The exploitation of host autophagy and ubiquitin machinery by Mycobacterium tuberculosis in shaping immune responses and host defense during infection

References

• Mizushima N, Levine B, Longo DL. Autophagy in human diseases. N Engl J Med. 2020 Oct 15;383(16):1564–1576. 10.1056/NEJMra2022774
   PubMed Web of Science ®Google Scholar
• Mizushima N, Yoshimori T, Ohsumi Y. The role of Atg proteins in autophagosome formation. Annu Rev Cell Dev Biol. 2011;27(1):107–132.
   PubMed Web of Science ®Google Scholar
• Kimmey JM, Stallings CL. Bacterial Pathogens versus Autophagy: implications for Therapeutic Interventions. Trends Mol Med. 2016 Dec;22(12):1060–1076.
   PubMed Web of Science ®Google Scholar
• Swatek KN, Komander D. Ubiquitin modifications. Cell Res. 2016 Apr;26(4):399–422.
   PubMed Web of Science ®Google Scholar
• Hershko A, Ciechanover A. The ubiquitin system. Annu Rev Biochem. 1998;67(1):425–479.
   PubMedGoogle Scholar
• Kerscher O, Felberbaum R, Hochstrasser M. Modification of proteins by ubiquitin and ubiquitin-like proteins. Annu Rev Cell Dev Biol. 2006;22(1):159–180.
   PubMedGoogle Scholar
• Lin YH, Machner MP. Exploitation of the host cell ubiquitin machinery by microbial effector proteins. J Cell Sci. 2017 Jun 15; 130(12):1985–1996. 10.1242/jcs.188482
   PubMed Web of Science ®Google Scholar
• Liu J, Qian C, Cao X. Post-Translational Modification Control of Innate Immunity. Immunity. 2016 Jul 19;45(1):15–30. 10.1016/j.immuni.2016.06.020
   PubMed Web of Science ®Google Scholar
• Ribet D, Cossart P. Ubiquitin, SUMO, and NEDD8: key Targets of Bacterial Pathogens. Trends Cell Biol. 2018 Nov;28(11):926–940.
   PubMed Web of Science ®Google Scholar
• Liu CH, Liu H, Ge B. Innate immunity in tuberculosis: host defense vs pathogen evasion. Cell Mol Immunol. 2017 Dec;14(12):963–975.
   PubMed Web of Science ®Google Scholar
• Jo EK. Autophagy as an innate defense against mycobacteria. Pathog Dis. 2013 Mar;67(2):108–118.
   PubMed Web of Science ®Google Scholar
• Chai Q, Wang L, Liu CH, et al. New insights into the evasion of host innate immunity by Mycobacterium tuberculosis. Cell Mol Immunol. 2020 Sep;17(9):901–913. DOI:10.1038/s41423-020-0502-z.
   PubMed Web of Science ®Google Scholar
• Deretic V, Delgado M, Vergne I, et al. Autophagy in immunity against mycobacterium tuberculosis: a model system to dissect immunological roles of autophagy. Curr Top Microbiol Immunol. 2009;335:169–188.
   PubMed Web of Science ®Google Scholar
• Vergne I, Chua J, Deretic V. Mycobacterium tuberculosis phagosome maturation arrest: selective targeting of PI3P-dependent membrane trafficking. Traffic. 2003 Sep;4(9):600–606.
   PubMed Web of Science ®Google Scholar
• Jamwal SV, Mehrotra P, Singh A, et al. Mycobacterial escape from macrophage phagosomes to the cytoplasm represents an alternate adaptation mechanism. Sci Rep. 2016 Mar 16;6(1):23089. 10.1038/srep23089
   PubMedGoogle Scholar
• Simeone R, Bobard A, Lippmann J, et al. Phagosomal rupture by Mycobacterium tuberculosis results in toxicity and host cell death. PLoS Pathog. 2012 Feb;8(2):e1002507. DOI:10.1371/journal.ppat.1002507.
   PubMed Web of Science ®Google Scholar
• Chen RH, Chen YH, Huang TY. Ubiquitin-mediated regulation of autophagy. J Biomed Sci. 2019 Oct 21;26(1):80. 10.1186/s12929-019-0569-y
   PubMed Web of Science ®Google Scholar
• Li J, Chai QY, Liu CH. The ubiquitin system: a critical regulator of innate immunity and pathogen-host interactions. Cell Mol Immunol. 2016 Sep;13(5):560–576.
   PubMed Web of Science ®Google Scholar
• Bussi C, Gutierrez MG. Mycobacterium tuberculosis infection of host cells in space and time. FEMS Microbiol Rev. 2019 Jul 1;43(4):341–361. 10.1093/femsre/fuz006
   PubMed Web of Science ®Google Scholar
• Lerner TR, Borel S, Greenwood DJ, et al. Mycobacterium tuberculosis replicates within necrotic human macrophages. J Cell Biol. 2017 Mar 6;216(3):583–594. 10.1083/jcb.201603040
   PubMed Web of Science ®Google Scholar
• Romagnoli A, Etna MP, Giacomini E, et al. ESX-1 dependent impairment of autophagic flux by Mycobacterium tuberculosis in human dendritic cells. Autophagy. 2012 Sep;8(9):1357–1370. DOI:10.4161/auto.20881.
   PubMed Web of Science ®Google Scholar
• Kumar A, Rani M, Ehtesham NZ, et al. Commentary: modification of host responses by Mycobacteria. Front Immunol. 2017;8:466.
   PubMed Web of Science ®Google Scholar
• Kumar A, Alam A, Rani M, et al. Biofilms: survival and defense strategy for pathogens. Int J Med Microbiol. 2017 Dec;307(8):481–489. DOI:10.1016/j.ijmm.2017.09.016.
   PubMed Web of Science ®Google Scholar
• Kumar A, Alam A, Grover S, et al. Peptidyl-prolyl isomerase-B is involved in Mycobacterium tuberculosis biofilm formation and a generic target for drug repurposing-based intervention. NPJ Biofilms Microbiomes. 2019;5(1):3. DOI:10.1038/s41522-018-0075-0.
   PubMedGoogle Scholar
• Singh Y, Kohli S, Sowpati DT, et al. Gene cooption in mycobacteria and search for virulence attributes: comparative proteomic analyses of Mycobacterium tuberculosis, Mycobacterium indicus pranii and other mycobacteria. Int J Med Microbiol. 2014 Jul;304(5–6):742–748. DOI:10.1016/j.ijmm.2014.05.006.
   PubMed Web of Science ®Google Scholar
• Saini V, Raghuvanshi S, Khurana JP, et al. Massive gene acquisitions in Mycobacterium indicus pranii provide a perspective on mycobacterial evolution. Nucleic Acids Res. 2012 Nov;40(21):10832–10850. DOI:10.1093/nar/gks793.
   PubMed Web of Science ®Google Scholar
• Kohli S, Singh Y, Sharma K, et al. Comparative genomic and proteomic analyses of PE/PPE multigene family of Mycobacterium tuberculosis H(3)(7)Rv and H(3)(7)Ra reveal novel and interesting differences with implications in virulence. Nucleic Acids Res. 2012 Aug;40(15):7113–7122. DOI:10.1093/nar/gks465.
   PubMed Web of Science ®Google Scholar
• Kumar A, Alam A, Tripathi D, et al. Protein adaptations in extremophiles: an insight into extremophilic connection of mycobacterial proteome. Semin Cell Dev Biol. 2018 Dec;84:147–157.
   PubMed Web of Science ®Google Scholar
• Grover S, Gupta P, Kahlon PS, et al. Analyses of methyltransferases across the pathogenicity spectrum of different mycobacterial species point to an extremophile connection. Mol Biosyst. 2016 May 26;12(5):1615–1625. 10.1039/C5MB00810G
   PubMedGoogle Scholar
• Pickart CM, Eddins MJ. Ubiquitin: structures, functions, mechanisms. Biochim Biophys Acta. 2004 Nov 29;1695(1–3):55–72. 10.1016/j.bbamcr.2004.09.019
   PubMed Web of Science ®Google Scholar
• Komander D, Rape M. The ubiquitin code. Annu Rev Biochem. 2012;81(1):203–229.
