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Chatterjee BK, Alam M, Chakravorty A, Lacy SM, Rech J, Brooks CL, Arvan PD, Truttmann MC. Small molecule FICD inhibitors suppress endogenous and pathologic FICD-mediated protein AMPylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.13.603377. [PMID: 39071275 PMCID: PMC11275912 DOI: 10.1101/2024.07.13.603377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
The AMP transferase, FICD, is an emerging drug target finetuning stress signaling in the endoplasmic reticulum (ER). FICD is a bi-functional enzyme, catalyzing both AMP addition (AMPylation) and removal (deAMPylation) from the ER resident chaperone BiP/GRP78. Despite increasing evidence linking excessive BiP/GRP78 AMPylation to human diseases, small molecules to inhibit pathogenic FICD variants are lacking. Using an in-vitro high-throughput screen, we identify two small-molecule FICD inhibitors, C22 and C73. Both molecules significantly inhibit FICD-mediated BiP/GRP78 AMPylation in intact cells while only weakly inhibiting BiP/GRP78 deAMPylation. C22 and C73 also efficiently inhibit pathogenic FICD variants and improve proinsulin processing in β cells. Our study identifies and validates FICD inhibitors, highlighting a novel therapeutic avenue against pathologic protein AMPylation.
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Lobato AG, Ortiz-Vega N, Canic T, Tao X, Bucan N, Ruan K, Rebelo AP, Schule R, Zuchner S, Syed S, Zhai RG. Loss of Fic causes progressive neurodegeneration in a Drosophila model of hereditary spastic paraplegia. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167348. [PMID: 38986817 DOI: 10.1016/j.bbadis.2024.167348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 07/03/2024] [Accepted: 07/03/2024] [Indexed: 07/12/2024]
Abstract
Hereditary Spastic Paraplegia (HSP) is a group of rare inherited disorders characterized by progressive weakness and spasticity of the legs. Recent newly discovered biallelic variants in the gene FICD were found in patients with a highly similar phenotype to early onset HSP. FICD encodes filamentation induced by cAMP domain protein. FICD is involved in the AMPylation and deAMPylation protein modifications of the endoplasmic reticulum (ER) chaperone BIP, a major constituent of the ER that regulates the unfolded protein response. Although several biochemical properties of FICD have been characterized, the neurological function of FICD and the pathological mechanism underlying HSP are unknown. We established a Drosophila model to gain mechanistic understanding of the function of FICD in HSP pathogenesis, and specifically the role of BIP in neuromuscular physiology. Our studies on Drosophila Fic null mutants uncovered that loss of Fic resulted in locomotor impairment and reduced levels of BIP in the motor neuron circuitry, as well as increased reactive oxygen species (ROS) in the ventral nerve cord of Fic null mutants. Finally, feeding Drosophila Fic null mutants with chemical chaperones PBA or TUDCA, or treatment of patient fibroblasts with PBA, reduced the ROS accumulation. The neuronal phenotypes of Fic null mutants recapitulate several clinical features of HSP patients and further reveal cellular patho-mechanisms. By modeling FICD in Drosophila, we provide potential targets for intervention for HSP, and advance fundamental biology that is important for understanding related rare and common neuromuscular diseases.
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Affiliation(s)
- Amanda G Lobato
- Department of Neurology, University of Chicago, Chicago, IL, USA; Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL, USA; Graduate Program in Human Genetics and Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Natalie Ortiz-Vega
- Department of Neurology, University of Chicago, Chicago, IL, USA; Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL, USA; Graduate Program in Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, FL, USA
| | - Tijana Canic
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL, USA; Graduate Program in Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, FL, USA
| | - Xianzun Tao
- Department of Neurology, University of Chicago, Chicago, IL, USA; Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Nika Bucan
- Undergraduate Program in Neuroscience, University of Miami, Coral Gables, FL, USA
| | - Kai Ruan
- Department of Neurology, University of Chicago, Chicago, IL, USA; Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Adriana P Rebelo
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Rebecca Schule
- Hertie Institute for Clinical Brain Research (HIH), Center of Neurology, University of Tübingen, Tübingen, Germany; German Center for Neurodegenerative Diseases (DZNE), University of Tübingen, Tübingen, Germany
| | - Stephan Zuchner
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sheyum Syed
- Department of Physics, University of Miami, Coral Gables, FL, USA
| | - R Grace Zhai
- Department of Neurology, University of Chicago, Chicago, IL, USA; Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL, USA.
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3
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Casey AK, Stewart NM, Zaidi N, Gray HF, Cox A, Fields HA, Orth K. FicD regulates adaptation to the unfolded protein response in the murine liver. Biochimie 2024; 225:114-124. [PMID: 38740171 DOI: 10.1016/j.biochi.2024.05.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/07/2024] [Accepted: 05/10/2024] [Indexed: 05/16/2024]
Abstract
The unfolded protein response (UPR) is a cellular stress response that is activated when misfolded proteins accumulate in the endoplasmic reticulum (ER). Regulation of the UPR response must be adapted to the needs of the cell as prolonged UPR responses can result in disrupted cellular function and tissue damage. Previously, we discovered that the enzyme FicD (also known as Fic or HYPE) through its AMPylation and deAMPylation activity can modulate the UPR response via post-translational modification of BiP. FicD AMPylates BiP during homeostasis and deAMPylates BiP during stress. We hypothesized that FicD regulation of the UPR will play a role in mitigating the deleterious effects of UPR activation in tissues with frequent physiological stress. Here, we explore the role of FicD in the murine liver. As seen in our pancreatic studies, livers lacking FicD exhibit enhanced UPR signaling in response to short term physiologic fasting and feeding stress. However, in contrast to studies on the pancreas, livers, as a more regenerative tissue, remained remarkably resilient in the absence of FicD. The livers of FicD-/- did not show marked changes in UPR signaling or damage after either chronic high fat diet (HFD) feeding or acute pathological UPR induction. Intriguingly, FicD-/- mice showed changes in UPR induction and weight loss patterns following repeated pathological UPR induction. These findings indicate that FicD regulates UPR responses during mild physiological stress and in adaptation to repeated stresses, but there are tissue specific differences in the requirement for FicD regulation.
