1
|
Aakko J, Pietilä S, Suomi T, Mahmoudian M, Toivonen R, Kouvonen P, Rokka A, Hänninen A, Elo LL. Data-Independent Acquisition Mass Spectrometry in Metaproteomics of Gut Microbiota—Implementation and Computational Analysis. J Proteome Res 2019; 19:432-436. [DOI: 10.1021/acs.jproteome.9b00606] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Juhani Aakko
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Sami Pietilä
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Tomi Suomi
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Mehrad Mahmoudian
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
- Department of Future Technologies, University of Turku, Turku 20014, Finland
| | - Raine Toivonen
- Department of Medical Microbiology and Immunology, University of Turku, Turku 20520, Finland
| | - Petri Kouvonen
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Anne Rokka
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Arno Hänninen
- Department of Medical Microbiology and Immunology, University of Turku, Turku 20520, Finland
- TYKS Microbiology, Turku University Central Hospital, Turku 20521, Finland
| | - Laura L. Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
| |
Collapse
|
2
|
Eerola SK, Santio NM, Rinne S, Kouvonen P, Corthals GL, Scaravilli M, Scala G, Serra A, Greco D, Ruusuvuori P, Latonen L, Rainio EM, Visakorpi T, Koskinen PJ. Phosphorylation of NFATC1 at PIM1 target sites is essential for its ability to promote prostate cancer cell migration and invasion. Cell Commun Signal 2019; 17:148. [PMID: 31730483 PMCID: PMC6858710 DOI: 10.1186/s12964-019-0463-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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] [Received: 06/18/2019] [Accepted: 10/22/2019] [Indexed: 12/11/2022] Open
Abstract
Background Progression of prostate cancer from benign local tumors to metastatic carcinomas is a multistep process. Here we have investigated the signaling pathways that support migration and invasion of prostate cancer cells, focusing on the role of the NFATC1 transcription factor and its post-translational modifications. We have previously identified NFATC1 as a substrate for the PIM1 kinase and shown that PIM1-dependent phosphorylation increases NFATC1 activity without affecting its subcellular localization. Both PIM kinases and NFATC1 have been reported to promote cancer cell migration, invasion and angiogenesis, but it has remained unclear whether the effects of NFATC1 are phosphorylation-dependent and which downstream targets are involved. Methods We used mass spectrometry to identify PIM1 phosphorylation target sites in NFATC1, and analysed their functional roles in three prostate cancer cell lines by comparing phosphodeficient mutants to wild-type NFATC1. We used luciferase assays to determine effects of phosphorylation on NFAT-dependent transcriptional activity, and migration and invasion assays to evaluate effects on cell motility. We also performed a microarray analysis to identify novel PIM1/NFATC1 targets, and validated one of them with both cellular expression analyses and in silico in clinical prostate cancer data sets. Results Here we have identified ten PIM1 target sites in NFATC1 and found that prevention of their phosphorylation significantly decreases the transcriptional activity as well as the pro-migratory and pro-invasive effects of NFATC1 in prostate cancer cells. We observed that also PIM2 and PIM3 can phosphorylate NFATC1, and identified several novel putative PIM1/NFATC1 target genes. These include the ITGA5 integrin, which is differentially expressed in the presence of wild-type versus phosphorylation-deficient NFATC1, and which is coexpressed with PIM1 and NFATC1 in clinical prostate cancer specimens. Conclusions Based on our data, phosphorylation of PIM1 target sites stimulates NFATC1 activity and enhances its ability to promote prostate cancer cell migration and invasion. Therefore, inhibition of the interplay between PIM kinases and NFATC1 may have therapeutic implications for patients with metastatic forms of cancer. Graphical abstract ![]()
Collapse
Affiliation(s)
- Sini K Eerola
- Department of Biology, University of Turku, Vesilinnantie 5, FI-20500, Turku, Finland.,Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Niina M Santio
- Department of Biology, University of Turku, Vesilinnantie 5, FI-20500, Turku, Finland
| | - Sanni Rinne
- Department of Biology, University of Turku, Vesilinnantie 5, FI-20500, Turku, Finland
| | - Petri Kouvonen
- Turku Centre for Biotechnology, University of Turku, Turku, Finland
| | - Garry L Corthals
- Turku Centre for Biotechnology, University of Turku, Turku, Finland
| | - Mauro Scaravilli
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland.,Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Giovanni Scala
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland.,University of Helsinki, Helsinki, Finland
| | - Angela Serra
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Dario Greco
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland.,University of Helsinki, Helsinki, Finland
| | - Pekka Ruusuvuori
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland.,Signal processing laboratory, Tampere University of Technology, Pori, Finland
| | - Leena Latonen
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland.,Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Eeva-Marja Rainio
- Department of Biology, University of Turku, Vesilinnantie 5, FI-20500, Turku, Finland
| | - Tapio Visakorpi
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland.,Fimlab Laboratories, Tampere, Finland
| | - Päivi J Koskinen
- Department of Biology, University of Turku, Vesilinnantie 5, FI-20500, Turku, Finland.
