1
|
Matzinger M, Schmücker A, Yelagandula R, Stejskal K, Krššáková G, Berger F, Mechtler K, Mayer RL. Micropillar arrays, wide window acquisition and AI-based data analysis improve comprehensiveness in multiple proteomic applications. Nat Commun 2024; 15:1019. [PMID: 38310095 PMCID: PMC10838342 DOI: 10.1038/s41467-024-45391-z] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 01/19/2024] [Indexed: 02/05/2024] Open
Abstract
Comprehensive proteomic analysis is essential to elucidate molecular pathways and protein functions. Despite tremendous progress in proteomics, current studies still suffer from limited proteomic coverage and dynamic range. Here, we utilize micropillar array columns (µPACs) together with wide-window acquisition and the AI-based CHIMERYS search engine to achieve excellent proteomic comprehensiveness for bulk proteomics, affinity purification mass spectrometry and single cell proteomics. Our data show that µPACs identify ≤50% more peptides and ≤24% more proteins, while offering improved throughput, which is critical for large (clinical) proteomics studies. Combining wide precursor isolation widths of m/z 4-12 with the CHIMERYS search engine identified +51-74% and +59-150% more proteins and peptides, respectively, for single cell, co-immunoprecipitation, and multi-species samples over a conventional workflow at well-controlled false discovery rates. The workflow further offers excellent precision, with CVs <7% for low input bulk samples, and accuracy, with deviations <10% from expected fold changes for regular abundance two-proteome mixes. Compared to a conventional workflow, our entire optimized platform discovered 92% more potential interactors in a protein-protein interaction study on the chromatin remodeler Smarca5/Snf2h. These include previously described Smarca5 binding partners and undescribed ones including Arid1a, another chromatin remodeler with key roles in neurodevelopmental and malignant disorders.
Collapse
Affiliation(s)
- Manuel Matzinger
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria.
| | - Anna Schmücker
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
- MRC (Medical Research Council) London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK
- Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Ramesh Yelagandula
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
- Laboratory of Epigenetics, Cell Fate & Disease, Centre for DNA Fingerprinting and Diagnostics (CDFD), Uppal, Hyderabad, India
| | - Karel Stejskal
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Gabriela Krššáková
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Frédéric Berger
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria.
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.
| | - Rupert L Mayer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria.
| |
Collapse
|
2
|
Starkl P, Jonsson G, Artner T, Turnes BL, Serhan N, Oliveira T, Gail LM, Stejskal K, Channon KM, Köcher T, Stary G, Klang V, Gaudenzio N, Knapp S, Woolf CJ, Penninger JM, Cronin SJ. Mast cell-derived BH4 is a critical mediator of postoperative pain. bioRxiv 2023:2023.01.24.525378. [PMID: 37293068 PMCID: PMC10245978 DOI: 10.1101/2023.01.24.525378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Postoperative pain affects most patients after major surgery and can transition to chronic pain. Here, we discovered that postoperative pain hypersensitivity correlated with markedly increased local levels of the metabolite BH4. Gene transcription and reporter mouse analyses after skin injury identified neutrophils, macrophages and mast cells as primary postoperative sources of GTP cyclohydrolase-1 (Gch1) expression, the rate-limiting enzyme in BH4 production. While specific Gch1 deficiency in neutrophils or macrophages had no effect, mice deficient in mast cells or mast cell-specific Gch1 showed drastically decreased postoperative pain after surgery. Skin injury induced the nociceptive neuropeptide substance P, which directly triggers the release of BH4-dependent serotonin in mouse and human mast cells. Substance P receptor blockade substantially ameliorated postoperative pain. Our findings underline the unique position of mast cells at the neuro-immune interface and highlight substance P-driven mast cell BH4 production as promising therapeutic targets for the treatment of postoperative pain.
Collapse
Affiliation(s)
- Philipp Starkl
- Research Division of Infection Biology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Gustav Jonsson
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Tyler Artner
- Research Division of Infection Biology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
- Department of Internal Medicine II, Medical University of Vienna, Vienna, Austria
| | - Bruna Lenfers Turnes
- Department of Neurobiology, Harvard Medical School, Boston, United States
- F.M. Kirby Neurobiology Research Center, Boston Children’s Hospital, Boston, United States, Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Nadine Serhan
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), Inserm UMR1291 CNRS UMR5051, University of Toulouse III, Toulouse, France
| | - Tiago Oliveira
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Laura-Marie Gail
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
- LBI-RUD – Ludwig-Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Karel Stejskal
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Keith M. Channon
- Radcliffe Department of, British Heart Foundation Centre of Research Excellence, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Thomas Köcher
- Vienna BioCenter Core Facilities (VBCF), 1030 Vienna, Austria
| | - Georg Stary
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
- LBI-RUD – Ludwig-Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Victoria Klang
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Nicolas Gaudenzio
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), Inserm UMR1291 CNRS UMR5051, University of Toulouse III, Toulouse, France
- Genoskin SAS, Toulouse, France
| | - Sylvia Knapp
- Research Division of Infection Biology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Clifford J. Woolf
- Department of Neurobiology, Harvard Medical School, Boston, United States
- F.M. Kirby Neurobiology Research Center, Boston Children’s Hospital, Boston, United States, Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Josef M. Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Shane J.F. Cronin
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| |
Collapse
|
3
|
Stejskal K, Jeff ODB, Matzinger M, Dürnberger G, Boychenko A, Jacobs P, Mechtler K. Deep Proteome Profiling with Reduced Carryover Using Superficially Porous Microfabricated nanoLC Columns. Anal Chem 2022; 94:15930-15938. [PMID: 36356180 PMCID: PMC9685595 DOI: 10.1021/acs.analchem.2c01196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
![]()
In the field of liquid chromatography–mass spectrometry
(LC–MS)-based proteomics, increases in the sampling depth and
proteome coverage have mainly been accomplished by rapid advances
in mass spectrometer technology. The comprehensiveness and quality
of the data that can be generated do, however, also depend on the
performance provided by nano-liquid chromatography (nanoLC) separations.
