Mutation Research 475 (2001) 169184

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 identied. 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 citric acid cycle, fatty acid oxidation, the initial reaction of the urea cycle, the respiratory chain, and a variety of carriers or transporters. They are the organelles responsible for the synthesis of the high-energy compound, 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 (OXPHOS). 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: cberdani@hestia.fcs.uga.edu (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 encoded by the mitochondrial (mt) DNA. This review will discuss this genome and its expression with respect 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 [114]. Fig. 1 shows the human 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: S 0 0 2 7 - 5 1 0 7 ( 0 1 ) 0 0 0 6 8 - 9

170

C.D. Berdanier, H.B. Everts / Mutation Research 475 (2001) 169184

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

genes [314]. In rat, the size of the mt genome is 16,298 bp; in humans it is 16,569 bp. The mt genome has been sequenced and mapped for many species yet the regulation of its expression is poorly understood. The mtDNA encodes 22 transfer RNAs, 2 ribosomal RNAs, and 13 structural genes. These structural genes encode 13 components of OXPHOS. The structural genes encode 7 of the 39 subunit proteins of Complex I (ND1, 2, 3, 4, 4L, 5, and 6), 1 of the 10 subunit proteins of complex (Cyt b), 3 of the 13 subunit proteins of complex IV (CO I, II and III), and 2 subunit proteins of the F0 portion of complex V, the F1 F0

ATPase. Approximately 6% of the bases in the mt genome are noncoding. The 97% of this noncoding DNA is located in the two controller regions, the 30 bp origin of replication for the light strand (OL ), and the 898 bp unit called the D-loop. The strands of mtDNA have been named light and heavy according to their buoyancy through a denaturing cesium chloride gradient. The heavy strand is the main coding strand, and codes for 2 rRNA species, 14 tRNA species and 12 structural genes. The light strand codes for 8 tRNA species and 1 structural gene for a subunit of NADH

C.D. Berdanier, H.B. Everts / Mutation Research 475 (2001) 169184

171

dehydrogenase. The genome sequence shows extreme economy in that very few genes have noncoding bases between them [38]. In fact, the largest space between two genes is a 5 bp sequence between the genes for tRNAGlu and the cytochrome b gene. The controller region has more of these noncoding regions yet they are few in number compared to the nuclear genome. There is gene overlap as well. In six instances, the shared nucleotides are not really shared; they are on the heavy and light strands such that the shared bases are on the 3 -ends of the two genes. In the other three instances, the shared bases are actually frame shifts that allow the same nucleotides to code for two different proteins. The genes that share nucleotides include the ATPase 6 and 8 genes that share 52 bp, ND4 and ND4L that share seven, the tRNASer and the tRNALeu that share one, ND5 and ND6 that share 31, the tRNASer and the cytochrome oxidase I gene that share four and lastly, the tRNAIle and tRNAGln genes that share 3 bp. Of interest is the observation that only 56 bp are all that separate the different genes on the mt genome and that 98 bp are shared by neighboring genes. 1.2. Mitochondrial gene transcription Early studies revealed that transcription is symmetrical [15] and is initiated within the D-loop. Light strand transcription moves clockwise and the heavy strand transcription moves counterclockwise [5,16,17]. The light strand has a longer half life and there is roughly twice as much of this strand as the heavy strand. The light strand is transcribed as one polycistron while the heavy strand is transcribed as two polycistrons [18]. One of the heavy strand polycistrons encodes all of the heavy strand, while the other encodes the two rRNAs. Three distinct promoter sequences, one for the light strand and two for the heavy strand, have been described [6,13,1923]. In addition, the light strand promoter (LSP) region also primes the replication of the heavy strand [24,25] forming a RNADNA primer that is cleaved by the RNase mt RNA processing (MRP) enzyme. This cleavage occurs at the origin of heavy strand replication [26]. There are three sequence blocks that are conserved among a number of species [27]. These sequences are involved in this RNADNA cleavage. In humans, both the LSP and the heavy strand promoter (HSP) sequences contain regions near the

start site containing specic nucleotides required for transcription initiation. There are also upstream regulatory regions. In mouse, the LSP contains three domains. The rst consists of nucleotides 10 to +9 (relative to transcription initiation) that are required for accurate transcription initiation. The second domain (nt-11 to -29) facilitates the formation of the preinitiation complex and the third domain (nt-30 to -88) affects transcriptional efciency. In contrast, specic nucleotides are not required near or at the transcription start sites for heavy strand transcription initiation. There is an essential upstream element for the start site of the mouse HSP. Promoter sequences are not highly conserved among species and there are some cross species activities. For example, mouse RNA polymerase is active on rat mtDNA. This suggests that the rat and mouse promoters are similar. Between the mouse and the human there is an additional difference in that the two HSP start sites are close together in the mouse but not in the human. In humans, the main start site is near the D-loop/tPhe border with a minor start site between the tPhe and 12S gene. The main start site is thought to result in transcription of the two rRNA genes while the minor one initiates transcription of the whole heavy strand. At present, only two transcription factors have been well studied. Both of these are nuclear encoded. They are mitochondrial transcription factor A (mtTFA) that stimulates initiation [28,29] and mitochondrial transcription termination factor (mTERF) that is involved in the termination of the heavy strand after the rRNAs are formed [30]. There are probably many more factors that inuence mtDNA transcription but we are only now beginning to elucidate them. In vitro studies have shown that mtTFA binds to both promoter regions as well as to a region in-between two of the conserved sequence blocks. The mtTFA condenses, unwinds, and bends mtDNA [31,32]. In addition, in vitro, more mtTFA is needed to promote transcription of the heavy strand than to promote transcription of the light strand. This suggests that low levels of mtTFA may result in the activation of the light strand and be involved in replication. This suggestion is supported by the observation that mtTFA protein levels have been correlated with mtDNA copy number. A deciency in mtTFA results in mtDNA depletion [33,34]. Transgenic technology has provided further evidence of mtTFAs role in transcription and replication.

