1
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Bérouti M, Lammens K, Heiss M, Hansbauer L, Bauernfried S, Stöckl J, Pinci F, Piseddu I, Greulich W, Wang M, Jung C, Fröhlich T, Carell T, Hopfner KP, Hornung V. Lysosomal endonuclease RNase T2 and PLD exonucleases cooperatively generate RNA ligands for TLR7 activation. Immunity 2024; 57:1482-1496.e8. [PMID: 38697119 DOI: 10.1016/j.immuni.2024.04.010] [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: 10/16/2023] [Revised: 03/06/2024] [Accepted: 04/12/2024] [Indexed: 05/04/2024]
Abstract
Toll-like receptor 7 (TLR7) is essential for recognition of RNA viruses and initiation of antiviral immunity. TLR7 contains two ligand-binding pockets that recognize different RNA degradation products: pocket 1 recognizes guanosine, while pocket 2 coordinates pyrimidine-rich RNA fragments. We found that the endonuclease RNase T2, along with 5' exonucleases PLD3 and PLD4, collaboratively generate the ligands for TLR7. Specifically, RNase T2 generated guanosine 2',3'-cyclic monophosphate-terminated RNA fragments. PLD exonuclease activity further released the terminal 2',3'-cyclic guanosine monophosphate (2',3'-cGMP) to engage pocket 1 and was also needed to generate RNA fragments for pocket 2. Loss-of-function studies in cell lines and primary cells confirmed the critical requirement for PLD activity. Biochemical and structural studies showed that PLD enzymes form homodimers with two ligand-binding sites important for activity. Previously identified disease-associated PLD mutants failed to form stable dimers. Together, our data provide a mechanistic basis for the detection of RNA fragments by TLR7.
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Affiliation(s)
- Marleen Bérouti
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Katja Lammens
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Matthias Heiss
- Department of Chemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Larissa Hansbauer
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Stefan Bauernfried
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Jan Stöckl
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Francesca Pinci
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Ignazio Piseddu
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany; Department of Medicine II, University Hospital Munich, Munich, Germany
| | - Wilhelm Greulich
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Meiyue Wang
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Christophe Jung
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Thomas Fröhlich
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Thomas Carell
- Department of Chemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Karl-Peter Hopfner
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Veit Hornung
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany.
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2
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Ghosh G, Neely BA, Bland AM, Whitmer ER, Field CL, Duignan PJ, Janech MG. Identification of Candidate Protein Biomarkers Associated with Domoic Acid Toxicosis in Cerebrospinal Fluid of California Sea Lions ( Zalophus californianus). J Proteome Res 2024; 23:2419-2430. [PMID: 38807289 PMCID: PMC11232103 DOI: 10.1021/acs.jproteome.4c00103] [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: 02/13/2024] [Revised: 05/10/2024] [Accepted: 05/20/2024] [Indexed: 05/30/2024]
Abstract
Since 1998, California sea lion (Zalophus californianus) stranding events associated with domoic acid toxicosis (DAT) have consistently increased. Outside of direct measurement of domoic acid in bodily fluids at the time of stranding, there are no practical nonlethal clinical tests for the diagnosis of DAT that can be utilized in a rehabilitation facility. Proteomics analysis was conducted to discover candidate protein markers of DAT using cerebrospinal fluid from stranded California sea lions with acute DAT (n = 8), chronic DAT (n = 19), or without DAT (n = 13). A total of 2005 protein families were identified experiment-wide. A total of 83 proteins were significantly different in abundance across the three groups (adj. p < 0.05). MDH1, PLD3, ADAM22, YWHAG, VGF, and CLSTN1 could discriminate California sea lions with or without DAT (AuROC > 0.75). IGKV2D-28, PTRPF, KNG1, F2, and SNCB were able to discriminate acute DAT from chronic DAT (AuROC > 0.75). Proteins involved in alpha synuclein deposition were over-represented as classifiers of DAT, and many of these proteins have been implicated in a variety of neurodegenerative diseases. These proteins should be considered potential markers for DAT in California sea lions and should be prioritized for future validation studies as biomarkers.
