Mitochondrial DNA in Aging and Degenerative

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Mutation Research 475 (2001) 169–184 Review Mitochondrial DNA in aging and degenerative disease Carolyn D. Berdanier * , Helen B. Everts Department of Foods and Nutrition, University of Georgia, Athens, GA 30602, USA Received 24 March 2000; received in revised form 20 September 2000; accepted 24 September 2000 Abstract The mitochondrial DNA encodes only a few gene products compared to the nuclear DNA. These products, however, play a decisive role in determining cell function. Should this DNA mutate spontaneously or be damaged by free radicals the functionality of the gene products will be compromised. A number of mitochondrial genetic diseases have been identified. Some of these are quite serious and involve the central nervous system as well as muscle, heart, liver and kidney. Aging has been characterized by a gradual increase in base deletions in this DNA. This increase in deletion mutation has been suggested to be the cumulative result of exposure to free radicals. © 2001 Elsevier Science B.V. All rights reserved. Keywords: Mitochondrial DNA; Mitochondrial diseases; Aging; Oxidative stress 1. Introduction Mitochondria have long been known to serve as central integrators of intermediary metabolism. In this compartment can be found the enzymes of the cit- ric acid cycle, fatty acid oxidation, the initial reaction of the urea cycle, the respiratory chain, and a vari- ety of carriers or transporters. They are the organelles responsible for the synthesis of the high-energy com- pound, ATP. The synthesis of ATP is coupled to the respiratory chain that produces water by joining two molecules of hydrogen to one molecule of oxygen. This dual synthesis occurs in a stepwise sequence of reactions known as oxidative phosphorylation (OX- PHOS). Each of the components of OXPHOS must be present and active. If any one of the many proteins comprising OXPHOS is missing or abnormal due to * Corresponding author. Tel.: +1-706-542-4858; fax: +1-706-542-5059. E-mail address: [email protected] (C.D. Berdanier). one or more mutations in the genes encoding these proteins, then OXPHOS will be compromised. The majority of these proteins are encoded by the nuclear genome, synthesized on the ribosomes and imported into the mitochondria. Thirteen of the proteins are en- coded by the mitochondrial (mt) DNA. This review will discuss this genome and its expression with re- spect to aging, free radical damage and degenerative disease. 1.1. The mitochondrial genome In animals, the mtDNA exists as a double stranded closed circular molecule [1–14]. Fig. 1 shows the hu- man mt genome. The size of this genome ranges from approximately 16 kb in animals to more than 100 kb in plants. The expression of this genome more closely resembles that of prokaryotes than that of eukaryotes as suggested by the endosymbiotic hypothesis of mt origin. In animals, the mt DNA is about the same size and has the same organization and content of 0027-5107/01/$ – see front matter © 2001 Elsevier Science B.V. All rights reserved. PII:S0027-5107(01)00068-9

Transcript of Mitochondrial DNA in Aging and Degenerative

Page 1: Mitochondrial DNA in Aging and Degenerative

Mutation Research 475 (2001) 169–184

Review

Mitochondrial DNA in aging and degenerative disease

Carolyn D. Berdanier∗, Helen B. EvertsDepartment of Foods and Nutrition, University of Georgia, Athens, GA 30602, USA

Received 24 March 2000; received in revised form 20 September 2000; accepted 24 September 2000

Abstract

The mitochondrial DNA encodes only a few gene products compared to the nuclear DNA. These products, however, playa decisive role in determining cell function. Should this DNA mutate spontaneously or be damaged by free radicals thefunctionality of the gene products will be compromised. A number of mitochondrial genetic diseases have been identified.Some of these are quite serious and involve the central nervous system as well as muscle, heart, liver and kidney. Aging hasbeen characterized by a gradual increase in base deletions in this DNA. This increase in deletion mutation has been suggestedto be the cumulative result of exposure to free radicals. © 2001 Elsevier Science B.V. All rights reserved.

Keywords:Mitochondrial DNA; Mitochondrial diseases; Aging; Oxidative stress

1. Introduction

Mitochondria have long been known to serve ascentral integrators of intermediary metabolism. In thiscompartment can be found the enzymes of the cit-ric acid cycle, fatty acid oxidation, the initial reactionof the urea cycle, the respiratory chain, and a vari-ety of carriers or transporters. They are the organellesresponsible for the synthesis of the high-energy com-pound, ATP. The synthesis of ATP is coupled to therespiratory chain that produces water by joining twomolecules of hydrogen to one molecule of oxygen.This dual synthesis occurs in a stepwise sequence ofreactions known as oxidative phosphorylation (OX-PHOS). Each of the components of OXPHOS mustbe present and active. If any one of the many proteinscomprising OXPHOS is missing or abnormal due to

∗ Corresponding author. Tel.:+1-706-542-4858;fax: +1-706-542-5059.E-mail address:[email protected] (C.D. Berdanier).

one or more mutations in the genes encoding theseproteins, then OXPHOS will be compromised. Themajority of these proteins are encoded by the nucleargenome, synthesized on the ribosomes and importedinto the mitochondria. Thirteen of the proteins are en-coded by the mitochondrial (mt) DNA. This reviewwill discuss this genome and its expression with re-spect to aging, free radical damage and degenerativedisease.

