Disorders of phospholipid metabolism: an emerging class of mitochondrial disease due to defects in nuclear genes

Abstract

The human nuclear and mitochondrial genomes co-exist within each cell. While the mitochondrial genome encodes for a limited number of proteins, transfer RNAs, and ribosomal RNAs, the vast majority of mitochondrial proteins are encoded in the nuclear genome. Of the multitude of mitochondrial disorders known to date, only a fifth are maternally inherited. The recent characterization of the mitochondrial proteome therefore serves as an important step toward delineating the nosology of a large spectrum of phenotypically heterogeneous diseases. Following the identification of the first nuclear gene defect to underlie a mitochondrial disorder, a plenitude of genetic variants that provoke mitochondrial pathophysiology have been molecularly elucidated and classified into six categories that impact: (1) oxidative phosphorylation (subunits and assembly factors); (2) mitochondrial DNA maintenance and expression; (3) mitochondrial protein import and assembly; (4) mitochondrial quality control (chaperones and proteases); (5) iron-sulfur cluster homeostasis; and (6) mitochondrial dynamics (fission and fusion). Here, we propose that an additional class of genetic variant be included in the classification schema to acknowledge the role of genetic defects in phospholipid biosynthesis, remodeling, and metabolism in mitochondrial pathophysiology. This seventh class includes a small but notable group of nuclear-encoded proteins whose dysfunction impacts normal mitochondrial phospholipid metabolism. The resulting human disorders present with a diverse array of pathologic consequences that reflect the variety of functions that phospholipids have in mitochondria and highlight the important role of proper membrane homeostasis in mitochondrial biology.

Keywords: Barth syndrome; DCMA; MEGDEL; Sengers syndrome; cardiolipin; hereditary spastic paraplegia; mitochondrial disease; phospholipid metabolism.

FIGURE 1

Mammalian cardiolipin biosynthesis. CL biosynthesis likely involves PA sourced from multiple pathways. PA can be generated by LPAATs which acylate LPA; LPA can be made using glycerol 3-phosphate (G3P) and acyl-CoAs by mitochondrial and ER GPATs. Additionally, PA can be made on the OMM through the hydrolysis of CL by MitoPLD. In the OMM, PA recruits the phosphatase lipin-1 which dephosphorylates PA into DAG. In turn, DAG may traffic across the OMM and be phosphorylated by AGK forming PA in the context of the IMS-side of the IMM. Regardless of where it is made, PA must reach the matrix side of the IMM to gain access to the core CL biosynthetic machinery. Here, PA is converted to CDP-DAG by TAMM41, thus providing the precursor for the committed step in CL biosynthesis, PGP synthesis by PGS1. PGP is rapidly dephosphorylated by PTPMT1 and the produced PG is condensed with CDP-DAG by CLS generating CL. Dashed arrows describe uncharacterized steps and pathways.

FIGURE 2

Mammalian cardiolipin remodeling. CL that is synthesized by CLS on the matrix-facing leaflet of the IMM can by remodeled by three different pathways. While no single enzyme has been demonstrated to be required to initiate CL remodeling in mammals, several phospholipases of the iPLA₂ family have been demonstrated to have a role in the process. Additionally, the submitochondrial localization of the phospholipases and the mechanisms by which CL gains access to these enzymes are unknown. After a fatty acyl chain is hydrolyzed from CL, generating MLCL, MLCL can be acylated back to CL by acyltransferases or transacylases. MLCLAT1 on the matrix-leaflet of the IMM, TAZ on the IMS-facing leaflets of the OMM and IMM, and ALCAT1 on the ER MAM all have the capacity to re-acylate MLCL. The acyltransferases, ALCAT1 and MLCLAT1, use acyl-CoAs as an acyl chain donor to acylate MLCL. In contrast, the transacylase TAZ uses acyl chains donated from other phospholipids. The activity of TAZ is required to establish the steady state physiological CL molecular form. In contrast, the CL formed by ALCAT1 is more sensitive to oxidative damage and associated with pathologic states. Dashed arrows describe uncharacterized steps and pathways. In the phospholipid key, unremodeled CL corresponds to the newly synthesized CL that enters the pathway at the point of CLS (black head group). CL can undergo either physiologically relevant CL remodeling (green head group) or pathological remodeling (red head group).

