Accumulation of intracellular damage by reactive oxygen species accelerates biological aging, leading to the development of age-related lung diseases such as idiopathic pulmonary fibrosis (IPF). Mitochondrial dysfunction and mitochondria-related oxidative stress has been implicated in the pathogenesis of many age-related diseases. Selective autophagic degradation of mitochondria (mitophagy) is critical to maintain a proper pool of the organelle and preserve cellular energy homeostasis. Oxidative stress resulting from age-dependent defects in the quality of proteins and degradation of mitochondria promotes alveolar epithelial cell damage potentiating lung injury. Our research found diminished autophagy corresponding with elevated levels of oxidized proteins and lipofuscin in response to lung injury in old and middle-aged mice compared to younger animals. More importantly, older mice exposed to lung injury are characterized by deficient mitophagic responses. The pro-fibrotic cytokine transforming growth factor beta 1 (TGFβ1) plays a pivotal role in driving fibroblast-to-myofibroblast differentiation (FMD), an important feature of pulmonary fibrosis. TGFβ1-mediated FMD is characterized by reduced autophagy flux, altered mitophagy and defects in mitochondrial function. In accordance, PINK1 expression is reduced in the aging murine lung and biopsies from IPF patients compared to controls. "nOur research also revealed a decline in mitochondrial protein deacetylase sirtuin 3 (SIRT3) expression in the lungs of aging mice. Low levels of SIRT3 transcripts were observed in two different animal models of pulmonary fibrosis. SIRT3 expression was reduced in fibrotic regions of lung tissues from patients with fibrotic diseases. We demonstrated that down-regulation of SIRT3 by TGFβ1 promotes acetylation of major oxidative stress response regulators, such as superoxide dismutase 2 (SOD2) and isocitrate dehydrogenase 2 (IDH2), and that resveratrol induced SIRT3 expression and ameliorated acetylation changes induced by TGFβ1. Knockdown of SIRT3 expression by siRNA exacerbated TGFβ1-induced FMD. By contrast, promotion of SIRT3 expression attenuated the effect of TGFβ1 on myofibroblast differentiation. Finally, SIRT3-deficient mice were more susceptible to pulmonary fibrosis in response to bleomycin and had increased collagen deposition compared to control mice. Collectively, our research indicates that an age-related decline in autophagy, SIRT3 expression, and mitochondrial homeostasis may contribute to the promotion and/or perpetuation of pulmonary fibrosis. / Meredith L Sosulski

La mitophagie, la dégradation sélective des mitochondries par autophagie, est impliquée dans l’élimination des mitochondries endommagées ou superflues et requiert des régulateurs et protéines spécifiques. Chez la levure, Atg32, localisée dans la membrane externe mitochondriale, interagit avec Atg8, et permet le recrutement des mitochondries et leur séquestration à l’intérieur des autophagosomes. Atg8 est conjuguée à de la phosphatidyléthanolamine et est ainsi ancrée aux membranes du phagophore et des autophagosomes. Chez la levure, plusieurs voies de synthèse de PE existent mais leur contribution dans l’autophagie et la mitophagie est inconnue. Dans le premier chapitre, nous avons étudié la contribution des différentes enzymes de synthèse de PE, dans l’induction de l’autophagie et la mitophagie et nous avons démontré que Psd1, la phosphatidylsérine décarboxylase mitochondriale, est impliquée dans la mitophagie seulement en condition de carence azotée alors que Psd2, localisée dans les membranes vacuolaires, endosomales et de l’appareil de Golgi, est nécessaire en phase stationnaire de croissance. Dans le second chapitre, la relation entre Atg32, la mitophagie et le protéasome a été étudiée. Nous avons démontré que l’activité du promoteur d’ATG32 et la quantité de protéine Atg32 exprimée sont inversement régulées. En phase stationnaire de croissance, l’inhibition du protéasome empêche la diminution de l’expression d’Atg32 et la mitophagie est stimulée. Nos données montrent ainsi que la quantité d’Atg32 est reliée à l’activité du protéasome et que cette protéine pourrait être ubiquitinylée. Dans le troisième chapitre, nous nous sommes intéressés au rôle potentiel de Dep1, un composant du complexe nucléaire Rpd3 d’histones déacétylases, dans la mitophagie. Dans nos conditions, Dep1 semble être mitochondriale et elle est impliquée dans la régulation de la mitophagie. BRMS1L (Breast Cancer Metastasis suppressor 1-like) est l’homologue de Dep1 chez les mammifères. Cette protéine possède un rôle anti-métastatique dans des lignées de cancer du sein. Nous avons trouvé que l’expression de BRMS1L augmente en présence de stimuli pro-mitophagie. / Mitophagy, the selective degradation of mitochondria by autophagy, is implicated in the clearance of superfluous or damaged mitochondria and requires specific proteins and regulators. In yeast, Atg32, an outer mitochondrial membrane protein, interacts with Atg8, promoting mitochondria recruitment to the phagophore and their sequestration