1
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Tomasiunaite U, Kielkowski P, Krafczyk R, Forné I, Imhof A, Jung K. Decrypting the functional design of unmodified translation elongation factor P. Cell Rep 2024; 43:114063. [PMID: 38635400 DOI: 10.1016/j.celrep.2024.114063] [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] [Received: 09/20/2023] [Revised: 01/17/2024] [Accepted: 03/21/2024] [Indexed: 04/20/2024] Open
Abstract
Bacteria overcome ribosome stalling by employing translation elongation factor P (EF-P), which requires post-translational modification (PTM) for its full activity. However, EF-Ps of the PGKGP subfamily are unmodified. The mechanism behind the ability to avoid PTM while retaining active EF-P requires further examination. Here, we investigate the design principles governing the functionality of unmodified EF-Ps in Escherichia coli. We screen for naturally unmodified EF-Ps with activity in E. coli and discover that the EF-P from Rhodomicrobium vannielii rescues growth defects of a mutant lacking the modification enzyme EF-P-(R)-β-lysine ligase. We identify amino acids in unmodified EF-P that modulate its activity. Ultimately, we find that substitution of these amino acids in other marginally active EF-Ps of the PGKGP subfamily leads to fully functional variants in E. coli. These results provide strategies to improve heterologous expression of proteins with polyproline motifs in E. coli and give insights into cellular adaptations to optimize protein synthesis.
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Affiliation(s)
- Urte Tomasiunaite
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Pavel Kielkowski
- Department of Chemistry, Institut für Chemische Epigenetik (ICEM), Ludwig-Maximilians-Universität München, 81375 Munich, Germany
| | - Ralph Krafczyk
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Ignasi Forné
- Zentrallabor für Proteinanalytik, Biomedical Center Munich, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Axel Imhof
- Zentrallabor für Proteinanalytik, Biomedical Center Munich, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Kirsten Jung
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany.
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2
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Mostert D, Bubeneck WA, Rauh T, Kielkowski P, Itzen A, Jung K, Sieber SA. Pronucleotide Probes Reveal a Diverging Specificity for AMPylation vs UMPylation of Human and Bacterial Nucleotide Transferases. Biochemistry 2024; 63:651-659. [PMID: 38388156 PMCID: PMC10918828 DOI: 10.1021/acs.biochem.3c00568] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/23/2024] [Accepted: 02/07/2024] [Indexed: 02/24/2024]
Abstract
AMPylation is a post-translational modification utilized by human and bacterial cells to modulate the activity and function of specific proteins. Major AMPylators such as human FICD and bacterial VopS have been studied extensively for their substrate and target scope in vitro. Recently, an AMP pronucleotide probe also facilitated the in situ analysis of AMPylation in living cells. Based on this technology, we here introduce a novel UMP pronucleotide probe and utilize it to profile uninfected and Vibrio parahaemolyticus infected human cells. Mass spectrometric analysis of labeled protein targets reveals an unexpected promiscuity of human nucleotide transferases with an almost identical target set of AMP- and UMPylated proteins. Vice versa, studies in cells infected by V. parahaemolyticus and its effector VopS revealed solely AMPylation of host enzymes, highlighting a so far unknown specificity of this transferase for ATP. Taken together, pronucleotide probes provide an unprecedented insight into the in situ activity profile of crucial nucleotide transferases, which can largely differ from their in vitro activity.
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Affiliation(s)
- Dietrich Mostert
- Center
for Functional Protein Assemblies (CPA), Department of Chemistry,
Chair of Organic Chemistry II, Technical
University of Munich, 85748 Garching, Germany
| | - Wilhelm Andrei Bubeneck
- Center
for Functional Protein Assemblies (CPA), Department of Chemistry,
Chair of Organic Chemistry II, Technical
University of Munich, 85748 Garching, Germany
| | - Theresa Rauh
- Center
for Functional Protein Assemblies (CPA), Department of Chemistry,
Chair of Organic Chemistry II, Technical
University of Munich, 85748 Garching, Germany
| | - Pavel Kielkowski
- Department
of Chemistry, Ludwig-Maximilians-Universität
München, 81377 München, Germany
| | - Aymelt Itzen
- Department
of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany
| | - Kirsten Jung
- Department
of Biology I, Microbiology, Ludwig-Maximilians-Universität
München, 82152 Martinsried, Germany
| | - Stephan A. Sieber
- Center
for Functional Protein Assemblies (CPA), Department of Chemistry,
Chair of Organic Chemistry II, Technical
University of Munich, 85748 Garching, Germany
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3
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Wiest A, Kielkowski P. Cu-Catalyzed Azide-Alkyne-Thiol Reaction Forms Ubiquitous Background in Chemical Proteomic Studies. J Am Chem Soc 2024; 146:2151-2159. [PMID: 38214237 PMCID: PMC10811670 DOI: 10.1021/jacs.3c11780] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/13/2024]
Abstract
We report here a Cu-catalyzed azide-alkyne-thiol reaction forming thiotriazoles as the major byproduct under widely used bio-orthogonal protein labeling "click" conditions. The development of Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) had a tremendous impact on many biological discoveries. However, the considered chemoselectivity of CuAAC is hampered by the high reactivity of cysteine free thiols, yielding thiotriazole protein conjugates. The reaction byproducts generate false-positive protein hits in functional proteomic studies. The reported detail investigation of conjugates between chemical probes containing terminal alkynes, azide tags, and cell lysates reveals the formation of thiotriazoles, which can be readily detected by in-gel fluorescence scanning or after peptide and protein enrichment by mass spectrometry-based proteomics. In protein level identification and quantification experiments, the produced fluorescent bands or enriched proteins may not result from the important enzymatically driven reaction and can be falsely assigned as hits. This study provides a complete list of the most common background proteins. The knowledge of this previously overlooked reactivity now leads to the introduction of modified CuAAC conditions, which avoids the undesired product formation, diminishes the background, and hence improves the signal-to-noise ratio.