Proper selection of reversed-phase separation columns can be important
to provide the MS instrument with peptides at the highest possible
concentration and separated at the highest possible resolution. In
the current contribution, we evaluate the use of the prototype generation
2 μPAC nanoLC columns, which use C18-functionalized superficially
porous micropillars as a stationary phase. When compared to traditionally
used fully porous silica stationary phases, more precursors could
be characterized when performing single shot data-dependent LC–MS/MS
analyses of a human cell line tryptic digest. Up to 30% more protein
groups and 60% more unique peptides were identified for short gradients
(10 min) and limited sample amounts (10–100 ng of cell lysate
digest). With LC–MS gradient times of 10, 60, 120, and 180
min, respectively, we identified 2252, 6513, 7382, and 8174 protein
groups with 25, 500, 1000, and 2000 ng of the sample loaded on the
column. Reduction of sample carryover to the next run (up to 2 to
3%) and decreased levels of methionine oxidation (up to 3-fold) were
identified as additional figures of merit. When analyzing a disuccinimidyl
dibutyric urea-crosslinked synthetic library, 29 to 59 more unique
crosslinked peptides could be identified at an experimentally validated
false discovery rate of 1–2%.
Collapse
Affiliation(s)
- Karel Stejskal
- IMBA─Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Dr. Bohr Gasse 3, A-1030 Vienna, Austria
| | - Op de Beeck Jeff
- Thermo Fisher Scientific, Technologiepark-Zwijnaarde 82, B-9052 Gent, Belgium
| | - Manuel Matzinger
- IMP─Institute of Molecular Pathology, Campus-Vienna-Biocenter 1, A-1030 Vienna, Austria
| | - Gerhard Dürnberger
- Gregor Mendel Institute of Molecular Plant Biology of the Austrian Academy of Sciences, Dr. Bohr Gasse 3, A-1030 Vienna, Austria
| | | | - Paul Jacobs
- Thermo Fisher Scientific, Technologiepark-Zwijnaarde 82, B-9052 Gent, Belgium
| | - Karl Mechtler
- IMP─Institute of Molecular Pathology, Campus-Vienna-Biocenter 1, A-1030 Vienna, Austria
- IMBA─Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Dr. Bohr Gasse 3, A-1030 Vienna, Austria
- Gregor Mendel Institute of Molecular Plant Biology of the Austrian Academy of Sciences, Dr. Bohr Gasse 3, A-1030 Vienna, Austria
| |
Collapse
|
4
|
Zheng R, Stejskal K, Pynn C, Mechtler K, Boychenko A. Deep Single-Shot NanoLC-MS Proteome Profiling with a 1500 Bar UHPLC System, Long Fully Porous Columns, and HRAM MS. J Proteome Res 2022; 21:2545-2551. [PMID: 36068014 PMCID: PMC9552226 DOI: 10.1021/acs.jproteome.2c00270] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
This study demonstrates how the latest ultrahigh-performance
liquid
chromatography (UHPLC) technology can be combined with high-resolution
accurate-mass (HRAM) mass spectrometry (MS) and long columns packed
with fully porous particles to improve bottom-up proteomics analysis
with nanoflow liquid chromatography–mass spectrometry (nanoLC-MS)
methods. The increased back pressures from the UHPLC system enabled
the use of 75 μm I.D. × 75 cm columns packed with 2 μm
particles at a typical 300 nL/min flow rate as well as elevated and
reduced flow rates. The constant pressure pump operation at 1500 bar
reduced sample loading and column washing/equilibration stages and
overall overhead time, which maximizes MS utilization time. The versatility
of flow rate optimization to balance the sensitivity, throughput with
sample loading amount, and capability of using longer gradients contributes
to a greater number of peptide and protein identifications for single-shot
bottom-up proteomics experiments. The routine proteome profiling and
precise quantification of >7000 proteins with single-shot nanoLC-MS
analysis open possibilities for large-scale discovery studies with
a deep dive into the protein level alterations. Data are available
via ProteomeXchange with identifier PXD035665.
Collapse
Affiliation(s)
- Runsheng Zheng
- Thermo Fisher Scientific, Dornierstrasse 4, 82110 Germering, Germany
| | - Karel Stejskal
- IMP─Institute of Molecular Pathology, Campus-Vienna-Biocenter 1, A-1030 Vienna, Austria.,IMBA─Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Dr. Bohr Gasse 3, A-1030 Vienna, Austria.,Gregor Mendel Institute of Molecular Plant Biology of the Austrian Academy of Sciences, Dr. Bohr Gasse 3, A-1030 Vienna, Austria
| | - Christopher Pynn
- Thermo Fisher Scientific, Dornierstrasse 4, 82110 Germering, Germany
| | - Karl Mechtler
- IMP─Institute of Molecular Pathology, Campus-Vienna-Biocenter 1, A-1030 Vienna, Austria.,IMBA─Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Dr. Bohr Gasse 3, A-1030 Vienna, Austria.,Gregor Mendel Institute of Molecular Plant Biology of the Austrian Academy of Sciences, Dr. Bohr Gasse 3, A-1030 Vienna, Austria
| | | |
Collapse
|
5
|
Kolesar P, Stejskal K, Potesil D, Murray JM, Palecek JJ. Role of Nse1 Subunit of SMC5/6 Complex as a Ubiquitin Ligase. Cells 2022; 11:cells11010165. [PMID: 35011726 PMCID: PMC8750328 DOI: 10.3390/cells11010165] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 11/08/2021] [Revised: 12/15/2021] [Accepted: 01/01/2022] [Indexed: 11/16/2022] Open
Abstract
Structural Maintenance of Chromosomes (SMC) complexes are important for many aspects of the chromosomal organization. Unlike cohesin and condensin, the SMC5/6 complex contains a variant RING domain carried by its Nse1 subunit. RING domains are characteristic for ubiquitin ligases, and human NSE1 has been shown to possess ubiquitin-ligase activity in vitro. However, other studies were unable to show such activity. Here, we confirm Nse1 ubiquitin-ligase activity using purified Schizosaccharomyces pombe proteins. We demonstrate that the Nse1 ligase activity is stimulated by Nse3 and Nse4. We show that Nse1 specifically utilizes Ubc13/Mms2 E2 enzyme and interacts directly with ubiquitin. We identify the Nse1 mutation (R188E) that specifically disrupts its E3 activity and demonstrate that the Nse1-dependent ubiquitination is particularly important under replication stress. Moreover, we determine Nse4 (lysine K181) as the first known SMC5/6-associated Nse1 substrate. Interestingly, abolition of Nse4 modification at K181 leads to suppression of DNA-damage sensitivity of other SMC5/6 mutants. Altogether, this study brings new evidence for Nse1 ubiquitin ligase activity, significantly advancing our understanding of this enigmatic SMC5/6 function.