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Affiliation(s)
- Amanda K Casey
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA; Howard Hughes Medical Institute, Dallas, TX, 75390, USA
| | - Nathan M Stewart
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA; Howard Hughes Medical Institute, Dallas, TX, 75390, USA
| | - Naqi Zaidi
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Hillery F Gray
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA; Howard Hughes Medical Institute, Dallas, TX, 75390, USA
| | - Amelia Cox
- Washington and Lee University, Lexington, VA, 24450, USA
| | - Hazel A Fields
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Kim Orth
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA; Howard Hughes Medical Institute, Dallas, TX, 75390, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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4
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Casey AK, Stewart NM, Zaidi N, Gray HF, Cox A, Fields HA, Orth K. FicD regulates adaptation to the unfolded protein response in the murine liver. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.15.589620. [PMID: 38659954 PMCID: PMC11042336 DOI: 10.1101/2024.04.15.589620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The unfolded protein response (UPR) is a cellular stress response that is activated when misfolded proteins accumulate in the endoplasmic reticulum (ER). The UPR elicits a signaling cascade that results in an upregulation of protein folding machinery and cell survival signals. However, prolonged UPR responses can result in elevated cellular inflammation, damage, and even cell death. Thus, regulation of the UPR response must be tuned to the needs of the cell, sensitive enough to respond to the stress but pliable enough to be stopped after the crisis has passed. Previously, we discovered that the bi-functional enzyme FicD can modulate the UPR response via post-translational modification of BiP. FicD AMPylates BiP during homeostasis and deAMPylates BiP during stress. We found this activity is important for the physiological regulation of the exocrine pancreas. Here, we explore the role of FicD in the murine liver. Like our previous studies, livers lacking FicD exhibit enhanced UPR signaling in response to short term physiologic fasting and feeding stress. However, the livers of FicD -/- did not show marked changes in UPR signaling or damage after either chronic high fat diet (HFD) feeding or acute pathological UPR induction. Intriguingly, FicD -/- mice showed changes in UPR induction and weight loss patterns following repeated pathological UPR induction. These findings show that FicD regulates UPR responses during mild physiological stress and may play a role in maintaining resiliency of tissue through adaptation to repeated ER stress.
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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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Höpfner D, Cichy A, Pogenberg V, Krisp C, Mezouar S, Bach NC, Grotheer J, Zarza SM, Martinez E, Bonazzi M, Feige MJ, Sieber SA, Schlüter H, Itzen A. The DNA-binding induced (de)AMPylation activity of a Coxiella burnetii Fic enzyme targets Histone H3. Commun Biol 2023; 6:1124. [PMID: 37932372 PMCID: PMC10628234 DOI: 10.1038/s42003-023-05494-7] [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: 04/14/2023] [Accepted: 10/20/2023] [Indexed: 11/08/2023] Open
Abstract
The intracellular bacterial pathogen Coxiella burnetii evades the host response by secreting effector proteins that aid in establishing a replication-friendly niche. Bacterial filamentation induced by cyclic AMP (Fic) enzymes can act as effectors by covalently modifying target proteins with the posttranslational AMPylation by transferring adenosine monophosphate (AMP) from adenosine triphosphate (ATP) to a hydroxyl-containing side chain. Here we identify the gene product of C. burnetii CBU_0822, termed C. burnetii Fic 2 (CbFic2), to AMPylate host cell histone H3 at serine 10 and serine 28. We show that CbFic2 acts as a bifunctional enzyme, both capable of AMPylation as well as deAMPylation, and is regulated by the binding of DNA via a C-terminal helix-turn-helix domain. We propose that CbFic2 performs AMPylation in its monomeric state, switching to a deAMPylating dimer upon DNA binding. This study unveils reversible histone modification by a specific enzyme of a pathogenic bacterium.
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Affiliation(s)
- Dorothea Höpfner
- Institute of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246, Hamburg, Germany
| | - Adam Cichy
- Center for Integrated Protein Science Munich (CIPSM), Department Chemistry, Group of Proteinchemistry, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany
| | - Vivian Pogenberg
- Institute of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246, Hamburg, Germany
| | - Christoph Krisp
- Institute of Clinical Chemistry and Laboratory Medicine, Section Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246, Hamburg, Germany
| | - Soraya Mezouar
- Aix-Marseille University, Institut de Recherche pour la Développement (IRD), Assistance Publique-Hôpitaux de Marseille (APHM), Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Boulevard Jean Moulin, 13005, Marseille, France
| | - Nina C Bach
- Technical University of Munich (TUM), TUM School of Natural Sciences, Department of Biosciences, Chair of Organic Chemistry II, Center for Functional Protein Assemblies (CPA), Ernst-Otto-Fischer Straße 8, 85748, Garching, Germany
| | - Jan Grotheer
- Institute of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246, Hamburg, Germany
| | - Sandra Madariaga Zarza
- Aix-Marseille University, Institut de Recherche pour la Développement (IRD), Assistance Publique-Hôpitaux de Marseille (APHM), Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Boulevard Jean Moulin, 13005, Marseille, France
| | - Eric Martinez
- Cellular and Molecular Biology of Bacterial Infections, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, UMR 9004 - Centre national de la recherche scientifique (CNRS), 1919 Route de Mende, 34293, Montpellier, France
| | - Matteo Bonazzi
- Cellular and Molecular Biology of Bacterial Infections, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, UMR 9004 - Centre national de la recherche scientifique (CNRS), 1919 Route de Mende, 34293, Montpellier, France
| | - Matthias J Feige
- Center for Functional Protein Assemblies (CPA), Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Stephan A Sieber
- Technical University of Munich (TUM), TUM School of Natural Sciences, Department of Biosciences, Chair of Organic Chemistry II, Center for Functional Protein Assemblies (CPA), Ernst-Otto-Fischer Straße 8, 85748, Garching, Germany
| | - Hartmut Schlüter
- Institute of Clinical Chemistry and Laboratory Medicine, Section Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf (UKE), 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 (UKE), Martinistraße 52, 20246, Hamburg, Germany.
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7
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Shekhar S, Moehlman AT, Park B, Ewnetu M, Tracy C, Titos I, Pawłowski K, Tagliabracci VS, Krämer H. Allnighter pseudokinase-mediated feedback links proteostasis and sleep in Drosophila. Nat Commun 2023; 14:2932. [PMID: 37217484 DOI: 10.1038/s41467-023-38485-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 05/04/2023] [Indexed: 05/24/2023] Open
Abstract
In nervous systems, retrograde signals are key for organizing circuit activity and maintaining neuronal homeostasis. We identify the conserved Allnighter (Aln) pseudokinase as a cell non-autonomous regulator of proteostasis responses necessary for normal sleep and structural plasticity of Drosophila photoreceptors. In aln mutants exposed to extended ambient light, proteostasis is dysregulated and photoreceptors develop striking, but reversible, dysmorphology. The aln gene is widely expressed in different neurons, but not photoreceptors. However, secreted Aln protein is retrogradely endocytosed by photoreceptors. Inhibition of photoreceptor synaptic release reduces Aln levels in lamina neurons, consistent with secreted Aln acting in a feedback loop. In addition, aln mutants exhibit reduced night time sleep, providing a molecular link between dysregulated proteostasis and sleep, two characteristics of ageing and neurodegenerative diseases.
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Affiliation(s)
- Shashank Shekhar
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX; O'Donnell Brain Institute, Dallas, USA.
| | - Andrew T Moehlman
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX; O'Donnell Brain Institute, Dallas, USA
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Brenden Park
- Department of Molecular Biology UT Southwestern Medical Center, Dallas, TX, USA
| | - Michael Ewnetu
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX; O'Donnell Brain Institute, Dallas, USA
| | - Charles Tracy
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX; O'Donnell Brain Institute, Dallas, USA
| | - Iris Titos
- Molecular Medicine Program, University of Utah, School of Medicine, Salt Lake City, UT, USA
| | - Krzysztof Pawłowski
- Department of Molecular Biology UT Southwestern Medical Center, Dallas, TX, USA
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences, Warsaw, 02-776, Poland
| | - Vincent S Tagliabracci
- Department of Molecular Biology UT Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, Maryland, USA
| | - Helmut Krämer
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX; O'Donnell Brain Institute, Dallas, USA.