| |
Collapse
|
3
|
Miikkulainen P, Högel H, Rantanen K, Suomi T, Kouvonen P, Elo LL, Jaakkola PM. HIF prolyl hydroxylase PHD3 regulates translational machinery and glucose metabolism in clear cell renal cell carcinoma. Cancer Metab 2017; 5:5. [PMID: 28680592 PMCID: PMC5496173 DOI: 10.1186/s40170-017-0167-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [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] [Received: 01/06/2017] [Accepted: 06/25/2017] [Indexed: 12/03/2022] Open
Abstract
Background A key feature of clear cell renal cell carcinoma (ccRCC) is the inactivation of the von Hippel-Lindau tumour suppressor protein (pVHL) that leads to the activation of hypoxia-inducible factor (HIF) pathway also in well-oxygenated conditions. Important regulator of HIF-α, prolyl hydroxylase PHD3, is expressed in high amounts in ccRCC. Although several functions and downstream targets for PHD3 in cancer have been suggested, the role of elevated PHD3 expression in ccRCC is not clear. Methods To gain insight into the functions of high PHD3 expression in ccRCC, we used PHD3 knockdown by siRNA in 786-O cells under normoxic and hypoxic conditions and performed discovery mass spectrometry (LC-MS/MS) of the purified peptide samples. The LC-MS/MS results were analysed by label-free quantification of proteome data using a peptide-level expression-change averaging procedure and subsequent gene ontology enrichment analysis. Results Our data reveals an intriguingly widespread effect of PHD3 knockdown with 91 significantly regulated proteins. Under hypoxia, the response to PHD3 silencing was wider than under normoxia illustrated by both the number of regulated proteins and by the range of protein expression levels. The main cellular functions regulated by PHD3 expression were glucose metabolism, protein translation and messenger RNA (mRNA) processing. PHD3 silencing led to downregulation of most glycolytic enzymes from glucose transport to lactate production supported by the reduction in extracellular acidification and lactate production and increase in cellular oxygen consumption rate. Moreover, upregulation of mRNA processing-related proteins and alteration in a number of ribosomal proteins was seen as a response to PHD3 silencing. Further studies on upstream effectors of the translational machinery revealed a possible role for PHD3 in regulation of mTOR pathway signalling. Conclusions Our findings suggest crucial involvement of PHD3 in the maintenance of key cellular functions including glycolysis and protein synthesis in ccRCC. Electronic supplementary material The online version of this article (doi:10.1186/s40170-017-0167-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Petra Miikkulainen
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520 Turku, Finland.,Department of Medical Biochemistry, Faculty of Medicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland
| | - Heidi Högel
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520 Turku, Finland.,Department of Medical Biochemistry, Faculty of Medicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland
| | - Krista Rantanen
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520 Turku, Finland.,Department of Medical Biochemistry, Faculty of Medicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland
| | - Tomi Suomi
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520 Turku, Finland.,Department of Information Technology, Faculty of Mathematics and Natural Sciences, University of Turku, Vesilinnantie 5, 20520 Turku, Finland
| | - Petri Kouvonen
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520 Turku, Finland
| | - Laura L Elo
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520 Turku, Finland
| | - Panu M Jaakkola
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520 Turku, Finland.,Department of Medical Biochemistry, Faculty of Medicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland.,Department of Oncology and Radiotherapy, Turku University Hospital, Hämeentie 11, 20520 Turku, Finland
| |
Collapse
|
4
|
Bulanova DR, Akimov YA, Rokka A, Laajala TD, Aittokallio T, Kouvonen P, Pellinen T, Kuznetsov SG. Orphan G protein-coupled receptor GPRC5A modulates integrin β1-mediated epithelial cell adhesion. Cell Adh Migr 2017; 11:434-446. [PMID: 27715394 PMCID: PMC5810789 DOI: 10.1080/19336918.2016.1245264] [Citation(s) in RCA: 7] [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: 01/13/2023] Open
Abstract
G-Protein Coupled Receptor (GPCR), Class C, Group 5, Member A (GPRC5A) has been implicated in several malignancies. The underlying mechanisms, however, remain poorly understood. Using a panel of human cell lines, we demonstrate that CRISPR/Cas9-mediated knockout and RNAi-mediated depletion of GPRC5A impairs cell adhesion to integrin substrates: collagens I and IV, fibronectin, as well as to extracellular matrix proteins derived from the Engelbreth-Holm-Swarm (EHS) mouse sarcoma (Matrigel). Consistent with the phenotype, knock-out of GPRC5A correlated with a reduced integrin β1 (ITGB1) protein expression, impaired phosphorylation of the focal adhesion kinase (FAK), and lower activity of small GTPases RhoA and Rac1. Furthermore, we provide the first evidence for a direct interaction between GPRC5A and a receptor tyrosine kinase EphA2, an upstream regulator of FAK, although its contribution to the observed adhesion phenotype is unclear. Our findings reveal an unprecedented role for GPRC5A in regulation of the ITGB1-mediated cell adhesion and it's downstream signaling, thus indicating a potential novel role for GPRC5A in human epithelial cancers.