within autophagosomes. Atg8 is anchored to the phagophore and autophagosome membranes thanks to phosphatidylethanolamine (PE). In yeast, several PE synthesis pathways have been characterized, but their contribution to autophagy and mitophagy is unknown. In the first chapter, we investigated the contribution of the different enzymes responsible for PE synthesis in autophagy and mitophagy and we demonstrated that Psd1, the mitochondrial phosphatidylserine decarboxylase, is involved in mitophagy induction only in nitrogen starvation, whereas Psd2, located in vacuole/Golgi apparatus/endosome membranes, is required preferentially for mitophagy induction in stationary phase of growth. In the second chapter, we were interested in the relationship between Atg32, mitophagy and the proteasome. We demonstrated that ATG32 promoter activity and protein expression are inversely regulated. During stationary phase of growth, proteasome inhibition abolishes the decrease in Atg32 expression and mitophagy is enhanced. Our data indicate that Atg32 protein is regulated by the proteasome activity and could be ubiquitinated. In the third chapter, we investigated the involvement of Dep1, a member of the nuclear Rpd3L histone deacetylase complex, in mitophagy. In our conditions, Dep1 seems to be located in mitochondria and is a novel effector of mitophagy both in nitrogen starvation and stationary phase of growth. BRMS1L (Breast Cancer Metastasis suppressor 1-like) is the mammalian homolog of Dep1 and has been described in breast cancer metastasis suppression. We found that BRMS1L protein expression increases upon pro-mitophagy stimuli.

Mitochondria not only supply the energy for cell function, but also take part in cell signaling. This review describes the dysfunctions of mitochondria in aging and neurodegenerative diseases, and the signaling pathways leading to mitochondrial biogenesis (including PGC-1 family proteins, SIRT1, AMPK) and mitophagy (parkin-Pink1 pathway). Understanding the regulation of these mitochondrial pathways may be beneficial in finding pharmacological approaches or lifestyle changes (caloric restrict or exercise) to modulate mitochondrial biogenesis and/or to activate mitophagy for the removal of damaged mitochondria, thus reducing the onset and/or severity of neurodegenerative diseases.

Omi/HtrA2 is a mitochondrial serine protease with a dual and opposite function depending on its subcellular localization. Most of the previous studies focused on Omi/HtrA2’s pro-apoptotic function when the protein is released to the cytoplasm. It is becoming apparent that the main function of Omi/HtrA2 is within the mitochondria, where it has a pro-survival role. However, its mechanism is still poorly understood. To this end, we used the yeast two-hybrid system to dissect the Omi/HtrA2 pathway by identifying novel interactors and substrates. Our studies revealed a novel function of Omi/HtrA2 in the regulation of a deubiquitinating (DUB) complex. In addition we found that Omi/HtrA2 participates in mitophagy by regulating Mulan E3 ubiquitin ligase, which recruits GABARAP (gamma-amino-butyric acid receptor-associated protein) to the mitochondria. Abro1 is the scaffold protein of the DUB complex known as BRISC (BRCC36 isopeptidase complex) that is specific for Lys-63 deubiquitination. This complex is similar to the BRCA-1 complex, a known and important player in DNA damage response. Using the yeast two-hybrid screen and a bait consisting of the unique carboxy-terminus of the Abro1 protein, we identified three transcription factors which are members of the activating protein 1 (AP-1) family, namely ATF4, ATF5 and JunD. The AP-1 family member ATF4 is ubiquitously expressed, like Abro1, and important in cell cycle regulation and survival, thus we further analyzed this interaction. Abro1’s interaction with ATF4 was specific and present only when cells are under cellular stress. When Abro1 protein level is increased it provides protection against stress-induced cell iv death, but interaction between Abro1 and ATF4 is necessary to achieve this protection. The significance of this interaction was the translocation of Abro1 from the cytoplasm to the nucleus. These results establish a new cytoprotective function of cytoplasmic Omi/HtrA2 as a regulator of the BRISC DUB complex. Under normal conditions Omi/HtrA2 is localized in the intermembrane space (IMS) of the mitochondria. We have recently identified that the mitochondrial Mulan E3 ubiquitin ligase is a substrate of Omi/HtrA2 protease. Mulan, along with MARCH5/MITOL and RNF185, are the only three mitochondrial E3 ubiquitin ligases identified thus far. The function of Mulan has been linked to cell growth, cell death and autophagy/mitophagy. In addition, we showed that Omi/HtrA2, through regulation of the Mulan protein level, controls mitophagy, especially during mitochondrial stress. To understand Mulan’s function and its control by Omi/HtrA2, we set out to identify E2 conjugating enzymes that form a complex with Mulan E3 ligase. We isolated four specific interacting E2’s, namely Ube2E2, Ube2E3, Ube2G2 