172

C.D. Berdanier, H.B. Everts / Mutation Research 475 (2001) 169184

First, overexpression of mtTFA in HeLa cells and in isolated liver mitochondria were shown to increase mt transcription [35]. Second, heterozygous m-mtTFA (also called Tfam) knockout mice were shown to have reduced mtDNA copy number in heart, kidney and liver, reduced mt transcription in the heart, and reduced respiratory chain function in the heart [36]. The kidney, liver and skeletal muscle were variable in this respect. Interestingly, the protein levels of mitochondrially encoded cytochrome c oxidase subunit II and ATP synthase subunit 8 were normal in all tissues studied in these mice. Using knockout technology it was found that if the gene for the mtTFA was completely absent, this absence was lethal. Thus, there are no homozygous knockout mice. These data, in combination with the in vitro data, support the idea that mtTFA is essential for mt replication, primed from the LSP; but is not solely responsible for regulating heavy strand transcription. It is altogether likely that mt transcription depends on the presence of other transcription factors as well. Because genes occur in both the nuclear and mt genomes that encode components of OXPHOS, there must be a mechanism available that coordinates the expression of both. The nuclear respiratory factors (NRF) 1 and 2 and the general transcription factor Sp1 serve this function. They simultaneously regulate the expression of mtTFA as well as several nuclear OXPHOS genes [3742]. During rapid cell proliferation this coordinated expression has been shown to occur. However, such coordination has not been found under all circumstances. For example, in either hypoor hyper-thyroidism discoordination rather than coordination has been observed [4347]. The transcription factor Sp1 was shown to both activate and repress the adenine nucleotide translocator 2 and F1 ATPase promoters [48] confusing the issue of coordinated regulation. The regulation of OXPHOS gene expression has been found to occur in an uncoordinated fashion by others as well [40,4953]. These studies suggest that the regulation of mt gene expression is a complicated tissue-specic process occurring at the levels of transcription, mRNA stability and translation. Mt gene expression can also be regulated by growth and development in a tissue-specic manner [5459]. The mechanism of growth from conception to maturity involves a plethora of hormones, cytokines, eicosanoids, nutrients and so forth, all of which are

orchestrated such that an orderly process occurs. Very little research has been conducted with respect to the specic effects these substances have on mt gene expression. There are a few studies on the effect of growth on specic mt genes and their expression. In the heart, growth affects transcription [43,54]. In rat heart, mt transcripts increased between days 1 and 90 then decreased between 90 and 540 days of age. In the liver, mRNA stability [55] and translational efciency [56] were shown to be regulated by growth. Ostronoff et al. [55,56] found that in neonates the half lives of mt-mRNA was much longer than in adult liver and that translational efciency peaked 1 h after birth. This response to growth was seen in both the nuclear encoded and mitochondria encoded OXPHOS genes [57,58]. The mechanism for this post-transcriptional regulation has been explained for the nuclear encoded F1 ATPase subunit [43,59]. The 3 -untranslated region (UTR) of this gene contains a translational enhancer that functionally resembles an internal-ribosomal-entry-site. During fetal development, a protein (3 -FBP) binds to this region and inhibits translation. Within 1 h of birth this protein no longer binds the 3 -UTR, unmasking the enhancer. This produces a spike in F1 ATPase protein levels. In the adult, this protein is present again and translation is once again inhibited. This protein has not been isolated and identied nor do we know whether such a masking mechanism exists for the mt genes. We do know that the import of the F1 ATPase subunit can trigger mt translation in cancer cells [60]. Whether this occurs in normal cells has not been established. In addition to the above, some local tuning may occur in the mitochondria compartment. There are some data that suggest that receptors analogous to those that inuence nuclear transcription also function in the mitochondria compartment. Fig. 2 shows where putative glucocorticoid (GRE), Vitamin D (VDRE), thyroid hormone (TRE), and retinoic acid (RARE) response elements have been identied in the D-loop [1921,28,6169]. The glucocorticoid receptor (GR) and a variant of the thyroid receptor (TR) have been shown to bind this region of mtDNA in vitro [61,62]. It was originally thought that thyroid hormone only increased mt transcription by increasing mtTFA [66]. However, Enriquez et al. [63] showed in isolated mitochondria that the thyroid hormone directly increased the transcription of all the mRNAs encoded on the

C.D. Berdanier, H.B. Everts / Mutation Research 475 (2001) 169184

173

Fig. 2. Putative nuclear receptor response elements (HRE) found in the mitochondrial D-loop, the mitochondrial promoter region. Highlighted are the putative nuclear receptor response elements with 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. They were unable to show that this occurred by binding to the putative TRE. They did show a proteinDNA interaction near the transcription start sites (but not the termination sites) that was affected by thyroid hormone. In addition, it was recently demonstrated that a variant form of a thyroid receptor (p43) is rapidly imported into the mitochondria. This receptor binds to three putative TREs and increases mt transcription in a thyroid dependent manner [65]. Two of these putative TREs are located in the D-loop and were shown to increase mt transcription in the presence of p43 and thyroid hormone in a nuclear CAT assay. One of these TREs is a direct repeat with two spaces. This element has also been shown to act as a RARE. This suggests the involvement of retinoic acid in mt transcription. In addition, the binding of glucocorticoid [61] and thyroid [66] receptors were demonstrated in regions outside the D-loop, suggesting that they might have other effects on transcription in addition to transcription initiation. Perhaps they might inuence mRNA processing and translation as well. The mitochondrially encoded ATP synthase subunit 6 and 8 genes were found to be regulated by Vitamin D status in a tissue-specic manner [62,67]. Renal tissue was responsive while hepatic tissue was not. This is due to the tissue difference in the Vitamin D binding protein. It is present in kidney but not in liver. Retinoic acid has been shown to up regulate NADH dehydrogenase subunit 5 mRNA [68], as well as cytochrome c oxidase subunit I and 16S rRNA [69]. In addition, retinoid X receptor knockout mice

