1
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Burns AR, Wiedrick J, Feryn A, Maes M, Midha MK, Baxter DH, Morrone SR, Prokop TJ, Kapil C, Hoopmann MR, Kusebauch U, Deutsch EW, Rappaport N, Watanabe K, Moritz RL, Miller RA, Lapidus JA, Orwoll ES. Proteomic changes induced by longevity-promoting interventions in mice. GeroScience 2024; 46:1543-1560. [PMID: 37653270 PMCID: PMC10828338 DOI: 10.1007/s11357-023-00917-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/20/2023] [Indexed: 09/02/2023] Open
Abstract
Using mouse models and high-throughput proteomics, we conducted an in-depth analysis of the proteome changes induced in response to seven interventions known to increase mouse lifespan. This included two genetic mutations, a growth hormone receptor knockout (GHRKO mice) and a mutation in the Pit-1 locus (Snell dwarf mice), four drug treatments (rapamycin, acarbose, canagliflozin, and 17α-estradiol), and caloric restriction. Each of the interventions studied induced variable changes in the concentrations of proteins across liver, kidney, and gastrocnemius muscle tissue samples, with the strongest responses in the liver and limited concordance in protein responses across tissues. To the extent that these interventions promote longevity through common biological mechanisms, we anticipated that proteins associated with longevity could be identified by characterizing shared responses across all or multiple interventions. Many of the proteome alterations induced by each intervention were distinct, potentially implicating a variety of biological pathways as being related to lifespan extension. While we found no protein that was affected similarly by every intervention, we identified a set of proteins that responded to multiple interventions. These proteins were functionally diverse but tended to be involved in peroxisomal oxidation and metabolism of fatty acids. These results provide candidate proteins and biological mechanisms related to enhancing longevity that can inform research on therapeutic approaches to promote healthy aging.
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Affiliation(s)
- Adam R Burns
- Biostatistics & Design Program, Oregon Health & Science University, Portland, OR, USA.
| | - Jack Wiedrick
- Biostatistics & Design Program, Oregon Health & Science University, Portland, OR, USA
| | - Alicia Feryn
- Biostatistics & Design Program, Oregon Health & Science University, Portland, OR, USA
| | - Michal Maes
- Institute for Systems Biology, Seattle, WA, USA
| | | | | | | | | | - Charu Kapil
- Institute for Systems Biology, Seattle, WA, USA
| | | | | | | | | | | | | | - Richard A Miller
- Department of Pathology and Geriatrics Center, University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Jodi A Lapidus
- School of Public Health, Oregon Health & Science University-Portland State University, Portland, OR, USA
| | - Eric S Orwoll
- Department of Endocrinology, Oregon Health & Science University, Portland, OR, USA
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2
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Watanabe K, Wilmanski T, Baloni P, Robinson M, Garcia GG, Hoopmann MR, Midha MK, Baxter DH, Maes M, Morrone SR, Crebs KM, Kapil C, Kusebauch U, Wiedrick J, Lapidus J, Pflieger L, Lausted C, Roach JC, Glusman G, Cummings SR, Schork NJ, Price ND, Hood L, Miller RA, Moritz RL, Rappaport N. Author Correction: Lifespan-extending interventions induce consistent patterns of fatty acid oxidation in mouse livers. Commun Biol 2023; 6:1208. [PMID: 38012377 PMCID: PMC10682460 DOI: 10.1038/s42003-023-05549-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023] Open
Affiliation(s)
| | | | - Priyanka Baloni
- School of Health Sciences, Purdue University, West Lafayette, IN, USA
| | | | - Gonzalo G Garcia
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, MI, USA
| | | | | | | | - Michal Maes
- Institute for Systems Biology, Seattle, WA, USA
| | | | | | - Charu Kapil
- Institute for Systems Biology, Seattle, WA, USA
| | | | - Jack Wiedrick
- Oregon Health and Science University, Portland, OR, USA
| | - Jodi Lapidus
- Oregon Health and Science University, Portland, OR, USA
| | - Lance Pflieger
- Institute for Systems Biology, Seattle, WA, USA
- Phenome Health, Seattle, WA, USA
| | | | | | | | - Steven R Cummings
- San Francisco Coordinating Center, California Pacific Medical Center Research Institute, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Nicholas J Schork
- Department of Quantitative Medicine, The Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
- Department of Population Sciences and Molecular and Cell Biology, The City of Hope National Medical Center, Duarte, CA, USA
| | - Nathan D Price
- Institute for Systems Biology, Seattle, WA, USA
- Thorne HealthTech, New York, NY, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Leroy Hood
- Institute for Systems Biology, Seattle, WA, USA.