and Ube2L3. To identify substrates for each unique Mulan-E2 complex we used fusion baits in a second yeast two-hybrid screening. One of the interactors isolated against the Mulan-Ube2E3 bait was the GABARAP protein, a member of the Atg8 (autophagy) family. The mammalian Atg8 family is composed of seven members that have been linked to important roles in autophagy/mitophagy. We characterized this interaction both in vitro and in vivo and its role in mitophagy. Our results suggest that Mulan participates in various pathways, depending on the nature of its partner E2 conjugating enzyme. In addition, we identified the pathway by which Mulan participates in mitophagy by recruiting GABARAP to the mitochondria. v I want to dedicate this hard work to the people who mean the most to me, the people who have been more than supportive in these past five years; they are my very small, but very loud and loving, family. My brother Raffaello has always been proud of me and always told his friends how his sister was a "doctor." My father, Alvaro, always told me I had to be better than him, a man who has a master’s degree in chemistry. Finally, but most importantly to me, I want to dedicate this work and degree to my mother, Maria Aparecida Troncon, a woman who is like no other. She has always supported me, and with small gestures like having snacks ready when I came to visit after work or coming with me to lab on the weekends so I would not be alone, she told me every day that she was proud of me. Every time she met someone she told them I was her doctor and she said it with the biggest smile on her face. Unfortunately she passed away on December 17th, 2012, just months shy of the completion of my degree. I remember how proud she was when I received my bachelor’s and I can only imagine the size of her smile when I walk across the stage this time as a Ph.D. I love you mom, you are my rock and my strength; without your constant support and dedication I would have not reached this point. I know you are smiling at me from above. Last but not least I want to dedicate this to the man who is my better-half. Thank you for all your love and support, Guillermo. I love you.

La plupart des voies de signalisation qui régule la croissance cellulaire et le métabolisme sont sous le contrôle du mécanisme du complexe I de la rapamycine (mTORC1). L'un des régulateurs en amont de mTORC1, impliqués dans la détection des acides aminés et l'autophagie, est complexe SEA, chez la levure, et le complexe GATOR, chez les mammifères. Plusieurs composants de GATOR sont dérégulés dans de nombreux cancers et maladies neurodégénératives. Malgré l'intérêt scientifique vis à vis du complexe SEA / GATOR, de nombreux détails concernant sa fonction et son implication dans différents troubles humains sont encore inconnus et restent à investiguer.L'objectif principal de ma thèse était d’élargir notre connaissance sur le complexe SEA / GATOR, et plus particulièrement en ce qui concerne son rôle dans la modulation des voies de signalisation cellulaire. Étant donné que le SEA / GATOR est très conservé, j'ai effectué les expériences en utilisant deux modèles cellulaires : levure S. cerevisiae et lignées cellulaires humaines. Les résultats obtenus ont permis de démontrer un nouveau rôle pour le NPRL2, composant de GATOR, distinct de sa fonction dans la régulation de la voie mTORC1. Nous avons constaté que l'expression ectopique de la NPRL2 induit un stress oxydant et conduit aux dommages de l'ADN et à l'apoptose. Les études sur la levure ont révélé que le complexe SEA relie la voie mTORC1 et la régulation du contrôle de la qualité des mitochondries. Par conséquent, le complexe SEA / GATOR émerge en tant que régulateur multifonctionnel de plusieurs processus cellulaires. / The major signaling pathway that regulates cell growth and metabolism is under the control of the mechanistic target of rapamycin complex 1 (mTORC1). One of the mTORC1 upstream regulators involved in amino acid sensing and autophagy is called the SEA complex in yeast and GATOR in mammalian cells. Several GATOR components are deregulated in many cancers and neurodegenerative diseases. Despite of the growing interest to the SEA/GATOR, many details concerning its function and implication in different human disorders are still unknown.The main objective of my thesis was to extend our knowledge about the SEA/GATOR, especially what concerns its role in the modulating cellular signaling network. Because the SEA/GATOR is highly conserved I performed the experiments using two model systems - budding yeast S. cerevisiae and human cells lines. The results I obtained allowed to demonstrate a new role for the GATOR component NPRL2, distinct from its function in mTORC1 regulation. We found that ectopic expression of NPRL2 induces oxidative stress and leads to the DNA damage and apoptosis. The studies in yeast revealed that the SEA complex connects the TORC1 pathway and the regulation of mitochondria quality control. Therefore, the SEA/GATOR complex is emerging as a multifunctional regulator of several cellular processes.