Collapse
Affiliation(s)
- Peter Kolesar
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
- Correspondence: (P.K.); (J.J.P.)
| | - Karel Stejskal
- Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (K.S.); (D.P.)
| | - David Potesil
- Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (K.S.); (D.P.)
| | - Johanne M. Murray
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RH, UK;
| | - Jan J. Palecek
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
- Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (K.S.); (D.P.)
- Correspondence: (P.K.); (J.J.P.)
| |
Collapse
|
6
|
Abstract
![]()
Single-cell proteomics
workflows have considerably improved in
sensitivity and reproducibility to characterize as-yet unknown biological
phenomena. With the emergence of multiplexed single-cell proteomics,
studies increasingly present single-cell measurements in conjunction
with an abundant congruent carrier to improve the precursor selection
and enhance identifications. While these extreme carrier spikes are
often >100× more abundant than the investigated samples, the
total ion current undoubtably increases but the quantitative accuracy
possibly is affected. We here focus on narrowly titrated carrier spikes
(i.e., <20×) and assess their elimination for a comparable
sensitivity with superior accuracy. We find that subtle changes in
the carrier ratio can severely impact the measurement variability
and describe alternative multiplexing strategies to evaluate data
quality. Lastly, we demonstrate elevated replicate overlap while preserving
acquisition throughput at an improved quantitative accuracy with DIA-TMT
and discuss optimized experimental designs for multiplexed proteomics
of trace samples. This comprehensive benchmarking gives an overview
of currently available techniques and guides the conceptualization
of the optimal single-cell proteomics experiment.
Collapse
Affiliation(s)
- Claudia Ctortecka
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus Vienna Biocenter 1, 1030 Vienna, Austria
| | - Karel Stejskal
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus Vienna Biocenter 1, 1030 Vienna, Austria.,Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria.,The Gregor Mendel Institute of Molecular Plant Biology of the Austrian Academy of Sciences (GMI), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Gabriela Krššáková
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus Vienna Biocenter 1, 1030 Vienna, Austria.,Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria.,The Gregor Mendel Institute of Molecular Plant Biology of the Austrian Academy of Sciences (GMI), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Sasha Mendjan
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus Vienna Biocenter 1, 1030 Vienna, Austria.,Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria.,The Gregor Mendel Institute of Molecular Plant Biology of the Austrian Academy of Sciences (GMI), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| |
Collapse
|
7
|
Ctortecka C, Krššáková G, Stejskal K, Penninger JM, Mendjan S, Mechtler K, Stadlmann J. Comparative proteome signatures of trace samples by multiplexed Data-Independent Acquisition. Mol Cell Proteomics 2021; 21:100177. [PMID: 34793982 PMCID: PMC8717550 DOI: 10.1016/j.mcpro.2021.100177] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 04/19/2021] [Revised: 11/04/2021] [Accepted: 11/10/2021] [Indexed: 01/01/2023] Open
Abstract
Single-cell transcriptomics has revolutionized our understanding of basic biology and disease. Since transcript levels often do not correlate with protein expression, it is crucial to complement transcriptomics approaches with proteome analyses at single-cell resolution. Despite continuous technological improvements in sensitivity, mass-spectrometry-based single-cell proteomics ultimately faces the challenge of reproducibly comparing the protein expression profiles of thousands of individual cells. Here, we combine two hitherto opposing analytical strategies, DIA and Tandem-Mass-Tag (TMT)-multiplexing, to generate highly reproducible, quantitative proteome signatures from ultralow input samples. We developed a novel, identification-independent proteomics data-analysis pipeline that allows to quantitatively compare DIA-TMT proteome signatures across hundreds of samples independent of their biological origin to identify cell types and single protein knockouts. These proteome signatures overcome the need to impute quantitative data due to accumulating detrimental amounts of missing data in standard multibatch TMT experiments. We validate our approach using integrative data analysis of different human cell lines and standard database searches for knockouts of defined proteins. Our data establish a novel and reproducible approach to markedly expand the numbers of proteins one detects from ultralow input samples. DIA-TMT provides reproducible, quantitative proteome signatures at high throughput. Proteome signature inferred cell type characterization is highly accurate. Proteome signatures accurately highlight underrepresented cell types. ID-independent DIA-TMT is more reproducible than standard DDA acquisition strategies.
Collapse
Affiliation(s)
- Claudia Ctortecka
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Gabriela Krššáková
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria; Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria; The Gregor Mendel Institute of Molecular Plant Biology of the Austrian Academy of Sciences (GMI), Vienna BioCenter (VBC), Vienna, Austria
| | - Karel Stejskal
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria; Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria; The Gregor Mendel Institute of Molecular Plant Biology of the Austrian Academy of Sciences (GMI), Vienna BioCenter (VBC), Vienna, Austria
| | - Josef M Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria; Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver Campus, Vancouver, British Columbia, Canada
| | - Sasha Mendjan
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria; Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria; The Gregor Mendel Institute of Molecular Plant Biology of the Austrian Academy of Sciences (GMI), Vienna BioCenter (VBC), Vienna, Austria
| | - Johannes Stadlmann
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria; Institute of Biochemistry, Department of Chemistry, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria.
| |
Collapse
|
8
|
Stejskal K, Op de Beeck J, Dürnberger G, Jacobs P, Mechtler K. Ultrasensitive NanoLC-MS of Subnanogram Protein Samples Using Second Generation Micropillar Array LC Technology with Orbitrap Exploris 480 and FAIMS PRO. Anal Chem 2021; 93:8704-8710. [PMID: 34137250 PMCID: PMC8253486 DOI: 10.1021/acs.analchem.1c00990] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [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: 03/06/2021] [Accepted: 06/03/2021] [Indexed: 12/14/2022]
Abstract
In the light of the ongoing single-cell revolution, scientific disciplines are combining forces to retrieve as much relevant data as possible from trace amounts of biological material. For single-cell proteomics, this implies optimizing the entire workflow from initial cell isolation down to sample preparation, liquid chromatography (LC) separation, mass spectrometer (MS) data acquisition, and data analysis. To demonstrate the potential for single-cell and limited sample proteomics, we report on a series of benchmarking experiments where we combine LC separation on a new generation of micropillar array columns with state-of-the-art Orbitrap MS/MS detection and high-field asymmetric waveform ion mobility spectrometry (FAIMS). This dedicated limited sample column has a reduced cross section and micropillar dimensions that have been further downscaled (interpillar distance and pillar diameter by a factor of 2), resulting in improved chromatography at reduced void times. A dilution series of a HeLa tryptic digest (5-0.05 ng/μL) was used to explore the sensitivity that can be achieved. Comparative processing of the MS/MS data with Sequest HT, MS Amanda, Mascot, and SpectroMine pointed out the benefits of using Sequest HT together with INFERYS when analyzing sample amounts below 1 ng. Here, 2855 protein groups were identified from just 1 ng of HeLa tryptic digest hereby increasing detection sensitivity as compared to a previous contribution by a factor well above 10. By successfully identifying 1486 protein groups from as little as 250 pg of HeLa tryptic digest, we demonstrate outstanding sensitivity with great promise for use in limited sample proteomics workflows.
