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Reynaud K, McGeachy AM, Noble D, Meacham ZA, Ingolia NT. Surveying the global landscape of post-transcriptional regulators. Nat Struct Mol Biol 2023; 30:740-752. [PMID: 37231154 PMCID: PMC10279529 DOI: 10.1038/s41594-023-00999-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 04/17/2023] [Indexed: 05/27/2023]
Abstract
Numerous proteins regulate gene expression by modulating mRNA translation and decay. To uncover the full scope of these post-transcriptional regulators, we conducted an unbiased survey that quantifies regulatory activity across the budding yeast proteome and delineates the protein domains responsible for these effects. Our approach couples a tethered function assay with quantitative single-cell fluorescence measurements to analyze ~50,000 protein fragments and determine their effects on a tethered mRNA. We characterize hundreds of strong regulators, which are enriched for canonical and unconventional mRNA-binding proteins. Regulatory activity typically maps outside the RNA-binding domains themselves, highlighting a modular architecture that separates mRNA targeting from post-transcriptional regulation. Activity often aligns with intrinsically disordered regions that can interact with other proteins, even in core mRNA translation and degradation factors. Our results thus reveal networks of interacting proteins that control mRNA fate and illuminate the molecular basis for post-transcriptional gene regulation.
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Affiliation(s)
- Kendra Reynaud
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
| | - Anna M McGeachy
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - David Noble
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Zuriah A Meacham
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Nicholas T Ingolia
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
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2
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Zahumenský J, Mota Fernandes C, Veselá P, Del Poeta M, Konopka JB, Malínský J. Microdomain Protein Nce102 Is a Local Sensor of Plasma Membrane Sphingolipid Balance. Microbiol Spectr 2022; 10:e0196122. [PMID: 35758748 PMCID: PMC9431316 DOI: 10.1128/spectrum.01961-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 06/06/2022] [Indexed: 01/17/2023] Open
Abstract
Sphingolipids are essential building blocks of eukaryotic membranes and important signaling molecules that are regulated tightly in response to environmental and physiological inputs. While their biosynthetic pathway has been well-described, the mechanisms that facilitate the perception of sphingolipid levels at the plasma membrane remain to be uncovered. In Saccharomyces cerevisiae, the Nce102 protein has been proposed to function as a sphingolipid sensor as it changes its plasma membrane distribution in response to sphingolipid biosynthesis inhibition. We show that Nce102 redistributes specifically in regions of increased sphingolipid demand, e.g., membranes of nascent buds. Furthermore, we report that the production of Nce102 increases following sphingolipid biosynthesis inhibition and that Nce102 is internalized when excess sphingolipid precursors are supplied. This finding suggests that the total amount of Nce102 in the plasma membrane is a measure of the current need for sphingolipids, whereas its local distribution marks sites of high sphingolipid demand. The physiological role of Nce102 in the regulation of sphingolipid synthesis is demonstrated by mass spectrometry analysis showing reduced levels of hydroxylated complex sphingolipids in response to heat stress in the nce102Δ deletion mutant. We also demonstrate that Nce102 behaves analogously in the widespread human fungal pathogen Candida albicans, suggesting a conserved principle of local sphingolipid control across species. IMPORTANCE Microorganisms are challenged constantly by their rapidly changing environment. To survive, they have developed diverse mechanisms to quickly perceive stressful situations and adapt to them appropriately. The primary site of both stress sensing and adaptation is the plasma membrane. We identified the yeast protein Nce102 as a marker of local sphingolipid levels and fluidity in the plasma membrane. Nce102 is an important structural and functional component of the membrane compartment Can1 (MCC), a plasma membrane microdomain stabilized by a large cytosolic hemitubular protein scaffold, the eisosome. The MCC/eisosomes are widely conserved among fungi and unicellular algae. To determine if Nce102 carries out similar functions in other organisms, we analyzed the human fungal pathogen Candida albicans and found that Nce102 responds to sphingolipid levels also in this organism, which has potential applications for the development of novel therapeutic approaches. The presented study represents a valuable model for how organisms regulate plasma membrane sphingolipids.
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Affiliation(s)
- Jakub Zahumenský
- Department of Functional Organization of Biomembranes, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Caroline Mota Fernandes
- Department of Microbiology and Immunology, School of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Petra Veselá
- Department of Functional Organization of Biomembranes, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Maurizio Del Poeta
- Department of Microbiology and Immunology, School of Medicine, Stony Brook University, Stony Brook, New York, USA
- Division of Infectious Diseases, School of Medicine, Stony Brook University, Stony Brook, New York, USA
- Veterans Administration Medical Center, Northport, New York, USA
| | - James B. Konopka
- Department of Microbiology and Immunology, School of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Jan Malínský
- Department of Functional Organization of Biomembranes, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Prague, Czech Republic
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3
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Schmitt K, Kraft AA, Valerius O. A Multi-Perspective Proximity View on the Dynamic Head Region of the Ribosomal 40S Subunit. Int J Mol Sci 2021; 22:ijms222111653. [PMID: 34769086 PMCID: PMC8583833 DOI: 10.3390/ijms222111653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/23/2021] [Accepted: 10/25/2021] [Indexed: 11/25/2022] Open
Abstract
A comparison of overlapping proximity captures at the head region of the ribosomal 40S subunit (hr40S) in Saccharomyces cerevisiae from four adjacent perspectives, namely Asc1/RACK1, Rps2/uS5, Rps3/uS3, and Rps20/uS10, corroborates dynamic co-localization of proteins that control activity and fate of both ribosomes and mRNA. Co-locating factors that associate with the hr40S are involved in (i) (de)ubiquitination of ribosomal proteins (Hel2, Bre5-Ubp3), (ii) clamping of inactive ribosomal subunits (Stm1), (iii) mRNA surveillance and vesicular transport (Smy2, Syh1), (iv) degradation of mRNA (endo- and exonucleases Ypl199c and Xrn1, respectively), (v) autophagy (Psp2, Vps30, Ykt6), and (vi) kinase signaling (Ste20). Additionally, they must be harmonized with translation initiation factors (eIF3, cap-binding protein Cdc33, eIF2A) and mRNA-binding/ribosome-charging proteins (Scp160, Sro9). The Rps/uS-BioID perspectives revealed substantial Asc1/RACK1-dependent hr40S configuration indicating a function of the β-propeller in context-specific spatial organization of this microenvironment. Toward resolving context-specific constellations, a Split-TurboID analysis emphasized the ubiquitin-associated factors Def1 and Lsm12 as neighbors of Bre5 at hr40S. These shuttling proteins indicate a common regulatory axis for the fate of polymerizing machineries for the biosynthesis of proteins in the cytoplasm and RNA/DNA in the nucleus.
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4
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Abstract
Top-down proteomics is a key mass spectrometry-based technology for comprehensive analysis of proteoforms. Proteoforms exhibit multiple high charge states and isotopic forms in full MS scans. The dissociation behavior of proteoforms in different charge states and subjected to different collision energies is highly variable. The current widely employed data-dependent acquisition (DDA) method selects a narrow m/z range (corresponding to a single proteoform charge state) for dissociation from the most abundant precursors. We describe here Mesh, a novel dissociation strategy, to dissociate multiple charge states of one proteoform with multiple collision energies. We show that the Mesh strategy has the potential to generate fragment ions with improved sequence coverage and improve identification ratios in top-down proteomic analyses of complex samples. The strategy is implemented within an open-source instrument control software program named MetaDrive to perform real time deconvolution and precursor selection.
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Affiliation(s)
- Lei Lu
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Michael R. Shortreed
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Lloyd M. Smith
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
- Corresponding Author Phone: (608) 263-2594. Fax: (608) 265-6780.
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5
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Abstract
Large-scale proteomic methods are essential for the functional characterization of proteins in their native cellular context. However, proteomics has lagged far behind genomic approaches in scalability, standardization, and cost. Here, we introduce in vivo mRNA display, a technology that converts a variety of proteomics applications into a DNA sequencing problem. In vivo-expressed proteins are coupled with their encoding messenger RNAs (mRNAs) via a high-affinity stem-loop RNA binding domain interaction, enabling high-throughput identification of proteins with high sensitivity and specificity by next generation DNA sequencing. We have generated a high-coverage in vivo mRNA display library of the Saccharomyces cerevisiae proteome and demonstrated its potential for characterizing subcellular localization and interactions of proteins expressed in their native cellular context. In vivo mRNA display libraries promise to circumvent the limitations of mass spectrometry-based proteomics and leverage the exponentially improving cost and throughput of DNA sequencing to systematically characterize native functional proteomes.
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Affiliation(s)
- Panos Oikonomou
- Department of Biological Sciences, Columbia University, New York, NY 10027;
- Department of Systems Biology, Columbia University, New York, NY 10032
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY10032
| | - Roberto Salatino
- Department of Systems Biology, Columbia University, New York, NY 10032
| | - Saeed Tavazoie
- Department of Biological Sciences, Columbia University, New York, NY 10027;
- Department of Systems Biology, Columbia University, New York, NY 10032
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY10032
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6
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van‘t Klooster JS, Bianchi F, Doorn RB, Lorenzon M, Lusseveld JH, Punter CM, Poolman B. Extracellular loops matter - subcellular location and function of the lysine transporter Lyp1 from Saccharomyces cerevisiae. FEBS J 2020; 287:4401-4414. [PMID: 32096906 PMCID: PMC7687128 DOI: 10.1111/febs.15262] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/05/2020] [Accepted: 02/24/2020] [Indexed: 12/01/2022]
Abstract
Yeast amino acid transporters of the APC superfamily are responsible for the proton motive force-driven uptake of amino acids into the cell, which for most secondary transporters is a reversible process. The l-lysine proton symporter Lyp1 of Saccharomyces cerevisiae is special in that the Michaelis constant from out-to-in transport ( K m out → in ) is much lower than K m in → out , which allows accumulation of l-lysine to submolar concentration. It has been proposed that high intracellular lysine is part of the antioxidant mechanism of the cell. The molecular basis for the unique kinetic properties of Lyp1 is unknown. We compared the sequence of Lyp1 with APC para- and orthologues and find structural features that set Lyp1 apart, including differences in extracellular loop regions. We screened the extracellular loops by alanine mutagenesis and determined Lyp1 localization and activity and find positions that affect either the localization or activity of Lyp1. Half of the affected mutants are located in the extension of extracellular loop 3 or in a predicted α-helix in extracellular loop 4. Our data indicate that extracellular loops not only connect the transmembrane helices but also serve functionally important roles.
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Affiliation(s)
- Joury S. van‘t Klooster
- Department of BiochemistryGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenThe Netherlands
| | - Frans Bianchi
- Department of BiochemistryGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenThe Netherlands
| | - Ruben B. Doorn
- Department of BiochemistryGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenThe Netherlands
| | - Mirco Lorenzon
- Department of BiochemistryGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenThe Netherlands
| | - Jarnick H. Lusseveld
- Department of BiochemistryGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenThe Netherlands
| | - Christiaan M. Punter
- Department of BiochemistryGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenThe Netherlands
| | - Bert Poolman
- Department of BiochemistryGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenThe Netherlands
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7
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Herzog PL, Borghi E, Traxlmayr MW, Obinger C, Sikes HD, Peterbauer CK. Developing a cell-bound detection system for the screening of oxidase activity using the fluorescent peroxide sensor roGFP2-Orp1. Protein Eng Des Sel 2020; 33:gzaa019. [PMID: 32930800 PMCID: PMC7720637 DOI: 10.1093/protein/gzaa019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 06/02/2020] [Accepted: 07/08/2020] [Indexed: 11/14/2022] Open
Abstract
Accurate yet efficient high-throughput screenings have emerged as essential technology for enzyme engineering via directed evolution. Modern high-throughput screening platforms for oxidoreductases are commonly assisted by technologies such as surface display and rely on emulsification techniques to facilitate single-cell analysis via fluorescence-activated cell sorting. Empowered by the dramatically increased throughput, the screening of significantly larger sequence spaces in acceptable time frames is achieved but usually comes at the cost of restricted applicability. In this work, we tackle this problem by utilizing roGFP2-Orp1 as a fluorescent one-component detection system for enzymatic H2O2 formation. We determined the kinetic parameters of the roGFP2-Orp1 reaction with H2O2 and established an efficient immobilization technique for the sensor on Saccharomyces cerevisiae cells employing the lectin Concanavalin A. This allowed to realize a peroxide-sensing shell on enzyme-displaying cells, a system that was successfully employed to screen for H2O2 formation of enzyme variants in a whole-cell setting.