- Phenome Health, Seattle, WA, USA.
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA.
- Department of Immunology, University of Washington, Seattle, WA, USA.
| | - Richard A Miller
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, MI, USA
- University of Michigan Geriatrics Center, Ann Arbor, MI, USA
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3
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Watanabe K, Wilmanski T, Baloni P, Robinson M, Garcia GG, Hoopmann MR, Midha MK, Baxter DH, Maes M, Morrone SR, Crebs KM, Kapil C, Kusebauch U, Wiedrick J, Lapidus J, Pflieger L, Lausted C, Roach JC, Glusman G, Cummings SR, Schork NJ, Price ND, Hood L, Miller RA, Moritz RL, Rappaport N. Lifespan-extending interventions induce consistent patterns of fatty acid oxidation in mouse livers. Commun Biol 2023; 6:768. [PMID: 37481675 PMCID: PMC10363145 DOI: 10.1038/s42003-023-05128-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 07/10/2023] [Indexed: 07/24/2023] Open
Abstract
Aging manifests as progressive deteriorations in homeostasis, requiring systems-level perspectives to investigate the gradual molecular dysregulation of underlying biological processes. Here, we report systemic changes in the molecular regulation of biological processes under multiple lifespan-extending interventions. Differential Rank Conservation (DIRAC) analyses of mouse liver proteomics and transcriptomics data show that mechanistically distinct lifespan-extending interventions (acarbose, 17α-estradiol, rapamycin, and calorie restriction) generally tighten the regulation of biological modules. These tightening patterns are similar across the interventions, particularly in processes such as fatty acid oxidation, immune response, and stress response. Differences in DIRAC patterns between proteins and transcripts highlight specific modules which may be tightened via augmented cap-independent translation. Moreover, the systemic shifts in fatty acid metabolism are supported through integrated analysis of liver transcriptomics data with a mouse genome-scale metabolic model. Our findings highlight the power of systems-level approaches for identifying and characterizing the biological processes involved in aging and longevity.
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Affiliation(s)
| | | | - Priyanka Baloni
- School of Health Sciences, Purdue University, West Lafayette, IN, USA
| | | | - Gonzalo G Garcia
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, MI, USA
| | | | | | | | - Michal Maes
- Institute for Systems Biology, Seattle, WA, USA
| | | | | | - Charu Kapil
- Institute for Systems Biology, Seattle, WA, USA
| | | | - Jack Wiedrick
- Oregon Health and Science University, Portland, OR, USA
| | - Jodi Lapidus
- Oregon Health and Science University, Portland, OR, USA
| | - Lance Pflieger
- Institute for Systems Biology, Seattle, WA, USA
- Phenome Health, Seattle, WA, USA
| | | | | | | | - Steven R Cummings
- San Francisco Coordinating Center, California Pacific Medical Center Research Institute, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Nicholas J Schork
- Department of Quantitative Medicine, The Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
- Department of Population Sciences and Molecular and Cell Biology, The City of Hope National Medical Center, Duarte, CA, USA
| | - Nathan D Price
- Institute for Systems Biology, Seattle, WA, USA
- Thorne HealthTech, New York, NY, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Leroy Hood
- Institute for Systems Biology, Seattle, WA, USA.
- Phenome Health, Seattle, WA, USA.
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA.
- Department of Immunology, University of Washington, Seattle, WA, USA.