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Affiliation(s)
- Andreas Wiest
- Department of Chemistry, LMU Munich, Würmtalstr. 201, 81375 Munich, Germany
| | - Pavel Kielkowski
- Department of Chemistry, LMU Munich, Würmtalstr. 201, 81375 Munich, Germany
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4
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Makarov D, Kielkowski P. Chemical Proteomics Reveals Protein Tyrosination Extends Beyond the Alpha-Tubulins in Human Cells. Chembiochem 2022; 23:e202200414. [PMID: 36218090 PMCID: PMC10099736 DOI: 10.1002/cbic.202200414] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 10/10/2022] [Indexed: 01/25/2023]
Abstract
Tubulin detyrosination-tyrosination cycle regulates the stability of microtubules. With respect to α-tubulins, the tyrosination level is maintained by a single tubulin-tyrosine ligase (TTL). However, the precise dynamics and tubulin isoforms which undergo (de)tyrosination in neurons are unknown. Here, we exploit the substrate promiscuity of the TTL to introduce an O-propargyl-l-tyrosine to neuroblastoma cells and neurons. Mass spectrometry-based chemical proteomics in neuroblastoma cells using the O-propargyl-l-tyrosine probe revealed previously discussed tyrosination of TUBA4A, MAPRE1, and other non-tubulin proteins. This finding was further corroborated in differentiating neurons. Together we present the method for tubulin tyrosination profiling in living cells. Our results show that detyrosination-tyrosination is not restricted to α-tubulins with coded C-terminal tyrosine and is thus involved in fine-tuning of the tubulin and non-tubulin proteins during neuronal differentiation.
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Affiliation(s)
- Dmytro Makarov
- LMU München, Department of Chemistry, Institute for Chemical Epigenetics - Munich (ICEM), Würmtalstrasse 201, 81375, Munich, Germany
| | - Pavel Kielkowski
- LMU München, Department of Chemistry, Institute for Chemical Epigenetics - Munich (ICEM), Würmtalstrasse 201, 81375, Munich, Germany
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5
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Makarov D, Kielkowski P. Chemical Proteomics Reveals Protein Tyrosination Extends Beyond the Alpha‐Tubulins in Human Cells**. Chembiochem 2022. [DOI: 10.1002/cbic.202200648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Dmytro Makarov
- LMU München Department of Chemistry Institute for Chemical Epigenetics – Munich (ICEM) Würmtalstrasse 201 81375 Munich Germany
| | - Pavel Kielkowski
- LMU München Department of Chemistry Institute for Chemical Epigenetics – Munich (ICEM) Würmtalstrasse 201 81375 Munich Germany
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6
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Becker T, Wiest A, Telek A, Bejko D, Hoffmann-Röder A, Kielkowski P. Transforming Chemical Proteomics Enrichment into a High-Throughput Method Using an SP2E Workflow. JACS Au 2022; 2:1712-1723. [PMID: 35911458 PMCID: PMC9326820 DOI: 10.1021/jacsau.2c00284] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Protein post-translational modifications (PTMs) play a critical role in the regulation of protein catalytic activity, localization, and protein-protein interactions. Attachment of PTMs onto proteins significantly diversifies their structure and function, resulting in proteoforms. However, the sole identification of post-translationally modified proteins, which are often cell type and disease-specific, is still a highly challenging task. Substoichiometric amounts and modifications of low abundant proteins necessitate the purification or enrichment of the modified proteins. Although the introduction of mass spectrometry-based chemical proteomic strategies has enabled the screening of protein PTMs with increased throughput, sample preparation remains highly time-consuming and tedious. Here, we report an optimized workflow for the enrichment of PTM proteins in a 96-well plate format, which could be extended to robotic automation. This platform allows us to significantly lower the input of total protein, which opens up the opportunity to screen specialized and difficult-to-culture cell lines in a high-throughput manner. The presented SP2E protocol is robust and time- and cost-effective, as well as suitable for large-scale screening of proteoforms. The application of the SP2E protocol will thus enable the characterization of proteoforms in various processes such as neurodevelopment, neurodegeneration, and cancer. This may contribute to an overall acceleration of the recently launched Human Proteoform Project.
