These are all transmitted by Mendelian inheritance and include 6 major subgroups.
Mutations in genes encoding subunits of the respiratory chain (“direct hits”). As noted above, mtDNA encodes only 13 subunits of the respiratory chain, while nDNA encodes all subunits of complex II, most subunits of the other 4 complexes, as well as CoQ10 and cytochrome c. Nuclear DNA mutations can affect respiratory chain complexes directly or indirectly.
Direct "hits,” that is, mutations in genes encoding respiratory chain subunits, are known mostly for 2 complexes (complex 1 and complex 2). In general – and in keeping with the all-or-none effects of mendelian mutations (most of which are recessive), as opposed to the variegated effects of heteroplasmic mtDNA mutations – disorders due to “direct hits” manifest at or soon after birth and are very severe, often lethal in infancy. Most of these mutations have been associated with autosomal recessive forms of Leigh syndrome, a disorder that reflects the ravages of energy shortage on the developing nervous system. The neuropathological (or neuroradiological) hallmarks of Leigh syndrome are bilateral symmetric lesions all along the nervous system, but especially in the basal ganglia, thalamus, brainstem, and cerebellar roof nuclei. Microscopically, there is neuronal loss, proportional loss of myelin, reactive astrocytosis, and proliferation of cerebral microvessels (DiMauro et al 2013).
Mutations in assembly proteins (“indirect hits”). Even when all nDNA-encoded subunits of the various complexes are expressed correctly, they have to be translated, imported into mitochondria, and directed to the mitochondrial inner membrane, where they assemble with their mtDNA-encoded and nDNA-encoded counterparts.
The search for the molecular basis of COX-deficient Leigh syndrome led to the simultaneous discovery by 2 laboratories of the first mutant assembly gene, SURF1 (Tiranti et al 1998; Zhu et al 1998). Mutant assembly factors have been found through whole exome sequencing (WES) of patients with specific respiratory chain complex deficiencies, such as children with complex I deficiency (Calvo et al 2010).
The clinical manifestations of indirect hits in complex I tend to be more heterogeneous than those associated with direct hits (Fernandez-Vizarra et al 2009; Tucker et al 2012). All described patients had encephalopathy clinically resembling Leigh syndrome, but often with leukodystrophy rather than grey matter involvement. Cardiomyopathy was more common and often the dominating feature.
The first assembly defect in complex III was identified in 2002 in Finnish infants with an extremely severe syndrome named GRACILE that summarizes acronymically the main symptoms and signs: growth retardation, aminoaciduria, cholestasis, iron overload, and early death (before 5 months of age) (Visapaa et al 2002). The mutated protein, BCS1L, is needed for the insertion of the Rieske FeS subunit into the complex.
Mutations in the assembly protein SURF1 are among the most common causes of Leigh syndrome, and SURF1 ought to be sequenced in all children with COX-deficient Leigh syndrome.
Mutations in at least 7 more COX assembly factors have been associated with human diseases; although all cause encephalopathy, each also involves 1 other tissue preferentially. Thus, mutations in SCO2 cause severe cardiopathy, as do mutations in COX10, COX15, and COA5, whereas mutations in SCO1 cause hepatopathy (DiMauro et al 2012).
The function of complex V depends on the integrity of 2 partners, the adenine nucleotide transporter (ANT1) and the inorganic phosphate carrier (PIC). Whereas mutations in ANT1 affect mostly mtDNA maintenance (see below), mutations in SCL25A3, the gene encoding the heart and muscle isoform of PIC, affect ATP synthesis and caused infantile and rapidly fatal cardiopathy and myopathy in 2 sisters (Mayr et al 2007).
We include among the indirect hits a relative new group of disorders due to coenzyme Q10 (CoQ10) deficiency. In this case, mutations in a cascade of biosynthetic enzymes result in the deficiency of 1 relatively simple component of the respiratory chain. CoQ10 (ubiquinone) is a small lipophilic molecule comprising a redox active benzoquinone ring and a polyisoprene tail consisting of 10 units in humans.