| | - Richard A Miller
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, MI, USA
- University of Michigan Geriatrics Center, Ann Arbor, MI, USA
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Midha MK, Kapil C, Maes M, Baxter DH, Morrone SR, Prokop TJ, Moritz RL. Vacuum Insulated Probe Heated Electrospray Ionization Source Enhances Microflow Rate Chromatography Signals in the Bruker timsTOF Mass Spectrometer. J Proteome Res 2023; 22:2525-2537. [PMID: 37294184 PMCID: PMC11060334 DOI: 10.1021/acs.jproteome.3c00305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
By far the largest contribution to ion detectability in liquid chromatography-driven mass spectrometry-based proteomics is the efficient generation of peptide molecular ions by the electrospray source. To maximize the transfer of peptides from the liquid to gaseous phase and allow molecular ions to enter the mass spectrometer at microspray flow rates, an efficient electrospray process is required. Here we describe the superior performance of newly design vacuum insulated probe heated electrospray ionization (VIP-HESI) source coupled to a Bruker timsTOF PRO mass spectrometer operated in microspray mode. VIP-HESI significantly improves chromatography signals in comparison to electrospray ionization (ESI) and nanospray ionization using the captivespray (CS) source and provides increased protein detection with higher quantitative precision, enhancing reproducibility of sample injection amounts. Protein quantitation of human K562 lymphoblast samples displayed excellent chromatographic retention time reproducibility (<10% coefficient of variation (CV)) with no signal degradation over extended periods of time, and a mouse plasma proteome analysis identified 12% more plasma protein groups allowing large-scale analysis to proceed with confidence (1,267 proteins at 0.4% CV). We show that the Slice-PASEF VIP-HESI mode is sensitive in identifying low amounts of peptide without losing quantitative precision. We demonstrate that VIP-HESI coupled with microflow rate chromatography achieves a higher depth of coverage and run-to-run reproducibility for a broad range of proteomic applications. Data and spectral libraries are available via ProteomeXchange (PXD040497).
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Affiliation(s)
- Mukul K Midha
- Institute for Systems Biology, 401 Terry Avenue N, Seattle, Washington 98109, United States
| | - Charu Kapil
- Institute for Systems Biology, 401 Terry Avenue N, Seattle, Washington 98109, United States
| | - Michal Maes
- Institute for Systems Biology, 401 Terry Avenue N, Seattle, Washington 98109, United States
| | - David H Baxter
- Institute for Systems Biology, 401 Terry Avenue N, Seattle, Washington 98109, United States
| | - Seamus R Morrone
- Institute for Systems Biology, 401 Terry Avenue N, Seattle, Washington 98109, United States
| | - Timothy J Prokop
- Institute for Systems Biology, 401 Terry Avenue N, Seattle, Washington 98109, United States
| | - Robert L Moritz
- Institute for Systems Biology, 401 Terry Avenue N, Seattle, Washington 98109, United States
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5
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Midha MK, Kapil C, Maes M, Baxter DH, Morrone SR, Prokop TJ, Moritz RL. Vacuum Insulated Probe Heated ElectroSpray Ionization source (VIP-HESI) enhances micro flow rate chromatography signals in the Bruker timsTOF mass spectrometer. bioRxiv 2023:2023.02.15.528699. [PMID: 36824828 PMCID: PMC9949110 DOI: 10.1101/2023.02.15.528699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
By far the largest contribution to ion detectability in liquid chromatography-driven mass spectrometry-based proteomics is the efficient generation of peptide ions by the electrospray source. To maximize the transfer of peptides from liquid to a gaseous phase to allow molecular ions to enter the mass spectrometer at micro-spray flow rates, an efficient electrospray process is required. Here we describe superior performance of new Vacuum-Insulated-Probe-Heated-ElectroSpray-Ionization source (VIP-HESI) coupled with micro-spray flow rate chromatography and Bruker timsTOF PRO mass spectrometer. VIP-HESI significantly improves chromatography signals in comparison to nano-spray ionization using the CaptiveSpray source and provides increased protein detection with higher quantitative precision, enhancing reproducibility of sample injection amounts. Protein quantitation of human K562 lymphoblast samples displayed excellent chromatographic retention time reproducibility (<10% coefficient-of-variation (CV)) with no signal degradation over extended periods of time, and a mouse plasma proteome analysis identified 12% more plasma protein groups allowing large-scale analysis to proceed with confidence (1,267 proteins at 0.4% CV). We show that Slice-PASEF mode with VIP-HESI setup is sensitive in identifying low amounts of peptide without losing quantitative precision. We demonstrate that VIP-HESI coupled with micro-flow-rate chromatography achieves higher depth of coverage and run-to-run reproducibility for a broad range of proteomic applications.
