1
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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] [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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2
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Weigert Muñoz A, Zhao W, Sieber SA. Monitoring host-pathogen interactions using chemical proteomics. RSC Chem Biol 2024; 5:73-89. [PMID: 38333198 PMCID: PMC10849124 DOI: 10.1039/d3cb00135k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/09/2023] [Indexed: 02/10/2024] Open
Abstract
With the rapid emergence and the dissemination of microbial resistance to conventional chemotherapy, the shortage of novel antimicrobial drugs has raised a global health threat. As molecular interactions between microbial pathogens and their mammalian hosts are crucial to establish virulence, pathogenicity, and infectivity, a detailed understanding of these interactions has the potential to reveal novel therapeutic targets and treatment strategies. Bidirectional molecular communication between microbes and eukaryotes is essential for both pathogenic and commensal organisms to colonise their host. In particular, several devastating pathogens exploit host signalling to adjust the expression of energetically costly virulent behaviours. Chemical proteomics has emerged as a powerful tool to interrogate the protein interaction partners of small molecules and has been successfully applied to advance host-pathogen communication studies. Here, we present recent significant progress made by this approach and provide a perspective for future studies.
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Affiliation(s)
- Angela Weigert Muñoz
- Center for Functional Protein Assemblies, Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich Ernst-Otto-Fischer-Straße 8 D-85748 Garching Germany
| | - Weining Zhao
- College of Pharmacy, Shenzhen Technology University Shenzhen 518118 China
| | - Stephan A Sieber
- Center for Functional Protein Assemblies, Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich Ernst-Otto-Fischer-Straße 8 D-85748 Garching Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Germany
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3
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Gulen B, Kinch LN, Servage KA, Blevins A, Stewart NM, Gray HF, Casey AK, Orth K. FicD Sensitizes Cellular Response to Glucose Fluctuations in Mouse Embryonic Fibroblasts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.576705. [PMID: 38328056 PMCID: PMC10849547 DOI: 10.1101/2024.01.22.576705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
During homeostasis, the endoplasmic reticulum (ER) maintains productive transmembrane and secretory protein folding that is vital for proper cellular function. The ER-resident HSP70 chaperone, BiP, plays a pivotal role in sensing ER stress to activate the unfolded protein response (UPR). BiP function is regulated by the bifunctional enzyme FicD that mediates AMPylation and deAMPylation of BiP in response to changes in ER stress. AMPylated BiP acts as a molecular rheostat to regulate UPR signaling, yet little is known about the molecular consequences of FicD loss. In this study, we investigate the role of FicD in mouse embryonic fibroblast (MEF) response to pharmacologically and metabolically induced ER stress. We find differential BiP AMPylation signatures when comparing robust chemical ER stress inducers to physiological glucose starvation stress and recovery. Wildtype MEFs respond to pharmacological ER stress by downregulating BiP AMPylation. Conversely, BiP AMPylation in wildtype MEFs increases upon metabolic stress induced by glucose starvation. Deletion of FicD results in widespread gene expression changes under baseline growth conditions. In addition, FicD null MEFs exhibit dampened UPR signaling, altered cell stress recovery response, and unconstrained protein secretion. Taken together, our findings indicate that FicD is important for tampering UPR signaling, stress recovery, and the maintenance of secretory protein homeostasis. Significance Statement The chaperone BiP plays a key quality control role in the endoplasmic reticulum, the cellular location for the production, folding, and transport of secreted proteins. The enzyme FicD regulates BiP's activity through AMPylation and deAMPylation. Our study unveils the importance of FicD in regulating BiP and the unfolded protein response (UPR) during stress. We identify distinct BiP AMPylation signatures for different stressors, highlighting FicD's nuanced control. Deletion of FicD causes widespread gene expression changes, disrupts UPR signaling, alters stress recovery, and perturbs protein secretion in cells. These observations underscore the pivotal contribution of FicD for preserving secretory protein homeostasis. Our findings deepen the understanding of FicD's role in maintaining cellular resilience and open avenues for therapeutic strategies targeting UPR-associated diseases.