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Affiliation(s)
- Gautam Ghosh
- Department of Biology, Grice Marine Laboratory, College of Charleston, Charleston, South Carolina 29412, United States
| | - Benjamin A Neely
- National Institute of Standards and Technology (NIST) Charleston, Charleston, South Carolina 29412, United States
| | - Alison M Bland
- Department of Biology, Grice Marine Laboratory, College of Charleston, Charleston, South Carolina 29412, United States
- Hollings Marine Laboratory, College of Charleston, Charleston, South Carolina 29412, United States
| | - Emily R Whitmer
- The Marine Mammal Center, 2000 Bunker Road, Sausalito, California 94965, United States
| | - Cara L Field
- The Marine Mammal Center, 2000 Bunker Road, Sausalito, California 94965, United States
| | - Pádraig J Duignan
- The Marine Mammal Center, 2000 Bunker Road, Sausalito, California 94965, United States
| | - Michael G Janech
- Department of Biology, Grice Marine Laboratory, College of Charleston, Charleston, South Carolina 29412, United States
- Hollings Marine Laboratory, College of Charleston, Charleston, South Carolina 29412, United States
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3
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Yuan M, Peng L, Huang D, Gavin A, Luan F, Tran J, Feng Z, Zhu X, Matteson J, Wilson IA, Nemazee D. Structural and mechanistic insights into disease-associated endolysosomal exonucleases PLD3 and PLD4. Structure 2024; 32:766-779.e7. [PMID: 38537643 PMCID: PMC11162324 DOI: 10.1016/j.str.2024.02.019] [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: 12/04/2023] [Revised: 02/12/2024] [Accepted: 02/29/2024] [Indexed: 04/09/2024]
Abstract
Endolysosomal exonucleases PLD3 and PLD4 (phospholipases D3 and D4) are associated with autoinflammatory and autoimmune diseases. We report structures of these enzymes, and the molecular basis of their catalysis. The structures reveal an intra-chain dimer topology forming a basic active site at the interface. Like other PLD superfamily members, PLD3 and PLD4 carry HxKxxxxD/E motifs and participate in phosphodiester-bond cleavage. The enzymes digest ssDNA and ssRNA in a 5'-to-3' manner and are blocked by 5'-phosphorylation. We captured structures in apo, intermediate, and product states and revealed a "link-and-release" two-step catalysis. We also unexpectedly demonstrated phosphatase activity via a covalent 3-phosphohistidine intermediate. PLD4 contains an extra hydrophobic clamp that stabilizes substrate and could affect oligonucleotide substrate preference and product release. Biochemical and structural analysis of disease-associated mutants of PLD3/4 demonstrated reduced enzyme activity or thermostability and the possible basis for disease association. Furthermore, these findings provide insight into therapeutic design.
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Affiliation(s)
- Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Linghang Peng
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Deli Huang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Amanda Gavin
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Fangkun Luan
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jenny Tran
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ziqi Feng
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jeanne Matteson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - David Nemazee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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4
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Roske Y, Cappel C, Cremer N, Hoffmann P, Koudelka T, Tholey A, Heinemann U, Daumke O, Damme M. Structural analysis of PLD3 reveals insights into the mechanism of lysosomal 5' exonuclease-mediated nucleic acid degradation. Nucleic Acids Res 2024; 52:370-384. [PMID: 37994783 PMCID: PMC10783504 DOI: 10.1093/nar/gkad1114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 10/31/2023] [Accepted: 11/15/2023] [Indexed: 11/24/2023] Open
Abstract
The phospholipase D (PLD) family is comprised of enzymes bearing phospholipase activity towards lipids or endo- and exonuclease activity towards nucleic acids. PLD3 is synthesized as a type II transmembrane protein and proteolytically cleaved in lysosomes, yielding a soluble active form. The deficiency of PLD3 leads to the slowed degradation of nucleic acids in lysosomes and chronic activation of nucleic acid-specific intracellular toll-like receptors. While the mechanism of PLD phospholipase activity has been extensively characterized, not much is known about how PLDs bind and hydrolyze nucleic acids. Here, we determined the high-resolution crystal structure of the luminal N-glycosylated domain of human PLD3 in its apo- and single-stranded DNA-bound forms. PLD3 has a typical phospholipase fold and forms homodimers with two independent catalytic centers via a newly identified dimerization interface. The structure of PLD3 in complex with an ssDNA-derived thymidine product in the catalytic center provides insights into the substrate binding mode of nucleic acids in the PLD family. Our structural data suggest a mechanism for substrate binding and nuclease activity in the PLD family and provide the structural basis to design immunomodulatory drugs targeting PLD3.
