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

Intracellular pathogens have evolved various efficient molecular armaments to subvert innate defenses. Cellular ubiquitination, a normal physiological process to maintain homeostasis, is emerging one such exploited mechanism. Ubiquitin (Ub), a small protein modifier, is conjugated to diverse protein substrates to regulate many functions. Structurally diverse linkages of poly-Ub to target proteins allow enormous functional diversity with specificity being governed by evolutionarily conserved enzymes (E3-Ub ligases). The Ub-binding domain (UBD) and LC3-interacting region (LIR) are critical features of macroautophagy/autophagy receptors that recognize Ub-conjugated on protein substrates. Emerging evidence suggests that E3-Ub ligases unexpectedly protect against intracellular pathogens by tagging poly-Ub on their surfaces and targeting them to phagophores. Two E3-Ub ligases, PRKN and SMURF1, provide immunity against Mycobacterium tuberculosis (M. tb). Both enzymes conjugate K63 and K48-linked poly-Ub to M. tb for successful delivery to phagophores. Intriguingly, M. tb exploits virulence factors to effectively dampen host-directed autophagy utilizing diverse mechanisms. Autophagy receptors contain LIR-motifs that interact with conserved Atg8-family proteins to modulate phagophore biogenesis and fusion to the lysosome. Intracellular pathogens have evolved a vast repertoire of virulence effectors to subdue host-immunity via hijacking the host ubiquitination process. This review highlights the xenophagy-mediated clearance of M. tb involving host E3-Ub ligases and counter-strategy of autophagy inhibition by M. tb using virulence factors. The role of Ub-binding receptors and their mode of autophagy regulation is also explained. We also discuss the co-opting and utilization of the host Ub system by M. tb for its survival and virulence. Abbreviations: APC: anaphase promoting complex/cyclosome; ATG5: autophagy related 5; BCG: bacille Calmette-Guerin; C2: Ca2+-binding motif; CALCOCO2: calcium binding and coiled-coil domain 2; CUE: coupling of ubiquitin conjugation to ER degradation domains; DUB: deubiquitinating enzyme; GABARAP: GABA type A receptor-associated protein; HECT: homologous to the E6-AP carboxyl terminus; IBR: in-between-ring fingers; IFN: interferon; IL1B: interleukin 1 beta; KEAP1: kelch like ECH associated protein 1; LAMP1: lysosomal associated membrane protein 1; LGALS: galectin; LIR: LC3-interacting region; MAPK11/p38: mitogen-activated protein kinase 11; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MAP3K7/TAK1: mitogen-activated protein kinase kinase kinase 7; MAPK8/JNK: mitogen-activated protein kinase 8; MHC-II: major histocompatibility complex-II; MTOR: mechanistic target of rapamycin kinase; NBR1: NBR1 autophagy cargo receptor; NFKB1/p50: nuclear factor kappa B subunit 1; OPTN: optineurin; PB1: phox and bem 1; PE/PPE: proline-glutamic acid/proline-proline-glutamic acid; PknG: serine/threonine-protein kinase PknG; PRKN: parkin RBR E3 ubiquitin protein ligase; RBR: RING-in between RING; RING: really interesting new gene; RNF166: RING finger protein 166; ROS: reactive oxygen species; SMURF1: SMAD specific E3 ubiquitin protein ligase 1; SQSTM1: sequestosome 1; STING1: stimulator of interferon response cGAMP interactor 1; TAX1BP1: Tax1 binding protein 1; TBK1: TANK binding kinase 1; TNF: tumor necrosis factor; TRAF6: TNF receptor associated factor 6; Ub: ubiquitin; UBA: ubiquitin-associated; UBAN: ubiquitin-binding domain in ABIN proteins and NEMO; UBD: ubiquitin-binding domain; UBL: ubiquitin-like; ULK1: unc-51 like autophagy activating kinase 1.