PrimaryCoQ10 deficiencies can cause 5 major syndromes: (1) a predominantly myopathic disorder with recurrent myoglobinuria but also CNS involvement (seizures, ataxia, mental retardation) (Ogasahara et al 1989); (2) a predominantly encephalopathic disorder with ataxia and cerebellar atrophy; (3) an isolated myopathy, with ragged-red fibers and lipid storage; (4) a generalized mitochondrial encephalomyopathy, usually with onset in infancy; (5) nephropathy alone or associated with encephalopathy (Quinzii and Hirano 2010; Emmanuele et al 2012); and (6) a wide spectrum of mitochondrial disorders due to mutations in COQ4 (Brea-Calvo et al 2015). Examples of secondary CoQ10 deficiency include ataxia oculomotor apraxia (AOA1) associated with mutations in the aprataxin (APTX) gene, the myopathic presentation of glutaric aciduria type II due to mutations in the electron transfer flavoprotein dehydrogenase (ETFDH) gene (Gempel et al 2007), and autosomal recessive spinocerebellar ataxia (SCAR) due to mutations in ANO10 (Balreira et al 2014). Examples of primary CoQ10 deficiency include mutations in the biosynthetic genes, COQ1 (PDSS1 and PDSS2), COQ2, COQ9, COQ6, COQ4, and CABC1/ADCK3. Irrespective of etiology, diagnosis is important because most patients with CoQ10 deficiency respond to high-dose CoQ10 supplementation (Quinzii and Hirano 2010; Emmanuele et al 2012).
In a novel type of indirect hit, the second whammy is toxic instead of structural, as illustrated by ethylmalonic encephalomyopathy (EE), a devastating early-onset disorder with encephalopathy, microangiopathy, chronic diarrhea, and massively increased levels of ethylmalonic acid and short-chain acylcarnitines in body fluids. This disorder is due to mutations in the ETHE1 gene, whose product, ETHE1, is a mitochondrial matrix thioesterase. Studies of an Ethe1-null mouse led to the discovery that thiosulfate and sulfide accumulate excessively both in the animal model and in affected children due to the lack of sulfur dioxygenase activity (Tiranti et al 2009). As sulfide is a powerful COX inhibitor, this turned out to be an indirect hit of a toxic kind and likely the prototype of other similar pathogenic mechanisms.
Because a prerequisite for the assembly of any respiratory chain complex is the import of nDNA-encoded subunits from the cytoplasm into mitochondria, it seems plausible to add one more category to the indirect hits, defects of mitochondrial protein importation. An example is the X-linked deafness-dystonia syndrome (Mohr-Tranebjaerg syndrome), characterized by progressive sensorineural deafness, dystonia, cortical blindness, and psychiatric symptoms. This disorder is due to mutations in TIMM8A, which encodes the deafness-dystonia protein (DDP1), a component of the mitochondrial protein import machinery located in the intermembrane space (Roesch et al 2002).
This field of research has important theoretical and practical implications. From an investigative point of view, these disorders are teaching us a lot about the structural and functional complexity of the respiratory chain. At a more practical level, identification of mutations in these genes allows prenatal diagnosis and suggests approaches to therapy.
Defects of mtDNA maintenance (intergenomic signaling). As noted above, the mtDNA has become the slave of nDNA and depends on numerous factors encoded by nuclear genes. Mutations in these genes cause Mendelian disorders characterized by qualitative or quantitative alterations of mtDNA. Two important features of this group of diseases ought to be considered. First, although inheritance is unequivocally Mendelian, these disorders share much of the clinical heterogeneity of primary mtDNA-related diseases, presumably because the polyploid mtDNA is involved in both conditions. Second, we had been lured into the simplistic concept that mtDNA depletion and mtDNA multiple deletions were distinct conditions with characteristic and distinguishable phenotypes. Largely due to the application of whole genome sequencing, we have been disabused of this idea and now realize that the 2 conditions often coexist and that mutations in the same genes can cause either predominantly mtDNA depletion in infants or children or predominantly mtDNA multiple deletions in adults (DiMauro et al 2013).
Examples of qualitative alterations include autosomal dominant or recessive multiple mtDNA deletions of mtDNA, usually accompanied clinically by progressive external ophthalmoplegia (PEO) plus a variety of other symptoms and signs. Several of these conditions have been characterized at the molecular level. Mutations in the gene TYMP for thymidine phosphorylase are responsible for an autosomal recessive multisystemic syndrome called mitochondrial neurogastrointestinal encephalomyopathy (MNGIE) (Hirano et al 1994). Mutations in the gene for 1 isoform of the adenine nucleotide translocator (ANT1) have been identified in patients with autosomal dominant progressive external ophthalmoplegia (Kaukonen et al 2000). Mutations in the PEO1 gene, encoding Twinkle, a helicase, are also associated with autosomal dominant progressive external ophthalmoplegia (Spelbrink et al 2001).
