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Říhová K, Lapčík P, Veselá B, Knopfová L, Potěšil D, Pokludová J, Šmarda J, Matalová E, Bouchal P, Beneš P. Caspase-9 Is a Positive Regulator of Osteoblastic Cell Migration Identified by diaPASEF Proteomics. J Proteome Res 2024. [PMID: 38498986 DOI: 10.1021/acs.jproteome.3c00641] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Caspase-9 is traditionally considered the initiator caspase of the intrinsic apoptotic pathway. In the past decade, however, other functions beyond initiation/execution of cell death have been described including cell type-dependent regulation of proliferation, differentiation/maturation, mitochondrial, and endosomal/lysosomal homeostasis. As previous studies revealed nonapoptotic functions of caspases in osteogenesis and bone homeostasis, this study was performed to identify proteins and pathways deregulated by knockout of caspase-9 in mouse MC3T3-E1 osteoblasts. Data-independent acquisition-parallel accumulation serial fragmentation (diaPASEF) proteomics was used to compare protein profiles of control and caspase-9 knockout cells. A total of 7669 protein groups were quantified, and 283 upregulated/141 downregulated protein groups were associated with the caspase-9 knockout phenotype. The deregulated proteins were mainly enriched for those associated with cell migration and motility and DNA replication/repair. Altered migration was confirmed in MC3T3-E1 cells with the genetic and pharmacological inhibition of caspase-9. ABHD2, an established regulator of cell migration, was identified as a possible substrate of caspase-9. We conclude that caspase-9 acts as a modulator of osteoblastic MC3T3-E1 cell migration and, therefore, may be involved in bone remodeling and fracture repair.
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Affiliation(s)
- Kamila Říhová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital, Brno 602 00, Czech Republic
| | - Petr Lapčík
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
| | - Barbora Veselá
- Laboratory of Odontogenesis and Osteogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno 602 00, Czech Republic
| | - Lucia Knopfová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital, Brno 602 00, Czech Republic
| | - David Potěšil
- Proteomics Core Facility, Central European Institute for Technology, Masaryk University, Brno 625 00, Czech Republic
| | - Jana Pokludová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital, Brno 602 00, Czech Republic
| | - Jan Šmarda
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
| | - Eva Matalová
- Laboratory of Odontogenesis and Osteogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno 602 00, Czech Republic
- Department of Physiology, Faculty of Veterinary Medicine, University of Veterinary Sciences, Brno 612 42, Czech Republic
| | - Pavel Bouchal
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
| | - Petr Beneš
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital, Brno 602 00, Czech Republic
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Vyhlídalová Kotrbová A, Gömöryová K, Mikulová A, Plešingerová H, Sladeček S, Kravec M, Hrachovinová Š, Potěšil D, Dunsmore G, Blériot C, Bied M, Kotouček J, Bednaříková M, Hausnerová J, Minář L, Crha I, Felsinger M, Zdráhal Z, Ginhoux F, Weinberger V, Bryja V, Pospíchalová V. Proteomic analysis of ascitic extracellular vesicles describes tumour microenvironment and predicts patient survival in ovarian cancer. J Extracell Vesicles 2024; 13:e12420. [PMID: 38490958 PMCID: PMC10942866 DOI: 10.1002/jev2.12420] [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: 07/08/2023] [Accepted: 02/08/2024] [Indexed: 03/17/2024] Open
Abstract
High-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type of ovarian cancer, ranks among the deadliest malignancies. Many HGSC patients have excess fluid in the peritoneum called ascites. Ascites is a tumour microenvironment (TME) containing various cells, proteins and extracellular vesicles (EVs). We isolated EVs from patients' ascites by orthogonal methods and analyzed them by mass spectrometry. We identified not only a set of 'core ascitic EV-associated proteins' but also defined their subset unique to HGSC ascites. Using single-cell RNA sequencing data, we mapped the origin of HGSC-specific EVs to different types of cells present in ascites. Surprisingly, EVs did not come predominantly from tumour cells but from non-malignant cell types such as macrophages and fibroblasts. Flow cytometry of ascitic cells in combination with analysis of EV protein composition in matched samples showed that analysis of cell type-specific EV markers in HGSC has more substantial prognostic potential than analysis of ascitic cells. To conclude, we provide evidence that proteomic analysis of EVs can define the cellular composition of HGSC TME. This finding opens numerous avenues both for a better understanding of EV's role in tumour promotion/prevention and for improved HGSC diagnostics.
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Affiliation(s)
| | - Kristína Gömöryová
- Department of Experimental Biology, Faculty of ScienceMasaryk UniversityBrnoCzech Republic
| | - Antónia Mikulová
- Department of Experimental Biology, Faculty of ScienceMasaryk UniversityBrnoCzech Republic
| | - Hana Plešingerová
- Department of Experimental Biology, Faculty of ScienceMasaryk UniversityBrnoCzech Republic
| | - Stanislava Sladeček
- Department of Experimental Biology, Faculty of ScienceMasaryk UniversityBrnoCzech Republic
| | - Marek Kravec
- Department of Experimental Biology, Faculty of ScienceMasaryk UniversityBrnoCzech Republic
| | - Šárka Hrachovinová
- Department of Experimental Biology, Faculty of ScienceMasaryk UniversityBrnoCzech Republic
| | - David Potěšil
- Central European Institute of TechnologyMasaryk UniversityBrnoCzech Republic
| | | | - Camille Blériot
- Institut Gustave Roussy, INSERM U1015VillejuifFrance
- Institut Necker Enfants Malades, IMMEDIABParisFrance
| | - Mathilde Bied
- Institut Gustave Roussy, INSERM U1015VillejuifFrance
| | - Jan Kotouček
- Department of Pharmacology and ToxicologyVeterinary Research InstituteBrnoCzech Republic
| | - Markéta Bednaříková
- Department of Internal Medicine ‐ Hematology & Oncology, University Hospital Brno and Medical FacultyMasaryk UniversityBrnoCzech Republic
| | - Jitka Hausnerová
- Department of Pathology, University Hospital Brno and Medical FacultyMasaryk UniversityBrnoCzech Republic
| | - Luboš Minář
- Department of Obstetrics and Gynecology, University Hospital Brno and Medical FacultyMasaryk UniversityBrnoCzech Republic
| | - Igor Crha
- Department of Health Sciences, Faculty of MedicineMasaryk UniversityBrnoCzech Republic
| | - Michal Felsinger
- Department of Obstetrics and Gynecology, University Hospital Brno and Medical FacultyMasaryk UniversityBrnoCzech Republic
| | - Zbyněk Zdráhal
- Central European Institute of TechnologyMasaryk UniversityBrnoCzech Republic
| | | | - Vít Weinberger
- Department of Obstetrics and Gynecology, University Hospital Brno and Medical FacultyMasaryk UniversityBrnoCzech Republic
| | - Vitězslav Bryja
- Department of Experimental Biology, Faculty of ScienceMasaryk UniversityBrnoCzech Republic
| | - Vendula Pospíchalová
- Department of Experimental Biology, Faculty of ScienceMasaryk UniversityBrnoCzech Republic
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3
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Martinková P, Konečná H, Gintar P, Kryštofová K, Potěšil D, Trtílek M, Zdráhal Z. Benchmarking of Two Peptide Clean-Up Protocols: SP2 and Ethyl Acetate Extraction for Sodium Dodecyl Sulfate or Polyethylene Glycol Removal from Plant Samples before LC-MS/MS. Int J Mol Sci 2023; 24:17347. [PMID: 38139176 PMCID: PMC10743447 DOI: 10.3390/ijms242417347] [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: 11/09/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
The success of bottom-up proteomic analysis frequently depends on the efficient removal of contaminants from protein or peptide samples before LC-MS/MS. For a peptide clean-up workflow, single-pot solid-phase-enhanced peptide sample preparation on carboxylate-modified paramagnetic beads (termed SP2) was evaluated for sodium dodecyl sulfate or polyethylene glycol removal from Arabidopsis thaliana tryptic peptides. The robust and efficient 40-min SP2 protocol, tested for 10-ng, 250-ng, and 10-µg peptide samples, was proposed and benchmarked thoroughly against the ethyl acetate extraction protocol. The SP2 protocol on carboxylated magnetic beads proved to be the most robust approach, even for the simultaneous removal of massive sodium dodecyl sulfate (SDS) and polyethylene glycol (PEG) contaminations from AT peptide samples in respect of the LC-MS/MS data outperforming ethyl acetate extraction.
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Affiliation(s)
- Petra Martinková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; (P.M.); (P.G.); (K.K.); (D.P.)
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Hana Konečná
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; (P.M.); (P.G.); (K.K.); (D.P.)
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Petr Gintar
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; (P.M.); (P.G.); (K.K.); (D.P.)
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Karolína Kryštofová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; (P.M.); (P.G.); (K.K.); (D.P.)
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - David Potěšil
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; (P.M.); (P.G.); (K.K.); (D.P.)
| | - Martin Trtílek
- Photon Systems Instruments, Spol. s r.o., Průmyslová 470, 664 24 Drásov, Czech Republic
| | - Zbyněk Zdráhal
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; (P.M.); (P.G.); (K.K.); (D.P.)
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
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Klodová B, Potěšil D, Steinbachová L, Michailidis C, Lindner AC, Hackenberg D, Becker JD, Zdráhal Z, Twell D, Honys D. Correction: Regulatory dynamics of gene expression in the developing male gametophyte of Arabidopsis. Plant Reprod 2023:10.1007/s00497-023-00471-w. [PMID: 37318658 PMCID: PMC10363072 DOI: 10.1007/s00497-023-00471-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 05/23/2023] [Indexed: 06/16/2023]
Affiliation(s)
- Božena Klodová
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02, Prague 6, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, Praha 2, 128 00, Czech Republic
| | - David Potěšil
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Lenka Steinbachová
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02, Prague 6, Czech Republic
| | - Christos Michailidis
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02, Prague 6, Czech Republic
| | - Ann-Cathrin Lindner
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | - Dieter Hackenberg
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
- KWS SAAT SE & Co. KGaA, Grimsehlstraße 31, 37574, Einbeck, Germany
| | - Jörg D Becker
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2780-157, Oeiras, Portugal
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | - Zbyněk Zdráhal
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - David Twell
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK.
| | - David Honys
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02, Prague 6, Czech Republic.
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Zapletalová M, Rancurel C, Industri B, Bardin M, Le Brigand K, Nicot P, Magnone V, Seassau A, Barbry P, Potěšil D, Zdráhal Z, Ponchet M, Lochman J. BABA-induced pathogen resistance: a multi-omics analysis of the tomato response reveals a hyper-receptive status involving ethylene. Hortic Res 2023; 10:uhad068. [PMID: 37287445 PMCID: PMC10243938 DOI: 10.1093/hr/uhad068] [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] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 04/05/2023] [Indexed: 06/09/2023]
Abstract
Prior exposure to microbial-associated molecular patterns or specific chemical compounds can promote plants into a primed state with stronger defence responses. β-aminobutyric acid (BABA) is an endogenous stress metabolite that induces resistance protecting various plants towards diverse stresses. In this study, by integrating BABA-induced changes in selected metabolites with transcriptome and proteome data, we generated a global map of the molecular processes operating in BABA-induced resistance (BABA-IR) in tomato. BABA significantly restricts the growth of the pathogens Oidium neolycopersici and Phytophthora parasitica but not Botrytis cinerea. A cluster analysis of the upregulated processes showed that BABA acts mainly as a stress factor in tomato. The main factor distinguishing BABA-IR from other stress conditions was the extensive induction of signaling and perception machinery playing a key role in effective resistance against pathogens. Interestingly, the signalling processes and immune response activated during BABA-IR in tomato differed from those in Arabidopsis with substantial enrichment of genes associated with jasmonic acid (JA) and ethylene (ET) signalling and no change in Asp levels. Our results revealed key differences between the effect of BABA on tomato and other model plants studied until now. Surprisingly, salicylic acid (SA) is not involved in BABA downstream signalization whereas ET and JA play a crucial role.