were shown to have alterations in mt gene expression [70]. We have shown that retinoic acid up regulates ATPase 6 gene expression and optimizes OXPHOS in diabetes-prone BHE/Cdb rats [71,72]. We have found retinoic acid receptors (RAR) , and in isolated rat liver mitochondria [72]. Interestingly, we have also observed that Vitamin A restoration to Vitamin A depleted BHE/Cdb rats results in an increase in mitochondria number as well as an increase in mtTFA. BHE/Cdb rats have two base substitutions in the ATPase 6 gene that associate with impaired glucose tolerance and mitochondria function [73,74]. These rats also have an increased need for dietary Vitamin A in order to maintain normal OXPHOS function [72]. The mode of action of this vitamin in these rats was at the level of mt gene expression. Increases in Vitamin A intake resulted in increased expression of mtATPase 6 gene. Vitamin A as retinoic acid (the gene active form of the vitamin) could also have effects on nuclear gene expression as evidenced by the increase in mtTFA and the increase in mitochondria number. Dietary Vitamin A (as retinol palmitate) was converted to retinoic acid and it was this form that up regulated mt gene expression. In vitro studies using primary cultures of hepatocytes have conrmed these observations (unpublished data). Huang et al. [75] showed that insulin increased mt gene expression while having no effect on mt gene copy number. These workers examined the expression of the ND1 and COX1 genes in control and diabetic subjects. They suggested that there might be an insulin response element (IRE) in the promoter region. Others [76,77] have reported that insulin increases the expression of mt genes in liver and heart. Huang et al. [75] searched the genome for sequence similarity with known IREs and found a locus (position 413446) that had an 83% matched sequence similarity to the 29 bp IRE of mouse amylase. This locus also contains the IRE sequence motif T(G/A) TTTTG [78,79]. Its position is near the 5 end of the 12s rRNA gene and might 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 and translation of the mt genome are regulated processes. Any disease or abnormal nutritional state that affects the above hormones or nutrients will likely affect mt gene expression. Whether these actions are direct or indirect is subject to speculation. However, there are

174

C.D. Berdanier, H.B. Everts / Mutation Research 475 (2001) 169184

indications that some of the proteins that inuence nuclear gene expression action may have similar actions with respect to mt gene expression. Studies of these actions are in progress in several laboratories particularly as we attempt to unravel the pathophysiology of the various diseases that are associated with mutations in the mtDNA. 1.3. Mitochondrial diseases A number of human diseases are thought to be caused by mutations of the mt genome [2,9,80100]. Among these are premature aging, cancer, diabetes mellitus, Parkinsons disease, Alzheimers disease, epilepsy, sensory losses (hearing and vision), and a
Table 1 Diseases attributed to mitochondrial mutations Human disease Leighs syndrome KearnsSayre LHONa Mutated gene

variety of syndromes involving the muscles and the central nervous system. Table 1 lists these diseases as well as the mutations thought to be responsible for the condition. Note that more than one mutation can phenotype as a single disease and that more than one disease will associate with a single mutation. Some of these diseases have been well studied while others have not. The mitochondria diseases include Leighs syndrome, KearnsSayre syndrome, progressive external ophthalmoplegia (PEO), mitochondria encephalomyopathy, lactic acidosis and stroke-like syndrome (MELAS), Lebers hereditary optic neuropathy (LHON), myotonic epilepsy and ragged red ber disease (MERRF), and neurogenic muscle weakness, ataxia, retinitis pigmentosa (NARP). Other

Position of mutation 8993 3394, 3460, 4160, 4216 4917, 5244 11, 778 13, 708 14, 484 7444 15, 257 8993, 8860, 8894 3243, 3252, 3256, 3271, 3290, 3291, 12308 3316, 3348, 3394, 3396, 3423, 3434, 3438, 3447, 3480, 3483, 4216 4917 5780 7476 8245, 8251 8344 10, 398 11, 778 14, 709 15904, 15924, 15927, 15928 16069, 16093, 16126 8993 3243 8344, 8356 15, 990 3302

Diabetes mellitus

ATPase 6 Numerous multiple deletions/duplications ND1 ND2 ND4 ND5 ND6 COI Cyt b ATPase 6b tRNALeu ND1 ND2 tRNACys tRNASer COXII tRNALys ND3 ND4 tRNAGlu tRNAThr D-loop ATPase 6 tRNALeu tRNALys tRNAPro tRNALeu

NARPc MELASd MERFe Myopathy

a

Lebers hereditary optic neuropathy. 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 ber disease.
b

C.D. Berdanier, H.B. Everts / Mutation Research 475 (2001) 169184

175

diseases associated with mtDNA mutations include diabetes mellitus [8392], Parkinsons disease [93] and Alzheimers disease [9496]. The linkage between the latter two diseases and mtDNA mutation is not as tight as with the other diseases. Both Parkinsons disease and Alzheimers disease are known to involve the brain and the central nervous system. The mtDNA mutations have been found in patients with these disorders. Yet there is the possibility that the mutations found in these patients might not be pathogenic. They may be secondary features of the disorder rather than causal. Most of the above diseases are characterized by abnormal glucose homeostasis, a key feature of diabetes mellitus. This suggests that inadequate mt function might explain several of the secondary characteristics of diabetes in general. The genotypes that phenotype as diabetes are numerous and among them are mutations in the tRNALeu , ND1, ND2 tRNACys , COX II, tRNALeu(uur) tRNAGlu , tRNAThr , ATPase 6 genes, and the D-loop. To date 42 mutations in the mtDNA have been found that phenotype as diabetes in humans. The population with mt diabetes is not large. Estimates of the percentage of the diabetic population with mtDNA mutations range from 0.1 to 10% of the total. Of special interest is the group of people with mt diabetes that also have hearing loss. This is explained by the need for ATP by the neuronal tract that is part of the auditory system. Most frequently these people have a mutation in the tRNALeu(UUR) gene. This may be an etiological hot spot for mtDNA mutation [98]. So far, 11 disease related mutations have been described for this gene. Of these, six are associated with type 2 diabetes mellitus. Mutations in this particular gene account for 60% of all the mt tRNA gene mutations and collectively account for majority of people with mt diabetes. An A/G transition at bp 3252 has been found to associate with mt encephalomyopathy, pigmented retinopathy, dementia, hypothyroidism, and diabetes [97]. Point mutation in the codes for the 13 structural genes as well as in the codes for the tRNAs have been reported as well as mutations in the controller regions. Controller region sequence mutation has been reported to occur at rates faster than mutation rates elsewhere in the genome [2,9,8082]. Rates of base pair substitution in this region vary among the different sites. These sites are distributed along the region rather than being clustered. Polymorphic variation occurs as well