1.1. The mitochondrial genome

In animals, the mtDNA exists as a double strandedclosed circular molecule [1–14]. Fig. 1 shows the hu-man mt genome. The size of this genome ranges fromapproximately 16 kb in animals to more than 100 kbin plants. The expression of this genome more closelyresembles that of prokaryotes than that of eukaryotesas suggested by the endosymbiotic hypothesis of mtorigin. In animals, the mt DNA is about the samesize and has the same organization and content of

0027-5107/01/$ – see front matter © 2001 Elsevier Science B.V. All rights reserved.PII: S0027-5107(01)00068-9

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Fig. 1. Map of the human mitochondrial genome. The location of the various genes is consistent between species however the lengthvaries from one species to another.

genes [3–14]. In rat, the size of the mt genome is16,298 bp; in humans it is 16,569 bp. The mt genomehas been sequenced and mapped for many species yetthe regulation of its expression is poorly understood.

The mtDNA encodes 22 transfer RNAs, 2 ribosomalRNAs, and 13 structural genes. These structural genesencode 13 components of OXPHOS. The structuralgenes encode 7 of the 39 subunit proteins of ComplexI (ND1, 2, 3, 4, 4L, 5, and 6), 1 of the 10 subunitproteins of complex (Cyt b), 3 of the 13 subunit pro-teins of complex IV (CO I, II and III), and 2 subunitproteins of the F0 portion of complex V, the F1F0

ATPase. Approximately 6% of the bases in the mtgenome are noncoding. The 97% of this noncodingDNA is located in the two controller regions, the30 bp origin of replication for the light strand (OL),and the 898 bp unit called the D-loop. The strands ofmtDNA have been named light and heavy according totheir buoyancy through a denaturing cesium chloridegradient.

The heavy strand is the main coding strand, andcodes for 2 rRNA species, 14 tRNA species and 12structural genes. The light strand codes for 8 tRNAspecies and 1 structural gene for a subunit of NADH

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dehydrogenase. The genome sequence shows extremeeconomy in that very few genes have noncoding basesbetween them [3–8]. In fact, the largest space betweentwo genes is a 5 bp sequence between the genes fortRNAGlu and the cytochromeb gene. The controllerregion has more of these noncoding regions yet theyare few in number compared to the nuclear genome.There is gene overlap as well. In six instances, theshared nucleotides are not really shared; they are on theheavy and light strands such that the shared bases areon the 3′-ends of the two genes. In the other three in-stances, the shared bases are actually frame shifts thatallow the same nucleotides to code for two differentproteins. The genes that share nucleotides include theATPase 6 and 8 genes that share 52 bp, ND4 and ND4Lthat share seven, the tRNASer and the tRNALeu thatshare one, ND5 and ND6 that share 31, the tRNASer

and the cytochrome oxidase I gene that share fourand lastly, the tRNAIle and tRNAGln genes that share3 bp. Of interest is the observation that only 56 bp areall that separate the different genes on the mt genomeand that 98 bp are shared by neighboring genes.

1.2. Mitochondrial gene transcription

Early studies revealed that transcription is sym-metrical [15] and is initiated within the D-loop. Lightstrand transcription moves clockwise and theheavy strand transcription moves counterclockwise[5,16,17]. The light strand has a longer half life andthere is roughly twice as much of this strand as theheavy strand. The light strand is transcribed as onepolycistron while the heavy strand is transcribed astwo polycistrons [18]. One of the heavy strand poly-cistrons encodes all of the heavy strand, while theother encodes the two rRNAs. Three distinct promotersequences, one for the light strand and two for theheavy strand, have been described [6,13,19–23]. Inaddition, the light strand promoter (LSP) region alsoprimes the replication of the heavy strand [24,25]forming a RNA–DNA primer that is cleaved by theRNase mt RNA processing (MRP) enzyme. Thiscleavage occurs at the origin of heavy strand repli-cation [26]. There are three sequence blocks that areconserved among a number of species [27]. Thesesequences are involved in this RNA–DNA cleavage.

In humans, both the LSP and the heavy strandpromoter (HSP) sequences contain regions near the

start site containing specific nucleotides required fortranscription initiation. There are also upstream reg-ulatory regions. In mouse, the LSP contains threedomains. The first consists of nucleotides−10 to+9(relative to transcription initiation) that are requiredfor accurate transcription initiation. The second do-main (nt-11 to -29) facilitates the formation of thepreinitiation complex and the third domain (nt-30to -88) affects transcriptional efficiency. In contrast,specific nucleotides are not required near or at thetranscription start sites for heavy strand transcriptioninitiation. There is an essential upstream element forthe start site of the mouse HSP. Promoter sequencesare not highly conserved among species and thereare some cross species activities. For example, mouseRNA polymerase is active on rat mtDNA. This sug-gests that the rat and mouse promoters are similar.Between the mouse and the human there is an addi-tional difference in that the two HSP start sites areclose together in the mouse but not in the human. Inhumans, the main start site is near the D-loop/tPheborder with a minor start site between the tPhe and12S gene. The main start site is thought to result intranscription of the two rRNA genes while the minorone initiates transcription of the whole heavy strand.