Collapse
Affiliation(s)
- Karel Stejskal
- IMBA
- Institute of Molecular Biotechnology of the Austrian Academy of
Sciences, Dr. Bohr Gasse
3, A-1030 Vienna, Austria
- IMP
- Institute of Molecular Pathology, Campus-Vienna-Biocenter 1, A-1030 Vienna, Austria
- Gregor
Mendel Institute of Molecular Plant Biology of the Austrian Academy
of Sciences, Dr. Bohr
Gasse 3, A-1030 Vienna, Austria
| | - Jeff Op de Beeck
- PharmaFluidics, Technologiepark-Zwijnaarde 82, B-9052 Gent, Belgium
| | - Gerhard Dürnberger
- IMBA
- Institute of Molecular Biotechnology of the Austrian Academy of
Sciences, Dr. Bohr Gasse
3, A-1030 Vienna, Austria
- IMP
- Institute of Molecular Pathology, Campus-Vienna-Biocenter 1, A-1030 Vienna, Austria
- Gregor
Mendel Institute of Molecular Plant Biology of the Austrian Academy
of Sciences, Dr. Bohr
Gasse 3, A-1030 Vienna, Austria
| | - Paul Jacobs
- PharmaFluidics, Technologiepark-Zwijnaarde 82, B-9052 Gent, Belgium
| | - Karl Mechtler
- IMBA
- Institute of Molecular Biotechnology of the Austrian Academy of
Sciences, Dr. Bohr Gasse
3, A-1030 Vienna, Austria
- IMP
- Institute of Molecular Pathology, Campus-Vienna-Biocenter 1, A-1030 Vienna, Austria
- Gregor
Mendel Institute of Molecular Plant Biology of the Austrian Academy
of Sciences, Dr. Bohr
Gasse 3, A-1030 Vienna, Austria
| |
Collapse
|
9
|
Chiva C, Mendes Maia T, Panse C, Stejskal K, Douché T, Matondo M, Loew D, Helm D, Rettel M, Mechtler K, Impens F, Nanni P, Shevchenko A, Sabidó E. Quality standards in proteomics research facilities: Common standards and quality procedures are essential for proteomics facilities and their users. EMBO Rep 2021; 22:e52626. [PMID: 34009726 PMCID: PMC8183401 DOI: 10.15252/embr.202152626] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 02/11/2021] [Indexed: 11/23/2022] Open
Affiliation(s)
- Cristina Chiva
- Centre de Regulació Genòmica, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Univeristat Pompeu Fabra, Barcelona, Spain
| | - Teresa Mendes Maia
- VIB Proteomics Core, VIB, Ghent, Belgium.,VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Christian Panse
- Functional Genomics Center Zurich, University/ETH Zurich, Zurich, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Karel Stejskal
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.,IMBA Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Thibaut Douché
- Institut Pasteur, Proteomics Platform, Mass Spectrometry for Biology Unit, USR CNRS 2000 MSBio Unit, CNRS, Paris, France
| | - Mariette Matondo
- Institut Pasteur, Proteomics Platform, Mass Spectrometry for Biology Unit, USR CNRS 2000 MSBio Unit, CNRS, Paris, France
| | - Damarys Loew
- Institut Curie, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, PSL Research University, Paris cedex 05, France
| | - Dominic Helm
- Proteomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany.,MS based Protein analysis Unit, Genomics Proteomics Core Facilities, DKFZ, Heidelberg, Germany
| | - Mandy Rettel
- Proteomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.,IMBA Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria.,Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter 7 (VBC), Vienna, Austria
| | - Francis Impens
- VIB Proteomics Core, VIB, Ghent, Belgium.,VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Paolo Nanni
- Functional Genomics Center Zurich, University/ETH Zurich, Zurich, Switzerland
| | - Anna Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Eduard Sabidó
- Centre de Regulació Genòmica, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Univeristat Pompeu Fabra, Barcelona, Spain
| |
Collapse
|
10
|
Leca I, Phillips AW, Hofer I, Landler L, Ushakova L, Cushion TD, Dürnberger G, Stejskal K, Mechtler K, Keays DA. A proteomic survey of microtubule-associated proteins in a R402H TUBA1A mutant mouse. PLoS Genet 2020; 16:e1009104. [PMID: 33137126 PMCID: PMC7660477 DOI: 10.1371/journal.pgen.1009104] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 04/06/2020] [Revised: 11/12/2020] [Accepted: 09/08/2020] [Indexed: 11/25/2022] Open
Abstract
Microtubules play a critical role in multiple aspects of neurodevelopment, including the generation, migration and differentiation of neurons. A recurrent mutation (R402H) in the α-tubulin gene TUBA1A is known to cause lissencephaly with cerebellar and striatal phenotypes. Previous work has shown that this mutation does not perturb the chaperone-mediated folding of tubulin heterodimers, which are able to assemble and incorporate into the microtubule lattice. To explore the molecular mechanisms that cause the disease state we generated a new conditional mouse line that recapitulates the R402H variant. We show that heterozygous mutants present with laminar phenotypes in the cortex and hippocampus, as well as a reduction in striatal size and cerebellar abnormalities. We demonstrate that homozygous expression of the R402H allele causes neuronal death and exacerbates a cell intrinsic defect in cortical neuronal migration. Microtubule sedimentation assays coupled with quantitative mass spectrometry demonstrated that the binding and/or levels of multiple microtubule associated proteins (MAPs) are perturbed by the R402H mutation including VAPB, REEP1, EZRIN, PRNP and DYNC1l1/2. Consistent with these data we show that the R402H mutation impairs dynein-mediated transport which is associated with a decoupling of the nucleus to the microtubule organising center. Our data support a model whereby the R402H variant is able to fold and incorporate into microtubules, but acts as a gain of function by perturbing the binding of MAPs. Microtubules are polymers composed of tubulin proteins, which play an important role in the development of the human brain. Genetic mutations in tubulin genes are known to cause neurodevelopmental diseases, including lissencephaly which is characterised by an impairment in the migration of neurons. In this study we investigate how a common mutation (R402H) in TUBA1A causes lissencephaly by generating and characterising a mouse with the same variant. We show that affected animals recapitulate multiple aspects of the human disease; including laminar perturbations in the cortex and hippocampus, attributable to defects in neuronal migration at key developmental time points. To characterize the molecular implications of the R402H mutation we purified microtubules from the developing brain, and analysed the proteins present by mass spectrometry. This revealed that the binding of DYNC1I1/2 to microtubules is altered in mice with the R402H mutation. Our results provide insight into the molecular pathology underlying tubulin related disease states, and provide a foundation for the rational design of therapeutic interventions.