   PubMedGoogle Scholar
• Ikeda F, Dikic I. Atypical ubiquitin chains: new molecular signals. ‘protein modifications: beyond the usual suspects’ review series. EMBO Rep. 2008 Jun;9(6):536–542.
   PubMed Web of Science ®Google Scholar
• Vucic D, Dixit VM, Wertz IE. Ubiquitylation in apoptosis: a post-translational modification at the edge of life and death. Nat Rev Mol Cell Biol. 2011 Jun 23;12(7):439–452. 10.1038/nrm3143
   PubMed Web of Science ®Google Scholar
• Corn JE, Vucic D. Ubiquitin in inflammation: the right linkage makes all the difference. Nat Struct Mol Biol. 2014 Apr;21(4):297–300.
   PubMed Web of Science ®Google Scholar
• Haakonsen DL, Rape M. Branching out: improved signaling by heterotypic ubiquitin chains. Trends Cell Biol. 2019 Sep;29(9):704–716.
   PubMed Web of Science ®Google Scholar
• D’Andrea A, Pellman D. Deubiquitinating enzymes: a new class of biological regulators. Crit Rev Biochem Mol Biol. 1998;33(5):337–352.
   PubMed Web of Science ®Google Scholar
• Komander D, Clague MJ, Urbe S. Breaking the chains: structure and function of the deubiquitinases. Nat Rev Mol Cell Biol. 2009 Aug;10(8):550–563.
   PubMed Web of Science ®Google Scholar
• Husnjak K, Dikic I. Ubiquitin-binding proteins: decoders of ubiquitin-mediated cellular functions. Annu Rev Biochem. 2012;81(1):291–322.
   PubMedGoogle Scholar
• Dikic I, Wakatsuki S, Walters KJ. Ubiquitin-binding domains - from structures to functions. Nat Rev Mol Cell Biol. 2009 Oct;10(10):659–671.
   PubMed Web of Science ®Google Scholar
• Dieckmann T, Withers-Ward ES, Jarosinski MA, et al. Structure of a human DNA repair protein UBA domain that interacts with HIV-1 Vpr. Nat Struct Biol. 1998 Dec;5(12):1042–1047. DOI:10.1038/4220.
   PubMedGoogle Scholar
• Mueller TD, Feigon J. Solution structures of UBA domains reveal a conserved hydrophobic surface for protein-protein interactions. J Mol Biol. 2002 Jun 21;319(5):1243–1255. 10.1016/S0022-2836(02)00302-9
   PubMed Web of Science ®Google Scholar
• Hicke L, Schubert HL, Hill CP. Ubiquitin-binding domains. Nat Rev Mol Cell Biol. 2005 Aug;6(8):610–621.
   PubMed Web of Science ®Google Scholar
• Deshaies RJ, Joazeiro CA. RING domain E3 ubiquitin ligases. Annu Rev Biochem. 2009;78(1):399–434.
   PubMedGoogle Scholar
• Smit JJ, Sixma TK. RBR E3-ligases at work. EMBO Rep. 2014 Feb;15(2):142–154.
   PubMed Web of Science ®Google Scholar
• Weber J, Polo S, Maspero E. HECT E3 ligases: a tale with multiple facets. Front Physiol. 2019;10:370.
   PubMed Web of Science ®Google Scholar
• George AJ, Hoffiz YC, Charles AJ, et al. A comprehensive atlas of E3 ubiquitin ligase mutations in neurological disorders. Front Genet. 2018;9:29.
   PubMed Web of Science ®Google Scholar
• Galdeano C. Drugging the undruggable: targeting challenging E3 ligases for personalized medicine. Future Med Chem. 2017 Mar;9(4):347–350.
   PubMed Web of Science ®Google Scholar
• Berndsen CE, Wolberger C. New insights into ubiquitin E3 ligase mechanism. Nat Struct Mol Biol. 2014 Apr;21(4):301–307.
   PubMed Web of Science ®Google Scholar
• Ohi MD, Vander Kooi CW, Rosenberg JA, et al. Structural insights into the U-box, a domain associated with multi-ubiquitination. Nat Struct Biol. 2003 Apr;10(4):250–255. DOI:10.1038/nsb906.
   PubMedGoogle Scholar
• Vander Kooi CW, Ohi MD, Rosenberg JA, et al. The Prp19 U-box crystal structure suggests a common dimeric architecture for a class of oligomeric E3 ubiquitin ligases. Biochemistry. 2006 Jan 10;45(1):121–130. 10.1021/bi051787e
   PubMed Web of Science ®Google Scholar
• Verdecia MA, Joazeiro CA, Wells NJ, et al. Conformational flexibility underlies ubiquitin ligation mediated by the WWP1 HECT domain E3 ligase. Mol Cell. 2003 Jan;11(1):249–259. DOI:10.1016/S1097-2765(02)00774-8.
   PubMed Web of Science ®Google Scholar
• Rotin D, Kumar S. Physiological functions of the HECT family of ubiquitin ligases. Nat Rev Mol Cell Biol. 2009 Jun;10(6):398–409.
   PubMed Web of Science ®Google Scholar
• Spratt DE, Walden H, Shaw GS. RBR E3 ubiquitin ligases: new structures, new insights, new questions. Biochem J. 2014 Mar 15;458(3):421–437. 10.1042/BJ20140006
   PubMedGoogle Scholar
• Deretic V. Autophagy in immunity and cell-autonomous defense against intracellular microbes. Immunol Rev. 2011 Mar;240(1):92–104.
   PubMed Web of Science ®Google Scholar
• Selleck EM, Orchard RC, Lassen KG, et al. A Noncanonical Autophagy Pathway Restricts Toxoplasma gondii Growth in a Strain-Specific Manner in IFN-gamma-Activated Human Cells. mBio. 2015 Sep 8;6(5):e01157–15. 10.1128/mBio.01157-15
   PubMed Web of Science ®Google Scholar
• Joubert PE, Meiffren G, Gregoire IP, et al. Autophagy induction by the pathogen receptor CD46. Cell Host Microbe. 2009 Oct 22;6(4):354–366. 10.1016/j.chom.2009.09.006
   PubMed Web of Science ®Google Scholar
• Thurston TL, Ryzhakov G, Bloor S, et al. The TBK1 adaptor and autophagy receptor NDP52 restricts the proliferation of ubiquitin-coated bacteria. Nat Immunol. 2009 Nov;10(11):1215–1221. DOI:10.1038/ni.1800.
   PubMed Web of Science ®Google Scholar
• Case ED, Chong A, Wehrly TD, et al. The Francisella O-antigen mediates survival in the macrophage cytosol via autophagy avoidance. Cell Microbiol. 2014 Jun;16(6):862–877. DOI:10.1111/cmi.12246.
   PubMed Web of Science ®Google Scholar
• Ogawa M, Yoshimori T, Suzuki T, et al. Escape of intracellular Shigella from autophagy. Science. 2005 Feb 4;307(5710):727–731. 10.1126/science.1106036
   PubMed Web of Science ®Google Scholar
• Jo EK, Yuk JM, Shin DM, et al. Roles of autophagy in elimination of intracellular bacterial pathogens. Front Immunol. 2013;4:97.
   PubMed Web of Science ®Google Scholar
• Heath RJ, Goel G, Baxt LA, et al. RNF166 Determines Recruitment of Adaptor Proteins during Antibacterial Autophagy. Cell Rep. 2016 Nov 22;17(9):2183–2194. 10.1016/j.celrep.2016.11.005
   PubMed Web of Science ®Google Scholar
• Shahnazari S, Yen WL, Birmingham CL, et al. A diacylglycerol-dependent signaling pathway contributes to regulation of antibacterial autophagy. Cell Host Microbe. 2010 Aug 19;8(2):137–146. 10.1016/j.chom.2010.07.002
   PubMed Web of Science ®Google Scholar
• Thurston TL, Wandel MP, Von Muhlinen N, et al. Galectin 8 targets damaged vesicles for autophagy to defend cells against bacterial invasion. Nature. 2012 Jan 15;482(7385):414–418. 10.1038/nature10744
   PubMed Web of Science ®Google Scholar
• Jia J, Abudu YP, Claude-Taupin A, et al. Galectins control MTOR and AMPK in response to lysosomal damage to induce autophagy. Autophagy. 2019 Jan;15(1):169–171. DOI:10.1080/15548627.2018.1505155.
