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Ravenhill BJ, Boyle KB, von Muhlinen N, Ellison CJ, Masson GR, Otten EG, Foeglein A, Williams R, Randow F. The Cargo Receptor NDP52 Initiates Selective Autophagy by Recruiting the ULK Complex to Cytosol-Invading Bacteria. Mol Cell 2019; 74:320-329.e6. [PMID: 30853402 PMCID: PMC6477152 DOI: 10.1016/j.molcel.2019.01.041] [Citation(s) in RCA: 188] [Impact Index Per Article: 37.6] [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: 06/01/2018] [Revised: 11/19/2018] [Accepted: 01/29/2019] [Indexed: 12/27/2022]
Abstract
Xenophagy, a selective autophagy pathway that protects the cytosol against bacterial invasion, relies on cargo receptors that juxtapose bacteria and phagophore membranes. Whether phagophores are recruited from a constitutive pool or are generated de novo at prospective cargo remains unknown. Phagophore formation in situ would require recruitment of the upstream autophagy machinery to prospective cargo. Here, we show that, essential for anti-bacterial autophagy, the cargo receptor NDP52 forms a trimeric complex with FIP200 and SINTBAD/NAP1, which are subunits of the autophagy-initiating ULK and the TBK1 kinase complex, respectively. FIP200 and SINTBAD/NAP1 are each recruited independently to bacteria via NDP52, as revealed by selective point mutations in their respective binding sites, but only in their combined presence does xenophagy proceed. Such recruitment of the upstream autophagy machinery by NDP52 reveals how detection of cargo-associated “eat me” signals, induction of autophagy, and juxtaposition of cargo and phagophores are integrated in higher eukaryotes. NDP52 recruits upstream autophagy machinery to damaged Salmonella-containing vacuoles NDP52 trimerizes with the ULK subunit FIP200 and the TBK1 adaptor SINTBAD NDP52-dependent recruitment of FIP200-ULK and SINTBAD-TBK1 required for xenophagy Recruitment of ULK and TBK1 complexes promotes phagophore formation in situ
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Affiliation(s)
- Benjamin J Ravenhill
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Keith B Boyle
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Natalia von Muhlinen
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Cara J Ellison
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Glenn R Masson
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Elsje G Otten
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Agnes Foeglein
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Roger Williams
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Felix Randow
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Addenbrooke's Hospital, Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK.
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Thurston TL, Boyle KB, Allen M, Ravenhill BJ, Karpiyevich M, Bloor S, Kaul A, Noad J, Foeglein A, Matthews SA, Komander D, Bycroft M, Randow F. Recruitment of TBK1 to cytosol-invading Salmonella induces WIPI2-dependent antibacterial autophagy. EMBO J 2016; 35:1779-92. [PMID: 27370208 PMCID: PMC5010046 DOI: 10.15252/embj.201694491] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 05/24/2016] [Indexed: 01/01/2023] Open
Abstract
Mammalian cells deploy autophagy to defend their cytosol against bacterial invaders. Anti‐bacterial autophagy relies on the core autophagy machinery, cargo receptors, and “eat‐me” signals such as galectin‐8 and ubiquitin that label bacteria as autophagy cargo. Anti‐bacterial autophagy also requires the kinase TBK1, whose role in autophagy has remained enigmatic. Here we show that recruitment of WIPI2, itself essential for anti‐bacterial autophagy, is dependent on the localization of catalytically active TBK1 to the vicinity of cytosolic bacteria. Experimental manipulation of TBK1 recruitment revealed that engagement of TBK1 with any of a variety of Salmonella‐associated “eat‐me” signals, including host‐derived glycans and K48‐ and K63‐linked ubiquitin chains, suffices to restrict bacterial proliferation. Promiscuity in recruiting TBK1 via independent signals may buffer TBK1 functionality from potential bacterial antagonism and thus be of evolutionary advantage to the host.