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX, USA.
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8
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Perera LA, Hattersley AT, Harding HP, Wakeling MN, Flanagan SE, Mohsina I, Raza J, Gardham A, Ron D, De Franco E. Infancy-onset diabetes caused by de-regulated AMPylation of the human endoplasmic reticulum chaperone BiP. EMBO Mol Med 2023; 15:e16491. [PMID: 36704923 PMCID: PMC9994480 DOI: 10.15252/emmm.202216491] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 12/08/2022] [Accepted: 12/09/2022] [Indexed: 01/28/2023] Open
Abstract
Dysfunction of the endoplasmic reticulum (ER) in insulin-producing beta cells results in cell loss and diabetes mellitus. Here we report on five individuals from three different consanguineous families with infancy-onset diabetes mellitus and severe neurodevelopmental delay caused by a homozygous p.(Arg371Ser) mutation in FICD. The FICD gene encodes a bifunctional Fic domain-containing enzyme that regulates the ER Hsp70 chaperone, BiP, via catalysis of two antagonistic reactions: inhibitory AMPylation and stimulatory deAMPylation of BiP. Arg371 is a conserved residue in the Fic domain active site. The FICDR371S mutation partially compromises BiP AMPylation in vitro but eliminates all detectable deAMPylation activity. Overexpression of FICDR371S or knock-in of the mutation at the FICD locus of stressed CHO cells results in inappropriately elevated levels of AMPylated BiP and compromised secretion. These findings, guided by human genetics, highlight the destructive consequences of de-regulated BiP AMPylation and raise the prospect of tuning FICD's antagonistic activities towards therapeutic ends.
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Affiliation(s)
- Luke A Perera
- Cambridge Institute for Medical ResearchUniversity of CambridgeCambridgeUK
- Present address:
The Francis Crick InstituteLondonUK
| | - Andrew T Hattersley
- Institute of Biomedical and Clinical Science, College of Medicine and HealthUniversity of ExeterExeterUK
| | - Heather P Harding
- Cambridge Institute for Medical ResearchUniversity of CambridgeCambridgeUK
| | - Matthew N Wakeling
- Institute of Biomedical and Clinical Science, College of Medicine and HealthUniversity of ExeterExeterUK
| | - Sarah E Flanagan
- Institute of Biomedical and Clinical Science, College of Medicine and HealthUniversity of ExeterExeterUK
| | - Ibrahim Mohsina
- Department of Endocrine and DiabetesNational Institute of Child HealthKarachiPakistan
| | - Jamal Raza
- Department of Endocrine and DiabetesNational Institute of Child HealthKarachiPakistan
| | | | - David Ron
- Cambridge Institute for Medical ResearchUniversity of CambridgeCambridgeUK
| | - Elisa De Franco
- Institute of Biomedical and Clinical Science, College of Medicine and HealthUniversity of ExeterExeterUK
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9
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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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10
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Liu M, Li L, Wang Z, Wang S, Tang X. Catalytic deAMPylation in AMPylation-inhibitory/assistant forms of FICD protein. Front Chem 2023; 11:1077188. [PMID: 36762200 PMCID: PMC9905249 DOI: 10.3389/fchem.2023.1077188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 01/10/2023] [Indexed: 01/27/2023] Open
Abstract
DeAMPylation, as a reversible reaction of AMPylation and mediated by the endoplasmic reticulum-localized enzyme FICD (filamentation induced by cAMP domain protein, also known as HYPE), is an important process in protein posttranslational modifications (PTMs). Elucidating the function and catalytic details of FICD is of vital importance to provide a comprehensive understanding of protein folding homeostasis. However, the detailed deAMPylation mechanism is still unclear. Furthermore, the role of a conserved glutamine (Glu234), that plays an inhibitory role in the AMPylation response, is still an open question in the deAMPylation process. In the present work, the elaborated deAMPylation mechanisms with AMPylation-inhibitory/assistant forms of FICD (wild type and Glu234Ala mutant) were investigated based on the QM(DFT)/MM MD approach. The results revealed that deAMPylation was triggered by proton transfer from protonated histidine (His363) to AMPylated threonine, instead of a nucleophilic attack of water molecules adding to the phosphorus of AMP. The free energy barrier of deAMPylation in the wild type (∼17.3 kcal/mol) is consistent with that in the Glu234Ala mutant of FICD (∼17.1 kcal/mol), suggesting that the alteration of the Glu234 residue does not affect the deAMPylation reaction and indirectly verifying the inducement of deAMPylation in FICD. In the wild type, the proton in the nucleophilic water molecule is transferred to Glu234, whereas it is delivered to Asp367 through the hydrogen-bond network of coordinated water molecules in the Glu234Ala mutant. The present findings were inspirational for understanding the catalytic and inhibitory mechanisms of FICD-mediated AMP transfer, paving the way for further studies on the physiological role of FICD protein.
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Affiliation(s)
- Meili Liu
- Department of Medical Chemistry, School of Pharmacy, Qingdao University, Qingdao, China,Department of Civil and Architectural Engineering, University of Miami, Coral Gables, FL, United States
| | - Li Li
- Department of Medical Chemistry, School of Pharmacy, Qingdao University, Qingdao, China
| | - Zhiqin Wang
- Department of Medical Chemistry, School of Pharmacy, Qingdao University, Qingdao, China
| | - Shuang Wang
- Department of Medical Chemistry, School of Pharmacy, Qingdao University, Qingdao, China,Department of Stomatology, Huangdao District Central Hospital, Qingdao, China,*Correspondence: Shuang Wang, ; Xiaowen Tang,
| | - Xiaowen Tang
- Department of Medical Chemistry, School of Pharmacy, Qingdao University, Qingdao, China,*Correspondence: Shuang Wang, ; Xiaowen Tang,
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11
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Casey AK, Gray HF, Chimalapati S, Hernandez G, Moehlman AT, Stewart N, Fields HA, Gulen B, Servage KA, Stefanius K, Blevins A, Evers BM, Krämer H, Orth K. Fic-mediated AMPylation tempers the unfolded protein response during physiological stress. Proc Natl Acad Sci U S A 2022; 119:e2208317119. [PMID: 35914137 PMCID: PMC9371680 DOI: 10.1073/pnas.2208317119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/09/2022] [Indexed: 12/14/2022] Open
Abstract
The proper balance of synthesis, folding, modification, and degradation of proteins, also known as protein homeostasis, is vital to cellular health and function. The unfolded protein response (UPR) is activated when the mechanisms maintaining protein homeostasis in the endoplasmic reticulum become overwhelmed. However, prolonged or strong UPR responses can result in elevated inflammation and cellular damage. Previously, we discovered that the enzyme filamentation induced by cyclic-AMP (Fic) can modulate the UPR response via posttranslational modification of binding immunoglobulin protein (BiP) by AMPylation during homeostasis and deAMPylation during stress. Loss of fic in Drosophila leads to vision defects and altered UPR activation in the fly eye. To investigate the importance of Fic-mediated AMPylation in a mammalian system, we generated a conditional null allele of Fic in mice and characterized the effect of Fic loss on the exocrine pancreas. Compared to controls, Fic-/- mice exhibit elevated serum markers for pancreatic dysfunction and display enhanced UPR signaling in the exocrine pancreas in response to physiological and pharmacological stress. In addition, both fic-/- flies and Fic-/- mice show reduced capacity to recover from damage by stress that triggers the UPR. These findings show that Fic-mediated AMPylation acts as a molecular rheostat that is required to temper the UPR response in the mammalian pancreas during physiological stress. Based on these findings, we propose that repeated physiological stress in differentiated tissues requires this rheostat for tissue resilience and continued function over the lifetime of an animal.
