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Wang T, Song X, Tan J, Xian W, Zhou X, Yu M, Wang X, Xu Y, Wu T, Yuan K, Ran Y, Yang B, Fan G, Liu X, Zhou Y, Zhu Y. Legionella effector LnaB is a phosphoryl AMPylase that impairs phosphosignalling. Nature 2024; 631:393-401. [PMID: 38776962 DOI: 10.1038/s41586-024-07573-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 05/16/2024] [Indexed: 05/25/2024]
Abstract
AMPylation is a post-translational modification in which AMP is added to the amino acid side chains of proteins1,2. Here we show that, with ATP as the ligand and actin as the host activator, the effector protein LnaB of Legionella pneumophila exhibits AMPylase activity towards the phosphoryl group of phosphoribose on PRR42-Ub that is generated by the SidE family of effectors, and deubiquitinases DupA and DupB in an E1- and E2-independent ubiquitination process3-7. The product of LnaB is further hydrolysed by an ADP-ribosylhydrolase, MavL, to Ub, thereby preventing the accumulation of PRR42-Ub and ADPRR42-Ub and protecting canonical ubiquitination in host cells. LnaB represents a large family of AMPylases that adopt a common structural fold, distinct from those of the previously known AMPylases, and LnaB homologues are found in more than 20 species of bacterial pathogens. Moreover, LnaB also exhibits robust phosphoryl AMPylase activity towards phosphorylated residues and produces unique ADPylation modifications in proteins. During infection, LnaB AMPylates the conserved phosphorylated tyrosine residues in the activation loop of the Src family of kinases8,9, which dampens downstream phosphorylation signalling in the host. Structural studies reveal the actin-dependent activation and catalytic mechanisms of the LnaB family of AMPylases. This study identifies, to our knowledge, an unprecedented molecular regulation mechanism in bacterial pathogenesis and protein phosphorylation.
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Affiliation(s)
- Ting Wang
- Department of Gastroenterology of the Second Affiliated Hospital, School of Medicine and College of Animal Sciences, Life Sciences Institute, Zhejiang University, Hangzhou, China
- MOE Key Laboratory of Biosystems Homeostasis and Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xiaonan Song
- Department of Gastroenterology of the Second Affiliated Hospital, School of Medicine and College of Animal Sciences, Life Sciences Institute, Zhejiang University, Hangzhou, China
- MOE Key Laboratory of Biosystems Homeostasis and Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jiaxing Tan
- Department of Gastroenterology of the Second Affiliated Hospital, School of Medicine and College of Animal Sciences, Life Sciences Institute, Zhejiang University, Hangzhou, China
- MOE Key Laboratory of Biosystems Homeostasis and Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Shanghai Institute for Advanced Study, Zhejiang University, Shanghai, China
| | - Wei Xian
- Department of Microbiology and Infectious Disease Center, NHC Key Laboratory of Medical Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Xingtong Zhou
- Department of Gastroenterology of the Second Affiliated Hospital, School of Medicine and College of Animal Sciences, Life Sciences Institute, Zhejiang University, Hangzhou, China
- MOE Key Laboratory of Biosystems Homeostasis and Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Mingru Yu
- Department of Gastroenterology of the Second Affiliated Hospital, School of Medicine and College of Animal Sciences, Life Sciences Institute, Zhejiang University, Hangzhou, China
- MOE Key Laboratory of Biosystems Homeostasis and Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xiaofei Wang
- Department of Gastroenterology of the Second Affiliated Hospital, School of Medicine and College of Animal Sciences, Life Sciences Institute, Zhejiang University, Hangzhou, China
- MOE Key Laboratory of Biosystems Homeostasis and Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Yan Xu
- Department of Gastroenterology of the Second Affiliated Hospital, School of Medicine and College of Animal Sciences, Life Sciences Institute, Zhejiang University, Hangzhou, China
- MOE Key Laboratory of Biosystems Homeostasis and Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Ting Wu
- MOE Key Laboratory of Biosystems Homeostasis and Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Keke Yuan
- Department of Gastroenterology of the Second Affiliated Hospital, School of Medicine and College of Animal Sciences, Life Sciences Institute, Zhejiang University, Hangzhou, China
- MOE Key Laboratory of Biosystems Homeostasis and Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yu Ran
- MOE Key Laboratory of Biosystems Homeostasis and Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Bing Yang
- MOE Key Laboratory of Biosystems Homeostasis and Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Gaofeng Fan
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xiaoyun Liu
- Department of Microbiology and Infectious Disease Center, NHC Key Laboratory of Medical Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.
| | - Yan Zhou
- Department of Gastroenterology of the Second Affiliated Hospital, School of Medicine and College of Animal Sciences, Life Sciences Institute, Zhejiang University, Hangzhou, China.