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4
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Gulen B, Casey A, Orth K. AMPylation of small GTPases by Fic enzymes. FEBS Lett 2023; 597:883-891. [PMID: 36239538 PMCID: PMC10050140 DOI: 10.1002/1873-3468.14516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/17/2022] [Accepted: 10/06/2022] [Indexed: 12/14/2022]
Abstract
Small GTPases orchestrate numerous cellular pathways, acting as molecular switches and regulatory hubs to transmit molecular signals and because of this, they are often the target of pathogens. During infection, pathogens manipulate host cellular networks using post-translational modifications (PTMs). AMPylation, the modification of proteins with AMP, has been identified as a common PTM utilized by pathogens to hijack GTPase signalling during infection. AMPylation is primarily carried out by enzymes with a filamentation induced by cyclic-AMP (Fic) domain. Modification of small GTPases by AMP renders GTPases impervious to upstream regulatory inputs, resulting in unregulated downstream effector outputs for host cellular processes. Here, we overview Fic-mediated AMPylation of small GTPases by pathogens and other related PTMs catalysed by Fic enzymes on GTPases.
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Affiliation(s)
- Burak Gulen
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Amanda Casey
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kim Orth
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX and Howard Hughes Medical Institute, Dallas, TX, USA
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5
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Ramanathan R, Hatzios SK. Activity-based Tools for Interrogating Host Biology During Infection. Isr J Chem 2023; 63:e202200095. [PMID: 37744997 PMCID: PMC10512441 DOI: 10.1002/ijch.202200095] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Indexed: 02/18/2023]
Abstract
Host cells sense and respond to pathogens by dynamically regulating cell signaling. The rapid modulation of signaling pathways is achieved by post-translational modifications (PTMs) that can alter protein structure, function, and/or binding interactions. By using chemical probes to broadly profile changes in enzyme function or side-chain reactivity, activity-based protein profiling (ABPP) can reveal PTMs that regulate host-microbe interactions. While ABPP has been widely utilized to uncover microbial mechanisms of pathogenesis, in this review, we focus on more recent applications of this technique to the discovery of host PTMs and enzymes that modulate signaling within infected cells. Collectively, these advances underscore the importance of ABPP as a tool for interrogating the host response to infection and identifying potential targets for host-directed therapies.
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Affiliation(s)
- Renuka Ramanathan
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520 USA
- Microbial Sciences Institute, Yale University, West Haven, CT 06516 USA
| | - Stavroula K. Hatzios
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520 USA
- Microbial Sciences Institute, Yale University, West Haven, CT 06516 USA
- Department of Chemistry, Yale University, New Haven, CT 06520 USA
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6
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Frese M, Saumer P, Yuan Y, Herzog D, Höpfner D, Itzen A, Marx A. The Alarmone Diadenosine Tetraphosphate as a Cosubstrate for Protein AMPylation. Angew Chem Int Ed Engl 2023; 62:e202213279. [PMID: 36524454 PMCID: PMC10107192 DOI: 10.1002/anie.202213279] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/18/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022]
Abstract
Diadenosine polyphosphates (Apn As) are non-canonical nucleotides whose cellular concentrations increase during stress and are therefore termed alarmones, signaling homeostatic imbalance. Their cellular role is poorly understood. In this work, we assessed Apn As for their usage as cosubstrates for protein AMPylation, a post-translational modification in which adenosine monophosphate (AMP) is transferred to proteins. In humans, AMPylation mediated by the AMPylator FICD with ATP as a cosubstrate is a response to ER stress. Herein, we demonstrate that Ap4 A is proficiently consumed for AMPylation by FICD. By chemical proteomics using a new chemical probe, we identified new potential AMPylation targets. Interestingly, we found that AMPylation targets of FICD may differ depending on the nucleotide cosubstrate. These results may suggest that signaling at elevated Ap4 A levels during cellular stress differs from when Ap4 A is present at low concentrations, allowing response to extracellular cues.