Collapse
Affiliation(s)
- Ines Leca
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | | | - Iris Hofer
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Lukas Landler
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
- Institute of Zoology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Lyubov Ushakova
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Thomas David Cushion
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Gerhard Dürnberger
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Karel Stejskal
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - David Anthony Keays
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
- Department of Anatomy and Neuroscience, University of Melbourne, Parkville, Australia
- Division of Neurobiology, Department Biology II, Ludwig-Maximilians-University Munich, Planegg-Martinsried 82152, Germany
- * E-mail:
| |
Collapse
|
11
|
Majerská J, Schrumpfová PP, Dokládal L, Schořová Š, Stejskal K, Obořil M, Honys D, Kozáková L, Polanská PS, Sýkorová E. Correction to: Tandem affinity purification of AtTERT reveals putative interaction partners of plant telomerase in vivo. Protoplasma 2018; 255:715. [PMID: 29442174 DOI: 10.1007/s00709-018-1224-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In the published online version, the affiliations were mixed up. Corrected affiliation section is shown below. Also, the update has also been reflected in the author group section above.
Collapse
Affiliation(s)
- Jana Majerská
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i, Královopolská 135, CZ-61265, Brno, Czech Republic
- Central European Institute of Technology and Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Petra Procházková Schrumpfová
- Central European Institute of Technology and Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
| | - Ladislav Dokládal
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i, Královopolská 135, CZ-61265, Brno, Czech Republic
| | - Šárka Schořová
- Central European Institute of Technology and Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
| | - Karel Stejskal
- Central European Institute of Technology and Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
| | - Michal Obořil
- Central European Institute of Technology and Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
| | - David Honys
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic v.v.i, Rozvojová 263, CZ-16502, Prague, Czech Republic
| | - Lucie Kozáková
- Central European Institute of Technology and Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
| | - Pavla Sováková Polanská
- Central European Institute of Technology and Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
| | - Eva Sýkorová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i, Královopolská 135, CZ-61265, Brno, Czech Republic.
| |
Collapse
|
12
|
Hellerschmied D, Roessler M, Lehner A, Gazda L, Stejskal K, Imre R, Mechtler K, Dammermann A, Clausen T. UFD-2 is an adaptor-assisted E3 ligase targeting unfolded proteins. Nat Commun 2018; 9:484. [PMID: 29396393 PMCID: PMC5797217 DOI: 10.1038/s41467-018-02924-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 01/09/2018] [Indexed: 11/09/2022] Open
Abstract
Muscle development requires the coordinated activities of specific protein folding and degradation factors. UFD-2, a U-box ubiquitin ligase, has been reported to play a central role in this orchestra regulating the myosin chaperone UNC-45. Here, we apply an integrative in vitro and in vivo approach to delineate the substrate-targeting mechanism of UFD-2 and elucidate its distinct mechanistic features as an E3/E4 enzyme. Using Caenorhabditis elegans as model system, we demonstrate that UFD-2 is not regulating the protein levels of UNC-45 in muscle cells, but rather shows the characteristic properties of a bona fide E3 ligase involved in protein quality control. Our data demonstrate that UFD-2 preferentially targets unfolded protein segments. Moreover, the UNC-45 chaperone can serve as an adaptor protein of UFD-2 to poly-ubiquitinate unfolded myosin, pointing to a possible role of the UFD-2/UNC-45 pair in maintaining proteostasis in muscle cells.
Collapse
Affiliation(s)
- Doris Hellerschmied
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030, Vienna, Austria.,Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06511, USA
| | - Max Roessler
- Max F. Perutz Laboratories (MFPL), University of Vienna, Doktor-Bohr-Gasse 9, 1030, Vienna, Austria
| | - Anita Lehner
- Vienna Biocenter Core Facilities, Doktor-Bohr-Gasse 3, 1030, Vienna, Austria
| | - Linn Gazda
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030, Vienna, Austria
| | - Karel Stejskal
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030, Vienna, Austria
| | - Richard Imre
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030, Vienna, Austria
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030, Vienna, Austria
| | - Alexander Dammermann
- Max F. Perutz Laboratories (MFPL), University of Vienna, Doktor-Bohr-Gasse 9, 1030, Vienna, Austria.
| | - Tim Clausen
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030, Vienna, Austria. .,Medical University of Vienna, Vienna BioCenter (VBC), 1030, Vienna, Austria.
| |
Collapse
|
13
|
Majerská J, Schrumpfová PP, Dokládal L, Schořová Š, Stejskal K, Obořil M, Honys D, Kozáková L, Polanská PS, Sýkorová E. Tandem affinity purification of AtTERT reveals putative interaction partners of plant telomerase in vivo. Protoplasma 2017; 254:1547-1562. [PMID: 27853871 DOI: 10.1007/s00709-016-1042-3] [Citation(s) in RCA: 10] [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] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 11/04/2016] [Indexed: 05/15/2023]
Abstract
The life cycle of telomerase involves dynamic and complex interactions between proteins within multiple macromolecular networks. Elucidation of these associations is a key to understanding the regulation of telomerase under diverse physiological and pathological conditions from telomerase biogenesis, through telomere recruitment and elongation, to its non-canonical activities outside of telomeres. We used tandem affinity purification coupled to mass spectrometry to build an interactome of the telomerase catalytic subunit AtTERT, using Arabidopsis thaliana suspension cultures. We then examined interactions occurring at the AtTERT N-terminus, which is thought to fold into a discrete domain connected to the rest of the molecule via a flexible linker. Bioinformatic analyses revealed that interaction partners of AtTERT have a range of molecular functions, a subset of which is specific to the network around its N-terminus. A significant number of proteins co-purifying with the N-terminal constructs have been implicated in cell cycle and developmental processes, as would be expected of bona fide regulatory interactions and we have confirmed experimentally the direct nature of selected interactions. To examine AtTERT protein-protein interactions from another perspective, we also analysed AtTERT interdomain contacts to test potential dimerization of AtTERT. In total, our results provide an insight into the composition and architecture of the plant telomerase complex and this will aid in delineating molecular mechanisms of telomerase functions.
