References
- Armstrong JA, Hart PD. Response of cultured macrophages to Mycobacterium tuberculosis, with observations on fusion of lysosomes with phagosomes. J Exp Med. 1971;134:713–740.
- Rich KA, Burkett C, Webster P. Cytoplasmic bacteria can be targets for autophagy. Cell Microbiol. 2003;5:455–468.
- Gutierrez MG, Master SS, Singh SB, et al. Autophagy is a defense mechanism inhibiting BCG and Mycobacterium tuberculosis survival in infected macrophages. Cell. 2004;119:753–766.
- Nakagawa I, Amano A, Mizushima N, et al. Autophagy defends cells against invading group A Streptococcus. Science. 2004;306:1037–1040.
- Deretic V, Levine B. Autophagy, immunity, and microbial adaptations. Cell Host Microbe. 2018;8:527–549.
- Huang J, Brumell JH. Bacteria-autophagy interplay: a battle for survival. Nat Rev Microbiol. 2014;12:101–114.
- Birmingham CL, Smith AC, Bakowski MA, et al. Autophagy controls Salmonella infection in response to damage to the Salmonella-containing vacuole. J Biol Chem. 2006;281:11374–11383.
- Zheng YT, Shahnazari S, Brech A, et al. The adaptor protein p62/SQSTM1 targets invading bacteria to the autophagy pathway. J Immunol. 2009;183:5909–5916.
- Fujita N, Morita E, Itoh T, et al. Recruitment of the autophagic machinery to endosomes during infection is mediated by ubiquitin. J Cell Biol. 2013;203:115–128.
- Alpuche-Aranda CM, Racoosin EL, Swanson JA, et al. Salmonella stimulate macrophage macropinocytosis and persist within spacious phagosomes. J Exp Med. 1994;179:601–608.
- McGourty K, Thurston TL, Matthews SA, et al. Salmonella inhibits retrograde trafficking of mannose-6-phosphate receptors and lysosome function. Science. 2012;338:963–967.
- Tattoli I, Sorbara MT, Vuckovic D, et al. Amino acid starvation induced by invasive bacterial pathogens triggers an innate host defense program. Cell Host Microbe. 2012;11:563–575.
- Ganesan R, Hos NJ, Gutierrez S, et al. Salmonella Typhimurium disrupts Sirt1/AMPK checkpoint control of mTOR to impair autophagy. PLoS Pathog. 2017;13:e1006227.
- Benjamin JL, Sumpter R Jr., Levine B, et al. Intestinal epithelial autophagy is essential for host defense against invasive bacteria. Cell Host Microbe. 2013;13:723–734.
- Travassos LH, Carneiro LA, Ramjeet M, et al. Nod1 and Nod2 direct autophagy by recruiting ATG16L1 to the plasma membrane at the site of bacterial entry. Nat Immunol. 2010;11:55–62.
- Shoji-Kawata S, Sumpter R, Leveno M, et al. Identification of a candidate therapeutic autophagy-inducing peptide. Nature. 2013;494:201–206.
- Chauhan S, Ahmed Z, Bradfute SB, et al. Pharmaceutical screen identifies novel target processes for activation of autophagy with a broad translational potential. Nat Commun. 2015;6:8620.
- Kuo SY, Castoreno AB, Aldrich LN, et al. Small-molecule enhancers of autophagy modulate cellular disease phenotypes suggested by human genetics. Proc Natl Acad Sci U S A. 2015;112:E4281–7.
- Lapierre LR, De Magalhaes Filho CD, McQuary PR, et al. The TFEB orthologue HLH-30 regulates autophagy and modulates longevity in Caenorhabditis elegans. Nat Commun. 2013;4:2267.
- Najibi M, Labed SA, Visvikis O, et al. An evolutionarily conserved PLC-PKD-TFEB pathway for host defense. Cell Rep. 2016;15:1728–1742.
- Sardiello M, Palmieri M, Di Ronza A, et al. A gene network regulating lysosomal biogenesis and function. Science. 2009;325:473–477.
- Settembre C, Di Malta C, Polito VA, et al. TFEB links autophagy to lysosomal biogenesis. Science. 2011;332:1429–1433.
- Roczniak-Ferguson A, Petit CS, Froehlich F, et al. The transcription factor TFEB links mTORC1 signaling to transcriptional control of lysosome homeostasis. Sci Signal. 2012;5:ra42.