   PubMed Web of Science ®Google Scholar
• Fiskin E, Bionda T, Dikic I, et al. Global Analysis of Host and Bacterial Ubiquitinome in Response to Salmonella Typhimurium Infection. Mol Cell. 2016 Jun 16;62(6):967–981. 10.1016/j.molcel.2016.04.015
   PubMed Web of Science ®Google Scholar
• Katsuragi Y, Ichimura Y, Komatsu M. p62/SQSTM1 functions as a signaling hub and an autophagy adaptor. FEBS J. 2015 Dec;282(24):4672–4678.
   PubMed Web of Science ®Google Scholar
• Khaminets A, Behl C, Dikic I. Ubiquitin-Dependent And Independent Signals In Selective Autophagy. Trends Cell Biol. 2016 Jan;26(1):6–16.
   PubMed Web of Science ®Google Scholar
• Vainshtein A, Grumati P. Selective Autophagy by Close Encounters of the Ubiquitin Kind. Cells. 2020 Oct 24;9(11):2349. 10.3390/cells9112349
   PubMed Web of Science ®Google Scholar
• Budzik JM, Swaney DL, Jimenez-Morales D, et al. Dynamic post-translational modification profiling of Mycobacterium tuberculosis-infected primary macrophages. Elife. 2020 Jan 17;9. 10.7554/eLife.51461
   PubMed Web of Science ®Google Scholar
• Sharma V, Verma S, Seranova E, et al. Selective Autophagy and Xenophagy in Infection and Disease. Front Cell Dev Biol. 2018;6:147.
   PubMed Web of Science ®Google Scholar
• Verlhac P, Gregoire IP, Azocar O, et al. Autophagy receptor NDP52 regulates pathogen-containing autophagosome maturation. Cell Host Microbe. 2015 Apr 8;17(4):515–525. 10.1016/j.chom.2015.02.008
   PubMed Web of Science ®Google Scholar
• Judith D, Mostowy S, Bourai M, et al. Species-specific impact of the autophagy machinery on Chikungunya virus infection. EMBO Rep. 2013 Jun;14(6):534–544. DOI:10.1038/embor.2013.51.
   PubMed Web of Science ®Google Scholar
• Deng Q, Wang Y, Zhang Y, et al. Pseudomonas aeruginosa Triggers Macrophage Autophagy To Escape Intracellular Killing by Activation of the NLRP3 Inflammasome. Infect Immun. 2016 Jan;84(1):56–66. DOI:10.1128/IAI.00945-15.
   PubMed Web of Science ®Google Scholar
• Kuang E, Okumura CY, Sheffy-Levin S, et al. Regulation of ATG4B stability by RNF5 limits basal levels of autophagy and influences susceptibility to bacterial infection. PLoS Genet. 2012;8(10):e1003007. DOI:10.1371/journal.pgen.1003007.
   PubMed Web of Science ®Google Scholar
• Kuang E, Qi J, Ronai Z. Emerging roles of E3 ubiquitin ligases in autophagy. Trends Biochem Sci. 2013 Sep;38(9):453–460.
   PubMed Web of Science ®Google Scholar
• Li F, Zeng J, Gao Y, et al. G9a Inhibition Induces Autophagic Cell Death via AMPK/mTOR Pathway in Bladder Transitional Cell Carcinoma. PLoS One. 2015;10(9):e0138390. DOI:10.1371/journal.pone.0138390.
   PubMed Web of Science ®Google Scholar
• McEwan DG, Dikic I. Cullins keep autophagy under control. Dev Cell. 2014 Dec 22;31(6):675–676. 10.1016/j.devcel.2014.12.010
   PubMed Web of Science ®Google Scholar
• Manzanillo PS, Ayres JS, Watson RO, et al. The ubiquitin ligase parkin mediates resistance to intracellular pathogens. Nature. 2013 Sep 26;501(7468):512–516. 10.1038/nature12566
   PubMed Web of Science ®Google Scholar
• Noad J, Von der Malsburg A, Pathe C, et al. LUBAC-synthesized linear ubiquitin chains restrict cytosol-invading bacteria by activating autophagy and NF-kappaB. Nat Microbiol. 2017 May 8;2(7):17063. 10.1038/nmicrobiol.2017.63
   PubMed Web of Science ®Google Scholar
• van Wijk SJL, Fricke F, Herhaus L, et al. Linear ubiquitination of cytosolic Salmonella Typhimurium activates NF-kappaB and restricts bacterial proliferation. Nat Microbiol. 2017 May 8;2(7):17066. 10.1038/nmicrobiol.2017.66
   PubMed Web of Science ®Google Scholar
• Franco LH, Nair VR, Scharn CR, et al. The ubiquitin ligase smurf1 functions in selective autophagy of mycobacterium tuberculosis and anti-tuberculous host defense. Cell Host Microbe. 2017 Jan 11;21(1):59–72. 10.1016/j.chom.2016.11.002
   PubMed Web of Science ®Google Scholar
• Siqueira MDS, Ribeiro RM, Travassos LH. Autophagy and its interaction with intracellular bacterial pathogens. Front Immunol. 2018;9:935.
   PubMed Web of Science ®Google Scholar
• Deng L, Meng T, Chen L, et al. The role of ubiquitination in tumorigenesis and targeted drug discovery. Signal Transduct Target Ther. 2020 Feb 29;5(1):11. 10.1038/s41392-020-0107-0
   PubMed Web of Science ®Google Scholar
• Bielskiene K, Bagdoniene L, Mozuraitiene J, et al. E3 ubiquitin ligases as drug targets and prognostic biomarkers in melanoma. Medicina (Kaunas). 2015;51(1):1–9. DOI:10.1016/j.medici.2015.01.007.
   PubMed Web of Science ®Google Scholar
• Dove KK, Klevit RE. RING-between-RING E3 ligases: emerging themes amid the variations. J Mol Biol. 2017 Nov 10;429(22):3363–3375. 10.1016/j.jmb.2017.08.008
   PubMed Web of Science ®Google Scholar
• Gladkova C, Maslen SL, Skehel JM, et al. Mechanism of parkin activation by PINK1. Nature. 2018 Jul;559(7714):410–414. DOI:10.1038/s41586-018-0224-x.
   PubMed Web of Science ®Google Scholar
• Sauve V, Sung G, Soya N, et al. Mechanism of parkin activation by phosphorylation. Nat Struct Mol Biol. 2018 Jul;25(7):623–630. DOI:10.1038/s41594-018-0088-7.
   PubMed Web of Science ®Google Scholar
• Johnson BN, Berger AK, Cortese GP, et al. The ubiquitin E3 ligase parkin regulates the proapoptotic function of bax. Proc Natl Acad Sci U S A. 2012 Apr 17;109(16):6283–6288. 10.1073/pnas.1113248109
   PubMed Web of Science ®Google Scholar
• de Leseleuc L, Orlova M, Cobat A, et al. PARK2 mediates interleukin 6 and monocyte chemoattractant protein 1 production by human macrophages. PLoS Negl Trop Dis. 2013;7(1):e2015. DOI:10.1371/journal.pntd.0002015.
   PubMed Web of Science ®Google Scholar
• Klein C, Westenberger A. Genetics of parkinson’s disease. Cold Spring Harb Perspect Med. 2012 Jan;2(1):a008888.
   PubMed Web of Science ®Google Scholar
• Marin I, Ferrus A. Comparative genomics of the RBR family, including the Parkinson’s disease-related gene parkin and the genes of the ariadne subfamily. Mol Biol Evol. 2002 Dec;19(12):2039–2050.