FIGURE 3

Inter-organelle and intra-organelle phospholipid trafficking. The existence of ER- and vacuole-mitochondria contacts is highly conserved from yeast to humans. By generating closely appositioned membranes, the inter-organelle and intra-organelle tethers are hypothesized to promote movement of lipids across the aqueous cytosol and IMS, respectively. Within the mitochondrion, phospholipid trafficking may involve contacts between the OMM and the IMM mediated by MICOS complexes or NM23-H4. In addition, PRELI transports PA from the OMM to the IMM. PLS3 activity stimulates CL externalization on OMM. It may directly transport CL from the IMM to the OMM or instead function as a scramblase that redistributes CL between both leaflets of the IMM. CL now exposed to IMS-side of IMM would then be transported to the OMM by other mechanisms. With the possible exception of EMC, it is presently unclear if any of the known tethers has specificity for a defined phospholipid(s); as such, they are shown to promote the flux of phospholipids (PLs) in bulk. If a specific phospholipid is impacted by mutations in a complex/protein (levels and/or composition), the lipid is indicated. Solid lines indicate known transport mechanisms. Dashed lines describe possible trafficking routes and/or highlight transport events whose mechanisms have not been resolved. The ERMES complex is found only in yeast and color-coded pink. For the remaining proteins/complexes, those found only in mammals are in blue and those that are likely to be conserved across species are colored gray. See text for additional details.

FIGURE 4

Biological functions of cardiolipin. As the signature phospholipid of the mitochondrion, CL is intimately involved in a number of mitochondrial processes. (A) Anionic CL on the IMM can function as a proton trap by attracting (and providing) a local pool of protons that can be funneled towards the ATP synthase. Moreover, CL is associated with every OXPHOS component and can promote their assembly into respiratory supercomplexes. Such supramolecular assemblies are thought to enhance electron transfer and reduce ROS leakage from the electron transport chain. (B) CL associates with dynamin-related GTPases that are intimately involved in fusion and fission and (C) contributes to the assembly and function of IMM and OMM translocases vital for mitochondrial biogenesis. (D) Besides enhancing OXPHOS by stabilizing SCs, CL also promotes the assembly of ATP synthase oligomers that provide a structural scaffold required for establishing the characteristic shape of mitochondrial cristae. (E) Externalization of CL on the surface of the mitochondrion is involved in signaling the execution of either mitophagy or apoptotic cell death.

FIGURE 5

Potential mechanisms of DCMA mitochondrial dysfunction. (A) Under physiological conditions, DNAJC19 is targeted to TIM17B by MAGMAS and associates with components of the TIM23 translocation machinery, forming translocase B. DNAJC19 is homologous to yeast Pam18p which stimulates the mtHsp70 activity of the PAM (presequence-associated motor) complex and stabilizes binding of incoming precursors. Moreover, DNAJC19 also interacts with prohibitin-2 (PHB) of the PHB complexes. PHB1/PHB2 oligomers form ring-like complexes that are modeled to delineate specialized membrane domains. Functional segregation of CL and TAZ in such domains may confer acyl chain specificity to TAZ, allowing it to perform physiologically relevant CL remodeling (green). Thus, DNAJC19 may participate in both mitochondrial presequence protein import as well as formation of membrane domains that are important for TAZ-based CL remodeling. (B) In the absence of DNAJC19, the ability of the TIM23 machinery to import proteins across the IMM may be compromised. Consequently, the biogenesis of mitochondrial proteins, such as subunits of respiratory complexes, may be reduced. (C) Further, loss of DNAJC19 prevents the PHB complex-based generation of privileged membrane domains. In the absence of such domains, TAZ remodeling, which may still occur, lacks specificity (red). For clarity, not all components of the TOM, TIM, and PAM complexes are depicted.

FIGURE 6

Potential consequences of the absence of SERAC1 activity. (A) PG that is generated on the matrix-leaflet of the IMM is trafficked out of the mitochondrion and remodeled by SERAC1 on the ER MAMs. Remodeled PG can subsequently serve as substrate for BMP and CL synthesis. BMP in the endosomsal/lysosomal compartments regulates (green arrow) cholesterol esterification and trafficking out of the compartment. (B) In the absence of a functional SERAC1, PG is not remodeled and accumulates shorter acyl chain moieties. The decrease in acyl chain length somehow reduces overall BMP levels, perhaps because the unremodeled PG is a poor precursor for BMP synthesis. Reduced BMP levels in the endosome/lysosome impairs cholesterol esterification (inhibition in red) and leads to decreased (red arrows) cholesterol efflux. The lack of SERAC1 also changes the steady state composition of CL acyl chains. Blue arrows denote enzymatic reactions and lipid movements. Dashed arrows describe uncharacterized steps and pathways.