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Affiliation(s)
- Tobias Becker
- Institute
for Chemical Epigenetics Munich, LMU Munich, 81375 Munich, Germany
| | - Andreas Wiest
- Institute
for Chemical Epigenetics Munich, LMU Munich, 81375 Munich, Germany
| | - András Telek
- Institute
for Chemical Epigenetics Munich, LMU Munich, 81375 Munich, Germany
| | - Daniel Bejko
- Institute
for Chemical Epigenetics Munich, LMU Munich, 81375 Munich, Germany
| | | | - Pavel Kielkowski
- Institute
for Chemical Epigenetics Munich, LMU Munich, 81375 Munich, Germany
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7
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Makarov D, Telek A, Becker T, von Wrisberg MK, Schneider S, Kielkowski P. Clickable report tags for identification of modified peptides by mass spectrometry. J Mass Spectrom 2022; 57:e4812. [PMID: 35156258 DOI: 10.1002/jms.4812] [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: 11/08/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 06/14/2023]
Abstract
The identification and quantification of modified peptides are critical for the functional characterization of post-translational protein modifications (PTMs) to elucidate their biological function. Nowadays, quantitative mass spectrometry coupled with various bioinformatic pipelines has been successfully used for the determination of a wide range of PTMs. However, direct characterization of low abundant protein PTMs in bottom-up proteomic workflow remains challenging. Here, we present the synthesis and evaluation of tandem mass spectrometry tags (TMT) which are introduced via click-chemistry into peptides bearing alkyne handles. The fragmentation properties of the two mass tags were validated and used for screening in a model system and analysis of AMPylated proteins. The presented tags provide a valuable tool for diagnostic peak generation to increase confidence in the identification of modified peptides and potentially for direct peptide-PTM quantification from various experimental conditions.
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Affiliation(s)
| | - András Telek
- Department of Chemistry, LMU Munich, Munich, Germany
- Department of Applied Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary
| | - Tobias Becker
- Department of Chemistry, LMU Munich, Munich, Germany
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8
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Becker T, Cappel C, Di Matteo F, Sonsalla G, Kaminska E, Spada F, Cappello S, Damme M, Kielkowski P. AMPylation profiling during neuronal differentiation reveals extensive variation on lysosomal proteins. iScience 2021; 24:103521. [PMID: 34917898 PMCID: PMC8668991 DOI: 10.1016/j.isci.2021.103521] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 07/20/2021] [Accepted: 11/23/2021] [Indexed: 12/02/2022] Open
Abstract
Protein AMPylation is a posttranslational modification with an emerging role in neurodevelopment. In metazoans two highly conserved protein AMP-transferases together with a diverse group of AMPylated proteins have been identified using chemical proteomics and biochemical techniques. However, the function of AMPylation remains largely unknown. Particularly problematic is the localization of thus far identified AMPylated proteins and putative AMP-transferases. We show that protein AMPylation is likely a posttranslational modification of luminal lysosomal proteins characteristic in differentiating neurons. Through a combination of chemical proteomics, gel-based separation of modified and unmodified proteins, and an activity assay, we determine that the modified, lysosomal soluble form of exonuclease PLD3 increases dramatically during neuronal maturation and that AMPylation correlates with its catalytic activity. Together, our findings indicate that AMPylation is a so far unknown lysosomal posttranslational modification connected to neuronal differentiation and it may provide a molecular rationale behind lysosomal storage diseases and neurodegeneration. Profiling of AMPylation during neuronal differentiation AMPylation is a potential PTM of luminal lysosomal proteins Phos-tag gel enables the separation of non-AMPylated and AMPylated proteins The modified lysosomal soluble form of PLD3 increases during neuronal maturation
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Affiliation(s)
- Tobias Becker
- LMU Munich, Department of Chemistry, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Cedric Cappel
- University of Kiel, Institute of Biochemistry, Olshausenstr. 40, 24098 Kiel, Germany
| | - Francesco Di Matteo
- Max Planck Institute of Psychiatry, Kraepelinstraße 2, 80804 Munich, Germany.,International Max Planck Research School for Translational Psychiatry (IMPRS-TP), Kraepelinstraße 2-10, 80804 Munich, Germany
| | - Giovanna Sonsalla
- LMU Munich, Department of Physiological Genomics, Biomedical Center (BMC), Großhadernerstr. 9, 82152 Planegg, Germany.,Helmholtz Zentrum München, Institute for Stem Cell Research, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany.,Graduate School of Systemic Neurosciences (GSN), Großhadernerstr. 2, 82152 Planegg, Germany
| | - Ewelina Kaminska
- LMU Munich, Department of Chemistry, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Fabio Spada
- LMU Munich, Department of Chemistry, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Silvia Cappello
- Max Planck Institute of Psychiatry, Kraepelinstraße 2, 80804 Munich, Germany
| | - Markus Damme
- University of Kiel, Institute of Biochemistry, Olshausenstr. 40, 24098 Kiel, Germany
| | - Pavel Kielkowski
- LMU Munich, Department of Chemistry, Butenandtstr. 5-13, 81377 Munich, Germany
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9