   PubMed Web of Science ®Google Scholar
• Ingham RJ, Gish G, Pawson T. The Nedd4 family of E3 ubiquitin ligases: functional diversity within a common modular architecture. Oncogene. 2004 Mar 15;23(11):1972–1984. 10.1038/sj.onc.1207436
   PubMed Web of Science ®Google Scholar
• Shearwin-Whyatt L, Dalton HE, Foot N, et al. Regulation of functional diversity within the Nedd4 family by accessory and adaptor proteins. Bioessays. 2006 Jun;28(6):617–628. DOI:10.1002/bies.20422.
   PubMed Web of Science ®Google Scholar
• Macias MJ, Wiesner S, Sudol M. WW and SH3 domains, two different scaffolds to recognize proline-rich ligands. FEBS Lett. 2002 Feb 20;513(1):30–37. 10.1016/S0014-5793(01)03290-2
   PubMed Web of Science ®Google Scholar
• Wei X, Wang X, Zhan J, et al. Smurf1 inhibits integrin activation by controlling Kindlin-2 ubiquitination and degradation. J Cell Biol. 2017 May 1;216(5):1455–1471. 10.1083/jcb.201609073
   PubMed Web of Science ®Google Scholar
• Cao Y, Zhang L. A Smurf1 tale: function and regulation of an ubiquitin ligase in multiple cellular networks. Cell Mol Life Sci. 2013 Jul;70(13):2305–2317.
   PubMed Web of Science ®Google Scholar
• Orvedahl A, Sumpter R Jr., Xiao G, et al. Image-based genome-wide siRNA screen identifies selective autophagy factors. Nature. 2011 Dec 1;480(7375):113–117. 10.1038/nature10546
   PubMed Web of Science ®Google Scholar
• Yuan C, Qi J, Zhao X, et al. Smurf1 protein negatively regulates interferon-gamma signaling through promoting STAT1 protein ubiquitination and degradation. J Biol Chem. 2012 May 18;287(21):17006–17015. 10.1074/jbc.M112.341198
   PubMed Web of Science ®Google Scholar
• Kimmey JM, Huynh JP, Weiss LA, et al. Unique role for ATG5 in neutrophil-mediated immunopathology during M. tuberculosis infection. Nature. 2015 Dec 24;528(7583):565–569. 10.1038/nature16451
   PubMed Web of Science ®Google Scholar
• Rogov VV, Stolz A, Ravichandran AC, et al. Structural and functional analysis of the GABARAP interaction motif (GIM). EMBO Rep. 2017 Aug;18(8):1382–1396. DOI:10.15252/embr.201643587.
   PubMed Web of Science ®Google Scholar
• Abdrakhmanov A, Gogvadze V, Zhivotovsky B. To eat or to die: deciphering selective forms of autophagy. Trends Biochem Sci. 2020 Apr;45(4):347–364.
   PubMed Web of Science ®Google Scholar
• Shaid S, Brandts CH, Serve H, et al. Ubiquitination and selective autophagy. Cell Death Differ. 2013 Jan;20(1):21–30. DOI:10.1038/cdd.2012.72.
   PubMed Web of Science ®Google Scholar
• Huang J, Brumell JH. Bacteria-autophagy interplay: a battle for survival. Nat Rev Microbiol. 2014 Feb;12(2):101–114.
   PubMed Web of Science ®Google Scholar
• Whang MI, Tavares RM, Benjamin DI, et al. The ubiquitin binding protein TAX1BP1 mediates autophagasome induction and the metabolic transition of activated t cells. Immunity. 2017 Mar 21;46(3):405–420. 10.1016/j.immuni.2017.02.018
   PubMed Web of Science ®Google Scholar
• Fu T, Liu J, Wang Y, et al. Mechanistic insights into the interactions of NAP1 with the SKICH domains of NDP52 and TAX1BP1. Proc Natl Acad Sci U S A. 2018 Dec 11;115(50):E11651–E11660. 10.1073/pnas.1811421115
   PubMed Web of Science ®Google Scholar
• Ceregido MA, Spinola Amilibia M, Buts L, et al. The structure of TAX1BP1 UBZ1+2 provides insight into target specificity and adaptability. J Mol Biol. 2014 Feb 6;426(3):674–690. 10.1016/j.jmb.2013.11.006
   PubMed Web of Science ®Google Scholar
• Tumbarello DA, Manna PT, Allen M, et al. The autophagy receptor TAX1BP1 and the molecular motor myosin VI are required for clearance of salmonella typhimurium by autophagy. PLoS Pathog. 2015 Oct;11(10):e1005174. DOI:10.1371/journal.ppat.1005174.
   PubMed Web of Science ®Google Scholar
• Chai Q, Wang X, Qiang L, et al. A Mycobacterium tuberculosis surface protein recruits ubiquitin to trigger host xenophagy. Nat Commun. 2019 Apr 29;10(1):1973. 10.1038/s41467-019-09955-8
   PubMed Web of Science ®Google Scholar
• Lin C, Nozawa T, Minowa-Nozawa A, Toh H, Aikawa C, Nakagawa I. LAMTOR2/LAMTOR1 complex is required for TAX1BP1-mediated xenophagy. Cell Microbiol. 2019;21(4): e12981. 10.1111/cmi.12981
   PubMed Web of Science ®Google Scholar
• Furuya N, Kakuta S, Sumiyoshi K, Ando M, Nonaka R, Suzuki A, Kazuno S, Saiki S, Hattori N. NDP52 interacts with mitochondrial RNA poly(A) polymerase to promote mitophagy. EMBO Rep. 2018;19(12). 10.15252/embr.201846363
   PubMed Web of Science ®Google Scholar
• Verlhac P, Viret C, Faure M. Dual function of CALCOCO2/NDP52 during xenophagy. Autophagy. 2015;11(6): 965–966. 10.1080/15548627.2015.1046672
   PubMed Web of Science ®Google Scholar
• Ryan T A, Tumbarello D A. (). Optineurin: A Coordinator of Membrane-Associated Cargo Trafficking and Autophagy. Front Immunol. 2018;9:1024. 10.3389/fimmu.2018.01024
   PubMed Web of Science ®Google Scholar
• Shen W, Li H, Chen G, Chern Y, Tu P. Mutations in the ubiquitin-binding domain of OPTN/optineurin interfere with autophagy-mediated degradation of misfolded proteins by a dominant-negative mechanism. Autophagy. 2015;11(4), 685–700. 10.4161/auto.36098
   PubMed Web of Science ®Google Scholar
• Wild P et al. Phosphorylation of the autophagy receptor optineurin restricts Salmonella growth. Science. 2011;333(6039): 228–233. 10.1126/science.1205405
   PubMed Web of Science ®Google Scholar
• Bjørkøy G, Lamark T, Brech A, Outzen H, Perander M, Overvatn A, Stenmark H, Johansen T. 2005p62/SQSTM1 forms protein aggregates degraded by autophagy and has a protective effect on huntingtin-induced cell death. J Cell Biol. 2005;171(4):603–614. 10.1083/jcb.200507002
   PubMed Web of Science ®Google Scholar
• Tsuchiya M, Ogawa H, Koujin T, Mori C, Osakada H, Kobayashi S, Hiraoka Y, Haraguchi T. p62/SQSTM1 promotes rapid ubiquitin conjugation to target proteins after endosome rupture during xenophagy. FEBS Open Bio. 2018;8(3): 470–480. 10.1002/2211-5463.12385
   PubMed Web of Science ®Google Scholar
• Yamada T, Dawson T M, Yanagawa T, Iijima M, Sesaki H. SQSTM1/p62 promotes mitochondrial ubiquitination independently of PINK1 and PRKN/parkin in mitophagy. Autophagy. 2019;15(11): 2012–2018. 10.1080/15548627.2019.1643185
   PubMed Web of Science ®Google Scholar
• Hafren A, Hofius D. NBR1-mediated antiviral xenophagy in plant immunity. Autophagy. 2017;13(11): 2000–2001.