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Affiliation(s)
| | | | - Benoit Industri
- UMR Institut Sophia Agrobiotech INRAE 1355, CNRS 6254, Université Côte d’Azur, 400, Route des Chappes, 06903 Sophia Antipolis, France
| | - Marc Bardin
- Unité 407 Pathologie végétale, INRAE, Domaine Saint-Maurice, 84143 Montfavet cedex, France
| | - Kevin Le Brigand
- UMR Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d’Azur, CNRS 7275, 660 Route des Lucioles 06560 Valbonne, France
| | - Philippe Nicot
- Unité 407 Pathologie végétale, INRAE, Domaine Saint-Maurice, 84143 Montfavet cedex, France
| | - Virginie Magnone
- UMR Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d’Azur, CNRS 7275, 660 Route des Lucioles 06560 Valbonne, France
| | - Aurélie Seassau
- UMR Institut Sophia Agrobiotech INRAE 1355, CNRS 6254, Université Côte d’Azur, 400, Route des Chappes, 06903 Sophia Antipolis, France
| | - Pascal Barbry
- UMR Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d’Azur, CNRS 7275, 660 Route des Lucioles 06560 Valbonne, France
| | - David Potěšil
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Michel Ponchet
- UMR Institut Sophia Agrobiotech INRAE 1355, CNRS 6254, Université Côte d’Azur, 400, Route des Chappes, 06903 Sophia Antipolis, France
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Montaser AB, Kuiri J, Natunen T, Hruška P, Potěšil D, Auriola S, Hiltunen M, Terasaki T, Lehtonen M, Jalkanen A, Huttunen KM. Enhanced drug delivery by a prodrug approach effectively relieves neuroinflammation in mice. Life Sci 2022; 310:121088. [PMID: 36257461 DOI: 10.1016/j.lfs.2022.121088] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 09/30/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022]
Abstract
AIMS Neuroinflammation is a prominent hallmark in several neurodegenerative diseases (NDs). Halting neuroinflammation can slow down the progression of NDs. Improving the efficacy of clinically available non-steroidal anti-inflammatory drugs (NSAIDs) is a promising approach that may lead to fast-track and effective disease-modifying therapies for NDs. Here, we aimed to utilize the L-type amino acid transporter 1 (LAT1) to improve the efficacy of salicylic acid as an example of an NSAID prodrug, for which brain uptake and intracellular localization have been reported earlier. MAIN METHODS Firstly, we confirmed the improved LAT1 utilization of the salicylic acid prodrug (SA-AA) in freshly isolated primary mouse microglial cells. Secondly, we performed behavioural rotarod, open field, and four-limb hanging tests in mice, and a whole-brain proteome analysis. KEY FINDINGS The SA-AA prodrug alleviated the lipopolysaccharide (LPS)-induced inflammation in the rotarod and hanging tests. The proteome analysis indicated decreased neuroinflammation at the molecular level. We identified 399 proteins linked to neuroinflammation out of 7416 proteins detected in the mouse brain. Among them, Gps2, Vamp8, Slc6a3, Slc18a2, Slc5a7, Rgs9, Lrrc1, Ppp1r1b, Gnal, and Adcy5/6 were associated with the drug's effects. The SA-AA prodrug attenuated the LPS-induced neuroinflammation through the regulation of critical pathways of neuroinflammation such as the cellular response to stress and transmission across chemical synapses. SIGNIFICANCE The efficacy of NSAIDs can be improved via the utilization of LAT1 and repurposed for the treatment of neuroinflammation. This improved brain delivery and microglia localisation can be applied to other inflammatory modulators to achieve effective and targeted CNS therapies.
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Affiliation(s)
- Ahmed B Montaser
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland.
| | - Janita Kuiri
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Teemu Natunen
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Pavel Hruška
- Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - David Potěšil
- Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Seppo Auriola
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Mikko Hiltunen
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Tetsuya Terasaki
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Marko Lehtonen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Aaro Jalkanen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Kristiina M Huttunen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
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7
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Klodová B, Potěšil D, Steinbachová L, Michailidis C, Lindner AC, Hackenberg D, Becker JD, Zdráhal Z, Twell D, Honys D. Regulatory dynamics of gene expression in the developing male gametophyte of Arabidopsis. Plant Reprod 2022:10.1007/s00497-022-00452-5. [PMID: 36282332 PMCID: PMC10363097 DOI: 10.1007/s00497-022-00452-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Sexual reproduction in angiosperms requires the production and delivery of two male gametes by a three-celled haploid male gametophyte. This demands synchronized gene expression in a short developmental window to ensure double fertilization and seed set. While transcriptomic changes in developing pollen are known for Arabidopsis, no studies have integrated RNA and proteomic data in this model. Further, the role of alternative splicing has not been fully addressed, yet post-transcriptional and post-translational regulation may have a key role in gene expression dynamics during microgametogenesis. We have refined and substantially updated global transcriptomic and proteomic changes in developing pollen for two Arabidopsis accessions. Despite the superiority of RNA-seq over microarray-based platforms, we demonstrate high reproducibility and comparability. We identify thousands of long non-coding RNAs as potential regulators of pollen development, hundreds of changes in alternative splicing and provide insight into mRNA translation rate and storage in developing pollen. Our analysis delivers an integrated perspective of gene expression dynamics in developing Arabidopsis pollen and a foundation for studying the role of alternative splicing in this model.
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Affiliation(s)
- Božena Klodová
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02, Prague 6, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, Praha 2, 128 00, Czech Republic
| | - David Potěšil
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Lenka Steinbachová
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02, Prague 6, Czech Republic
| | - Christos Michailidis
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02, Prague 6, Czech Republic
| | - Ann-Cathrin Lindner
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | - Dieter Hackenberg
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
- KWS SAAT SE & Co. KGaA, Grimsehlstraße 31, 37574, Einbeck, Germany
| | - Jörg D Becker
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2780-157, Oeiras, Portugal
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | - Zbyněk Zdráhal
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - David Twell
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK.
| | - David Honys
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02, Prague 6, Czech Republic.
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8
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Hluchý M, Gajdušková P, Ruiz de Los Mozos I, Rájecký M, Kluge M, Berger BT, Slabá Z, Potěšil D, Weiß E, Ule J, Zdráhal Z, Knapp S, Paruch K, Friedel CC, Blazek D. CDK11 regulates pre-mRNA splicing by phosphorylation of SF3B1. Nature 2022; 609:829-834. [PMID: 36104565 DOI: 10.1038/s41586-022-05204-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 08/08/2022] [Indexed: 11/09/2022]
Abstract
RNA splicing, the process of intron removal from pre-mRNA, is essential for the regulation of gene expression. It is controlled by the spliceosome, a megadalton RNA-protein complex that assembles de novo on each pre-mRNA intron through an ordered assembly of intermediate complexes1,2. Spliceosome activation is a major control step that requires substantial protein and RNA rearrangements leading to a catalytically active complex1-5. Splicing factor 3B subunit 1 (SF3B1) protein-a subunit of the U2 small nuclear ribonucleoprotein6-is phosphorylated during spliceosome activation7-10, but the kinase that is responsible has not been identified. Here we show that cyclin-dependent kinase 11 (CDK11) associates with SF3B1 and phosphorylates threonine residues at its N terminus during spliceosome activation. The phosphorylation is important for the association between SF3B1 and U5 and U6 snRNAs in the activated spliceosome, termed the Bact complex, and the phosphorylation can be blocked by OTS964, a potent and selective inhibitor of CDK11. Inhibition of CDK11 prevents spliceosomal transition from the precatalytic complex B to the activated complex Bact and leads to widespread intron retention and accumulation of non-functional spliceosomes on pre-mRNAs and chromatin. We demonstrate a central role of CDK11 in spliceosome assembly and splicing regulation and characterize OTS964 as a highly selective CDK11 inhibitor that suppresses spliceosome activation and splicing.
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Affiliation(s)
- Milan Hluchý
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Pavla Gajdušková
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Igor Ruiz de Los Mozos
- The Francis Crick Institute, London, UK
- Department of Personalized Medicine, NASERTIC, Government of Navarra, Pamplona, Spain
- Center for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Michal Rájecký
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Michael Kluge
- Institut für Informatik, Ludwig-Maximilians-Universität München, München, Germany
| | - Benedict-Tilman Berger
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences (BMLS), Goethe University Frankfurt am Main, Frankfurt am Main, Germany
- Institut für Pharmazeutische Chemie, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - Zuzana Slabá
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - David Potěšil
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Elena Weiß
- Institut für Informatik, Ludwig-Maximilians-Universität München, München, Germany
| | - Jernej Ule
- The Francis Crick Institute, London, UK
- UK Dementia Research Institute, King's College London, London, UK
| | - Zbyněk Zdráhal
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Stefan Knapp
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences (BMLS), Goethe University Frankfurt am Main, Frankfurt am Main, Germany
- Institut für Pharmazeutische Chemie, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - Kamil Paruch
- Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St Anne's University Hospital in Brno, Brno, Czech Republic
| | - Caroline C Friedel
- Institut für Informatik, Ludwig-Maximilians-Universität München, München, Germany
| | - Dalibor Blazek
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.
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9
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Muresan XM, Slabáková E, Procházková J, Drápela S, Fedr R, Pícková M, Vacek O, Víchová R, Suchánková T, Bouchal J, Kürfürstová D, Král M, Hulínová T, Sýkora RP, Študent V, Hejret V, van Weerden WM, Puhr M, Pustka V, Potěšil D, Zdráhal Z, Culig Z, Souček K. Toll-Like Receptor 3 Overexpression Induces Invasion of Prostate Cancer Cells, whereas Its Activation Triggers Apoptosis. Am J Pathol 2022; 192:1321-1335. [PMID: 35750257 DOI: 10.1016/j.ajpath.2022.05.009] [Citation(s) in RCA: 1] [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] [Received: 12/15/2021] [Revised: 04/29/2022] [Accepted: 05/17/2022] [Indexed: 01/27/2023]
Abstract
Toll-like receptor 3 (TLR3) is an endosomal receptor expressed in several immune and epithelial cells. Recent studies have highlighted its expression also in solid tumors, including prostate cancer (PCa), and described its role mainly in the proinflammatory response and induction of apoptosis. It has been found up-regulated in some castration-resistant prostate cancers. However, the role of TLR3 in prostate cancer progression remains largely unknown. We have experimentally demonstrated that exogenous TLR3 activation in PCa cell lines leads to the significant induction of secretion of the cytokines IL-6, IL-8, and interferon-β, depending on the model and chemoresistance status. Transcriptomic analysis of TLR3-overexpressing cells revealed a functional program that is enriched for genes involved in the regulation of cell motility, migration, and tumor invasiveness. Increased motility, migration, and invasion in TLR3-overexpressing cell line were confirmed by several in vitro assays and using an orthotopic prostate xenograft model in vivo. Furthermore, TLR3-ligand induced apoptosis via cleavage of caspase-3/7 and poly (ADP-ribose) polymerase, predominantly in TLR3-overexpressing cells. We conclude that TLR3 may be involved in prostate cancer progression and metastasis; however, it might also represent an Achilles heel of PCa, which can be exploited for targeted therapy.
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Affiliation(s)
- Ximena M Muresan
- Department of Cytokinetics, Institute of Biophysics of Czech Academy of Sciences, Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital in Brno, Brno, Czech Republic
| | - Eva Slabáková
- Department of Cytokinetics, Institute of Biophysics of Czech Academy of Sciences, Brno, Czech Republic
| | - Jiřina Procházková
- Department of Cytokinetics, Institute of Biophysics of Czech Academy of Sciences, Brno, Czech Republic
| | - Stanislav Drápela
- Department of Cytokinetics, Institute of Biophysics of Czech Academy of Sciences, Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital in Brno, Brno, Czech Republic; Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Radek Fedr
- Department of Cytokinetics, Institute of Biophysics of Czech Academy of Sciences, Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital in Brno, Brno, Czech Republic
| | - Markéta Pícková
- Department of Cytokinetics, Institute of Biophysics of Czech Academy of Sciences, Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital in Brno, Brno, Czech Republic; Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Ondřej Vacek
- Department of Cytokinetics, Institute of Biophysics of Czech Academy of Sciences, Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital in Brno, Brno, Czech Republic; Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Ráchel Víchová
- Department of Cytokinetics, Institute of Biophysics of Czech Academy of Sciences, Brno, Czech Republic
| | - Tereza Suchánková
- Department of Cytokinetics, Institute of Biophysics of Czech Academy of Sciences, Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital in Brno, Brno, Czech Republic
| | - Jan Bouchal
- Department of Clinical and Molecular Pathology, Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University, Olomouc, Czech Republic
| | | | - Milan Král
- Department of Urology, University Hospital, Olomouc, Czech Republic
| | - Tereza Hulínová
- Department of Clinical and Molecular Pathology, Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University, Olomouc, Czech Republic; Department of Clinical and Molecular Pathology, University Hospital, Ostrava, Czech Republic
| | - Radek P Sýkora
- Department of Urology, University Hospital, Ostrava, Czech Republic
| | - Vladimír Študent
- Department of Urology, University Hospital, Olomouc, Czech Republic
| | - Václav Hejret
- Bioinformatics Core Facility Central European Institute of Technology, Masaryk University, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Wytske M van Weerden
- Department of Urology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Martin Puhr
- Proteomics Core Facility Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Václav Pustka
- Department of Urology, Experimental Urology, Innsbruck Medical University, Innsbruck, Austria
| | - David Potěšil
- Department of Urology, Experimental Urology, Innsbruck Medical University, Innsbruck, Austria
| | - Zbyněk Zdráhal
- Department of Urology, Experimental Urology, Innsbruck Medical University, Innsbruck, Austria
| | - Zoran Culig
- International Clinical Research Center, St. Anne's University Hospital in Brno, Brno, Czech Republic; Proteomics Core Facility Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Karel Souček
- Department of Cytokinetics, Institute of Biophysics of Czech Academy of Sciences, Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital in Brno, Brno, Czech Republic; Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic.
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10
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Colville C, Alcaraz AJ, Green D, Park B, Xia J, Soufan O, Hruṧka P, Potěšil D, Zdráhal Z, Crump D, Basu N, Hogan N, Hecker M. Characterizing toxicity pathways of fluoxetine to predict adverse outcomes in adult fathead minnows (Pimephales promelas). Sci Total Environ 2022; 817:152747. [PMID: 35026279 DOI: 10.1016/j.scitotenv.2021.152747] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/09/2021] [Accepted: 12/24/2021] [Indexed: 05/17/2023]
Abstract
Current ecotoxicity testing programs are impeded as they predominantly rely on slow and expensive animal tests measuring adverse outcomes. Therefore, new approach methodologies (NAMs) increasingly involve short-term mechanistic assays that employ molecular endpoints to predict adverse outcomes of regulatory relevance. This study aimed to elucidate the application of NAMs in adult fathead minnows using fluoxetine (FLX) as a model compound. Fish were exposed to three FLX concentrations (measured: 2.42, 10.7, and 56.7 μgL-1) and a control. After 96 h, molecular toxicity signatures were characterized using proteomics and transcriptomics analyses in livers and brains of a sub-set of fish. The remaining fish were sampled at 21 days and assessed for liver histopathology and morphometric measurements. Fecundity was monitored throughout the study. In the livers, 56.7 μgL-1 FLX caused enrichment of PPAR signaling in the proteome and fatty acid-related pathways in the transcriptome, potential upstream responses that led to lipid-type vacuolation of hepatocytes, observed via histopathology. Upregulated genes in the brain suggested alterations in serotonin-related signaling processes and reproductive behaviour, which may explain the observed significant decrease in fecundity. While the relationships between molecular responses and adverse outcomes remain complex, this research provided important insights into the mechanistic toxicity of FLX.