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Affiliation(s)
- P L Herzog
- Food Biotechnology Laboratory, Department of Food Science and Technology, BOKU – University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria
| | - E Borghi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 287, 41124 Modena, Italy
| | - M W Traxlmayr
- Institute of Biochemistry, Department of Chemistry, BOKU – University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - C Obinger
- Institute of Biochemistry, Department of Chemistry, BOKU – University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - H D Sikes
- Department of Chemical Engineering, MIT – Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge 02139, MA, USA
| | - C K Peterbauer
- Food Biotechnology Laboratory, Department of Food Science and Technology, BOKU – University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria
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8
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Abstract
The unbiased selection of peptide precursors makes data-independent acquisition (DIA) an advantageous alternative to data-dependent acquisition (DDA) for discovery proteomics, but traditional multiplexed quantification approaches employing mass difference labeling or isobaric tagging are incompatible with DIA. Here, we describe a strategy that permits multiplexed quantification by DIA using mass defect-based N,N-dimethyl leucine (mdDiLeu) tags and high-resolution tandem mass spectrometry (MS2) analysis. Millidalton mass differences between mdDiLeu isotopologues produce fragment ion multiplet peaks separated in mass by as little as 5.8 mDa, enabling up to 4-plex quantification in DIA MS2 spectra. Quantitative analysis of yeast samples displayed comparable accuracy and precision for MS2-based DIA and MS1-based DDA methods. Multiplexed DIA analysis of cerebrospinal fluid revealed the dynamic proteome changes in Alzheimer's disease, demonstrating its utility for discovery of potential clinical biomarkers. We show that the mdDiLeu tagging approach for multiplexed DIA is a viable methodology for investigating proteome changes, particularly for low-abundance proteins, in different biological matrices.
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Affiliation(s)
- Xiaofang Zhong
- School of Pharmacy, University of Wisconsin–Madison, Madison, WI 53705, USA
| | - Dustin C. Frost
- School of Pharmacy, University of Wisconsin–Madison, Madison, WI 53705, USA
| | - Qinying Yu
- School of Pharmacy, University of Wisconsin–Madison, Madison, WI 53705, USA
| | - Miyang Li
- Department of Chemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Ting-Jia Gu
- School of Pharmacy, University of Wisconsin–Madison, Madison, WI 53705, USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin–Madison, Madison, WI 53705, USA
- Department of Chemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
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9
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Abstract
Transcript levels powerfully influence cell behavior and phenotype and are carefully regulated at several steps. Recently developed single cell approaches such as RNA single molecule fluorescence in-situ hybridization (smFISH) have produced advances in our understanding of how these steps work within the cell. In comparison to single-cell sequencing, smFISH provides more accurate quantification of RNA levels. Additionally, transcript subcellular localization is directly visualized, enabling the analysis of transcription (initiation and elongation), RNA export and degradation. As part of our efforts to investigate how this type of analysis can generate improved models of gene expression, we used smFISH to quantify the kinetic expression of STL1 and CTT1 mRNAs in single Saccharomyces cerevisiae cells upon 0.2 and 0.4 M NaCl osmotic stress. In this Data Descriptor, we outline our procedure along with our data in the form of raw images and processed mRNA counts. We discuss how these data can be used to develop single cell modelling approaches, to study fundamental processes in transcription regulation and develop single cell image processing approaches.
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Affiliation(s)
- Guoliang Li
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN, 37232, USA
| | - Gregor Neuert
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN, 37232, USA.
- Department of Biomedical Engineering, School of Engineering, Vanderbilt University, Nashville, TN, 37232, USA.
- Department of Pharmacology, School of Medicine, Vanderbilt University, Nashville, TN, 37232, USA.
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10
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Guo W, Kumar S, Görlitz F, Garcia E, Alexandrov Y, Munro I, Kelly DJ, Warren S, Thorpe P, Dunsby C, French P. Automated Fluorescence Lifetime Imaging High-Content Analysis of Förster Resonance Energy Transfer between Endogenously Labeled Kinetochore Proteins in Live Budding Yeast Cells. SLAS Technol 2019; 24:308-320. [PMID: 30629461 PMCID: PMC6537140 DOI: 10.1177/2472630318819240] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 11/16/2018] [Accepted: 11/23/2018] [Indexed: 11/23/2022]
Abstract
We describe an open-source automated multiwell plate fluorescence lifetime imaging (FLIM) methodology to read out Förster resonance energy transfer (FRET) between fluorescent proteins (FPs) labeling endogenous kinetochore proteins (KPs) in live budding yeast cells. The low copy number of many KPs and their small spatial extent present significant challenges for the quantification of donor fluorescence lifetime in the presence of significant cellular autofluorescence and photobleaching. Automated FLIM data acquisition was controlled by µManager and incorporated wide-field time-gated imaging with optical sectioning to reduce background fluorescence. For data analysis, we used custom MATLAB-based software tools to perform kinetochore foci segmentation and local cellular background subtraction and fitted the fluorescence lifetime data using the open-source FLIMfit software. We validated the methodology using endogenous KPs labeled with mTurquoise2 FP and/or yellow FP and measured the donor fluorescence lifetimes for foci comprising 32 kinetochores with KP copy numbers as low as ~2 per kinetochore under an average labeling efficiency of 50%. We observed changes of median donor lifetime ≥250 ps for KPs known to form dimers. Thus, this FLIM high-content analysis platform enables the screening of relatively low-copy-number endogenous protein-protein interactions at spatially confined macromolecular complexes.
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Affiliation(s)
- Wenjun Guo
- Photonics Group, Department of Physics,
Imperial College London, London, UK
- Francis Crick Institute, London,
UK
| | - Sunil Kumar
- Photonics Group, Department of Physics,
Imperial College London, London, UK
- Francis Crick Institute, London,
UK
| | - Frederik Görlitz
- Photonics Group, Department of Physics,
Imperial College London, London, UK
| | - Edwin Garcia
- Photonics Group, Department of Physics,
Imperial College London, London, UK
| | - Yuriy Alexandrov
- Photonics Group, Department of Physics,
Imperial College London, London, UK
- Francis Crick Institute, London,
UK
| | - Ian Munro
- Photonics Group, Department of Physics,
Imperial College London, London, UK
| | - Douglas J. Kelly
- Photonics Group, Department of Physics,
Imperial College London, London, UK
- RIKEN Center for Biodynamic Systems
Research, Kobe, Japan
| | - Sean Warren
- Garvan Institute of Medical Research,
University of New South Wales, Sydney, New South Wales, Australia
| | - Peter Thorpe
- Francis Crick Institute, London,
UK
- Queen Mary University of London, London,
UK
| | - Christopher Dunsby
- Photonics Group, Department of Physics,
Imperial College London, London, UK
- Francis Crick Institute, London,
UK
- Centre for Pathology, Imperial College
London, London, UK
| | - Paul French
- Photonics Group, Department of Physics,
Imperial College London, London, UK
- Francis Crick Institute, London,
UK
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11
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Datki Z, Olah Z, Macsai L, Pakaski M, Galik B, Mihaly G, Kalman J. Application of BisANS fluorescent dye for developing a novel protein assay. PLoS One 2019; 14:e0215863. [PMID: 31002721 PMCID: PMC6474611 DOI: 10.1371/journal.pone.0215863] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 04/09/2019] [Indexed: 11/23/2022] Open
Abstract
In many biology- and chemistry-related research fields and experiments the quantification of the peptide and/or protein concentration in samples are essential. Every research environment has unique requirements, e.g. metal ions, incubation times, photostability, pH, protease inhibitors, chelators, detergents, etc. A new protein assay may be adequate in different experiments beyond or instead of the well-known standard protocols (e.g. Qubit, Bradford or bicinchoninic acid) in related conceptions. Based on our previous studies, we developed a novel protein assay applying the 4,4′-Dianilino-1,1′-binaphthyl-5,5′-disulfonic acid dipotassium salt (BisANS) fluorescent dye. This molecule has several advantageous properties related to protein detection: good solubility in water, high photostability at adequate pH, quick interaction kinetics (within seconds) with proteins and no exclusionary sensitivity to the chelator, detergent and inhibitor ingredients. The protocol described in this work is highly sensitive in a large spectrum to detect protein (100-fold diluted samples) concentrations (from 0.28 up to more than 100 μg/mL). The BisANS protein assay is valid and applicable for quantification of the amount of protein in different biological and/or chemical samples.
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Affiliation(s)
- Zsolt Datki
- Department of Psychiatry, Faculty of Medicine, University of Szeged, Szeged, Hungary
- * E-mail: ,
| | - Zita Olah
- Department of Psychiatry, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Lilla Macsai
- Department of Psychiatry, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Magdolna Pakaski
- Department of Psychiatry, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Bence Galik
- Department of Clinical Molecular Biology, Medical University of Bialystok, Bialystok, Poland
| | - Gabor Mihaly
- Department of Psychiatry, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Janos Kalman
- Department of Psychiatry, Faculty of Medicine, University of Szeged, Szeged, Hungary
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12
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Nightingale DJ, Geladaki A, Breckels LM, Oliver SG, Lilley KS. The subcellular organisation of Saccharomyces cerevisiae. Curr Opin Chem Biol 2019; 48:86-95. [PMID: 30503867 PMCID: PMC6391909 DOI: 10.1016/j.cbpa.2018.10.026] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 10/29/2018] [Accepted: 10/31/2018] [Indexed: 01/06/2023]
Abstract
Subcellular protein localisation is essential for the mechanisms that govern cellular homeostasis. The ability to understand processes leading to this phenomenon will therefore enhance our understanding of cellular function. Here we review recent developments in this field with regard to mass spectrometry, fluorescence microscopy and computational prediction methods. We highlight relative strengths and limitations of current methodologies focussing particularly on studies in the yeast Saccharomyces cerevisiae. We further present the first cell-wide spatial proteome map of S. cerevisiae, generated using hyperLOPIT, a mass spectrometry-based protein correlation profiling technique. We compare protein subcellular localisation assignments from this map, with two published fluorescence microscopy studies and show that confidence in localisation assignment is attained using multiple orthogonal methods that provide complementary data.
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Affiliation(s)
- Daniel Jh Nightingale
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, United Kingdom; Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Aikaterini Geladaki
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, United Kingdom; Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, United Kingdom; Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, United Kingdom
| | - Lisa M Breckels
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, United Kingdom; Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Stephen G Oliver
- Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, United Kingdom; Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, United Kingdom.
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13
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Crickard JB, Kwon Y, Sung P, Greene EC. Dynamic interactions of the homologous pairing 2 (Hop2)-meiotic nuclear divisions 1 (Mnd1) protein complex with meiotic presynaptic filaments in budding yeast. J Biol Chem 2019; 294:490-501. [PMID: 30420424 PMCID: PMC6333877 DOI: 10.1074/jbc.ra118.006146] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 11/02/2018] [Indexed: 12/19/2022] Open
Abstract
Homologous recombination (HR) is a universally conserved DNA repair pathway that can result in the exchange of genetic material. In eukaryotes, HR has evolved into an essential step in meiosis. During meiosis many eukaryotes utilize a two-recombinase pathway. This system consists of Rad51 and the meiosis-specific recombinase Dmc1. Both recombinases have distinct activities during meiotic HR, despite being highly similar in sequence and having closely related biochemical activities, raising the question of how these two proteins can perform separate functions. A likely explanation for their differential regulation involves the meiosis-specific recombination proteins Hop2 and Mnd1, which are part of a highly conserved eukaryotic protein complex that participates in HR, albeit through poorly understood mechanisms. To better understand how Hop2-Mnd1 functions during HR, here we used DNA curtains in conjunction with single-molecule imaging to measure and quantify the binding of the Hop2-Mnd1 complex from Saccharomyces cerevisiae to recombination intermediates comprising Rad51- and Dmc1-ssDNA in real time. We found that yeast Hop2-Mnd1 bound rapidly to Dmc1-ssDNA filaments with high affinity and remained bound for ∼1.3 min before dissociating. We also observed that this binding interaction was highly specific for Dmc1 and found no evidence for an association of Hop2-Mnd1 with Rad51-ssDNA or RPA-ssDNA. Our findings provide new quantitative insights into the binding dynamics of Hop2-Mnd1 with the meiotic presynaptic complex. On the basis of these findings, we propose a model in which recombinase specificities for meiotic accessory proteins enhance separation of the recombinases' functions during meiotic HR.