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, China.
| | - Yongqun Zhu
- Department of Gastroenterology of the Second Affiliated Hospital, School of Medicine and College of Animal Sciences, Life Sciences Institute, Zhejiang University, Hangzhou, China.
- MOE Key Laboratory of Biosystems Homeostasis and Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China.
- Shanghai Institute for Advanced Study, Zhejiang University, Shanghai, China.
- State Key Laboratory of Transvascular Implantation Devices, Hangzhou, China.
- MOA Key Laboratory of Animal Virology, Center for Veterinary Sciences, Zhejiang University, Hangzhou, China.
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2
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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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3
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Fatima N, Best OG, Belov L, Christopherson RI. The effect of HYPE knock-out on the AMPylome of human OSU-CLL leukemia cells. Leuk Lymphoma 2024; 65:242-249. [PMID: 37933638 DOI: 10.1080/10428194.2023.2275530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/22/2023] [Indexed: 11/08/2023]
Abstract
In humans, AMPylation of cellular proteins is carried out by Huntingtin yeast-interacting protein E (HYPE), activated under conditions of endoplasmic reticulum stress, such as in cancer cells. Extracts of the human chronic lymphocytic leukemia cell line, OSU-CLL, were fractionated using immuno-precipitation with antibodies against adenosine-phosphate and then AMP-Tyr. The proteins isolated were modified with AMP, the 'AMPylome.' AMP-labelled peptides isolated from HYPE wild-type (WT) and HYPE knock-out (KO) cells were identified using tandem mass spectrometry. A total of 213 proteins were identified from WT cell extracts, while only 23 of these were pulled down from KO cells, consistent with the presence of another AMPylator, besides HYPE. The KO cells were more sensitive to fludarabine nucleoside (2-FaraA) than WT cells. Ingenuity Pathway Analysis of the AMPylated proteins identified in WT cells clustered actin binding proteins of the cytoskeleton, and proteins of the RHO GTPase pathway that would jointly stimulate cell proliferation.
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Affiliation(s)
- Narjis Fatima
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - O Giles Best
- College of Medicine and Public Health, Flinders University, Bedford Park, South Australia, Australia
| | - Larissa Belov
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
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JIang W, Dong J, Zhang W, Huang Z, Guo T, Zhang K, Jiang X, Du T. Development and Validation of a Prognostic Model based on 11 E3-related Genes for Colon Cancer Patients. Curr Pharm Des 2024; 30:935-951. [PMID: 38898815 DOI: 10.2174/0113816128292398240306160051] [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: 11/14/2023] [Accepted: 02/06/2024] [Indexed: 06/21/2024]
Abstract
BACKGROUND Colon cancer is a common tumor in the gastrointestinal tract with a poor prognosis. According to research reports, ubiquitin-dependent modification systems have been found to play a crucial role in the development and advancement of different types of malignant tumors, including colon cancer. However, further investigation is required to fully understand the mechanism of ubiquitination in colon cancer. METHODS We collected the RNA expression matrix of the E3 ubiquitin ligase-related genes (E3RGs) from the patients with colon adenocarcinoma (COAD) using The Cancer Genome Atlas program (TCGA). The "limma" package was used to obtain differentially expressed E3RGs between COAD and adjacent normal tissues. Then, univariate COX regression and least absolute shrinkage and selection operator (LASSO) analysis were performed to construct the prognostic signature and nomogram model. Afterward, we used the original copy number variation data of COAD to find potential somatic mutation and employed the "pRRophetic" package to investigate the disparity in the effectiveness of chemotherapy drugs between high and low-risk groups. The RT-qPCR was also implied to detect mRNA expression levels in tumor tissues. RESULTS A total of 137 differentially expressed E3RG3 were screened and 11 genes (CORO2B, KCTD9, RNF32, BACH2, RBCK1, DPH7, WDR78, UCHL1, TRIM58, WDR72, and ZBTB18) were identified for the construction of prognostic signatures. The Kaplan-Meier curve showed a worse prognosis for patients with high risk both in the training and test cohorts (P = 1.037e-05, P = 5.704e-03), and the area under the curve (AUC) was 0.728 and 0.892 in the training and test cohorts, respectively. Based on the stratified analysis, this 11- E3RGs signature was a novel and attractive prognostic model independent of several clinicopathological parameters (age, sex, stage, TNM) in COAD. The DEGs were subjected to GO and KEGG analysis, which identified pathways associated with cancer progression. These pathways included the cAMP signaling pathway, calcium signaling pathway, Wnt signaling pathway, signaling pathways regulating stem cell pluripotency, and proteoglycans in cancer. Additionally, immune infiltration analysis revealed significant differences in the infiltration of macrophages M0, T cells follicular helper, and plasma cells between the two groups. CONCLUSION We developed a novel independent risk model consisting of 11 E3RGs and verified the effectiveness of this model in test cohorts, providing important insights into survival prediction in COAD and several promising targets for COAD therapy.