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Kyrousi C, O’Neill AC, Brazovskaja A, He Z, Kielkowski P, Coquand L, Di Giaimo R, D’ Andrea P, Belka A, Forero Echeverry A, Mei D, Lenge M, Cruceanu C, Buchsbaum IY, Khattak S, Fabien G, Binder E, Elmslie F, Guerrini R, Baffet AD, Sieber SA, Treutlein B, Robertson SP, Cappello S. Extracellular LGALS3BP regulates neural progenitor position and relates to human cortical complexity. Nat Commun 2021; 12:6298. [PMID: 34728600 PMCID: PMC8564519 DOI: 10.1038/s41467-021-26447-w] [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: 10/28/2020] [Accepted: 09/26/2021] [Indexed: 12/15/2022] Open
Abstract
Basal progenitors (BPs), including intermediate progenitors and basal radial glia, are generated from apical radial glia and are enriched in gyrencephalic species like humans, contributing to neuronal expansion. Shortly after generation, BPs delaminate towards the subventricular zone, where they further proliferate before differentiation. Gene expression alterations involved in BP delamination and function in humans are poorly understood. Here, we study the role of LGALS3BP, so far known as a cancer biomarker, which is a secreted protein enriched in human neural progenitors (NPCs). We show that individuals with LGALS3BP de novo variants exhibit altered local gyrification, sulcal depth, surface area and thickness in their cortex. Additionally, using cerebral organoids, human fetal tissues and mice, we show that LGALS3BP regulates the position of NPCs. Single-cell RNA-sequencing and proteomics reveal that LGALS3BP-mediated mechanisms involve the extracellular matrix in NPCs' anchoring and migration within the human brain. We propose that its temporal expression influences NPCs' delamination, corticogenesis and gyrification extrinsically.
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Affiliation(s)
- Christina Kyrousi
- grid.419548.50000 0000 9497 5095Max Planck Institute of Psychiatry, 80804 Munich, Germany ,grid.5216.00000 0001 2155 0800Present Address: First Department of Psychiatry, Medical School, National and Kapodistrian University of Athens, Greece and University Mental Health, Neurosciences and Precision Medicine Research Institute “Costas Stefanis”, Athens, Greece
| | - Adam C. O’Neill
- grid.29980.3a0000 0004 1936 7830Department of Women’s and Children’s Health, University of Otago, 9054 Dunedin, New Zealand
| | - Agnieska Brazovskaja
- grid.419518.00000 0001 2159 1813Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Zhisong He
- grid.419518.00000 0001 2159 1813Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany ,grid.5801.c0000 0001 2156 2780ETH Zurich, Department of Biosystems Science and Engineering, 4058 Basel, Switzerland
| | - Pavel Kielkowski
- grid.6936.a0000000123222966Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Garching, Germany ,grid.5252.00000 0004 1936 973XPresent Address: Department Chemie Ludwig-Maximilians-Universität München Butenandtstr. 5-13, 81377 München, Germany
| | - Laure Coquand
- grid.4444.00000 0001 2112 9282Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d’Ulm, F-75005 Paris, France
| | - Rossella Di Giaimo
- grid.419548.50000 0000 9497 5095Max Planck Institute of Psychiatry, 80804 Munich, Germany ,grid.4691.a0000 0001 0790 385XDepartment of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Pierpaolo D’ Andrea
- grid.419548.50000 0000 9497 5095Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Alexander Belka
- grid.419548.50000 0000 9497 5095Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | | | - Davide Mei
- grid.413181.e0000 0004 1757 8562Neuroscience Department, Children’s Hospital A. Meyer-University of Florence, 50139 Florence, Italy
| | - Matteo Lenge
- grid.413181.e0000 0004 1757 8562Neuroscience Department, Children’s Hospital A. Meyer-University of Florence, 50139 Florence, Italy
| | - Cristiana Cruceanu
- grid.419548.50000 0000 9497 5095Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Isabel Y. Buchsbaum
- grid.419548.50000 0000 9497 5095Max Planck Institute of Psychiatry, 80804 Munich, Germany ,grid.5252.00000 0004 1936 973XGraduate School of Systemic Neurosciences, Ludwig-Maximilians-University, 82152 Munich Planegg, Germany
| | - Shahryar Khattak
- grid.4488.00000 0001 2111 7257DFG-Research Center and Cluster of Excellence for Regenerative Therapies (CRTD), School of Medicine, Technical University Dresden, 01307 Dresden, Germany ,grid.4912.e0000 0004 0488 7120Present Address: Royal College of Surgeons Ireland (RCSI) in Bahrain, Adliya, Kingdom of Bahrain
| | - Guimiot Fabien
- grid.50550.350000 0001 2175 4109Unité de Foetopathologie, Assistance Publique-Hôpitaux de Paris, CHU Robert Debré, F-75019 Paris, France
| | - Elisabeth Binder
- grid.419548.50000 0000 9497 5095Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Frances Elmslie
- grid.4464.20000 0001 2161 2573South West Thames Regional Genetics Service, St George’s, University of London, London, SW17 0RE UK
| | - Renzo Guerrini
- grid.413181.e0000 0004 1757 8562Neuroscience Department, Children’s Hospital A. Meyer-University of Florence, 50139 Florence, Italy
| | - Alexandre D. Baffet
- grid.4444.00000 0001 2112 9282Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d’Ulm, F-75005 Paris, France
| | - Stephan A. Sieber
- grid.6936.a0000000123222966Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Garching, Germany
| | - Barbara Treutlein
- grid.419518.00000 0001 2159 1813Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany ,grid.5801.c0000 0001 2156 2780ETH Zurich, Department of Biosystems Science and Engineering, 4058 Basel, Switzerland
| | - Stephen P. Robertson
- grid.29980.3a0000 0004 1936 7830Department of Women’s and Children’s Health, University of Otago, 9054 Dunedin, New Zealand
| | - Silvia Cappello