Collapse
Affiliation(s)
- Jana Majerská
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, CZ-61265, Brno, Czech Republic
- Central European Institute of Technology and Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Petra Procházková Schrumpfová
- Central European Institute of Technology and Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Ladislav Dokládal
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, CZ-61265, Brno, Czech Republic
| | - Šárka Schořová
- Central European Institute of Technology and Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
| | - Karel Stejskal
- Central European Institute of Technology and Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
| | - Michal Obořil
- Central European Institute of Technology and Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
| | - David Honys
- Institute of Experimental Biology, Academy of Sciences of the Czech Republic, v.v.i., Rozvojová 263, CZ-165 02, Prague, Czech Republic
| | - Lucie Kozáková
- Central European Institute of Technology and Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
| | - Pavla Sováková Polanská
- Central European Institute of Technology and Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
| | - Eva Sýkorová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, CZ-61265, Brno, Czech Republic.
| |
Collapse
|
14
|
Grochalová M, Konečná H, Stejskal K, Potěšil D, Fridrichová D, Srbová E, Ornerová K, Zdráhal Z. Deep coverage of the beer proteome. J Proteomics 2017; 162:119-124. [DOI: 10.1016/j.jprot.2017.05.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 04/12/2017] [Accepted: 05/01/2017] [Indexed: 11/25/2022]
|
15
|
Stejskal S, Stepka K, Tesarova L, Stejskal K, Matejkova M, Simara P, Zdrahal Z, Koutna I. Cell cycle-dependent changes in H3K56ac in human cells. Cell Cycle 2016; 14:3851-63. [PMID: 26645646 DOI: 10.1080/15384101.2015.1106760] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The incorporation of histone H3 with an acetylated lysine 56 (H3K56ac) into the nucleosome is important for chromatin remodeling and serves as a marker of new nucleosomes during DNA replication and repair in yeast. However, in human cells, the level of H3K56ac is greatly reduced, and its role during the cell cycle is controversial. Our aim was to determine the potential of H3K56ac to regulate cell cycle progression in different human cell lines. A significant increase in the number of H3K56ac foci, but not in H3K56ac protein levels, was observed during the S and G2 phases in cancer cell lines, but was not observed in embryonic stem cell lines. Despite this increase, the H3K56ac signal was not present in late replication chromatin, and H3K56ac protein levels did not decrease after the inhibition of DNA replication. H3K56ac was not tightly associated with the chromatin and was primarily localized to active chromatin regions. Our results support the role of H3K56ac in transcriptionally active chromatin areas but do not confirm H3K56ac as a marker of newly synthetized nucleosomes in DNA replication.
Collapse
Affiliation(s)
- Stanislav Stejskal
- a Centre for Biomedical Image Analysis; Faculty of Informatics; Masaryk University ; Brno , Czech Republic
| | - Karel Stepka
- a Centre for Biomedical Image Analysis; Faculty of Informatics; Masaryk University ; Brno , Czech Republic
| | - Lenka Tesarova
- a Centre for Biomedical Image Analysis; Faculty of Informatics; Masaryk University ; Brno , Czech Republic
| | - Karel Stejskal
- b Research Group - Proteomics; Central European Institute of Technology; Masaryk University ; Brno , Czech Republic.,c National Centre for Biomolecular Research; Faculty of Science; Masaryk University ; Brno , Czech Republic
| | - Martina Matejkova
- a Centre for Biomedical Image Analysis; Faculty of Informatics; Masaryk University ; Brno , Czech Republic
| | - Pavel Simara
- a Centre for Biomedical Image Analysis; Faculty of Informatics; Masaryk University ; Brno , Czech Republic
| | - Zbynek Zdrahal
- b Research Group - Proteomics; Central European Institute of Technology; Masaryk University ; Brno , Czech Republic.,c National Centre for Biomolecular Research; Faculty of Science; Masaryk University ; Brno , Czech Republic
| | - Irena Koutna
- a Centre for Biomedical Image Analysis; Faculty of Informatics; Masaryk University ; Brno , Czech Republic
| |
Collapse
|
16
|
Kozakova L, Vondrova L, Stejskal K, Charalabous P, Kolesar P, Lehmann AR, Uldrijan S, Sanderson CM, Zdrahal Z, Palecek JJ. The melanoma-associated antigen 1 (MAGEA1) protein stimulates the E3 ubiquitin-ligase activity of TRIM31 within a TRIM31-MAGEA1-NSE4 complex. Cell Cycle 2015; 14:920-30. [PMID: 25590999 PMCID: PMC4614679 DOI: 10.1080/15384101.2014.1000112] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The MAGE (Melanoma-associated antigen) protein family members are structurally related to each other by a MAGE-homology domain comprised of 2 winged helix motifs WH/A and WH/B. This family specifically evolved in placental mammals although single homologs designated NSE3 (non-SMC element) exist in most eukaryotes. NSE3, together with its partner proteins NSE1 and NSE4 form a tight subcomplex of the structural maintenance of chromosomes SMC5–6 complex. Previously, we showed that interactions of the WH/B motif of the MAGE proteins with their NSE4/EID partners are evolutionarily conserved (including the MAGEA1-NSE4 interaction). In contrast, the interaction of the WH/A motif of NSE3 with NSE1 diverged in the MAGE paralogs. We hypothesized that the MAGE paralogs acquired new RING-finger-containing partners through their evolution and form MAGE complexes reminiscent of NSE1-NSE3-NSE4 trimers. In this work, we employed the yeast 2-hybrid system to screen a human RING-finger protein library against several MAGE baits. We identified a number of potential MAGE-RING interactions and confirmed several of them (MDM4, PCGF6, RNF166, TRAF6, TRIM8, TRIM31, TRIM41) in co-immunoprecipitation experiments. Among these MAGE-RING pairs, we chose to examine MAGEA1-TRIM31 in detail and showed that both WH/A and WH/B motifs of MAGEA1 bind to the coiled-coil domain of TRIM31 and that MAGEA1 interaction stimulates TRIM31 ubiquitin-ligase activity. In addition, TRIM31 directly binds to NSE4, suggesting the existence of a TRIM31-MAGEA1-NSE4 complex reminiscent of the NSE1-NSE3-NSE4 trimer. These results suggest that MAGEA1 functions as a co-factor of TRIM31 ubiquitin-ligase and that the TRIM31-MAGEA1-NSE4 complex may have evolved from an ancestral NSE1-NSE3-NSE4 complex.