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Affiliation(s)
- Wanju JIang
- Department of Gastrointestinal Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Jiaxing Dong
- Department of Gastrointestinal Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Wenjia Zhang
- Department of Respiratory Medicine, Shanghai Tenth Peoples Hospital, Tongji University, Shanghai 200072, China
| | - Zhiye Huang
- Department of Gastrointestinal Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Taohua Guo
- Department of Gastrointestinal Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Kehui Zhang
- Department of Gastrointestinal Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Xiaohua Jiang
- Department of Gastrointestinal Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Tao Du
- Department of Gastrointestinal Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai 200092, China
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5
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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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6
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Ghosh S, Kundu R, Chandana M, Das R, Anand A, Beura S, Bobde RC, Jain V, Prabhu SR, Behera PK, Mohanty AK, Chakrapani M, Satyamoorthy K, Suryawanshi AR, Dixit A, Padmanaban G, Nagaraj VA. Distinct evolution of type I glutamine synthetase in Plasmodium and its species-specific requirement. Nat Commun 2023; 14:4216. [PMID: 37452051 PMCID: PMC10349072 DOI: 10.1038/s41467-023-39670-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/22/2023] [Indexed: 07/18/2023] Open
Abstract
Malaria parasite lacks canonical pathways for amino acid biosynthesis and depends primarily on hemoglobin degradation and extracellular resources for amino acids. Interestingly, a putative gene for glutamine synthetase (GS) is retained despite glutamine being an abundant amino acid in human and mosquito hosts. Here we show Plasmodium GS has evolved as a unique type I enzyme with distinct structural and regulatory properties to adapt to the asexual niche. Methionine sulfoximine (MSO) and phosphinothricin (PPT) inhibit parasite GS activity. GS is localized to the parasite cytosol and abundantly expressed in all the life cycle stages. Parasite GS displays species-specific requirement in Plasmodium falciparum (Pf) having asparagine-rich proteome. Targeting PfGS affects asparagine levels and inhibits protein synthesis through eIF2α phosphorylation leading to parasite death. Exposure of artemisinin-resistant Pf parasites to MSO and PPT inhibits the emergence of viable parasites upon artemisinin treatment.
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Affiliation(s)
- Sourav Ghosh
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
- Regional Centre for Biotechnology, Faridabad, 121001, Haryana, India
| | - Rajib Kundu
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
- Regional Centre for Biotechnology, Faridabad, 121001, Haryana, India
| | - Manjunatha Chandana
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, 751024, Odisha, India
| | - Rahul Das
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
- Regional Centre for Biotechnology, Faridabad, 121001, Haryana, India
| | - Aditya Anand
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
- Regional Centre for Biotechnology, Faridabad, 121001, Haryana, India
| | - Subhashree Beura
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
| | - Ruchir Chandrakant Bobde
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
- Regional Centre for Biotechnology, Faridabad, 121001, Haryana, India
| | - Vishal Jain
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
| | - Sowmya Ramakant Prabhu
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | | | - Akshaya Kumar Mohanty
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
- Ispat General Hospital, Sector 19, Rourkela, 769005, Odisha, India
| | - Mahabala Chakrapani
- Department of Medicine, Kasturba Medical College, Mangalore, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | | | - Anshuman Dixit
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
| | - Govindarajan Padmanaban
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, Karnataka, India
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7
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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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8
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Abstract
RNA ligases are present across all forms of life. While enzymatic RNA ligation between 5'-PO4 and 3'-OH termini is prevalent in viruses, fungi, and plants, such RNA ligases are yet to be identified in vertebrates. Here, using a nucleotide-based chemical probe targeting human AMPylated proteome, we have enriched and identified the hitherto uncharacterised human protein chromosome 12 open reading frame 29 (C12orf29) as a human enzyme promoting RNA ligation between 5'-PO4 and 3'-OH termini. C12orf29 catalyses ATP-dependent RNA ligation via a three-step mechanism, involving tandem auto- and RNA AMPylation. Knock-out of C12ORF29 gene impedes the cellular resilience to oxidative stress featuring concurrent RNA degradation, which suggests a role of C12orf29 in maintaining RNA integrity. These data provide the groundwork for establishing a human RNA repair pathway.