   PubMed Web of Science ®Google Scholar
• Barnett T C, Liebl D, Seymour LM et al. The globally disseminated M1T1 clone of group A Streptococcus evades autophagy for intracellular replication. Cell Host Microbe. 2013;14(6): 675–682. 10.1016/j.chom.2013.11.003
   PubMed Web of Science ®Google Scholar
• Xie X, Li F, Wang Y, et al. Molecular basis of ubiquitin recognition by the autophagy receptor CALCOCO2. Autophagy. 2015;11(10):1775–1789. DOI:10.1080/15548627.2015.1082025.
   PubMed Web of Science ®Google Scholar
• Watson RO, Manzanillo PS, Cox JS. Extracellular M. tuberculosis DNA targets bacteria for autophagy by activating the host DNA-sensing pathway. Cell. 2012 Aug 17;150(4):803–815. 10.1016/j.cell.2012.06.040
   PubMed Web of Science ®Google Scholar
• Mostowy S, Sancho-Shimizu V, Hamon MA, et al. p62 and NDP52 proteins target intracytosolic shigella and listeria to different autophagy pathways. J Biol Chem. 2011 Jul 29;286(30):26987–26995. 10.1074/jbc.M111.223610
   PubMed Web of Science ®Google Scholar
• Richter B, Sliter DA, Herhaus L, et al. Phosphorylation of OPTN by TBK1 enhances its binding to Ub chains and promotes selective autophagy of damaged mitochondria. Proc Natl Acad Sci U S A. 2016 Apr 12;113(15):4039–4044. 10.1073/pnas.1523926113
   PubMed Web of Science ®Google Scholar
• Heo JM, Ordureau A, Paulo JA, et al. The PINK1-PARKIN mitochondrial ubiquitylation pathway drives a program of OPTN/NDP52 recruitment and TBK1 activation to promote mitophagy. Mol Cell. 2015 Oct 1;60(1):7–20. 10.1016/j.molcel.2015.08.016
   PubMed Web of Science ®Google Scholar
• Lazarou M, Sliter DA, Kane LA, et al. The ubiquitin kinase PINK1 recruits autophagy receptors to induce mitophagy. Nature. 2015 Aug 20;524(7565):309–314. 10.1038/nature14893
   PubMed Web of Science ®Google Scholar
• Rahighi S, Ikeda F, Kawasaki M, et al. Specific recognition of linear ubiquitin chains by NEMO is important for NF-kappaB activation. Cell. 2009 Mar 20;136(6):1098–1109. 10.1016/j.cell.2009.03.007
   PubMed Web of Science ®Google Scholar
• Clark K, Nanda S, Cohen P. Molecular control of the NEMO family of ubiquitin-binding proteins. Nat Rev Mol Cell Biol. 2013 Oct;14(10):673–685.
   PubMed Web of Science ®Google Scholar
• Morton S, Hesson L, Peggie M, et al. Enhanced binding of TBK1 by an optineurin mutant that causes a familial form of primary open angle glaucoma. FEBS Lett. 2008 Mar 19;582(6):997–1002. 10.1016/j.febslet.2008.02.047
   PubMed Web of Science ®Google Scholar
• Li F, Xie X, Wang Y, et al. Structural insights into the interaction and disease mechanism of neurodegenerative disease-associated optineurin and TBK1 proteins. Nat Commun. 2016 Sep 13;7(1):12708. 10.1038/ncomms12708
   PubMedGoogle Scholar
• Li F, Xu D, Wang Y, et al. Structural insights into the ubiquitin recognition by OPTN (optineurin) and its regulation by TBK1-mediated phosphorylation. Autophagy. 2018;14(1):66–79. DOI:10.1080/15548627.2017.1391970.
   PubMed Web of Science ®Google Scholar
• Puri M, La Pietra L, Mraheil MA, et al. Listeriolysin O regulates the expression of optineurin, an autophagy adaptor that inhibits the growth of listeria monocytogenes. Toxins (Basel). 2017 Sep 5;9(9):273. 10.3390/toxins9090273
   PubMed Web of Science ®Google Scholar
• Munoz-Sanchez S, van der Vaart M, Meijer AH. Autophagy and Lc3-associated phagocytosis in zebrafish models of bacterial infections. Cells. 2020 Oct 29;9(11):2372. 10.3390/cells9112372
   PubMed Web of Science ®Google Scholar
• Zhang R, Varela M, Vallentgoed W, et al. The selective autophagy receptors optineurin and p62 are both required for zebrafish host resistance to mycobacterial infection. PLoS Pathog. 2019 Feb;15(2):e1007329. DOI:10.1371/journal.ppat.1007329.
   PubMed Web of Science ®Google Scholar
• Pankiv S, Clausen TH, Lamark T, et al. p62/SQSTM1 binds directly to Atg8/LC3 to facilitate degradation of ubiquitinated protein aggregates by autophagy. J Biol Chem. 2007 Aug 17;282(33):24131–24145. 10.1074/jbc.M702824200
   PubMed Web of Science ®Google Scholar
• Komatsu M, Waguri S, Koike M, et al. Homeostatic levels of p62 control cytoplasmic inclusion body formation in autophagy-deficient mice. Cell. 2007 Dec 14;131(6):1149–1163. 10.1016/j.cell.2007.10.035
   PubMed Web of Science ®Google Scholar
• Itakura E, Mizushima N. Targeting to the autophagosome formation site requires self-oligomerization but not LC3 binding. J Cell Biol. [2011 Jan 10];192(1):17–27. p62 DOI:10.1083/jcb.201009067.
   PubMed Web of Science ®Google Scholar
• Kim BW, Kwon DH, Song HK. Structure biology of selective autophagy receptors. BMB Rep. 2016 Feb;49(2):73–80.
   PubMed Web of Science ®Google Scholar
• Clausen TH, Lamark T, Isakson P, et al. p62/SQSTM1 and ALFY interact to facilitate the formation of p62 bodies/ALIS and their degradation by autophagy. Autophagy. 2010 Apr;6(3):330–344. DOI:10.4161/auto.6.3.11226.
   PubMed Web of Science ®Google Scholar
• Filimonenko M, Isakson P, Finley KD, et al. The selective macroautophagic degradation of aggregated proteins requires the PI3P-binding protein Alfy. Mol Cell. 2010 Apr 23;38(2):265–279. 10.1016/j.molcel.2010.04.007
   PubMed Web of Science ®Google Scholar
• Zhang Y, Mun SR, Linares JF, et al. ZZ-dependent regulation of p62/SQSTM1 in autophagy. Nat Commun. 2018 Oct 22;9(1):4373. 10.1038/s41467-018-06878-8
   PubMed Web of Science ®Google Scholar
• Cha-Molstad H, Yu JE, Feng Z, et al. p62/SQSTM1/Sequestosome-1 is an N-recognin of the N-end rule pathway which modulates autophagosome biogenesis. Nat Commun. 2017 Jul 24;8(1):102. 10.1038/s41467-017-00085-7
   PubMedGoogle Scholar
• Orvedahl A, MacPherson S, Sumpter R Jr., et al. Autophagy protects against Sindbis virus infection of the central nervous system. Cell Host Microbe. 2010 Feb 18;7(2):115–127. 10.1016/j.chom.2010.01.007
   PubMed Web of Science ®Google Scholar
• Yoshikawa Y, Ogawa M, Hain T, et al. Listeria monocytogenes ActA-mediated escape from autophagic recognition. Nat Cell Biol. 2009 Oct;11(10):1233–1240. DOI:10.1038/ncb1967.