Collapse
Affiliation(s)
- Daria R Bulanova
- a Institute for Molecular Medicine Finland (FIMM), University of Helsinki , Helsinki , Finland
| | - Yevhen A Akimov
- a Institute for Molecular Medicine Finland (FIMM), University of Helsinki , Helsinki , Finland
| | - Anne Rokka
- c Turku Centre for Biotechnology , University of Turku and Abo Academy , Turku , Finland
| | - Teemu D Laajala
- a Institute for Molecular Medicine Finland (FIMM), University of Helsinki , Helsinki , Finland.,b Department of Mathematics and Statistics , University of Turku , Turku , Finland
| | - Tero Aittokallio
- a Institute for Molecular Medicine Finland (FIMM), University of Helsinki , Helsinki , Finland.,b Department of Mathematics and Statistics , University of Turku , Turku , Finland
| | - Petri Kouvonen
- c Turku Centre for Biotechnology , University of Turku and Abo Academy , Turku , Finland
| | - Teijo Pellinen
- a Institute for Molecular Medicine Finland (FIMM), University of Helsinki , Helsinki , Finland
| | - Sergey G Kuznetsov
- a Institute for Molecular Medicine Finland (FIMM), University of Helsinki , Helsinki , Finland
| |
Collapse
|
5
|
Abstract
Blood protein measurements are used frequently in the clinic in the assessment of patient health. Nevertheless, there remains the need for new biomarkers with better diagnostic specificities. With the advent of improved technology for bioanalysis and the growth of biobanks including collections from specific disease risk cohorts, the plasma proteome has remained a target of proteomics research toward the characterization of disease-related biomarkers. The following protocol presents a workflow for serum/plasma proteomics including details of sample preparation both with and without immunoaffinity depletion of the most abundant plasma proteins and methodology for selected reaction monitoring mass spectrometry validation.
Collapse
Affiliation(s)
| | - Robert Moulder
- Turku Centre for Biotechnology, University of Turku, Turku, Finland
| | - Petri Kouvonen
- Turku Centre for Biotechnology, University of Turku, Turku, Finland
| | - Riitta Lahesmaa
- Turku Centre for Biotechnology, University of Turku, Turku, Finland
| | - David R Goodlett
- Turku Centre for Biotechnology, University of Turku, Turku, Finland. .,Department of Pharmaceutical Science, University of Maryland, 20 North Pine Street, Baltimore, MD, 21201, USA.
| |
Collapse
|
6
|
Vuorijoki L, Isojärvi J, Kallio P, Kouvonen P, Aro EM, Corthals GL, Jones PR, Muth-Pawlak D. Development of a Quantitative SRM-Based Proteomics Method to Study Iron Metabolism of Synechocystis sp. PCC 6803. J Proteome Res 2015; 15:266-79. [DOI: 10.1021/acs.jproteome.5b00800] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Linda Vuorijoki
- Molecular
Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
| | - Janne Isojärvi
- Molecular
Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
| | - Pauli Kallio
- Molecular
Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
| | - Petri Kouvonen
- Turku
Proteomics Facility, Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20014 Turku, Finland
| | - Eva-Mari Aro
- Molecular
Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
| | - Garry L. Corthals
- Turku
Proteomics Facility, Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20014 Turku, Finland
- Van’t
Hoff Institute for Molecular Sciences, University of Amsterdam, 1018 WV Amsterdam, The Netherlands
| | - Patrik R. Jones
- Department
of Life Sciences, Imperial College London, Sir Alexander Fleming Building, London SW7 2AZ, United Kingdom
| | - Dorota Muth-Pawlak
- Molecular
Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
- Turku
Proteomics Facility, Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20014 Turku, Finland
| |
Collapse
|
7
|
Konert G, Trotta A, Kouvonen P, Rahikainen M, Durian G, Blokhina O, Fagerstedt K, Muth D, Corthals GL, Kangasjärvi S. Protein phosphatase 2A (PP2A) regulatory subunit B'γ interacts with cytoplasmic ACONITASE 3 and modulates the abundance of AOX1A and AOX1D in Arabidopsis thaliana. New Phytol 2015; 205:1250-1263. [PMID: 25307043 DOI: 10.1111/nph.13097] [Citation(s) in RCA: 16] [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] [Received: 05/30/2014] [Accepted: 09/11/2014] [Indexed: 05/09/2023]
Abstract