At present, only two transcription factors have beenwell studied. Both of these are nuclear encoded. Theyare mitochondrial transcription factor A (mtTFA) thatstimulates initiation [28,29] and mitochondrial tran-scription termination factor (mTERF) that is involvedin the termination of the heavy strand after the rRNAsare formed [30]. There are probably many more fac-tors that influence mtDNA transcription but we areonly now beginning to elucidate them.

In vitro studies have shown that mtTFA binds toboth promoter regions as well as to a region in-betweentwo of the conserved sequence blocks. The mtTFAcondenses, unwinds, and bends mtDNA [31,32]. In ad-dition, in vitro, more mtTFA is needed to promote tran-scription of the heavy strand than to promote transcrip-tion of the light strand. This suggests that low levels ofmtTFA may result in the activation of the light strandand be involved in replication. This suggestion is sup-ported by the observation that mtTFA protein levelshave been correlated with mtDNA copy number. A de-ficiency in mtTFA results in mtDNA depletion [33,34].

Transgenic technology has provided further evi-dence of mtTFAs role in transcription and replication.

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First, overexpression of mtTFA in HeLa cells and inisolated liver mitochondria were shown to increasemt transcription [35]. Second, heterozygousm-mtTFA(also calledTfam) knockout mice were shown tohave reduced mtDNA copy number in heart, kidneyand liver, reduced mt transcription in the heart, andreduced respiratory chain function in the heart [36].The kidney, liver and skeletal muscle were variable inthis respect. Interestingly, the protein levels of mito-chondrially encoded cytochrome c oxidase subunit IIand ATP synthase subunit 8 were normal in all tissuesstudied in these mice. Using knockout technology itwas found that if the gene for the mtTFA was com-pletely absent, this absence was lethal. Thus, there areno homozygous knockout mice. These data, in com-bination with the in vitro data, support the idea thatmtTFA is essential for mt replication, primed fromthe LSP; but is not solely responsible for regulatingheavy strand transcription. It is altogether likely thatmt transcription depends on the presence of othertranscription factors as well.

Because genes occur in both the nuclear and mtgenomes that encode components of OXPHOS, theremust be a mechanism available that coordinates theexpression of both. The nuclear respiratory factors(NRF) 1 and 2 and the general transcription factorSp1 serve this function. They simultaneously regulatethe expression of mtTFA as well as several nuclearOXPHOS genes [37–42]. During rapid cell prolifer-ation this coordinated expression has been shown tooccur. However, such coordination has not been foundunder all circumstances. For example, in either hypo-or hyper-thyroidism discoordination rather than coor-dination has been observed [43–47]. The transcriptionfactor Sp1 was shown to both activate and repress theadenine nucleotide translocator 2 and F1 ATPasebpromoters [48] confusing the issue of coordinated reg-ulation. The regulation of OXPHOS gene expressionhas been found to occur in an uncoordinated fashionby others as well [40,49–53]. These studies suggestthat the regulation of mt gene expression is a compli-cated tissue-specific process occurring at the levels oftranscription, mRNA stability and translation.

Mt gene expression can also be regulated by growthand development in a tissue-specific manner [54–59].The mechanism of growth from conception to ma-turity involves a plethora of hormones, cytokines,eicosanoids, nutrients and so forth, all of which are

orchestrated such that an orderly process occurs. Verylittle research has been conducted with respect tothe specific effects these substances have on mt geneexpression. There are a few studies on the effect ofgrowth on specific mt genes and their expression. Inthe heart, growth affects transcription [43,54]. In ratheart, mt transcripts increased between days 1 and 90then decreased between 90 and 540 days of age. Inthe liver, mRNA stability [55] and translational effi-ciency [56] were shown to be regulated by growth.Ostronoff et al. [55,56] found that in neonates thehalf lives of mt-mRNA was much longer than inadult liver and that translational efficiency peaked1 h after birth. This response to growth was seen inboth the nuclear encoded and mitochondria encodedOXPHOS genes [57,58]. The mechanism for thispost-transcriptional regulation has been explained forthe nuclear encoded F1 ATPaseb subunit [43,59]. The3′-untranslated region (UTR) of this gene contains atranslational enhancer that functionally resembles aninternal-ribosomal-entry-site. During fetal develop-ment, a protein (3′-bFBP) binds to this region andinhibits translation. Within 1 h of birth this protein nolonger binds the 3′-UTR, unmasking the enhancer.This produces a spike inb F1 ATPase protein levels.In the adult, this protein is present again and transla-tion is once again inhibited. This protein has not beenisolated and identified nor do we know whether sucha masking mechanism exists for the mt genes. We doknow that the import of the F1 ATPaseb subunit cantrigger mt translation in cancer cells [60]. Whetherthis occurs in normal cells has not been established.

