| Category | Specific detail | Evidence type (review/primary) | Key recent citation(s) with year + DOI URL |
|---|---|---|---|
| Protein/complex | **AFG3L2 = human mitochondrial inner-membrane m-AAA protease subunit** (UniProt Q9Y4W6); assembles as **homo-hexamers** or **hetero-hexamers with SPG7/paraplegin** to form the matrix-facing m-AAA protease complex (pqac-00000001, pqac-00000002, pqac-00000003) | Review + primary | Dastidar et al., 2024, *Mol Neurobiol*, https://doi.org/10.1007/s12035-023-03768-z; Franchino et al., 2024, *Brain*, https://doi.org/10.1093/brain/awad340 |
| Localization/topology | **Inner mitochondrial membrane (IMM)**, catalytic sites/AAA+ module **facing the matrix**; IM-anchored metalloprotease involved in protein quality control and mitochondrial biogenesis (pqac-00000001, pqac-00000006, pqac-00000008) | Review + primary | Khalimonchuk & Becker, 2023, *Antioxid Redox Signal*, https://doi.org/10.1089/ars.2022.0124; Franchino et al., 2024, *Brain*, https://doi.org/10.1093/brain/awad340 |
| Catalytic activities | Dual function: **AAA+ ATPase/unfoldase-translocase** plus **zinc metalloprotease**; ATP-driven substrate engagement/translocation feeds substrates to a C-terminal Zn-dependent protease site (pqac-00000002, pqac-00000003, pqac-00000006) | Review | Dastidar et al., 2024, *Mol Neurobiol*, https://doi.org/10.1007/s12035-023-03768-z; Khalimonchuk & Becker, 2023, *Antioxid Redox Signal*, https://doi.org/10.1089/ars.2022.0124 |
| Substrate: SLC25A39 | **SLC25A39 glutathione transporter** is an experimentally supported AFG3L2 substrate; mitochondrial GSH depletion stabilizes SLC25A39 by reducing AFG3L2-dependent turnover, whereas GSH supplementation restores rapid degradation (pqac-00000014, pqac-00000008, pqac-00000009) | Primary + review | Liu et al., 2023, *Science*, https://doi.org/10.1126/science.adf4154; Chandragiri et al., 2024, *bioRxiv*, https://doi.org/10.1101/2024.09.27.615438 |
| Substrate: MRPL32 / bL32m | AFG3L2/m-AAA supports **biogenesis/processing of mitochondrial ribosomal bL32m (MRPL32)**, linking proteolysis to mitochondrial ribosome assembly and protein synthesis (pqac-00000008, pqac-00000010, pqac-00000012) | Review + primary | Khalimonchuk & Becker, 2023, *Antioxid Redox Signal*, https://doi.org/10.1089/ars.2022.0124; Chandragiri et al., 2024, *bioRxiv*, https://doi.org/10.1101/2024.09.27.615438 |
| Substrate: EMRE | AFG3L2/m-AAA contributes to **EMRE maturation/turnover**, thereby regulating the mitochondrial calcium uniporter machinery and mitochondrial Ca²⁺ handling (pqac-00000008, pqac-00000010, pqac-00000012) | Review + primary | Khalimonchuk & Becker, 2023, *Antioxid Redox Signal*, https://doi.org/10.1089/ars.2022.0124; Chandragiri et al., 2024, *bioRxiv*, https://doi.org/10.1101/2024.09.27.615438 |
| Substrate: TIMMDC1 | **TIMMDC1**, a complex I assembly factor, is degraded by AFG3L2, linking m-AAA proteolysis to respiratory-chain assembly control (pqac-00000008, pqac-00000009) | Primary | Chandragiri et al., 2024, *bioRxiv*, https://doi.org/10.1101/2024.09.27.615438 |
| Substrate/regulator: TMBIM5 (GHITM) | **TMBIM5/GHITM** is both an **AFG3L2 substrate** and an **inhibitor/modulator** of AFG3L2, connecting the protease to mitochondrial Ca²⁺/H⁺ homeostasis and stress adaptation (pqac-00000008, pqac-00000011) | Primary | Chandragiri et al., 2024, *bioRxiv*, https://doi.org/10.1101/2024.09.27.615438 |
| Substrates: RNA metabolism factors | Recent proteomics identified AFG3L2 substrates in **mitochondrial RNA metabolism/gene expression**, including **LRPPRC, SLIRP, MTPAP, POLRMT, TFB2M, DHX30, GRSF1**, plus import factors (**PAM16, DNAJC15, TIMM17A**), especially under hypoxia (pqac-00000005, pqac-00000009, pqac-00000011, pqac-00000015) | Primary | Chandragiri et al., 2024, *bioRxiv*, https://doi.org/10.1101/2024.09.27.615438 |