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Affiliation(s)
- Matthias Frese
- Department of Chemistry, Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Philip Saumer
- Department of Chemistry, Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Yizhi Yuan
- Department of Chemistry, Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Doreen Herzog
- Department of Chemistry, Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Dorothea Höpfner
- Institute of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246, Hamburg, Germany.,Center for Structural Systems Biology (CSSB), University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Aymelt Itzen
- Institute of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246, Hamburg, Germany.,Center for Structural Systems Biology (CSSB), University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Andreas Marx
- Department of Chemistry, Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
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7
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Hernandez-Lima MA, Champion M, Mattiola Z, Truttmann MC. The AMPylase FIC-1 modulates TGF-β signaling in Caenorhabditis elegans. Front Mol Neurosci 2022; 15:912734. [PMID: 36504677 PMCID: PMC9730714 DOI: 10.3389/fnmol.2022.912734] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 11/03/2022] [Indexed: 11/25/2022] Open
Abstract
Post-translational protein modifications are essential for the spatio-temporal regulation of protein function. In this study, we examine how the activity of the Caenorhabditis elegans AMPylase FIC-1 modulates physiological processes in vivo. We find that over-expression (OE) of the constitutive AMPylase FIC-1(E274G) impairs C. elegans development, fertility, and stress resilience. We also show that FIC-1(E274G) OE inhibits pathogen avoidance behavior by selectively suppressing production of the Transforming Growth Factor-β (TGF-β) ligands DAF-7 and DBL-1 in ASI sensory neurons. Finally, we demonstrate that FIC-1 contributes to the regulation of adult body growth, cholinergic neuron function, and larval entry into dauer stage; all processes controlled by TGF-β signaling. Together, our results suggest a role for FIC-1 in regulating TGF-β signaling in C. elegans.
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Affiliation(s)
- Mirella A. Hernandez-Lima
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, United States,Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, United States
| | - Margaret Champion
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, United States
| | - Zachary Mattiola
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, United States
| | - Matthias C. Truttmann
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, United States,Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, United States,Geriatrics Center, University of Michigan, Ann Arbor, MI, United States,*Correspondence: Matthias C. Truttmann,
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8
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Ji Y, Sun L, Chen Y, Qin H, Xuan W. Sirtuin‐Derived Covalent Binder for the Selective Recognition of Protein Crotonylation. Angew Chem Int Ed Engl 2022; 61:e202205522. [DOI: 10.1002/anie.202205522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Yanli Ji
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Lin Sun
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Yao Chen
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences (CAS) Dalian 116023 China
| | - Hongqiang Qin
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences (CAS) Dalian 116023 China
| | - Weimin Xuan
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
- School of Life Sciences Tianjin University Tianjin 300072 China
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9
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Sirtuin‐Derived Covalent Binder for the Selective Recognition of Protein Crotonylation. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202205522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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10
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Fromm K, Dehio C. The Impact of Bartonella VirB/VirD4 Type IV Secretion System Effectors on Eukaryotic Host Cells. Front Microbiol 2022; 12:762582. [PMID: 34975788 PMCID: PMC8714903 DOI: 10.3389/fmicb.2021.762582] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 10/29/2021] [Indexed: 12/14/2022] Open
Abstract
Bartonella spp. are facultative intracellular pathogens that infect a wide range of mammalian hosts including humans. The VirB/VirD4 type IV secretion system (T4SS) is a key virulence factor utilized to translocate Bartonella effector proteins (Beps) into host cells in order to subvert their functions. Crucial for effector translocation is the C-terminal Bep intracellular delivery (BID) domain that together with a positively charged tail sequence forms a bipartite translocation signal. Multiple BID domains also evolved secondary effector functions within host cells. The majority of Beps possess an N-terminal filamentation induced by cAMP (FIC) domain and a central connecting oligonucleotide binding (OB) fold. FIC domains typically mediate AMPylation or related post-translational modifications of target proteins. Some Beps harbor other functional modules, such as tandem-repeated tyrosine-phosphorylation (EPIYA-related) motifs. Within host cells the EPIYA-related motifs are phosphorylated, which facilitates the interaction with host signaling proteins. In this review, we will summarize our current knowledge on the molecular functions of the different domains present in Beps and highlight examples of Bep-dependent host cell modulation.
