RAB7A phosphorylation by TBK1 promotes mitophagy via the PINK-PARKIN pathway

Heo, Jin‐Mi; Ordureau, Alban; Swarup, Sharan; Paulo, João A.; Shen, Kuang; Sabatini, David M.; Harper, J. Wade

doi:10.1126/sciadv.aav0443

Cited by 146 publications

(157 citation statements)

References 54 publications

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“…The PPM1H related, PPM1M enzyme ( Figure 5B) also dephosphorylated Rab10 when overexpressed in cells, to a lower extent than PPM1H ( Figure 5A). In corresponding biochemical studies, we also found that PPM1M displayed weak activity towards phosphorylated Rab10 ( [16], including Rab7A phosphorylated at Ser72 by TBK1 [51] or LRRK1 [52] and Rab1 that is phosphorylated at Thr75 by TAK1 [53]. It will be interesting to probe whether PPM1M, PPM1J or indeed PPM1H might dephosphorylate other Rab proteins.…”

Section: Discussionmentioning

confidence: 81%

PPM1H phosphatase counteracts LRRK2 signaling by selectively dephosphorylating Rab proteins

Berndsen

Lis

Yeshaw

et al. 2019

Preprint

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Mutations that activate LRRK2 protein kinase cause Parkinson's disease. LRRK2 phosphorylates a subset of Rab GTPases within their Switch-II motif controlling interaction with effectors. An siRNA screen of all protein phosphatases revealed that a poorly studied protein phosphatase, PPM1H, counteracts LRRK2 signaling by specifically dephosphorylating Rab proteins. PPM1H knock out increased endogenous Rab phosphorylation and inhibited Rab dephosphorylation. Overexpression of PPM1H suppressed LRRK2-mediated Rab phosphorylation. PPM1H also efficiently and directly dephosphorylated Rab8A in biochemical studies. A "substrate-trapping" PPM1H mutant (Asp288Ala) binds with high affinity to endogenous, LRRK2-phosphorylated Rab proteins, thereby blocking dephosphorylation seen upon addition of LRRK2 inhibitors. PPM1H is localized to the Golgi and its knockdown suppresses primary cilia formation, similar to pathogenic LRRK2. Thus, PPM1H acts as a key modulator of LRRK2 signaling by controlling dephosphorylation of Rab proteins. PPM1H activity enhancers could offer a new therapeutic approach to prevent or treat Parkinson's disease.

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Section: Discussionmentioning

confidence: 81%

PPM1H phosphatase counteracts LRRK2 signaling by selectively dephosphorylating Rab proteins

Berndsen

Lis

Yeshaw

et al. 2019

Preprint

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“…The rationale for this study stemmed from our lack of current knowledge concerning the molecular mechanisms that underpin mitophagy in skeletal muscle. Much of the research that informs our understanding of the mechanisms governing mitophagy has been conducted in immortalized mammalian cells harboring systems that stably express non‐native PINK1 and/ or Parkin . In skeletal muscle, our understanding of mitophagy, and how it changes in response to physiological stimuli such as exercise and aging, has been largely informed by the assessment of mitophagy markers, rather than measuring mitophagy directly.…”

Section: Discussionmentioning

confidence: 99%

“…TANK‐binding kinase 1 (TBK1) is thought to be an important signaling node in this process, activating autophagy receptors that link ubiquitylated cargo to the autophagosome . TBK1 is known to be activated following phosphorylation at Ser 172 and recent work has suggested that its activation upon mitochondrial depolarization requires both PINK1 and Parkin . Despite these advances, much of the research that underpins our current understanding of PINK1‐Parkin mediated mitophagy has been conducted in mammalian cells that stably express non‐native PINK1 and/ or Parkin .…”

Section: Introductionmentioning

confidence: 99%

“…TBK1 is known to be activated following phosphorylation at Ser 172 and recent work has suggested that its activation upon mitochondrial depolarization requires both PINK1 and Parkin . Despite these advances, much of the research that underpins our current understanding of PINK1‐Parkin mediated mitophagy has been conducted in mammalian cells that stably express non‐native PINK1 and/ or Parkin . Furthermore, murine models have shown that basal mitophagy occurs in skeletal muscle even in the absence of PINK1 .…”