Organellar reactive oxygen species (ROS) signalling is a key mechanism that promotes the onset of defensive measures in stress-exposed plants. The underlying molecular mechanisms and feedback regulation loops, however, still remain poorly understood. Our previous work has shown that a specific regulatory B'γ subunit of protein phosphatase 2A (PP2A) is required to control organellar ROS signalling and associated metabolic adjustments in Arabidopsis thaliana. Here, we addressed the mechanisms through which PP2A-B'γ impacts on organellar metabolic crosstalk and ROS homeostasis in leaves. Genetic, biochemical and pharmacological approaches, together with a combination of data-dependent acquisition (DDA) and selected reaction monitoring (SRM) MS techniques, were utilized to assess PP2A-B'γ-dependent adjustments in Arabidopsis thaliana. We show that PP2A-B'γ physically interacts with the cytoplasmic form of aconitase, a central metabolic enzyme functionally connected with mitochondrial respiration, oxidative stress responses and regulation of cell death in plants. Furthermore, PP2A-B'γ impacts ROS homeostasis by controlling the abundance of specific alternative oxidase isoforms, AOX1A and AOX1D, in leaf mitochondria. We conclude that PP2A-B'γ-dependent regulatory actions modulate the functional status of metabolic enzymes that essentially contribute to intracellular ROS signalling and metabolic homeostasis in plants.
Collapse
Affiliation(s)
- Grzegorz Konert
- Department of Biochemistry, Molecular Plant Biology, University of Turku, FI-20014, Turku, Finland
| | - Andrea Trotta
- Department of Biochemistry, Molecular Plant Biology, University of Turku, FI-20014, Turku, Finland
| | - Petri Kouvonen
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20014, Turku, Finland
| | - Moona Rahikainen
- Department of Biochemistry, Molecular Plant Biology, University of Turku, FI-20014, Turku, Finland
| | - Guido Durian
- Department of Biochemistry, Molecular Plant Biology, University of Turku, FI-20014, Turku, Finland
| | - Olga Blokhina
- Department of Biosciences, University of Helsinki, FI-00014, Helsinki, Finland
| | - Kurt Fagerstedt
- Department of Biosciences, University of Helsinki, FI-00014, Helsinki, Finland
| | - Dorota Muth
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20014, Turku, Finland
| | - Garry L Corthals
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20014, Turku, Finland
| | - Saijaliisa Kangasjärvi
- Department of Biochemistry, Molecular Plant Biology, University of Turku, FI-20014, Turku, Finland
| |
Collapse
|
8
|
Rosenberger G, Koh CC, Guo T, Röst HL, Kouvonen P, Collins BC, Heusel M, Liu Y, Caron E, Vichalkovski A, Faini M, Schubert OT, Faridi P, Ebhardt HA, Matondo M, Lam H, Bader SL, Campbell DS, Deutsch EW, Moritz RL, Tate S, Aebersold R. A repository of assays to quantify 10,000 human proteins by SWATH-MS. Sci Data 2014; 1:140031. [PMID: 25977788 PMCID: PMC4322573 DOI: 10.1038/sdata.2014.31] [Citation(s) in RCA: 292] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 08/06/2014] [Indexed: 12/30/2022] Open
Abstract
Mass spectrometry is the method of choice for deep and reliable exploration of the (human) proteome. Targeted mass spectrometry reliably detects and quantifies pre-determined sets of proteins in a complex biological matrix and is used in studies that rely on the quantitatively accurate and reproducible measurement of proteins across multiple samples. It requires the one-time, a priori generation of a specific measurement assay for each targeted protein. SWATH-MS is a mass spectrometric method that combines data-independent acquisition (DIA) and targeted data analysis and vastly extends the throughput of proteins that can be targeted in a sample compared to selected reaction monitoring (SRM). Here we present a compendium of highly specific assays covering more than 10,000 human proteins and enabling their targeted analysis in SWATH-MS datasets acquired from research or clinical specimens. This resource supports the confident detection and quantification of 50.9% of all human proteins annotated by UniProtKB/Swiss-Prot and is therefore expected to find wide application in basic and clinical research. Data are available via ProteomeXchange (PXD000953-954) and SWATHAtlas (SAL00016-35).