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Affiliation(s)
- Yvette Roske
- Structural Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Cedric Cappel
- Biochemical Institute, Kiel University, Kiel, Germany
| | - Nils Cremer
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Straβe 10, 13125 Berlin, Germany
| | | | - Tomas Koudelka
- Institute of Experimental Medicine, Kiel University, 24188 Kiel, Germany
| | - Andreas Tholey
- Institute of Experimental Medicine, Kiel University, 24188 Kiel, Germany
| | - Udo Heinemann
- Structural Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Oliver Daumke
- Structural Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Markus Damme
- Biochemical Institute, Kiel University, Kiel, Germany
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5
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Yuan M, Peng L, Huang D, Gavin A, Luan F, Tran J, Feng Z, Zhu X, Matteson J, Wilson IA, Nemazee D. Structural and mechanistic insights into disease-associated endolysosomal exonucleases PLD3 and PLD4. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.20.567917. [PMID: 38045427 PMCID: PMC10690185 DOI: 10.1101/2023.11.20.567917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Endolysosomal exonucleases PLD3 and PLD4 (phospholipases D3 and D4) are associated with autoinflammatory and autoimmune diseases. We report structures of these enzymes, and the molecular basis of their catalysis. The structures reveal an intra-chain dimer topology forming a basic active site at the interface. Like other PLD superfamily members, PLD3 and PLD4 carry HxKxxxxD/E motifs and participate in phosphodiester-bond cleavage. The enzymes digest ssDNA and ssRNA in a 5'-to-3' manner and are blocked by 5'-phosphorylation. We captured structures in apo, intermediate, and product states and revealed a 'link-and-release' two-step catalysis. We also unexpectedly demonstrated phosphatase activity via a covalent 3' phosphistidine intermediate. PLD4 contains an extra hydrophobic clamp that stabilizes substrate and could affect oligonucleotide substrate preference and product release. Biochemical and structural analysis of disease-associated mutants of PLD3/4 demonstrated reduced enzyme activity or thermostability and the possible basis for disease association. Furthermore, these findings provide insight into therapeutic design.
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Affiliation(s)
- Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- These authors contribute equally
| | - Linghang Peng
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- These authors contribute equally
| | - Deli Huang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- These authors contribute equally
- Present address: Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Amanda Gavin
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Fangkun Luan
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jenny Tran
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ziqi Feng
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jeanne Matteson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - David Nemazee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
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6
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Van Acker ZP, Perdok A, Hellemans R, North K, Vorsters I, Cappel C, Dehairs J, Swinnen JV, Sannerud R, Bretou M, Damme M, Annaert W. Phospholipase D3 degrades mitochondrial DNA to regulate nucleotide signaling and APP metabolism. Nat Commun 2023; 14:2847. [PMID: 37225734 DOI: 10.1038/s41467-023-38501-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 05/04/2023] [Indexed: 05/26/2023] Open
Abstract
Phospholipase D3 (PLD3) polymorphisms are linked to late-onset Alzheimer's disease (LOAD). Being a lysosomal 5'-3' exonuclease, its neuronal substrates remained unknown as well as how a defective lysosomal nucleotide catabolism connects to AD-proteinopathy. We identified mitochondrial DNA (mtDNA) as a major physiological substrate and show its manifest build-up in lysosomes of PLD3-defective cells. mtDNA accretion creates a degradative (proteolytic) bottleneck that presents at the ultrastructural level as a marked abundance of multilamellar bodies, often containing mitochondrial remnants, which correlates with increased PINK1-dependent mitophagy. Lysosomal leakage of mtDNA to the cytosol activates cGAS-STING signaling that upregulates autophagy and induces amyloid precursor C-terminal fragment (APP-CTF) and cholesterol accumulation. STING inhibition largely normalizes APP-CTF levels, whereas an APP knockout in PLD3-deficient backgrounds lowers STING activation and normalizes cholesterol biosynthesis. Collectively, we demonstrate molecular cross-talks through feedforward loops between lysosomal nucleotide turnover, cGAS-STING and APP metabolism that, when dysregulated, result in neuronal endolysosomal demise as observed in LOAD.