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Affiliation(s)
- J Brooks Crickard
- From the Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032
| | - Youngho Kwon
- the Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, and
- the Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas 78229
| | - Patrick Sung
- the Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, and
- the Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas 78229
| | - Eric C Greene
- From the Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032,
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14
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Men D, Zhou J, Li W, Wei CH, Chen YY, Zhou K, Zheng Y, Xu K, Zhang ZP, Zhang XE. Self-Assembly of Antigen Proteins into Nanowires Greatly Enhances the Binding Affinity for High-Efficiency Target Capture. ACS Appl Mater Interfaces 2018; 10:41019-41025. [PMID: 30388367 DOI: 10.1021/acsami.8b12511] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
High-efficiency target capture is an essential prerequisite for sensitive immunoassays. However, the current available immunoassay approaches are subject to deficient binding affinities between predator-prey molecules that greatly restrict the target capture efficiency and immunoassay sensitivity. Herein, we present a new strategy through the self-assembly of antigen proteins into nanowires to enhance the binding affinity between an antigen and antibody. Through the genetic fusion of antigen proteins (e.g., HIV p24) with the yeast amyloid protein Sup35 self-assembly domain, specific antigen nanowires (Ag nanowires) were constructed and demonstrated a remarkable enhancement in binding affinity compared with that of the monomeric antigen molecule. The Ag nanowires were further combined with magnetic beads to form a 3D magnetic probe based on a seed-induced self-assembly strategy. Taking advantage of both the strong binding affinity and the rapid magnetic separation and enrichment capacity, the specific 3D magnetic probe achieved a 100-fold improvement in detection sensitivity within a significantly shorter period of 20 min over that of the conventional enzyme-linked immunosorbent assay method.
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Affiliation(s)
- Dong Men
- State Key Laboratory of Virology, Wuhan Institute of Virology , Chinese Academy of Sciences , Wuhan 430071 , PR China
| | - Juan Zhou
- State Key Laboratory of Virology, Wuhan Institute of Virology , Chinese Academy of Sciences , Wuhan 430071 , PR China
| | - Wei Li
- College of Life Sciences , Hubei University , Wuhan 430062 , China
| | - Cui-Hua Wei
- State Key Laboratory of Virology, Wuhan Institute of Virology , Chinese Academy of Sciences , Wuhan 430071 , PR China
| | | | - Kun Zhou
- State Key Laboratory of Virology, Wuhan Institute of Virology , Chinese Academy of Sciences , Wuhan 430071 , PR China
| | - Ying Zheng
- State Key Laboratory of Virology, Wuhan Institute of Virology , Chinese Academy of Sciences , Wuhan 430071 , PR China
| | - Ke Xu
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai , Chinese Academy of Sciences, University of Chinese Academy of Sciences , Shanghai 200031 , China
| | - Zhi-Ping Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology , Chinese Academy of Sciences , Wuhan 430071 , PR China
| | - Xian-En Zhang
- National Key Laboratory of Biomacromolecules, Institute of Biophysics , Chinese Academy of Sciences , Beijing 100101 , China
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15
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Razban RM, Gilson AI, Durfee N, Strobelt H, Dinkla K, Choi JM, Pfister H, Shakhnovich EI. ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms' proteomes. Bioinformatics 2018; 34:3557-3565. [PMID: 29741573 PMCID: PMC6184454 DOI: 10.1093/bioinformatics/bty370] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 03/27/2018] [Accepted: 05/03/2018] [Indexed: 01/27/2023] Open
Abstract
Motivation Protein evolution spans time scales and its effects span the length of an organism. A web app named ProteomeVis is developed to provide a comprehensive view of protein evolution in the Saccharomyces cerevisiae and Escherichia coli proteomes. ProteomeVis interactively creates protein chain graphs, where edges between nodes represent structure and sequence similarities within user-defined ranges, to study the long time scale effects of protein structure evolution. The short time scale effects of protein sequence evolution are studied by sequence evolutionary rate (ER) correlation analyses with protein properties that span from the molecular to the organismal level. Results We demonstrate the utility and versatility of ProteomeVis by investigating the distribution of edges per node in organismal protein chain universe graphs (oPCUGs) and putative ER determinants. S.cerevisiae and E.coli oPCUGs are scale-free with scaling constants of 1.79 and 1.56, respectively. Both scaling constants can be explained by a previously reported theoretical model describing protein structure evolution. Protein abundance most strongly correlates with ER among properties in ProteomeVis, with Spearman correlations of -0.49 (P-value < 10-10) and -0.46 (P-value < 10-10) for S.cerevisiae and E.coli, respectively. This result is consistent with previous reports that found protein expression to be the most important ER determinant. Availability and implementation ProteomeVis is freely accessible at http://proteomevis.chem.harvard.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Rostam M Razban
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Amy I Gilson
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Niamh Durfee
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Hendrik Strobelt
- School of Engineering & Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Kasper Dinkla
- School of Engineering & Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Jeong-Mo Choi
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Hanspeter Pfister
- School of Engineering & Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Eugene I Shakhnovich
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA, USA
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16
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Bierla K, Lobinski R, Szpunar J. Determination of Proteinaceous Selenocysteine in Selenized Yeast. Int J Mol Sci 2018; 19:E543. [PMID: 29439473 PMCID: PMC5855765 DOI: 10.3390/ijms19020543] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 01/29/2018] [Accepted: 01/31/2018] [Indexed: 11/16/2022] Open
Abstract
A method for the quantitation of proteinaceous selenocysteine (SeCys) in Se-rich yeast was developed. The method is based on the reduction of the Se-Se and S-Se bridges with dithiotretiol, derivatization with iodoacetamide (carbamidomethylation), followed by HPLC-ICP MS. The chromatographic conditions were optimized for the total recovery of the proteinaceous selenocysteine, the minimum number of peaks in the chromatogram (reduction of derivatization products of other Se-species present) and the baseline separation. A typical chromatogram of a proteolytic digest of selenized yeast protein consisted of up to five peaks (including SeMet, carbamidomethylated (CAM)-SeCys, and Se(CAM)₂) identified by retention time matching with available standards and electrospray MS. Inorganic selenium non-specifically attached to proteins and selenomethionine could be quantified (in the form of Se(CAM)₂) along with SeCys. Selenocysteine, selenomethionine, inorganic selenium, and the water soluble-metabolite fraction accounted for the totality of selenium species in Se-rich yeast.
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Affiliation(s)
- Katarzyna Bierla
- Institute of Analytical Sciences, IPREM, UMR 5254, CNRS-UPPA, Hélioparc, 2 Avenue Angot, 64053 Pau, France.
| | - Ryszard Lobinski
- Institute of Analytical Sciences, IPREM, UMR 5254, CNRS-UPPA, Hélioparc, 2 Avenue Angot, 64053 Pau, France.
| | - Joanna Szpunar
- Institute of Analytical Sciences, IPREM, UMR 5254, CNRS-UPPA, Hélioparc, 2 Avenue Angot, 64053 Pau, France.
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17
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Denis CL, Richardson R, Park S, Zhang C, Xi W, Laue TM, Wang X. Defining the protein complexome of translation termination factor eRF1: Identification of four novel eRF1-containing complexes that range from 20S to 57S in size. Proteins 2018; 86:177-191. [PMID: 29139201 PMCID: PMC5897186 DOI: 10.1002/prot.25422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 11/09/2017] [Accepted: 11/10/2017] [Indexed: 12/23/2022]
Abstract
The eukaryotic eRF1 translation termination factor plays an important role in recognizing stop codons and initiating the end to translation. However, which exact complexes contain eRF1 and at what abundance is not clear. We have used analytical ultracentrifugation with fluorescent detection system to identify the protein complexome of eRF1 in the yeast Saccharomyces cerevisiae. In addition to eRF1 presence in translating polysomes, we found that eRF1 associated with five other macromolecular complexes: 77S, 57S, 39S, 28S, and 20S in size. Generally equal abundances of each of these complexes were found. The 77S complex primarily contained the free 80S ribosome consistent with in vitro studies and did not appear to contain significant levels of the monosomal translating complex that co-migrates with the free 80S ribosome. The 57S and 39S complexes represented, respectively, free 60S and 40S ribosomal subunits bound to eRF1, associations not previously reported. The novel 28S and 20S complexes (containing minimal masses of 830 KDa and 500 KDa, respectively) lacked significant RNA components and appeared to be oligomeric, as eRF1 has a mass of 49 KDa. The majority of polysomal complexes containing eRF1 were both substantially deadenylated and lacking in closed-loop factors eIF4E and eIF4G. The thirteen percent of such translating polysomes that contained poly(A) tails had equivalent levels of eIF4E and eIF4G, suggesting these complexes were in a closed-loop structure. The identification of eRF1 in these unique and previously unrecognized complexes suggests a variety of new roles for eRF1 in the regulation of cellular processes.
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Affiliation(s)
- Clyde L. Denis
- Department of Molecular, Cellular, and Biomedical Sciences, 46 College Road, Rudman Hall, University of New Hampshire, Durham, NH 03824, 603-862-2427, FAX: 603-862-4013
| | - Roy Richardson
- Department of Molecular, Cellular, and Biomedical Sciences, 46 College Road, Rudman Hall, University of New Hampshire, Durham, NH 03824, 603-862-2427, FAX: 603-862-4013
| | - Shiwha Park
- Department of Molecular, Cellular, and Biomedical Sciences, 46 College Road, Rudman Hall, University of New Hampshire, Durham, NH 03824, 603-862-2427, FAX: 603-862-4013
| | - Chongxu Zhang
- Department of Molecular, Cellular, and Biomedical Sciences, 46 College Road, Rudman Hall, University of New Hampshire, Durham, NH 03824, 603-862-2427, FAX: 603-862-4013
| | - Wen Xi
- Department of Molecular, Cellular, and Biomedical Sciences, 46 College Road, Rudman Hall, University of New Hampshire, Durham, NH 03824, 603-862-2427, FAX: 603-862-4013
| | - Thomas M. Laue
- Department of Molecular, Cellular, and Biomedical Sciences, 46 College Road, Rudman Hall, University of New Hampshire, Durham, NH 03824, 603-862-2427, FAX: 603-862-4013
| | - Xin Wang
- Department of Molecular, Cellular, and Biomedical Sciences, 46 College Road, Rudman Hall, University of New Hampshire, Durham, NH 03824, 603-862-2427, FAX: 603-862-4013
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18
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Belov AM, Viner R, Santos MR, Horn DM, Bern M, Karger BL, Ivanov AR. Analysis of Proteins, Protein Complexes, and Organellar Proteomes Using Sheathless Capillary Zone Electrophoresis - Native Mass Spectrometry. J Am Soc Mass Spectrom 2017; 28:2614-2634. [PMID: 28875426 PMCID: PMC5709234 DOI: 10.1007/s13361-017-1781-1] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 08/09/2017] [Accepted: 08/09/2017] [Indexed: 05/04/2023]
Abstract
Native mass spectrometry (MS) is a rapidly advancing field in the analysis of proteins, protein complexes, and macromolecular species of various types. The majority of native MS experiments reported to-date has been conducted using direct infusion of purified analytes into a mass spectrometer. In this study, capillary zone electrophoresis (CZE) was coupled online to Orbitrap mass spectrometers using a commercial sheathless interface to enable high-performance separation, identification, and structural characterization of limited amounts of purified proteins and protein complexes, the latter with preserved non-covalent associations under native conditions. The performance of both bare-fused silica and polyacrylamide-coated capillaries was assessed using mixtures of protein standards known to form non-covalent protein-protein and protein-ligand complexes. High-efficiency separation of native complexes is demonstrated using both capillary types, while the polyacrylamide neutral-coated capillary showed better reproducibility and higher efficiency for more complex samples. The platform was then evaluated for the determination of monoclonal antibody aggregation and for analysis of proteomes of limited complexity using a ribosomal isolate from E. coli. Native CZE-MS, using accurate single stage and tandem-MS measurements, enabled identification of proteoforms and non-covalent complexes at femtomole levels. This study demonstrates that native CZE-MS can serve as an orthogonal and complementary technique to conventional native MS methodologies with the advantages of low sample consumption, minimal sample processing and losses, and high throughput and sensitivity. This study presents a novel platform for analysis of ribosomes and other macromolecular complexes and organelles, with the potential for discovery of novel structural features defining cellular phenotypes (e.g., specialized ribosomes). Graphical Abstract ᅟ.