   PubMed Web of Science ®Google Scholar
• Zheng YT, Shahnazari S, Brech A, et al. The adaptor protein p62/SQSTM1 targets invading bacteria to the autophagy pathway. J Immunol. 2009 Nov 1;183(9):5909–5916. 10.4049/jimmunol.0900441
   PubMed Web of Science ®Google Scholar
• Pilli M, Arko-Mensah J, Ponpuak M, et al. TBK-1 promotes autophagy-mediated antimicrobial defense by controlling autophagosome maturation. Immunity. 2012 Aug 24;37(2):223–234. 10.1016/j.immuni.2012.04.015
   PubMed Web of Science ®Google Scholar
• Lee Y, Weihl CC. Regulation of SQSTM1/p62 via UBA domain ubiquitination and its role in disease. Autophagy. 2017 Sep 2;13(9):1615–1616. 10.1080/15548627.2017.1339845
   PubMed Web of Science ®Google Scholar
• Fusco C, Micale L, Egorov M, et al. The E3-ubiquitin ligase TRIM50 interacts with HDAC6 and p62, and promotes the sequestration and clearance of ubiquitinated proteins into the aggresome. PLoS One. 2012;7(7):e40440. DOI:10.1371/journal.pone.0040440.
   PubMed Web of Science ®Google Scholar
• Komatsu M, Kurokawa H, Waguri S, et al. The selective autophagy substrate p62 activates the stress responsive transcription factor Nrf2 through inactivation of Keap1. Nat Cell Biol. 2010 Mar;12(3):213–223. DOI:10.1038/ncb2021.
   PubMed Web of Science ®Google Scholar
• Lau A, Wang XJ, Zhao F, et al. A noncanonical mechanism of Nrf2 activation by autophagy deficiency: direct interaction between Keap1 and p62. Mol Cell Biol. 2010 Jul;30(13):3275–3285. DOI:10.1128/MCB.00248-10.
   PubMed Web of Science ®Google Scholar
• Moscat J, Diaz-Meco MT. p62 at the crossroads of autophagy, apoptosis, and cancer. Cell. 2009 Jun 12;137(6):1001–1004. 10.1016/j.cell.2009.05.023
   PubMed Web of Science ®Google Scholar
• Lee Y, Chou TF, Pittman SK, et al. Keap1/Cullin3 Modulates p62/SQSTM1 activity via UBA domain ubiquitination. Cell Rep. 2017 Apr 4;19(1):188–202. 10.1016/j.celrep.2017.03.030
   PubMed Web of Science ®Google Scholar
• Ponpuak M, Davis AS, Roberts EA, et al. Delivery of cytosolic components by autophagic adaptor protein p62 endows autophagosomes with unique antimicrobial properties. Immunity. 2010 Mar 26;32(3):329–341. 10.1016/j.immuni.2010.02.009
   PubMed Web of Science ®Google Scholar
• Seto S, Tsujimura K, Horii T, et al. Autophagy adaptor protein p62/SQSTM1 and autophagy-related gene Atg5 mediate autophagosome formation in response to Mycobacterium tuberculosis infection in dendritic cells. PLoS One. 2013;8(12):e86017. DOI:10.1371/journal.pone.0086017.
   PubMed Web of Science ®Google Scholar
• Prabakaran T, Bodda C, Krapp C, et al. Attenuation of cGAS-STING signaling is mediated by a p62/SQSTM1-dependent autophagy pathway activated by TBK1. EMBO J. 2018 Apr 13;37(8). 10.15252/embj.201797858.
   PubMed Web of Science ®Google Scholar
• Lange S, Xiang F, Yakovenko A, et al. The kinase domain of titin controls muscle gene expression and protein turnover. Science. 2005 Jun 10;308(5728):1599–1603. 10.1126/science.1110463
   PubMed Web of Science ®Google Scholar
• Whitehouse CA, Waters S, Marchbank K, et al. Neighbor of Brca1 gene (Nbr1) functions as a negative regulator of postnatal osteoblastic bone formation and p38 MAPK activity. Proc Natl Acad Sci U S A. 2010 Jul 20;107(29):12913–12918. 10.1073/pnas.0913058107
   PubMed Web of Science ®Google Scholar
• Lamark T, Perander M, Outzen H, et al. Interaction codes within the family of mammalian phox and bem1p domain-containing proteins. J Biol Chem. 2003 Sep 5;278(36):34568–34581. 10.1074/jbc.M303221200
   PubMed Web of Science ®Google Scholar
• Rogov V, Dotsch V, Johansen T, et al. Interactions between autophagy receptors and ubiquitin-like proteins form the molecular basis for selective autophagy. Mol Cell. 2014 Jan 23;53(2):167–178. 10.1016/j.molcel.2013.12.014
   PubMed Web of Science ®Google Scholar
• Kirkin V, Lamark T, Sou YS, et al. A role for NBR1 in autophagosomal degradation of ubiquitinated substrates. Mol Cell. 2009 Feb 27;33(4):505–516. 10.1016/j.molcel.2009.01.020
   PubMed Web of Science ®Google Scholar
• Svenning S, Lamark T, Krause K, et al. Plant NBR1 is a selective autophagy substrate and a functional hybrid of the mammalian autophagic adapters NBR1 and p62/SQSTM1. Autophagy. 2011 Sep;7(9):993–1010. DOI:10.4161/auto.7.9.16389.
   PubMed Web of Science ®Google Scholar
• Deosaran E, Larsen KB, Hua R, et al. NBR1 acts as an autophagy receptor for peroxisomes. J Cell Sci. 2013 Feb 15;126(Pt 4):939–952. 10.1242/jcs.114819
   PubMed Web of Science ®Google Scholar
• Guirado E, Schlesinger LS. Modeling the mycobacterium tuberculosis granuloma - the critical battlefield in host immunity and disease. Front Immunol. 2013;4:98.
   PubMed Web of Science ®Google Scholar
• Xu G, Wang J, Gao GF, et al. Insights into battles between Mycobacterium tuberculosis and macrophages. Protein Cell. 2014 Oct;5(10):728–736. DOI:10.1007/s13238-014-0077-5.
   PubMed Web of Science ®Google Scholar
• Keane J, Remold HG, Kornfeld H. Virulent Mycobacterium tuberculosis strains evade apoptosis of infected alveolar macrophages. J Immunol. 2000 Feb 15;164(4):2016–2020.
   PubMed Web of Science ®Google Scholar
• Welin A, Eklund D, Stendahl O, et al. Human macrophages infected with a high burden of ESAT-6-expressing M. tuberculosis undergo caspase-1- and cathepsin B-independent necrosis. PLoS One. 2011;6(5):e20302. DOI:10.1371/journal.pone.0020302.
   PubMed Web of Science ®Google Scholar
• Ahmad J, Farhana A, Pancsa R, et al. Contrasting function of structured N-terminal and unstructured C-terminal segments of Mycobacterium tuberculosis PPE37 protein. mBio. 2018 Jan 23;9(1). 10.1128/mBio.01712-17.
   PubMed Web of Science ®Google Scholar
• Grover S, Sharma T, Singh Y, et al. The PGRS domain of Mycobacterium tuberculosis PE_PGRS protein Rv0297 is involved in endoplasmic reticulum stress-mediated apoptosis through toll-like receptor 4. mBio. 2018 Jun 19;9(3). 10.1128/mBio.01017-18.
   PubMed Web of Science ®Google Scholar
• Tundup S, Mohareer K, Hasnain SE. Mycobacterium tuberculosis PE25/PPE41 protein complex induces necrosis in macrophages: role in virulence and disease reactivation? FEBS Open Bio. 2014;4(1):822–828.
   PubMedGoogle Scholar
• Arora SK, Alam A, Naqvi N, et al. Immunodominant mycobacterium tuberculosis protein Rv1507A elicits Th1 response and modulates host macrophage effector functions. Front Immunol. 2020;11:1199.
   PubMedGoogle Scholar
• Ahmad J, Khubaib M, Sheikh JA, et al. Disorder-to-order transition in PE-PPE proteins of Mycobacterium tuberculosis augments the pro-pathogen immune response. FEBS Open Bio. 2020 Jan;10(1):70–85. DOI:10.1002/2211-5463.12749.
   PubMed Web of Science ®Google Scholar
• Khubaib M, Sheikh JA, Pandey S, et al. Mycobacterium tuberculosis Co-operonic PE32/PPE65 proteins alter host immune responses by hampering Th1 Response. Front Microbiol. 2016;7:719.