In addition to the above, some local tuning may oc-cur in the mitochondria compartment. There are somedata that suggest that receptors analogous to thosethat influence nuclear transcription also function inthe mitochondria compartment. Fig. 2 shows whereputative glucocorticoid (GRE), Vitamin D (VDRE),thyroid hormone (TRE), and retinoic acid (RARE)response elements have been identified in the D-loop[19–21,28,61–69]. The glucocorticoid receptor (GR)and a variant of the thyroid receptor (TR) have beenshown to bind this region of mtDNA in vitro [61,62].It was originally thought that thyroid hormone onlyincreased mt transcription by increasing mtTFA [66].However, Enriquez et al. [63] showed in isolated mi-tochondria that the thyroid hormone directly increasedthe transcription of all the mRNAs encoded on the

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Fig. 2. Putative nuclear receptor response elements (HRE) foundin the mitochondrial D-loop, the mitochondrial promoter region.Highlighted are the putative nuclear receptor response elementswith indications of the origin of the heavy strand replication (Oh),the light strand promoter (LSP), and the heavy strand promoter(HSP).

heavy strand without increasing mt rRNAs. Theywere unable to show that this occurred by binding tothe putative TRE. They did show a protein–DNA in-teraction near the transcription start sites (but not thetermination sites) that was affected by thyroid hor-mone. In addition, it was recently demonstrated thata variant form of a thyroid receptor (p43) is rapidlyimported into the mitochondria. This receptor bindsto three putative TREs and increases mt transcriptionin a thyroid dependent manner [65]. Two of these pu-tative TREs are located in the D-loop and were shownto increase mt transcription in the presence of p43 andthyroid hormone in a nuclear CAT assay. One of theseTREs is a direct repeat with two spaces. This elementhas also been shown to act as a RARE. This suggeststhe involvement of retinoic acid in mt transcription.

In addition, the binding of glucocorticoid [61] andthyroid [66] receptors were demonstrated in regionsoutside the D-loop, suggesting that they might haveother effects on transcription in addition to transcrip-tion initiation. Perhaps they might influence mRNAprocessing and translation as well.

The mitochondrially encoded ATP synthase sub-unit 6 and 8 genes were found to be regulated byVitamin D status in a tissue-specific manner [62,67].Renal tissue was responsive while hepatic tissue wasnot. This is due to the tissue difference in the VitaminD binding protein. It is present in kidney but not inliver. Retinoic acid has been shown to up regulateNADH dehydrogenase subunit 5 mRNA [68], as wellas cytochrome c oxidase subunit I and 16S rRNA[69]. In addition, retinoid X receptora knockout mice

were shown to have alterations in mt gene expression[70]. We have shown that retinoic acid up regulatesATPase 6 gene expression and optimizes OXPHOS indiabetes-prone BHE/Cdb rats [71,72]. We have foundretinoic acid receptors (RAR)b, andg in isolated ratliver mitochondria [72]. Interestingly, we have alsoobserved that Vitamin A restoration to Vitamin Adepleted BHE/Cdb rats results in an increase in mito-chondria number as well as an increase in mtTFA.

BHE/Cdb rats have two base substitutions in theATPase 6 gene that associate with impaired glucosetolerance and mitochondria function [73,74]. Theserats also have an increased need for dietary VitaminA in order to maintain normal OXPHOS function[72]. The mode of action of this vitamin in these ratswas at the level of mt gene expression. Increases inVitamin A intake resulted in increased expression ofmtATPase 6 gene. Vitamin A as retinoic acid (thegene active form of the vitamin) could also have ef-fects on nuclear gene expression as evidenced by theincrease in mtTFA and the increase in mitochondrianumber. Dietary Vitamin A (as retinol palmitate) wasconverted to retinoic acid and it was this form that upregulated mt gene expression. In vitro studies usingprimary cultures of hepatocytes have confirmed theseobservations (unpublished data).

Huang et al. [75] showed that insulin increased mtgene expression while having no effect on mt genecopy number. These workers examined the expressionof the ND1 andCOX1genes in control and diabeticsubjects. They suggested that there might be an in-sulin response element (IRE) in the promoter region.Others [76,77] have reported that insulin increases theexpression of mt genes in liver and heart. Huang et al.[75] searched the genome for sequence similarity withknown IREs and found a locus (position 413–446) thathad an 83% matched sequence similarity to the 29 bpIRE of mouse amylase. This locus also contains theIRE sequence motif T(G/A) TTTTG [78,79]. Its po-sition is near the 5’ end of the 12s rRNA gene andmight serve as a response element for insulin. Thus,insulin may serve to enhance mt gene transcription.

It is clear from the above text that transcription andtranslation of the mt genome are regulated processes.Any disease or abnormal nutritional state that affectsthe above hormones or nutrients will likely affect mtgene expression. Whether these actions are direct orindirect is subject to speculation. However, there are

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indications that some of the proteins that influence nu-clear gene expression action may have similar actionswith respect to mt gene expression. Studies of theseactions are in progress in several laboratories particu-larly as we attempt to unravel the pathophysiology ofthe various diseases that are associated with mutationsin the mtDNA.