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Affiliation(s)
- Zoë P Van Acker
- Laboratory for Membrane Trafficking, VIB Center for Brain & Disease Research, Herestraat 49, box 602, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Herestraat 49, box 602, Leuven, Belgium
| | - Anika Perdok
- Laboratory for Membrane Trafficking, VIB Center for Brain & Disease Research, Herestraat 49, box 602, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Herestraat 49, box 602, Leuven, Belgium
| | - Ruben Hellemans
- Laboratory for Membrane Trafficking, VIB Center for Brain & Disease Research, Herestraat 49, box 602, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Herestraat 49, box 602, Leuven, Belgium
| | - Katherine North
- Laboratory for Membrane Trafficking, VIB Center for Brain & Disease Research, Herestraat 49, box 602, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Herestraat 49, box 602, Leuven, Belgium
| | - Inge Vorsters
- Laboratory for Membrane Trafficking, VIB Center for Brain & Disease Research, Herestraat 49, box 602, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Herestraat 49, box 602, Leuven, Belgium
| | - Cedric Cappel
- Laboratory for Molecular Cell Biology and Transgenic Research, Institute of Biochemistry, Christian-Albrechts-University Kiel, Otto-Hahn-Platz 9, Kiel, Germany
| | - Jonas Dehairs
- Laboratory of Lipid Metabolism & Cancer, Department of Oncology, KU Leuven, B-3000, Leuven, Belgium
| | - Johannes V Swinnen
- Laboratory of Lipid Metabolism & Cancer, Department of Oncology, KU Leuven, B-3000, Leuven, Belgium
| | - Ragna Sannerud
- Laboratory for Membrane Trafficking, VIB Center for Brain & Disease Research, Herestraat 49, box 602, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Herestraat 49, box 602, Leuven, Belgium
| | - Marine Bretou
- Laboratory for Membrane Trafficking, VIB Center for Brain & Disease Research, Herestraat 49, box 602, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Herestraat 49, box 602, Leuven, Belgium
| | - Markus Damme
- Laboratory for Molecular Cell Biology and Transgenic Research, Institute of Biochemistry, Christian-Albrechts-University Kiel, Otto-Hahn-Platz 9, Kiel, Germany
| | - Wim Annaert
- Laboratory for Membrane Trafficking, VIB Center for Brain & Disease Research, Herestraat 49, box 602, Leuven, Belgium.
- Department of Neurosciences, KU Leuven, Herestraat 49, box 602, Leuven, Belgium.
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7
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The role of lysosomes in metabolic and autoimmune diseases. Nat Rev Nephrol 2023; 19:366-383. [PMID: 36894628 DOI: 10.1038/s41581-023-00692-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2023] [Indexed: 03/11/2023]
Abstract
Lysosomes are catabolic organelles that contribute to the degradation of intracellular constituents through autophagy and of extracellular components through endocytosis, phagocytosis and macropinocytosis. They also have roles in secretory mechanisms, the generation of extracellular vesicles and certain cell death pathways. These functions make lysosomes central organelles in cell homeostasis, metabolic regulation and responses to environment changes including nutrient stresses, endoplasmic reticulum stress and defects in proteostasis. Lysosomes also have important roles in inflammation, antigen presentation and the maintenance of long-lived immune cells. Their functions are tightly regulated by transcriptional modulation via TFEB and TFE3, as well as by major signalling pathways that lead to activation of mTORC1 and mTORC2, lysosome motility and fusion with other compartments. Lysosome dysfunction and alterations in autophagy processes have been identified in a wide variety of diseases, including autoimmune, metabolic and kidney diseases. Deregulation of autophagy can contribute to inflammation, and lysosomal defects in immune cells and/or kidney cells have been reported in inflammatory and autoimmune pathologies with kidney involvement. Defects in lysosomal activity have also been identified in several pathologies with disturbances in proteostasis, including autoimmune and metabolic diseases such as Parkinson disease, diabetes mellitus and lysosomal storage diseases. Targeting lysosomes is therefore a potential therapeutic strategy to regulate inflammation and metabolism in a variety of pathologies.