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Affiliation(s)
- Arseniy M Belov
- Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, MA, 02115, USA
| | - Rosa Viner
- Thermo Fisher Scientific, San Jose, CA, 95134, USA
| | | | - David M Horn
- Thermo Fisher Scientific, San Jose, CA, 95134, USA
| | | | - Barry L Karger
- Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, MA, 02115, USA
| | - Alexander R Ivanov
- Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, MA, 02115, USA.
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19
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Belov AM, Viner R, Santos MR, Horn DM, Bern M, Karger BL, Ivanov AR. Analysis of Proteins, Protein Complexes, and Organellar Proteomes Using Sheathless Capillary Zone Electrophoresis - Native Mass Spectrometry. J Am Soc Mass Spectrom 2017; 28:2614-2634. [PMID: 28875426 DOI: 10.1007/s13361-13017-11781-13361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 08/09/2017] [Accepted: 08/09/2017] [Indexed: 05/25/2023]
Abstract
Native mass spectrometry (MS) is a rapidly advancing field in the analysis of proteins, protein complexes, and macromolecular species of various types. The majority of native MS experiments reported to-date has been conducted using direct infusion of purified analytes into a mass spectrometer. In this study, capillary zone electrophoresis (CZE) was coupled online to Orbitrap mass spectrometers using a commercial sheathless interface to enable high-performance separation, identification, and structural characterization of limited amounts of purified proteins and protein complexes, the latter with preserved non-covalent associations under native conditions. The performance of both bare-fused silica and polyacrylamide-coated capillaries was assessed using mixtures of protein standards known to form non-covalent protein-protein and protein-ligand complexes. High-efficiency separation of native complexes is demonstrated using both capillary types, while the polyacrylamide neutral-coated capillary showed better reproducibility and higher efficiency for more complex samples. The platform was then evaluated for the determination of monoclonal antibody aggregation and for analysis of proteomes of limited complexity using a ribosomal isolate from E. coli. Native CZE-MS, using accurate single stage and tandem-MS measurements, enabled identification of proteoforms and non-covalent complexes at femtomole levels. This study demonstrates that native CZE-MS can serve as an orthogonal and complementary technique to conventional native MS methodologies with the advantages of low sample consumption, minimal sample processing and losses, and high throughput and sensitivity. This study presents a novel platform for analysis of ribosomes and other macromolecular complexes and organelles, with the potential for discovery of novel structural features defining cellular phenotypes (e.g., specialized ribosomes). Graphical Abstract ᅟ.
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Affiliation(s)
- Arseniy M Belov
- Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, MA, 02115, USA
| | - Rosa Viner
- Thermo Fisher Scientific, San Jose, CA, 95134, USA
| | | | - David M Horn
- Thermo Fisher Scientific, San Jose, CA, 95134, USA
| | | | - Barry L Karger
- Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, MA, 02115, USA
| | - Alexander R Ivanov
- Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, MA, 02115, USA.
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20
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Bubis JA, Levitsky LI, Ivanov MV, Tarasova IA, Gorshkov MV. Comparative evaluation of label-free quantification methods for shotgun proteomics. Rapid Commun Mass Spectrom 2017; 31:606-612. [PMID: 28097710 DOI: 10.1002/rcm.7829] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 12/24/2016] [Accepted: 01/15/2017] [Indexed: 06/06/2023]
Abstract
RATIONALE Label-free quantification (LFQ) is a popular strategy for shotgun proteomics. A variety of LFQ algorithms have been developed recently. However, a comprehensive comparison of the most commonly used LFQ methods is still rare, in part due to a lack of clear metrics for their evaluation and an annotated and quantitatively well-characterized data set. METHODS Five LFQ methods were compared: spectral counting based algorithms SIN , emPAI, and NSAF, and approaches relying on the extracted ion chromatogram (XIC) intensities, MaxLFQ and Quanti. We used three criteria for performance evaluation: coefficient of variation (CV) of protein abundances between replicates; analysis of variance (ANOVA); and the root-mean-square error of logarithmized calculated concentration ratios, referred to as standard quantification error (SQE). Comparison was performed using a quantitatively annotated publicly available data set. RESULTS The best results in terms of inter-replicate reproducibility were observed for MaxLFQ and NSAF, although they exhibited larger standard quantification errors. Using NSAF, all quantitatively annotated proteins were correctly identified in the Bonferronni-corrected results of the ANOVA test. SIN was found to be the most accurate in terms of SQE. Finally, the current implementations of XIC-based LFQ methods did not outperform the methods based on spectral counting for the data set used in this study. CONCLUSIONS Surprisingly, the performances of XIC-based approaches measured using three independent metrics were found to be comparable with more straightforward and simple MS/MS-based spectral counting approaches. The study revealed no clear leader among the latter. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Julia A Bubis
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 119334, Moscow, Russia
- Moscow Institute of Physics and Technology (State University), 141700, Dolgoprudny, Russia
| | - Lev I Levitsky
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 119334, Moscow, Russia
- Moscow Institute of Physics and Technology (State University), 141700, Dolgoprudny, Russia
| | - Mark V Ivanov
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 119334, Moscow, Russia
- Moscow Institute of Physics and Technology (State University), 141700, Dolgoprudny, Russia
| | - Irina A Tarasova
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 119334, Moscow, Russia
| | - Mikhail V Gorshkov
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 119334, Moscow, Russia
- Moscow Institute of Physics and Technology (State University), 141700, Dolgoprudny, Russia
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21
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Queralt E, Rodriguez-Rodriguez JA. A New Methodology for the Quantification of In Vivo Cdc14 Phosphatase Activity. Methods Mol Biol 2017; 1505:89-96. [PMID: 27826859 DOI: 10.1007/978-1-4939-6502-1_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The phosphatase Cdc14 has a pivotal function in the mitotic exit of Saccharomyces cerevisiae. During interphase, Cdc14 remains inactive in the nucleolus bound to the inhibitor Net1. Cdc14 activation occurs in the metaphase to anaphase transition and it is promoted by at least two signaling pathways called FEAR (CdcFourteen Early Anaphase Release) and MEN (Mitotic Exit Network). These two pathways act in parallel and target the phosphorylation of Net1, thus decreasing Net1 affinity for Cdc14. The activity of Cdc14 can be used as a readout to assay functional interactions of different components of the mitotic exit signaling pathways.
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Affiliation(s)
- Ethel Queralt
- Cancer Epigenetics & Biology Program, IDIBELL,Hospitalet de Llobregat, Barcelona, Spain.
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22
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Caydasi AK, Pereira G. Evaluation of the Dynamicity of Mitotic Exit Network and Spindle Position Checkpoint Components on Spindle Pole Bodies by Fluorescence Recovery After Photobleaching (FRAP). Methods Mol Biol 2017; 1505:167-182. [PMID: 27826864 DOI: 10.1007/978-1-4939-6502-1_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Fluorescence recovery after photobleaching (FRAP) is a powerful technique to study in vivo binding and diffusion dynamics of fluorescently labeled proteins. In this chapter, we describe how to determine spindle pole body (SPB) binding dynamics of mitotic exit network (MEN) and spindle position checkpoint (SPOC) proteins using FRAP microscopy. Procedures presented here include the growth of the yeast cultures, sample preparation, image acquisition and analysis.
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Affiliation(s)
- Ayse Koca Caydasi
- DKFZ-ZMBH Alliance, German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 280, Heidelberg, 69120, Germany
- Centre for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 230, Heidelberg, 69120, Germany
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze/Kocaeli, 41400, Turkey
| | - Gislene Pereira
- DKFZ-ZMBH Alliance, German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 280, Heidelberg, 69120, Germany.
- Centre for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 230, Heidelberg, 69120, Germany.
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Abstract
The budding yeast Saccharomyces cerevisiae is a very powerful genetic model that has been extensively used in cell cycle studies. Despite the fact that its small size has made imaging studies challenging (haploid cells have a diameter of approximately 4-5 μm that is very close to the maximal optical microscope resolution, ca. 0.20-0.25 μm), the continual improvement of imaging tags and techniques has made it possible to visualize organelles and macromolecules also in this organism. The possibility to easily epitope-tag endogenous proteins and follow them during synchronized cell cycles has proved critical for understanding the distribution of Mitotic Exit Network (MEN) components and gathering insights into their regulation. In this chapter, we describe a detailed protocol for indirect immunofluorescence of fixed cells outlining fixation strategies, cell wall digestion, and the use of primary and secondary antibodies conjugated to fluorescent moieties. This protocol can be used to successfully localize endogenously expressed yeast proteins including MEN components.
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Affiliation(s)
- Francesca Senic-Matuglia
- Department of Experimental Oncology, European Institute of Oncology, via Adamello 16, Milan, 20139, Italy
| | - Rosella Visintin
- Department of Experimental Oncology, European Institute of Oncology, via Adamello 16, Milan, 20139, Italy.
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24
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Abstract
The budding index and the morphology of the spindle and the nucleus are excellent markers for the analysis of the progression through the different stages of the cell cycle in Saccharomyces cerevisiae. Here, we describe a protocol to evaluate the budding index in this model organism using phase contrast microscopy. We also describe an indirect immunofluorescence method designed for the visualization of microtubules and the nucleus in S. cerevisiae. Finally, we explain how both methodologies can be used in order to analyze cell cycle progression in the budding yeast.
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Affiliation(s)
- Marta Muñoz-Barrera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas (CSIC), Avda. Américo Vespucio, s/n, P.C.T. Cartuja 93, 41092, Sevilla, Spain
| | - Fernando Monje-Casas
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas (CSIC), Avda. Américo Vespucio, s/n, P.C.T. Cartuja 93, 41092, Sevilla, Spain.
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25
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Landgraf D, Huh D, Hallacli E, Lindquist S. Scarless Gene Tagging with One-Step Transformation and Two-Step Selection in Saccharomyces cerevisiae and Schizosaccharomyces pombe. PLoS One 2016; 11:e0163950. [PMID: 27736907 PMCID: PMC5063382 DOI: 10.1371/journal.pone.0163950] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 09/16/2016] [Indexed: 11/24/2022] Open
Abstract
Gene tagging with fluorescent proteins is commonly applied to investigate the localization and dynamics of proteins in their cellular environment. Ideally, a fluorescent tag is genetically inserted at the endogenous locus at the N- or C- terminus of the gene of interest without disrupting regulatory sequences including the 5’ and 3’ untranslated region (UTR) and without introducing any extraneous unwanted “scar” sequences, which may create unpredictable transcriptional or translational effects. We present a reliable, low-cost, and highly efficient method for the construction of such scarless C-terminal and N-terminal fusions with fluorescent proteins in yeast. The method relies on sequential positive and negative selection and uses an integration cassette with long flanking regions, which is assembled by two-step PCR, to increase the homologous recombination frequency. The method also enables scarless tagging of essential genes with no need for a complementing plasmid. To further ease high-throughput strain construction, we have computationally automated design of the primers, applied the primer design code to all open reading frames (ORFs) of the budding yeast Saccharomyces cerevisiae (S. cerevisiae) and the fission yeast Schizosaccharomyces pombe (S. pombe), and provide here the computed sequences. To illustrate the scarless N- and C-terminal gene tagging methods in S. cerevisiae, we tagged various genes including the E3 ubiquitin ligase RSP5, the proteasome subunit PRE1, and the eleven Rab GTPases with yeast codon-optimized mNeonGreen or mCherry; several of these represent essential genes. We also implemented the scarless C-terminal gene tagging method in the distantly related organism S. pombe using kanMX6 and HSV1tk as positive and negative selection markers, respectively, as well as ura4. The scarless gene tagging methods presented here are widely applicable to visualize and investigate the functional roles of proteins in living cells.