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Affiliation(s)
- Teresa Lm Thurston
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Keith B Boyle
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Mark Allen
- Division of Structural Studies, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Benjamin J Ravenhill
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Maryia Karpiyevich
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Stuart Bloor
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Annie Kaul
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Jessica Noad
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Agnes Foeglein
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Sophie A Matthews
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - David Komander
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Mark Bycroft
- Division of Structural Studies, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Felix Randow
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
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Loucaides EM, von Kirchbach JC, Foeglein A, Sharps J, Fodor E, Digard P. Nuclear dynamics of influenza A virus ribonucleoproteins revealed by live-cell imaging studies. Virology 2009; 394:154-63. [PMID: 19744689 PMCID: PMC2771073 DOI: 10.1016/j.virol.2009.08.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2009] [Revised: 07/06/2009] [Accepted: 08/07/2009] [Indexed: 11/25/2022]
Abstract
The negative sense RNA genome of influenza A virus is transcribed and replicated in the nuclei of infected cells by the viral RNA polymerase. Only four viral polypeptides are required but multiple cellular components are potentially involved. We used fluorescence recovery after photobleaching (FRAP) to characterise the dynamics of GFP-tagged viral ribonucleoprotein (RNP) components in living cells. The nucleoprotein (NP) displayed very slow mobility that significantly increased on formation of transcriptionally active RNPs. Conversely, single or dimeric polymerase subunits showed fast nuclear dynamics that decreased upon formation of heterotrimers, suggesting increased interaction of the full polymerase complex with a relatively immobile cellular component(s). Treatment with inhibitors of cellular transcription indicated that in part, this reflected an interaction with cellular RNA polymerase II. Analysis of mutated influenza virus polymerase complexes further suggested that this was through an interaction between PB2 and RNA Pol II separate from PB2 cap-binding activity.
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Affiliation(s)
- Eva M Loucaides
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
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Foeglein A, Walter H. Determination of HIV-1 coreceptor tropism in clinical practise. Eur J Med Res 2007; 12:473-482. [PMID: 17933729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023] Open
Abstract
Several studies showed that the upcoming drug class of CCR5 coreceptor antagonists have potent virological and immunological activity in treatment experienced patients. In patients failing a CCR5 antagonists-based regimen, the emergence of CXCR4-tropic viral variants has been demonstrated. Clonal analysis of viral isolates from a limited number of patients revealed that these CXCR4-tropic strains did not develop by mutation of a CCR5-tropic virus during therapy, but emerged from a minor population of CXCR4-tropic variants already present in the patients at baseline. Obviously, screening for CXCR4-tropic strains with a functional assay and subsequent exclusion of positive individuals from clinical studies could not completely avoid the selection of CXCR4-tropic strains during failure. But emergence of CXCR4-tropic viruses on therapy may require a critical threshold of CXCR4 viral load at baseline, which may not be the case in patients with a very low proportion of CXCR4-using variants. Therefore, this review addresses to what extent currently available methods are suitable to detect CXCR4-tropic strains in clinical settings. Available functional assays are based on recombinant viruses. These assays are generally restricted to a few laboratories and cannot be easily included in daily clinical settings. Whereas minority detection limits of sequence analyses are generally high with 15 to 30%, functional assays achieve lower detection limits for minorities of 5%. Sequence analyses require an additional interpretation step, and the accuracy of interpretation from clinical samples by current predictions systems has to be improved. In consequence, new methods are arising: genotyping may be improved by hybridisation assays, which quantify CXCR4-tropic viruses by their homology down to 1% minorities, and functional non-infectious cell fusion assays may overcome security restrictions and make phenotypic methods suitable for routine clinical laboratory practise. The highly sensitive detection of CXCR4-tropic viruses may provide the opportunity to clarify the conditions of clinical relevance for CXCR4-tropic minorities.
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Affiliation(s)
- Agnes Foeglein
- National Reference Center for Human Retroviruses, Institute for Clinical and Molecular Virology at the University of Erlangen-Nuremberg, Germany
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