- grid.419548.50000 0000 9497 5095Max Planck Institute of Psychiatry, 80804 Munich, Germany
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10
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Pinheiro B, Scheidler CM, Kielkowski P, Schmid M, Forné I, Ye S, Reiling N, Takano E, Imhof A, Sieber SA, Schneider S, Jung K. Structure and Function of an Elongation Factor P Subfamily in Actinobacteria. Cell Rep 2021; 30:4332-4342.e5. [PMID: 32234471 DOI: 10.1016/j.celrep.2020.03.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 08/20/2019] [Revised: 02/06/2020] [Accepted: 03/02/2020] [Indexed: 12/28/2022] Open
Abstract
Translation of consecutive proline motifs causes ribosome stalling and requires rescue via the action of a specific translation elongation factor, EF-P in bacteria and archaeal/eukaryotic a/eIF5A. In Eukarya, Archaea, and all bacteria investigated so far, the functionality of this translation elongation factor depends on specific and rather unusual post-translational modifications. The phylum Actinobacteria, which includes the genera Corynebacterium, Mycobacterium, and Streptomyces, is of both medical and economic significance. Here, we report that EF-P is required in these bacteria in particular for the translation of proteins involved in amino acid and secondary metabolite production. Notably, EF-P of Actinobacteria species does not need any post-translational modification for activation. While the function and overall 3D structure of this EF-P type is conserved, the loop containing the conserved lysine is flanked by two essential prolines that rigidify it. Actinobacteria's EF-P represents a unique subfamily that works without any modification.
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Affiliation(s)
- Bruno Pinheiro
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | | | - Pavel Kielkowski
- Department of Chemistry, Technische Universität München, Garching, Germany
| | - Marina Schmid
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Ignasi Forné
- Biomedical Center Munich, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Suhui Ye
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, University of Manchester, Manchester, UK
| | - Norbert Reiling
- RG Microbial Interface Biology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Eriko Takano
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, University of Manchester, Manchester, UK
| | - Axel Imhof
- Biomedical Center Munich, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Stephan A Sieber
- Department of Chemistry, Technische Universität München, Garching, Germany
| | - Sabine Schneider
- Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany.
| | - Kirsten Jung
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany.
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11
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Abstract
![]()
Bacteria utilize versatile strategies
to propagate infections within
human cells, e.g., by the injection of effector proteins,
which alter crucial signaling pathways. One class of such virulence-associated
proteins is involved in the AMPylation of eukaryotic Rho GTPases with
devastating effects on viability. In order to get an inventory of
AMPylated proteins, several technologies have been developed. However,
as they were designed for the analysis of cell lysates, knowledge
about AMPylation targets in living cells is largely lacking. Here,
we implement a chemical-proteomic method for deciphering AMPylated
host proteins in situ during bacterial infection.
HeLa cells treated with a previously established cell permeable pronucleotide
probe (pro-N6pA) were infected with Vibrio parahaemolyticus, and modified host proteins were identified upon probe enrichment
and LC-MS/MS analysis. Three already known targets of the AMPylator
VopS—Rac1, RhoA, and Cdc42—could be confirmed, and several
other Rho GTPases were additionally identified. These hits were validated
in comparative studies with V. parahaemolyticus wild type and a mutant producing an inactive VopS (H348A). The method
further allowed to decipher the sites of modification and facilitated
a time-dependent analysis of AMPylation during infection. Overall,
the methodology provides a reliable detection of host AMPylation in situ and thus a versatile tool in monitoring infection
processes.
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Affiliation(s)
- Theresa Rauh
- Department of Chemistry, Chair of Organic Chemistry II, Center for Functional Protein Assemblies (CPA), Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Sophie Brameyer
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Pavel Kielkowski
- Department of Chemistry, Ludwig-Maximilians-Universität München, 81377 München, Germany
| | - Kirsten Jung
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Stephan A. Sieber
- Department of Chemistry, Chair of Organic Chemistry II, Center for Functional Protein Assemblies (CPA), Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
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12
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Becker T, Kielkowski P. Protein-AMPylierungs-Identifikation in lebenden Zellen. ACTA ACUST UNITED AC 2020; 26:743-746. [PMID: 33250577 PMCID: PMC7686442 DOI: 10.1007/s12268-020-1491-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Protein AMPylation is a prevalent protein post-translational modification in human cells involved in endoplasmic reticulum stress regulation and neural development. In this article we describe the design, synthesis and application of a pronucleotide probe suitable for in situ fluorescence imaging and chemical protemics profiling of AMPylated proteins. Our probe utilizes straightforward strain-promoted azidealkyne click reaction for fluorescence labeling in living cells.