Neurons are metabolically active cells that depend on mitochondria for ATP production and calcium homeostasis. Within a single neuron, the demand for mitochondrial function is highly variable both spatially and temporally. This need-based distribution is reflected in high local density of mitochondria at presynaptic endings, post-synaptic densities, nodes of Ranvier, and in growth cones, where mitochondrial function is required to sustain neuronal activity. To meet local demand, mitochondria are mobile organelles that move along microtubule cytoskeleton in axons and dendrites. Due to their role in oxidative phosphorylation, mitochondria are prone to oxidative damage that can in turn jeopardize the cell. To minimize cellular damage, an autophagic process, known as mitophagy, has evolved to clear dysfunctional mitochondria. Defects in mitochondrial clearance are implicated in neurodegenerative diseases such as Parkinson's disease (PD). In neurons, it was thought that mitochondria with reduced membrane potential are retrogradely transported to the soma where they are degraded. In this dissertation, I present a new paradigm where damaged mitochondria are arrested and undergo mitophagy locally in axons. In chapter 2 we report that mitochondrial damage causes arrest of mitochondrial motility in neuronal axons through the action of Parkin, an E3 ubiquitin ligase implicated in PD. Parkin accumulates on the surface of depolarized mitochondria and triggers proteosomal degradation of the mitochondrial motor adaptor protein, Miro, thereby detaching mitochondria from the kinesin and dynein motor complex. This arrest of mitochondria would serve to quarantine them in preparation for their subsequent degradation. In chapter 3, I demonstrate that damage to a small population of axonal mitochondria triggers a pathway of mitophagy that occurs locally in distal axons. Two PD-associated proteins, PINK1, a mitochondrial kinase mutated, and Parkin are both required for axonal mitophagy. In chapter 4, I present preliminary studies examining the turnover rate of neuronal PINK1 in order to characterize its mechanism of activation in distal axons. In conclusion, I have characterized a pathway for quality control of mitochondria in neuronal axons showing that clearance of defective mitochondria oocurs locally in distal axons without a need for their retrograde transport to the soma.

Autophagy is a physiological process by which the cell eliminates damaged organelles, toxic agents, and long-lived proteins by degradation through lysosomal system. Mitophagy, the specific autophagic elimination of mitochondria, regulates mitochondrial number to match metabolic demand and is a core machinery of quality control to remove damaged mitochondria. A neuroprotective role of physiological autophagy/mitophagy has been discovered. However, recent studies suggested that highly accelerated autophagy/mitophagy might contribute to neuronal death in various pathological situations including cerebral ischemia. In this study, we aimed to investigate the activation of excessive autophagy, particularly, the more specific mitophagy, in neuronal tissues and its contribution to ischemia/hypoxia (I/H)-induced delayed neuronal death. I/H injury was induced by oxygen and glucose deprivation (OGD) followed by reperfusion (RP) on primary cortical neurons in vitro. Cerebral ischemia was induced by unilateral common carotid artery occlusion and hypoxia in neonatal mice in vivo. In order to determine the extent to which autophagy contributes to neuronal death in cerebral ischemia, we performed multiple methods and found that in both primary cortical neurons and SH-SY5Y cells exposed to OGD for 6 h and RP for 24, 48, and 72 h, respectively, an increase of autophagy was observed as determined by the increased ratio of LC3-II to LC3-I and Beclin 1 expression. Using