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Affiliation(s)
- Katja Fromm
- Biozentrum, University of Basel, Basel, Switzerland
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11
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Xin X, Zhang Y, Gaetani M, Lundström SL, Zubarev RA, Zhou Y, Corkery DP, Wu YW. Ultrafast and Selective Labeling of Endogenous Proteins Using Affinity-based Benzotriazole Chemistry. Chem Sci 2022; 13:7240-7246. [PMID: 35799822 PMCID: PMC9214888 DOI: 10.1039/d1sc05974b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 05/27/2022] [Indexed: 11/21/2022] Open
Abstract
Chemical modification of proteins is enormously useful for characterizing protein function in complex biological systems and for drug development. Selective labeling of native or endogenous proteins is challenging owing to the existence of distinct functional groups in proteins and in living systems. Chemistry for rapid and selective labeling of proteins remains in high demand. Here we have developed novel affinity labeling probes using benzotriazole (BTA) chemistry. We showed that affinity-based BTA probes selectively and covalently label a lysine residue in the vicinity of the ligand binding site of a target protein with a reaction half-time of 28 s. The reaction rate constant is comparable to the fastest biorthogonal chemistry. This approach was used to selectively label different cytosolic and membrane proteins in vitro and in live cells. BTA chemistry could be widely useful for labeling of native/endogenous proteins, target identification and development of covalent inhibitors. Affinity-based benzotriazole (BTA) probes selectively and covalently label native proteins or endogenous proteins in cells with a fast reaction rate. It is enormously useful for characterizing protein function in biological systems and for drug development.![]()
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Affiliation(s)
- Xiaoyi Xin
- Department of Chemistry, Umeå Centre for Microbial Research (UCMR), Umeå University Umeå 90187 Sweden
| | - Yu Zhang
- Department of Chemistry, Umeå Centre for Microbial Research (UCMR), Umeå University Umeå 90187 Sweden
| | - Massimiliano Gaetani
- Division of Physiological Chemistry I, Chemical Proteomics Core Facility, Department of Medical Biochemistry and Biophysics, Karolinska Institute Stockholm 17177 Sweden
- Chemical Proteomics, Science for Life Laboratory (SciLifeLab) Stockholm 17177 Sweden
| | - Susanna L Lundström
- Division of Physiological Chemistry I, Chemical Proteomics Core Facility, Department of Medical Biochemistry and Biophysics, Karolinska Institute Stockholm 17177 Sweden
- Chemical Proteomics, Science for Life Laboratory (SciLifeLab) Stockholm 17177 Sweden
| | - Roman A Zubarev
- Division of Physiological Chemistry I, Chemical Proteomics Core Facility, Department of Medical Biochemistry and Biophysics, Karolinska Institute Stockholm 17177 Sweden
- Chemical Proteomics, Science for Life Laboratory (SciLifeLab) Stockholm 17177 Sweden
| | - Yuan Zhou
- School of Medical Technology, Xuzhou Medical University Xuzhou 221004 China
| | - Dale P Corkery
- Department of Chemistry, Umeå Centre for Microbial Research (UCMR), Umeå University Umeå 90187 Sweden
| | - Yao-Wen Wu
- Department of Chemistry, Umeå Centre for Microbial Research (UCMR), Umeå University Umeå 90187 Sweden
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12
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Gulen B, Itzen A. Revisiting AMPylation through the lens of Fic enzymes. Trends Microbiol 2021; 30:350-363. [PMID: 34531089 DOI: 10.1016/j.tim.2021.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 08/04/2021] [Accepted: 08/09/2021] [Indexed: 11/30/2022]
Abstract
AMPylation, a post-translational modification (PTM) first discovered in the late 1960s, is catalyzed by adenosine monophosphate (AMP)-transferring enzymes. The observation that filamentation-induced-by-cyclic-AMP (fic) enzymes are associated with this unique PTM revealed that AMPylation plays a major role in hijacking of host signaling by pathogenic bacteria during infection. Studies over the past decade showed that AMPylation is conserved across all kingdoms of life and, outside their role in infection, also modulates cellular functions. Many aspects of AMPylation are yet to be uncovered. In this review we present the advancement in research on AMPylation and Fic enzymes as well as other distinct classes of enzymes that catalyze AMPylation.