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Affiliation(s)
- Tobias Becker
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, D-81377 München, Deutschland
| | - Pavel Kielkowski
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, D-81377 München, Deutschland
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13
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Sieber SA, Cappello S, Kielkowski P. From Young to Old: AMPylation Hits the Brain. Cell Chem Biol 2020; 27:773-779. [PMID: 32521229 DOI: 10.1016/j.chembiol.2020.05.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 02/19/2020] [Revised: 04/19/2020] [Accepted: 05/20/2020] [Indexed: 01/08/2023]
Abstract
Protein post-translational modifications (PTMs) are implicated in numerous physiological processes and significantly contribute to complex regulatory networks of protein functions. Recently, a protein PTM called AMPylation was found to play a role in modulation of neurodevelopment and neurodegeneration. Combination of biochemical and chemical proteomic studies has uncovered the prevalence of this PTM in regulation of diverse metabolic pathways. In metazoans, thus far two protein AMP transferases have been identified to introduce AMPylation: FICD and SELO. These two proteins were found to be involved in unfolded protein response and redox homeostasis on the cellular level and in the case of FICD to adjust the development of glial cells and neurons in Drosophila and cerebral organoids, respectively. Together with findings on AMPylation and its association with toxic protein aggregation, we summarize in this Perspective the knowledge and putative future directions of protein AMPylation research.
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Affiliation(s)
- Stephan A Sieber
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Silvia Cappello
- Max Planck Institute of Psychiatry, Kraepelinstraße 2, 80804 München, Germany
| | - Pavel Kielkowski
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377 München, Germany.
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14
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Pfab M, Kielkowski P, Krafczyk R, Volkwein W, Sieber SA, Lassak J, Jung K. Synthetic post-translational modifications of elongation factor P using the ligase EpmA. FEBS J 2020; 288:663-677. [PMID: 32337775 DOI: 10.1111/febs.15346] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 01/25/2020] [Revised: 03/24/2020] [Accepted: 04/23/2020] [Indexed: 12/20/2022]
Abstract
Canonically, tRNA synthetases charge tRNA. However, the lysyl-tRNA synthetase paralog EpmA catalyzes the attachment of (R)-β-lysine to the ε-amino group of lysine 34 of the translation elongation factor P (EF-P) in Escherichia coli. This modification is essential for EF-P-mediated translational rescue of ribosomes stalled at consecutive prolines. In this study, we determined the kinetics of EpmA and its variant EpmA_A298G to catalyze the post-translational modification of K34 in EF-P with eight noncanonical substrates. In addition, acetylated EF-P was generated using an amber suppression system. The impact of these synthetically modified EF-P variants on in vitro translation of a polyproline-containing NanoLuc luciferase reporter was analyzed. Our results show that natural (R)-β-lysylation was more effective in rescuing stalled ribosomes than any other synthetic modification tested. Thus, our work not only provides new biochemical insights into the function of EF-P, but also opens a new route to post-translationally modify proteins using EpmA.
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Affiliation(s)
- Miriam Pfab
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Germany
| | - Pavel Kielkowski
- Organic Chemistry II, Technical University of Munich, Garching, Germany
| | - Ralph Krafczyk
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Germany
| | - Wolfram Volkwein
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Germany
| | - Stephan A Sieber
- Organic Chemistry II, Technical University of Munich, Garching, Germany
| | - Jürgen Lassak
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Germany
| | - Kirsten Jung
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Germany
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15
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Buchsbaum IY, Kielkowski P, Giorgio G, O'Neill AC, Di Giaimo R, Kyrousi C, Khattak S, Sieber SA, Robertson SP, Cappello S. ECE2 regulates neurogenesis and neuronal migration during human cortical development. EMBO Rep 2020; 21:e48204. [PMID: 32207244 PMCID: PMC7202216 DOI: 10.15252/embr.201948204] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [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: 04/01/2019] [Revised: 02/18/2020] [Accepted: 02/21/2020] [Indexed: 11/24/2022] Open
Abstract
During embryonic development, excitatory projection neurons migrate in the cerebral cortex giving rise to organised layers. Periventricular heterotopia (PH) is a group of aetiologically heterogeneous disorders in which a subpopulation of newborn projection neurons fails to initiate their radial migration to the cortex, ultimately resulting in bands or nodules of grey matter lining the lateral ventricles. Although a number of genes have been implicated in its cause, currently they only satisfactorily explain the pathogenesis of the condition for 50% of patients. Novel gene discovery is complicated by the extreme genetic heterogeneity recently described to underlie its cause. Here, we study the neurodevelopmental role of endothelin‐converting enzyme‐2 (ECE2) for which two biallelic variants have been identified in two separate patients with PH. Our results show that manipulation of ECE2 levels in human cerebral organoids and in the developing mouse cortex leads to ectopic localisation of neural progenitors and neurons. We uncover the role of ECE2 in neurogenesis, and mechanistically, we identify its involvement in the generation and secretion of extracellular matrix proteins in addition to cytoskeleton and adhesion.