with few or no effects on the activities of the gene products [1,3]. In contrast to diseases caused by mutations in nuclear DNA, mutations in mtDNA might not be fully expressed. This is because there are many mitochondria in each cell. The liver, for example, has between 500 and 2500 mitochondria per cell with an average of about 1300. Each mitochondrion has 810 copies of the genome. Since cells differ in the number of mitochondria, the range for copy number is broad (100010,000 copies per cell). This is in contrast to nuclear DNA of which there are only two copies per cell. If some of the mtDNA copies have a normal base sequence and others have a mutated sequence the cell is heteroplasmic. If all of the DNA has a mutated sequence (or a normal sequence) then the cell is homoplasmic. Heteroplasmy with low percent-mutated mtDNA will likely be unnoticed. Some base substitutions are without effect on the gene product because they are silent. That is, the triplet of which they are a part, will be translated identically to the usual triplet of bases. In a number of instances more than one triplet can be used for a single amino acid. These polymorphisms or variations in base sequence are useful in dening an individual mt code but have no bearing on either the gene product or its function. However, should the percent-mutated DNA be large with a mutation at a critical point in the gene product, a disease state will be observed. With mt diseases there is the concept of threshold burden. This means that when the percent-mutated DNA rises above a certain level, noticeable symptoms will be present. When the percent-mutated DNA far exceeds this threshold then an acute (and sometimes lethal) condition will be observed. Mitochondrial diseases are transmitted as maternal traits because mtDNA is of maternal origin [1]. Very little mtDNA is contributed to the fertilized egg by the sperm [101104]. The mitochondria (and its DNA) in the sperm are located in the mid-piece of the tail. This mid-piece is eliminated early in the process of fertilization. The mechanism for this elimination is not well understood. Thus, while the head of the sperm contributes its nuclear DNA to the fertilized egg, the mtDNA in the tail is eliminated. As a result, mt mutations are inherited from the mother not the father. Both heteroplasmic and homoplasmic base pair deletions have been reported. Deletion events have

176

C.D. Berdanier, H.B. Everts / Mutation Research 475 (2001) 169184

been found to accumulate with age [105111] and with exposure to oxidizing chemicals such as radicalized unsaturated fatty acids [112116], zidovudine (AZT) [117,118] and streptozotocin [119]. These compounds are generally referred to as free radicals and are assessed as compounds that react with thiobarbituric acid (TBA-reactive compounds). Some repair of this damage is possible [120,121]. Deletion mutations can occur due to slipped mispairing between repeated sequences during DNA replication or by erroneous RNA splicing [49]. Domains containing tandemly repeated DNA sequences are often highly polymorphic in length due to the propensity of repeat units to undergo addition or deletion events [7,12]. Slipped mispairing between adjacent or nearby repeat sequences during replication is one of several proposed mechanisms for mtDNA deletion mutation. Slipped mispairing between distant repeats can also occur and may be responsible for larger scale deletions associated with a variety of neuromuscular diseases in humans [2,9,12,50,97,105111]. Madsen et al. [49] have investigated the mechanism of slipped mispairing. They analyzed a repeat domain present in porcine mtDNA. This domain was located at the 5 -end of the D-loop between conserved sequence blocks 1 and 2. This sequence consisted of 1429 copies of a 10 bp, self complimentary, tandemly repeated sequence, CGTGCGTACA. Upon passage into E. coli, a recombinant plasmid containing this domain displayed a unique polymorphic pattern that was different from that seen in the pig. Using either single or double stranded templates containing the repeat domain, these investigators showed that slippage replication could account for the observed mammalian deletion mutation. Because certain genomes may have more areas of direct repeats and because deletions are more likely to occur in or near these areas, these genomes might be more vulnerable to this type of mutation [7,8,122]. Heteroplasmy can have different consequences depending on whether it is a point mutation or a deletion mutation. In the instance of the heteroplasmic cell with the deletion mutation there is the tendency to drift towards deletion mutation homoplasmy. The reason this drift occurs is subject to speculation. Brown et al. [51] showed that mitochondria reproduce themselves at a rate that is 510 times faster than the rate of cell replication. Poulton et al. [123,124], Larsson

et al. [125] and others [126129] have suggested that the rates of propagation of deleted mtDNA could be different than for normal DNA and that shorter strands of DNA may be replicated at a faster rate than strands of normal length. This would suggest that deletion mutation confers a replicative advantage to the mtDNA molecule until it has overwhelmed the wild type mtDNA. All of these investigators hypothesize that accumulations of deletion mutation might be attributed to this differential replication mechanism. Thus, a deletion mutation might become evident faster than a point mutation all other factors being equal. In this scenario, age is a critical determinant of the percentage of the mtDNA with a deletion mutation. As the animal or human ages, there is a drift towards an increase in the percent deletion mutation. Whether replication speed can explain this accumulation is subject to discussion. One could argue that it is not replication speed but the possibility that there are certain hot spots in the genome that are targets for repeated deletion events. If this occurs frequently there would be an age-related accumulation of deletion mutation not because of differences in replication speed but because certain deletions are made repeatedly. Several investigators have reported that age, as well as dietary fat as a source of free radicals, are critical factors in the accumulation of both base substitution and deletion mutation [79,105111,131141]. In part this might be due to the above described drift but it could also be explained by differences in vulnerability of certain areas of the DNA to mutation events. As mentioned, regions of direct repeats create a hot spot for mutation [122]. If those regions are continuously present, then mutations could accumulate because of a continuous free radical attack on the genome at these hot spots. Such free radical attack has been documented by the detection of various base modications particularly 8-hydroxyguanosine [138]. These modications could lead to point mutations because of mispairing or to deletions. The mtDNA fragmentation has also been observed in relation to oxidative damage and this fragmentation could lead to deletion mutation. As mentioned, mt diseases can be due to either a homoplasmic mutation or a heteroplasmic one. In the case of a heteroplasmic mutation, the disease state develops only after a threshold level of mutation has been achieved. Not all tissues have the same distribution of mutated DNA. Those with a heavy burden of mutated