Collapse
Affiliation(s)
- George Rosenberger
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland ; PhD Program in Systems Biology, University of Zurich and ETH Zurich , CH-8093 Zurich, Switzerland
| | - Ching Chiek Koh
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland ; Ruprecht Karls University of Heidelberg , DE-69117 Heidelberg, Germany
| | - Tiannan Guo
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland
| | - Hannes L Röst
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland ; PhD Program in Systems Biology, University of Zurich and ETH Zurich , CH-8093 Zurich, Switzerland
| | - Petri Kouvonen
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland
| | - Ben C Collins
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland
| | - Moritz Heusel
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland ; PhD Program in Molecular and Translational Biomedicine, Competence Centre for Systems Physiology and Metabolic Diseases (CC-SPMD), University of Zurich and ETH Zurich , CH-8093 Zurich, Switzerland
| | - Yansheng Liu
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland
| | - Etienne Caron
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland
| | - Anton Vichalkovski
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland
| | - Marco Faini
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland
| | - Olga T Schubert
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland ; PhD Program in Systems Biology, University of Zurich and ETH Zurich , CH-8093 Zurich, Switzerland
| | - Pouya Faridi
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland ; Department of Phytopharmaceuticals (Traditional Pharmacy), School of Pharmacy and Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, 71345-1583 Shiraz, Iran
| | - H Alexander Ebhardt
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland
| | - Mariette Matondo
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland
| | - Henry Lam
- Division of Biomedical Engineering and Department of Chemical and Biomolecular Engineering, The Hong Kong University of Science and Technology, Clear Water Bay , Hong Kong, China
| | - Samuel L Bader
- Institute for Systems Biology , Seattle, Washington 98109-5234, USA
| | - David S Campbell
- Institute for Systems Biology , Seattle, Washington 98109-5234, USA
| | - Eric W Deutsch
- Institute for Systems Biology , Seattle, Washington 98109-5234, USA
| | - Robert L Moritz
- Institute for Systems Biology , Seattle, Washington 98109-5234, USA
| | | | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland ; Faculty of Science, University of Zurich , CH-8057 Zurich, Switzerland
| |
Collapse
|
9
|
Rantanen K, Kouvonen P, Corthals G, Jaakkola P. 364: VHL-dependent changes in global kinome expression in renal cell carcinoma. Eur J Cancer 2014. [DOI: 10.1016/s0959-8049(14)50324-3] [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: 11/24/2022]
|
10
|
Araújo J, Oliveira E, Kouvonen P, Corthals G, Lodeiro C, Santos H, Capelo J. A journey through PROTEOSONICS. Talanta 2014; 121:71-80. [DOI: 10.1016/j.talanta.2013.12.054] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 12/16/2013] [Accepted: 12/24/2013] [Indexed: 10/25/2022]
|
11
|
Santos HM, Kouvonen P, Capelo JL, Corthals GL. On-target ultrasonic digestion of proteins. Proteomics 2013; 13:1423-7. [DOI: 10.1002/pmic.201200241] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2012] [Revised: 02/06/2013] [Accepted: 02/18/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Hugo M. Santos
- Departamento de Química; Centro de Química Fina e Biotecnologia; (CQFB); REQUIMTE; Faculdade de Ciências e Tecnologia, (FCT); Universidade Nova de Lisboa, (UNL); Caparica Portugal
| | - Petri Kouvonen
- Turku Centre for Biotechnology; University of Turku and Åbo Akademi University; Turku Finland
- Department of Biology; Institute of Molecular Systems Biology; ETH; Zurich Switzerland
| | - Jose-Luis Capelo
- Departamento de Química; Centro de Química Fina e Biotecnologia; (CQFB); REQUIMTE; Faculdade de Ciências e Tecnologia, (FCT); Universidade Nova de Lisboa, (UNL); Caparica Portugal
| | - Garry L. Corthals
- Turku Centre for Biotechnology; University of Turku and Åbo Akademi University; Turku Finland
| |
Collapse
|
12
|
Santos HM, Kouvonen P, Capelo JL, Corthals GL. Isotopic labelling of peptides in tissues enhances mass spectrometric profiling. Rapid Commun Mass Spectrom 2012; 26:254-262. [PMID: 22223310 DOI: 10.1002/rcm.5325] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
RATIONALE There is a need in imaging mass spectrometry to use the acquired isotope distribution to unequivocally determine the identity of a peptide ion. A way of achieving unambiguous differentiation of ions from protonated peptides from other [M + H](+) ions in a tissue would be via the direct on-tissue incorporation of (18)O into peptides. METHODS Tissues were first digested with trypsin for 3 h at 37 °C in a humidified chamber. For the (18)O-labelling of digested peptides 1 μL of H(2)(18)O/50 mM ammonium acetate (at pH 6.75) was added to the array of tryptic spots and incubated at room temperature for 20 min. α-Cyano-4-hydroxycinnamic acid was used as a matrix modifier. The mass spectral analysis of tissue sections was carried out using a matrix-assisted laser desorption/ionisation tandem time-of-flight (MALDI-TOF-TOF) instrument. RESULTS On-tissue incorporation of (18)O into peptides cannot be carried out during the digestion step inside a humidified chamber. After tissue digestion for 3 h at 37 °C in an humidified chamber, (18)O labelling was carried out for 20 min at room temperature (no humidified chamber). No trypsin was needed to enhance the labelling. CONCLUSIONS For first time the feasibility of (18)O-labelling of peptides in situ for tissues has been demonstrated. The method decouples protein digestion from peptide labelling and is performed in sequential steps. Furthermore, we observed that (18)O incorporation produces characteristic isotopic peptide distributions, thus making facile distinguishing peptides from other tissue molecular components that ionise in the MALDI ion source.