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Affiliation(s)
- Amanda K. Casey
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Hillery F. Gray
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- HHMI, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Suneeta Chimalapati
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- HHMI, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Genaro Hernandez
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Andrew T. Moehlman
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Nathan Stewart
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- HHMI, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Hazel A. Fields
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Burak Gulen
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Kelly A. Servage
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- HHMI, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Karoliina Stefanius
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- HHMI, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Aubrie Blevins
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Bret M. Evers
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Helmut Krämer
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Kim Orth
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- HHMI, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390
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12
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Virolainen MS, Søltoft CL, Pedersen PA, Ellgaard L. Production of an Active, Human Membrane Protein in Saccharomyces cerevisiae: Full-Length FICD. Int J Mol Sci 2022; 23:ijms23052458. [PMID: 35269596 PMCID: PMC8910494 DOI: 10.3390/ijms23052458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 12/10/2022] Open
Abstract
The human Fic domain-containing protein (FICD) is a type II endoplasmic reticulum (ER) membrane protein that is important for the maintenance of ER proteostasis. Structural and in vitro biochemical characterisation of FICD AMPylase and deAMPylase activity have been restricted to the soluble ER-luminal domain produced in Escherichia coli. Information about potentially important features, such as structural motifs, modulator binding sites or other regulatory elements, is therefore missing for the approximately 100 N-terminal residues including the transmembrane region of FICD. Expressing and purifying the required quantity and quality of membrane proteins is demanding because of the low yields and poor stability often observed. Here, we produce full-length FICD by combining a Saccharomyces cerevisiae-based platform with green fluorescent protein (GFP) tagging to optimise the conditions for expression, solubilisation and purification. We subsequently employ these conditions to purify milligram quantities of His-tagged FICD per litre of culture, and show that the purified, detergent-solubilised membrane protein is an active deAMPylating enzyme. Our work provides a straightforward methodology for producing not only full-length FICD, but also other membrane proteins in S. cerevisiae for structural and biochemical characterisation.
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Affiliation(s)
- Minttu S. Virolainen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark; (M.S.V.); (C.L.S.)
| | - Cecilie L. Søltoft
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark; (M.S.V.); (C.L.S.)
| | - Per A. Pedersen
- Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2200 Copenhagen, Denmark
- Correspondence: (P.A.P.); (L.E.)
| | - Lars Ellgaard
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark; (M.S.V.); (C.L.S.)
- Correspondence: (P.A.P.); (L.E.)
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13
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Zhang S, Wang H, Melick CH, Jeong MH, Curukovic A, Tiwary S, Lama-Sherpa TD, Meng D, Servage KA, James NG, Jewell JL. AKAP13 couples GPCR signaling to mTORC1 inhibition. PLoS Genet 2021; 17:e1009832. [PMID: 34673774 PMCID: PMC8570464 DOI: 10.1371/journal.pgen.1009832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 11/05/2021] [Accepted: 09/21/2021] [Indexed: 01/14/2023] Open
Abstract
The mammalian target of rapamycin complex 1 (mTORC1) senses multiple stimuli to regulate anabolic and catabolic processes. mTORC1 is typically hyperactivated in multiple human diseases such as cancer and type 2 diabetes. Extensive research has focused on signaling pathways that can activate mTORC1 such as growth factors and amino acids. However, less is known about signaling cues that can directly inhibit mTORC1 activity. Here, we identify A-kinase anchoring protein 13 (AKAP13) as an mTORC1 binding protein, and a crucial regulator of mTORC1 inhibition by G-protein coupled receptor (GPCR) signaling. GPCRs paired to Gαs proteins increase cyclic adenosine 3’5’ monophosphate (cAMP) to activate protein kinase A (PKA). Mechanistically, AKAP13 acts as a scaffold for PKA and mTORC1, where PKA inhibits mTORC1 through the phosphorylation of Raptor on Ser 791. Importantly, AKAP13 mediates mTORC1-induced cell proliferation, cell size, and colony formation. AKAP13 expression correlates with mTORC1 activation and overall lung adenocarcinoma patient survival, as well as lung cancer tumor growth in vivo. Our study identifies AKAP13 as an important player in mTORC1 inhibition by GPCRs, and targeting this pathway may be beneficial for human diseases with hyperactivated mTORC1. The mammalian target of rapamycin complex 1 (mTORC1) can sense multiple upstream stimuli to regulate cell growth and metabolism. Increased mTORC1 activation results in many human diseases such as cancer. Small molecules like rapamycin that target and inhibit mTORC1, are available in the clinic with limited success. Thus, decoding the mechanisms involved in mTORC1 regulation is crucial. Most of the research has focused on stimuli that activate mTORC1. Less is known about signaling pathways that can directly inhibit mTORC1 activity. G-protein coupled receptors (GPCRs) coupled to Gαs proteins signal to and potently inhibit mTORC1. In this study, we have identified AKAP13 to play a crucial role in mTORC1 inhibition by GPCR signaling. Importantly, GPCRs are the largest family of drug targets with many approved FDA compounds. Targeting this signaling pathway may be beneficial for human diseases with hyperactivated mTORC1.