C.D. Berdanier, H.B. Everts / Mutation Research 475 (2001) 169184

177

DNA will manifest mt dysfunction while those with only a modest burden will not. If the tissue in question has a high mutation load and a high requirement for ATP then the function of that tissue will be aberrant. The CNS is a case in point. This system has a very high requirement for ATP and should the cells of this system have a substantial impairment in ATP production, the symptoms of mt disease will become apparent. The liver or the adipose tissue on the other hand might not be as affected given the same level of mtDNA mutation. Cells in these tissues have multiple metabolic pathways that in turn can compensate (in part) for mt dysfunction. Thus, symptoms of CNS disease due to a high percentage of mutated mtDNA are acute and can be lethal while those of diabetes chronic and manageable. People with mt diabetes live long enough to pass their mutations on to their progeny while those with a high burden of mutated mtDNA observed as MELAS, LHON, MERRF and NARP usually do not. Actually, it is the infants and children with these conditions that lead to genetic testing of the parents. In these parents the mother is usually found to have a percent mutation that may or may not compromise her health but yet is sufcient to result in a compromise of her metabolism. She in turn passes the mutation to the infant. The degree to which the infant is affected depends in turn on how much of the mutated DNA is passed to the fertilized egg at conception. Whether the distribution of normal versus mutated DNA is by chance alone or if there is some sort of preferential allocation is subject to much argument. Accumulations of deleted mutant mtDNA have been observed in terminally differentiated cells. However, the question arises as to whether mutations accumulate in oocytes. Rapid changes in mtDNA variants between generations have led to the bottleneck theory [139,140]. This theory proposes that there is a dramatic reduction in mtDNA during early oogenesis and that mutant mtDNA could be a major contributor of the mtDNA as the oocyte develops. This theory suggests that if by chance, mutant DNA instead of normal DNA contributes to subsequent mtDNA in the oocyte, then, the resultant egg might then result in an infant with a heavy burden of mutant mtDNA. This theory however attractive, does not explain all instances of mt disease nor all instances of mtDNA transmission from mother to child [141]. Families can have several affected children and within a family there can be degrees of mutation severity

or percent-mutated DNA. This latter observation does not support the bottleneck theory. If a bottleneck does occur it would affect all children equally. 1.4. Oxidative stress as a mutagen of mtDNA Until recently, it has been assumed that the major targets for free radical attack were the plasma and intracellular membranes and the nuclear genome. Now, however, with the knowledge about the importance of the mtDNA and mt function in cellular metabolism, the research on oxidative stress has shifted. It is now recognized that the mitochondria produce nearly 90% of the free radicals generated in the living cell and for proximity reasons, are also the prime targets of these reactive oxygen species. The nutrients that serve as antioxidants and free radical suppressants should function in the mt compartment. Indeed, Kristal et al. [142] have shown that antioxidants are active in this respect. Vitamin E in particular regulates mt peroxide formation by serving as an antioxidant in this compartment [143,144]. The BHE/Cdb rat with a mutation in the ATPase 6 gene is more vulnerable to free radical attack and this rat requires substantially more dietary Vitamin E than normal rats [145,146]. Humans with mutations that result in a similar reduction in OXPHOS efciency likewise might be more vulnerable to oxidative stress and also require more Vitamin E but such studies have not been conducted. The free radicals are produced in the inter-mt membrane space and must diffuse across the inner membrane in order to attack the mtDNA. Fortunately, there is a very active enzyme in the mt compartment (manganese-superoxide dismutase) that converts the free oxygen radical to a less reactive oxygen compound, peroxide. The peroxide is then converted to water. This reaction is not 100% efcient in capturing all of the oxygen radicals immediately upon their creation, so some do escape and attack not only the mt membranes but also the mtDNA. The attack on the mtDNA is random. That is, there is no specic target within the DNA molecule. Yet there are some sequences that are more vulnerable than others. Those regions that have multiple repeats are more vulnerable than regions without such repeats [122]. Because the mtDNA has little protection of its structure, free radical damage is more likely. There is some evidence of the existence of protective histone-like proteins in the

178

C.D. Berdanier, H.B. Everts / Mutation Research 475 (2001) 169184

mt compartment but a full histone coat of the DNA is generally agreed to be absent. Further, although there is some repair [120,121], this repair is not as efcient as that which occurs in the nucleus. Excision of the damaged sequences occurs and there is repair of alkalated bases. However, recombination as is common in nuclear repair, is not a signicant mtDNA repair mechanism [130]. Actually, mtDNA damage is far more persistent than is nDNA damage [134]. This is not, however, a critical or an acute situation under most conditions. Each mitochondrion has so many copies of its genome and each cell has so many mitochondria that damage to a few DNA molecules is unlikely to have a signicant effect on cellular function. If a few cells have a few copies damaged by free radical attack there will be no immediate cause for concern. If there is an overwhelming attack however, there would be noticeable loss in function. This happens when an individual is exposed to toxic levels of free radical generating chemicals, i.e. some pesticides. In this instance, damage could be extensive and the loss of mt function could likewise be significant, perhaps lethal. This is an uncommon event. More common are the subtle but cumulative changes in mt function that occur with age. In part, some of these changes are due to age changes in the membrane lipids and changes in the proteins embedded in that lipid. However, there is gathering evidence that age carries with it an accumulation of free radical induced damage to the mt genome. The products of this genome might have lost a measure of its normal function and thereby explain age-related declines in mt function. 1.5. Aging and mitochondrial function Yu et al. [112], Wei et al. [105,106,109111] and others [107,108,113,131,135138,147149] have reported that humans as well as animals have an increase in the number of base pair deletions as they age. There is also an increase in the number of base pair duplications. These mutations are translated into proteins that have less than normal function. For decades researchers have reported on the age-related decline in mt function and some have suggested that cell aging was caused by oxidative stress [133,136]. An age-related increase in mt 8-hydroxyguanosine has been reported [138]. Because mitochondria turn