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Affiliation(s)
- Burak Gulen
- Department of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), Martinistr. 52, 20246, Hamburg, Germany; Present address: Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Aymelt Itzen
- Department of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), Martinistr. 52, 20246, Hamburg, Germany.
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13
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Deletion of mFICD AMPylase alters cytokine secretion and affects visual short-term learning in vivo. J Biol Chem 2021; 297:100991. [PMID: 34419450 PMCID: PMC8441161 DOI: 10.1016/j.jbc.2021.100991] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/07/2021] [Accepted: 07/19/2021] [Indexed: 11/21/2022] Open
Abstract
Fic domain-containing AMP transferases (fic AMPylases) are conserved enzymes that catalyze the covalent transfer of AMP to proteins. This posttranslational modification regulates the function of several proteins, including the ER-resident chaperone Grp78/BiP. Here we introduce a mouse FICD (mFICD) AMPylase knockout mouse model to study fic AMPylase function in vertebrates. We find that mFICD deficiency is well tolerated in unstressed mice. We also show that mFICD-deficient mouse embryonic fibroblasts are depleted of AMPylated proteins. mFICD deletion alters protein synthesis and secretion in splenocytes, including that of IgM, an antibody secreted early during infections, and the proinflammatory cytokine IL-1β, without affecting the unfolded protein response. Finally, we demonstrate that visual nonspatial short-term learning is stronger in old mFICD−/− mice than in wild-type controls while other measures of cognition, memory, and learning are unaffected. Together, our results suggest a role for mFICD in adaptive immunity and neuronal plasticity in vivo.
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14
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Fauser J, Itzen A, Gulen B. Current Advances in Covalent Stabilization of Macromolecular Complexes for Structural Biology. Bioconjug Chem 2021; 32:879-890. [PMID: 33861574 DOI: 10.1021/acs.bioconjchem.1c00118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Structural characterization of macromolecular assemblies is often limited by the transient nature of the interactions. The development of specific chemical tools to covalently tether interacting proteins to each other has played a major role in various fundamental discoveries in recent years. To this end, protein engineering techniques such as mutagenesis, incorporation of unnatural amino acids, and methods using synthetic substrate/cosubstrate derivatives were employed. In this review, we give an overview of both commonly used and recently developed biochemical methodologies for covalent stabilization of macromolecular complexes enabling structural investigation via crystallography, nuclear magnetic resonance, and cryo-electron microscopy. We divided the strategies into nonenzymatic- and enzymatic-driven cross-linking and further categorized them in either naturally occurring or engineered covalent linkage. This review offers a compilation of recent advances in diverse scientific fields where the structural characterization of macromolecular complexes was achieved by the aid of intermolecular covalent linkage.