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Affiliation(s)
- Dirk Landgraf
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Dann Huh
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Erinc Hallacli
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
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26
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Säll A, Persson H, Ohlin M, Borrebaeck CAK, Wingren C. Advancing the global proteome survey platform by using an oriented single chain antibody fragment immobilization approach. N Biotechnol 2016; 33:503-13. [PMID: 26703809 DOI: 10.1016/j.nbt.2015.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 11/27/2015] [Accepted: 12/03/2015] [Indexed: 11/17/2022]
Abstract
Increasing the understanding of a proteome and how its protein composition is affected by for example different diseases, such as cancer, has the potential to improve strategies for early diagnosis and therapeutics. The Global Proteome Survey or GPS is a method that combines mass spectrometry and affinity enrichment with the use of antibodies. The technology enables profiling of complex proteomes in a species independent manner. The sensitivity of GPS, and other methods relying on affinity enrichment, is largely affected by the activity of the exploited affinity reagent. We here present an improvement of the GPS platform by utilizing an antibody immobilization approach which ensures a controlled immobilization process of the antibody to the magnetic bead support. More specifically, we make use of an antibody format that enables site-directed biotinylation and use this in combination with streptavidin coated magnetic beads. The performance of the expanded GPS platform was evaluated by profiling yeast proteome samples. We demonstrate that the oriented antibody immobilization strategy increases the ability of the GPS platform and results in larger fraction of functional antibodies. Additionally, we show that this new antibody format enabled in-solution capture, i.e. immobilization of the antibodies after sample incubation. A workflow has been established that permit the use of an oriented immobilization strategy for the GPS platform.
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Affiliation(s)
- Anna Säll
- Department of Immunotechnology, Lund University, Medicon Village (House 406), SE-223 81 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, Stockholm, Sweden
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, Medicon Village (House 406), SE-223 81 Lund, Sweden
| | - Carl A K Borrebaeck
- Department of Immunotechnology, Lund University, Medicon Village (House 406), SE-223 81 Lund, Sweden.
| | - Christer Wingren
- Department of Immunotechnology, Lund University, Medicon Village (House 406), SE-223 81 Lund, Sweden.
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27
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Zheng S, Bai X, Tian S, Wang G, Zhai G, Guo Z, Bi W, Shen L, Zhang K. Identification of hydroxylation at aromatic amino acid residues in yeast kinase using mass spectrometry with affinity enrichment. Rapid Commun Mass Spectrom 2016; 30 Suppl 1:185-189. [PMID: 27539436 DOI: 10.1002/rcm.7644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
RATIONALE Protein kinases represent the key elements in phosphorylation-based signal transmission. Recent studies suggest that hydroxylation may mediate activities of protein kinases. This paper aims to examine the hydroxylation in protein kinases for improving our understanding of the protein modification. METHODS We combined affinity-based protein purification with MS analysis for identification of novel hydroxylation at aromatic amino acid residues in yeast kinases. RESULTS We identified 17 hydroxylation at aromatic amino acid residues (10 at Phe, 1 at Tyr and 6 at Trp) using MS analysis. We further characterized the localization and studied the potential significance of these modifications. CONCLUSIONS This is a new report on the identification of hydroxylation at aromatic amino acid residues in yeast kinases. This study expands the catalog of hydroxylation in kinases and suggests the potential function of hydroxylation. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Shuzhen Zheng
- Department of Chemistry, Nankai University, Tianjin, 300071, China
| | - Xue Bai
- Department of Chemistry, Nankai University, Tianjin, 300071, China
| | - Shanshan Tian
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin, 300070, China
| | - Guojuan Wang
- Department of Chemistry, Nankai University, Tianjin, 300071, China
| | - Guijin Zhai
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin, 300070, China
| | - Zhenchang Guo
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin, 300070, China
| | - Wenjing Bi
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin, 300070, China
| | - Lijin Shen
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin, 300070, China
| | - Kai Zhang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin, 300070, China
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Paulo JA, O'Connell JD, Everley RA, O'Brien J, Gygi MA, Gygi SP. Quantitative mass spectrometry-based multiplexing compares the abundance of 5000 S. cerevisiae proteins across 10 carbon sources. J Proteomics 2016; 148:85-93. [PMID: 27432472 DOI: 10.1016/j.jprot.2016.07.005] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 06/26/2016] [Accepted: 07/07/2016] [Indexed: 12/18/2022]
Abstract
UNLABELLED The budding yeast Saccharomyces cerevisiae is a model system for investigating biological processes. Cellular events are known to be dysregulated due to shifts in carbon sources. However, the comprehensive proteomic alterations thereof have not been fully investigated. Here we examined proteomic alterations in S. cerevisiae due to the adaptation of yeast from glucose to nine different carbon sources - maltose, trehalose, fructose, sucrose, glycerol, acetate, pyruvate, lactic acid, and oleate. Isobaric tag-based mass spectrometry techniques are at the forefront of global proteomic investigations. As such, we used a TMT10-plex strategy to study multiple growth conditions in a single experiment. The SPS-MS3 method on an Orbitrap Fusion Lumos mass spectrometer enabled the quantification of over 5000 yeast proteins across ten carbon sources at a 1% protein-level FDR. On average, the proteomes of yeast cultured in fructose and sucrose deviated the least from those cultured in glucose. As expected, gene ontology classification revealed the major alteration in protein abundances occurred in metabolic pathways and mitochondrial proteins. Our protocol lays the groundwork for further investigation of carbon source-induced protein alterations. Additionally, these data offer a hypothesis-generating resource for future studies aiming to investigate both characterized and uncharacterized genes. BIOLOGICAL SIGNIFICANCE We investigate the proteomic alterations in S. cerevisiae resulting from adaptation of yeast from glucose to nine different carbon sources - maltose, trehalose, fructose, sucrose, glycerol, acetate, pyruvate, lactic acid, and oleate. SPS-MS3 TMT10plex analysis is used for quantitative proteomic analysis. We showcase a technique that allows the quantification of over 5000 yeast proteins, the highest number to date in S. cerevisiae, across 10 growth conditions in a single experiment. As expected, gene ontology classification of proteins with the major alterations in abundances occurred in metabolic pathways and mitochondrial proteins, reflecting the degree of metabolic stress when cellular machinery shifts from growth on glucose to an alternative carbon source. Our protocol lays the groundwork for further investigation of carbon source-induced protein alterations. Improving depth of coverage - measuring abundance changes of over 5000 proteins - increases our understanding of difficult-to-study genes in the model system S. cerevisiae and by homology human cell biology. We submit this highly comprehensive dataset as a hypothesis generating resource for targeted studies on uncharacterized genes.
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Affiliation(s)
- Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, United States.
| | - Jeremy D O'Connell
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, United States
| | - Robert A Everley
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, United States
| | - Jonathon O'Brien
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, United States
| | - Micah A Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, United States
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, United States.
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29
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Jensen MS, Costa SR, Theorin L, Christensen JP, Pomorski TG, López-Marqués RL. Application of image cytometry to characterize heterologous lipid flippases in yeast. Cytometry A 2016; 89:673-80. [PMID: 27272389 DOI: 10.1002/cyto.a.22886] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Lipid flippases are integral membrane proteins that play a central role in moving lipids across cellular membranes. Some of these transporters are ATPases that couple lipid translocation to ATP hydrolysis, whereas others function without any discernible metabolic energy input. A growing number of lipid flippases has been identified but key features of their activity remain to be elucidated. A well-established method to characterize ATP-driven flippases is based on their heterologous expression in yeast, followed by incubation of the cells with fluorescent lipids. Internalization of these probes is typically monitored by flow cytometry, a costly and maintenance-intensive method. Here, we have optimized a protocol to use an automated image-based cell counter to accurately measure lipid uptake by heterologous lipid flippases expressed in yeast. The method was validated by comparison with the classical flow cytometric evaluation of lipid-labeled cells. In addition, we demonstrated that expression of fluorescently tagged flippase complexes can be directly co-related with fluorescent lipid uptake using the image-based cell counter system. The method extends the number of techniques available for characterization of lipid flippase activity, and should be readily adaptable to analyze a variety of other transport systems in yeast, parasites, and mammalian cells. © 2016 International Society for Advancement of Cytometry.
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Affiliation(s)
- Maria S Jensen
- Centre for Membrane Pumps in Cells and Disease - PUMPKIN, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Sara R Costa
- Centre for Membrane Pumps in Cells and Disease - PUMPKIN, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Lisa Theorin
- Centre for Membrane Pumps in Cells and Disease - PUMPKIN, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | | | - Thomas Günther Pomorski
- Centre for Membrane Pumps in Cells and Disease - PUMPKIN, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
- Faculty of Chemistry and Biochemistry, Department of Molecular Biochemistry, Ruhr University Bochum, Universitätstrasse 150, Bochum, D-44780, Germany
| | - Rosa L López-Marqués
- Centre for Membrane Pumps in Cells and Disease - PUMPKIN, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
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30
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Yuan SM, Nie WC, He F, Jia ZW, Gao XD. Kin2, the Budding Yeast Ortholog of Animal MARK/PAR-1 Kinases, Localizes to the Sites of Polarized Growth and May Regulate Septin Organization and the Cell Wall. PLoS One 2016; 11:e0153992. [PMID: 27096577 PMCID: PMC4838231 DOI: 10.1371/journal.pone.0153992] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 04/06/2016] [Indexed: 11/18/2022] Open
Abstract
MARK/PAR-1 protein kinases play important roles in cell polarization in animals. Kin1 and Kin2 are a pair of MARK/PAR-1 orthologs in the budding yeast Saccharomyces cerevisiae. They participate in the regulation of secretion and ER stress response. However, neither the subcellular localization of these two kinases nor whether they may have other cellular functions is clear. Here, we show that Kin2 localizes to the sites of polarized growth in addition to localization on the plasma membrane. The localization to polarity sites is mediated by two targeting domains-TD1 and TD2. TD1 locates in the N-terminal region that spans the protein kinase domain whereas TD2 locates in the C-terminal end that covers the KA1 domain. We also show that an excess of Kin2 activity impaired growth, septin organization, and chitin deposition in the cell wall. Both TD1 and TD2 contribute to this function. Moreover, we find that the C-terminal region of Kin2 interacts with Cdc11, a septin subunit, and Pea2, a component of the polarisome that is known to play a role in septin organization. These findings suggest that Kin2 may play a role in the regulation of the septin cytoskeleton and the cell wall. Finally, we show that the C-terminal region of Kin2 interacts with Rho3, a Rho GTPase, whereas the N-terminal region of Kin2 interacts with Bmh1, a 14-3-3 protein. We speculate that Kin2 may be regulated by Bmh1, Rho3, or Pea2 in vivo. Our study provides new insight in the localization, function, and regulation of Kin2.
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Affiliation(s)
- Si-Min Yuan
- Department of Microbiology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Wen-Chao Nie
- Department of Microbiology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Fei He
- Department of Microbiology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhi-Wen Jia
- Department of Microbiology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiang-Dong Gao
- Department of Microbiology, College of Life Sciences, Wuhan University, Wuhan, China
- Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Wuhan, China
- * E-mail:
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31
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Abstract
Prions, infectious proteins, can transmit diseases or be the basis of heritable traits (or both), mostly based on amyloid forms of the prion protein. A single protein sequence can be the basis for many prion strains/variants, with different biological properties based on different amyloid conformations, each rather stably propagating. Prions are unique in that evolution and selection work at both the level of the chromosomal gene encoding the protein, and on the prion itself selecting prion variants. Here, we summarize what is known about the evolution of prion proteins, both the genes and the prions themselves. We contrast the one known functional prion, [Het-s] of Podospora anserina, with the known disease prions, the yeast prions [PSI+] and [URE3] and the transmissible spongiform encephalopathies of mammals.
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Affiliation(s)
- Reed B Wickner
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes Digestive and Kidney Diseases, National Institutes of Health, Bldg. 8, Room 225, 8 Center Drive MSC 0830, Bethesda, MD, 20892-0830, USA.
| | - Amy C Kelly
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes Digestive and Kidney Diseases, National Institutes of Health, Bldg. 8, Room 225, 8 Center Drive MSC 0830, Bethesda, MD, 20892-0830, USA.
- NCAUR, Agricultural Research Service, U.S. Department of Agriculture, 1815 N. University St., Peoria, IL, 61604, USA.
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32
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Pérez-Magariño S, Martínez-Lapuente L, Bueno-Herrera M, Ortega-Heras M, Guadalupe Z, Ayestarán B. Use of Commercial Dry Yeast Products Rich in Mannoproteins for White and Rosé Sparkling Wine Elaboration. J Agric Food Chem 2015; 63:5670-5681. [PMID: 26027899 DOI: 10.1021/acs.jafc.5b01336] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In sparkling wines, mannoproteins released during yeast autolysis largely affect their final quality. This process is very slow and may take several months. The aim of this work was to study the effect of several commercial dry yeast autolysates on the chemical composition, foam, and sensory properties of white and rosé sparkling wines aged on lees for 9 months during two consecutive vintages. The addition of these products in the tirage phase did not affect either the content of phenolic compounds, amino acids, and biogenic amines or the foam properties. The commercial product with the highest mannoprotein content and the highest purity caused significant changes in the volatile composition of the wines and enhanced the fruity aromas in both Verdejo and Godello sparkling wines.