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Affiliation(s)
- Isabel Y Buchsbaum
- Max Planck Institute of Psychiatry, Munich, Germany.,Graduate School of Systemic Neurosciences, Ludwig-Maximilians-University Munich, Planegg, Germany
| | - Pavel Kielkowski
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Garching bei München, Germany
| | - Grazia Giorgio
- Max Planck Institute of Psychiatry, Munich, Germany.,Graduate School of Systemic Neurosciences, Ludwig-Maximilians-University Munich, Planegg, Germany
| | - Adam C O'Neill
- Department of Women's and Children's Health, University of Otago, Dunedin, New Zealand
| | - Rossella Di Giaimo
- Max Planck Institute of Psychiatry, Munich, Germany.,Department of Biology, University of Naples Federico II, Naples, Italy
| | | | - Shahryar Khattak
- DFG Center for Regenerative Therapies, Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Stephan A Sieber
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Garching bei München, Germany
| | - Stephen P Robertson
- Department of Women's and Children's Health, University of Otago, Dunedin, New Zealand
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16
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Kielkowski P, Buchsbaum IY, Becker T, Bach K, Cappello S, Sieber SA. A Pronucleotide Probe for Live-Cell Imaging of Protein AMPylation. Chembiochem 2020; 21:1285-1287. [PMID: 32027064 PMCID: PMC7317759 DOI: 10.1002/cbic.201900716] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Indexed: 12/17/2022]
Abstract
Conjugation of proteins to AMP (AMPylation) is a prevalent post‐translational modification (PTM) in human cells, involved in the regulation of unfolded protein response and neural development. Here we present a tailored pronucleotide probe suitable for in situ imaging and chemical proteomics profiling of AMPylated proteins. Using straightforward strain‐promoted azide–alkyne click chemistry, the probe provides stable fluorescence labelling in living cells.
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Affiliation(s)
- Pavel Kielkowski
- Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Isabel Y Buchsbaum
- Max Planck Institute of Psychiatry, Kraepelinstrasse 2, 80804, Munich, Germany.,Graduate School of Systemic Neurosciences, LMU Munich, Grosshaderner Strasse 2, 82152, Munich, Germany
| | - Tobias Becker
- Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Kathrin Bach
- Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Silvia Cappello
- Max Planck Institute of Psychiatry, Kraepelinstrasse 2, 80804, Munich, Germany
| | - Stephan A Sieber
- Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
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17
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Stahl M, Korotkov VS, Balogh D, Kick LM, Gersch M, Pahl A, Kielkowski P, Richter K, Schneider S, Sieber SA. Selektive Aktivierung der humanen caseinolytischen Protease P (ClpP). Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201808189] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Matthias Stahl
- Fakultät für Chemie; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
- Department of Oncology-Pathology; Science for Life Laboratory; Karolinska Institutet; Tomtebodavägen 23A 171 65 Solna Schweden
| | - Vadim S. Korotkov
- Fakultät für Chemie; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Dóra Balogh
- Fakultät für Chemie; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Leonhard M. Kick
- Fakultät für Chemie; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Malte Gersch
- Fakultät für Chemie; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
- Medical Research Council Laboratory of, Molecular Biology; Francis Crick Avenue CB2 0QH Cambridge Großbritannien
| | - Axel Pahl
- Fakultät für Chemie; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
- Max-Planck-Institut für Molekulare Physiologie; Compound Management and Screening Center (COMAS); Otto-Hahn-Straße 11 44227 Dortmund Deutschland
| | - Pavel Kielkowski
- Fakultät für Chemie; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Klaus Richter
- Fakultät für Chemie; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Sabine Schneider
- Fakultät für Chemie; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Stephan A. Sieber
- Fakultät für Chemie; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
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18
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Stahl M, Korotkov VS, Balogh D, Kick LM, Gersch M, Pahl A, Kielkowski P, Richter K, Schneider S, Sieber SA. Selective Activation of Human Caseinolytic Protease P (ClpP). Angew Chem Int Ed Engl 2018; 57:14602-14607. [DOI: 10.1002/anie.201808189] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 08/15/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Matthias Stahl
- Department of Chemistry; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
- Present address: Department of Oncology-Pathology; Science for Life Laboratory; Karolinska Institutet; Tomtebodavägen 23A 171 65 Solna Sweden
| | - Vadim S. Korotkov
- Department of Chemistry; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
| | - Dóra Balogh
- Department of Chemistry; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
| | - Leonhard M. Kick
- Department of Chemistry; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
| | - Malte Gersch
- Department of Chemistry; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
- Present address; Medical Research Council Laboratory of Molecular Biology; Francis Crick Avenue CB2 0QH Cambridge UK
| | - Axel Pahl
- Department of Chemistry; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
- Present address: Max-Planck-Institut für Molekulare Physiologie; Compound Management and Screening Center (COMAS); Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Pavel Kielkowski
- Department of Chemistry; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
| | - Klaus Richter
- Department of Chemistry; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
| | - Sabine Schneider
- Department of Chemistry; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
| | - Stephan A. Sieber
- Department of Chemistry; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
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19
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Cahová H, Panattoni A, Kielkowski P, Fanfrlík J, Hocek M. 5-Substituted Pyrimidine and 7-Substituted 7-Deazapurine dNTPs as Substrates for DNA Polymerases in Competitive Primer Extension in the Presence of Natural dNTPs. ACS Chem Biol 2016; 11:3165-3171. [PMID: 27668519 DOI: 10.1021/acschembio.6b00714] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A complete series of 5-substituted uracil or cytosine, as well as 7-substituted 7-deazaadenine and 7-deazaguanine 2'-deoxyribonucleoside triphosphates (dNTPs) bearing substituents of increasing bulkiness (H, Me, vinyl, ethynyl, and phenyl) were systematically studied in competitive primer extension in the presence of their natural counterparts (nonmodified dNTPs), and their kinetic data were determined. The results show that modified dNTPs bearing π-electron-containing substituents (vinyl, ethynyl, Ph) are typically excellent substrates for DNA polymerases comparable to or better than natural dNTPs. The kinetic studies revealed that these modified dNTPs have higher affinity to the active site of the enzyme-primer-template complex, and the calculations (semiempirical quantum mechanical scoring function) suggest that it is due to the cation-π interaction of the modified dNTP with Arg629 in the active site of Bst DNA polymerase.