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8
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Wang X, Liu S, Xiao R, Hu J, Li L, Ning Y, Lu F. Graphene-oxide-based bioassay for the fluorometric determination of agrC gene transcription in methicillin-resistant Staphylococcus aureus that uses nicking-enzyme-assisted target recycling and a hybridization chain reaction. Talanta 2022; 250:123714. [PMID: 35779362 DOI: 10.1016/j.talanta.2022.123714] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 06/18/2022] [Accepted: 06/23/2022] [Indexed: 10/17/2022]
Abstract
Herein, we report the development of a graphene-oxide-based (GO-based) fluorescent bioassay for determining agrC gene transcription (mRNA) in methicillin-resistant Staphylococcus aureus (MRSA). The design is based on nicking-enzyme-assisted (Nb.BbvcI-assisted) target recycling amplification (NATR) and a hybridization chain reaction (HCR). The system consists of a helper probe (HP), a molecular beacon (MB) probe, four hairpins, and endonuclease Nb.BbvcI, which plays a role in target recycling and signal amplification. In the absence of the target, all of the carboxyfluorescein-labeled (FAM-labeled) hairpins are adsorbed through π-stacking interactions onto the surface of GO, resulting in FAM signal quenching. When the target is added, three nucleic acid chains hybridize together to form a triple complex that is recognized by Nb.BbvCI. The MB probe is then cleaved by Nb.BbvCI to generate an HP/target complex and two new DNA fragments; the former is hybridized to another MB probe and enters the next round of reaction. The two newly reproduced DNA fragments induce a HCR with the assistance of hairpins 1-4 to create double-stranded DNA (dsDNA) products. These dsDNA products are repelled by GO and generate strong fluorescence at excitation/emission wavelengths of 480/514 nm. Importantly, synergy between FAM and the dsDNA-SYBR Green I duplex structure led to significantly amplified fluorescence and enhanced sensitivity. The bioassay showed a detection limit of 7.5 fM toward the target and a good linearity in the 10 fM to 100 pM range. The developed method was applied to monitor biofilm formation and study the mechanism of drug action, with satisfactory results obtained.
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Affiliation(s)
- Xiaoqi Wang
- Department of Microbiology, The Medicine School of Hunan University of Chinese Medicine, Changsha, Hunan, 410208, People's Republic of China
| | - Shiwu Liu
- Department of Microbiology, The Medicine School of Hunan University of Chinese Medicine, Changsha, Hunan, 410208, People's Republic of China
| | - Rong Xiao
- Department of Microbiology, The Medicine School of Hunan University of Chinese Medicine, Changsha, Hunan, 410208, People's Republic of China
| | - Jue Hu
- Department of Microbiology, The Medicine School of Hunan University of Chinese Medicine, Changsha, Hunan, 410208, People's Republic of China
| | - Ling Li
- Experimental Center of Molecular Biology, The Medicine School of Hunan University of Chinese Medicine, Changsha, Hunan, 410208, People's Republic of China
| | - Yi Ning
- Department of Microbiology, The Medicine School of Hunan University of Chinese Medicine, Changsha, Hunan, 410208, People's Republic of China.
| | - Fangguo Lu
- Department of Microbiology, The Medicine School of Hunan University of Chinese Medicine, Changsha, Hunan, 410208, People's Republic of China.