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Affiliation(s)
- Joel Fauser
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, 85747 Garching, Germany
- Department of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany
| | - Aymelt Itzen
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, 85747 Garching, Germany
- Department of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany
| | - Burak Gulen
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, 85747 Garching, Germany
- Department of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany
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15
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Chatterjee BK, Truttmann MC. Fic and non-Fic AMPylases: protein AMPylation in metazoans. Open Biol 2021; 11:210009. [PMID: 33947243 PMCID: PMC8097203 DOI: 10.1098/rsob.210009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Protein AMPylation refers to the covalent attachment of an AMP moiety to the amino acid side chains of target proteins using ATP as nucleotide donor. This process is catalysed by dedicated AMP transferases, called AMPylases. Since this initial discovery, several research groups have identified AMPylation as a critical post-translational modification relevant to normal and pathological cell signalling in both bacteria and metazoans. Bacterial AMPylases are abundant enzymes that either regulate the function of endogenous bacterial proteins or are translocated into host cells to hijack host cell signalling processes. By contrast, only two classes of metazoan AMPylases have been identified so far: enzymes containing a conserved filamentation induced by cAMP (Fic) domain (Fic AMPylases), which primarily modify the ER-resident chaperone BiP, and SelO, a mitochondrial AMPylase involved in redox signalling. In this review, we compare and contrast bacterial and metazoan Fic and non-Fic AMPylases, and summarize recent technological and conceptual developments in the emerging field of AMPylation.
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Affiliation(s)
- Bhaskar K Chatterjee
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Matthias C Truttmann
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA.,Geriatrics Center, University of Michigan, Ann Arbor, MI 48109, USA
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16
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Specificity of AMPylation of the human chaperone BiP is mediated by TPR motifs of FICD. Nat Commun 2021; 12:2426. [PMID: 33893288 PMCID: PMC8065156 DOI: 10.1038/s41467-021-22596-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 03/18/2021] [Indexed: 02/02/2023] Open
Abstract
To adapt to fluctuating protein folding loads in the endoplasmic reticulum (ER), the Hsp70 chaperone BiP is reversibly modified with adenosine monophosphate (AMP) by the ER-resident Fic-enzyme FICD/HYPE. The structural basis for BiP binding and AMPylation by FICD has remained elusive due to the transient nature of the enzyme-substrate-complex. Here, we use thiol-reactive derivatives of the cosubstrate adenosine triphosphate (ATP) to covalently stabilize the transient FICD:BiP complex and determine its crystal structure. The complex reveals that the TPR-motifs of FICD bind specifically to the conserved hydrophobic linker of BiP and thus mediate specificity for the domain-docked conformation of BiP. Furthermore, we show that both AMPylation and deAMPylation of BiP are not directly regulated by the presence of unfolded proteins. Together, combining chemical biology, crystallography and biochemistry, our study provides structural insights into a key regulatory mechanism that safeguards ER homeostasis.
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17
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Savitskiy S, Itzen A. SopD from Salmonella specifically inactivates Rab8. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140661. [PMID: 33872771 DOI: 10.1016/j.bbapap.2021.140661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 04/09/2021] [Accepted: 04/12/2021] [Indexed: 10/21/2022]
Abstract
Salmonella outer protein D (SopD) is secreted into a host during the first stages of the Salmonella infection and contributes to the systemic virulence of the bacterium. SopD2 is a SopD homolog and possesses GTPase activating protein (GAP) activity towards Rab32. Here, we identified Rab-proteins as putative SopD-targets using a yeast two-hybrid approach. In vitro investigations subsequently revealed Rab8a as an exclusive SopD substrate in contrast to SopD2, which has a broader specificity targeting Rab29, Rab32 and Rab38 in vitro. Additionally, we determined the catalytic efficiencies of SopD and SopD2 towards their physiologically relevant substrates. Moreover, mutagenesis studies provided insights into possible key residues of the Rab-protein and the GAP involved in the conversion of active to inactive GTPase. In conclusion, we demonstrate that Salmonella SopD and SopD2 act as RabGAPs and can inactivate Rab signaling.
