To eat or not to eat mitochondria? How do host cells cope with mitophagy upon bacterial infection?

Abstract

Mitochondria fulfil a plethora of cellular functions ranging from energy production to regulation of inflammation and cell death control. The fundamental role of mitochondria makes them a target of choice for invading pathogens, with either an intracellular or extracellular lifestyle. Indeed, the modulation of mitochondrial functions by several bacterial pathogens has been shown to be beneficial for bacterial survival inside their host. However, so far, relatively little is known about the importance of mitochondrial recycling and degradation pathways through mitophagy in the outcome (success or failure) of bacterial infection. On the one hand, mitophagy could be considered as a defensive response triggered by the host upon infection to maintain mitochondrial homeostasis. However, on the other hand, the pathogen itself may initiate the host mitophagy to escape from mitochondrial-mediated inflammation or antibacterial oxidative stress. In this review, we will discuss the diversity of various mechanisms of mitophagy in a general context, as well as what is currently known about the different bacterial pathogens that have developed strategies to manipulate the host mitophagy.

Fig 1. Autophagosome formation machinery.

(1) The initiation of autophagosome formation requires the activation of the ULK complex (composed of ULK1/2 (unc-51-like kinases 1 and 2), ATG13, ATG101, and FIP200 (also known as RB1CC1)), which further activates ATG13 inducing its translocation to the ER where autophagosome formation occurs. (2) The ULK complex also activates and recruits (3) the class III PI3K lipid kinase complex (composed of VPS34, VPS15, Beclin 1, and ATG14) to the ER. (4) There, the PI3K III complex phosphorylates surrounding PI2P from the ER membrane, generating a PI3P-rich membrane. (5) The local PI3P enrichment of the ER membrane allows the recruitment of PI3P-binding proteins such as DFCP1 promoting the formation of a particular compartment termed “omegasome” from which autophagosomes are generated. (6) Other PI3P-binding proteins such as WIPI proteins are required for the formation of the isolation membrane of the future autophagosome, also called phagophore. WIPI proteins bind to and bring the ATG5-ATG12-ATG16L1 complex to the isolation membrane where it acts as a conjugating system, with ATG3, ATG4, and ATG7. (7) This machinery conjugates a PE to the LC3 type I protein converting it into LC3 type II (or LC3-PE), which is therefore incorporated in the isolation membrane, allowing its elongation and closure into an autophagosome. (8) LC3-PE then interacts with the targeted cargo to be degraded through specific adapters that harbour an LIR motif, allowing its sequestration inside the autophagosome, and further degradation through the lysosomal pathway. Created with BioRender.com. DFCP1, double FYVE-containing protein 1; ER, endoplasmic reticulum; LIR, LC3-interacting region; PE, phosphatidylethanolamine; PI2P, phosphatidylinositol-2-phosphate; PI3K, phosphatidylinositol-3-phosphate kinase; PI3P, phosphatidylinositol-3-phosphate; ULK, unc-51-like kinase; VPS34, vacuolar sorting protein 34; WIPI, WD repeat domain phosphoinositide-interacting.

Fig 2. Ubiquitin-dependent and independent pathways of mitophagy.

(A) Canonical ubiquitin-dependent mitophagy. In basal conditions, the PINK1 serine/threonine protein kinase precursor is targeted to healthy mitochondria thanks to its MTS, allowing its interaction with the TOMM complex and its import from the OMM to the IMM in an MMP-dependent way. (1) PINK1 then undergoes controlled proteolysis at its N-terminal part by the IMM-resident PARL protease. (2) Cleaved PINK1 is then released into the cytosol where it is fully degraded by the UPS. (3) However, upon a drop in MMP, PINK1 is no more cleaved at the IMM but is stabilised at the OMM where it accumulates as a dimeric form and activates through autophosphorylation. (4) PINK1 then phosphorylates ubiquitin (at serine 65) as well as Parkin (at the N-terminal ubiquitin-like domain serine 65 residue) which is found in the cytosol in an autoinhibited form. PINK1 phosphorylation of ubiquitin has been shown to be necessary for partial activation of Parkin, revealing its ubiquitin-binding domain and allowing PINK1 recognition and phosphorylation of Parkin, converting it in its fully active form. (5) Parkin is then recruited at the OMM through a still unclear mechanism in which ubiquitinated OMM proteins (OMP) (through the resident mitochondrial E3 ubiquitin ligase MITOL/March5) subsequently phosphorylated by PINK1 would serve as recruitment platform for activated Parkin. (6) Parkin recruitment at the OMM favours the nonselective polyubiquitination of OMM proteins in a positive feedforward amplification loop since PINK1-dependent polyphosphorylation of ubiquitin acts as a receptor for activated Parkin, therefore enhancing OMM protein polyubiquitination. Nonselective polyubiquitination of OMM proteins can also be performed by MUL1 independently of PINK1. (7) Polyubiquitin chains are then recognised by protein adapters such as p62 (also called SQSTM1), TAX1BP1, NDP52, or OPTN, previously activated by TBK1. (8) These adapters will finally recruit LC3-positive phagophores to form mitophagosomes. (B) Ubiquitin-independent or receptor-mediated mitophagy. Several LIR motif-containing receptors, which are expressed at the OMM upon different stresses, can directly interact with the LC3-positive phagophores to form mitophagosomes. FUNDC1 and BNIP3 (activated by ULK1) as well as BNIP3L and FKBP8 trigger mitophagy upon hypoxia. ATAD3B initiates mitophagy upon oxidative damage of mtDNA. PHB2 (activated by AURKA) induces mitophagy upon OMM rupture and IMM exposure to the cytoplasm. Cardiolipin is an IMM glycerophospholipid that is translocated to the OMM and triggers 6-OHDA-induced mitophagy. Bcl2-L-13 is another mitophagy receptor that requires ULK1 for proper interaction with LC3. Created with BioRender.com. FKBP8, FK506 binding protein 8; FUNDC1, FUN14 domain-containing protein 1; IMM, inner mitochondrial membrane; LIR, LC3-interacting region; MMP, mitochondrial membrane potential; MTS, mitochondria targeting signal; MUL1, mitochondrial ubiquitin ligase 1; NDP52, nuclear dot protein 52; OMM, outer mitochondrial membrane; OPTN, optineurin; PARL, presenilin-associated rhomboid-like protein; PHB2, Prohibitin 2;PINK1, phosphatase and tensin homolog-induced putative kinase 1; SQSTM1, sequestosome 1; TAX1BP1, tax 1 binding protein 1; TBK1, tank-binding kinase 1; TOMM, translocase of the outer mitochondrial membrane; UPS, ubiquitin-proteasome system.