over more rapidly than do the cells that contain them, free radical damage can have cumulative effects on cell function. As cell function, particularly mt function declines, cell (and tissue) aging accelerates. Thus, it should come as no surprise that mt genetic change predicts the rate at which the whole cell ages. Mitochondrial aging or the age-related decline in mt function due to an age-related mtDNA mutation is thought to explain some of the features of aging. For example, Correl-Debrinski et al. [150] reported that heart disease was associated with an increased number of mtDNA deletions in the heart muscle. They examined heart tissue from persons who had died from heart disease and their age matched controls who died from other causes. They found that a common mutation at 4977 bp was far more frequent in the persons with heart disease than in persons who died of other causes. The percent deletion mutation was quite low, however, probably too low to explain possible defective OXPHOS. There might have been other mtDNA changes as well but these were not reported. Tumor tissue from patients with breast cancer similarly had more frequent mtDNA deletions than people without this disease [151]. Both groups were heteroplasmic for a number of mt base sequences yet the patients with breast cancer went on to develop the disease. This suggests that there were other perhaps nongenomic factors that promoted the development of the cancer and that these factors were absent in the healthy controls. Cortopassi and Liu [152] reached these same conclusions and suggested that through understanding how these genes express themselves we might gain a better understanding of how the mt genes were transcribed and translated. Through this understanding we might be able to develop appropriate strategies for manipulating this expression. One such strategy is life long food restriction. Rodents that are food restricted have a signicantly longer life span than non-restricted rodents. The literature on this phenomenon is enormous. Within this literature are three reports that indicate that food restriction results in a reduction in the number of age-related mt deletions and other changes in mtDNA [153155]. In contrast, longevity and successful aging may be the result of inheriting mtDNA that is resistant to free radical induced mutation [156]. Some individuals apparently have mtDNA that resists the mutagenic actions of their environment. In others, perhaps their choice

C.D. Berdanier, H.B. Everts / Mutation Research 475 (2001) 169184

179

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

2. Summary The mt genome has been completely sequenced and mapped for a variety of species including man. The control of its expression via controls of transcription are now being investigated as we seek to understand how the phenotypic expression of the mt genotype can be manipulated. Mitochondrial diseases due to mutations in the mtDNA are of interest particularly as they relate to aging, degenerative disease and the response to dietary manipulation. Free radical damage and its suppression by nutrients may be important to our understanding of the aging process as well as age-related degenerative disease. Nutrient-mt gene interactions have not received much attention but perhaps as our knowledge about the role of the mtDNA in health and disease expands, these interactions will be explored.

Acknowledgements The authors would like to express their appreciation to all those who helped in the conduct of this work. Especially helpful was Ms. Kathie Wickwire. This work was supported by grants from Mitokor, The United States Department of Agriculture (Grant no. 98-35200-6049), The Georgia Agricultural Experiment Station and the UGA Diabetes Research Fund. References
[1] R.E. Giles, H. Blanc, H.M. Cann, D.C. Wallace, Maternal inheritance of human mtDNA, Proc. Natl. Acad. Sci. U.S.A. 77 (1980) 67156719. [2] D.C. Wallace, Diseases of the mtDNA, Ann. Rev. Biochem. 61 (1992) 11751212. [3] A. Tzagoloff, A.M. Myers, Biogenesis of mitochondrial genetics, Ann. Rev. Biochem. 55 (1986) 249285. [4] S. Anderson, A.T. Bankier, B.G. Barrell, M.H.L. Bruijin, A.R. Coulsen, J. Drouin, I.C. Eperon, D.P. Nierlich, B.A. Roe, F. Sanger, P.H. Schreier, A.J.H. Smith, R. Staden, I.G. Young, Sequence and organization of the human mitochondrial genome, Nature 290 (1981) 457465. [5] P. Cantatore, G. Attardi, Mapping the nascent light and heavy strand transcripts on the physical map of HeLa cell mtDNA, Nucl. Acid Res. 8 (1980) 26052625.

[6] D.D. Chang, D.A. Clayton, Precise identication of individual promoters for transcription of each strand of human mitochondrial DNA, Cell 36 (1984) 635643. [7] F. Mignotte, A. Gueride, A.M. Champagne, J.C. Mounolou, Direct repeats in the noncoding region of rabbit mtDNA: Involvement in the generation of intra and inter-individual heterogeneity, Eur. J. Biochem. 194 (1990) 561571. [8] R.J. Monnat, D.T. Reay, Nucleotide sequence identity of mitochondrial DNA from different human tissues, Gene 43 (1986) 205211. [9] J.M. Shoffner, D.C. Wallace, Oxidative phosphorylation disease and mitochondrial DNA mutations: diagnosis and treatment, Ann. Rev. Nutr. 14 (1994) 535568. [10] J.E. Walker, N.J. Gay, S.J. Powell, M. Kostina, M.R. Dyer, ATP synthase from bovine mitochondria: sequences of imported precursors of oligomycin sensitivity conferral protein, factor 6, and adenosinetriphosphatase inhibitor protein, Biochemistry 26 (1987) 86138619. [11] J.E. Walker, M.J. Runswick, L. Poulter, ATP synthase from bovine mitochondria. The characterization and sequence analysis of two membrane-associated subunits and of corresponding cDNAs, J. Mol. Biol. 197 (1987) 89100. [12] R.J. Britten, D.E. Kohne, Repeated sequences in DNA. Hundreds of thousands of copies of DNA sequences have been incorporated into the genomes of higher organisms, Science 161 (1968) 529540. [13] J.E. Hixson, D.A. Clayton, Initiation of transcription from each of the two human mitochondrial promoters requires unique nucleotides at the transcription start sites, Proc. Natl. Acad. Sci. U.S.A. 82 (1985) 26602664. [14] G. Gadaleta, G. Pepe, G. DeCandia, C. Quagliariello, E. Sbiss, C. Saccone C, The complete nucleotide sequence of the Rattus norvegicus mitochondrial genome: cryptic signals revealed by comparative analysis between vertebrates, J. Mol. Evol. 28 (1989) 497516. [15] Y. Aloni, G. Attardi, Symmetrical in vivo transcription of mitochondrial DNA in HeLa cells, Proc. Natl. Acad. Sci. U.S.A. 68 (1971) 17571761. [16] J. Montoya, T. Christianson, D. Levens, M. Rabinowitz, G. Attardi, Identication of initiation sites for heavy-strand and light-strand transcription in human mitochondrial DNA, Proc. Natl. Acad. Sci. U.S.A. 79 (1982) 71957199. [17] M.W. Walberg, D.A. Clayton, In vitro transcription of human mitochondrial DNA, J. Biol. Chem. 258 (1983) 12681275. [18] J. Montoya, G.L. Gaines, G. Attardi, The pattern of transcription of the human mitochondrial rRNA genes reveals two overlapping transcription units, Cell 34 (1983) 151159. [19] D.D. Chang, D.A. Clayton, Precise assignment of the light-strand promoter of mouse mitochondrial DNA: a functional promoter consists of multiple upstream domains, Mol. Cell. Biol. 6 (1986) 32533261. [20] D.D. Chang, D.A. Clayton, Precise assignment of the heavy-strand promoter of mouse mitochondrial DNA: cognate start sites are not required for transcriptional initiation, Mol. Cell. Biol. 6 (1986) 32623267. [21] D.F. Bogenhagen, E.F. Applegate, B.K. Yoza, Identication of a promoter for transcription of the heavy strand mtDNA:

180

C.D. Berdanier, H.B. Everts / Mutation Research 475 (2001) 169184 in vitro transcription and deletion mutagenesis, Cell 36 (1984) 11051113. D.D. Chang, J.E. Hixson, D.A. Clayton, Minor transcription initiation events indicate that both human mitochondrial promoters function bidirectionally, Mol. Cell. Biol. 6 (1986) 294301. J.N. Topper, D.A. Clayton, Identication of transcriptional regulatory elements in human mitochondrial DNA by linker substitution analysis, Mol. Cell. Biol. 9 (1989) 12001211. D.D. Chang, W.W. Hauswirth, D.A. Clayton, Replication priming and transcription initiation from precisely the same site in mouse mitochondrial DNA, EMBO J. 4 (1985) 15591567. D.D. Chang, D.A. Clayton, Priming of human mitochondrial DNA replication occurs at the light-strand promoter, Proc. Natl. Acad. Sci. U.S.A. 82 (1985) 351355. D.Y. Lee, D.A. Clayton, RNase mitochondrial RNA processing correctly cleaves a novel R-loop at the mitochondrial-DNA leading-strand origin of replication, Genes Develop. 11 (1997) 582592. M.W. Walberg, D.A. Clayton, Sequence and properties of the human KB cell and mouse L cell D-loop regions of mitochondrial DNA, Nucl. Acids Res. 9 (1981) 54115421. R.P. Fisher, D.A. Clayton, A transcription factor required for promoter recognition by human mitochondrial RNA polymerase: accurate initiation at the heavy- and light-strand promoters dissected and reconstituted in vitro, J. Biol. Chem. 260 (1985) 1133011338. R.P. Fisher, D.A. Clayton, Purication and characterization of human mitochondrial transcription factor 1, Mol. Cell. Biol. 8 (1988) 34963509. B. Kruse, N. Narasimhan, G. Attardi, Termination of transcription in human mitochondria: identication and purication of a DNA binding protein factor that promotes termination, Cell 58 (1989) 391397. R.P. Fisher, J.N. Topper, D.A. Clayton, Promoter selection in human mitochondria involves binding of transcription factor to orientation-independent upstream elements, Cell 50 (1987) 247258. R.P. Fisher, T. Lisowsky, M.A. Parisi, D.A. Clayton, DNA wrapping and bending by a mitochondrial high mobility group-like transcriptional activator protein, J. Biol. Chem. 267 (1992) 33583367. J. Poulton, K. Morten, C. Freeman-Emmerson, C. Potter, C. Sewry, V. Dubowitz, H. Kidd, J. Stephenson, W. Whitehouse, F.J. Hansen, M. Paris, G. Brown, Deciency of the human mitochondrial transcription factor h-mtTFA in infantile mitochondrial myopathy is associated with mtDNA depletion, Hum. Mol. Genet. 3 (1994) 17631769. N.-G. Larsson, A. Oldfors, E. Holme, D.A. Clayton, Low levels of mitochondrial transcription factor A in mitochondrial DNA depletion, Biochem. Biophys. Res. Commun. 200 (1994) 13741381. J. Montoya, A. Perez-Martos, H.L. Garstka, R.J. Wiesner, Regulation of mitochondrial transcription by mitochondrial transcription factor A, Mol. Cell. Biochem. 174 (1997) 227230. [36] N.-G. Larsson, J. Wang, H. Wilhelmsson, A. Oldfors, P. Rustin, M. Lewandoski, G.S. Barsh, D.A. Clayton, Mitochondrial transcription factor A is necessary for mtDNA maintenance and embryogenesis in mice, Nature Genet. 18 (1998) 231236. [37] H. Tomura, H. Endo, Y. Kagawa, S. Ohta, Novel regulatory enhancer in the nuclear gene of the human mitochondrial ATP synthase -subunit, J. Biol. Chem. 265 (1990) 6525 6527. [38] M.J. Evans, R.C. Scarpulla, NRF-1: a trans-activator of nuclear-encoded respiratory genes in animal cells, Genes Develop. 4 (1990) 10231034. [39] C.A. Chau, M.J. Evans, R.C. Scarpulla, Nuclear respiratory factor 1 activation sites in genes encoding the -subunit of ATP synthase, eukaryotic initiation factor 2, and tyrosine aminotransferase: specic interaction of puried NRF-1 with multiple target genes, J. Biol. Chem. 267 (1992) 69997006. [40] C.A. Virbasius, J.A. Virbasius, R.C. Scarpulla, NRF-1, an activator involved in nuclear-mitochondrial interactions, utilizes a new DNA-binding domain conserved in a family of developmental regulators, Genes Develop. 7 (1993) 24312445. [41] J.V. Virbasius, R.C. Scarpulla, Activation of the human mitochondrial transcription factor A gene by nuclear respiratory factors: a potential regulatory link between nuclear and mitochondrial gene expression in organelle biogenesis, Proc. Natl. Acad. Sci. U.S.A. 91 (1994) 13091313. [42] J.A. Enriquez, P. Fernadez-Silva, J. Montoya, Autonomous regulation in mammalian mitochondrial DNA transcription, Biol. Chem. 380 (1999) 737747. [43] J.M. Izquierdo, J.M. Cueza, Evidence of post-transcriptional regulation in mammalian mitochondrial biogenesis, Biochem. Biophys. Res. Commun. 196 (1993) 5560. [44] K. Luciakova, R. Li, B.D. Nelson, Differential regulation of the transcript levels of some nuclear-encoded and mitochondrial-encoded respiratory-chain components in response to growth activation, Eur. J. Biochem. 207 (1992) 253257. [45] R.J. Stevens, M.L. Nishio, D.A. Hood, Effect of hypothyroidism on the expression of cytochrome c and cytochrome c oxidase in heart and muscle during development, Mol. Cell. Biochem. 143 (1995) 119127. [46] B.D. Nelson, K. Luciakova, R. Li, S. Betina, The role of thyroid hormone and promoter diversity in the regulation of nuclear encoded mitochondrial proteins, Biochim. Biophys. Acta 1271 (1995) 8591. [47] J.M. Izquierdo, J. Ricart, L.K. Ostronoff, G. Egea, J.M. Cuezva, Changing patterns of transcriptional and posttranscriptional control of -F1 -ATPase gene expression during mitochondrial biogenesis in liver, J. Biol. Chem. 270 (1995) 1034210350. [48] N.E. Buroker, J.R. Brown, T.A. Gilbert, P.J. OHara, A.T. Beckenback, W.K. Thomas, M.J. Smith, Length heteroplasmy of sturgeon mtDNA: an illegitimate elongation model, Genetics 124 (1991) 157163. [49] C.S. Madsen, S.C. Ghivizzani, W.W. Hauswirth, In vivo and in vitro evidence for slipped mispairing in mammalian