Collapse
Affiliation(s)
- Lucie Kozakova
- a From the Mendel Center for Plant Genomics and Proteomics; Central European Institute of Technology; Masaryk University ; Brno , Czech Republic
| | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Matulova M, Varmuzova K, Sisak F, Havlickova H, Babak V, Stejskal K, Zdrahal Z, Rychlik I. Chicken innate immune response to oral infection with Salmonella enterica serovar Enteritidis. Vet Res 2013; 44:37. [PMID: 23687968 PMCID: PMC3663788 DOI: 10.1186/1297-9716-44-37] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 04/23/2013] [Indexed: 02/02/2023] Open
Abstract
The characterization of the immune response of chickens to Salmonella infection is usually limited to the quantification of expression of genes coding for cytokines, chemokines or antimicrobial peptides. However, processes occurring in the cecum of infected chickens are likely to be much more diverse. In this study we have therefore characterized the transcriptome and proteome in the chicken cecum after infection with Salmonella Enteritidis. Using a combination of 454 pyrosequencing, protein mass spectrometry and quantitative real-time PCR, we identified 48 down- and 56 up-regulated chicken genes after Salmonella Enteritidis infection. The most inducible gene was that coding for MMP7, exhibiting a 5952 fold induction 9 days post-infection. An induction of greater than 100 fold was observed for IgG, IRG1, SAA, ExFABP, IL-22, TRAP6, MRP126, IFNγ, iNOS, ES1, IL-1β, LYG2, IFIT5, IL-17, AVD, AH221 and SERPIN B. Since prostaglandin D2 synthase was upregulated and degrading hydroxyprostaglandin dehydrogenase was downregulated after the infection, prostaglandin must accumulate in the cecum of chickens infected with Salmonella Enteritidis. Finally, above mentioned signaling was dependent on the presence of a SPI1-encoded type III secretion system in Salmonella Enteritidis. The inflammation lasted for 2 weeks after which time the expression of the “inflammatory” genes returned back to basal levels and, instead, the expression of IgA and IgG increased. This points to an important role for immunoglobulins in the restoration of homeostasis in the cecum after infection.
Collapse
Affiliation(s)
- Marta Matulova
- Veterinary Research Institute, Hudcova 70, Brno 621 00, Czech Republic.
| | | | | | | | | | | | | | | |
Collapse
|
18
|
Affiliation(s)
- Karel Stejskal
- Research
Group Proteomics, Central European Institute of Technology and ‡National Centre
for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech
Republic
| | - David Potěšil
- Research
Group Proteomics, Central European Institute of Technology and ‡National Centre
for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech
Republic
| | - Zbyněk Zdráhal
- Research
Group Proteomics, Central European Institute of Technology and ‡National Centre
for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech
Republic
| |
Collapse
|
19
|
Dokládal L, Obořil M, Stejskal K, Zdráhal Z, Ptáčková N, Chaloupková R, Damborský J, Kašparovský T, Jeandroz S, Žd'árská M, Lochman J. Physiological and proteomic approaches to evaluate the role of sterol binding in elicitin-induced resistance. J Exp Bot 2012; 63:2203-15. [PMID: 22223811 PMCID: PMC3295402 DOI: 10.1093/jxb/err427] [Citation(s) in RCA: 12] [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] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Revised: 11/28/2011] [Accepted: 11/30/2011] [Indexed: 05/22/2023]
Abstract
Cryptogein is a proteinaceous elicitor secreted by Phytophthora cryptogea that can induce resistance to P. parasitica in tobacco plants. On the basis of previous computer modelling experiments, by site-directed mutagenesis a series of cryptogein variants was prepared with altered abilities to bind sterols, phospholipids or both. The sterol binding and phospholipid transfer activities corresponded well with the previously reported structural data. Induction of the synthesis of reactive oxygen species (ROS) in tobacco cells in suspension and proteomic analysis of intercellular fluid changes in tobacco leaves triggered by these mutant proteins were not proportional to their ability to bind or transfer sterols and phospholipids. However, changes in the intercellular proteome corresponded to transcription levels of defence genes and resistance to P. parasitica and structure-prediction of mutants did not reveal any significant changes in protein structure. These results suggest, contrary to previous proposals, that the sterol-binding ability of cryptogein and its mutants, and the associated conformational change in the ω-loop, might not be principal factors in either ROS production or resistance induction. Nevertheless, the results support the importance of the ω-loop for the interaction of the protein with the high affinity binding site on the plasma membrane.
Collapse
Affiliation(s)
- Ladislav Dokládal
- Department of Biochemistry, Faculty of Science, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic
| | - Michal Obořil
- Department of Biochemistry, Faculty of Science, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic
| | - Karel Stejskal
- Core Facility–Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Zbyněk Zdráhal
- Core Facility–Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Nikola Ptáčková
- Department of Biochemistry, Faculty of Science, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic
| | - Radka Chaloupková
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Substances in the Environment, Faculty of Science, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic
| | - Jiří Damborský
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Substances in the Environment, Faculty of Science, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic
| | - Tomáš Kašparovský
- Department of Biochemistry, Faculty of Science, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic
| | - Sylvain Jeandroz
- UMR AgroSup Dijon/CNRS/INRA/Université Bourgogne “Agroécologie”, 17 rue Sully, BP 86510, F-21065 Dijon cedex, France
| | - Markéta Žd'árská
- Core Facility–Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Jan Lochman
- Department of Biochemistry, Faculty of Science, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic
| |
Collapse
|
20
|
Cumová J, Jedličková L, Potěšil D, Sedo O, Stejskal K, Potáčová A, Zdráhal Z, Hájek R. [Comparative plasma proteomic analysis of patients with multiple myeloma treated with bortezomib-based regimens]. Klin Onkol 2012; 25:17-25. [PMID: 22348216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
BACKGROUNDS Recently, the term biomarker has become, especially in connection with the term clinical proteomics, one of the most frequent terms in the field of biomedical research. The aim of this work was to select an appropriate pre-fractionation method of blood plasma prior to a subsequent proteomic analysis of low-abundant fraction of proteins by two dimensional gel electrophoresis (2-DE) and mass spectrometry to improve the resolution of 2-DE maps and protein identification. MATERIALS AND METHODS First, we compared two prefractionation methods (MARS versus ProteoMiner) preceding 2-DE analysis using 10 blood plasma samples. Based on the results of the comparative experiments, low-abundant plasma protein fractions from 18 multiple myeloma patients treated with bortezomib were analyzed. Patients were divided into two groups: a group resistant to chemotherapy (9 patients--disease progression, stable disease) and a group with positive clinical response (9 patients--complete and partial remission). RESULTS AND CONCLUSION Samples prefractioned by ProteoMiner method yielded 2-DE maps with a significantly increased number of detected protein spots, as compared to immunodepletion method MARS (Multiple Affinity Removal System). Between groups of chemoresistant and sensitive patients treated with bortezomib, 15 differently intense spots were revealed by image analysis. These spots were found to correspond to 10 proteins, as confirmed by mass spectrometry. Seven proteins had significantly lower protein level in the group of chemosensitive patients (serum amyloid P, fibrinogen--gamma chain, retinol-binding protein 4, complement factor C4-A, apolipoprotein E, carboxypeptidase N and complement factor H-related protein 1) and 3 proteins showed significantly higher levels of protein (or were only detected) in the group of chemosensitive patients (serum paraoxonase 1, alpha-1-antitrypsin and complement factor B).