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Affiliation(s)
- Silvia Pérez-Magariño
- †Instituto Tecnológico Agrario de Castilla y León, Consejerı́a de Agricultura y Ganaderı́a, Ctra Burgos Km 119, Finca Zamadueñas, 47071 Valladolid, Spain
| | - Leticia Martínez-Lapuente
- §Instituto de las Ciencias de la Vid y del Vino (Universidad de la Rioja, CSIC y Gobierno de la Rioja), C/Madre de Dios 51, 26006 Logroño, Spain
| | - Marta Bueno-Herrera
- †Instituto Tecnológico Agrario de Castilla y León, Consejerı́a de Agricultura y Ganaderı́a, Ctra Burgos Km 119, Finca Zamadueñas, 47071 Valladolid, Spain
| | - Miriam Ortega-Heras
- †Instituto Tecnológico Agrario de Castilla y León, Consejerı́a de Agricultura y Ganaderı́a, Ctra Burgos Km 119, Finca Zamadueñas, 47071 Valladolid, Spain
| | - Zenaida Guadalupe
- §Instituto de las Ciencias de la Vid y del Vino (Universidad de la Rioja, CSIC y Gobierno de la Rioja), C/Madre de Dios 51, 26006 Logroño, Spain
| | - Belén Ayestarán
- §Instituto de las Ciencias de la Vid y del Vino (Universidad de la Rioja, CSIC y Gobierno de la Rioja), C/Madre de Dios 51, 26006 Logroño, Spain
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33
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Campos A, Díaz R, Martínez-Bartolomé S, Sierra J, Gallardo O, Sabidó E, López-Lucendo M, Ignacio Casal J, Pasquarello C, Scherl A, Chiva C, Borras E, Odena A, Elortza F, Azkargorta M, Ibarrola N, Canals F, Albar JP, Oliveira E. Multicenter experiment for quality control of peptide-centric LC-MS/MS analysis - A longitudinal performance assessment with nLC coupled to orbitrap MS analyzers. J Proteomics 2015; 127:264-74. [PMID: 25982386 DOI: 10.1016/j.jprot.2015.05.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 05/07/2015] [Accepted: 05/11/2015] [Indexed: 11/19/2022]
Abstract
Proteomic technologies based on mass spectrometry (MS) have greatly evolved in the past years, and nowadays it is possible to routinely identify thousands of peptides from complex biological samples in a single LC-MS/MS experiment. Despite the advancements in proteomic technologies, the scientific community still faces important challenges in terms of depth and reproducibility of proteomics analyses. Here, we present a multicenter study designed to evaluate long-term performance of LC-MS/MS platforms within the Spanish Proteomics Facilities Network (ProteoRed-ISCIII). The study was performed under well-established standard operating procedures, and demonstrated that it is possible to attain qualitative and quantitative reproducibility over time. Our study highlights the importance of deploying quality assessment metrics routinely in individual laboratories and in multi-laboratory studies. The mass spectrometry data have been deposited to the ProteomeXchange Consortium with the data set identifier PXD000205.This article is part of a Special Issue entitled: HUPO 2014.
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Affiliation(s)
- Alex Campos
- ProteoRed-ISCIII, Proteomics Platform, Barcelona Science Park, Barcelona, Spain; Integromics, Madrid, Spain.
| | - Ramón Díaz
- ProteoRed-ISCIII, Proteomics Platform, Barcelona Science Park, Barcelona, Spain
| | | | | | - Oscar Gallardo
- ProteoRed-ISCIII, CSIC/UAB Proteomics Laboratory, Instituto de Investigaciones Biomédicas de Barcelona, Spanish National Research Council, Barcelona, Spain
| | - Eduard Sabidó
- ProteoRed-ISCIII, Proteomics Unit, Universitat Pompeu Fabra (UPF) and Centre de Regulació Genòmica (CRG), Barcelona, Spain
| | - Maria López-Lucendo
- ProteoRed-ISCIII, Proteomics Facility and Functional Proteomics Laboratory, Centro de Investigaciones, Biológicas, Madrid, Spain
| | - J Ignacio Casal
- ProteoRed-ISCIII, Proteomics Facility and Functional Proteomics Laboratory, Centro de Investigaciones, Biológicas, Madrid, Spain
| | | | - Alexander Scherl
- Department of Human Protein Sciences, CMU, University of Geneva, Switzerland
| | - Cristina Chiva
- ProteoRed-ISCIII, Proteomics Unit, Universitat Pompeu Fabra (UPF) and Centre de Regulació Genòmica (CRG), Barcelona, Spain
| | - Eva Borras
- ProteoRed-ISCIII, Proteomics Unit, Universitat Pompeu Fabra (UPF) and Centre de Regulació Genòmica (CRG), Barcelona, Spain
| | - Antonia Odena
- ProteoRed-ISCIII, Proteomics Platform, Barcelona Science Park, Barcelona, Spain
| | - Félix Elortza
- ProteoRed-ISCIII, Proteomics Platform, CIC bioGUNE, CIBERehd, Technology Park of Bizkaia, Derio, Spain
| | - Mikel Azkargorta
- ProteoRed-ISCIII, Proteomics Platform, CIC bioGUNE, CIBERehd, Technology Park of Bizkaia, Derio, Spain
| | - Nieves Ibarrola
- ProteoRed-ISCIII, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Salamanca, Spain
| | - Francesc Canals
- ProteoRed-ISCIII, Proteomic Laboratory, Vall d'Hebron Institute of Oncology-VHIO, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Juan P Albar
- ProteoRed-ISCIII, Proteomics Facility, Centro Nacional de Biotecnología - CSIC, Madrid, Spain
| | - Eliandre Oliveira
- ProteoRed-ISCIII, Proteomics Platform, Barcelona Science Park, Barcelona, Spain
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34
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Bohnert M, Zerbes RM, Davies KM, Mühleip AW, Rampelt H, Horvath SE, Boenke T, Kram A, Perschil I, Veenhuis M, Kühlbrandt W, van der Klei IJ, Pfanner N, van der Laan M. Central role of Mic10 in the mitochondrial contact site and cristae organizing system. Cell Metab 2015; 21:747-55. [PMID: 25955210 DOI: 10.1016/j.cmet.2015.04.007] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 03/09/2015] [Accepted: 04/01/2015] [Indexed: 11/19/2022]
Abstract
The mitochondrial contact site and cristae organizing system (MICOS) is a conserved multi-subunit complex crucial for maintaining the characteristic architecture of mitochondria. Studies with deletion mutants identified Mic10 and Mic60 as core subunits of MICOS. Mic60 has been studied in detail; however, topogenesis and function of Mic10 are unknown. We report that targeting of Mic10 to the mitochondrial inner membrane requires a positively charged internal loop, but no cleavable presequence. Both transmembrane segments of Mic10 carry a characteristic four-glycine motif, which has been found in the ring-forming rotor subunit of F1Fo-ATP synthases. Overexpression of Mic10 profoundly alters the architecture of the inner membrane independently of other MICOS components. The four-glycine motifs are dispensable for interaction of Mic10 with other MICOS subunits but are crucial for the formation of large Mic10 oligomers. Our studies identify a unique role of Mic10 oligomers in promoting the formation of inner membrane crista junctions.
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Affiliation(s)
- Maria Bohnert
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany
| | - Ralf M Zerbes
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany; Faculty of Biology, Universität Freiburg, 79104 Freiburg, Germany
| | - Karen M Davies
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Alexander W Mühleip
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Heike Rampelt
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany
| | - Susanne E Horvath
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany
| | - Thorina Boenke
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany
| | - Anita Kram
- Molecular Cell Biology, University of Groningen, 9700 CC Groningen, the Netherlands
| | - Inge Perschil
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany
| | - Marten Veenhuis
- Molecular Cell Biology, University of Groningen, 9700 CC Groningen, the Netherlands
| | - Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Ida J van der Klei
- Molecular Cell Biology, University of Groningen, 9700 CC Groningen, the Netherlands
| | - Nikolaus Pfanner
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, Universität Freiburg, 79104 Freiburg, Germany.
| | - Martin van der Laan
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, Universität Freiburg, 79104 Freiburg, Germany.
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35
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Abstract
Recent advances in chromatography and mass spectrometry (MS) have made rapid and deep proteomic profiling possible. To maximize the performance of the recently produced Orbitrap hybrid mass spectrometer, we have developed a protocol that combines improved sample preparation (including optimized cellular lysis by extensive bead beating) and chromatographic conditions (specifically, 30-cm capillary columns packed with 1.7-μm bridged ethylene hybrid material) and the manufacture of a column heater (to accommodate flow rates of 350-375 nl/min) that increases the number of proteins identified across a single liquid chromatography-tandem MS (LC-MS/MS) separation, thereby reducing the need for extensive sample fractionation. This strategy allowed the identification of up to 4,002 proteins (at a 1% false discovery rate (FDR)) in yeast (Saccharomyces cerevisiae strain BY4741) over 70 min of LC-MS/MS analysis. Quintuplicate analysis of technical replicates reveals 83% overlap at the protein level, thus demonstrating the reproducibility of this procedure. This protocol, which includes cell lysis, overnight tryptic digestion, sample analysis and database searching, takes ∼24 h to complete. Aspects of this protocol, including chromatographic separation and instrument parameters, can be adapted for the optimal analysis of other organisms.
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Affiliation(s)
- Alicia L Richards
- 1] The Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin, USA. [2] Department of Chemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Alexander S Hebert
- 1] The Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin, USA. [2] Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Arne Ulbrich
- 1] The Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin, USA. [2] Department of Chemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Derek J Bailey
- 1] The Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin, USA. [2] Department of Chemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Emma E Coughlin
- The Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin, USA
| | - Michael S Westphall
- The Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin, USA
| | - Joshua J Coon
- 1] The Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin, USA. [2] Department of Chemistry, University of Wisconsin, Madison, Wisconsin, USA. [3] Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin, USA
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36
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Abstract
Import of secretory proteins into the Endoplasmic Reticulum (ER) is an established function of the Sec61 channel. The contribution of the Sec61 channel to export of misfolded proteins from the ER for degradation by proteasomes is still controversial, but the proteasome 19S regulatory particle (RP) is necessary and sufficient for extraction of specific misfolded proteins from the ER, and binds directly to the Sec61 channel. In this work we have identified an import-competent sec61 mutant, S353C, carrying a point mutation in ER-lumenal loop 7 which reduces affinity of the cytoplasmic face of the Sec61 channel for the 19S RP. This indicates that the interaction between the 19S RP and the Sec61 channel is dependent on conformational changes in Sec61p hinging on loop 7. The sec61-S353C mutant had no measurable ER import defects and did not cause ER stress in intact cells, but reduced ER-export of a 19S RP-dependent misfolded protein when proteasomes were limiting in a cell-free assay. Our data suggest that the interaction between the 19S RP and the Sec61 channel is essential for the export of specific substrates from the ER to the cytosol for proteasomal degradation.
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Affiliation(s)
- Marie-Luise Kaiser
- Department of Microbiology, Faculty of Natural Sciences and Technology VIII, Saarland University, 66123, Saarbrücken, Germany
| | - Karin Römisch
- Department of Microbiology, Faculty of Natural Sciences and Technology VIII, Saarland University, 66123, Saarbrücken, Germany
- * E-mail:
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37
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Abstract
Protein interactions occur at certain times and at specific cellular places. The past years have seen a massive accumulation of binary protein-protein interaction data. The rapid increase of this context-free information necessitates robust methods to monitor protein interactions with temporal and spatial resolution in single cells. We have developed a simple split-ubiquitin-based method (SPLIFF) that uses the ratio of two fluorescent reporters as a signal for protein-protein interactions. One protein of the pair of interest is attached to the linear fusion of mCherry, the C-terminal half of ubiquitin, and GFP (mCherry-Cub-GFP). The other potential binding partner is expressed as a C-terminal fusion to the N-terminal half of ubiquitin (Nub). Upon co-expression the interaction between the two proteins of interest induces the reassociation of Nub and Cub to the native-like ubiquitin. GFP is subsequently cleaved from the C-terminus of Cub and degraded whereas the red-fluorescent mCherry stays attached to the Cub-fusion protein. We first implemented this method in the model yeast Saccharomyces cerevisiae. One fusion protein is expressed in cells of the a-mating type and the complementary fusion protein in cells of the α-mating type. Upon mixing, both cell types fuse and the Nub- and Cub-fusion proteins are free to interact. The red and green fluorescence is monitored by two-channel fluorescence time-lapse microcopy. The moment of cell fusion defines the start of the analysis. The calculated ratio of green to red fluorescence allows mapping the spatiotemporal interaction profiles of the investigated proteins in single cells.