   PubMedGoogle Scholar
• Blundell TL, Gupta MN, Hasnain SE. Intrinsic disorder in proteins: relevance to protein assemblies, drug design and host-pathogen interactions. Prog Biophys Mol Biol. 2020 Jul 3;156:34–42.10.1016/j.pbiomolbio.2020.06.004
   PubMed Web of Science ®Google Scholar
• Gupta MN, Alam A, Hasnain SE. Protein promiscuity in drug discovery, drug-repurposing and antibiotic resistance. Biochimie. 2020 Aug;175:50–57.
   PubMed Web of Science ®Google Scholar
• Dev A, Iyer S, Razani B, et al. NF-kappaB and innate immunity. Curr Top Microbiol Immunol. 2011;349:115–143.
   PubMed Web of Science ®Google Scholar
• Chen J, Xie C, Tian L, et al. Participation of the p38 pathway in drosophila host defense against pathogenic bacteria and fungi. Proc Natl Acad Sci U S A. 2010 Nov 30;107(48):20774–20779. 10.1073/pnas.1009223107
   PubMed Web of Science ®Google Scholar
• Wang J, Ge P, Lei Z, et al. Mycobacterium tuberculosis protein kinase G acts as an unusual ubiquitinating enzyme to impair host immunity. EMBO Rep. 2021 Jun 4;22(6):e52175. 10.15252/embr.202052175
   PubMed Web of Science ®Google Scholar
• Wang J, Ge P, Qiang L, et al. The mycobacterial phosphatase PtpA regulates the expression of host genes and promotes cell proliferation. Nat Commun. 2017 Aug 15;8(1):244. 10.1038/s41467-017-00279-z
   PubMedGoogle Scholar
• Puri RV, Reddy PV, Tyagi AK. Secreted acid phosphatase (SapM) of Mycobacterium tuberculosis is indispensable for arresting phagosomal maturation and growth of the pathogen in Guinea pig tissues. PLoS One. 2013;8(7):e70514.
   PubMed Web of Science ®Google Scholar
• Maculins T, Fiskin E, Bhogaraju S, et al. Bacteria-host relationship: ubiquitin ligases as weapons of invasion. Cell Res. 2016 Apr;26(4):499–510. DOI:10.1038/cr.2016.30.
   PubMed Web of Science ®Google Scholar
• Ahmed N, Dobrindt U, Hacker J, et al. Genomic fluidity and pathogenic bacteria: applications in diagnostics, epidemiology and intervention. Nat Rev Microbiol. 2008 May;6(5):387–394. DOI:10.1038/nrmicro1889.
   PubMed Web of Science ®Google Scholar
• Shariq M, Quadir N, Sheikh JA, et al. Post translational modifications in tuberculosis: ubiquitination paradox. Autophagy. 2020 Nov 15;17(3):814–817. 10.1080/15548627.2020.1850009
   PubMed Web of Science ®Google Scholar
• Wang L, Wu J, Li J, et al. Host-mediated ubiquitination of a mycobacterial protein suppresses immunity. Nature. 2020 Jan;577(7792):682–688. DOI:10.1038/s41586-019-1915-7.
   PubMed Web of Science ®Google Scholar
• Dhiman R, Raje M, Majumdar S. Differential expression of NF-kappaB in mycobacteria infected THP-1 affects apoptosis. Biochim Biophys Acta. 2007 Apr;1770(4):649–658.
   PubMed Web of Science ®Google Scholar
• Cho JE, Park S, Cho SN, et al. c-Jun N-terminal kinase (JNK) and p38 mitogen-activated protein kinase (p38 MAPK) are involved in Mycobacterium tuberculosis-induced expression of Leukotactin-1. BMB Rep. 2012 Oct;45(10):583–588. DOI:10.5483/BMBRep.2012.45.10.120.
   PubMed Web of Science ®Google Scholar
• Wang J, Li BX, Ge PP, et al. Mycobacterium tuberculosis suppresses innate immunity by coopting the host ubiquitin system. Nat Immunol. 2015 Mar;16(3):237–245. DOI:10.1038/ni.3096.
   PubMed Web of Science ®Google Scholar
• Wang L, Liu Z, Wang J, et al. Oxidization of TGFbeta-activated kinase by MPT53 is required for immunity to Mycobacterium tuberculosis. Nat Microbiol. 2019 Aug;4(8):1378–1388. DOI:10.1038/s41564-019-0436-3.
   PubMed Web of Science ®Google Scholar
• Sakowski ET, Koster S, Portal Celhay C, et al. Ubiquilin 1 promotes IFN-gamma-induced xenophagy of Mycobacterium tuberculosis. PLoS Pathog. 2015 Jul;11(7):e1005076. DOI:10.1371/journal.ppat.1005076.
   PubMed Web of Science ®Google Scholar
• Cowley S, Ko M, Pick N, et al. The Mycobacterium tuberculosis protein serine/threonine kinase PknG is linked to cellular glutamate/glutamine levels and is important for growth in vivo. Mol Microbiol. 2004 Jun;52(6):1691–1702. DOI:10.1111/j.1365-2958.2004.04085.x.
   PubMed Web of Science ®Google Scholar
• Lisa MN, Gil M, Andre-Leroux G, et al. Molecular basis of the activity and the regulation of the eukaryotic-like S/T protein kinase PknG from Mycobacterium tuberculosis. Structure. 2015 Jun 2;23(6):1039–1048. 10.1016/j.str.2015.04.001
   PubMed Web of Science ®Google Scholar
• Walburger A, Koul A, Ferrari G, et al. Protein kinase G from pathogenic mycobacteria promotes survival within macrophages. Science. 2004 Jun 18;304(5678):1800–1804. 10.1126/science.1099384
   PubMed Web of Science ®Google Scholar
• Ehtram A, Shariq M, Ali S, et al. Teleological cooption of Mycobacterium tuberculosis PE/PPE proteins as porins: role in molecular immigration and emigration. Int J Med Microbiol. 2021 Apr;311(3):151495. DOI:10.1016/j.ijmm.2021.151495.
   PubMed Web of Science ®Google Scholar
• Akhter Y, Ehebauer MT, Mukhopadhyay S, et al. The PE/PPE multigene family codes for virulence factors and is a possible source of mycobacterial antigenic variation: perhaps more? Biochimie. 2012 Jan;94(1):110–116. DOI:10.1016/j.biochi.2011.09.026.
   PubMed Web of Science ®Google Scholar
• Sharma N, Shariq M, Quadir N, et al. Mycobacterium tuberculosis protein PE6 (Rv0335c), a novel TLR4 agonist, evokes an inflammatory response and modulates the cell death pathways in macrophages to enhance intracellular survival. Front Immunol. 2021;12:696491.
   PubMed Web of Science ®Google Scholar
• Strong EJ, Jurcic Smith KL, Saini NK, et al. Identification of autophagy-inhibiting factors of mycobacterium tuberculosis by high-throughput loss-of-function screening. Infect Immun. 2020 Nov 16;88(12). 10.1128/IAI.00269-20.
   PubMed Web of Science ®Google Scholar
• Saini NK, Baena A, Ng TW, et al. Suppression of autophagy and antigen presentation by Mycobacterium tuberculosis PE_PGRS47. Nat Microbiol. 2016 Aug 15;1(9):16133. 10.1038/nmicrobiol.2016.133
   PubMed Web of Science ®Google Scholar
• Strong EJ, Ng TW, Porcelli SA, et al. Mycobacterium tuberculosis PE_PGRS20 and PE_PGRS47 proteins inhibit autophagy by interaction with Rab1A. mSphere. 2021 Aug 25;6(4):e0054921. 10.1128/mSphere.00549-21
   PubMed Web of Science ®Google Scholar
• Deng W, Long Q, Zeng J, et al. Mycobacterium tuberculosis PE_PGRS41 Enhances the Intracellular Survival of M. smegmatis within Macrophages via blocking innate immunity and inhibition of host defense. Sci Rep. 2017 Apr 25;7(1):46716. 10.1038/srep46716
   PubMedGoogle Scholar
• Hu D, Wu J, Wang W, et al. Autophagy regulation revealed by SapM-induced block of autophagosome-lysosome fusion via binding RAB7. Biochem Biophys Res Commun. 2015 May 29;461(2):401–407. 10.1016/j.bbrc.2015.04.051
   PubMed Web of Science ®Google Scholar
• Shariq M, Quadir N, Sharma N, et al. Mycobacterium tuberculosis RipA dampens TLR4-mediated host protective response using a multi-pronged approach involving autophagy, apoptosis, metabolic repurposing, and immune modulation. Front Immunol. 2021;12:636644.