Collapse
Affiliation(s)
- J Cumová
- Babákova myelomová skupina, Ústav patologické fyziologie, LF MU Brno
| | | | | | | | | | | | | | | |
Collapse
|
21
|
Beklova M, Adam V, Stejskal K, Zitka O, Zeman L, Horna A, Kizek R. Liquid chromatography coupled with electrochemical detector as a tool for detection of fat-soluble vitamins in blood serum. Toxicol Lett 2008. [DOI: 10.1016/j.toxlet.2008.06.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
22
|
Mikelova R, Prokop Z, Stejskal K, Adam V, Beklova M, Trnkova L, Kulichova B, Horna A, Chaloupkova R, Damborsky J, Kizek R. Enzymatic Reaction Coupled with Flow-Injection Analysis with Charged Aerosol, Coulometric, or Amperometric Detection for Estimation of Contamination of the Environment by Pesticides. Chromatographia 2008. [DOI: 10.1365/s10337-008-0590-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
23
|
Kukacka J, Zitka O, Horna A, Stejskal K, Zehnalek J, Adam V, Havel L, Zeman L, Prusa R, Trnkova L, Kizek R. A new tool for distinguishing of different structural forms of lactoferrin. FASEB J 2007. [DOI: 10.1096/fasebj.21.5.a635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jiri Kukacka
- Dep. of Clinical Biochemistry and PathobiochemistryCharles University 2nd Medical SchoolV Uvalu 84Prague15006Czech Republic
| | - Ondrej Zitka
- Dep. of Chemistry and BiochemistryMendel University of Agriculture and ForestryZemedelska 1BrnoCzech Republic
| | - Ales Horna
- Radanal LtdOkruzni 613PardubiceCzech Republic
| | - Karel Stejskal
- Dep. of Chemistry and BiochemistryMendel University of Agriculture and ForestryZemedelska 1BrnoCzech Republic
| | - Josef Zehnalek
- Dep. of Chemistry and BiochemistryMendel University of Agriculture and ForestryZemedelska 1BrnoCzech Republic
| | - Vojtech Adam
- Dep. of Chemistry and BiochemistryMendel University of Agriculture and ForestryZemedelska 1BrnoCzech Republic
| | - Ladislav Havel
- Dep. of Chemistry and BiochemistryMendel University of Agriculture and ForestryZemedelska 1BrnoCzech Republic
| | - Ladislav Zeman
- Dep. of Chemistry and BiochemistryMendel University of Agriculture and ForestryZemedelska 1BrnoCzech Republic
| | - Richard Prusa
- Dep. of Clinical Biochemistry and PathobiochemistryCharles University 2nd Medical SchoolV Uvalu 84Prague15006Czech Republic
| | - Libuse Trnkova
- Dep. of Theoretical and Physical ChemistryMasaryk UniversityKotlarska 2BrnoCzech Republic
| | - Rene Kizek
- Dep. of Chemistry and BiochemistryMendel University of Agriculture and ForestryZemedelska 1BrnoCzech Republic
| |
Collapse
|
24
|
Krizkova S, Adam V, Petrlova J, Zitka O, Stejskal K, Zehnalek J, Sures B, Trnkova L, Beklova M, Kizek R. A Suggestion of Electrochemical Biosensor for Study of Platinum(II)-DNA Interactions. ELECTROANAL 2007. [DOI: 10.1002/elan.200603737] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
25
|
Petrlova J, Mikelova R, Stejskal K, Kleckerova A, Zitka O, Petrek J, Havel L, Zehnalek J, Vojtech A, Trnkova L, Kizek R. Simultaneous determination of eight biologically active thiol compounds using gradient elution-liquid chromatography with Coul-Array detection. J Sep Sci 2006; 29:1166-73. [PMID: 16830732 DOI: 10.1002/jssc.200500425] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The most active form of sulfur in biomolecules is the thiol group, present in a number of biologically active compounds. Here we present a comprehensive study of thiol analysis using flow injection analysis/HPLC with electrochemical detection. The effect of different potentials of working electrodes, of organic solvent contents in the mobile phase, and of isocratic and gradient elution on simultaneous determination of thiol compounds (cysteine, cystine, N-acetylcysteine, homocysteine, reduced and oxidised glutathione, desglycinephytochelatin, and phytochelatins) are described and discussed. These thiol compounds were well separated and detected under optimised HPLC-electrochemical detection conditions (mobile phase: 80 mM trifluoroacetic acid and methanol with a gradient profile starting at 97:3 (TFA:methanol), kept constant for the first 8 min, then decreasing to 85:15 during one minute, kept constant for 8 min, and finally increasing linearly up to 97:3 from 17 to 18 min; the flow rate was 0.8 mL/min, column and detector temperature 25 degrees C, and the electrode potential 900 mV). We were able to determine tens of femtomoles (3 S/N) of the thiols per injection (5 microL), except for phytochelatin5 whose detection limit was 2.1 pmole. This technique was consequently used for simultaneous determination of compounds of interest in biological samples (maize tissue and human blood serum).
Collapse
Affiliation(s)
- Jitka Petrlova
- Department of Chemistry and Biochemistry, Mendel University of Agriculture and Forestry, Brno, Czech Republic
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|