total of 1250 proteins were identified with an estimated false discovery rate below 1%. This represents 85% of all distinct annotated proteins and ∼90% of the expressed protein-coding genes. Genes that were detected at the transcript but not protein level, were found to be highly enriched in several genomic islands. Furthermore, genes that lacked an ortholog and a functional annotation were not detected at the protein level; these may represent examples of overprediction in genome annotations. A dramatic membrane proteome reorganization was observed, including differential regulation of autotransporters, adhesins, and hemin binding proteins. Particularly noteworthy was the complete membrane proteome coverage, which included expression of all members of the VirB/D4 type IV secretion system, a key virulence factor.
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Affiliation(s)
- Ulrich Omasits
- Quantitative Model Organism Proteomics, Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
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48
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León IR, Schwämmle V, Jensen ON, Sprenger RR. Quantitative assessment of in-solution digestion efficiency identifies optimal protocols for unbiased protein analysis. Mol Cell Proteomics 2013; 12:2992-3005. [PMID: 23792921 DOI: 10.1074/mcp.m112.025585] [Citation(s) in RCA: 178] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The majority of mass spectrometry-based protein quantification studies uses peptide-centric analytical methods and thus strongly relies on efficient and unbiased protein digestion protocols for sample preparation. We present a novel objective approach to assess protein digestion efficiency using a combination of qualitative and quantitative liquid chromatography-tandem MS methods and statistical data analysis. In contrast to previous studies we employed both standard qualitative as well as data-independent quantitative workflows to systematically assess trypsin digestion efficiency and bias using mitochondrial protein fractions. We evaluated nine trypsin-based digestion protocols, based on standard in-solution or on spin filter-aided digestion, including new optimized protocols. We investigated various reagents for protein solubilization and denaturation (dodecyl sulfate, deoxycholate, urea), several trypsin digestion conditions (buffer, RapiGest, deoxycholate, urea), and two methods for removal of detergents before analysis of peptides (acid precipitation or phase separation with ethyl acetate). Our data-independent quantitative liquid chromatography-tandem MS workflow quantified over 3700 distinct peptides with 96% completeness between all protocols and replicates, with an average 40% protein sequence coverage and an average of 11 peptides identified per protein. Systematic quantitative and statistical analysis of physicochemical parameters demonstrated that deoxycholate-assisted in-solution digestion combined with phase transfer allows for efficient, unbiased generation and recovery of peptides from all protein classes, including membrane proteins. This deoxycholate-assisted protocol was also optimal for spin filter-aided digestions as compared with existing methods.
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Affiliation(s)
- Ileana R León
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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49
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Proteome-wide selected reaction monitoring assays for the human pathogen Streptococcus pyogenes. Nat Commun 2013; 3:1301. [PMID: 23250431 PMCID: PMC3535367 DOI: 10.1038/ncomms2297] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 11/15/2012] [Indexed: 01/07/2023] Open
Abstract
Selected reaction monitoring mass spectrometry (SRM-MS) is a targeted proteomics technology used to identify and quantify proteins with high sensitivity, specificity and high reproducibility. Execution of SRM-MS relies on protein-specific SRM assays, a set of experimental parameters that requires considerable effort to develop. Here we present a proteome-wide SRM assay repository for the gram-positive human pathogen group A Streptococcus. Using a multi-layered approach we generated SRM assays for 10,412 distinct group A Streptococcus peptides followed by extensive testing of the selected reaction monitoring assays in >200 different group A Streptococcus protein pools. Based on the number of SRM assay observations we created a rule-based selected reaction monitoring assay-scoring model to select the most suitable assays per protein for a given cellular compartment and bacterial state. The resource described here represents an important tool for deciphering the group A Streptococcus proteome using selected reaction monitoring and we anticipate that concepts described here can be extended to other pathogens. Selected reaction monitoring mass spectrometry (SRM-MS) can quantify dynamic changes in protein expression with high sensitivity. Karlsson et al. define optimal detection parameters for 10,412 distinct group A Streptococcus pyogenes peptides, which facilitates proteome-wide SRM-MS studies in this bacterium.
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50
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Adav SS, Chao LT, Sze SK. Protein abundance in multiplexed samples (PAMUS) for quantitation of Trichoderma reesei secretome. J Proteomics 2013; 83:180-96. [DOI: 10.1016/j.jprot.2013.03.023] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2013] [Revised: 03/20/2013] [Accepted: 03/23/2013] [Indexed: 11/27/2022]
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