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Affiliation(s)
- Shihai Zhang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Huanyu Wang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Chase H. Melick
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Mi-Hyeon Jeong
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Adna Curukovic
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Shweta Tiwary
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Tshering D. Lama-Sherpa
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Delong Meng
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Kelly A. Servage
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Nicholas G. James
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii, United States of America
| | - Jenna L. Jewell
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- * E-mail:
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14
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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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15
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Structures of a deAMPylation complex rationalise the switch between antagonistic catalytic activities of FICD. Nat Commun 2021; 12:5004. [PMID: 34408154 PMCID: PMC8373988 DOI: 10.1038/s41467-021-25076-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 07/15/2021] [Indexed: 12/22/2022] Open
Abstract
The endoplasmic reticulum (ER) Hsp70 chaperone BiP is regulated by AMPylation, a reversible inactivating post-translational modification. Both BiP AMPylation and deAMPylation are catalysed by a single ER-localised enzyme, FICD. Here we present crystallographic and solution structures of a deAMPylation Michaelis complex formed between mammalian AMPylated BiP and FICD. The latter, via its tetratricopeptide repeat domain, binds a surface that is specific to ATP-state Hsp70 chaperones, explaining the exquisite selectivity of FICD for BiP’s ATP-bound conformation both when AMPylating and deAMPylating Thr518. The eukaryotic deAMPylation mechanism thus revealed, rationalises the role of the conserved Fic domain Glu234 as a gatekeeper residue that both inhibits AMPylation and facilitates hydrolytic deAMPylation catalysed by dimeric FICD. These findings point to a monomerisation-induced increase in Glu234 flexibility as the basis of an oligomeric state-dependent switch between FICD’s antagonistic activities, despite a similar mode of engagement of its two substrates — unmodified and AMPylated BiP. The ER chaperone BiP is regulated by FICD-mediated AMPylation and deAMPylation. Here, the authors characterise the structure of mammalian AMPylated BiP bound to FICD, by X-ray crystallography and neutron scattering, providing insights into the mechanism of BiP AMPylation and deAMPylation.
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16
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Sanyal A, Zbornik EA, Watson BG, Christoffer C, Ma J, Kihara D, Mattoo S. Kinetic and structural parameters governing Fic-mediated adenylylation/AMPylation of the Hsp70 chaperone, BiP/GRP78. Cell Stress Chaperones 2021; 26:639-656. [PMID: 33942205 PMCID: PMC8275707 DOI: 10.1007/s12192-021-01208-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 04/20/2021] [Accepted: 04/26/2021] [Indexed: 12/11/2022] Open
Abstract
Fic (filamentation induced by cAMP) proteins regulate diverse cell signaling events by post-translationally modifying their protein targets, predominantly by the addition of an AMP (adenosine monophosphate). This modification is called Fic-mediated adenylylation or AMPylation. We previously reported that the human Fic protein, HYPE/FicD, is a novel regulator of the unfolded protein response (UPR) that maintains homeostasis in the endoplasmic reticulum (ER) in response to stress from misfolded proteins. Specifically, HYPE regulates UPR by adenylylating the ER chaperone, BiP/GRP78, which serves as a sentinel for UPR activation. Maintaining ER homeostasis is critical for determining cell fate, thus highlighting the importance of the HYPE-BiP interaction. Here, we study the kinetic and structural parameters that determine the HYPE-BiP interaction. By measuring the binding and kinetic efficiencies of HYPE in its activated (Adenylylation-competent) and wild type (de-AMPylation-competent) forms for BiP in its wild type and ATP-bound conformations, we determine that HYPE displays a nearly identical preference for the wild type and ATP-bound forms of BiP in vitro and preferentially de-AMPylates the wild type form of adenylylated BiP. We also show that AMPylation at BiP's Thr366 versus Thr518 sites differentially affect its ATPase activity, and that HYPE does not adenylylate UPR accessory proteins like J-protein ERdJ6. Using molecular docking models, we explain how HYPE is able to adenylylate Thr366 and Thr518 sites in vitro. While a physiological role for AMPylation at both the Thr366 and Thr518 sites has been reported, our molecular docking model supports Thr518 as the structurally preferred modification site. This is the first such analysis of the HYPE-BiP interaction and offers critical insights into substrate specificity and target recognition.
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Affiliation(s)
- Anwesha Sanyal
- From the Department of Biological Sciences, Purdue University, 915 W. State St., LILY G-227, West Lafayette, IN, 47907, USA
| | - Erica A Zbornik
- From the Department of Biological Sciences, Purdue University, 915 W. State St., LILY G-227, West Lafayette, IN, 47907, USA
| | - Ben G Watson
- From the Department of Biological Sciences, Purdue University, 915 W. State St., LILY G-227, West Lafayette, IN, 47907, USA
| | - Charles Christoffer
- Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA
| | - Jia Ma
- Bindley Biosciences Center, Purdue University, West Lafayette, IN, 47907, USA
| | - Daisuke Kihara
- From the Department of Biological Sciences, Purdue University, 915 W. State St., LILY G-227, West Lafayette, IN, 47907, USA
- Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA
| | - Seema Mattoo
- From the Department of Biological Sciences, Purdue University, 915 W. State St., LILY G-227, West Lafayette, IN, 47907, USA.
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17
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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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18
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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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Aghaei M, Dastghaib S, Aftabi S, Aghanoori MR, Alizadeh J, Mokarram P, Mehrbod P, Ashrafizadeh M, Zarrabi A, McAlinden KD, Eapen MS, Sohal SS, Sharma P, Zeki AA, Ghavami S. The ER Stress/UPR Axis in Chronic Obstructive Pulmonary Disease and Idiopathic Pulmonary Fibrosis. Life (Basel) 2020; 11:1. [PMID: 33374938 PMCID: PMC7821926 DOI: 10.3390/life11010001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/14/2020] [Accepted: 12/18/2020] [Indexed: 12/18/2022] Open
Abstract
Cellular protein homeostasis in the lungs is constantly disrupted by recurrent exposure to various external and internal stressors, which may cause considerable protein secretion pressure on the endoplasmic reticulum (ER), resulting in the survival and differentiation of these cell types to meet the increased functional demands. Cells are able to induce a highly conserved adaptive mechanism, known as the unfolded protein response (UPR), to manage such stresses. UPR dysregulation and ER stress are involved in numerous human illnesses, such as metabolic syndrome, fibrotic diseases, and neurodegeneration, and cancer. Therefore, effective and specific compounds targeting the UPR pathway are being considered as potential therapies. This review focuses on the impact of both external and internal stressors on the ER in idiopathic pulmonary fibrosis (IPF) and chronic obstructive pulmonary disease (COPD) and discusses the role of the UPR signaling pathway activation in the control of cellular damage and specifically highlights the potential involvement of non-coding RNAs in COPD. Summaries of pathogenic mechanisms associated with the ER stress/UPR axis contributing to IPF and COPD, and promising pharmacological intervention strategies, are also presented.
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Affiliation(s)
- Mahmoud Aghaei
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada; (M.A.); (S.A.); (J.A.)
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan 8174673461, Iran
| | - Sanaz Dastghaib
- Department of Clinical Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz 7134845794, Iran; (S.D.); (P.M.)
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz 7134845794, Iran
| | - Sajjad Aftabi
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada; (M.A.); (S.A.); (J.A.)
- Medical Physics Department, Cancer Care Manitoba, University of Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - Mohamad-Reza Aghanoori
- Division of Neurodegenerative Disorders, St Boniface Hospital Albrechtsen Research Centre, University of Manitoba, Winnipeg, MB R2H 2A6, Canada;
- Department of Internal Medicine, University of Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - Javad Alizadeh
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada; (M.A.); (S.A.); (J.A.)