Fluoro-Jade C and monodansylcadaverine double-staining, and electron microscopy we found the increment in autophagy after OGD/RP was accompanied by increased autophagic cell death, and this increased cell death was inhibited by the specific autophagy inhibitor, 3-methyladenine. The presence of large autolysosomes and numerous autophagosomes in cortical neurons were confirmed by electron microscopy. Autophagy activities were increased dramatically in the ischemic brains 3-7 days postinjury from a rat model of neonatal cerebral I/H as shown by increased punctate LC3 staining and Beclin-1 expression. We thus obtained the conclusion that excessive activation of autophagy contributes to neuronal death in cerebral ischemia. BNIP3 (Bcl-2/adenovirus E19 kD interacting protein 3), a member of a unique subfamily of death-inducing mitochondrial proteins, is highly associated with mitochondrial dysfunction and delayed neuronal death in stroke. It is known that BNIP3-induced neuronal death is caspase-independent and characterized by early mitochondrial damage. Recent evidence suggested that the BNIP3 family of proteins might be important regulators of mitophagy. Here, using both stroke models, we found that homodimer (60 kD) of BNIP3/NIX (BNIP3L) were highly expressed in a ‘delayed’ manner. Particularly, significant mitophagic activation was confirmed by electron microscopy. In contrast, both neonatal mitophagy and apoptosis were significantly inhibited in the BNIP3 knockout (KO) mice after I/H, which was also accompanied by a significantly increased autophagic response. In addition, the infarct volume in the BNIP3 KO mice was significantly reduced as compared to wild-type (WT) mice after 7 or 28 days recovery, showing a prominent neuroprotection of BNIP3 gene silencing. A protein-to-protein interaction of mitochondria-localized BNIP3 (60 kD) with the autophagosome marker, LC3, was confirmed by co-ip, immunocytochemistry and further quantified by ELISA, indicating BNIP3 was an effective LC3-binding target on damaged mitochondria. These data demonstrated a novel role of BNIP3 in regulating neuronal mitophagy and cell death during ischemic stroke.

Mitochondrial dysfunction has been implicated as one of the primary causes of Parkinson's disease (PD). The proteins PINK1, a serine-threonine kinase, and Parkin, an E3 ubiquitin ligase, are mutated in many genetic cases of PD. In healthy individuals, Parkin is recruited to damaged mitochondria and leads to autophagic degradation of mitochondria in a process termed mitophagy. Following depolarization of the mitochondrial membrane, PINK1 is stabilized on the outer mitochondrial membrane, and triggers Parkin translocation from the cytosol to mitochondria. Precisely how this phenomenon is regulated is still unclear. We employed RNA interference (RNAi) technology in a 384-well format to identify novel genes that are required for Parkin recruitment to mitochondria. We identified ATPase inhibitory factor 1 (IF1) as the strongest hit required for Parkin recruitment following treatment with the protonophore CCCP. We show that IF1 is upstream of PINK1 and Parkin, and required to sense mitochondrial damage by allowing the loss of membrane potential. In cells treated with CCCP, the absence of IF1 permits the ATP synthase to run freely in reverse, consuming ATP to maintain potential across the inner mitochondrial membrane, thus blocking PINK1 and Parkin activation. Interestingly, Rho0 cells, that lack mitochondrial DNA, have downregulated endogenous expression of IF1 in order to maintain mitochondrial function. Overexpression of IF1 in Rho0 cells results in the depletion of mitochondrial membrane potential and the initiation of mitophagy. These data demonstrate a unique role for IF1 in the regulation of mitochondrial quality control that has not been explored in the etiology of PD.