   PubMedGoogle Scholar
• Meng QL, Liu F, Yang XY, et al. Identification of latent tuberculosis infection-related microRNAs in human U937 macrophages expressing Mycobacterium tuberculosis hsp16.3. BMC Microbiol. 2014 Feb 12;14(1):37. 10.1186/1471-2180-14-37
   PubMedGoogle Scholar
• Yang L, Zhang C, Zhao Y, et al. Effects of Mycobacterium tuberculosis mutant strain hsp16.3 gene on murine raw 264.7 macrophage autophagy. DNA Cell Biol. 2018 Jan;37(1):7–14. DOI:10.1089/dna.2016.3599.
   PubMed Web of Science ®Google Scholar
• Zheng Q, Li Z, Zhou S, et al. Heparin-binding hemagglutinin of mycobacterium tuberculosis is an inhibitor of autophagy. Front Cell Infect Microbiol. 2017;7:33.
   PubMed Web of Science ®Google Scholar
• Gengenbacher M, Nieuwenhuizen N, Vogelzang A, et al. Deletion of nuoG from the vaccine candidate mycobacterium bovis bcg deltaurec::hly improves protection against tuberculosis. mBio. 2016 May 24;7(3). 10.1128/mBio.00679-16.
   PubMed Web of Science ®Google Scholar
• Shin DM, Jeon BY, Lee HM, et al. Mycobacterium tuberculosis eis regulates autophagy, inflammation, and cell death through redox-dependent signaling. PLoS Pathog. 2010 Dec 16;6(12):e1001230. 10.1371/journal.ppat.1001230
   PubMed Web of Science ®Google Scholar
• Garg R, Borbora SM, Bansia H, et al. Mycobacterium tuberculosis calcium pump ctpf modulates the autophagosome in an mtor-dependent manner. Front Cell Infect Microbiol. 2020;10:461.
   PubMed Web of Science ®Google Scholar
• Mohanty S, Jagannathan L, Ganguli G, et al. A mycobacterial phosphoribosyltransferase promotes bacillary survival by inhibiting oxidative stress and autophagy pathways in macrophages and zebrafish. J Biol Chem. 2015 May 22;290(21):13321–13343. 10.1074/jbc.M114.598482
   PubMed Web of Science ®Google Scholar
• Huang D, Bao L. Mycobacterium tuberculosis EspB protein suppresses interferon-gamma-induced autophagy in murine macrophages. J Microbiol Immunol Infect. 2016 Dec;49(6):859–865.
   PubMedGoogle Scholar
• Yabaji SM, Dhamija E, Mishra AK, et al. ESAT-6 regulates autophagous response through SOD-2 and as a result induces intracellular survival of Mycobacterium bovis BCG. Biochim Biophys Acta Proteins Proteom. 2020 Oct;1868(10):140470. DOI:10.1016/j.bbapap.2020.140470.
   PubMed Web of Science ®Google Scholar
• Padhi A, Pattnaik K, Biswas M, et al. Mycobacterium tuberculosis LprE suppresses TLR2-dependent cathelicidin and autophagy expression to enhance bacterial survival in macrophages. J Immunol. 2019 Nov 15;203(10):2665–2678. 10.4049/jimmunol.1801301
   PubMed Web of Science ®Google Scholar
• Ge P, Lei Z, Yu Y, et al. M. tuberculosis PknG manipulates host autophagy flux to promote pathogen intracellular survival. Autophagy. 2021 Jun 7;1–19. DOI:10.1080/15548627.2021.1938912.
   PubMed Web of Science ®Google Scholar
• Jacomin AC, Samavedam S, Promponas V, et al. iLIR database: a web resource for LIR motif-containing proteins in eukaryotes. Autophagy. 2016 Oct 2;12(10):1945–1953. 10.1080/15548627.2016.1207016
   PubMed Web of Science ®Google Scholar
• Birgisdottir AB, Lamark T, Johansen T. The LIR motif - crucial for selective autophagy. J Cell Sci. 2013 Aug 1;126(Pt 15):3237–3247. 10.1242/jcs.126128
   PubMed Web of Science ®Google Scholar
• Deretic V. Autophagy in tuberculosis. Cold Spring Harb Perspect Med. 2014 Aug 28;4(11):a018481. 10.1101/cshperspect.a018481
   PubMed Web of Science ®Google Scholar
• Gutierrez MG, Master SS, Singh SB, et al. Autophagy is a defense mechanism inhibiting BCG and Mycobacterium tuberculosis survival in infected macrophages. Cell. 2004 Dec 17;119(6):753–766. 10.1016/j.cell.2004.11.038
   PubMed Web of Science ®Google Scholar
• Ye X, Zhou XJ, Zhang H. Exploring the role of autophagy-related gene 5 (ATG5) yields important insights into autophagy in autoimmune/autoinflammatory diseases. Front Immunol. 2018;9:2334.
   PubMed Web of Science ®Google Scholar
• Csizmadia T, Low P. The Role of Deubiquitinating Enzymes in the Various Forms of Autophagy. Int J Mol Sci. 2020 Jun 12;21(12):4196. 10.3390/ijms21124196
   PubMed Web of Science ®Google Scholar
• Grumati P, Dikic I. Ubiquitin signaling and autophagy. J Biol Chem. 2018 Apr 13;293(15):5404–5413. 10.1074/jbc.TM117.000117
   PubMed Web of Science ®Google Scholar
• Jacomin AC, Taillebourg E, Fauvarque MO. Deubiquitinating enzymes related to autophagy: new therapeutic opportunities? Cells. 2018 Aug 19;7(8):112. 10.3390/cells7080112
   PubMed Web of Science ®Google Scholar
• Jia R, Bonifacino JS. Negative regulation of autophagy by UBA6-BIRC6-mediated ubiquitination of LC3. Elife. 2019 Nov 6;8. 10.7554/eLife.50034
   Web of Science ®Google Scholar
• Nibe Y, Oshima S, Kobayashi M, et al. Novel polyubiquitin imaging system, PolyUb-FC, reveals that K33-linked polyubiquitin is recruited by SQSTM1/p62. Autophagy. 2018;14(2):347–358. DOI:10.1080/15548627.2017.1407889.
   PubMed Web of Science ®Google Scholar
• Chakaya JM, Marais B, Du Cros P, et al. Programmatic versus personalised approaches to managing the global epidemic of multidrug-resistant tuberculosis. Lancet Respir Med. 2020 Apr;8(4):334–335. DOI:10.1016/S2213-2600(20)30104-1.
   PubMed Web of Science ®Google Scholar
• Parsa K, Hasnain SE. Proteomics of multidrug resistant Mycobacterium tuberculosis clinical isolates: a peep show on mechanism of drug resistance & perhaps more. Indian J Med Res. 2015 Jan;141(1):8–9.
   PubMedGoogle Scholar
• Tiberi S, Du Plessis N, Walzl G, et al. Tuberculosis: progress and advances in development of new drugs, treatment regimens, and host-directed therapies. Lancet Infect Dis. 2018 Jul;18(7):e183–e198. DOI:10.1016/S1473-3099(18)30110-5.
   PubMed Web of Science ®Google Scholar
• Sheikh JA, Ehtesham NZ, Hasnain SE. Revisiting BCG to control tuberculosis: mucosal delivery and delipidation? Lancet Infect Dis. 2020 Mar;20(3):272–273.
   PubMed Web of Science ®Google Scholar