- Research Institute of Oncology and Hematology, Cancer Care Manitoba, University of Manitoba, Winnipeg, MB R3E 0V9, Canada
- Biology of Breathing Theme, Children Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - Pooneh Mokarram
- Department of Clinical Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz 7134845794, Iran; (S.D.); (P.M.)
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz 7134845794, Iran
| | - Parvaneh Mehrbod
- Influenza and Respiratory Viruses Department, Pasteur Institute of Iran, Tehran 1316943551, Iran;
| | - Milad Ashrafizadeh
- Faculty of Engineering and Natural Sciences, Sabanci University, Orta Mahalle, Üniversite Caddesi No. 27, Orhanlı, Tuzla, 34956 Istanbul, Turkey;
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Tuzla, 34956 Istanbul, Turkey;
| | - Ali Zarrabi
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Tuzla, 34956 Istanbul, Turkey;
| | - Kielan Darcy McAlinden
- Respiratory Translational Research Group, Department of Laboratory Medicine, School of Health Sciences, University of Tasmania, Launceston 7250, Tasmania, Australia; (K.D.M.); (M.S.E.); (S.S.S.)
| | - Mathew Suji Eapen
- Respiratory Translational Research Group, Department of Laboratory Medicine, School of Health Sciences, University of Tasmania, Launceston 7250, Tasmania, Australia; (K.D.M.); (M.S.E.); (S.S.S.)
| | - Sukhwinder Singh Sohal
- Respiratory Translational Research Group, Department of Laboratory Medicine, School of Health Sciences, University of Tasmania, Launceston 7250, Tasmania, Australia; (K.D.M.); (M.S.E.); (S.S.S.)
| | - Pawan Sharma
- Center for Translational Medicine, Jane & Leonard Korman Respiratory Institute, Thomas Jefferson University, Philadelphia, PA 19107, USA;
| | - Amir A. Zeki
- Davis School of Medicine, Department of Internal Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, UC Davis Lung Center, University of California, Davis, CA 95616, USA;
- Veterans Affairs Medical Center, Mather, CA 95655, USA
| | - Saeid Ghavami
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada; (M.A.); (S.A.); (J.A.)
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz 7134845794, Iran
- Research Institute of Oncology and Hematology, Cancer Care Manitoba, University of Manitoba, Winnipeg, MB R3E 0V9, Canada
- Biology of Breathing Theme, Children Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB R3E 0V9, Canada
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20
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Lu CH, McCloskey A, Chen FR, Nakayasu ES, Zhang LQ, Luo ZQ. Fic Proteins Inhibit the Activity of Topoisomerase IV by AMPylation in Diverse Bacteria. Front Microbiol 2020; 11:2084. [PMID: 32983060 PMCID: PMC7479194 DOI: 10.3389/fmicb.2020.02084] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 08/07/2020] [Indexed: 12/14/2022] Open
Abstract
The Fic (filamentation induced by cyclic AMP) domain is a widely distributed motif with a conserved sequence of HPFx[D/E]GN[G/K]R, some of which regulate cellular activity by catalyzing the transfer of the AMP moiety from ATP to protein substrates. Some Fic proteins, including Fic-1 from the soil bacterium Pseudomonas fluorescens strain 2P24, have been shown to inhibit bacterial DNA replication by AMPylating the subunit B of DNA gyrase (GyrB), but the biochemical activity and cellular target of most Fic proteins remain unknown. Here, we report that Fic-2, which is another Fic protein from strain 2P24 and Fic-1 AMPylate the topoisomerase IV ParE at Tyr109. We also examined Fic proteins from several phylogenetically diverse bacteria and found that those from Yersinia pseudotuberculosis and Staphylococcus aureus AMPylate ParE and GrlB, the counterpart of ParE in Gram-positive bacteria, respectively. Modification by Fic-1 of P. fluorescens and FicY of Y. pseudotuberculosis inhibits the relaxation activity of topoisomerase IV. Consistent with the inhibition of ParE activity, ectopic expression of these Fic proteins causes cell filamentation akin to the canonical par phenotype in which nucleoids are assembled in the center of elongated cells, a process accompanied by the induction of the SOS response. Our results establish that Fic proteins from diverse bacterial species regulate chromosome division and cell separation in bacteria by targeting ParE.
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Affiliation(s)
- Can-Hua Lu
- Yunnan Academy of Tobacco Agriculture Science, Kunming, China.,Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China.,Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
| | - Alix McCloskey
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
| | - Fu-Rong Chen
- Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Ernesto S Nakayasu
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Li-Qun Zhang
- Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Zhao-Qing Luo
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
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21
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Chimalapati S, de Souza Santos M, Lafrance AE, Ray A, Lee WR, Rivera-Cancel G, Vale G, Pawlowski K, Mitsche MA, McDonald JG, Liou J, Orth K. Vibrio deploys type 2 secreted lipase to esterify cholesterol with host fatty acids and mediate cell egress. eLife 2020; 9:58057. [PMID: 32808593 PMCID: PMC7434443 DOI: 10.7554/elife.58057] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 07/28/2020] [Indexed: 12/23/2022] Open
Abstract
Pathogens find diverse niches for survival including inside a host cell where replication occurs in a relatively protective environment. Vibrio parahaemolyticus is a facultative intracellular pathogen that uses its type 3 secretion system 2 (T3SS2) to invade and replicate inside host cells. Analysis of the T3SS2 pathogenicity island encoding the T3SS2 appeared to lack a mechanism for egress of this bacterium from the invaded host cell. Using a combination of molecular tools, we found that VPA0226, a constitutively secreted lipase, is required for escape of V. parahaemolyticus from the host cells. This lipase must be delivered into the host cytoplasm where it preferentially uses fatty acids associated with innate immune response to esterify cholesterol, weakening the plasma membrane and allowing egress of the bacteria. This study reveals the resourcefulness of microbes and the interplay between virulence systems and host cell resources to evolve an ingenious scheme for survival and escape.
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Affiliation(s)
- Suneeta Chimalapati
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, United States.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Marcela de Souza Santos
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Alexander E Lafrance
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Ann Ray
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Wan-Ru Lee
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Giomar Rivera-Cancel
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, United States
| | - Gonçalo Vale
- Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, United States
| | - Krzysztof Pawlowski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, United States.,Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Matthew A Mitsche
- Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Jeffrey G McDonald
- Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Jen Liou
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Kim Orth
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, United States.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, United States
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22
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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: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [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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23
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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: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [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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24
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FICD activity and AMPylation remodelling modulate human neurogenesis. Nat Commun 2020; 11:517. [PMID: 31980631 PMCID: PMC6981130 DOI: 10.1038/s41467-019-14235-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 12/16/2019] [Indexed: 12/18/2022] Open
Abstract
Posttranslational modification (PTM) of proteins represents an important cellular mechanism for controlling diverse functions such as signalling, localisation or protein–protein interactions. AMPylation (also termed adenylylation) has recently been discovered as a prevalent PTM for regulating protein activity. In human cells AMPylation has been exclusively studied with the FICD protein. Here we investigate the role of AMPylation in human neurogenesis by introducing a cell-permeable propargyl adenosine pronucleotide probe to infiltrate cellular AMPylation pathways and report distinct modifications in intact cancer cell lines, human-derived stem cells, neural progenitor cells (NPCs), neurons and cerebral organoids (COs) via LC–MS/MS as well as imaging methods. A total of 162 AMP modified proteins were identified. FICD-dependent AMPylation remodelling accelerates differentiation of neural progenitor cells into mature neurons in COs, demonstrating a so far unknown trigger of human neurogenesis. Protein AMPylation is a post-translational modification whose implications in cellular physiology are not fully understood. Here the authors develop a cell-permeable AMPylation probe and use it to identify new AMP modified proteins and investigate the role of FICD in neuronal differentiation using cerebral organoids.
