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Measuring Antibacterial Autophagy

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Autophagy

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1880))

Abstract

Bacteria that escape from membrane-enclosed vacuoles to the cytosol of cells are targeted by autophagy, which recognizes and captures bacteria into autophagosomes wherein their proliferation is restricted. Here we discuss two means by which antibacterial autophagy is assessed: (1) the visualization and enumeration of autophagy protein recruitment to the vicinity of cytosolic bacteria by means of immunofluorescence microscopy and (2) the measurement of autophagy-dependent restriction of bacterial proliferation by means of colony-forming unit assay.

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References

  1. Randow F, MacMicking JD, James LC (2013) Cellular self-defense: how cell-autonomous immunity protects against pathogens. Science 340:701–706. https://doi.org/10.1038/nm.3108

    Article  CAS  PubMed  Google Scholar 

  2. Deretic V, Saitoh T, Akira S (2013) Autophagy in infection, inflammation and immunity. Nat Rev Immunol 13:722–737. https://doi.org/10.1038/nri3532

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Boyle KB, Randow F (2013) The role of “eat-me” signals and autophagy cargo receptors in innate immunity. Curr Opin Microbiol 16:339–348. https://doi.org/10.1016/j.mib.2013.03.010

    Article  CAS  PubMed  Google Scholar 

  4. Huang J, Brumell JH (2014) Bacteria-autophagy interplay: a battle for survival. Nat Rev Microbiol 12:101–114. https://doi.org/10.1038/nrmicro3160

    Article  CAS  PubMed  Google Scholar 

  5. Noad J, von der Malsburg A, Pathe C et al (2017) LUBAC-synthesized linear ubiquitin chains restrict cytosol-invading bacteria by activating autophagy and NF-κB. Nat Microbiol 2:17063. https://doi.org/10.1038/nmicrobiol.2017.63

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Ogawa M, Yoshimori T, Suzuki T et al (2005) Escape of intracellular Shigella from autophagy. Science 307:727–731. https://doi.org/10.1126/science.1106036

    Article  CAS  PubMed  Google Scholar 

  7. Dupont N, Lacas-Gervais S, Bertout J et al (2009) Shigella phagocytic vacuolar membrane remnants participate in the cellular response to pathogen invasion and are regulated by autophagy. Cell Host Microbe 6:137–149

    Article  CAS  Google Scholar 

  8. Thurston TLM, Wandel MP, von Muhlinen N et al (2012) Galectin 8 targets damaged vesicles for autophagy to defend cells against bacterial invasion. Nature 482:414–418. https://doi.org/10.1038/nature10744

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Perrin AJ, Jiang X, Birmingham CL et al (2004) Recognition of bacteria in the cytosol of mammalian cells by the ubiquitin system. Curr Biol 14:806–811. https://doi.org/10.1016/j.cub.2004.04.033

    Article  CAS  PubMed  Google Scholar 

  10. Fiskin E, Bionda T, Dikic I, Behrends C (2016) Global analysis of host and bacterial ubiquitinome in response to Salmonella Typhimurium infection. Mol Cell 62:967–981. https://doi.org/10.1016/j.molcel.2016.04.015

    Article  CAS  PubMed  Google Scholar 

  11. Fujita N, Morita E, Itoh T et al (2013) Recruitment of the autophagic machinery to endosomes during infection is mediated by ubiquitin. J Cell Biol 203:115–128. https://doi.org/10.1083/jcb.201304188

    Article  PubMed  PubMed Central  Google Scholar 

  12. Thurston TLM, Ryzhakov G, Bloor S et al (2009) The TBK1 adaptor and autophagy receptor NDP52 restricts the proliferation of ubiquitin-coated bacteria. Nat Immunol 10:1215–1221. https://doi.org/10.1038/ni.1800

    Article  PubMed  Google Scholar 

  13. Patel JC, Hueffer K, Lam TT, Galan JE (2009) Diversification of a Salmonella virulence protein function by ubiquitin-dependent differential localization. Cell 137:283–294. https://doi.org/10.1016/j.cell.2009.01.056

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Mizushima N, Yoshimori T, Ohsumi Y (2011) The role of Atg proteins in autophagosome formation. Annu Rev Cell Dev Biol 27:107–132. https://doi.org/10.1146/annurev-cellbio-092910-154005

    Article  CAS  PubMed  Google Scholar 

  15. Shibutani ST, Yoshimori T (2014) Autophagosome formation in response to intracellular bacterial invasion. Cell Microbiol 16:1619–1626. https://doi.org/10.1111/cmi.12357

    Article  CAS  PubMed  Google Scholar 

  16. von Muhlinen N, Akutsu M, Ravenhill BJ et al (2012) LC3C, bound selectively by a noncanonical LIR motif in NDP52, is required for antibacterial autophagy. Mol Cell 48:329–342. https://doi.org/10.1016/j.molcel.2012.08.024

    Article  CAS  Google Scholar 

  17. Randow F, Sale JE (2006) Retroviral transduction of DT40. In: Buerstedde J-M, Takeda S (eds) Reviews and protocols in DT40 research: subcellular biochemistry. Springer, Dordrecht, pp 383–386

    Chapter  Google Scholar 

  18. Kageyama S, Omori H, Saitoh T et al (2011) The LC3 recruitment mechanism is separate from Atg9L1-dependent membrane formation in the autophagic response against Salmonella. Mol Biol Cell 22:2290–2300. https://doi.org/10.1091/mbc.E10-11-0893

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Sanjuan MA, Dillon CP, Tait SWG et al (2007) Toll-like receptor signalling in macrophages links the autophagy pathway to phagocytosis. Nature 450:1253–1257. https://doi.org/10.1038/nature06421

    Article  CAS  PubMed  Google Scholar 

  20. Mehta P, Henault J, Kolbeck R, Sanjuan MA (2014) Noncanonical autophagy: one small step for LC3, one giant leap for immunity. Curr Opin Immunol 26:69–75. https://doi.org/10.1016/j.coi.2013.10.012

    Article  CAS  PubMed  Google Scholar 

  21. Malik-Kale P, Winfree S, Steele-Mortimer O (2012) The bimodal lifestyle of intracellular Salmonella in epithelial cells: replication in the cytosol obscures defects in vacuolar replication. PLoS One 7:e38732. https://doi.org/10.1371/journal.pone.0038732

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Boettcher M, McManus MT (2015) Choosing the right tool for the job: RNAi, TALEN, or CRISPR. Mol Cell 58:575–585. https://doi.org/10.1016/j.molcel.2015.04.028

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgments

This work was supported by the MRC (U105170648) and the Wellcome Trust (WT104752MA).

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Correspondence to Felix Randow .

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Boyle, K.B., Randow, F. (2019). Measuring Antibacterial Autophagy. In: Ktistakis, N., Florey, O. (eds) Autophagy. Methods in Molecular Biology, vol 1880. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8873-0_45

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  • DOI: https://doi.org/10.1007/978-1-4939-8873-0_45

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-8872-3

  • Online ISBN: 978-1-4939-8873-0

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