胞内病原体已演化出多种高效的分子武器以破坏宿主天然免疫防御。细胞泛素化作为维持内稳态的正常生理过程，正被证实为此类病原体所劫持的关键机制之一。泛素（Ubiquitin, Ub）是一类小型蛋白修饰因子，可与多种蛋白质底物结合，从而调控诸多生物学功能。多聚泛素链与靶蛋白存在结构多样的连接方式，这赋予了其功能上的巨大多样性，而连接特异性则由进化保守的E3泛素连接酶（E3-Ub ligases）所调控。泛素结合结构域（Ubiquitin-binding domain, UBD）与LC3相互作用区域（LC3-interacting region, LIR）是自噬受体的核心特征，这类受体可识别结合于蛋白质底物表面的泛素链。越来越多的研究表明，E3泛素连接酶可通过在胞内病原体表面标记多聚泛素链并将其靶向至吞噬泡，从而发挥抗胞内病原体感染的防御作用，这一功能此前曾被意外发现。其中两种E3泛素连接酶——PRKN与SMURF1，可介导针对结核分枝杆菌（Mycobacterium tuberculosis, M. tb）的免疫防御。这两种酶均可将K63与K48连接型多聚泛素链结合至结核分枝杆菌表面，以成功将其递送至吞噬泡。有趣的是，结核分枝杆菌可通过多种机制利用毒力因子有效抑制宿主介导的自噬过程。自噬受体包含LIR基序，可与保守的Atg8家族蛋白相互作用，进而调控吞噬泡的生物发生及其与溶酶体的融合过程。胞内病原体已演化出大量毒力效应蛋白，通过劫持宿主泛素化过程来抑制宿主免疫防御。本综述重点阐述了依赖宿主E3泛素连接酶的异体自噬（xenophagy）介导的结核分枝杆菌清除机制，以及结核分枝杆菌利用毒力因子抑制自噬的对抗策略。本文还阐释了泛素结合受体的作用及其调控自噬的具体方式，并讨论了结核分枝杆菌如何劫持并利用宿主泛素系统以实现自身存活与毒力增强。 缩写： APC：后期促进复合物/周期体（anaphase promoting complex/cyclosome）； ATG5：自噬相关5（autophagy related 5）； BCG：卡介苗（bacille Calmette-Guerin）； C2：钙离子结合基序（Ca2+-binding motif）； CALCOCO2：钙结合卷曲螺旋结构域2（calcium binding and coiled-coil domain 2）； CUE：泛素结合与内质网降解偶联结构域（coupling of ubiquitin conjugation to ER degradation domains）； DUB：去泛素化酶（deubiquitinating enzyme）； GABARAP：GABA A型受体相关蛋白（GABA type A receptor-associated protein）； HECT：与E6-AP羧基末端同源结构域（homologous to the E6-AP carboxyl terminus）； IBR：环指之间结构域（in-between-ring fingers）； IFN：干扰素（interferon）； IL1B：白细胞介素1β（interleukin 1 beta）； KEAP1：Kelch样ECH结合蛋白1（kelch like ECH associated protein 1）； LAMP1：溶酶体相关膜蛋白1（lysosomal associated membrane protein 1）； LGALS：半乳糖凝集素（galectin）； LIR：LC3相互作用区域（LC3-interacting region）； MAPK11/p38：丝裂原活化蛋白激酶11（mitogen-activated protein kinase 11）； MAP1LC3/LC3：微管相关蛋白1轻链3（microtubule associated protein 1 light chain 3）； MAP3K7/TAK1：丝裂原活化蛋白激酶激酶激酶7（mitogen-activated protein kinase kinase kinase 7）； MAPK8/JNK：丝裂原活化蛋白激酶8（mitogen-activated protein kinase 8）； MHC-II：主要组织相容性复合体Ⅱ类（major histocompatibility complex-II）； MTOR：雷帕霉素机械靶标激酶（mechanistic target of rapamycin kinase）； NBR1：NBR1自噬货物受体（NBR1 autophagy cargo receptor）； NFKB1/p50：核因子κB亚基1（nuclear factor kappa B subunit 1）； OPTN：视神经萎缩蛋白（optineurin）； PB1：Phox与Bem1结构域（phox and bem 1）； PE/PPE：脯氨酸-谷氨酸/脯氨酸-脯氨酸-谷氨酸（proline-glutamic acid/proline-proline-glutamic acid）； PknG：丝氨酸/苏氨酸蛋白激酶PknG（serine/threonine-protein kinase PknG）； PRKN：帕金RBR E3泛素蛋白连接酶（parkin RBR E3 ubiquitin protein ligase）； RBR：环指-环指之间-环指结构域（RING-in between RING）； RING：环指结构域（really interesting new gene）； RNF166：环指蛋白166（RING finger protein 166）； ROS：活性氧（reactive oxygen species）； SMURF1：SMAD特异性E3泛素蛋白连接酶1（SMAD specific E3 ubiquitin protein ligase 1）； SQSTM1：隔离体1（sequestosome 1）； STING1：干扰素反应cGAMP互作因子1（stimulator of interferon response cGAMP interactor 1）； TAX1BP1：Tax1结合蛋白1（Tax1 binding protein 1）； TBK1：TANK结合激酶1（TANK binding kinase 1）； TNF：肿瘤坏死因子（tumor necrosis factor）； TRAF6：肿瘤坏死因子受体相关因子6（TNF receptor associated factor 6）； Ub：泛素（ubiquitin）； UBA：泛素相关结构域（ubiquitin-associated）； UBAN：ABIN蛋白与NEMO中的泛素结合结构域（ubiquitin-binding domain in ABIN proteins and NEMO）； UBD：泛素结合结构域（ubiquitin-binding domain）； UBL：泛素样结构域（ubiquitin-like）； ULK1：unc-51样自噬激活激酶1（unc-51 like autophagy activating kinase 1）。