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Affiliation(s)
- Carly Colville
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK S7N 5B3, Canada
| | - Alper James Alcaraz
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK S7N 5B3, Canada
| | - Derek Green
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK S7N 5B3, Canada
| | - Bradley Park
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK S7N 5B3, Canada
| | - Jianguo Xia
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC H9X 3V9, Canada
| | - Othman Soufan
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC H9X 3V9, Canada; Computer Science Department, St. Francis Xavier University, Antigonish, NS B2G 2W5, Canada
| | - Pavel Hruṧka
- Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic; RECETOX, Masaryk University, Brno 625 00, Czech Republic
| | - David Potěšil
- Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Doug Crump
- Environment and Climate Change Canada, National Wildlife Research Centre, Ottawa, ON K1A 0H3, Canada
| | - Niladri Basu
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC H9X 3V9, Canada
| | - Natacha Hogan
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK S7N 5B3, Canada; Department of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Markus Hecker
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK S7N 5B3, Canada; School of the Environment and Sustainability, University of Saskatchewan, Saskatoon, SK S7N 5C8, Canada.
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11
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Alcaraz AJG, Baraniuk S, Mikulášek K, Park B, Lane T, Burbridge C, Ewald J, Potěšil D, Xia J, Zdráhal Z, Schneider D, Crump D, Basu N, Hogan N, Brinkmann M, Hecker M. Comparative analysis of transcriptomic points-of-departure (tPODs) and apical responses in embryo-larval fathead minnows exposed to fluoxetine. Environ Pollut 2022; 295:118667. [PMID: 34896397 DOI: 10.1016/j.envpol.2021.118667] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 11/17/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
Current approaches in chemical hazard assessment face significant challenges because they rely on live animal testing, which is time-consuming, expensive, and ethically questionable. These concerns serve as an impetus to develop new approach methodologies (NAMs) that do not rely on live animal tests. This study explored a molecular benchmark dose (BMD) approach using a 7-day embryo-larval fathead minnow (FHM) assay to derive transcriptomic points-of-departure (tPODs) to predict apical BMDs of fluoxetine (FLX), a highly prescribed and potent selective serotonin reuptake inhibitor frequently detected in surface waters. Fertilized FHM embryos were exposed to graded concentrations of FLX (confirmed at < LOD, 0.19, 0.74, 3.38, 10.2, 47.5 μg/L) for 32 days. Subsets of fish were subjected to omics and locomotor analyses at 7 days post-fertilization (dpf) and to histological and biometric measurements at 32 dpf. Enrichment analyses of transcriptomics and proteomics data revealed significant perturbations in gene sets associated with serotonergic and axonal functions. BMD analysis resulted in tPOD values of 0.56 μg/L (median of the 20 most sensitive gene-level BMDs), 5.0 μg/L (tenth percentile of all gene-level BMDs), 7.51 μg/L (mode of the first peak of all gene-level BMDs), and 5.66 μg/L (pathway-level BMD). These tPODs were protective of locomotor and reduced body weight effects (LOEC of 10.2 μg/L) observed in this study and were reflective of chronic apical BMDs of FLX reported in the literature. Furthermore, the distribution of gene-level BMDs followed a bimodal pattern, revealing disruption of sensitive neurotoxic pathways at low concentrations and metabolic pathway perturbations at higher concentrations. This is one of the first studies to derive protective tPODs for FLX using a short-term embryo assay at a life stage not considered to be a live animal under current legislations.
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Affiliation(s)
| | - Shaina Baraniuk
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, S7N 5B3, Canada
| | - Kamil Mikulášek
- Central European Institute of Technology, Masaryk University, Brno, CZ-625 00, Czech Republic
| | - Bradley Park
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, S7N 5B3, Canada
| | - Taylor Lane
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, S7N 5B3, Canada; Department of Environment and Geography, University of York, Heslington, YO10 5NG, United Kingdom
| | - Connor Burbridge
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 0W9, Canada
| | - Jessica Ewald
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, H9X 3V9, Canada
| | - David Potěšil
- Central European Institute of Technology, Masaryk University, Brno, CZ-625 00, Czech Republic
| | - Jianguo Xia
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, H9X 3V9, Canada
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, Brno, CZ-625 00, Czech Republic
| | - David Schneider
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 0W9, Canada; School of the Environment and Sustainability, University of Saskatchewan, Saskatoon, SK, S7N 5C8, Canada
| | - Doug Crump
- Environment and Climate Change Canada, National Wildlife Research Centre, Ottawa, ON, K1A 0H3, Canada
| | - Niladri Basu
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, H9X 3V9, Canada
| | - Natacha Hogan
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, S7N 5B3, Canada; Department of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Markus Brinkmann
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, S7N 5B3, Canada; School of the Environment and Sustainability, University of Saskatchewan, Saskatoon, SK, S7N 5C8, Canada; Global Institute for Water Security, University of Saskatchewan, Saskatoon, SK, S7N 3H5, Canada
| | - Markus Hecker
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, S7N 5B3, Canada; School of the Environment and Sustainability, University of Saskatchewan, Saskatoon, SK, S7N 5C8, Canada; Global Institute for Water Security, University of Saskatchewan, Saskatoon, SK, S7N 3H5, Canada.
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12
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Covelo-Molares H, Obrdlik A, Poštulková I, Dohnálková M, Gregorová P, Ganji R, Potěšil D, Gawriyski L, Varjosalo M, Vaňáčová Š. The comprehensive interactomes of human adenosine RNA methyltransferases and demethylases reveal distinct functional and regulatory features. Nucleic Acids Res 2021; 49:10895-10910. [PMID: 34634806 PMCID: PMC8565353 DOI: 10.1093/nar/gkab900] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [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] [Received: 12/15/2020] [Revised: 09/18/2021] [Accepted: 09/22/2021] [Indexed: 12/26/2022] Open
Abstract
N6-methyladenosine (m6A) and N6,2′-O-dimethyladenosine (m6Am) are two abundant modifications found in mRNAs and ncRNAs that can regulate multiple aspects of RNA biology. They function mainly by regulating interactions with specific RNA-binding proteins. Both modifications are linked to development, disease and stress response. To date, three methyltransferases and two demethylases have been identified that modify adenosines in mammalian mRNAs. Here, we present a comprehensive analysis of the interactomes of these enzymes. PCIF1 protein network comprises mostly factors involved in nascent RNA synthesis by RNA polymerase II, whereas ALKBH5 is closely linked with most aspects of pre-mRNA processing and mRNA export to the cytoplasm. METTL16 resides in subcellular compartments co-inhabited by several other RNA modifiers and processing factors. FTO interactome positions this demethylase at a crossroad between RNA transcription, RNA processing and DNA replication and repair. Altogether, these enzymes share limited spatial interactomes, pointing to specific molecular mechanisms of their regulation.
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Affiliation(s)
- Helena Covelo-Molares
- Central European Institute of Technology (CEITEC), Masaryk University, Brno 62500, Czech Republic
| | - Ales Obrdlik
- Central European Institute of Technology (CEITEC), Masaryk University, Brno 62500, Czech Republic
| | - Ivana Poštulková
- Central European Institute of Technology (CEITEC), Masaryk University, Brno 62500, Czech Republic
| | - Michaela Dohnálková
- Central European Institute of Technology (CEITEC), Masaryk University, Brno 62500, Czech Republic
| | - Pavlína Gregorová
- Central European Institute of Technology (CEITEC), Masaryk University, Brno 62500, Czech Republic
| | - Ranjani Ganji
- Central European Institute of Technology (CEITEC), Masaryk University, Brno 62500, Czech Republic
| | - David Potěšil
- Central European Institute of Technology (CEITEC), Masaryk University, Brno 62500, Czech Republic
| | - Lisa Gawriyski
- Institute of Biotechnology & HiLIFE - Helsinki Institute of Life Science, University of Helsinki, Helsinki 00014, Finland
| | - Markku Varjosalo
- Institute of Biotechnology & HiLIFE - Helsinki Institute of Life Science, University of Helsinki, Helsinki 00014, Finland
| | - Štěpánka Vaňáčová
- Central European Institute of Technology (CEITEC), Masaryk University, Brno 62500, Czech Republic
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13
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Radaszkiewicz T, Nosková M, Gömöryová K, Vondálová Blanářová O, Radaszkiewicz KA, Picková M, Víchová R, Gybeľ T, Kaiser K, Demková L, Kučerová L, Bárta T, Potěšil D, Zdráhal Z, Souček K, Bryja V. RNF43 inhibits WNT5A-driven signaling and suppresses melanoma invasion and resistance to the targeted therapy. eLife 2021; 10:65759. [PMID: 34702444 PMCID: PMC8550759 DOI: 10.7554/elife.65759] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [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] [Received: 12/14/2020] [Accepted: 09/28/2021] [Indexed: 12/30/2022] Open
Abstract
RNF43 is an E3 ubiquitin ligase and known negative regulator of WNT/β-catenin signaling. We demonstrate that RNF43 is also a regulator of noncanonical WNT5A-induced signaling in human cells. Analysis of the RNF43 interactome using BioID and immunoprecipitation showed that RNF43 can interact with the core receptor complex components dedicated to the noncanonical Wnt pathway such as ROR1, ROR2, VANGL1, and VANGL2. RNF43 triggers VANGL2 ubiquitination and proteasomal degradation and clathrin-dependent internalization of ROR1 receptor and inhibits ROR2 activation. These activities of RNF43 are physiologically relevant and block pro-metastatic WNT5A signaling in melanoma. RNF43 inhibits responses to WNT5A, which results in the suppression of invasive properties of melanoma cells. Furthermore, RNF43 prevented WNT5A-assisted development of resistance to BRAF V600E and MEK inhibitors. Next, RNF43 acted as melanoma suppressor and improved response to targeted therapies in vivo. In line with these findings, RNF43 expression decreases during melanoma progression and RNF43-low patients have a worse prognosis. We conclude that RNF43 is a newly discovered negative regulator of WNT5A-mediated biological responses that desensitizes cells to WNT5A.
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Affiliation(s)
- Tomasz Radaszkiewicz
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Michaela Nosková
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Kristína Gömöryová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Olga Vondálová Blanářová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | | | - Markéta Picková
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic.,Department of Cytokinetics, Institute of Biophysics CAS, Brno, Czech Republic.,International Clinical Research Center FNUSA-ICRC, Brno, Czech Republic
| | - Ráchel Víchová
- Department of Cytokinetics, Institute of Biophysics CAS, Brno, Czech Republic
| | - Tomáš Gybeľ
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Karol Kaiser
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Lucia Demková
- Laboratory of Molecular Oncology, Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Bratislava, Slovakia
| | - Lucia Kučerová
- Laboratory of Molecular Oncology, Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Bratislava, Slovakia
| | - Tomáš Bárta
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic.,Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - David Potěšil
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Karel Souček
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic.,Department of Cytokinetics, Institute of Biophysics CAS, Brno, Czech Republic.,International Clinical Research Center FNUSA-ICRC, Brno, Czech Republic
| | - Vítězslav Bryja
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic.,Department of Cytokinetics, Institute of Biophysics CAS, Brno, Czech Republic
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14
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Alcaraz AJG, Mikulášek K, Potěšil D, Park B, Shekh K, Ewald J, Burbridge C, Zdráhal Z, Schneider D, Xia J, Crump D, Basu N, Hecker M. Assessing the Toxicity of 17α-Ethinylestradiol in Rainbow Trout Using a 4-Day Transcriptomics Benchmark Dose (BMD) Embryo Assay. Environ Sci Technol 2021; 55:10608-10618. [PMID: 34292719 DOI: 10.1021/acs.est.1c02401] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
There is an urgent demand for more efficient and ethical approaches in ecological risk assessment. Using 17α-ethinylestradiol (EE2) as a model compound, this study established an embryo benchmark dose (BMD) assay for rainbow trout (RBT; Oncorhynchus mykiss) to derive transcriptomic points-of-departure (tPODs) as an alternative to live-animal tests. Embryos were exposed to graded concentrations of EE2 (measured: 0, 1.13, 1.57, 6.22, 16.3, 55.1, and 169 ng/L) from hatch to 4 and up to 60 days post-hatch (dph) to assess molecular and apical responses, respectively. Whole proteome analyses of alevins did not show clear estrogenic effects. In contrast, transcriptomics revealed responses that were in agreement with apical effects, including excessive accumulation of intravascular and hepatic proteinaceous fluid and significant increases in mortality at 55.1 and 169 ng/L EE2 at later time points. Transcriptomic BMD analysis estimated the median of the 20th lowest geneBMD to be 0.18 ng/L, the most sensitive tPOD. Other estimates (0.78, 3.64, and 1.63 ng/L for the 10th percentile geneBMD, first peak geneBMD distribution, and median geneBMD of the most sensitive over-represented pathway, respectively) were within the same order of magnitude as empirically derived apical PODs for EE2 in the literature. This 4-day alternative RBT embryonic assay was effective in deriving tPODs that are protective of chronic effects of EE2.