Section: Introductionmentioning

confidence: 99%

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AMPK activation induces mitophagy and promotes mitochondrial fission while activating TBK1 in a PINK1‐Parkin independent manner

et al. 2020

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Abbreviations: ACC, acetyl-CoA carboxylase; AMP, adenosine monophosphate; AMPK, adenosine monophosphate activated protein kinase; CCCP, carbonyl cyanide m-chlorophenyl hydrazine; CISD1, CDGSH iron sulfur domain 1; DRP1, dynamin-related protein 1; GFP, green fluorescence protein; MFF, mitochondrial fission factor; MFN-1/2, mitofusin-1/2; mtFIS1 101-152 , mitochondrial targeting sequence of FIS1 (amino acids 101-152); NDP52, nuclear dot protein 52; OPA1, dynamin-like 120 kDa protein; OPTN, optineurin; OXPHOS, oxidative phosphorylation; PINK1, PTEN-induced kinase 1; SQSTM1/p62, sequestosome-1; TBK1, TANK-binding kinase 1; Ub, ubiquitin; UBA UBQLN1 , his-halo-ubiquilin1 UBA domain tetramer; ULK1, unc-51 like autophagy activating kinase 1. AbstractMitophagy is a key process regulating mitochondrial quality control. Several mechanisms have been proposed to regulate mitophagy, but these have mostly been studied using stably expressed non-native proteins in immortalized cell lines. In skeletal muscle, mitophagy and its molecular mechanisms require more thorough investigation. To measure mitophagy directly, we generated a stable skeletal muscle C2C12 cell line, expressing a mitophagy reporter construct (mCherry-green fluorescence protein-mtFIS1 101-152 ). Here, we report that both carbonyl cyanide m-chlorophenyl hydrazone (CCCP) treatment and adenosine monophosphate activated protein kinase (AMPK) activation by 991 promote mitochondrial fission via phosphorylation of MFF and induce mitophagy by ~20%. Upon CCCP treatment, but not 991, ubiquitin phosphorylation, a read-out of PTEN-induced kinase 1 (PINK1) activity, and Parkin E3 ligase activity toward CDGSH iron sulfur domain 1 (CISD1) were increased. Although the PINK1-Parkin signaling pathway is active in response to CCCP treatment, we observed no change in markers of mitochondrial protein content. Interestingly, our data shows that TANK-binding kinase 1 (TBK1) phosphorylation is increased after both CCCP and 991 treatments, suggesting TBK1 activation to be independent of both PINK1 and Parkin. Finally, we confirmed in non-muscle cell lines that TBK1 phosphorylation occurs in the absence of PINK1 and is regulated by AMPKdependent signaling. Thus, AMPK activation promotes mitophagy by enhancing mitochondrial fission (via MFF phosphorylation) and autophagosomal engulfment (via TBK1 activation) in a PINK1-Parkin independent manner.

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“…Rab7a is known to regulate endosomal transport and late endosome-lysosome fusion, but recent data specifically suggest a role in regulating autophagosome biogenesis during mitophagy, also known as mitophagsome formation (Tan & Tang, 2019;Yamano et al, 2014). It has been shown that Rab7A phosphorylation via TBK1 promotes mitophagy via the pink-parkin pathway (Heo et al, 2018). Rab7 GTP hydrolysis has also been implicated in regulating mitochondria-lysosomal contact sites, controlling mitochondrial fission (Wong et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

Lysosomal dysfunction impairs mitochondrial quality control and predicts neurodegeneration in TBCKE

Tintos-Hernández

Santana

Keller

et al. 2020

Preprint

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Biallelic variants in TBC1-domain containing kinase (TBCK) cause intellectual disability in children. It remains unclear how variants in TBCK lead to a neurodevelopmental disorder and what biological factors modulate the variability of clinical severity. Previous studies showed increased autophagosomes in patients sharing the truncating (p.R126X) Boricua homozygous TBCK variant, who exhibit a severe and progressive neurodegenerative phenotype. Since defects in mitophagy are linked to neurodegenerative disorders, we tested whether mitophagy and mitochondrial function are altered in TBCK -/fibroblasts. Our data shows significant accumulation of mitophagosomes, reduced mitochondrial respiratory capacity, and mtDNA depletion. Furthermore, mitochondrial dysfunction correlates with the severity of the neurological phenotype. Since effective mitophagy and degradation of mitophagosomes ultimately depends on successful lysosomal degradation, we also tested lysosomal function. Our data shows that lysosomal proteolytic function is significantly reduced in TBCK -/fibroblasts. Moreover, acidifying lysosomal nanoparticles rescue the mitochondrial respiratory defects, suggesting that impaired mitochondrial quality control secondary to lysosomal dysfunction, may play an important role in the pathogenicity of this rare neurodevelopmental disorder and predict the degree of disease progression and neurodegeneration.

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RAB7A phosphorylation by TBK1 promotes mitophagy via the PINK-PARKIN pathway

Abstract: TBK1 phosphorylates RAB7A-S72 to support multiple downstream steps in PARKIN-dependent mitophagy.

Cited by 146 publications

References 54 publications

PPM1H phosphatase counteracts LRRK2 signaling by selectively dephosphorylating Rab proteins

PPM1H phosphatase counteracts LRRK2 signaling by selectively dephosphorylating Rab proteins

AMPK activation induces mitophagy and promotes mitochondrial fission while activating TBK1 in a PINK1‐Parkin independent manner

Lysosomal dysfunction impairs mitochondrial quality control and predicts neurodegeneration in TBCKE

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