L’autophagie est un processus d’autodigestion qui se produit dans toutes les cellules eucaryotes et conduit à la dégradation d’éléments du cytoplasme (organites, macromolécules) par le lysosome. Elle peut se produire au hasard dans le cytoplasme où elle peut être sélective, par exemple d’un organite intracellulaire. Lorsque les mitochondries sont sélectivement dégradées par autophagie, on parle de mitophagie. L’autophagie et la mitophagie sont impliquées dans diverses pathologies comme les maladies neurodégénératives et le cancer car leur dérégulation peut grandement perturber l’homéostasie cellulaire.Mon projet de thèse porte sur le rôle de la protéine co-chaperonne BAG6 dans la régulation de la mitophagie.BAG6 est une protéine de 150 kDa, également appelée BAT3 ou Scythe, dont la fonction majeure réside dans le contrôle qualité du cytoplasme mais BAG6 est également impliquée dans l’immunité, l’apoptose ou l’autophagie. Nous montrons que son mécanisme d’action passe, tout d’abord, par la régulation de la morphologie mitochondriale en induisant la fission des mitochondries. Ensuite, la protéine BAG6 induit la mitophagie : les protéines impliquées dans la mitophagie (PINK1 et PARKIN) s’accumulent à la mitochondrie alors que les protéines de la mitochondrie (TOM20, TFAM et TIM23) voient leur expression diminuée. BAG6 diminue également la masse mitochondriale par un mécanisme dépendant de l’autophagie. L’analyse de la séquence de BAG6 montre qu’elle est composée de nombreux domaines protéiques incluant les domaines UBL et deux domaines LIR (LC3-Interacting Region) et nous avons montré que BAG6 interagit avec LC3 grâce à son domaine LIR2. Ces caractéristiques identifient la protéine BAG6 comme un nouveau récepteur potentiel de la mitophagie. / Autophagy, literally meaning self-eating, is a highly evolutionary conserved process in eukaryotes where elements of the cytoplasm (organelles, macromolecules) are degraded by lysosomes. Autophagy can occur randomly in the cytoplasm or can be selective of a specific organelle. Among other, the specific degradation of mitochondria is called mitophagy. Autophagy and mitophagy have been implicated in several physiopathologies such as neurodegenerative diseases or cancer. Deregulations of autophagy/mitophagy may profoundly affect homeostasis.The aim of my thesis is to characterize the role of the co-chaperonne protein BAG6 in the regulation of mitophagy.BAG6 is a 150kDa protein, also known as BAT3 or Scythe, which functions in the quality control of the cytoplasm. Moreover BAG6 is also involved in immunity, apoptosis or autophagy. Our work showed that it is implicated in the regulation of mitochondrial morphology by inducing mitochondrial fission. Also, BAG6 induces mitophagy: in presence of BAG6, mitophagy markers such as PINK1 and PARKIN are more localized at the mitochondria whereas the expression of mitochondrial specific protein’s (TOM20, TFAM and TIM23) decreases. After its sequence analysis, we discovered that BAG6 is composed of many domains such as the UBL domains and two LIR domains (LC3- Interacting Region) and that BAG6 interacts with LC3 through its LIR2 domain. These features lead to identify BAG6 as a new potential receptor of mitophagy.

Ubiquitin phosphorylation by PINK1 (PTEN-induced Putative Kinase 1) is crucial for mitochondrial quality control and loss or mutation of PINK1 can lead to autosomal recessive juvenile parkinsonism (AR-JP). PINK1 is an unusual kinase, as it is characterised by three unique insertions in its kinase N lobe and a C-terminal region after the kinase domain. Despite great effort, a structure of PINK1 could not be determined and the molecular mechanism of ubiquitin phosphorylation and the effect of the PINK1 AR-JP patient mutations remained elusive. The versatile modifier ubiquitin (Ub) is also an unusual kinase substrate, as its phosphorylation site (Ser65) is not exposed, but protected by the Ub fold. Hence, it was not clear how a kinase would be able to target Ser65 of Ub. This work shows that Ub needs to adopt a previously described conformation in order to be efficiently phosphorylated by PINK1. NMR experiments revealed that in a small population of Ub the last β-strand is retracted, resulting in a more accessible Ser65 loop. It could be shown that PINK1 binds the Ser65 loop in this C-terminally retracted conformation (Ub-CR), but not in the ‘common’ conformation. In addition, it could be shown that Ub trapped in the Ub-CR conformation by point mutations (Ub TVLN) is phosphorylated significantly faster than Ub wt, which only adopts the Ub-CR conformation at very low frequency. To further elucidate how PINK1 binds and phosphorylates Ub, the kinase domain of Pediculus humanus corporis (Ph)PINK1 was crystallised in complex with Ub TVLN stabilised by a nanobody. The structure revealed many peculiarities of PINK1, such as the architecture of the unique insertions and the C-terminal region. Together with NMR and mass spectrometry studies, the structure explains how PINK1 interacts with ubiquitin via insertion-3 and its activation segment, and how PINK1 utilises the Ub- CR conformation for efficient Ser65 phosphorylation. In addition, the structure shows that two autophosphorylation sites in the N lobe regulate PINK1, by stabilising the functionally important insertions. The structure helped our understanding of the molecular basis of over 40 AR-JP patient mutations and may guide the design of ARJP therapeutics in the future.