Fig 3. Intracellular pathogens have evolved strategies to escape the defensive mitophagy responses induced by the host.

(A) Pseudomonas aeruginosa induces the cell death of mammalian cells and an NLRC4 inflammatory response through a pyoverdine-dependent iron starvation response and subsequent mitochondrial damage. While host cells activate a defence mitophagy response through PINK1/p62- and PHB2-dependent axis correlated with increased bacterial clearance, this mitophagy also attenuates the host cell death and inflammation, which preserve P. aeruginosa replication niche. (B) Mycobacterium spp. can trigger in macrophages either a M1 or a M2 phenotype polarisation. In the case of M1 polarisation, the infected macrophage triggers a pro-inflammatory phenotype through the activation of HIF-1α and up-regulation of glycolysis. However, the BNIP3L-mediated mitophagy induced by M. tuberculosis and M. bovis through HIF-1α attenuates the M1 inflammatory response. In addition, M. bovis triggers the translocation of the phosphorylated form of TBK1 from the xenophagy machinery to the mitophagy machinery, therefore inhibiting xenophagy-mediated bacterial clearance. In both models, the pathogen has evolved mechanisms to escape the defensive mitophagy response triggered by the host. Created with BioRender.com. HIF-1α, hypoxia inducible factor 1 α; NLRC4, NOD-like receptor family caspase recruitment domain containing 4; PINK1, phosphatase and tensin homolog-induced putative kinase 1; TBK1, tank-binding kinase 1.

Fig 4. Intracellular pathogens actively induce mitophagy for bacterial survival and egress.

(A) Listeria monocytogenes virulence relies on LLO. LLO induces Mic10-dependent mitochondrial fragmentation correlated with an increase in mtROS production, which might be detrimental for the pathogen. However, LLO also triggers NLRX1-mediated mitophagy, which promotes the elimination of damage mitochondria and therefore inhibit mtROS accumulation for bacterial survival and egress. (B) Yersinia pestis manipulates its host cell mitochondria in a similar way as L. monocytogenes does. Y. pestis virulence relies on the YopH effector, which induces mitochondrial fragmentation, mtROS release, and PINK1/Parkin-mediated mitophagy. As for L. monocytogenes, this mitophagy response limits mtROS accumulation and enables bacterial survival. (C) Brucella abortus induces mitochondrial fragmentation and BNIP3-mediated mitophagy through a still unknown effector. This mitophagy response promote bacterial egress in addition with other autophagy actors such as ULK1, Beclin1, and ATG14L. In these three models, the pathogen manipulates mitochondrial morphology and degradation either to avoid oxidative stress and favour its own survival and/or to enable its dissemination in the host. Created with BioRender.com. LLO, listeriolysin O; mtROS, mitochondrial reactive oxygen species; NLRX1, NOD-like receptor X1; PINK1, phosphatase and tensin homolog-induced putative kinase 1.

Fig 5. Extracellular pathogens are also able to induce mitophagy to regulate the host cell death.

(A) Helicobacter pylori virulence relies on the VacA effector, which induces mitochondrial-mediated apoptosis, as well as PINK1/Parkin-mediated mitophagy, both leading to the host cell death. (B) Vibrio splendidus triggers an increase in mtROS accumulation causing mitochondrial damage and exacerbated accumulation of mtROS, which leads to host cell death through apoptosis. Mitochondrial damage induces in the host a defensive BNIP3-mediated mitophagy response, which eliminates damage mitochondria and limits host cell death. Created with BioRender.com. mtROS, mitochondrial reactive oxygen species; PINK1, phosphatase and tensin homolog-induced putative kinase 1; VacA, vacuolating cytotoxin A.