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9
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Becker T, Cappel C, Di Matteo F, Sonsalla G, Kaminska E, Spada F, Cappello S, Damme M, Kielkowski P. AMPylation profiling during neuronal differentiation reveals extensive variation on lysosomal proteins. iScience 2021; 24:103521. [PMID: 34917898 PMCID: PMC8668991 DOI: 10.1016/j.isci.2021.103521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 07/20/2021] [Accepted: 11/23/2021] [Indexed: 12/02/2022] Open
Abstract
Protein AMPylation is a posttranslational modification with an emerging role in neurodevelopment. In metazoans two highly conserved protein AMP-transferases together with a diverse group of AMPylated proteins have been identified using chemical proteomics and biochemical techniques. However, the function of AMPylation remains largely unknown. Particularly problematic is the localization of thus far identified AMPylated proteins and putative AMP-transferases. We show that protein AMPylation is likely a posttranslational modification of luminal lysosomal proteins characteristic in differentiating neurons. Through a combination of chemical proteomics, gel-based separation of modified and unmodified proteins, and an activity assay, we determine that the modified, lysosomal soluble form of exonuclease PLD3 increases dramatically during neuronal maturation and that AMPylation correlates with its catalytic activity. Together, our findings indicate that AMPylation is a so far unknown lysosomal posttranslational modification connected to neuronal differentiation and it may provide a molecular rationale behind lysosomal storage diseases and neurodegeneration. Profiling of AMPylation during neuronal differentiation AMPylation is a potential PTM of luminal lysosomal proteins Phos-tag gel enables the separation of non-AMPylated and AMPylated proteins The modified lysosomal soluble form of PLD3 increases during neuronal maturation
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Affiliation(s)
- Tobias Becker
- LMU Munich, Department of Chemistry, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Cedric Cappel
- University of Kiel, Institute of Biochemistry, Olshausenstr. 40, 24098 Kiel, Germany
| | - Francesco Di Matteo
- Max Planck Institute of Psychiatry, Kraepelinstraße 2, 80804 Munich, Germany.,International Max Planck Research School for Translational Psychiatry (IMPRS-TP), Kraepelinstraße 2-10, 80804 Munich, Germany
| | - Giovanna Sonsalla
- LMU Munich, Department of Physiological Genomics, Biomedical Center (BMC), Großhadernerstr. 9, 82152 Planegg, Germany.,Helmholtz Zentrum München, Institute for Stem Cell Research, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany.,Graduate School of Systemic Neurosciences (GSN), Großhadernerstr. 2, 82152 Planegg, Germany
| | - Ewelina Kaminska
- LMU Munich, Department of Chemistry, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Fabio Spada
- LMU Munich, Department of Chemistry, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Silvia Cappello
- Max Planck Institute of Psychiatry, Kraepelinstraße 2, 80804 Munich, Germany
| | - Markus Damme
- University of Kiel, Institute of Biochemistry, Olshausenstr. 40, 24098 Kiel, Germany
| | - Pavel Kielkowski
- LMU Munich, Department of Chemistry, Butenandtstr. 5-13, 81377 Munich, Germany
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10
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Van Acker ZP, Perdok A, Bretou M, Annaert W. The microglial lysosomal system in Alzheimer's disease: Guardian against proteinopathy. Ageing Res Rev 2021; 71:101444. [PMID: 34391945 DOI: 10.1016/j.arr.2021.101444] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/14/2021] [Accepted: 08/08/2021] [Indexed: 12/12/2022]
Abstract
Microglia, the brain-resident immune cells, play an essential role in the upkeep of brain homeostasis. They actively adapt into specific activation states based on cues from the microenvironment. One of these encompasses the activated response microglia (ARMs) phenotype. It arises along a healthy aging process and in a range of neurodegenerative diseases, including Alzheimer's disease (AD). As the phenotype is characterized by an increased lipid metabolism, phagocytosis rate, lysosomal protease content and secretion of neuroprotective agents, it leaves to reason that the phenotype is adapted in an attempt to restore homeostasis. This is important to the conundrum of inflammatory processes. Inflammation per se may not be deleterious; it is only when microglial reactions become chronic or the microglial subtype is made dysfunctional by (multiple) risk proteins with single-nucleotide polymorphisms that microglial involvement becomes deleterious instead of beneficial. Interestingly, the ARMs up- and downregulate many late-onset AD-associated risk factor genes, the products of which are particularly active in the endolysosomal system. Hence, in this review, we focus on how the endolysosomal system is placed at the crossroad of inflammation and microglial capacity to keep pace with degradation.