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6
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Martyn GD, Veggiani G, Kusebauch U, Morrone SR, Yates BP, Singer AU, Tong J, Manczyk N, Gish G, Sun Z, Kurinov I, Sicheri F, Moran MF, Moritz RL, Sidhu SS. Engineered SH2 Domains for Targeted Phosphoproteomics. ACS Chem Biol 2022; 17:1472-1484. [PMID: 35613471 DOI: 10.1021/acschembio.2c00051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A comprehensive analysis of the phosphoproteome is essential for understanding molecular mechanisms of human diseases. However, current tools used to enrich phosphotyrosine (pTyr) are limited in their applicability and scope. Here, we engineered new superbinder Src-Homology 2 (SH2) domains that enrich diverse sets of pTyr-peptides. We used phage display to select a Fes-SH2 domain variant (superFes; sFes1) with high affinity for pTyr and solved its structure bound to a pTyr-peptide. We performed systematic structure-function analyses of the superbinding mechanisms of sFes1 and superSrc-SH2 (sSrc1), another SH2 superbinder. We grafted the superbinder motifs from sFes1 and sSrc1 into 17 additional SH2 domains and confirmed increased binding affinity for specific pTyr-peptides. Using mass spectrometry (MS), we demonstrated that SH2 superbinders have distinct specificity profiles and superior capabilities to enrich pTyr-peptides. Finally, using combinations of SH2 superbinders as affinity purification (AP) tools we showed that unique subsets of pTyr-peptides can be enriched with unparalleled depth and coverage.
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Affiliation(s)
- Gregory D. Martyn
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Gianluca Veggiani
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
| | - Ulrike Kusebauch
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Seamus R. Morrone
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Bradley P. Yates
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
| | - Alex U. Singer
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
| | - Jiefei Tong
- Program in Cell biology, Hospital for Sick Children, Toronto M5G 0A4, Canada
| | - Noah Manczyk
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Gerald Gish
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Zhi Sun
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Igor Kurinov
- Department of Chemistry and Chemical Biology, Cornell University, NE-CAT, Argonne, Illinois 60439, United States
| | - Frank Sicheri
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Michael F. Moran
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Program in Cell biology, Hospital for Sick Children, Toronto M5G 0A4, Canada
- The Hospital for Sick Children, SPARC Biocentre, Toronto, Ontario M5G 0A4, Canada
| | - Robert L. Moritz
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Sachdev S. Sidhu
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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7
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Maixner F, Sarhan MS, Huang KD, Tett A, Schoenafinger A, Zingale S, Blanco-Míguez A, Manghi P, Cemper-Kiesslich J, Rosendahl W, Kusebauch U, Morrone SR, Hoopmann MR, Rota-Stabelli O, Rattei T, Moritz RL, Oeggl K, Segata N, Zink A, Reschreiter H, Kowarik K. Hallstatt miners consumed blue cheese and beer during the Iron Age and retained a non-Westernized gut microbiome until the Baroque period. Curr Biol 2021; 31:5149-5162.e6. [PMID: 34648730 PMCID: PMC8660109 DOI: 10.1016/j.cub.2021.09.031] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/16/2021] [Accepted: 09/14/2021] [Indexed: 02/06/2023]
Abstract
We subjected human paleofeces dating from the Bronze Age to the Baroque period (18th century AD) to in-depth microscopic, metagenomic, and proteomic analyses. The paleofeces were preserved in the underground salt mines of the UNESCO World Heritage site of Hallstatt in Austria. This allowed us to reconstruct the diet of the former population and gain insights into their ancient gut microbiome composition. Our dietary survey identified bran and glumes of different cereals as some of the most prevalent plant fragments. This highly fibrous, carbohydrate-rich diet was supplemented with proteins from broad beans and occasionally with fruits, nuts, or animal food products. Due to these traditional dietary habits, all ancient miners up to the Baroque period have gut microbiome structures akin to modern non-Westernized individuals whose diets are also mainly composed of unprocessed foods and fresh fruits and vegetables. This may indicate a shift in the gut community composition of modern Westernized populations due to quite recent dietary and lifestyle changes. When we extended our microbial survey to fungi present in the paleofeces, in one of the Iron Age samples, we observed a high abundance of Penicillium roqueforti and Saccharomyces cerevisiae DNA. Genome-wide analysis indicates that both fungi were involved in food fermentation and provides the first molecular evidence for blue cheese and beer consumption in Iron Age Europe. Gut microbiome and diet of European salt miners determined using paleofeces Until the Baroque, the microbiome resembled that of modern non-Westernized people Food-fermenting fungi in Iron Age feces indicates blue cheese and beer consumption
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Affiliation(s)
- Frank Maixner
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy.