Collapse
Affiliation(s)
- Hugo M Santos
- REQUIMTE-CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus de Caparica, 2829-516, Caparica, Portugal
| | | | | | | |
Collapse
|
13
|
Kouvonen P, Rainio EM, Suni V, Koskinen P, Corthals GL. Enrichment and sequencing of phosphopeptides on indium tin oxide coated glass slides. Mol Biosyst 2011; 7:1828-37. [PMID: 21523302 DOI: 10.1039/c0mb00269k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Unambiguous identification of phosphorylation sites is of premier importance to biologists, who seek to understand the role of phosphorylation from the perspective of site-specific control of biological phenomena. Despite this widely asked and highly specific information, many methods developed are aimed at analysis of complete proteomes, indeed even phospho-proteomes, surpassing the basic requests of many biologists. We have therefore further developed a simple method that specifically deals with the analysis of multiple phosphorylation sites on singular proteins or small collections of proteins. With this method, the whole purification process, from sample application to MALDI-MS analysis, can be performed on commercially available indium tin oxide (ITO) coated glass slides. We show that fifteen (15) samples can be purified within one hour, and that low femtomole sensitivity can be achieved. This limit of identification is demonstrated by the successful MS/MS-based identification of 6 fmol of monophosphopeptide from β-casein. We demonstrate that the method can be applied for identifying phosphorylation sites from recombinant and cell-derived biological protein samples. Since ITO-coated glass slides are inexpensive and available from several suppliers the method is readily and inexpensively available to other researchers. Taken together, the presented protocols and materials render this method as an extremely fast and sensitive phosphopeptide identification protocol that should aid biologists in discovery and validation of phosphorylation sites.
Collapse
Affiliation(s)
- Petri Kouvonen
- University of Turku, Centre for Biotechnology, Turku, Finland
| | | | | | | | | |
Collapse
|
14
|
Kouvonen P, Rainio EM, Suni V, Koskinen P, Corthals GL. Data combination from multiple matrix-assisted laser desorption/ionization (MALDI) matrices: opportunities and limitations for MALDI analysis. Rapid Commun Mass Spectrom 2010; 24:3493-3495. [PMID: 21072807 DOI: 10.1002/rcm.4785] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
|
15
|
Imanishi SY, Kouvonen P, Smått JH, Heikkilä M, Peuhu E, Mikhailov A, Ritala M, Lindén M, Corthals GL, Eriksson JE. Phosphopeptide enrichment with stable spatial coordination on a titanium dioxide coated glass slide. Rapid Commun Mass Spectrom 2009; 23:3661-3667. [PMID: 19899184 DOI: 10.1002/rcm.4291] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Recent advances in phosphoproteomics have established powerful tools to analyze phosphorylation events. However, their spatial localization is lost due to sample homogenization procedures prior to the analysis. Imaging mass spectrometry (IMS) has emerged as a method to visualize the spatial distribution of molecules in tissue samples, but its application is still limited to relatively abundant molecules. Due to low phosphorylation stoichiometry, direct detection and imaging of protein phosphorylation by MS has not been achieved yet. Therefore we have developed a novel phosphopeptide enrichment strategy as a potential tool for in situ affinity imaging MS (AIMS). A specific type of titanium dioxide (TiO2)-coated glass slides was designed and validated with casein tryptic digests for their ability to selectively retain phosphopeptides while maintaining their spatial coordination.