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Affiliation(s)
- Alexander Dünkler
- Institute of Molecular Genetics and Cell Biology, Department of Biology, Ulm University, James-Franck-Ring N27, 89081, Ulm, Germany
| | - Reinhild Rösler
- Institute of Molecular Genetics and Cell Biology, Department of Biology, Ulm University, James-Franck-Ring N27, 89081, Ulm, Germany
| | - Hans A Kestler
- Research Group for Bioinformatics and Systems Biology, Institute of Neural Information Processing, Ulm University, Ulm, Germany
| | - Daniel Moreno-Andrés
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstrasse 39, 72076, Tübingen, Germany
| | - Nils Johnsson
- Institute of Molecular Genetics and Cell Biology, Department of Biology, Ulm University, James-Franck-Ring N27, 89081, Ulm, Germany.
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38
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Lietz CB, Yu Q, Li L. Large-scale collision cross-section profiling on a traveling wave ion mobility mass spectrometer. J Am Soc Mass Spectrom 2014; 25:2009-2019. [PMID: 24845359 DOI: 10.1007/s13361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Revised: 04/16/2014] [Accepted: 04/20/2014] [Indexed: 05/23/2023]
Abstract
Ion mobility (IM) is a gas-phase electrophoretic method that separates ions according to charge and ion-neutral collision cross-section (CCS). Herein, we attempt to apply a traveling wave (TW) IM polyalanine calibration method to shotgun proteomics and create a large peptide CCS database. Mass spectrometry methods that utilize IM, such as HDMS(E), often use high transmission voltages for sensitive analysis. However, polyalanine calibration has only been demonstrated with low voltage transmission used to prevent gas-phase activation. If polyalanine ions change conformation under higher transmission voltages used for HDMS(E), the calibration may no longer be valid. Thus, we aimed to characterize the accuracy of calibration and CCS measurement under high transmission voltages on a TW IM instrument using the polyalanine calibration method and found that the additional error was not significant. We also evaluated the potential error introduced by liquid chromatography (LC)-HDMS(E) analysis, and found it to be insignificant as well, validating the calibration method. Finally, we demonstrated the utility of building a large-population peptide CCS database by investigating the effects of terminal lysine position, via LysC or LysN digestion, on the formation of two structural sub-families formed by triply charged ions.
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39
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Lietz CB, Yu Q, Li L. Large-scale collision cross-section profiling on a traveling wave ion mobility mass spectrometer. J Am Soc Mass Spectrom 2014; 25:2009-19. [PMID: 24845359 PMCID: PMC4224635 DOI: 10.1007/s13361-014-0920-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Revised: 04/16/2014] [Accepted: 04/20/2014] [Indexed: 05/25/2023]
Abstract
Ion mobility (IM) is a gas-phase electrophoretic method that separates ions according to charge and ion-neutral collision cross-section (CCS). Herein, we attempt to apply a traveling wave (TW) IM polyalanine calibration method to shotgun proteomics and create a large peptide CCS database. Mass spectrometry methods that utilize IM, such as HDMS(E), often use high transmission voltages for sensitive analysis. However, polyalanine calibration has only been demonstrated with low voltage transmission used to prevent gas-phase activation. If polyalanine ions change conformation under higher transmission voltages used for HDMS(E), the calibration may no longer be valid. Thus, we aimed to characterize the accuracy of calibration and CCS measurement under high transmission voltages on a TW IM instrument using the polyalanine calibration method and found that the additional error was not significant. We also evaluated the potential error introduced by liquid chromatography (LC)-HDMS(E) analysis, and found it to be insignificant as well, validating the calibration method. Finally, we demonstrated the utility of building a large-population peptide CCS database by investigating the effects of terminal lysine position, via LysC or LysN digestion, on the formation of two structural sub-families formed by triply charged ions.
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Affiliation(s)
| | - Qing Yu
- School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin, Madison, WI 53705, USA
- School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA
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40
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Bonomi M, Pellarin R, Kim SJ, Russel D, Sundin BA, Riffle M, Jaschob D, Ramsden R, Davis TN, Muller EGD, Sali A. Determining protein complex structures based on a Bayesian model of in vivo Förster resonance energy transfer (FRET) data. Mol Cell Proteomics 2014; 13:2812-23. [PMID: 25139910 PMCID: PMC4223474 DOI: 10.1074/mcp.m114.040824] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 08/13/2014] [Indexed: 12/24/2022] Open
Abstract
The use of in vivo Förster resonance energy transfer (FRET) data to determine the molecular architecture of a protein complex in living cells is challenging due to data sparseness, sample heterogeneity, signal contributions from multiple donors and acceptors, unequal fluorophore brightness, photobleaching, flexibility of the linker connecting the fluorophore to the tagged protein, and spectral cross-talk. We addressed these challenges by using a Bayesian approach that produces the posterior probability of a model, given the input data. The posterior probability is defined as a function of the dependence of our FRET metric FRETR on a structure (forward model), a model of noise in the data, as well as prior information about the structure, relative populations of distinct states in the sample, forward model parameters, and data noise. The forward model was validated against kinetic Monte Carlo simulations and in vivo experimental data collected on nine systems of known structure. In addition, our Bayesian approach was validated by a benchmark of 16 protein complexes of known structure. Given the structures of each subunit of the complexes, models were computed from synthetic FRETR data with a distance root-mean-squared deviation error of 14 to 17 Å. The approach is implemented in the open-source Integrative Modeling Platform, allowing us to determine macromolecular structures through a combination of in vivo FRETR data and data from other sources, such as electron microscopy and chemical cross-linking.
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Affiliation(s)
- Massimiliano Bonomi
- From the ‡Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, California 94158; §Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom;
| | - Riccardo Pellarin
- From the ‡Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, California 94158
| | - Seung Joong Kim
- From the ‡Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, California 94158
| | - Daniel Russel
- From the ‡Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, California 94158
| | - Bryan A Sundin
- ‖Department of Biochemistry, University of Washington, Seattle, Washington 98195
| | - Michael Riffle
- ‖Department of Biochemistry, University of Washington, Seattle, Washington 98195
| | - Daniel Jaschob
- ‖Department of Biochemistry, University of Washington, Seattle, Washington 98195
| | - Richard Ramsden
- ‖Department of Biochemistry, University of Washington, Seattle, Washington 98195
| | - Trisha N Davis
- ‖Department of Biochemistry, University of Washington, Seattle, Washington 98195
| | - Eric G D Muller
- ‖Department of Biochemistry, University of Washington, Seattle, Washington 98195
| | - Andrej Sali
- From the ‡Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, California 94158;
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41
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Cannon JR, Cammarata M, Robotham SA, Cotham VC, Shaw JB, Fellers RT, Early BP, Thomas PM, Kelleher NL, Brodbelt JS. Ultraviolet photodissociation for characterization of whole proteins on a chromatographic time scale. Anal Chem 2014; 86:2185-92. [PMID: 24447299 PMCID: PMC3958131 DOI: 10.1021/ac403859a] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 01/21/2014] [Indexed: 02/01/2023]
Abstract
Intact protein characterization using mass spectrometry thus far has been achieved at the cost of throughput. Presented here is the application of 193 nm ultraviolet photodissociation (UVPD) for top down identification and characterization of proteins in complex mixtures in an online fashion. Liquid chromatographic separation at the intact protein level coupled with fast UVPD and high-resolution detection resulted in confident identification of 46 unique sequences compared to 44 using HCD from prepared Escherichia coli ribosomes. Importantly, nearly all proteins identified in both the UVPD and optimized HCD analyses demonstrated a substantial increase in confidence in identification (as defined by an average decrease in E value of ∼40 orders of magnitude) due to the higher number of matched fragment ions. Also shown is the potential for high-throughput characterization of intact proteins via liquid chromatography (LC)-UVPD-MS of molecular weight-based fractions of a Saccharomyces cerevisiae lysate. In total, protein products from 215 genes were identified and found in 292 distinct proteoforms, 168 of which contained some type of post-translational modification.
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Affiliation(s)
- Joe R. Cannon
- Department
of Chemistry, University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, United States
| | - Michael
B. Cammarata
- Department
of Chemistry, University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, United States
| | - Scott A. Robotham
- Department
of Chemistry, University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, United States
| | - Victoria C. Cotham
- Department
of Chemistry, University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, United States
| | - Jared B. Shaw
- Department
of Chemistry, University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, United States
| | - Ryan T. Fellers
- Departments
of Chemistry and Molecular Biosciences and the Proteomics Center of
Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Bryan P. Early
- Departments
of Chemistry and Molecular Biosciences and the Proteomics Center of
Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Paul M. Thomas
- Departments
of Chemistry and Molecular Biosciences and the Proteomics Center of
Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Neil L. Kelleher
- Departments
of Chemistry and Molecular Biosciences and the Proteomics Center of
Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Jennifer S. Brodbelt
- Department
of Chemistry, University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, United States
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42
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Lv YJ, Wang X, Ma Q, Bai X, Li BZ, Zhang W, Yuan YJ. Proteomic analysis reveals complex metabolic regulation in Saccharomyces cerevisiae cells against multiple inhibitors stress. Appl Microbiol Biotechnol 2014; 98:2207-21. [PMID: 24442506 DOI: 10.1007/s00253-014-5519-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 12/20/2013] [Accepted: 12/28/2013] [Indexed: 11/24/2022]
Abstract
Toxic compounds including acids, furans, and phenols (AFP) were generated from the pretreatment of lignocellulose. We cultivated Saccharomyces cerevisiae cells in a batch mode, besides the cell culture of original yeast strain in AFP-free medium which was referred as C0, three independent subcultures were cultivated under multiple inhibitors AFP and were referred as C1, C2, and C3 in time sequence. Comparing to C0, the cell density was lowered while the ethanol yield was maintained stably in the three yeast cultures under AFP stress, and the lag phase of C1 was extended while the lag phases of C2 and C3 were not extended. In proteomic analysis, 194 and 215 unique proteins were identified as differently expressed proteins at lag phase and exponential phase, respectively. Specifically, the yeast cells co-regulated protein folding and protein synthesis process to prevent the generation of misfolded proteins and to save cellular energy, they increased the activity of glycolysis, redirected metabolic flux towards phosphate pentose pathway and the biosynthesis of ethanol instead of the biosynthesis of glycerol and acetic acid, and they upregulated several oxidoreductases especially at lag phase and induced programmed cell death at exponential phase. When the yeast cells were cultivated under AFP stress, the new metabolism homeostasis in favor of cellular energy and redox homeostasis was generated in C1, then it was inherited and optimized in C2 and C3, enabling the yeast cells in C2 and C3 to enter the exponential phase in a short period after inoculation, which thus significantly shortened the fermentation time.
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Affiliation(s)
- Ya-Jin Lv
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300072, People's Republic of China
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43
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Petelinc T, Polak T, Jamnik P. Insight into the molecular mechanisms of propolis activity using a subcellular proteomic approach. J Agric Food Chem 2013; 61:11502-11510. [PMID: 24195611 DOI: 10.1021/jf4042003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The effects of a fractionated 70% ethanolic extract of propolis were analyzed at the subproteome level by two-dimensional electrophoresis. Differential detergent fractionation was used to fractionate proteins from the yeast Saccharomyces cerevisiae according to their subcellular localization. Thus, four subcellular proteomes were obtained: cytosolic, membrane/organelle, nuclear, and cytoskeletal. Yeast treatment resulted in changes in the levels of proteins involved in carbohydrate and energy metabolism, antioxidant defense, actin filament dynamics, folding of proteins, and others. On the basis of this information, we can obtain better insights into the processes that are carried out in cells exposed to propolis extract.