| | - Mohamed S Sarhan
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy
| | - Kun D Huang
- Department CIBIO, University of Trento, Via Sommarive 9, 38123 Povo (Trento), Italy; Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, Via Edmund Mach 1, 38010 San Michele all'Adige (TN), Italy
| | - Adrian Tett
- Department CIBIO, University of Trento, Via Sommarive 9, 38123 Povo (Trento), Italy; CUBE (Division of Computational Systems Biology), Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Alexander Schoenafinger
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy; Institute of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | - Stefania Zingale
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy
| | - Aitor Blanco-Míguez
- Department CIBIO, University of Trento, Via Sommarive 9, 38123 Povo (Trento), Italy
| | - Paolo Manghi
- Department CIBIO, University of Trento, Via Sommarive 9, 38123 Povo (Trento), Italy
| | - Jan Cemper-Kiesslich
- Interfaculty Department of Legal Medicine & Department of Classics, University of Salzburg, Ignaz-Harrer-Straße 79, 5020 Salzburg, Austria
| | - Wilfried Rosendahl
- Reiss-Engelhorn-Museen, Zeughaus C5, 68159 Mannheim, Germany; Curt-Egelhorn-Zentrum Archäomtrie, D6,3, 61859 Mannheim, Germany
| | - Ulrike Kusebauch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA
| | - Seamus R Morrone
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA
| | - Michael R Hoopmann
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA
| | - Omar Rota-Stabelli
- Center Agriculture Food Environment (C3A), University of Trento, 38010 San Michele all'Adige (TN), Italy
| | - Thomas Rattei
- CUBE (Division of Computational Systems Biology), Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Robert L Moritz
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA
| | - Klaus Oeggl
- Institute of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | - Nicola Segata
- Department CIBIO, University of Trento, Via Sommarive 9, 38123 Povo (Trento), Italy
| | - Albert Zink
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy
| | - Hans Reschreiter
- Prehistoric Department, Museum of Natural History Vienna, Burgring 7, 1010 Vienna, Austria
| | - Kerstin Kowarik
- Prehistoric Department, Museum of Natural History Vienna, Burgring 7, 1010 Vienna, Austria.
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8
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Morrone SR, Lok SM. Structural perspectives of antibody-dependent enhancement of infection of dengue virus. Curr Opin Virol 2019; 36:1-8. [PMID: 30844538 DOI: 10.1016/j.coviro.2019.02.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 01/29/2019] [Accepted: 02/04/2019] [Indexed: 12/30/2022]
Abstract
Dengue virus (DENV) consists of four serotypes. Sequential serotype infections can cause increased disease severity, likely due to antibody-dependent enhancement (ADE) of infection. Here, we review two recent papers showing major advancements in the understanding of the ADE mechanism for both mature and immature DENV. The surface of both mature and immature DENV contains E and another protein - M in mature and prM in immature virus. On mature DENV, the orientation of anti-E antibody with respect to the virus surface determines the antibody enhancement properties. On the immature virus, binding of anti-prM antibody aids the dissociation of pr from the fusion loop of E protein allowing virus-endosomal membrane interaction, thus overcoming the hurdle in the early step of fusion.
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Affiliation(s)
- Seamus R Morrone
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, KTP Building, 8 College Road, Singapore 169857, Singapore; Centre for BioImaging Sciences, National University of Singapore, Singapore 117557, Singapore
| | - Shee-Mei Lok
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, KTP Building, 8 College Road, Singapore 169857, Singapore; Centre for BioImaging Sciences, National University of Singapore, Singapore 117557, Singapore.
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9
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Stratmann SA, Morrone SR, van Oijen AM, Sohn J. The innate immune sensor IFI16 recognizes foreign DNA in the nucleus by scanning along the duplex. eLife 2015; 4:e11721. [PMID: 26673078 PMCID: PMC4829420 DOI: 10.7554/elife.11721] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 12/15/2015] [Indexed: 12/31/2022] Open
Abstract
The ability to recognize foreign double-stranded (ds)DNA of pathogenic origin in the intracellular environment is an essential defense mechanism of the human innate immune system. However, the molecular mechanisms underlying distinction between foreign DNA and host genomic material inside the nucleus are not understood. By combining biochemical assays and single-molecule techniques, we show that the nuclear innate immune sensor IFI16 one-dimensionally tracks long stretches of exposed foreign dsDNA to assemble into supramolecular signaling platforms. We also demonstrate that nucleosomes represent barriers that prevent IFI16 from targeting host DNA by directly interfering with these one-dimensional movements. This unique scanning-assisted assembly mechanism allows IFI16 to distinguish friend from foe and assemble into oligomers efficiently and selectively on foreign DNA.