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Liu YH, Zhang HF, Jin JY, Wei YQ, Wang CY, Fan LL, Liu L. Case Report: A Homozygous Mutation (p.Y62X) of Phospholipase D3 May Lead to a New Leukoencephalopathy Syndrome. Front Aging Neurosci 2021; 13:671296. [PMID: 34267643 PMCID: PMC8276716 DOI: 10.3389/fnagi.2021.671296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/31/2021] [Indexed: 11/13/2022] Open
Abstract
Leukodystrophies are a heterogeneous group of inherited disorders with highly variable clinical manifestations and pathogenetic backgrounds. At present, variants in more than 20 genes have been described and may be responsible for different types of leukodystrophies. Members of the phospholipase D family of enzymes catalyze the hydrolysis of membrane phospholipids. Meanwhile, phospholipase D3 (PLD3) has also been found to exhibit single stranded DNA (ssDNA) acid 5' exonuclease activity. Variants in phospholipase D3 (PLD3) may increase the risk of Alzheimer's disease and spinocerebellar ataxia, but this hypothesis has not been fully confirmed. In this study, we identified a novel homozygous mutation (NM_012268.3: c.186C>G/ p.Y62X) of PLD3 in a consanguineous family with white matter lesions, hearing and vision loss, and kidney disease by whole exome sequencing. Real-time PCR revealed that the novel mutation may lead to non-sense-mediated messenger RNA (mRNA) decay. This may be the first case report on the homozygous mutation of PLD3 in patients worldwide. Our studies indicated that homozygous mutation of PLD3 may result in a novel leukoencephalopathy syndrome with white matter lesions, hearing and vision loss, and kidney disease.
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Affiliation(s)
- Yi-Hui Liu
- Department of Respiratory Medicine, Diagnosis and Treatment Center of Respiratory Disease, The Second Xiangya Hospital of Central South University, Changsha, China.,Department of Neurology, Affiliated Hospital of Yangzhou University, Yangzhou, China
| | - Hai-Feng Zhang
- Department of Neurology, Affiliated Hospital of Yangzhou University, Yangzhou, China
| | - Jie-Yuan Jin
- Department of Respiratory Medicine, Diagnosis and Treatment Center of Respiratory Disease, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Yan-Qiu Wei
- Department of Neurology, Affiliated Hospital of Yangzhou University, Yangzhou, China
| | - Chen-Yu Wang
- Department of Respiratory Medicine, Diagnosis and Treatment Center of Respiratory Disease, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Liang-Liang Fan
- Department of Respiratory Medicine, Diagnosis and Treatment Center of Respiratory Disease, The Second Xiangya Hospital of Central South University, Changsha, China.,Department of Cell Biology, The School of Life Sciences, Central South University, Changsha, China.,Hunan Key Laboratory of Animal Models for Human Disease, School of Life Sciences, Central South University, Changsha, China
| | - Lv Liu
- Department of Respiratory Medicine, Diagnosis and Treatment Center of Respiratory Disease, The Second Xiangya Hospital of Central South University, Changsha, China.,Department of Cell Biology, The School of Life Sciences, Central South University, Changsha, China
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Determination of Two Differently Manufactured Silicon Dioxide Nanoparticles by Cloud Point Extraction Approach in Intestinal Cells, Intestinal Barriers and Tissues. Int J Mol Sci 2021; 22:ijms22137035. [PMID: 34210022 PMCID: PMC8268481 DOI: 10.3390/ijms22137035] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/20/2021] [Accepted: 06/26/2021] [Indexed: 11/17/2022] Open
Abstract
Food additive amorphous silicon dioxide (SiO2) particles are manufactured by two different methods—precipitated and fumed procedures—which can induce different physicochemical properties and biological fates. In this study, precipitated and fumed SiO2 particles were characterized in terms of constituent particle size, hydrodynamic diameter, zeta potential, surface area, and solubility. Their fates in intestinal cells, intestinal barriers, and tissues after oral administration in rats were determined by optimizing Triton X-114-based cloud point extraction (CPE). The results demonstrate that the constituent particle sizes of precipitated and fumed SiO2 particles were similar, but their aggregate states differed from biofluid types, which also affect dissolution properties. Significantly higher cellular uptake, intestinal transport amount, and tissue accumulation of precipitated SiO2 than of fumed SiO2 was found. The intracellular fates of both types of particles in intestinal cells were primarily particle forms, but slowly decomposed into ions during intestinal transport and after distribution in the liver, and completely dissolved in the bloodstream and kidneys. These findings will provide crucial information for understanding and predicting the potential toxicity of food additive SiO2 after oral intake.
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