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Affiliation(s)
- Hana Cahová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic
| | - Alessandro Panattoni
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic
| | - Pavel Kielkowski
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic
- Department
of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, Prague-2 12843, Czech Republic
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20
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Kielkowski P, Fanfrlík J, Hocek M. 7-Aryl-7-deazaadenine 2′-Deoxyribonucleoside Triphosphates (dNTPs): Better Substrates for DNA Polymerases than dATP in Competitive Incorporations. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201404742] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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21
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Kielkowski P, Fanfrlík J, Hocek M. 7-Aryl-7-deazaadenine 2'-deoxyribonucleoside triphosphates (dNTPs): better substrates for DNA polymerases than dATP in competitive incorporations. Angew Chem Int Ed Engl 2014; 53:7552-5. [PMID: 24890276 DOI: 10.1002/anie.201404742] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Indexed: 01/31/2023]
Abstract
A series of 7-substituted 7-deazaadenine and 5-substituted cytosine 2'-deoxyribonucleoside triphosphates (dNTPs) were tested for their competitive incorporations (in the presence of dATP and dCTP) into DNA by several DNA polymerases by using analysis based on cleavage by restriction endonucleases. 7-Aryl-7-deazaadenine dNTPs were more efficient substrates than dATP because of their higher affinity for the active site of the enzyme, as proved by kinetic measurements and calculations.
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Affiliation(s)
- Pavel Kielkowski
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences & IOCB Research Center, Flemingovo nám. 2, 16610 Prague 6 (Czech Republic) http://www.uochb.cas.cz/hocekgroup
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22
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Abstract
Protecting group chemistry meets molecular biology: Chemically modified dATP carrying a bulky triethylsilylethynyl group was used in a PCR-based synthesis of a gene internally protected against cleavage by restriction endonucleases. The unmodified flanking regions were cleaved for cloning into a plasmid which was replicated by E. coli, and used for protein production.
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Affiliation(s)
- Pavel Kielkowski
- Institute of Organic Chemistry and Biochemistry, Academy of Science of the Czech Republic, Gilead Sciences & IOCB Research Center, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
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23
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Kielkowski P, Macíčková-Cahová H, Pohl R, Hocek M. Transient and Switchable (Triethylsilyl)ethynyl Protection of DNA against Cleavage by Restriction Endonucleases. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201102898] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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24
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Kielkowski P, Macíčková-Cahová H, Pohl R, Hocek M. Transient and Switchable (Triethylsilyl)ethynyl Protection of DNA against Cleavage by Restriction Endonucleases. Angew Chem Int Ed Engl 2011; 50:8727-30. [DOI: 10.1002/anie.201102898] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Revised: 06/30/2011] [Indexed: 12/13/2022]
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25
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Kielkowski P, Pohl R, Hocek M. Synthesis of acetylene linked double-nucleobase nucleos(t)ide building blocks and polymerase construction of DNA containing cytosines in the major groove. J Org Chem 2011; 76:3457-62. [PMID: 21425799 DOI: 10.1021/jo200436j] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
(Cytosin-5-yl)ethynyl derivatives of pyrimidine and 7-deazaadenine 2-deoxyribonucleosides and nucleoside triphosphates (dNTPs) were prepared in one step by the aqueous Sonogashira coupling of unprotected halogenated nucleos(t)ides with 5-ethynylcytosine. The modified dNTPs were good substrates for DNA polymerases suitable for primer extension or PCR construction of DNA bearing acetylene-linked cytosine(s) in the major groove mimicking the flipped-out nucleotide.
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Affiliation(s)
- Pavel Kielkowski
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences & IOCB Research Center, Flemingovo nam.2, CZ-16610 Prague 6, Czech Republic
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