- Parr C, Carzaniga R, Gentleman SM, et al. Glycogen synthase kinase 3 inhibition promotes lysosomal biogenesis and autophagic degradation of the amyloid-beta precursor protein. Mol Cell Biol. 2012;32:4410–4418.
- Settembre C, Zoncu R, Medina DL, et al. A lysosome-to-nucleus signalling mechanism senses and regulates the lysosome via mTOR and TFEB. Embo J. 2012;31:1095–1108.
- Medina DL, Di Paola S, Peluso I, et al. Lysosomal calcium signalling regulates autophagy through calcineurin and TFEB. Nat Cell Biol. 2015;17:288–299.
- Palmieri M, Pal R, Nelvagal HR, et al. mTORC1-independent TFEB activation via Akt inhibition promotes cellular clearance in neurodegenerative storage diseases. Nat Commun. 2017;8:14338.
- Mishra P, Dauphinee AN, Ward C, et al. Discovery of pan autophagy inhibitors through a high-throughput screen highlights macroautophagy as an evolutionarily conserved process across 3 eukaryotic kingdoms. Autophagy. 2017;13:1556–1572.
- Mishra P, Rai S, Manjithaya R. A novel dual luciferase based high throughput assay to monitor autophagy in real time in yeast S. cerevisiae. Biochem Biophys Rep. 2017;11:138–146.
- Kim JJ, Lee HM, Shin DM, et al. Host cell autophagy activated by antibiotics is required for their effective antimycobacterial drug action. Cell Host Microbe. 2012;11:457–468.
- Matsumoto G, Shimogori T, Hattori N, et al. TBK1 controls autophagosomal engulfment of polyubiquitinated mitochondria through p62/SQSTM1 phosphorylation. Hum Mol Genet. 2015;24:4429–4442.
- Parmar N, Tamanoi F. Rheb G-proteins and the activation of mTORC1. Enzymes. 2010;27:39–56.
- Casanova JE. Bacterial autophagy: offense and defense at the host-pathogen interface. Cell Mol Gastroenterol Hepatol. 2017;4:237–243.
- Escoll P, Rolando M, Buchrieser C. Modulation of host autophagy during bacterial infection: sabotaging host munitions for pathogen nutrition. Front Immunol. 2016;7:81.
- Zhang HW, Hu JJ, Fu RQ, et al. Flavonoids inhibit cell proliferation and induce apoptosis and autophagy through downregulation of PI3Kgamma mediated PI3K/AKT/mTOR/p70S6K/ULK signaling pathway in human breast cancer cells. Sci Rep. 2018;8:11255.
- Settembre C, Fraldi A, Medina DL, et al. Signals from the lysosome: a control centre for cellular clearance and energy metabolism. Nat Rev Mol Cell Biol. 2013;14:283–296.
- Martina JA, Chen Y, Gucek M, et al. MTORC1 functions as a transcriptional regulator of autophagy by preventing nuclear transport of TFEB. Autophagy. 2012;8:903–914.
- Puertollano R, Ferguson SM, Brugarolas J, et al. The complex relationship between TFEB transcription factor phosphorylation and subcellular localization. Embo J. 2018;37:e98804.
- Pastore N, Brady OA, Diab HI, et al. TFEB and TFE3 cooperate in the regulation of the innate immune response in activated macrophages. Autophagy. 2016;12:1240–1258.
- Gray MA, Choy CH, Dayam RM, et al. Phagocytosis enhances lysosomal and bactericidal properties by activating the transcription factor TFEB. Curr Biol. 2016;26:1955–1964.
- Visvikis O, Ihuegbu N, Labed SA, et al. Innate host defense requires TFEB-mediated transcription of cytoprotective and antimicrobial genes. Immunity. 2014;40:896–909.
- Conway KL, Kuballa P, Song JH, et al. Atg16l1 is required for autophagy in intestinal epithelial cells and protection of mice from Salmonella infection. Gastroenterology. 2013;145:1347–1357.
- Decressac M, Mattsson B, Weikop P, et al. TFEB-mediated autophagy rescues midbrain dopamine neurons from alpha-synuclein toxicity. Proc Natl Acad Sci U S A. 2013;110:E1817–26.
- Cheng B, Xu A, Qiao M, et al. BECN1s, a short splice variant of BECN1, functions in mitophagy. Autophagy. 2015;11:2048–2056.