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25
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Perera LA, Rato C, Yan Y, Neidhardt L, McLaughlin SH, Read RJ, Preissler S, Ron D. An oligomeric state-dependent switch in the ER enzyme FICD regulates AMPylation and deAMPylation of BiP. EMBO J 2019; 38:e102177. [PMID: 31531998 PMCID: PMC6826200 DOI: 10.15252/embj.2019102177] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/25/2019] [Accepted: 07/26/2019] [Indexed: 11/23/2022] Open
Abstract
AMPylation is an inactivating modification that alters the activity of the major endoplasmic reticulum (ER) chaperone BiP to match the burden of unfolded proteins. A single ER-localised Fic protein, FICD (HYPE), catalyses both AMPylation and deAMPylation of BiP. However, the basis for the switch in FICD's activity is unknown. We report on the transition of FICD from a dimeric enzyme, that deAMPylates BiP, to a monomer with potent AMPylation activity. Mutations in the dimer interface, or of residues along an inhibitory pathway linking the dimer interface to the enzyme's active site, favour BiP AMPylation in vitro and in cells. Mechanistically, monomerisation relieves a repressive effect allosterically propagated from the dimer interface to the inhibitory Glu234, thereby permitting AMPylation-competent binding of MgATP. Moreover, a reciprocal signal, propagated from the nucleotide-binding site, provides a mechanism for coupling the oligomeric state and enzymatic activity of FICD to the energy status of the ER.
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Affiliation(s)
- Luke A Perera
- Cambridge Institute for Medical ResearchUniversity of CambridgeCambridgeUK
| | - Claudia Rato
- Cambridge Institute for Medical ResearchUniversity of CambridgeCambridgeUK
| | - Yahui Yan
- Cambridge Institute for Medical ResearchUniversity of CambridgeCambridgeUK
| | - Lisa Neidhardt
- Cambridge Institute for Medical ResearchUniversity of CambridgeCambridgeUK
| | | | - Randy J Read
- Cambridge Institute for Medical ResearchUniversity of CambridgeCambridgeUK
| | - Steffen Preissler
- Cambridge Institute for Medical ResearchUniversity of CambridgeCambridgeUK
| | - David Ron
- Cambridge Institute for Medical ResearchUniversity of CambridgeCambridgeUK
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26
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Preissler S, Ron D. Early Events in the Endoplasmic Reticulum Unfolded Protein Response. Cold Spring Harb Perspect Biol 2019; 11:cshperspect.a033894. [PMID: 30396883 PMCID: PMC6442202 DOI: 10.1101/cshperspect.a033894] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The physiological consequences of the unfolded protein response (UPR) are mediated by changes in gene expression. Underlying them are rapid processes involving preexisting components. We review recent insights gained into the regulation of the endoplasmic reticulum (ER) Hsp70 chaperone BiP, whose incorporation into inactive oligomers and reversible AMPylation and de-AMPylation present a first line of response to fluctuating levels of unfolded proteins. BiP activity is tied to the regulation of the UPR transducers by a recently discovered cycle of ER-localized, J protein-mediated formation of a repressive IRE1-BiP complex, whose working we contrast to an alternative model for UPR regulation that relies on direct recognition of unfolded proteins. We conclude with a discussion of mechanisms that repress messenger RNA (mRNA) translation to limit the flux of newly synthesized proteins into the ER, a rapid adaptation that does not rely on new macromolecule biosynthesis.
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27
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Sengupta R, Poderycki MJ, Mattoo S. CryoAPEX - an electron tomography tool for subcellular localization of membrane proteins. J Cell Sci 2019; 132:132/6/jcs222315. [PMID: 30886003 DOI: 10.1242/jcs.222315] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 02/04/2019] [Indexed: 12/21/2022] Open
Abstract
We describe a method, termed cryoAPEX, which couples chemical fixation and high-pressure freezing of cells with peroxidase tagging (APEX) to allow precise localization of membrane proteins in the context of a well-preserved subcellular membrane architecture. Further, cryoAPEX is compatible with electron tomography. As an example, we apply cryoAPEX to obtain a high-resolution three-dimensional contextual map of the human FIC (filamentation induced by cAMP) protein, HYPE (also known as FICD). HYPE is a single-pass membrane protein that localizes to the endoplasmic reticulum (ER) lumen and regulates the unfolded protein response. Alternate cellular locations for HYPE have been suggested. CryoAPEX analysis shows that, under normal and/or resting conditions, HYPE localizes robustly within the subdomains of the ER and is not detected in the secretory pathway or other organelles. CryoAPEX is broadly applicable for assessing both lumenal and cytosol-facing membrane proteins.
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Affiliation(s)
- Ranjan Sengupta
- Department of Biological Sciences, Purdue University, 915 W. State St., LILY G-227, West Lafayette, IN 47907, USA
| | - Michael J Poderycki
- Department of Biological Sciences, Purdue University, 915 W. State St., LILY G-227, West Lafayette, IN 47907, USA
| | - Seema Mattoo
- Department of Biological Sciences, Purdue University, 915 W. State St., LILY G-227, West Lafayette, IN 47907, USA
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28
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Veyron S, Oliva G, Rolando M, Buchrieser C, Peyroche G, Cherfils J. A Ca 2+-regulated deAMPylation switch in human and bacterial FIC proteins. Nat Commun 2019; 10:1142. [PMID: 30850593 PMCID: PMC6408439 DOI: 10.1038/s41467-019-09023-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 02/07/2019] [Indexed: 12/13/2022] Open
Abstract
FIC proteins regulate molecular processes from bacteria to humans by catalyzing post-translational modifications (PTM), the most frequent being the addition of AMP or AMPylation. In many AMPylating FIC proteins, a structurally conserved glutamate represses AMPylation and, in mammalian FICD, also supports deAMPylation of BiP/GRP78, a key chaperone of the unfolded protein response. Currently, a direct signal regulating these FIC proteins has not been identified. Here, we use X-ray crystallography and in vitro PTM assays to address this question. We discover that Enterococcus faecalis FIC (EfFIC) catalyzes both AMPylation and deAMPylation and that the glutamate implements a multi-position metal switch whereby Mg2+ and Ca2+ control AMPylation and deAMPylation differentially without a conformational change. Remarkably, Ca2+ concentration also tunes deAMPylation of BiP by human FICD. Our results suggest that the conserved glutamate is a signature of AMPylation/deAMPylation FIC bifunctionality and identify metal ions as diffusible signals that regulate such FIC proteins directly. In many AMPylating FIC proteins a structurally conserved glutamate represses AMPylation. Here, the authors show that this glutamate supports deAMPylation in Enterococcus faecalis FIC (EfFIC), and that EfFIC switches from AMPylation to deAMPylation by binding Ca2+ at distinct sites.