The ultimate example of a single gene causing either mtDNA depletion or multiple mtDNA deletions and resulting in extremely diverse syndromes is POLG, the gene encoding Polg-A. Depending largely on which of the 3 domains of POLG (polymerase, exonuclease, linker region) harbors the mutation(s), the clinical phenotype ranges from a severe hepatocerebral disorder of infancy or childhood (Alpers syndrome) to adult-onset autosomal dominant or recessive progressive external ophthalmoplegia (AD- or AR-PEO) to parkinsonism and to other clinical phenotypes, including sensory ataxic neuropathy, dysarthria, and ophthalmoparesis (SANDO), and mitochondrial recessive ataxia syndrome (MIRAS) (Copeland 2008; Ylikallio and Suomalainen 2012). Similarly, mutations in the PEO1 gene encoding the Twinkle helicase usually cause adult-onset AD-PEO with multiple mtDNA deletions, but can also cause Alpers-like autosomal recessive hepatocerebral syndrome with mtDNA liver depletion, or infantile-onset spinocerebellar ataxia (IOSCA), a disease prevalent in the Finnish population and characterized by mtDNA depletion in the brain (Ylikallio and Suomalainen 2012).
Mutations in the gene POLG2, encoding the accessory subunit of POLG, can also cause autosomal dominant progressive external ophthalmoplegia and multiple deletions (Van Goethem et al 2001; Longley et al 2006). Finally, mutations in OPA1, which encodes a protein involved in mitochondrial dynamics (see below), besides causing dominant optic atrophy can also result in a syndrome that includes optic neuropathy, progressive external ophthalmoplegia, deafness, ataxia, and axonal neuropathy associated with multiple mtDNA deletions in the muscle biopsy (Amati-Bonneau et al 2008; Hudson et al 2008).
An iatrogenic form of mtDNA depletion may follow treatment with nucleoside analogs such as zidovudine (AZT) and will cause multiple mtDNA deletions (Payne et al 2015).
Examples of quantitative alterations of mtDNA include severe or partial mtDNA depletion, usually characterized clinically by congenital or childhood forms of autosomal recessively inherited myopathy or hepatopathy. Mutations in 9 genes, 7 of them involved in mitochondrial nucleotide homeostasis, have been associated with mtDNA depletion syndromes, although they still do not explain all cases (Suomalainen and Isohanni 2010). Mutations in the gene encoding thymidine kinase 2 (TK2) are typically seen in patients with myopathic mtDNA depletion syndromes, whereas mutations in the genes encoding the beta subunit (SUCLA2) or the alpha subunit (SUCLG1) of the mitochondrial matrix enzyme succinyl-CoA synthetase (SCS-A) cause both myopathy and encephalopathy. Mutations in DGUOK, encoding deoxyguanosine kinase, predominate in patients with hepatic or hepatocerebral mtDNA depletion syndromes, but mutations in POLG are the major causes of Alpers-Huttenlocher syndrome, a severe hepatocerebral syndrome with vulnerability to valproic acid (Naviaux and Nguyen 2004). Mutations in the gene MPV17, not involved in nucleotide pool homeostasis, have been associated with hepatocerebral syndrome (Spinazzola et al 2006) and with the Navajo neurohepatopathy syndrome, prevalent in the Navajo population of the southwestern Unites States (Karadimas et al 2006). Mutations in FBXL4 cause mtDNA depletion accompanied by early-onset mitochondrial encephalomyopathy (Bonnen et al 2013; Gai et al 2013). FBXL4 is localized in the intermembrane space, where it controls bioenergetic homeostasis and mtDNA maintenance.
Defects of mtDNA translation. The mitochondrial genome is translated into 9 monocistronic and 2 dicistronic mRNAs. Translation of these mRNAs into the 13 mtDNA-encoded respiratory chain subunits is effected by mitoribosomes that consist of 1 large subunit (48 proteins) and 1 small subunit (29 proteins). The translation process can be broken down into 4 phases, each requiring multiple ancillary factors (Christian and Spremulli 2012; Pearce et al 2013).
A group of defects of intergenomic communication is due to mutations in genes encoding those factors necessary for the faithful translation of mtDNA-encoded proteins (Christian and Spremulli 2012; Pearce et al 2013), including EFG1 (encoding elongation factor 1), MRPS16 (encoding small subunit protein), EFTu (encoding elongation factor Tu), TSFM (controlling the expression of both EFTs and EFTu), and PUS1 (encoding pseudouridine synthase 1). The resulting disorders usually affect infants and cause severe encephalomyopathy, cardiomyopathy, or sideroblastic anemia. Typically, both quality and quantity of mtDNA are normal in these patients, but there are – not surprisingly – multiple respiratory chain defects involving all complexes containing mtDNA-encoded subunits. Mutations in genes encoding mitochondrial amino acyl-tRNA synthetases cause a variety of syndromes. For example, mutations in DARS2 (encoding mitochondrial aspartyl-tRNA synthetase) cause leukoencephalopathy with brainstem and spinal cord involvement and lactate elevation (LBSL): surprisingly, no defects of respiratory chain enzymes were found in patients with LBSL, at least in fibroblasts and lymphoblasts (Scheper et al 2007). A novel mutation in the gene encoding aminoacyl-tRNA synthetase (AARS) caused Charcot-Marie-Tooth neuropathy in 1 family (Motley et al 2015).