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Affiliation(s)
| | - Seamus R Morrone
- Johns Hopkins University School of Medicine, Baltimore, United States
| | - Antoine M van Oijen
- University of Groningen, Groningen, Netherlands.,University of Wollongong, Wollongong, Australia
| | - Jungsan Sohn
- Johns Hopkins University School of Medicine, Baltimore, United States
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10
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Geertsema HJ, Schulte AC, Spenkelink LM, McGrath WJ, Morrone SR, Sohn J, Mangel WF, Robinson A, van Oijen AM. Single-molecule imaging at high fluorophore concentrations by local activation of dye. Biophys J 2015; 108:949-956. [PMID: 25692599 DOI: 10.1016/j.bpj.2014.12.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 12/08/2014] [Accepted: 12/10/2014] [Indexed: 10/24/2022] Open
Abstract
Single-molecule fluorescence microscopy is a powerful tool for observing biomolecular interactions with high spatial and temporal resolution. Detecting fluorescent signals from individual labeled proteins above high levels of background fluorescence remains challenging, however. For this reason, the concentrations of labeled proteins in in vitro assays are often kept low compared to their in vivo concentrations. Here, we present a new fluorescence imaging technique by which single fluorescent molecules can be observed in real time at high, physiologically relevant concentrations. The technique requires a protein and its macromolecular substrate to be labeled each with a different fluorophore. Making use of short-distance energy-transfer mechanisms, only the fluorescence from those proteins that bind to their substrate is activated. This approach is demonstrated by labeling a DNA substrate with an intercalating stain, exciting the stain, and using energy transfer from the stain to activate the fluorescence of only those labeled DNA-binding proteins bound to the DNA. Such an experimental design allowed us to observe the sequence-independent interaction of Cy5-labeled interferon-inducible protein 16 with DNA and the sliding via one-dimensional diffusion of Cy5-labeled adenovirus protease on DNA in the presence of a background of hundreds of nanomolar Cy5 fluorophore.
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Affiliation(s)
| | - Aartje C Schulte
- Zernike Institute for Advanced Materials, Groningen, The Netherlands
| | | | | | | | - Jungsan Sohn
- Johns Hopkins School of Medicine, Baltimore, Maryland
| | | | - Andrew Robinson
- Zernike Institute for Advanced Materials, Groningen, The Netherlands
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Morrone SR, Matyszewski M, Yu X, Delannoy M, Egelman EH, Sohn J. Assembly-driven activation of the AIM2 foreign-dsDNA sensor provides a polymerization template for downstream ASC. Nat Commun 2015. [PMID: 26197926 PMCID: PMC4525163 DOI: 10.1038/ncomms8827] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
AIM2 recognizes foreign dsDNA and assembles into the inflammasome, a filamentous supramolecular signalling platform required to launch innate immune responses. We show here that the pyrin domain of AIM2 (AIM2PYD) drives both filament formation and dsDNA binding. In addition, the dsDNA-binding domain of AIM2 also oligomerizes and assists in filament formation. The ability to oligomerize is critical for binding dsDNA, and in turn permits the size of dsDNA to regulate the assembly of the AIM2 polymers. The AIM2PYD oligomers define the filamentous structure, and the helical symmetry of the AIM2PYD filament is consistent with the filament assembled by the PYD of the downstream adaptor ASC. Our results suggest that the role of AIM2PYD is not autoinhibitory, but generating a structural template by coupling ligand binding and oligomerization is a key signal transduction mechanism in the AIM2 inflammasome. The AIM2 inflammasome complex is essential for defence against a number of human pathogens but how it assembles upon recognition of foreign DNA remains incompletely understood. Here Morrone et al. suggest the AIM2 pyrin domain acts in both DNA binding and filament assembly to generate a structural template for complex assembly.
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Affiliation(s)
- Seamus R Morrone
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine Baltimore, Maryland 21205, USA
| | - Mariusz Matyszewski
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine Baltimore, Maryland 21205, USA
| | - Xiong Yu
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine Charlottesville, Virginia 22908, USA
| | - Michael Delannoy
- Microscope Core Facilities, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine Charlottesville, Virginia 22908, USA
| | - Jungsan Sohn
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine Baltimore, Maryland 21205, USA
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