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Affiliation(s)
- Alper James G Alcaraz
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5B3
| | - Kamil Mikulášek
- Central European Institute of Technology, Masaryk University, Brno CZ-625 00, Czech Republic
| | - David Potěšil
- Central European Institute of Technology, Masaryk University, Brno CZ-625 00, Czech Republic
| | - Bradley Park
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5B3
| | - Kamran Shekh
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5B3
| | - Jessica Ewald
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada H9X 3V9
| | - Connor Burbridge
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 0W9
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, Brno CZ-625 00, Czech Republic
| | - David Schneider
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 0W9
- School of the Environment and Sustainability, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5C8
| | - Jianguo Xia
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada H9X 3V9
| | - Doug Crump
- Environment and Climate Change Canada, National Wildlife Research Centre, Ottawa, Ontario, Canada K1A 0H3
| | - Niladri Basu
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada H9X 3V9
| | - Markus Hecker
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5B3
- School of the Environment and Sustainability, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5C8
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15
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Bora P, Gahurova L, Hauserova A, Stiborova M, Collier R, Potěšil D, Zdráhal Z, Bruce AW. DDX21 is a p38-MAPK-sensitive nucleolar protein necessary for mouse preimplantation embryo development and cell-fate specification. Open Biol 2021; 11:210092. [PMID: 34255976 PMCID: PMC8277471 DOI: 10.1098/rsob.210092] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Successful navigation of the mouse preimplantation stages of development, during which three distinct blastocyst lineages are derived, represents a prerequisite for continued development. We previously identified a role for p38-mitogen-activated kinases (p38-MAPK) regulating blastocyst inner cell mass (ICM) cell fate, specifically primitive endoderm (PrE) differentiation, that is intimately linked to rRNA precursor processing, polysome formation and protein translation regulation. Here, we develop this work by assaying the role of DEAD-box RNA helicase 21 (DDX21), a known regulator of rRNA processing, in the context of p38-MAPK regulation of preimplantation mouse embryo development. We show nuclear DDX21 protein is robustly expressed from the 16-cell stage, becoming exclusively nucleolar during blastocyst maturation, a localization dependent on active p38-MAPK. siRNA-mediated clonal Ddx21 knockdown within developing embryos is associated with profound cell-autonomous and non-autonomous proliferation defects and reduced blastocyst volume, by the equivalent peri-implantation blastocyst stage. Moreover, ICM residing Ddx21 knockdown clones express the EPI marker NANOG but rarely express the PrE differentiation marker GATA4. These data contribute further significance to the emerging importance of lineage-specific translation regulation, as identified for p38-MAPK, during mouse preimplantation development.
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Affiliation(s)
- Pablo Bora
- Laboratory of Early Mammalian Developmental Biology (LEMDB), Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Lenka Gahurova
- Laboratory of Early Mammalian Developmental Biology (LEMDB), Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic.,Laboratory of Biochemistry and Molecular Biology of Germ Cells, Institute of Animal Physiology and Genetics, CAS, Rumburská 89, 27721 Liběchov, Czech Republic
| | - Andrea Hauserova
- Laboratory of Early Mammalian Developmental Biology (LEMDB), Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Martina Stiborova
- Laboratory of Early Mammalian Developmental Biology (LEMDB), Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Rebecca Collier
- Laboratory of Early Mammalian Developmental Biology (LEMDB), Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - David Potěšil
- Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic
| | - Alexander W Bruce
- Laboratory of Early Mammalian Developmental Biology (LEMDB), Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic
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Paclíková P, Radaszkiewicz TW, Potěšil D, Harnoš J, Zdráhal Z, Bryja V. Roles of individual human Dishevelled paralogs in the Wnt signalling pathways. Cell Signal 2021; 85:110058. [PMID: 34082011 DOI: 10.1016/j.cellsig.2021.110058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 12/21/2022]
Abstract
Dishevelled (DVL) proteins are key mediators of most Wnt pathways. In all vertebrates, three DVL paralogs are present (DVL1, DVL2 and DVL3) but it is poorly defined to what extent they are functionally redundant. Here, we generated T-REx HEK 293 cells with only one DVL paralog (i.e., DVL1-only, DVL2-only, and DVL3-only) and compared their response to Wnt-3a and Wnt-5a ligands with wild type and DVL triple knockout cells. We show that DVL is essential, in addition to the previously shown Wnt-3a-induced phosphorylation of LRP6 and transcriptional activation of TCF/LEF-dependent reporter, also for Wnt-3a-induced degradation of AXIN1 and Wnt-5a-induced phosphorylation of ROR1. We have quantified the molar ratios of DVL1:DVL2:DVL3 in our model to be approximately 4:80:16. Interestingly, DVL-only cells do not compensate for the lack of other paralogs and are still fully functional in all analyzed readouts with the exception of Wnt-3a-induced transcription assessed by TopFlash assay. In this assay, the DVL1-only cell line was the most potent; on the contrary, the DVL3-only cell line exhibited only the negligible capacity to mediate Wnt signals. Using a novel model system - complementation assays in T-REx HEK 293 with amplified Wnt signal response (RNF43/ZNRF3/DVL1/DVL2/DVL3 penta KO cells) we demonstrate that it is not the total amount of DVL but ratio of individual paralogs what decides the signal strength. In sum, this study contributes to our better understanding of the role of individual human DVL paralogs in the Wnt pathway.
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Affiliation(s)
- Petra Paclíková
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | | | - David Potěšil
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jakub Harnoš
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Vítězslav Bryja
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic; Institute of Biophysics, Academy of Sciences of Czech Republic, Brno, Czech Republic.
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17
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Alcaraz AJG, Potěšil D, Mikulášek K, Green D, Park B, Burbridge C, Bluhm K, Soufan O, Lane T, Pipal M, Brinkmann M, Xia J, Zdráhal Z, Schneider D, Crump D, Basu N, Hogan N, Hecker M. Development of a Comprehensive Toxicity Pathway Model for 17α-Ethinylestradiol in Early Life Stage Fathead Minnows ( Pimephales promelas). Environ Sci Technol 2021; 55:5024-5036. [PMID: 33755441 DOI: 10.1021/acs.est.0c05942] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
There is increasing pressure to develop alternative ecotoxicological risk assessment approaches that do not rely on expensive, time-consuming, and ethically questionable live animal testing. This study aimed to develop a comprehensive early life stage toxicity pathway model for the exposure of fish to estrogenic chemicals that is rooted in mechanistic toxicology. Embryo-larval fathead minnows (FHM; Pimephales promelas) were exposed to graded concentrations of 17α-ethinylestradiol (water control, 0.01% DMSO, 4, 20, and 100 ng/L) for 32 days. Fish were assessed for transcriptomic and proteomic responses at 4 days post-hatch (dph), and for histological and apical end points at 28 dph. Molecular analyses revealed core responses that were indicative of observed apical outcomes, including biological processes resulting in overproduction of vitellogenin and impairment of visual development. Histological observations indicated accumulation of proteinaceous fluid in liver and kidney tissues, energy depletion, and delayed or suppressed gonad development. Additionally, fish in the 100 ng/L treatment group were smaller than controls. Integration of omics data improved the interpretation of perturbations in early life stage FHM, providing evidence of conservation of toxicity pathways across levels of biological organization. Overall, the mechanism-based embryo-larval FHM model showed promise as a replacement for standard adult live animal tests.
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Affiliation(s)
- Alper James G Alcaraz
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B3, Canada
| | - David Potěšil
- Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
| | - Kamil Mikulášek
- Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
| | - Derek Green
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B3, Canada
| | - Bradley Park
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B3, Canada
| | - Connor Burbridge
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Kerstin Bluhm
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B3, Canada
| | - Othman Soufan
- Computer Science Department, St. Francis Xavier University, Antigonish, Nova Scotia B2G 2W5, Canada
| | - Taylor Lane
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B3, Canada
- Department of Environment and Geography, York University, York YO10 5NG, United Kingdom
| | - Marek Pipal
- RECETOX, Masaryk University, Brno 625 00, Czech Republic
| | - Markus Brinkmann
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B3, Canada
- School of the Environment and Sustainability, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5C8, Canada
- Global Institute for Water Security, University of Saskatchewan, Saskatoon, Saskatchewan S7N 3H5, Canada
| | - Jianguo Xia
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec H9X 3V9, Canada
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
| | - David Schneider
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, Saskatchewan S7N 0W9, Canada
- School of the Environment and Sustainability, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5C8, Canada
| | - Doug Crump
- Environment and Climate Change Canada, National Wildlife Research Centre, Ottawa, Ontario K1A 0H3, Canada
| | - Niladri Basu
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec H9X 3V9, Canada
| | - Natacha Hogan
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B3, Canada
- Department of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A8, Canada
| | - Markus Hecker
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B3, Canada
- School of the Environment and Sustainability, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5C8, Canada
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18
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Mikulášek K, Konečná H, Potěšil D, Holánková R, Havliš J, Zdráhal Z. SP3 Protocol for Proteomic Plant Sample Preparation Prior LC-MS/MS. Front Plant Sci 2021; 12:635550. [PMID: 33777071 PMCID: PMC7988192 DOI: 10.3389/fpls.2021.635550] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/17/2021] [Indexed: 05/25/2023]
Abstract
Quantitative protein extraction from biological samples, as well as contaminants removal before LC-MS/MS, is fundamental for the successful bottom-up proteomic analysis. Four sample preparation methods, including the filter-aided sample preparation (FASP), two single-pot solid-phase-enhanced sample preparations (SP3) on carboxylated or HILIC paramagnetic beads, and protein suspension trapping method (S-Trap) were evaluated for SDS removal and protein digestion from Arabidopsis thaliana (AT) lysate. Finally, the optimized carboxylated SP3 workflow was benchmarked closely against the routine FASP. Ultimately, LC-MS/MS analyses revealed that regarding the number of identifications, number of missed cleavages, proteome coverage, repeatability, reduction of handling time, and cost per assay, the SP3 on carboxylated magnetic particles proved to be the best alternative for SDS and other contaminants removal from plant sample lysate. A robust and efficient 2-h SP3 protocol for a wide range of protein input is presented, benefiting from no need to adjust the amount of beads, binding and rinsing conditions, or digestion parameters.
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Affiliation(s)
- Kamil Mikulášek
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Hana Konečná
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - David Potěšil
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Renata Holánková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Jan Havliš
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Zbyněk Zdráhal
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
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19
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Flores-Tornero M, Wang L, Potěšil D, Hafidh S, Vogler F, Zdráhal Z, Honys D, Sprunck S, Dresselhaus T. Comparative analyses of angiosperm secretomes identify apoplastic pollen tube functions and novel secreted peptides. Plant Reprod 2021; 34:47-60. [PMID: 33258014 PMCID: PMC7902602 DOI: 10.1007/s00497-020-00399-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 11/10/2020] [Indexed: 05/14/2023]
Abstract
KEY MESSAGE Analyses of secretomes of in vitro grown pollen tubes from Amborella, maize and tobacco identified many components of processes associated with the cell wall, signaling and metabolism as well as novel small secreted peptides. Flowering plants (angiosperms) generate pollen grains that germinate on the stigma and produce tubes to transport their sperm cells cargo deep into the maternal reproductive tissues toward the ovules for a double fertilization process. During their journey, pollen tubes secrete many proteins (secreted proteome or secretome) required, for example, for communication with the maternal reproductive tissues, to build a solid own cell wall that withstands their high turgor pressure while softening simultaneously maternal cell wall tissue. The composition and species specificity or family specificity of the pollen tube secretome is poorly understood. Here, we provide a suitable method to obtain the pollen tube secretome from in vitro grown pollen tubes of the basal angiosperm Amborella trichopoda (Amborella) and the Poaceae model maize. The previously published secretome of tobacco pollen tubes was used as an example of eudicotyledonous plants in this comparative study. The secretome of the three species is each strongly different compared to the respective protein composition of pollen grains and tubes. In Amborella and maize, about 40% proteins are secreted by the conventional "classic" pathway and 30% by unconventional pathways. The latter pathway is expanded in tobacco. Proteins enriched in the secretome are especially involved in functions associated with the cell wall, cell surface, energy and lipid metabolism, proteolysis and redox processes. Expansins, pectin methylesterase inhibitors and RALFs are enriched in maize, while tobacco secretes many proteins involved, for example, in proteolysis and signaling. While the majority of proteins detected in the secretome occur also in pollen grains and pollen tubes, and correlate in the number of mapped peptides with relative gene expression levels, some novel secreted small proteins were identified. Moreover, the identification of secreted proteins containing pro-peptides indicates that these are processed in the apoplast. In conclusion, we provide a proteome resource from three distinct angiosperm clades that can be utilized among others to study the localization, abundance and processing of known secreted proteins and help to identify novel pollen tube secreted proteins for functional studies.
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Affiliation(s)
- María Flores-Tornero
- Cell Biology and Plant Biochemistry, University of Regensburg, Universitätsstraße 31, 93053, Regensburg, Germany
| | - Lele Wang
- Cell Biology and Plant Biochemistry, University of Regensburg, Universitätsstraße 31, 93053, Regensburg, Germany
| | - David Potěšil
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Said Hafidh
- Laboratory of Pollen Biology, Institute of Experimental Botany ASCR, Rozvojová 263, 165 02, Prague 6, Czech Republic
| | - Frank Vogler
- Cell Biology and Plant Biochemistry, University of Regensburg, Universitätsstraße 31, 93053, Regensburg, Germany
| | - Zbyněk Zdráhal
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - David Honys
- Laboratory of Pollen Biology, Institute of Experimental Botany ASCR, Rozvojová 263, 165 02, Prague 6, Czech Republic
| | - Stefanie Sprunck
- Cell Biology and Plant Biochemistry, University of Regensburg, Universitätsstraße 31, 93053, Regensburg, Germany
| | - Thomas Dresselhaus
- Cell Biology and Plant Biochemistry, University of Regensburg, Universitätsstraße 31, 93053, Regensburg, Germany.