| Regulatory pathway: GSH-dependent dissociation | **Mitochondrial glutathione status regulates AFG3L2–SLC25A39 interaction**: low matrix GSH promotes SLC25A39 stabilization by diminishing AFG3L2-mediated degradation, forming an autoregulatory feedback loop for mitochondrial GSH import (pqac-00000014) | Primary | Liu et al., 2023, *Science*, https://doi.org/10.1126/science.adf4154 |
| Regulatory pathway: Hypoxia / HIF1α–mTORC1 | AFG3L2 proteolysis is **activated in hypoxia** along a **HIF1α–mTORC1 axis**; mTORC1 inhibition or amino-acid starvation increases turnover of multiple AFG3L2 substrates, whereas constitutive mTORC1 activity stabilizes them (pqac-00000004, pqac-00000008, pqac-00000011, pqac-00000015) | Primary | Chandragiri et al., 2024, *bioRxiv*, https://doi.org/10.1101/2024.09.27.615438 |
| Regulatory pathway: PHB scaffold | The **prohibitin (PHB) membrane scaffold complex** associates with m-AAA protease and can modulate **substrate-specific AFG3L2 activity**, including in hypoxic remodeling of the mitochondrial proteome (pqac-00000011) | Primary | Chandragiri et al., 2024, *bioRxiv*, https://doi.org/10.1101/2024.09.27.615438 |
| Regulatory pathway: OMA1–DELE1–HRI ISR | In AFG3L2 deficiency/mutation, **mitochondrial proteotoxic stress** causes **OMA1 overactivation**, excessive **OPA1 processing**, mitochondrial fragmentation, and activation of the **OMA1–DELE1–HRI integrated stress response (ISR)** with increased eIF2α phosphorylation and ATF4 signaling (pqac-00000001, pqac-00000020) | Primary | Franchino et al., 2024, *Brain*, https://doi.org/10.1093/brain/awad340 |
| Human disease: SCA28 | **Spinocerebellar ataxia type 28 (SCA28)**: typically **autosomal dominant**, usually from **heterozygous AFG3L2 variants**, characterized by slowly progressive gait/limb ataxia with frequent oculomotor abnormalities (pqac-00000016, pqac-00000017, pqac-00000018, pqac-00000020) | Review + primary | Franchino et al., 2024, *Brain*, https://doi.org/10.1093/brain/awad340; Dastidar et al., 2024, *Mol Neurobiol*, https://doi.org/10.1007/s12035-023-03768-z |
| Human disease: DOA12 / OPA12 | **Dominant optic atrophy 12 (DOA12/OPA12)**: generally **autosomal dominant**, associated especially with **heterozygous ATPase- or catalytic-domain variants**; may overlap with ophthalmoplegia and broader mitochondrial optic neuropathy phenotypes (pqac-00000016, pqac-00000019, pqac-00000020) | Review + primary | Franchino et al., 2024, *Brain*, https://doi.org/10.1093/brain/awad340; Dastidar et al., 2024, *Mol Neurobiol*, https://doi.org/10.1007/s12035-023-03768-z |
| Human disease: SPAX5 | **Spastic ataxia type 5 / early-onset spastic ataxia-neuropathy syndrome (SPAX5)**: **autosomal recessive**, caused by **biallelic AFG3L2 variants**; severe childhood-onset phenotype with cerebellar ataxia, spasticity, dystonia, neuropathy, and in some cases myoclonic epilepsy (pqac-00000016, pqac-00000018, pqac-00000019, pqac-00000020) | Review + primary | Franchino et al., 2024, *Brain*, https://doi.org/10.1093/brain/awad340; Dastidar et al., 2024, *Mol Neurobiol*, https://doi.org/10.1007/s12035-023-03768-z |
| Therapeutic/diagnostic implications | Current clinical use is mainly **genetic diagnosis/variant interpretation** (NGS panels, exome-based workup for ataxia/optic neuropathy). Preclinical 2024 evidence suggests **ISR potentiation with Sephin-1** can improve SPAX5 cellular and mouse phenotypes; molecular readouts include **eIF2α phosphorylation, ATF4 targets, CHOP/CHAC1/FGF21** (pqac-00000016, pqac-00000017, pqac-00000020) | Review + primary | Franchino et al., 2024, *Brain*, https://doi.org/10.1093/brain/awad340; Dastidar et al., 2024, *Mol Neurobiol*, https://doi.org/10.1007/s12035-023-03768-z |


*Table: This table condenses the core functional annotation of human AFG3L2, including complex identity, localization, catalytic mechanism, experimentally supported substrates, regulatory pathways, and associated human diseases. It is useful as a quick-reference map linking molecular function to disease relevance and recent literature.*