1.3. Mitochondrial diseases

A number of human diseases are thought to becaused by mutations of the mt genome [2,9,80–100].Among these are premature aging, cancer, diabetesmellitus, Parkinson’s disease, Alzheimer’s disease,epilepsy, sensory losses (hearing and vision), and a

Table 1Diseases attributed to mitochondrial mutations

Human disease Mutated gene Position of mutation

Leigh’s syndrome ATPase 6 8993Kearns–Sayre Numerous multiple deletions/duplicationsLHONa ND1 3394, 3460, 4160, 4216

ND2 4917, 5244ND4 11, 778ND5 13, 708ND6 14, 484COI 7444Cyt b 15, 257

Diabetes mellitus ATPase 6b 8993, 8860, 8894tRNALeu 3243, 3252, 3256, 3271, 3290, 3291, 12308ND1 3316, 3348, 3394, 3396, 3423, 3434,

3438, 3447, 3480, 3483, 4216ND2 4917tRNACys 5780tRNASer 7476COXII 8245, 8251tRNALys 8344ND3 10, 398ND4 11, 778tRNAGlu 14, 709tRNAThr 15904, 15924, 15927, 15928D-loop 16069, 16093, 16126

NARPc ATPase 6 8993MELASd tRNALeu 3243MERFe tRNALys 8344, 8356Myopathy tRNAPro 15, 990

tRNALeu 3302

a Leber’s hereditary optic neuropathy.b In the BHE/Cdb rat mutations have been found in the ATPase 6 gene at positions 8204 and 8289.c Neurogenic muscle weakness, ataxia, retinitis pigmentosa.d Mitochondrial encephalomyopathy, lactic acidosis, and stroke-like syndrome.e Myotonic epilepsy and ragged red fiber disease.

variety of syndromes involving the muscles and thecentral nervous system. Table 1 lists these diseasesas well as the mutations thought to be responsiblefor the condition. Note that more than one mutationcan phenotype as a single disease and that more thanone disease will associate with a single mutation.Some of these diseases have been well studied whileothers have not. The mitochondria diseases includeLeigh’s syndrome, Kearns–Sayre syndrome, progres-sive external ophthalmoplegia (PEO), mitochondriaencephalomyopathy, lactic acidosis and stroke-likesyndrome (MELAS), Lebers hereditary optic neu-ropathy (LHON), myotonic epilepsy and raggedred fiber disease (MERRF), and neurogenic muscleweakness, ataxia, retinitis pigmentosa (NARP). Other

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diseases associated with mtDNA mutations includediabetes mellitus [83–92], Parkinson’s disease [93]and Alzheimer’s disease [94–96]. The linkage be-tween the latter two diseases and mtDNA muta-tion is not as tight as with the other diseases. BothParkinson’s disease and Alzheimer’s disease areknown to involve the brain and the central nervoussystem. The mtDNA mutations have been found inpatients with these disorders. Yet there is the possi-bility that the mutations found in these patients mightnot be pathogenic. They may be secondary featuresof the disorder rather than causal.

Most of the above diseases are characterized by ab-normal glucose homeostasis, a key feature of diabetesmellitus. This suggests that inadequate mt functionmight explain several of the secondary characteristicsof diabetes in general. The genotypes that phenotypeas diabetes are numerous and among them are muta-tions in the tRNALeu, ND1, ND2 tRNACys, COX II,tRNALeu(uur) tRNAGlu, tRNAThr, ATPase 6 genes, andthe D-loop. To date 42 mutations in the mtDNA havebeen found that phenotype as diabetes in humans. Thepopulation with mt diabetes is not large. Estimates ofthe percentage of the diabetic population with mtDNAmutations range from 0.1 to 10% of the total. Of spe-cial interest is the group of people with mt diabetesthat also have hearing loss. This is explained by theneed for ATP by the neuronal tract that is part of theauditory system. Most frequently these people havea mutation in the tRNALeu(UUR) gene. This may bean etiological hot spot for mtDNA mutation [98]. Sofar, 11 disease related mutations have been describedfor this gene. Of these, six are associated with type 2diabetes mellitus. Mutations in this particular gene ac-count for 60% of all the mt tRNA gene mutations andcollectively account for majority of people with mtdiabetes. An A/G transition at bp 3252 has been foundto associate with mt encephalomyopathy, pigmentedretinopathy, dementia, hypothyroidism, and diabetes[97]. Point mutation in the codes for the 13 structuralgenes as well as in the codes for the tRNAs have beenreported as well as mutations in the controller regions.Controller region sequence mutation has been reportedto occur at rates faster than mutation rates elsewherein the genome [2,9,80–82]. Rates of base pair sub-stitution in this region vary among the different sites.These sites are distributed along the region rather thanbeing clustered. Polymorphic variation occurs as well

with few or no effects on the activities of the geneproducts [1,3].