Defects of the inner membrane lipid milieu. The function of the respiratory chain can be impaired by alterations in the lipid composition of the inner mitochondrial membrane, which does not act simply as a scaffold, but participates in the function of the respiratory chain. The first and prototypical disorder in this group is Barth syndrome, an X-linked recessive disorder characterized by mitochondrial myopathy, cardiopathy, and leukopenia (Barth et al 1999). The gene responsible for this disorder (TAZ) (Bione et al 1996) encodes a family of proteins (“tafazzins”) involved in the synthesis of phospholipids, and biochemical analysis has shown altered amounts and composition of cardiolipin, the main phospholipid component of the inner mitochondrial membrane (Schlame and Ren 2006).
Like Barth syndrome, Sengers syndrome also affects primarily heart and muscle, with the distinctive additional clinical feature of congenital cataracts. Muscle biopsy shows mitochondrial myopathy and respiratory chain dysfunction, with lactic acidosis and decreased activities of multiple respiratory chain enzymes. Although there was convincing evidence that ANT1 was missing in muscle of patients, no mutation was found in that gene, leading to postulations of defective transcription or translation. Whole exome sequencing solved the riddle when it revealed mutations in AGK, the gene encoding acylglycerol kinase (Mayr et al 2012). AGK catalyzes the phosphorylation of diacyl- and monoacylglycerol to form phosphatidic acid (PA) or lysophosphatidic acid (LPA), important intermediates in the synthesis of phospholipids. As PA is also a precursor of cardiolipin, there is a point of convergence with the pathogenesis of Barth syndrome, probably explaining some of the clinical similarities between the 2 disorders.
A third defect of the inner mitochondrial membrane lipid milieu is due to mutations in the gene encoding choline kinase beta (CHKB) that catalyzes the first step in the biosynthesis of phosphatidylcholine. The resulting clinical picture is a congenital mitochondrial myopathy morphologically characterized by giant mitochondria (“megaconial myopathy”) displaced to the periphery of the fibers (Mitsuhashi et al 2011a; 2011b; Gutierrez-Rios et al 2012; Quinlivan et al 2013).
Altered inner membrane phospholipid composition was documented in another disorder dubbed MEGDEL, an acronym referring to a syndrome characterized by 3-methylglutaconic aciduria type IV, deafness, and Leigh-like encephalopathy (Wortmann et al 2009). In this case, whole exome sequencing revealed mutations in the SERAC1 gene: SERAC controls the exchange of phospholipids between the endoplasmic reticulum and mitochondria (Wortmann et al 2012). Analysis of patient fibroblasts showed both altered distribution of phosphatidylglycerol species and altered composition of cardiolipin subspecies. Thus, quantitative or qualitative alterations in cardiolipin may be a common denominator in the pathogenesis of disorders other than Barth syndrome.
Finally, at least for now, recurrent muscle breakdown and myoglobinuria in children, a syndrome often occurring during febrile illnesses and rarely associated with known inborn errors of energy metabolism, has been attributed to mutations in LPIN1, a gene encoding the muscle-specific isoform of phosphatidic acid phosphatase (Zeharia et al 2008). Here, there is no direct evidence of mitochondrial dysfunction: rather, damage to the sarcolemma is postulated to occur through the detergent action of accumulated lysophospholipids.
Defects of mitochondrial motility, fusion, and fission. Defects of mitochondrial dynamics are taking center stage as causes of neurodegenerative disorders and do belong to the mitochondrial diseases sensu stricto because impairment of oxidative phosphorylation has been documented. Mitochondria travel on microtubular rails, propelled by motor proteins, usually GTPases, called kinesins or dyneins (Chan 2007). The first defect of mitochondrial motility was identified in a family with autosomal dominant hereditary spastic paraplegia and mutations in a gene (KIF5A) encoding 1 of the kinesins. Interestingly, the mutation affects a region of the protein involved in microtubule binding (Fichera et al 2004).
Mutations in OPA1 cause autosomal dominant optic atrophy, the Mendelian counterpart of Leber hereditary optic neuropathy. Mutations in MFN2, encoding mitofusin 2, cause an autosomal dominant axonal variant of Charcot-Marie-Tooth disease. Also, mutations in GDAP1, the gene encoding ganglioside-induced differentiation protein 1, which is located in the mitochondrial outer membrane and regulates the mitochondrial network, cause Charcot-Marie-Tooth disease type 4A, an autosomal recessive, severe, early-onset form of either demyelinating or axonal neuropathy (DiMauro et al 2013).