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Affiliation(s)
- Tanja Petelinc
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana , Ljubljana SI-1000, Slovenia
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44
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Randall SM, Cardasis HL, Muddiman DC. Factorial experimental designs elucidate significant variables affecting data acquisition on a quadrupole Orbitrap mass spectrometer. J Am Soc Mass Spectrom 2013; 24:1501-1512. [PMID: 23913023 DOI: 10.1007/s13361-013-0693-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 06/08/2013] [Accepted: 06/16/2013] [Indexed: 06/02/2023]
Abstract
Instrument parameter values for a quadrupole Orbitrap mass spectrometer were optimized for performing global proteomic analyses. Fourteen factors were evaluated for their influence on data-dependent acquisition with an emphasis on both the rate of sequencing and spectral quality by maximizing two individually tested response variables (unique peptides and protein groups). Of the 14 factors, 12 factors were assigned significant contrast values (P < 0.05) for both response variables. Fundamentally, when optimizing parameters, a balance between spectral quality and duty cycle needs to be reached in order to maximize proteome coverage. This is especially true when using a data-dependent approach for sequencing complex proteomes. For example, maximum ion injection time, automatic gain control settings, and minimum threshold settings for triggering MS/MS isolation and activation all heavily influence ion signal, the number of spectra collected, and spectral quality. To better assess the effect these parameters have on data acquisition, all MS/MS data were parsed according to ion abundance by calculating the percent of the AGC target reached for each MS/MS event and then compared with successful peptide-spectrum matches. This proved to be an effective approach for understanding the effect of ion abundance on successful peptide-spectrum matches and establishing minimum ion abundance thresholds for triggering MS/MS isolation and activation.
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Affiliation(s)
- Shan M Randall
- W. M. Keck Fourier Transform Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA
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45
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Gregori J, Villarreal L, Sánchez A, Baselga J, Villanueva J. An effect size filter improves the reproducibility in spectral counting-based comparative proteomics. J Proteomics 2013; 95:55-65. [PMID: 23770383 DOI: 10.1016/j.jprot.2013.05.030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 05/06/2013] [Accepted: 05/22/2013] [Indexed: 11/17/2022]
Abstract
UNLABELLED The microarray community has shown that the low reproducibility observed in gene expression-based biomarker discovery studies is partially due to relying solely on p-values to get the lists of differentially expressed genes. Their conclusions recommended complementing the p-value cutoff with the use of effect-size criteria. The aim of this work was to evaluate the influence of such an effect-size filter on spectral counting-based comparative proteomic analysis. The results proved that the filter increased the number of true positives and decreased the number of false positives and the false discovery rate of the dataset. These results were confirmed by simulation experiments where the effect size filter was used to evaluate systematically variable fractions of differentially expressed proteins. Our results suggest that relaxing the p-value cut-off followed by a post-test filter based on effect size and signal level thresholds can increase the reproducibility of statistical results obtained in comparative proteomic analysis. Based on our work, we recommend using a filter consisting of a minimum absolute log2 fold change of 0.8 and a minimum signal of 2-4 SpC on the most abundant condition for the general practice of comparative proteomics. The implementation of feature filtering approaches could improve proteomic biomarker discovery initiatives by increasing the reproducibility of the results obtained among independent laboratories and MS platforms. BIOLOGICAL SIGNIFICANCE Quality control analysis of microarray-based gene expression studies pointed out that the low reproducibility observed in the lists of differentially expressed genes could be partially attributed to the fact that these lists are generated relying solely on p-values. Our study has established that the implementation of an effect size post-test filter improves the statistical results of spectral count-based quantitative proteomics. The results proved that the filter increased the number of true positives whereas decreased the false positives and the false discovery rate of the datasets. The results presented here prove that a post-test filter applying a reasonable effect size and signal level thresholds helps to increase the reproducibility of statistical results in comparative proteomic analysis. Furthermore, the implementation of feature filtering approaches could improve proteomic biomarker discovery initiatives by increasing the reproducibility of results obtained among independent laboratories and MS platforms. This article is part of a Special Issue entitled: Standardization and Quality Control in Proteomics.
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Affiliation(s)
- Josep Gregori
- Vall d'Hebron Institute of Oncology (VHIO), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain; Statistics Department, University of Barcelona (UB), Barcelona, Spain
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46
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Weisbrod CR, Hoopmann MR, Senko MW, Bruce JE. Performance evaluation of a dual linear ion trap-Fourier transform ion cyclotron resonance mass spectrometer for proteomics research. J Proteomics 2013; 88:109-19. [PMID: 23590889 DOI: 10.1016/j.jprot.2013.04.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 03/28/2013] [Accepted: 04/05/2013] [Indexed: 11/18/2022]
Abstract
UNLABELLED A novel dual cell linear ion trap Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) and its performance characteristics are reported. A linear ion trap-Fourier transform ion cyclotron resonance mass spectrometer has been modified to incorporate a LTQ-Velos mass spectrometer. This modified instrument features efficient ion accumulation and fast MS/MS acquisition capabilities of dual cell linear RF ion trap instruments coupled to the high mass accuracy, resolution, and dynamic range of a FT-ICR for improved proteomic coverage. The ion accumulation efficiency is demonstrated to be an order of magnitude greater than that observed with LTQ-FT Ultra instrumentation. The proteome coverage with yeast was shown to increase over the previous instrument generation by 50% (100% increase on the peptide level). In addition, many lower abundance level yeast proteins were only detected with this modified instrument. This novel configuration also enables beam type CID fragmentation using a dual cell RF ion trap mass spectrometer. This technique involves accelerating ions between traps while applying an elevated DC offset to one of the traps to accelerate ions and induce fragmentation. This instrument design may serve as a useful option for labs currently considering purchasing new instrumentation or upgrading existing instruments. BIOLOGICAL SIGNIFICANCE A novel hybrid mass spectrometer that allows increased MS/MS acquisition rates with high mass measurement accuracy and new ion fragmentation methods greatly improves the number of proteins, posttranslational modifications and protein-protein interactions that can be identified from cells.
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Affiliation(s)
- Chad R Weisbrod
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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47
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Lobas AA, Verenchikov AN, Goloborodko AA, Levitsky LI, Gorshkov MV. Combination of Edman degradation of peptides with liquid chromatography/mass spectrometry workflow for peptide identification in bottom-up proteomics. Rapid Commun Mass Spectrom 2013; 27:391-400. [PMID: 23280970 DOI: 10.1002/rcm.6462] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 11/01/2012] [Accepted: 11/02/2012] [Indexed: 06/01/2023]
Abstract
RATIONALE High-throughput methods of proteomics are essential for identification of proteins in a cell or tissue under certain conditions. Most of these methods require tandem mass spectrometry (MS/MS). A multidimensional approach including predictive chromatography and partial chemical degradation could be a valuable alternative and/or addition to MS/MS. METHODS In the proposed strategy peptides are identified in a three-dimensional (3D) search space consisting of retention time (RT), mass, and reduced mass after one-step partial Edman degradation. The strategy was evaluated in silico for two databases: baker's yeast and human proteins. Rates of unambiguous identifications were estimated for mass accuracies from 0.001 to 0.05 Da and RT prediction accuracies from 0.1 to 5 min. Rates of Edman reactions were measured for test peptides. RESULTS A 3D description of proteolytic peptides allowing unambiguous identification without employing MS/MS of up to 95% and 80% of tryptic peptides from the yeast and human proteomes, respectively, was considered. Further extension of the search space to a four-dimensional one by incorporating the second N-terminal amino acid residue as the fourth dimension was also considered and was shown to result in up to 90% of human peptides being identified unambiguously. CONCLUSIONS The proposed 3D search space can be a useful alternative to MS/MS-based peptide identification approach. Experimental implementations of the proposed method within the on-line liquid chromatography/mass spectrometry (LC/MS) and off-line matrix-assisted laser desorption/ionization (MALDI) workflows are in progress.
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Affiliation(s)
- Anna A Lobas
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
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48
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Picotti P, Clément-Ziza M, Lam H, Campbell DS, Schmidt A, Deutsch EW, Röst H, Sun Z, Rinner O, Reiter L, Shen Q, Michaelson JJ, Frei A, Alberti S, Kusebauch U, Wollscheid B, Moritz RL, Beyer A, Aebersold R. A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis. Nature 2013; 494:266-70. [PMID: 23334424 PMCID: PMC3951219 DOI: 10.1038/nature11835] [Citation(s) in RCA: 257] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Accepted: 11/30/2012] [Indexed: 12/25/2022]
Abstract
Experience from different fields of life sciences suggests that accessible, complete reference maps of the components of the system under study are highly beneficial research tools. Examples of such maps include libraries of the spectroscopic properties of molecules, or databases of drug structures in analytical or forensic chemistry. Such maps, and methods to navigate them, constitute reliable assays to probe any sample for the presence and amount of molecules contained in the map. So far, attempts to generate such maps for any proteome have failed to reach complete proteome coverage. Here we use a strategy based on high-throughput peptide synthesis and mass spectrometry to generate an almost complete reference map (97% of the genome-predicted proteins) of the Saccharomyces cerevisiae proteome. We generated two versions of this mass-spectrometric map, one supporting discovery-driven (shotgun) and the other supporting hypothesis-driven (targeted) proteomic measurements. Together, the two versions of the map constitute a complete set of proteomic assays to support most studies performed with contemporary proteomic technologies. To show the utility of the maps, we applied them to a protein quantitative trait locus (QTL) analysis, which requires precise measurement of the same set of peptides over a large number of samples. Protein measurements over 78 S. cerevisiae strains revealed a complex relationship between independent genetic loci, influencing the levels of related proteins. Our results suggest that selective pressure favours the acquisition of sets of polymorphisms that adapt protein levels but also maintain the stoichiometry of functionally related pathway members.
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Affiliation(s)
- Paola Picotti
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich CH-8093, Switzerland.
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Lund MN, Hoff S, Berner TS, Lametsch R, Andersen ML. Effect of pasteurization on the protein composition and oxidative stability of beer during storage. J Agric Food Chem 2012; 60:12362-12370. [PMID: 23210737 DOI: 10.1021/jf303044a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The impacts of pasteurization of a lager beer on protein composition and the oxidative stability were studied during storage at 22 °C for 426 days in the dark. Pasteurization clearly improved the oxidative stability of beer determined by ESR spectroscopy, whereas it had a minor negative effect on the volatile profile by increasing volatile compounds that is generally associated with heat treatment and a loss of fruity ester aroma. A faster rate of radical formation in unpasteurized beer was consistent with a faster consumption of sulfite. Beer proteins in the unpasteurized beer were more degraded, most likely due to proteolytic enzyme activity of yeast remnants and more precipitation of proteins was also observed. The differences in soluble protein content and composition are suggested to result in differences in the contents of prooxidative metals as a consequence of the proteins ability to bind metals. This also contributes to the differences in oxidative stabilities of the beers.
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Affiliation(s)
- Marianne N Lund
- Department of Food Science, University of Copenhagen, Frederiksberg C, Denmark.
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Cirulli C, Coccetti P, Alberghina L, Tripodi F. A surface-activated chemical ionization approach allows quantitative phosphorylation analysis of the cyclin-dependent kinase inhibitor Sic1 phosphorylated on Ser201. Rapid Commun Mass Spectrom 2012; 26:1527-1532. [PMID: 22638969 DOI: 10.1002/rcm.6251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
RATIONALE Quantitative phosphoproteomics represents a front line for functional proteomics and hence for systems biology. Here we present a new application of the surface-activated chemical ionization (SACI) technology for quantitative phosphoproteomics analysis. The main advantages of SACI-MS technology are high sensitivity, quantitative accuracy and matrix effect reduction, which allow quantitative estimations. METHODS A SACI-MS approach was used to investigate the quantitative in vivo phosphorylation of the cyclin-dependent kinase inhibitor Sic1, a low-abundance protein of Saccharomyces cerevisiae, which is phosphorylated on Ser201 by casein kinase 2 (CK2) and compared its phosphorylation status in cells growing in two different carbon sources (glucose or ethanol). RESULTS Our relative quantification indicated that the Sic1-Ser201 phosphorylation level is about 2-fold higher in ethanol- than in glucose-growing cells, proportional to the Sic1 protein level. This finding is coherent with results of western blot analysis using anti-phospho-Ser201-specific antibody, validating the results obtained with this new SACI approach. CONCLUSIONS The findings presented in this paper indicate that the innovative LC/SACI-MS method, coupled with immunoprecipitation, is a powerful device to obtain quantitative information on the phosphorylation state of low abundance proteins.
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Affiliation(s)
- Claudia Cirulli
- Università degli Studi di Milano-Bicocca, Dipartimento di Biotecnologie e Bioscienze, Piazza della Scienza 2, 20126 Milano, Italy.
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