In contrast to diseases caused by mutations in nu-clear DNA, mutations in mtDNA might not be fullyexpressed. This is because there are many mitochon-dria in each cell. The liver, for example, has between500 and 2500 mitochondria per cell with an averageof about 1300. Each mitochondrion has 8–10 copiesof the genome. Since cells differ in the number ofmitochondria, the range for copy number is broad(1000–10,000 copies per cell). This is in contrast tonuclear DNA of which there are only two copies percell. If some of the mtDNA copies have a normal basesequence and others have a mutated sequence the cellis heteroplasmic. If all of the DNA has a mutatedsequence (or a normal sequence) then the cell is ho-moplasmic. Heteroplasmy with low percent-mutatedmtDNA will likely be unnoticed. Some base substitu-tions are without effect on the gene product becausethey are silent. That is, the triplet of which they are apart, will be translated identically to the usual tripletof bases. In a number of instances more than onetriplet can be used for a single amino acid. Thesepolymorphisms or variations in base sequence areuseful in defining an individual mt code but have nobearing on either the gene product or its function.However, should the percent-mutated DNA be largewith a mutation at a critical point in the gene product,a disease state will be observed.

With mt diseases there is the concept of thresh-old burden. This means that when the percent-mutatedDNA rises above a certain level, noticeable symptomswill be present. When the percent-mutated DNA farexceeds this threshold then an acute (and sometimeslethal) condition will be observed.

Mitochondrial diseases are transmitted as maternaltraits because mtDNA is of maternal origin [1]. Verylittle mtDNA is contributed to the fertilized egg by thesperm [101–104]. The mitochondria (and its DNA) inthe sperm are located in the mid-piece of the tail. Thismid-piece is eliminated early in the process of fer-tilization. The mechanism for this elimination is notwell understood. Thus, while the head of the spermcontributes its nuclear DNA to the fertilized egg, themtDNA in the tail is eliminated. As a result, mt mu-tations are inherited from the mother not the father.

Both heteroplasmic and homoplasmic base pairdeletions have been reported. Deletion events have

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been found to accumulate with age [105–111] andwith exposure to oxidizing chemicals such as radi-calized unsaturated fatty acids [112–116], zidovudine(AZT) [117,118] and streptozotocin [119]. Thesecompounds are generally referred to as free radi-cals and are assessed as compounds that react withthiobarbituric acid (TBA-reactive compounds). Somerepair of this damage is possible [120,121].

Deletion mutations can occur due to slipped mis-pairing between repeated sequences during DNA repli-cation or by erroneous RNA splicing [49]. Domainscontaining tandemly repeated DNA sequences are of-ten highly polymorphic in length due to the propensityof repeat units to undergo addition or deletion events[7,12]. Slipped mispairing between adjacent or nearbyrepeat sequences during replication is one of severalproposed mechanisms for mtDNA deletion mutation.Slipped mispairing between distant repeats can alsooccur and may be responsible for larger scale deletionsassociated with a variety of neuromuscular diseases inhumans [2,9,12,50,97,105–111].

Madsen et al. [49] have investigated the mecha-nism of slipped mispairing. They analyzed a repeatdomain present in porcine mtDNA. This domain waslocated at the 5′-end of the D-loop between conservedsequence blocks 1 and 2. This sequence consisted of14–29 copies of a 10 bp, self complimentary, tandemlyrepeated sequence, CGTGCGTACA. Upon passageinto E. coli, a recombinant plasmid containing thisdomain displayed a unique polymorphic pattern thatwas different from that seen in the pig. Using eithersingle or double stranded templates containing the re-peat domain, these investigators showed that slippagereplication could account for the observed mam-malian deletion mutation. Because certain genomesmay have more areas of direct repeats and becausedeletions are more likely to occur in or near theseareas, these genomes might be more vulnerable tothis type of mutation [7,8,122].

Heteroplasmy can have different consequencesdepending on whether it is a point mutation or a dele-tion mutation. In the instance of the heteroplasmiccell with the deletion mutation there is the tendency todrift towards deletion mutation homoplasmy. The rea-son this drift occurs is subject to speculation. Brownet al. [51] showed that mitochondria reproduce them-selves at a rate that is 5–10 times faster than the rateof cell replication. Poulton et al. [123,124], Larsson

et al. [125] and others [126–129] have suggested thatthe rates of propagation of deleted mtDNA couldbe different than for normal DNA and that shorterstrands of DNA may be replicated at a faster ratethan strands of normal length. This would suggestthat deletion mutation confers a replicative advantageto the mtDNA molecule until it has overwhelmed thewild type mtDNA. All of these investigators hypothe-size that accumulations of deletion mutation might beattributed to this differential replication mechanism.Thus, a deletion mutation might become evident fasterthan a point mutation all other factors being equal.In this scenario, age is a critical determinant of thepercentage of the mtDNA with a deletion mutation.As the animal or human ages, there is a drift towardsan increase in the percent deletion mutation. Whetherreplication speed can explain this accumulation issubject to discussion. One could argue that it is notreplication speed but the possibility that there arecertain hot spots in the genome that are targets for re-peated deletion events. If this occurs frequently therewould be an age-related accumulation of deletion mu-tation not because of differences in replication speedbut because certain deletions are made repeatedly.