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20
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Kolářová H, Víteček J, Černá A, Černík M, Přibyl J, Skládal P, Potěšil D, Ihnatová I, Zdráhal Z, Hampl A, Klinke A, Kubala L. Myeloperoxidase mediated alteration of endothelial function is dependent on its cationic charge. Free Radic Biol Med 2021; 162:14-26. [PMID: 33271281 DOI: 10.1016/j.freeradbiomed.2020.11.008] [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] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 11/02/2020] [Accepted: 11/10/2020] [Indexed: 12/20/2022]
Abstract
Endothelial cell (EC) glycocalyx (GLX) comprise a multicomponent layer of proteoglycans and glycoproteins. Alteration of its integrity contributes to chronic vascular inflammation and leads to the development of cardiovascular diseases. Myeloperoxidase (MPO), a highly abundant enzyme released by polymorphonuclear neutrophils, binds to the GLX and deleteriously affects vascular EC functions. The focus of this study was to elucidate the mechanisms of MPO-mediated alteration of GLX molecules, and to unravel subsequent changes in endothelial integrity and function. MPO binding to GLX of human ECs and subsequent internalization was mediated by cell surface heparan sulfate chains. Moreover, interaction of MPO, which is carrying a cationic charge, with anionic glycosaminoglycans (GAGs) resulted in reduction of their relative charge. By means of micro-viscometry and atomic force microscopy, we disclosed that MPO can crosslink GAG chains. MPO-dependent modulation of GLX structure was further supported by alteration of wheat germ agglutinin staining. Increased expression of ICAM-1 documented endothelial cell activation by both catalytically active and also inactive MPO. Furthermore, MPO increased vascular permeability connected with reorganization of intracellular junctions, however, this was dependent on MPO's catalytic activity. Novel proteins interacting with MPO during transcytosis were identified by proteomic analysis. Altogether, these findings provide evidence that MPO through interaction with GAGs modulates overall charge of the GLX, causing modification of its structure and thus affecting EC function. Importantly, our results also suggest a number of proteins interacting with MPO that possess a variety of cellular localizations and functions.
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Affiliation(s)
- Hana Kolářová
- Department of Biophysics of Immune System, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, Brno, Czech Republic
| | - Jan Víteček
- Department of Biophysics of Immune System, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, Brno, Czech Republic
| | - Anna Černá
- Department of Biophysics of Immune System, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, Brno, Czech Republic
| | - Marek Černík
- Department of Biophysics of Immune System, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, Brno, Czech Republic
| | - Jan Přibyl
- Central European Institute for Technology, Masaryk University, Kamenice 5, Brno, Czech Republic
| | - Petr Skládal
- Central European Institute for Technology, Masaryk University, Kamenice 5, Brno, Czech Republic
| | - David Potěšil
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Ivana Ihnatová
- Institute of Biostatistics and Analyses, Masaryk University, Kamenice 3, Brno, Czech Republic
| | - Zbyněk Zdráhal
- Central European Institute for Technology, Masaryk University, Kamenice 5, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Aleš Hampl
- Faculty of Medicine, Department of Histology and Embryology, Masaryk University, Kamenice 3, 625 00, Brno, Czech Republic
| | - Anna Klinke
- Clinic of General and Interventional Cardiology/Angiology, Agnes Wittenborg Institute of Translational Cardiovascular Research, Herz- und Diabeteszentrum NRW, Ruhr-Universität Bochum, Bad Oeynhausen, Germany
| | - Lukáš Kubala
- Department of Biophysics of Immune System, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, Brno, Czech Republic.
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Flores-Tornero M, Vogler F, Mutwil M, Potěšil D, Ihnatová I, Zdráhal Z, Sprunck S, Dresselhaus T. Transcriptomic and Proteomic Insights into Amborella trichopoda Male Gametophyte Functions. Plant Physiol 2020; 184:1640-1657. [PMID: 32989009 PMCID: PMC7723084 DOI: 10.1104/pp.20.00837] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/16/2020] [Indexed: 05/27/2023]
Abstract
Flowering plants (angiosperms) are characterized by pollen tubes (PTs; male gametophytes) carrying two immobile sperm cells that grow over long distances through the carpel toward the ovules, where double fertilization is executed. It is not understood how these reproductive structures evolved, which genes occur de novo in male gametophytes of angiosperms, and to which extent PT functions are conserved among angiosperms. To contribute to a deeper understanding of the evolution of gametophyte functions, we generated RNA sequencing data from seven reproductive and two vegetative control tissues of the basal angiosperm Amborella trichopoda and complemented these with proteomic data of pollen grains (PGs) and PTs. The eudicot model plant Arabidopsis (Arabidopsis thaliana) served as a reference organism for data analysis, as more than 200 genes have been associated with male gametophyte functions in this species. We describe methods to collect bicellular A. trichopoda PGs, to induce their germination in vitro, and to monitor PT growth and germ cell division. Transcriptomic and proteomic analyses indicate that A. trichopoda PGs are prepared for germination requiring lipids, energy, but likely also reactive oxygen species, while PTs are especially characterized by catabolic/biosynthetic and transport processes including cell wall biosynthesis and gene regulation. Notably, a number of pollen-specific genes were lacking in Arabidopsis, and the number of genes involved in pollen signaling is significantly reduced in A. trichopoda In conclusion, we provide insight into male gametophyte functions of the most basal angiosperm and establish a valuable resource for future studies on the evolution of flowering plants.
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Affiliation(s)
- María Flores-Tornero
- Cell Biology and Plant Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Frank Vogler
- Cell Biology and Plant Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - David Potěšil
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, CZ-62500 Brno, Czech Republic
| | - Ivana Ihnatová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, CZ-62500 Brno, Czech Republic
- RECETOX, Faculty of Science, Masaryk University, CZ-62500 Brno, Czech Republic
| | - Zbyněk Zdráhal
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, CZ-62500 Brno, Czech Republic
| | - Stefanie Sprunck
- Cell Biology and Plant Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Thomas Dresselhaus
- Cell Biology and Plant Biochemistry, University of Regensburg, 93053 Regensburg, Germany
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22
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Shrestha A, Mishra AK, Matoušek J, Steinbachová L, Potěšil D, Nath VS, Awasthi P, Kocábek T, Jakse J, Drábková LZ, Zdráhal Z, Honys D, Steger G. Integrated Proteo-Transcriptomic Analyses Reveal Insights into Regulation of Pollen Development Stages and Dynamics of Cellular Response to Apple Fruit Crinkle Viroid (AFCVd)-Infection in Nicotiana tabacum. Int J Mol Sci 2020; 21:E8700. [PMID: 33218043 PMCID: PMC7698868 DOI: 10.3390/ijms21228700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/15/2020] [Accepted: 11/17/2020] [Indexed: 02/06/2023] Open
Abstract
Tobacco (Nicotiana tabacum) pollen is a well-suited model for studying many fundamental biological processes owing to its well-defined and distinct development stages. It is also one of the major agents involved in the transmission of infectious viroids, which is the primary mechanism of viroid pathogenicity in plants. However, some viroids are non-transmissible and may be possibly degraded or eliminated during the gradual process of pollen development maturation. The molecular details behind the response of developing pollen against the apple fruit crinkle viroid (AFCVd) infection and viroid eradication is largely unknown. In this study, we performed an integrative analysis of the transcriptome and proteome profiles to disentangle the molecular cascade of events governing the three pollen development stages: early bicellular pollen (stage 3, S3), late bicellular pollen (stage 5, S5), and 6 h-pollen tube (PT6). The integrated analysis delivered the molecular portraits of the developing pollen against AFCVd infection, including mechanistic insights into the viroid eradication during the last steps of pollen development. The isobaric tags for label-free relative quantification (iTRAQ) with digital gene expression (DGE) experiments led us to reliably identify subsets of 5321, 5286, and 6923 proteins and 64,033, 60,597, and 46,640 expressed genes in S3, S5, and PT6, respectively. In these subsets, 2234, 2108 proteins and 9207 and 14,065 mRNAs were differentially expressed in pairwise comparisons of three stages S5 vs. S3 and PT6 vs. S5 of control pollen in tobacco. Correlation analysis between the abundance of differentially expressed mRNAs (DEGs) and differentially expressed proteins (DEPs) in pairwise comparisons of three stages of pollen revealed numerous discordant changes in mRNA/protein pairs. Only a modest correlation was observed, indicative of divergent transcription, and its regulation and importance of post-transcriptional events in the determination of the fate of early and late pollen development in tobacco. The functional and enrichment analysis of correlated DEGs/DEPs revealed the activation in pathways involved in carbohydrate metabolism, amino acid metabolism, lipid metabolism, and cofactor as well as vitamin metabolism, which points to the importance of these metabolic pathways in pollen development. Furthermore, the detailed picture of AFCVd-infected correlated DEGs/DEPs was obtained in pairwise comparisons of three stages of infected pollen. The AFCVd infection caused the modulation of several genes involved in protein degradation, nuclear transport, phytohormone signaling, defense response, and phosphorylation. Intriguingly, we also identified several factors including, DNA-dependent RNA-polymerase, ribosomal protein, Argonaute (AGO) proteins, nucleotide binding proteins, and RNA exonucleases, which may plausibly involve in viroid stabilization and eradication during the last steps of pollen development. The present study provides essential insights into the transcriptional and translational dynamics of tobacco pollen, which further strengthens our understanding of plant-viroid interactions and support for future mechanistic studies directed at delineating the functional role of candidate factors involved in viroid elimination.
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Affiliation(s)
- Ankita Shrestha
- Biology Centre, Czech Academy of Sciences, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic; (A.S.); (J.M.); (V.S.N.); (P.A.); (T.K.)
| | - Ajay Kumar Mishra
- Biology Centre, Czech Academy of Sciences, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic; (A.S.); (J.M.); (V.S.N.); (P.A.); (T.K.)
| | - Jaroslav Matoušek
- Biology Centre, Czech Academy of Sciences, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic; (A.S.); (J.M.); (V.S.N.); (P.A.); (T.K.)
| | - Lenka Steinbachová
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6-Lysolaje, Czech Republic; (L.S.); (L.Z.D.); (D.H.)
| | - David Potěšil
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; (D.P.); (Z.Z.)
| | - Vishnu Sukumari Nath
- Biology Centre, Czech Academy of Sciences, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic; (A.S.); (J.M.); (V.S.N.); (P.A.); (T.K.)
| | - Praveen Awasthi
- Biology Centre, Czech Academy of Sciences, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic; (A.S.); (J.M.); (V.S.N.); (P.A.); (T.K.)
| | - Tomáš Kocábek
- Biology Centre, Czech Academy of Sciences, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic; (A.S.); (J.M.); (V.S.N.); (P.A.); (T.K.)
| | - Jernej Jakse
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia;
| | - Lenka Záveská Drábková
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6-Lysolaje, Czech Republic; (L.S.); (L.Z.D.); (D.H.)
| | - Zbyněk Zdráhal
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; (D.P.); (Z.Z.)
| | - David Honys
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6-Lysolaje, Czech Republic; (L.S.); (L.Z.D.); (D.H.)
| | - Gerhard Steger
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, D-40204 Düsseldorf, Germany;
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23
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Roudnický P, Potěšil D, Zdráhal Z, Gelnar M, Kašný M. Laser capture microdissection in combination with mass spectrometry: Approach to characterization of tissue-specific proteomes of Eudiplozoon nipponicum (Monogenea, Polyopisthocotylea). PLoS One 2020; 15:e0231681. [PMID: 32555742 PMCID: PMC7299319 DOI: 10.1371/journal.pone.0231681] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 05/25/2020] [Indexed: 12/14/2022] Open
Abstract
Eudiplozoon nipponicum (Goto, 1891) is a hematophagous monogenean ectoparasite which inhabits the gills of the common carp (Cyprinus carpio). Heavy infestation can lead to anemia and in conjunction with secondary bacterial infections cause poor health and eventual death of the host. This study is based on an innovative approach to protein localization which has never been used in parasitology before. Using laser capture microdissection, we dissected particular areas of the parasite body without contaminating the samples by surrounding tissue and in combination with analysis by mass spectrometry obtained tissue-specific proteomes of tegument, intestine, and parenchyma of our model organism, E. nipponicum. We successfully verified the presence of certain functional proteins (e.g. cathepsin L) in tissues where their presence was expected (intestine) and confirmed that there were no traces of these proteins in other tissues (tegument and parenchyma). Additionally, we identified a total of 2,059 proteins, including 72 peptidases and 33 peptidase inhibitors. As expected, the greatest variety was found in the intestine and the lowest variety in the parenchyma. Our results are significant on two levels. Firstly, we demonstrated that one can localize all proteins in one analysis and without using laboratory animals (antibodies for immunolocalization of single proteins). Secondly, this study offers the first complex proteomic data on not only the E. nipponicum but within the whole class of Monogenea, which was from this point of view until recently neglected.
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Affiliation(s)
- Pavel Roudnický
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
- * E-mail:
| | - David Potěšil
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Milan Gelnar
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Martin Kašný
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
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24
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Matoušek J, Steinbachová L, Drábková LZ, Kocábek T, Potěšil D, Mishra AK, Honys D, Steger G. Elimination of Viroids from Tobacco Pollen Involves a Decrease in Propagation Rate and an Increase of the Degradation Processes. Int J Mol Sci 2020; 21:E3029. [PMID: 32344786 PMCID: PMC7216239 DOI: 10.3390/ijms21083029] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/19/2020] [Accepted: 04/20/2020] [Indexed: 12/13/2022] Open
Abstract
Some viroids-single-stranded, non-coding, circular RNA parasites of plants-are not transmissible through pollen to seeds and to next generation. We analyzed the cause for the elimination of apple fruit crinkle viroid (AFCVd) and citrus bark cracking viroid (CBCVd) from male gametophyte cells of Nicotiana tabacum by RNA deep sequencing and molecular methods using infected and transformed tobacco pollen tissues at different developmental stages. AFCVd was not transferable from pollen to seeds in reciprocal pollinations, due to a complete viroid eradication during the last steps of pollen development and fertilization. In pollen, the viroid replication pathway proceeds with detectable replication intermediates, but is dramatically depressed in comparison to leaves. Specific and unspecific viroid degradation with some preference for (-) chains occurred in pollen, as detected by analysis of viroid-derived small RNAs, by quantification of viroid levels and by detection of viroid degradation products forming "comets" on Northern blots. The decrease of viroid levels during pollen development correlated with mRNA accumulation of several RNA-degrading factors, such as AGO5 nuclease, DICER-like and TUDOR S-like nuclease. In addition, the functional status of pollen, as a tissue with high ribosome content, could play a role during suppression of AFCVd replication involving transcription factors IIIA and ribosomal protein L5.