Collapse
Affiliation(s)
- Susumu Y Imanishi
- Turku Centre for Biotechnology, University of Turku and Abo Akademi University, FIN-20521 Turku, Finland
| | | | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Kouvonen P, McDonnell LA, Heeren RMA, Corthals GL. Nitromatrix provides improved LC-MALDI signals and more protein identifications. Proteomics 2009; 9:1662-71. [DOI: 10.1002/pmic.200800302] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
17
|
Blomster HA, Hietakangas V, Wu J, Kouvonen P, Hautaniemi S, Sistonen L. Novel proteomics strategy brings insight into the prevalence of SUMO-2 target sites. Mol Cell Proteomics 2009; 8:1382-90. [PMID: 19240082 DOI: 10.1074/mcp.m800551-mcp200] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Small ubiquitin-like modifier (SUMO) is covalently conjugated to its target proteins thereby altering their activity. The mammalian SUMO protein family includes four members (SUMO-1-4) of which SUMO-2 and SUMO-3 are conjugated in a stress-inducible manner. The vast majority of known SUMO substrates are recognized by the single SUMO E2-conjugating enzyme Ubc9 binding to a consensus tetrapeptide (PsiKXE where Psi stands for a large hydrophobic amino acid) or extended motifs that contain phosphorylated or negatively charged amino acids called PDSM (phosphorylation-dependent sumoylation motif) and NDSM (negatively charged amino acid-dependent sumoylation motif), respectively. We identified 382 SUMO-2 targets using a novel method based on SUMO protease treatment that improves separation of SUMO substrates on SDS-PAGE before LC-ESI-MS/MS. We also implemented a software SUMOFI (SUMO motif finder) to facilitate identification of motifs for SUMO substrates from a user-provided set of proteins and to classify the substrates according to the type of SUMO-targeting consensus site. Surprisingly more than half of the substrates lacked any known consensus site, suggesting that numerous SUMO substrates are recognized by a yet unknown consensus site-independent mechanism. Gene ontology analysis revealed that substrates in distinct functional categories display strikingly different prevalences of NDSM sites. Given that different types of motifs are bound by Ubc9 using alternative mechanisms, our data suggest that the preference of SUMO-2 targeting mechanism depends on the biological function of the substrate.
Collapse
Affiliation(s)
- Henri A Blomster
- Department of Biology, Abo Akademi University and University of Turku, FI-20521 Turku, Finland
| | | | | | | | | | | |
Collapse
|
18
|
Mattinen L, Somervuo P, Nykyri J, Nissinen R, Kouvonen P, Corthals G, Auvinen P, Aittamaa M, Valkonen JPT, Pirhonen M. Microarray profiling of host-extract-induced genes and characterization of the type VI secretion cluster in the potato pathogen Pectobacterium atrosepticum. Microbiology (Reading) 2008; 154:2387-2396. [PMID: 18667571 DOI: 10.1099/mic.0.2008/017582-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Pectobacterium atrosepticum is a Gram-negative plant-pathogenic bacterium that rots potato stems and tubers. Microarray analysis was used to identify genes that were differentially expressed when host extracts were added to the growth medium. Potato extracts downregulated the expression of ribosomal genes and genes related to uptake and metabolism of nutrients, and upregulated genes needed for nitrate or phosphonate use. Some of the observed changes in gene expression in host-extract-induced cultures are similar to those during attachment of the bacterium to host tissues. Other responses indicated defence against toxic metabolites in the extract. Tuber extract induced a large gene cluster having homology to type VI secretion genes shown to be virulence determinants in many, but not all, animal and human pathogens. Two of the genes in the type VI cluster were found to be expressed during infection in potato tubers and stems, and mutants with knockouts of the corresponding genes had increased virulence on potato. One of the type VI secretion mutants was further characterized and found to grow to higher cell density in culture in the presence of host extract and to produce slightly more extracellular tissue-macerating enzymes than the wild-type strain. Analysis of secreted proteins showed that this type VI mutant was affected in the production of haemolysin-coregulated proteins (Hcps), which have been suggested to be secreted by the type VI pathway in other bacteria. The results suggest that the type VI secretion system of P. atrosepticum is needed for secretion of Hcps but not for virulence on its host plant, potato.