Several investigators have reported that age, as wellas dietary fat as a source of free radicals, are criticalfactors in the accumulation of both base substitutionand deletion mutation [79,105–111,131–141]. In partthis might be due to the above described drift but itcould also be explained by differences in vulnerabil-ity of certain areas of the DNA to mutation events. Asmentioned, regions of direct repeats create a hot spotfor mutation [122]. If those regions are continuouslypresent, then mutations could accumulate because of acontinuous free radical attack on the genome at thesehot spots. Such free radical attack has been docu-mented by the detection of various base modificationsparticularly 8-hydroxyguanosine [138]. These modifi-cations could lead to point mutations because of mis-pairing or to deletions. The mtDNA fragmentation hasalso been observed in relation to oxidative damage andthis fragmentation could lead to deletion mutation.

As mentioned, mt diseases can be due to either ahomoplasmic mutation or a heteroplasmic one. In thecase of a heteroplasmic mutation, the disease state de-velops only after a threshold level of mutation has beenachieved. Not all tissues have the same distribution ofmutated DNA. Those with a heavy burden of mutated

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DNA will manifest mt dysfunction while those withonly a modest burden will not. If the tissue in questionhas a high mutation load and a high requirement forATP then the function of that tissue will be aberrant.The CNS is a case in point. This system has a very highrequirement for ATP and should the cells of this sys-tem have a substantial impairment in ATP production,the symptoms of mt disease will become apparent. Theliver or the adipose tissue on the other hand might notbe as affected given the same level of mtDNA mu-tation. Cells in these tissues have multiple metabolicpathways that in turn can compensate (in part) for mtdysfunction. Thus, symptoms of CNS disease due to ahigh percentage of mutated mtDNA are acute and canbe lethal while those of diabetes chronic and manage-able. People with mt diabetes live long enough to passtheir mutations on to their progeny while those with ahigh burden of mutated mtDNA observed as MELAS,LHON, MERRF and NARP usually do not. Actually,it is the infants and children with these conditions thatlead to genetic testing of the parents. In these par-ents the mother is usually found to have a percentmutation that may or may not compromise her healthbut yet is sufficient to result in a compromise of hermetabolism. She in turn passes the mutation to the in-fant. The degree to which the infant is affected dependsin turn on how much of the mutated DNA is passedto the fertilized egg at conception. Whether the dis-tribution of normal versus mutated DNA is by chancealone or if there is some sort of preferential alloca-tion is subject to much argument. Accumulations ofdeleted mutant mtDNA have been observed in termi-nally differentiated cells. However, the question arisesas to whether mutations accumulate in oocytes. Rapidchanges in mtDNA variants between generations haveled to the bottleneck theory [139,140]. This theoryproposes that there is a dramatic reduction in mtDNAduring early oogenesis and that mutant mtDNA couldbe a major contributor of the mtDNA as the oocytedevelops. This theory suggests that if by chance, mu-tant DNA instead of normal DNA contributes to sub-sequent mtDNA in the oocyte, then, the resultant eggmight then result in an infant with a heavy burden ofmutant mtDNA. This theory however attractive, doesnot explain all instances of mt disease nor all instancesof mtDNA transmission from mother to child [141].Families can have several affected children and withina family there can be degrees of mutation severity

or percent-mutated DNA. This latter observation doesnot support the bottleneck theory. If a bottleneck doesoccur it would affect all children equally.

1.4. Oxidative stress as a mutagen of mtDNA

Until recently, it has been assumed that the majortargets for free radical attack were the plasma and in-tracellular membranes and the nuclear genome. Now,however, with the knowledge about the importance ofthe mtDNA and mt function in cellular metabolism,the research on oxidative stress has shifted. It is nowrecognized that the mitochondria produce nearly 90%of the free radicals generated in the living cell andfor proximity reasons, are also the prime targets ofthese reactive oxygen species. The nutrients that serveas antioxidants and free radical suppressants shouldfunction in the mt compartment. Indeed, Kristal et al.[142] have shown that antioxidants are active in thisrespect. Vitamin E in particular regulates mt perox-ide formation by serving as an antioxidant in thiscompartment [143,144]. The BHE/Cdb rat with amutation in the ATPase 6 gene is more vulnerable tofree radical attack and this rat requires substantiallymore dietary Vitamin E than normal rats [145,146].Humans with mutations that result in a similar reduc-tion in OXPHOS efficiency likewise might be morevulnerable to oxidative stress and also require moreVitamin E but such studies have not been conducted.

The free radicals are produced in the inter-mtmembrane space and must diffuse across the innermembrane in order to attack the mtDNA. Fortunately,there is a very active enzyme in the mt compartment(manganese-superoxide dismutase) that converts thefree oxygen radical to a less reactive oxygen com-pound, peroxide. The peroxide is then converted towater. This reaction is not 100% efficient in captur-ing all of the oxygen radicals immediately upon theircreation, so some do escape and attack not only themt membranes but also the mtDNA. The attack onthe mtDNA is random. That is, there is no specifictarget within the DNA molecule. Yet there are somesequences that are more vulnerable than others. Thoseregions that have multiple repeats are more vulnerablethan regions without such repeats [122]. Because themtDNA has little protection of its structure, free radi-cal damage is more likely. There is some evidence ofthe existence of protective histone-like proteins in the

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mt compartment but a full histone coat of the DNAis generally agreed to be absent.