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Affiliation(s)
- Jaroslav Matoušek
- Biology Centre of the Czech Academy of Sciences, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic; (J.M.); (T.K.); (A.K.M.)
| | - Lenka Steinbachová
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic; (L.S.); (L.Z.D.); (D.H.)
| | - Lenka Záveská Drábková
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic; (L.S.); (L.Z.D.); (D.H.)
| | - Tomáš Kocábek
- Biology Centre of the Czech Academy of Sciences, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic; (J.M.); (T.K.); (A.K.M.)
| | - David Potěšil
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic;
| | - Ajay Kumar Mishra
- Biology Centre of the Czech Academy of Sciences, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic; (J.M.); (T.K.); (A.K.M.)
| | - David Honys
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic; (L.S.); (L.Z.D.); (D.H.)
| | - Gerhard Steger
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, D-40204 Düsseldorf, Germany
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25
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Fíla J, Klodová B, Potěšil D, Juříček M, Šesták P, Zdráhal Z, Honys D. The beta Subunit of Nascent Polypeptide Associated Complex Plays A Role in Flowers and Siliques Development of Arabidopsis thaliana. Int J Mol Sci 2020; 21:E2065. [PMID: 32192231 PMCID: PMC7139743 DOI: 10.3390/ijms21062065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/11/2020] [Accepted: 03/14/2020] [Indexed: 01/06/2023] Open
Abstract
The nascent polypeptide-associated (NAC) complex was described in yeast as a heterodimer composed of two subunits, α and β, and was shown to bind to the nascent polypeptides newly emerging from the ribosomes. NAC function was widely described in yeast and several information are also available about its role in plants. The knock down of individual NAC subunit(s) led usually to a higher sensitivity to stress. In Arabidopsis thaliana genome, there are five genes encoding NACα subunit, and two genes encoding NACβ. Double homozygous mutant in both genes coding for NACβ was acquired, which showed a delayed development compared to the wild type, had abnormal number of flower organs, shorter siliques and greatly reduced seed set. Both NACβ genes were characterized in more detail-the phenotype of the double homozygous mutant was complemented by a functional NACβ copy. Then, both NACβ genes were localized to nuclei and cytoplasm and their promoters were active in many organs (leaves, cauline leaves, flowers, pollen grains, and siliques together with seeds). Since flowers were the most affected organs by nacβ mutation, the flower buds' transcriptome was identified by RNA sequencing, and their proteome by gel-free approach. The differential expression analyses of transcriptomic and proteomic datasets suggest the involvement of NACβ subunits in stress responses, male gametophyte development, and photosynthesis.
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Affiliation(s)
- Jan Fíla
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, 16502 Praha 6, Czech Republic; (B.K.); (D.H.)
| | - Božena Klodová
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, 16502 Praha 6, Czech Republic; (B.K.); (D.H.)
- Department of Experimental Plant Biology, Faculty of Science, Charles University, 12800 Praha 2, Czech Republic
| | - David Potěšil
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (D.P.); (Z.Z.)
| | - Miloslav Juříček
- Station of Apple Breeding for Disease Resistance, Institute of Experimental Botany of the Czech Academy of Sciences, 16502 Praha 6, Czech Republic;
| | - Petr Šesták
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, 16502 Praha 6, Czech Republic; (B.K.); (D.H.)
- Department of Experimental Plant Biology, Faculty of Science, Charles University, 12800 Praha 2, Czech Republic
| | - Zbyněk Zdráhal
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (D.P.); (Z.Z.)
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | - David Honys
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, 16502 Praha 6, Czech Republic; (B.K.); (D.H.)
- Department of Experimental Plant Biology, Faculty of Science, Charles University, 12800 Praha 2, Czech Republic
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26
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Hanáková K, Bernatík O, Kravec M, Micka M, Kumar J, Harnoš J, Ovesná P, Paclíková P, Rádsetoulal M, Potěšil D, Tripsianes K, Čajánek L, Zdráhal Z, Bryja V. Comparative phosphorylation map of Dishevelled 3 links phospho-signatures to biological outputs. Cell Commun Signal 2019; 17:170. [PMID: 31870452 PMCID: PMC6927192 DOI: 10.1186/s12964-019-0470-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [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] [Received: 09/02/2019] [Accepted: 10/22/2019] [Indexed: 12/28/2022] Open
Abstract
Background Dishevelled (DVL) is an essential component of the Wnt signaling cascades. Function of DVL is controlled by phosphorylation but the molecular details are missing. DVL3 contains 131 serines and threonines whose phosphorylation generates complex barcodes underlying diverse DVL3 functions. In order to dissect the role of DVL phosphorylation we analyzed the phosphorylation of human DVL3 induced by previously reported (CK1ε, NEK2, PLK1, CK2α, RIPK4, PKCδ) and newly identified (TTBK2, Aurora A) DVL kinases. Methods Shotgun proteomics including TiO2 enrichment of phosphorylated peptides followed by liquid chromatography tandem mass spectrometry on immunoprecipitates from HEK293T cells was used to identify and quantify phosphorylation of DVL3 protein induced by 8 kinases. Functional characterization was performed by in-cell analysis of phospho-mimicking/non-phosphorylatable DVL3 mutants and supported by FRET assays and NMR spectroscopy. Results We used quantitative mass spectrometry and calculated site occupancies and quantified phosphorylation of > 80 residues. Functional validation demonstrated the importance of CK1ε-induced phosphorylation of S268 and S311 for Wnt-3a-induced β-catenin activation. S630–643 cluster phosphorylation by CK1, NEK2 or TTBK2 is essential for even subcellular distribution of DVL3 when induced by CK1 and TTBK2 but not by NEK2. Further investigation showed that NEK2 utilizes a different mechanism to promote even localization of DVL3. NEK2 triggered phosphorylation of PDZ domain at S263 and S280 prevents binding of DVL C-terminus to PDZ and promotes an open conformation of DVL3 that is more prone to even subcellular localization. Conclusions We identify unique phosphorylation barcodes associated with DVL function. Our data provide an example of functional synergy between phosphorylation in structured domains and unstructured IDRs that together dictate the biological outcome. Video Abtract.
Graphical abstract ![]()
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Affiliation(s)
- Kateřina Hanáková
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Ondřej Bernatík
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic.,Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Marek Kravec
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Miroslav Micka
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Jitender Kumar
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Jakub Harnoš
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Petra Ovesná
- Institute of Biostatistics and Analyses, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Petra Paclíková
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Matěj Rádsetoulal
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - David Potěšil
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Konstantinos Tripsianes
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Lukáš Čajánek
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Zbyněk Zdráhal
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic. .,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic.
| | - Vítězslav Bryja
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic. .,Department of Cytokinetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
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27
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Roudnický P, Vorel J, Ilgová J, Benovics M, Norek A, Jedličková L, Mikeš L, Potěšil D, Zdráhal Z, Dvořák J, Gelnar M, Kašný M. Identification and partial characterization of a novel serpin from Eudiplozoon nipponicum (Monogenea, Polyopisthocotylea). ACTA ACUST UNITED AC 2018; 25:61. [PMID: 30516130 PMCID: PMC6280883 DOI: 10.1051/parasite/2018062] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 11/16/2018] [Indexed: 12/14/2022]
Abstract
Background: Serpins are a superfamily of serine peptidase inhibitors that participate in the regulation of many physiological and cell peptidase-mediated processes in all organisms (e.g. in blood clotting, complement activation, fibrinolysis, inflammation, and programmed cell death). It was postulated that in the blood-feeding members of the monogenean family Diplozoidae, serpins could play an important role in the prevention of thrombus formation, activation of complement, inflammation in the host, and/or in the endogenous regulation of protein degradation. Results: In silico analysis showed that the DNA and primary protein structures of serpin from Eudiplozoon nipponicum (EnSerp1) are similar to other members of the serpin superfamily. The inhibitory potential of EnSerp1 on four physiologically-relevant serine peptidases (trypsin, factor Xa, kallikrein, and plasmin) was demonstrated and its presence in the worm’s excretory-secretory products (ESPs) was confirmed. Conclusion: EnSerp1 influences the activity of peptidases that play a role in blood coagulation, fibrinolysis, and complement activation. This inhibitory potential, together with the serpin’s presence in ESPs, suggests that it is likely involved in host-parasite interactions and could be one of the molecules involved in the control of feeding and prevention of inflammatory responses.
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Affiliation(s)
- Pavel Roudnický
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic
| | - Jiří Vorel
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic
| | - Jana Ilgová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic
| | - Michal Benovics
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic
| | - Adam Norek
- Veterinary Research Institute, Hudcova 296/70, 62100 Brno, Czech Republic
| | - Lucie Jedličková
- Department of Parasitology, Faculty of Science, Charles University, Viničná 7, 12844 Prague 2, Czech Republic
| | - Libor Mikeš
- Department of Parasitology, Faculty of Science, Charles University, Viničná 7, 12844 Prague 2, Czech Republic
| | - David Potěšil
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic - National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic
| | - Jan Dvořák
- School of Biological Sciences, Medical Biology Centre, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, United Kingdom - Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences in Prague, Kamýcká 129, 16521 Prague, Czech Republic
| | - Milan Gelnar
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic
| | - Martin Kašný
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic - Department of Parasitology, Faculty of Science, Charles University, Viničná 7, 12844 Prague 2, Czech Republic
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28
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Kaurov I, Vancová M, Schimanski B, Cadena LR, Heller J, Bílý T, Potěšil D, Eichenberger C, Bruce H, Oeljeklaus S, Warscheid B, Zdráhal Z, Schneider A, Lukeš J, Hashimi H. The Diverged Trypanosome MICOS Complex as a Hub for Mitochondrial Cristae Shaping and Protein Import. Curr Biol 2018; 28:3393-3407.e5. [PMID: 30415698 DOI: 10.1016/j.cub.2018.09.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/02/2018] [Accepted: 09/04/2018] [Indexed: 12/20/2022]
Abstract
The mitochondrial contact site and cristae organization system (MICOS) is a multiprotein complex responsible for cristae formation. Even though cristae are found in all mitochondria capable of oxidative phosphorylation, only Mic10 and Mic60 appear to be conserved throughout eukaryotes. The remaining 4 or 5 known MICOS subunits are specific to the supergroup Opisthokonta, which includes yeast and mammals that are the only organisms in which this complex has been analyzed experimentally. We have isolated the MICOS from Trypanosoma brucei, a member of the supergroup Excavata that is profoundly diverged from opisthokonts. We show that it is required for the maintenance of the unique discoidal cristae that typify excavates, such as euglenids and kinetoplastids, the latter of which include trypanosomes. The trypanosome MICOS consists of 9 subunits, most of which are essential for normal growth. Unlike in opisthokonts, it contains two distinct Mic10 orthologs and an unconventional putative Mic60 that lacks a mitofilin domain. Interestingly, one of the essential trypanosomatid-specific MICOS subunits called TbMic20 is a thioredoxin-like protein that appears to be involved in import of intermembrane space proteins, including respiratory chain complex assembly factors. This result points to trypanosome MICOS coordinating cristae shaping and population of its membrane with proteins involved in respiration, the latter via the catalytic activity of TbMic20. Thus, trypanosome MICOS allows us to define which of its features are conserved in all eukaryotes and decipher those that represent lineage-specific adaptations.
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Affiliation(s)
- Iosif Kaurov
- Institute of Parasitology, Biology Center, Czech Academy of Sciences, 37005 České Budějovice, Czech Republic; Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - Marie Vancová
- Institute of Parasitology, Biology Center, Czech Academy of Sciences, 37005 České Budějovice, Czech Republic; Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - Bernd Schimanski
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Lawrence Rudy Cadena
- Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - Jiří Heller
- Institute of Parasitology, Biology Center, Czech Academy of Sciences, 37005 České Budějovice, Czech Republic
| | - Tomáš Bílý
- Institute of Parasitology, Biology Center, Czech Academy of Sciences, 37005 České Budějovice, Czech Republic; Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - David Potěšil
- Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic
| | - Claudia Eichenberger
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Hannah Bruce
- Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - Silke Oeljeklaus
- Faculty of Biology, Biochemistry and Functional Proteomics, Institute of Biology II, University of Freiburg, 79104 Freiburg, Germany
| | - Bettina Warscheid
- Faculty of Biology, Biochemistry and Functional Proteomics, Institute of Biology II, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic
| | - André Schneider
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Julius Lukeš
- Institute of Parasitology, Biology Center, Czech Academy of Sciences, 37005 České Budějovice, Czech Republic; Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - Hassan Hashimi
- Institute of Parasitology, Biology Center, Czech Academy of Sciences, 37005 České Budějovice, Czech Republic; Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic.