Collapse
Affiliation(s)
- Laura Mattinen
- Department of Applied Biology, FIN-00014 University of Helsinki, Finland
| | - Panu Somervuo
- Institute of Biotechnology, PO Box 56, FIN-00014 University of Helsinki, Finland.,Department of Applied Biology, FIN-00014 University of Helsinki, Finland
| | - Johanna Nykyri
- Department of Applied Biology, FIN-00014 University of Helsinki, Finland
| | - Riitta Nissinen
- Department of Applied Biology, FIN-00014 University of Helsinki, Finland
| | - Petri Kouvonen
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FIN-20521 Turku, Finland
| | - Garry Corthals
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FIN-20521 Turku, Finland
| | - Petri Auvinen
- Institute of Biotechnology, PO Box 56, FIN-00014 University of Helsinki, Finland
| | - Marja Aittamaa
- Department of Applied Biology, FIN-00014 University of Helsinki, Finland
| | - Jari P T Valkonen
- Department of Applied Biology, FIN-00014 University of Helsinki, Finland
| | - Minna Pirhonen
- Department of Applied Biology, FIN-00014 University of Helsinki, Finland
| |
Collapse
|
19
|
Filén JJ, Filén S, Moulder R, Tuomela S, Ahlfors H, West A, Kouvonen P, Kantola S, Björkman M, Katajamaa M, Rasool O, Nyman TA, Lahesmaa R. Quantitative proteomics reveals GIMAP family proteins 1 and 4 to be differentially regulated during human T helper cell differentiation. Mol Cell Proteomics 2008; 8:32-44. [PMID: 18701445 DOI: 10.1074/mcp.m800139-mcp200] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
T helper (Th) cells differentiate into functionally distinct effector cell subsets of which Th1 and Th2 cells are best characterized. Besides T cell receptor signaling, IL-12-induced STAT4 and T-bet- and IL-4-induced STAT6 and GATA3 signaling pathways are the major players regulating the Th1 and Th2 differentiation process, respectively. However, there are likely to be other yet unknown factors or pathways involved. In this study we used quantitative proteomics exploiting cleavable ICAT labeling and LC-MS/MS to identify IL-4-regulated proteins from the microsomal fractions of CD4(+) cells extracted from umbilical cord blood. We were able to identify 557 proteins of which 304 were also quantified. This study resulted in the identification of the down-regulation of small GTPases GIMAP1 and GIMAP4 by IL-4 during Th2 differentiation. We also showed that both GIMAP1 and GIMAP4 genes are up-regulated by IL-12 and other Th1 differentiation-inducing cytokines in cells induced to differentiate toward Th1 lineage and down-regulated by IL-4 in cells induced to Th2. Our results indicate that the GIMAP (GTPase of the immunity-associated protein) family of proteins is differentially regulated during Th cell differentiation.
Collapse
Affiliation(s)
- Jan-Jonas Filén
- Turku Centre for Biotechnology, University of Turku and Abo Akademi University, Tykistökatu 6B, FI-20520 Turku, Finland
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Korolainen MA, Corthals GL, Kouvonen P, Kurkinen KMA, Nyman TA. 3rd Annual FinnProt Meeting: from cells to systems. Expert Rev Proteomics 2008; 5:389-91. [PMID: 18532906 DOI: 10.1586/14789450.5.3.389] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The Finnish Proteomics Society, FinnProt ( www.finnprot.org ), was founded in November 2004 as the Proteomics Division of the Societas biochemica, biophysica et microbiologica Fenniae ( www.biobio.org ). The mission of FinnProt is to make proteomics research readily available for the large scientific community in Finland, promote research and education in proteomics and protein chemistry, and act as the official Finnish collaborative body to international proteomics organizations such as the European Proteomics Association.
Collapse
Affiliation(s)
- Minna A Korolainen
- Department of Neurology, University of Kuopio, PO Box 1627, FIN-70211, Kuopio, Finland.
| | | | | | | | | |
Collapse
|
21
|
Buggiotti L, Primmer CR, Kouvonen P, Bureš S, Corthals GL, Leder EH. Identification of differentially expressed proteins inFicedula flycatchers. Proteomics 2008; 8:2150-3. [DOI: 10.1002/pmic.200701006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
22
|
Takatalo MS, Kouvonen P, Corthals G, Nyman TA, Rönnholm RH. Identification of new Golgi complex specific proteins by direct organelle proteomic analysis. Proteomics 2006; 6:3502-8. [PMID: 16691549 DOI: 10.1002/pmic.200500516] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [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: 11/07/2022]
Abstract
The Golgi complex is in the crossroad of the endocytic and secretory pathways. Its function is to post-translationally modify and sort proteins and lipids, and regulate the membrane balance in the cell. To understand the structure-function relationship of the Golgi complex the Golgi proteome has to be identified first. We have used a direct organelle proteomic analysis to identify new Golgi complex proteins. Enriched stacked Golgi membrane fractions from rat livers were isolated, and the proteins from these membranes were subsequently digested into peptides. The peptides were fractionated by cation-exchange chromatography followed by protein identification by automated capillary-LC/ESI-MS/MS analysis and database searches. Two different search programs, ProID and MASCOT were used. This resulted in a total of 1125 protein identifications in two experiments. In addition to the known Golgi resident proteins, a significant number of unknown proteins were identified. Some of these were further characterized in silico using different programs to provide insight into their structure, intracellular localization and biological functions. The Golgi localization of two of these newly identified proteins was also confirmed by indirect immunofluorescence.
Collapse
Affiliation(s)
- Maarit S Takatalo
- Department of Bio- and Environmental Sciences, Division of Biochemistry, University of Helsinki, Finland
| | | | | | | | | |
Collapse
|