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Affiliation(s)
- Simon Veyron
- CNRS and Ecole normale supérieure Paris-Saclay, Laboratoire de Biologie et Pharmacologie Appliquée, 61 Avenue du Président Wilson, 94235, Cachan CEDEX, France
| | - Giulia Oliva
- Institut Pasteur and CNRS UMR 3525, Biologie des Bactéries Intracellulaires, 25-28 Rue du Dr Roux, 75015, Paris, France.,Sorbonne Université, Collège doctoral, 75005, Paris, France
| | - Monica Rolando
- Institut Pasteur and CNRS UMR 3525, Biologie des Bactéries Intracellulaires, 25-28 Rue du Dr Roux, 75015, Paris, France
| | - Carmen Buchrieser
- Institut Pasteur and CNRS UMR 3525, Biologie des Bactéries Intracellulaires, 25-28 Rue du Dr Roux, 75015, Paris, France
| | - Gérald Peyroche
- CNRS and Ecole normale supérieure Paris-Saclay, Laboratoire de Biologie et Pharmacologie Appliquée, 61 Avenue du Président Wilson, 94235, Cachan CEDEX, France
| | - Jacqueline Cherfils
- CNRS and Ecole normale supérieure Paris-Saclay, Laboratoire de Biologie et Pharmacologie Appliquée, 61 Avenue du Président Wilson, 94235, Cachan CEDEX, France.
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29
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Veyron S, Peyroche G, Cherfils J. FIC proteins: from bacteria to humans and back again. Pathog Dis 2018; 76:4898014. [PMID: 29617857 DOI: 10.1093/femspd/fty012] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 02/21/2018] [Indexed: 01/18/2023] Open
Abstract
During the last decade, FIC proteins have emerged as a large family comprised of a variety of bacterial enzymes and a single member in animals. The air de famille of FIC proteins stems from a domain of conserved structure, which catalyzes the post-translational modification of proteins (PTM) by a phosphate-containing compound. In bacteria, examples of FIC proteins include the toxin component of toxin/antitoxin modules, such as Doc-Phd and VbhT-VbhA, toxins secreted by pathogenic bacteria to divert host cell processes, such as VopS, IbpA and AnkX, and a vast majority of proteins of unknown functions. FIC proteins catalyze primarily the transfer of AMP (AMPylation), but they are not restricted to this PTM and also carry out other modifications, for example by phosphocholine or phosphate. In a recent twist, animal FICD/HYPE was shown to catalyze both AMPylation and de-AMPylation of the endoplasmic reticulum BIP chaperone to regulate the unfolded protein response. FICD shares structural features with some bacterial FIC proteins, raising the possibility that bacteria also encode such dual activities. In this review, we discuss how structural, biochemical and cellular approaches have fertilized each other to understand the mechanism, regulation and function of FIC proteins from bacterial pathogens to humans.
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Affiliation(s)
- Simon Veyron
- CNRS and Ecole normale supérieure Paris-Saclay, 94235 Cachan, France
| | - Gérald Peyroche
- CNRS and Ecole normale supérieure Paris-Saclay, 94235 Cachan, France
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30
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Moehlman AT, Casey AK, Servage K, Orth K, Krämer H. Adaptation to constant light requires Fic-mediated AMPylation of BiP to protect against reversible photoreceptor degeneration. eLife 2018; 7:e38752. [PMID: 30015618 PMCID: PMC6066327 DOI: 10.7554/elife.38752] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 07/16/2018] [Indexed: 12/13/2022] Open
Abstract
In response to environmental, developmental, and pathological stressors, cells engage homeostatic pathways to maintain their function. Among these pathways, the Unfolded Protein Response protects cells from the accumulation of misfolded proteins in the ER. Depending on ER stress levels, the ER-resident Fic protein catalyzes AMPylation or de-AMPylation of BiP, the major ER chaperone and regulator of the Unfolded Protein Response. This work elucidates the importance of the reversible AMPylation of BiP in maintaining the Drosophila visual system in response to stress. After 72 hr of constant light, photoreceptors of fic-null and AMPylation-resistant BiPT366A mutants, but not wild-type flies, display loss of synaptic function, disintegration of rhabdomeres, and excessive activation of ER stress reporters. Strikingly, this phenotype is reversible: photoreceptors regain their structure and function within 72 hr once returned to a standard light:dark cycle. These findings show that Fic-mediated AMPylation of BiP is required for neurons to adapt to transient stress demands.
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Affiliation(s)
- Andrew T Moehlman
- Department of NeuroscienceUT Southwestern Medical CenterDallasUnited States
| | - Amanda K Casey
- Department of Molecular BiologyUT Southwestern Medical CenterDallasUnited States
| | - Kelly Servage
- Department of Molecular BiologyUT Southwestern Medical CenterDallasUnited States
- Department of BiochemistryUT Southwestern Medical CenterDallasUnited States
- Howard Hughes Medical InstituteDallasUnited States
| | - Kim Orth
- Department of Molecular BiologyUT Southwestern Medical CenterDallasUnited States
- Department of BiochemistryUT Southwestern Medical CenterDallasUnited States
- Howard Hughes Medical InstituteDallasUnited States
| | - Helmut Krämer
- Department of NeuroscienceUT Southwestern Medical CenterDallasUnited States
- Department of Cell BiologyUT Southwestern Medical CenterDallasUnited States
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31
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Abstract
Posttranslational modifications are covalent changes made to proteins that typically alter the function or location of the protein. AMPylation is an emerging posttranslational modification that involves the addition of adenosine monophosphate (AMP) to a protein. Like other, more well-studied posttranslational modifications, AMPylation is predicted to regulate the activity of the modified target proteins. However, the scope of this modification both in bacteria and in eukaryotes remains to be fully determined. In this review, we provide an up to date overview of the known AMPylating enzymes, the regulation of these enzymes, and the effect of this modification on target proteins.
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Affiliation(s)
- Amanda K. Casey
- Department of Molecular Biology, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard NA5.120F, Dallas, Texas 75390-9148, United States
| | - Kim Orth
- Department of Molecular Biology, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard NA5.120F, Dallas, Texas 75390-9148, United States
- Howard Hughes Medical Institute, 6000 Harry Hines Boulevard NA5.120F, Dallas, Texas 75390-9148, United States
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