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29
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Hafidh S, Potěšil D, Müller K, Fíla J, Michailidis C, Herrmannová A, Feciková J, Ischebeck T, Valášek LS, Zdráhal Z, Honys D. Dynamics of the Pollen Sequestrome Defined by Subcellular Coupled Omics. Plant Physiol 2018; 178:258-282. [PMID: 30007911 PMCID: PMC6130014 DOI: 10.1104/pp.18.00648] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 06/27/2018] [Indexed: 05/19/2023]
Abstract
Reproduction success in angiosperm plants depends on robust pollen tube growth through the female pistil tissues to ensure successful fertilization. Accordingly, there is an apparent evolutionary trend to accumulate significant reserves during pollen maturation, including a population of stored mRNAs, that are utilized later for a massive translation of various proteins in growing pollen tubes. Here, we performed a thorough transcriptomic and proteomic analysis of stored and translated transcripts in three subcellular compartments of tobacco (Nicotiana tabacum), long-term storage EDTA/puromycin-resistant particles, translating polysomes, and free ribonuclear particles, throughout tobacco pollen development and in in vitro-growing pollen tubes. We demonstrated that the composition of the aforementioned complexes is not rigid and that numerous transcripts were redistributed among these complexes during pollen development, which may represent an important mechanism of translational regulation. Therefore, we defined the pollen sequestrome as a distinct and highly dynamic compartment for the storage of stable, translationally repressed transcripts and demonstrated its dynamics. We propose that EDTA/puromycin-resistant particle complexes represent aggregated nontranslating monosomes as the primary mediators of messenger RNA sequestration. Such organization is extremely useful in fast tip-growing pollen tubes, where rapid and orchestrated protein synthesis must take place in specific regions.
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Affiliation(s)
- Said Hafidh
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, 165 00 Prague 6, Czech Republic
| | - David Potěšil
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Karel Müller
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany of the Czech Academy of Sciences, 165 00 Prague 6, Czech Republic
| | - Jan Fíla
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, 165 00 Prague 6, Czech Republic
| | - Christos Michailidis
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, 165 00 Prague 6, Czech Republic
| | - Anna Herrmannová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, 142 20 Prague 4, Czech Republic
| | - Jana Feciková
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, 165 00 Prague 6, Czech Republic
| | - Till Ischebeck
- Department of Plant Biochemistry, Albrecht-von-Haller Institute for Plant Sciences, University of Goettingen, 37077 Goettingen, Germany
| | - Leoš Shivaya Valášek
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, 142 20 Prague 4, Czech Republic
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - David Honys
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, 165 00 Prague 6, Czech Republic
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Hamáková K, Potěšil D, Bernatik O, Červenka I, Rádsetoulal M, Bryja V, Zdráhal Z. Semiquantitative Assessment of Dishevelled-3 Phosphorylation Status by Mass Spectrometry. Hungarian Journal of Industry and Chemistry 2018. [DOI: 10.1515/hjic-2018-0002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
The focus of this paper is the human Dishevelled 3 protein (hDvl3), an essential component of the Wnt signalling pathway that contributes to their regulation. Mass spectrometry-based analysis of hDvl3 phosphorylations induced by eight associated kinases was performed revealing several dozens of phosphorylation sites. The main outcome of this study was the description of Dvl phosphorylation “patterns” induced by individual kinases
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Verlande A, Krafčíková M, Potěšil D, Trantírek L, Zdráhal Z, Elkalaf M, Trnka J, Souček K, Rauch N, Rauch J, Kolch W, Uldrijan S. Metabolic stress regulates ERK activity by controlling KSR-RAF heterodimerization. EMBO Rep 2018; 19:320-336. [PMID: 29263201 PMCID: PMC5797961 DOI: 10.15252/embr.201744524] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 11/15/2017] [Accepted: 11/24/2017] [Indexed: 12/24/2022] Open
Abstract
Altered cell metabolism is a hallmark of cancer, and targeting specific metabolic nodes is considered an attractive strategy for cancer therapy. In this study, we evaluate the effects of metabolic stressors on the deregulated ERK pathway in melanoma cells bearing activating mutations of the NRAS or BRAF oncogenes. We report that metabolic stressors promote the dimerization of KSR proteins with CRAF in NRAS-mutant cells, and with oncogenic BRAF in BRAFV600E-mutant cells, thereby enhancing ERK pathway activation. Despite this similarity, the two genomic subtypes react differently when a higher level of metabolic stress is induced. In NRAS-mutant cells, the ERK pathway is even more stimulated, while it is strongly downregulated in BRAFV600E-mutant cells. We demonstrate that this is caused by the dissociation of mutant BRAF from KSR and is mediated by activated AMPK. Both types of ERK regulation nevertheless lead to cell cycle arrest. Besides studying the effects of the metabolic stressors on ERK pathway activity, we also present data suggesting that for efficient therapies of both genomic melanoma subtypes, specific metabolic targeting is necessary.
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Affiliation(s)
- Amandine Verlande
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Michaela Krafčíková
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - David Potěšil
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Lukáš Trantírek
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Moustafa Elkalaf
- Laboratory for Metabolism and Bioenergetics, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jan Trnka
- Laboratory for Metabolism and Bioenergetics, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Karel Souček
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
- Laboratory of Cytokinetics, Institute of Biophysics, Academy of Sciences, Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Nora Rauch
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
- Conway Institute, University College Dublin, Dublin, Ireland
- School of Medicine, University College Dublin, Dublin, Ireland
| | - Jens Rauch
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
- Conway Institute, University College Dublin, Dublin, Ireland
- School of Medicine, University College Dublin, Dublin, Ireland
| | - Walter Kolch
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
- Conway Institute, University College Dublin, Dublin, Ireland
- School of Medicine, University College Dublin, Dublin, Ireland
| | - Stjepan Uldrijan
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
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Ilgová J, Jedličková L, Dvořáková H, Benovics M, Mikeš L, Janda L, Vorel J, Roudnický P, Potěšil D, Zdráhal Z, Gelnar M, Kašný M. A novel type I cystatin of parasite origin with atypical legumain-binding domain. Sci Rep 2017; 7:17526. [PMID: 29235483 PMCID: PMC5727476 DOI: 10.1038/s41598-017-17598-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [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: 06/15/2017] [Accepted: 11/28/2017] [Indexed: 12/26/2022] Open
Abstract
Parasite inhibitors of cysteine peptidases are known to influence a vast range of processes linked to a degradation of either the parasites' own proteins or proteins native to their hosts. We characterise a novel type I cystatin (stefin) found in a sanguinivorous fish parasite Eudiplozoon nipponicum (Platyhelminthes: Monogenea). We have identified a transcript of its coding gene in the transcriptome of adult worms. Its amino acid sequence is similar to other stefins except for containing a legumain-binding domain, which is in this type of cystatins rather unusual. As expected, the recombinant form of E. nipponicum stefin (rEnStef) produced in Escherichia coli inhibits clan CA peptidases - cathepsins L and B of the worm - via the standard papain-binding domain. It also blocks haemoglobinolysis by cysteine peptidases in the worm's excretory-secretory products and soluble extracts. Furthermore, we had confirmed its ability to inhibit clan CD asparaginyl endopeptidase (legumain). The presence of a native EnStef in the excretory-secretory products of adult worms, detected by mass spectrometry, suggests that this protein has an important biological function at the host-parasite interface. We discuss the inhibitor's possible role in the regulation of blood digestion, modulation of antigen presentation, and in the regeneration of host tissues.
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Affiliation(s)
- Jana Ilgová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, 611 37, Czech Republic.
| | - Lucie Jedličková
- Department of Parasitology, Faculty of Science, Charles University, Prague, 128 44, Czech Republic
| | - Hana Dvořáková
- Department of Parasitology, Faculty of Science, Charles University, Prague, 128 44, Czech Republic
| | - Michal Benovics
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, 611 37, Czech Republic
| | - Libor Mikeš
- Department of Parasitology, Faculty of Science, Charles University, Prague, 128 44, Czech Republic
| | - Lubomír Janda
- Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic
| | - Jiří Vorel
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, 611 37, Czech Republic
| | - Pavel Roudnický
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, 611 37, Czech Republic
| | - David Potěšil
- Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic
| | - Milan Gelnar
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, 611 37, Czech Republic
| | - Martin Kašný
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, 611 37, Czech Republic.,Department of Parasitology, Faculty of Science, Charles University, Prague, 128 44, Czech Republic
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Garlíková Z, Silva AC, Rabata A, Potěšil D, Ihnatová I, Dumková J, Koledová Z, Zdráhal Z, Vinarský V, Hampl A, Pinto-do-Ó P, Nascimento DS. Generation of a Close-to-Native In Vitro System to Study Lung Cells-Extracellular Matrix Crosstalk. Tissue Eng Part C Methods 2017; 24:1-13. [PMID: 28895470 DOI: 10.1089/ten.tec.2017.0283] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [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: 01/11/2023] Open
Abstract
Extracellular matrix (ECM) is an essential component of the tissue microenvironment, actively shaping cellular behavior. In vitro culture systems are often poor in ECM constituents, thus not allowing for naturally occurring cell-ECM interactions. This study reports on a straightforward and efficient method for the generation of ECM scaffolds from lung tissue and its subsequent in vitro application using primary lung cells. Mouse lung tissue was subjected to decellularization with 0.2% sodium dodecyl sulfate, hypotonic solutions, and DNase. Resultant ECM scaffolds were devoid of cells and DNA, whereas lung ECM architecture of alveolar region and blood and airway networks were preserved. Scaffolds were predominantly composed of core ECM and ECM-associated proteins such as collagens I-IV, nephronectin, heparan sulfate proteoglycan core protein, and lysyl oxidase homolog 1, among others. When homogenized and applied as coating substrate, ECM supported the attachment of lung fibroblasts (LFs) in a dose-dependent manner. After ECM characterization and biocompatibility tests, a novel in vitro platform for three-dimensional (3D) matrix repopulation that permits live imaging of cell-ECM interactions was established. Using this system, LFs colonized the ECM scaffolds, displaying a close-to-native morphology in intimate interaction with the ECM fibers, and showed nuclear translocation of the mechanosensor yes-associated protein (YAP), when compared with cells cultured in two dimensions. In conclusion, we developed a 3D-like culture system, by combining an efficient decellularization method with a live-imaging culture platform, to replicate in vitro native lung cell-ECM crosstalk. This is a valuable system that can be easily applied to other organs for ECM-related drug screening, disease modeling, and basic mechanistic studies.
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Affiliation(s)
- Zuzana Garlíková
- 1 Department of Histology and Embryology, Faculty of Medicine, Masaryk University , Brno, Czech Republic .,2 FNUSA-ICRC-International Clinical Research Center of St. Anne University Hospital Brno , Brno, Czech Republic
| | - Ana Catarina Silva
- 3 i3S-Instituto de Investigação e Inovação em Saúde , Porto, Portugal .,4 INEB-Instituto Nacional de Engenharia Biomédica , Porto, Portugal .,5 ICBAS-Instituto de Ciências Biomédicas de Abel Salazar , Porto, Portugal .,6 Gladstone Institutes, University of California San Francisco , San Francisco, California
| | - Anas Rabata
- 1 Department of Histology and Embryology, Faculty of Medicine, Masaryk University , Brno, Czech Republic
| | - David Potěšil
- 7 CEITEC-Central European Institute for Technology, Research Group Proteomics, Masaryk University , Brno, Czech Republic
| | - Ivana Ihnatová
- 7 CEITEC-Central European Institute for Technology, Research Group Proteomics, Masaryk University , Brno, Czech Republic
| | - Jana Dumková
- 1 Department of Histology and Embryology, Faculty of Medicine, Masaryk University , Brno, Czech Republic
| | - Zuzana Koledová
- 1 Department of Histology and Embryology, Faculty of Medicine, Masaryk University , Brno, Czech Republic
| | - Zbyněk Zdráhal
- 7 CEITEC-Central European Institute for Technology, Research Group Proteomics, Masaryk University , Brno, Czech Republic
| | - Vladimír Vinarský
- 2 FNUSA-ICRC-International Clinical Research Center of St. Anne University Hospital Brno , Brno, Czech Republic
| | - Aleš Hampl
- 1 Department of Histology and Embryology, Faculty of Medicine, Masaryk University , Brno, Czech Republic .,2 FNUSA-ICRC-International Clinical Research Center of St. Anne University Hospital Brno , Brno, Czech Republic
| | - Perpétua Pinto-do-Ó
- 3 i3S-Instituto de Investigação e Inovação em Saúde , Porto, Portugal .,4 INEB-Instituto Nacional de Engenharia Biomédica , Porto, Portugal .,5 ICBAS-Instituto de Ciências Biomédicas de Abel Salazar , Porto, Portugal
| | - Diana Santos Nascimento
- 3 i3S-Instituto de Investigação e Inovação em Saúde , Porto, Portugal .,4 INEB-Instituto Nacional de Engenharia Biomédica , Porto, Portugal
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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]
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Brabencová S, Ihnatová I, Potěšil D, Fojtová M, Fajkus J, Zdráhal Z, Lochmanová G. Variations of Histone Modification Patterns: Contributions of Inter-plant Variability and Technical Factors. Front Plant Sci 2017; 8:2084. [PMID: 29270186 PMCID: PMC5725443 DOI: 10.3389/fpls.2017.02084] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 11/22/2017] [Indexed: 05/07/2023]
Abstract
Inter-individual variability of conspecific plants is governed by differences in their genetically determined growth and development traits, environmental conditions, and adaptive responses under epigenetic control involving histone post-translational modifications. The apparent variability in histone modifications among plants might be increased by technical variation introduced in sample processing during epigenetic analyses. Thus, to detect true variations in epigenetic histone patterns associated with given factors, the basal variability among samples that is not associated with them must be estimated. To improve knowledge of relative contribution of biological and technical variation, mass spectrometry was used to examine histone modification patterns (acetylation and methylation) among Arabidopsis thaliana plants of ecotypes Columbia 0 (Col-0) and Wassilewskija (Ws) homogenized by two techniques (grinding in a cryomill or with a mortar and pestle). We found little difference in histone modification profiles between the ecotypes. However, in comparison of the biological and technical components of variability, we found consistently higher inter-individual variability in histone mark levels among Ws plants than among Col-0 plants (grown from seeds collected either from single plants or sets of plants). Thus, more replicates of Ws would be needed for rigorous analysis of epigenetic marks. Regarding technical variability, the cryomill introduced detectably more heterogeneity in the data than the mortar and pestle treatment, but mass spectrometric analyses had minor apparent effects. Our study shows that it is essential to consider inter-sample variance and estimate suitable numbers of biological replicates for statistical analysis for each studied organism when investigating changes in epigenetic histone profiles.