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Affiliation(s)
- Sergey Savitskiy
- Institute of Biochemistry and Signal Transduction, University Medical Centre Hamburg-Eppendorf (UKE), Martinistrasse 52, 20246 Hamburg, Germany; Center for Integrated Protein Science Munich (CIPSM), Department Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Aymelt Itzen
- Institute of Biochemistry and Signal Transduction, University Medical Centre Hamburg-Eppendorf (UKE), Martinistrasse 52, 20246 Hamburg, Germany; Center for Integrated Protein Science Munich (CIPSM), Department Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany; Centre for Structural Systems Biology (CSSB), University Medical Centre Hamburg-Eppendorf (UKE), Hamburg, Germany.
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18
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Du J, Wrisberg MKV, Gulen B, Stahl M, Pett C, Hedberg C, Lang K, Schneider S, Itzen A. Rab1-AMPylation by Legionella DrrA is allosterically activated by Rab1. Nat Commun 2021; 12:460. [PMID: 33469029 PMCID: PMC7815794 DOI: 10.1038/s41467-020-20702-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 12/16/2020] [Indexed: 01/29/2023] Open
Abstract
Legionella pneumophila infects eukaryotic cells by forming a replicative organelle - the Legionella containing vacuole. During this process, the bacterial protein DrrA/SidM is secreted and manipulates the activity and post-translational modification (PTM) states of the vesicular trafficking regulator Rab1. As a result, Rab1 is modified with an adenosine monophosphate (AMP), and this process is referred to as AMPylation. Here, we use a chemical approach to stabilise low-affinity Rab:DrrA complexes in a site-specific manner to gain insight into the molecular basis of the interaction between the Rab protein and the AMPylation domain of DrrA. The crystal structure of the Rab:DrrA complex reveals a previously unknown non-conventional Rab-binding site (NC-RBS). Biochemical characterisation demonstrates allosteric stimulation of the AMPylation activity of DrrA via Rab binding to the NC-RBS. We speculate that allosteric control of DrrA could in principle prevent random and potentially cytotoxic AMPylation in the host, thereby perhaps ensuring efficient infection by Legionella.
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Affiliation(s)
- Jiqing Du
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, Garching, 85748, Germany.,Center for Experimental Medicine, Institute of Biochemistry and Signal Transduction, Universitätsklinikum Hamburg-Eppendorf (UKE), Hamburg, 20246, Germany
| | - Marie-Kristin von Wrisberg
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, Institute for Advanced Study, Garching, 85748, Germany
| | - Burak Gulen
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, Garching, 85748, Germany.,Center for Experimental Medicine, Institute of Biochemistry and Signal Transduction, Universitätsklinikum Hamburg-Eppendorf (UKE), Hamburg, 20246, Germany
| | - Matthias Stahl
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, Garching, 85748, Germany.,Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Box 1031, 171 21 Solna, Stockholm, Sweden
| | - Christian Pett
- Chemical Biology Center (KBC), Department of Chemistry, Umeå University, Linnaeus väg 10, 90187, Umeå, Sweden
| | - Christian Hedberg
- Chemical Biology Center (KBC), Department of Chemistry, Umeå University, Linnaeus väg 10, 90187, Umeå, Sweden
| | - Kathrin Lang
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, Institute for Advanced Study, Garching, 85748, Germany.
| | - Sabine Schneider
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Ludwig-Maximilians-University Munich, München, 81377, Germany.
| | - Aymelt Itzen
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, Garching, 85748, Germany. .,Center for Experimental Medicine, Institute of Biochemistry and Signal Transduction, Universitätsklinikum Hamburg-Eppendorf (UKE), Hamburg, 20246, Germany. .,Center for Structural Systems Biology (CSSB), University Medical Centre Hamburg-Eppendorf (UKE), Hamburg, Germany.
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19
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Rauh T, Brameyer S, Kielkowski P, Jung K, Sieber SA. MS-Based in Situ Proteomics Reveals AMPylation of Host Proteins during Bacterial Infection. ACS Infect Dis 2020; 6:3277-3289. [PMID: 33259205 PMCID: PMC9558369 DOI: 10.1021/acsinfecdis.0c00740] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
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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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