Further, although there is some repair [120,121],this repair is not as efficient as that which occurs inthe nucleus. Excision of the damaged sequences oc-curs and there is repair of alkalated bases. However,recombination as is common in nuclear repair, is not asignificant mtDNA repair mechanism [130]. Actually,mtDNA damage is far more persistent than is nDNAdamage [134]. This is not, however, a critical or anacute situation under most conditions. Each mitochon-drion has so many copies of its genome and each cellhas so many mitochondria that damage to a few DNAmolecules is unlikely to have a significant effect oncellular function. If a few cells have a few copies dam-aged by free radical attack there will be no immediatecause for concern. If there is an overwhelming attackhowever, there would be noticeable loss in function.This happens when an individual is exposed to toxiclevels of free radical generating chemicals, i.e. somepesticides. In this instance, damage could be extensiveand the loss of mt function could likewise be signif-icant, perhaps lethal. This is an uncommon event.

More common are the subtle but cumulativechanges in mt function that occur with age. In part,some of these changes are due to age changes in themembrane lipids and changes in the proteins embed-ded in that lipid. However, there is gathering evidencethat age carries with it an accumulation of free radicalinduced damage to the mt genome. The products ofthis genome might have lost a measure of its normalfunction and thereby explain age-related declines inmt function.

1.5. Aging and mitochondrial function

Yu et al. [112], Wei et al. [105,106,109–111]and others [107,108,113,131,135–138,147–149] havereported that humans as well as animals have an in-crease in the number of base pair deletions as theyage. There is also an increase in the number of basepair duplications. These mutations are translated intoproteins that have less than normal function. Fordecades researchers have reported on the age-relateddecline in mt function and some have suggested thatcell aging was caused by oxidative stress [133,136].An age-related increase in mt 8-hydroxyguanosinehas been reported [138]. Because mitochondria turn

over more rapidly than do the cells that contain them,free radical damage can have cumulative effects oncell function. As cell function, particularly mt func-tion declines, cell (and tissue) aging accelerates. Thus,it should come as no surprise that mt genetic changepredicts the rate at which the whole cell ages.

Mitochondrial aging or the age-related decline inmt function due to an age-related mtDNA mutation isthought to explain some of the features of aging. Forexample, Correl-Debrinski et al. [150] reported thatheart disease was associated with an increased num-ber of mtDNA deletions in the heart muscle. Theyexamined heart tissue from persons who had diedfrom heart disease and their age matched controlswho died from other causes. They found that a com-mon mutation at 4977 bp was far more frequent in thepersons with heart disease than in persons who diedof other causes. The percent deletion mutation wasquite low, however, probably too low to explain possi-ble defective OXPHOS. There might have been othermtDNA changes as well but these were not reported.

Tumor tissue from patients with breast cancersimilarly had more frequent mtDNA deletions thanpeople without this disease [151]. Both groups wereheteroplasmic for a number of mt base sequences yetthe patients with breast cancer went on to develop thedisease. This suggests that there were other perhapsnongenomic factors that promoted the developmentof the cancer and that these factors were absent in thehealthy controls. Cortopassi and Liu [152] reachedthese same conclusions and suggested that throughunderstanding how these genes express themselveswe might gain a better understanding of how the mtgenes were transcribed and translated. Through thisunderstanding we might be able to develop appropri-ate strategies for manipulating this expression.

One such strategy is life long food restriction.Rodents that are food restricted have a significantlylonger life span than non-restricted rodents. The liter-ature on this phenomenon is enormous. Within this lit-erature are three reports that indicate that food restric-tion results in a reduction in the number of age-relatedmt deletions and other changes in mtDNA [153–155].In contrast, longevity and successful aging may be theresult of inheriting mtDNA that is resistant to free rad-ical induced mutation [156]. Some individuals appar-ently have mtDNA that resists the mutagenic actionsof their environment. In others, perhaps their choice

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of nutrients and their other lifestyle choices result ina protection of their mtDNA from such change.

2. Summary

The mt genome has been completely sequenced andmapped for a variety of species including man. Thecontrol of its expression via controls of transcriptionare now being investigated as we seek to understandhow the phenotypic expression of the mt genotype canbe manipulated. Mitochondrial diseases due to muta-tions in the mtDNA are of interest particularly as theyrelate to aging, degenerative disease and the responseto dietary manipulation. Free radical damage and itssuppression by nutrients may be important to our un-derstanding of the aging process as well as age-relateddegenerative disease. Nutrient-mt gene interactionshave not received much attention but perhaps as ourknowledge about the role of the mtDNA in health anddisease expands, these interactions will be explored.

Acknowledgements

The authors would like to express their apprecia-tion to all those who helped in the conduct of thiswork. Especially helpful was Ms. Kathie Wickwire.This work was supported by grants from Mitokor,The United States Department of Agriculture (Grantno. 98-35200-6049), The Georgia Agricultural Exper-iment Station and the UGA Diabetes Research Fund.

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