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Affiliation(s)
- Sylva Brabencová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Ivana Ihnatová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - David Potěšil
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Zbyněk Zdráhal
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Gabriela Lochmanová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
- *Correspondence: Gabriela Lochmanová,
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Hafidh S, Potěšil D, Fíla J, Čapková V, Zdráhal Z, Honys D. Quantitative proteomics of the tobacco pollen tube secretome identifies novel pollen tube guidance proteins important for fertilization. Genome Biol 2016; 17:81. [PMID: 27139692 PMCID: PMC4853860 DOI: 10.1186/s13059-016-0928-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 03/24/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND As in animals, cell-cell communication plays a pivotal role in male-female recognition during plant sexual reproduction. Prelaid peptides secreted from the female reproductive tissues guide pollen tubes towards ovules for fertilization. However, the elaborate mechanisms for this dialogue have remained elusive, particularly from the male perspective. RESULTS We performed genome-wide quantitative liquid chromatography-tandem mass spectrometry analysis of a pistil-stimulated pollen tube secretome and identified 801 pollen tube-secreted proteins. Interestingly, in silico analysis reveals that the pollen tube secretome is dominated by proteins that are secreted unconventionally, representing 57 % of the total secretome. In support, we show that an unconventionally secreted protein, translationally controlled tumor protein, is secreted to the apoplast. Remarkably, we discovered that this protein could be secreted by infiltrating through the initial phases of the conventional secretory pathway and could reach the apoplast via exosomes, as demonstrated by co-localization with Oleisin1 exosome marker. We demonstrate that translationally controlled tumor protein-knockdown Arabidopsis thaliana plants produce pollen tubes that navigate poorly to the target ovule and that the mutant allele is poorly transmitted through the male. Further, we show that regulators of the endoplasmic reticulum-trans-Golgi network protein secretory pathway control secretion of Nicotiana tabacum Pollen tube-secreted cysteine-rich protein 2 and Lorelei-like GPI-anchor protein 3 and that a regulator of endoplasmic reticulum-trans-Golgi protein translocation is essential for pollen tube growth, pollen tube guidance and ovule-targeting competence. CONCLUSIONS This work, the first study on the pollen tube secretome, identifies novel genome-wide pollen tube-secreted proteins with potential functions in pollen tube guidance towards ovules for sexual reproduction. Functional analysis highlights a potential mechanism for unconventional secretion of pollen tube proteins and reveals likely regulators of conventional pollen tube protein secretion. The association of pollen tube-secreted proteins with marker proteins shown to be secreted via exosomes in other species suggests exosome secretion is a possible mechanism for cell-cell communication between the pollen tube and female reproductive cells.
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Affiliation(s)
- Said Hafidh
- Laboratory of Pollen Biology, Institute of Experimental Botany ASCR, Rozvojová 263, 165 02, Prague 6, Czech Republic.
| | - David Potěšil
- Research group Proteomics, CEITEC-MU, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Jan Fíla
- Laboratory of Pollen Biology, Institute of Experimental Botany ASCR, Rozvojová 263, 165 02, Prague 6, Czech Republic
| | - Věra Čapková
- Laboratory of Pollen Biology, Institute of Experimental Botany ASCR, Rozvojová 263, 165 02, Prague 6, Czech Republic
| | - Zbyněk Zdráhal
- Research group Proteomics, CEITEC-MU, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - David Honys
- Laboratory of Pollen Biology, Institute of Experimental Botany ASCR, Rozvojová 263, 165 02, Prague 6, Czech Republic.
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Pernikářová V, Sedláček V, Potěšil D, Procházková I, Zdráhal Z, Bouchal P, Kučera I. Proteome-wide dataset generated by iTRAQ-3DLCMS/MS technique for studying the role of FerB protein in oxidative stress in Paracoccus denitrificans. Data Brief 2015; 4:390-4. [PMID: 26306309 PMCID: PMC4534580 DOI: 10.1016/j.dib.2015.06.015] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 06/22/2015] [Indexed: 11/17/2022] Open
Abstract
3DLC protein- and peptide-fractionation technique combined with iTRAQ-peptide labeling and Orbitrap mass spectrometry was employed to quantitate Paracoccus dentirificans total proteome with maximal coverage. This resulted in identification of 24,948 peptides representing 2627 proteins (FDR<0.01) in P. dentirificans wild type and ferB mutant strains grown in the presence or absence of methyl viologen as an oxidative stressor. The data were generated for assessment of FerB protein role in oxidative stress as published by Pernikářová et al.; proteomic responses to a methyl viologen-induced oxidative stress in the wild type and FerB mutant strains of P. denitrificans, J. Proteomics 2015;125:68–75. Dataset is supplied in the article.
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Affiliation(s)
- Vendula Pernikářová
- Department of Biochemistry, Faculty of Science, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic
| | - Vojtěch Sedláček
- Department of Biochemistry, Faculty of Science, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic
| | - David Potěšil
- Central European Institute for Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Iva Procházková
- Department of Biochemistry, Faculty of Science, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Žlutý kopec 7, 65653 Brno, Czech Republic
| | - Zbyněk Zdráhal
- Central European Institute for Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Pavel Bouchal
- Department of Biochemistry, Faculty of Science, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Žlutý kopec 7, 65653 Brno, Czech Republic
- Corresponding authors.
| | - Igor Kučera
- Department of Biochemistry, Faculty of Science, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic
- Corresponding authors.
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Lattová E, Brabcová A, Bartová V, Potěšil D, Bárta J, Zdráhal Z. Correction to N-glycome profiling of patatins from different potato species of solanum genus. J Agric Food Chem 2015; 63:4262. [PMID: 25885359 DOI: 10.1021/acs.jafc.5b01760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
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Lattová E, Brabcová A, Bartová V, Potěšil D, Bárta J, Zdráhal Z. N-glycome profiling of patatins from different potato species of Solanum genus. J Agric Food Chem 2015; 63:3243-3250. [PMID: 25763881 DOI: 10.1021/acs.jafc.5b00426] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
It is hypothesized that oligosaccharides are another potential source of immunological cross-reaction between different plant allergens. Patatin is the most abundant glycoprotein in potato and has been described to have an oligosaccharide of composition Man3(Xyl)GlcNAc2(Fuc). In this work, N-glycosylation profiles of patatin proteins isolated from tubers of different potato species were investigated and compared. Oligosaccharides were released by enzymatic digestion with PNAGase A and analyzed primarily by matrix-assisted laser desorption ionization mass spectrometry. For glycan labeling, a modified version of on-target derivatization with phenylhydrazine was applied. This study found the presence of glycan structures not described previously in patatins of potato tubers, and their glycan profiles significantly differed. This knowledge about the glycosylation of potato patatins may be helpful for correct choice of potato species to decrease the presence of specific glycan epitopes causing food allergy as well as for utilization of potatoes for the manufacture of therapeutic proteins.
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Affiliation(s)
| | - Adéla Brabcová
- ‡Department of Plant Production and Agroecology, Faculty of Agriculture, University of South Bohemia in Ceske Budejovice, Studentska 13, 370 05 Ceske Budejovice, Czech Republic
| | - Veronika Bartová
- ‡Department of Plant Production and Agroecology, Faculty of Agriculture, University of South Bohemia in Ceske Budejovice, Studentska 13, 370 05 Ceske Budejovice, Czech Republic
| | | | - Jan Bárta
- ‡Department of Plant Production and Agroecology, Faculty of Agriculture, University of South Bohemia in Ceske Budejovice, Studentska 13, 370 05 Ceske Budejovice, Czech Republic
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Lacina K, Konhefr M, Novotný J, Potěšil D, Zdráhal Z, Skládal P. Combining ferrocene, thiophene and a boronic acid: a hybrid ligand for reagentless electrochemical sensing of cis-diols. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.04.036] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Potěšil D, Stejskal S, Borský M, Šimara P, Havelková M, Rázga F, Koutná I, Dvořáková D, Mayer J, Ráčil Z, Zdráhal Z. Determination of Imatinib in the Blood Cells of Chronic Myelogenous Leukemia Patients by Ion-Trap Mass Spectrometry. ANAL LETT 2014. [DOI: 10.1080/00032719.2013.860538] [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: 10/25/2022]
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Lochmanová G, Jedličková L, Potěšil D, Tomancová A, Verner J, Pospíšilová S, Doubek M, Mayer J, Zdráhal Z. Potential biomarkers for early detection of acute graft-versus-host disease. Proteomics Clin Appl 2013; 6:351-63. [PMID: 22927351 DOI: 10.1002/prca.201100104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Acute graft-versus-host disease (aGVHD) is the main complication of allogeneic hematopoietic stem cell transplantation (HCT), resulting in considerable morbidity and mortality. Currently, the diagnosis of aGVHD is largely made based on clinical parameters and invasive biopsies. For the past 20 years, researchers have been trying to find reliable biomarkers to enable early and accurate diagnosis of aGVHD. Although a number of potential aGVHD biomarkers have been published, as yet, no validated diagnostic test is available. Proteomics encompasses a broad range of rapidly developing technologies, which have shown tremendous promise for early detection of aGVHD. In this article, we review the current state of aGVHD biomarker discovery, provide a summary of the key proteins of interest and the most common analytical procedures for the clinic, as well as outlining the significant challenges faced in their use.
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Affiliation(s)
- Gabriela Lochmanová
- Core Facility-Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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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
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Žd'árská M, Zatloukalová P, Benítez M, Šedo O, Potěšil D, Novák O, Svačinová J, Pešek B, Malbeck J, Vašíčková J, Zdráhal Z, Hejátko J. Proteome analysis in Arabidopsis reveals shoot- and root-specific targets of cytokinin action and differential regulation of hormonal homeostasis. Plant Physiol 2013; 161:918-30. [PMID: 23209126 PMCID: PMC3561029 DOI: 10.1104/pp.112.202853] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The plant hormones cytokinins (CKs) regulate multiple developmental and physiological processes in Arabidopsis (Arabidopsis thaliana). Responses to CKs vary in different organs and tissues (e.g. the response to CKs has been shown to be opposite in shoot and root samples). However, the tissue-specific targets of CKs and the mechanisms underlying such specificity remain largely unclear. Here, we show that the Arabidopsis proteome responds with strong tissue and time specificity to the aromatic CK 6-benzylaminopurine (BAP) and that fast posttranscriptional and/or posttranslational regulation of protein abundance is involved in the contrasting shoot and root proteome responses to BAP. We demonstrate that BAP predominantly regulates proteins involved in carbohydrate and energy metabolism in the shoot as well as protein synthesis and destination in the root. Furthermore, we found that BAP treatment affects endogenous hormonal homeostasis, again with strong tissue specificity. In the shoot, BAP up-regulates the abundance of proteins involved in abscisic acid (ABA) biosynthesis and the ABA response, whereas in the root, BAP rapidly and strongly up-regulates the majority of proteins in the ethylene biosynthetic pathway. This was further corroborated by direct measurements of hormone metabolites, showing that BAP increases ABA levels in the shoot and 1-aminocyclopropane-1-carboxylic acid, the rate-limiting precursor of ethylene biosynthesis, in the root. In support of the physiological importance of these findings, we identified the role of proteins mediating BAP-induced ethylene production, METHIONINE SYNTHASE1 and ACC OXIDASE2, in the early root growth response to BAP.
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Konečná H, Müller L, Dosoudilová H, Potěšil D, Buršíková J, Sedo O, Márová I, Zdráhal Z. Exploration of beer proteome using OFFGEL prefractionation in combination with two-dimensional gel electrophoresis with narrow pH range gradients. J Agric Food Chem 2012; 60:2418-2426. [PMID: 22353030 DOI: 10.1021/jf204475e] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [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
Two-dimensional gel electrophoresis in combination with mass spectrometry has already been applied successfully to study beer proteome. Due to the abundance of protein Z in beer samples, prefractionation techniques might help to improve beer proteome coverage. Proteins from four lager beers of different origins were separated by two-dimensional electrophoresis (2-DE) followed by tandem mass spectrometric analysis. Initially 52 proteins mostly from Hordeum vulgare (22 proteins) and Saccharomyces species (25 proteins) were identified. Preparative isoelectric focusing by OFFGEL Fractionator was applied prior to 2-DE to improve its resolution power. As a result of this combined approach, a total of 70 beer proteins from Hordeum vulgare (30 proteins), from Saccharomyces species (31 proteins), and from other sources (9 proteins) were identified. Of these, 37 proteins have not been previously reported in beer samples.
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Affiliation(s)
- Hana Konečná
- Core Facility-Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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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).
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Affiliation(s)
- J Cumová
- Babákova myelomová skupina, Ústav patologické fyziologie, LF MU Brno
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Petrlová J, Blaštík O, Průša R, Kukačka J, Potěšil D, Mikelová R, Adam V, Zehnálek J, Kizek R. USING OF ELECTROCHEMICAL METHODS FOR STUDYING OF METALLOTHIONEIN CONTENT IN THE HUMAN BLOOD SERUM OF A PATIENT POISONED BY LEAD AND TREATED BY PLATINUM. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2005. [DOI: 10.5507/bp.2005.086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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