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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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Rebelo AP, Ruiz A, Dohrn MF, Wayand M, Farooq A, Danzi MC, Beijer D, Aaron B, Vandrovcova J, Houlden H, Matalonga L, Abreu L, Rouleau G, Estiar MA, Van de Vondel L, Gan-Or Z, Baets J, Schüle R, Zuchner S. BiP inactivation due to loss of the deAMPylation function of FICD causes a motor neuron disease. Genet Med 2022; 24:2487-2500. [PMID: 36136088 DOI: 10.1016/j.gim.2022.08.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 08/21/2022] [Accepted: 08/22/2022] [Indexed: 12/14/2022] Open
Abstract
PURPOSE The chaperone protein BiP is the master regulator of the unfolded protein response in the endoplasmic reticulum. BiP chaperone activity is regulated by the post-translational modification AMPylation, exclusively provided by FICD. We investigated whether FICD variants identified in patients with motor neuron disease could interfere with BiP activity regulation. METHODS Exome sequencing was performed to identify causative pathogenic variants associated with motor neuron diseases. Functional studies were conducted on fibroblasts from patients to explore the molecular mechanism of the disease. RESULTS We identified biallelic variants in FICD causing a neurodegenerative disease of upper and lower motor neurons. Affected individuals harbor a specific missense variant, Arg374His, positioned in the catalytic motif of the enzyme and important for adenosine triphosphate binding. The mutated residue abolishes intramolecular interaction with the regulatory residue Glu234, essential to inhibit AMPylation and to promote de-AMPylation by FICD. Consequently, fibroblasts from patients with FICD variants have abnormally increased levels of AMPylated and thus inactivated BiP. CONCLUSION Loss of BiP chaperone activity in patients likely results in a chronic impairment of the protein quality control system in the endoplasmic reticulum. These findings will guide the development of therapeutic strategies for motoneuron and related diseases linked to proteotoxic stress.
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Affiliation(s)
- Adriana P Rebelo
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL
| | - Ariel Ruiz
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL
| | - Maike F Dohrn
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL; Department of Neurology, Medical Faculty RWTH Aachen University, Aachen, Germany
| | - Melanie Wayand
- 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
| | - Amjad Farooq
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL
| | - Matt C Danzi
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL
| | - Danique Beijer
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL
| | - Brooke Aaron
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL
| | - Jana Vandrovcova
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Leslie Matalonga
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Lisa Abreu
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL
| | - Guy Rouleau
- Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada; The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montreal, Quebec, Canada; Department of Neurology and Neurosurgery, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
| | - Mehrdad A Estiar
- Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada; The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montreal, Quebec, Canada; Department of Neurology and Neurosurgery, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
| | - Liedewei Van de Vondel
- Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Ziv Gan-Or
- Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada; The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montreal, Quebec, Canada; Department of Neurology and Neurosurgery, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
| | - Jonathan Baets
- Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium; Neuromuscular Reference Center, Antwerp University Hospital and Faculty of Medicine University of Antwerp, Antwerp, Belgium
| | - Rebecca Schüle
- 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, Miller School of Medicine, University of Miami, Miami, FL.
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11
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Weixler L, Ikenga NJ, Voorneveld J, Aydin G, Bolte TMHR, Momoh J, Bütepage M, Golzmann A, Lüscher B, Filippov DV, Žaja R, Feijs KLH. Protein and RNA ADP-ribosylation detection is influenced by sample preparation and reagents used. Life Sci Alliance 2022; 6:6/1/e202201455. [PMID: 36368907 PMCID: PMC9652768 DOI: 10.26508/lsa.202201455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 10/18/2022] [Accepted: 10/19/2022] [Indexed: 11/13/2022] Open
Abstract
The modification of substrates with ADP-ribose (ADPr) is important in, for example, antiviral immunity and cancer. Recently, several reagents were developed to detect ADP-ribosylation; however, it is unknown whether they recognise ADPr, specific amino acid-ADPr linkages, or ADPr with the surrounding protein backbone. We first optimised methods to prepare extracts containing ADPr-proteins and observe that depending on the amino acid modified, the modification is heatlabile. We tested the reactivity of available reagents with diverse ADP-ribosylated protein and RNA substrates and observed that not all reagents are equally suited for all substrates. Next, we determined cross-reactivity with adenylylated RNA, AMPylated proteins, and metabolites, including NADH, which are detected by some reagents. Lastly, we analysed ADP-ribosylation using confocal microscopy, where depending on the fixation method, either mitochondrion, nucleus, or nucleolus is stained. This study allows future work dissecting the function of ADP-ribosylation in cells, both on protein and on RNA substrates, as we optimised sample preparation methods and have defined the reagents suitable for specific methods and substrates.
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Affiliation(s)
- Lisa Weixler
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Nonso Josephat Ikenga
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Jim Voorneveld
- Leiden Institute of Chemistry, Leiden University Department of Bioorganic Synthesis, Leiden, Netherlands
| | - Gülcan Aydin
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Timo MHR Bolte
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Jeffrey Momoh
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Mareike Bütepage
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Alexandra Golzmann
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Dmitri V Filippov
- Leiden Institute of Chemistry, Leiden University Department of Bioorganic Synthesis, Leiden, Netherlands
| | - Roko Žaja
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Karla LH Feijs
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany,Correspondence: ;
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12
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Mukherjee M, Sreelatha A. Identification of selenoprotein O substrates using a biotinylated ATP analog. Methods Enzymol 2021; 662:275-296. [PMID: 35101215 DOI: 10.1016/bs.mie.2021.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Selenoprotein O is one of 25 human selenoproteins that incorporate the 21st amino acid selenocysteine. Recent studies have revealed a previously undocumented mechanism of redox regulation by which SelO protects cells from oxidative damage. SelO catalyzes the covalent addition of AMP from ATP to the hydroxyl side chain of protein substrates in a post translational modification known as AMPylation. Although AMPylation was discovered over 50 years ago, methods to detect and enrich substrates are limited. Here, we describe protocols to clone, purify, and identify the substrates of bacterial SelO using a biotinylated ATP analog. Identification of SelO substrates and the functional consequences of AMPylation will illuminate the significance of this evolutionarily conserved selenoprotein.
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Affiliation(s)
- Meghomukta Mukherjee
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Anju Sreelatha
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, United States; Center for Mineral Metabolism and Clinical Research, University of Texas Southwestern Medical Center, Dallas, TX, United States.
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13
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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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14
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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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15
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Rauh T, Brameyer S, Kielkowski P, Jung K, Sieber SA. MS-Based in Situ Proteomics Reveals AMPylation of Host Proteins during Bacterial Infection. ACS Infect Dis 2020; 6:3277-3289. [PMID: 33259205 PMCID: PMC9558369 DOI: 10.1021/acsinfecdis.0c00740] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
![]()
Bacteria utilize versatile strategies
to propagate infections within
human cells, e.g., by the injection of effector proteins,
which alter crucial signaling pathways. One class of such virulence-associated
proteins is involved in the AMPylation of eukaryotic Rho GTPases with
devastating effects on viability. In order to get an inventory of
AMPylated proteins, several technologies have been developed. However,
as they were designed for the analysis of cell lysates, knowledge
about AMPylation targets in living cells is largely lacking. Here,
we implement a chemical-proteomic method for deciphering AMPylated
host proteins in situ during bacterial infection.
HeLa cells treated with a previously established cell permeable pronucleotide
probe (pro-N6pA) were infected with Vibrio parahaemolyticus, and modified host proteins were identified upon probe enrichment
and LC-MS/MS analysis. Three already known targets of the AMPylator
VopS—Rac1, RhoA, and Cdc42—could be confirmed, and several
other Rho GTPases were additionally identified. These hits were validated
in comparative studies with V. parahaemolyticus wild type and a mutant producing an inactive VopS (H348A). The method
further allowed to decipher the sites of modification and facilitated
a time-dependent analysis of AMPylation during infection. Overall,
the methodology provides a reliable detection of host AMPylation in situ and thus a versatile tool in monitoring infection
processes.
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Affiliation(s)
- Theresa Rauh
- Department of Chemistry, Chair of Organic Chemistry II, Center for Functional Protein Assemblies (CPA), Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Sophie Brameyer
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Pavel Kielkowski
- Department of Chemistry, Ludwig-Maximilians-Universität München, 81377 München, Germany
| | - Kirsten Jung
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Stephan A. Sieber
- Department of Chemistry, Chair of Organic Chemistry II, Center for Functional Protein Assemblies (CPA), Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
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