[22]

[23]

[24]

[25]

[26]

[27]

[28]

[29]

[30]

[31]

[32]

[33]

[34]

[35]

C.D. Berdanier, H.B. Everts / Mutation Research 475 (2001) 169184 mitochondria, Proc. Natl. Acad. Sci. U.S.A. 90 (1993) 76717675. M. Zeviani, N. Bresolin, C. Gellera, A. Bordoni, M. Pannacci, P. Amati, M. Moggio, S. Servidei, G. Scarlato, S. DiDonato, Nucleus driven multiple large scale deletions of the human mitochondrial genome: a new autosomal dominant disease, Am. J. Hum. Genet. 47 (1990) 904914. W.M. Brown, M.M. George, A.C. Wilson, Rapid evolution of animal mtDNA, Proc. Natl. Acad. Sci. U.S.A. 76 (1979) 19671971. A. Zaid, R. Li, K. Luciakova, P. Barath, S. Nery, B.D. Nelson, On the role of the general transcription factor Sp1 in the activation and repression of diverse mammalian oxidative phosphorylation genes, J. Bioenergetics Biomembranes 31 (1999) 129135. K. Luciakova, B.D. Nelson, Transcript levels for nuclearencoded mammalian mitochondrial respiratory-chain components are regulated by thyroid hormone in an uncoordinated fashion, Eur. J. Biochem. 207 (1992) 247251. J. Marin-Garcia, R. Ananthakrishnan, M.J. Goldenthal, Mitochondrial gene expression in rat heart and liver during growth and development, Biochem. Cell Biol. 75 (1997) 137142. L.K. Ostronoff, J.M. Izquierdo, J.M. Cuezva, Mt-mRNA stability regulates the expression of the mitochondrial genome during liver development, Biochem. Biophys. Res. Commun. 217 (1995) 10941098. L.K. Ostronoff, J.M. Izquierdo, J.A. Enriquez, J. Montoya, J.M. Cuezva, Transient activation of mitochondrial translation regulates the expression of the mitochondrial genome during mammalian mitochondrial differentiation, Biochem. J. 316 (1996) 183191. J.M. Izquierdo, E. Jimenez, J.M. Cuezva, Hypothyroidism affects the expression of the -F1 -ATPase gene and limits mitochondrial proliferation in rat liver at all stages of development, Eur. J. Biochem. 232 (1995) 344350. A.M. Luis, J.M. Izquierdo, L.K. Ostronoff, M. Salinas, J.F. Santaren, J.M. Cuezva, Translational regulation of mitochondrial differentiation in neonatal rat liver: specic increase in the translational efciency of the nuclear-encoded mitochondrial -F1 -ATPase mRNA, J. Biol. Chem. 268 (1993) 18681875. J.M. Izquierdo, J.M. Cueza, Internal-ribosome-entry-site functional activity of the 3 -untranslated region of the mRNA for the subunit of mitochondrial h+-ATP synthase, Biochem. J. 346 (2000) 849855. M.L. DeHeredia, J.M. Izquierdo, J.M. Cuezvas, A conserved mechanism for controlling the translation of -F1ATPase between the fetal liver and cancer cells, J. Biol. Chem. 275 (2000) 74307437. C.V. Demonacos, N. Karayanni, E. Hatzoglou, C. Tsiriyiotis, D.A. Spandidos, C.E. Sekeris, Mitochondrial genes as sites of primary action of steroid hormones, Steroids 61 (1996) 226232. K. Umesono, K.K. Murakami, C.C. Thompson, R.M. Evans, Direct repeats as selective response elements for the thyroid hormone, retinoic acid, and Vitamin D3 receptors, Cell 65 (1991) 12551266.

181

[50]

[51]

[52]

[53]

[54]

[55]

[56]

[57]

[58]

[59]

[60]

[61]

[62]

[63] J.A. Enriquez, P. Fernadez-Silva, N. Garrido-Perez, M.J. Lopez-Perez, A. Perez-Martos, J. Montoya, Direct regulation of mitochondrial RNA synthesis by thyroid hormone, Mol. Cell. Biol. 19 (1999) 657670. [64] H.L. Garstka, M. Facke, J.R. Escribano, R.J. Wiesner, Stoichiometry of mitochondrial transcripts and regulation of gene expression by mitochondrial transcription factor a, Biochem. Biophys. Res. Commun. 200 (1994) 619626. [65] F. Casas, P. Rochard, A. Rodier, I. Casar-Malek, S. Marchal-Victorian, R.J. Weisner, G. Cabello, C. Wrutniak, A variant form of the nuclear triiodothyronine receptor c-ErbA1 plays a direct role in regulation of mitochondrial RNA synthesis, Mol. Cell. Biol. 19 (1999) 79137924. [66] T. Iglesias, J. Caubin, A. Zaballos, J.A. Bernal, J.A. Munoz, Identication of the mitochondrial NADH dehydrogenase subunit 3 (ND3) as a thyroid hormone regulated gene by whole genome PCR analysis, Biochem. Biophys. Res. Commun. 210 (1995) 9951000. [67] S.-Y. Chou, S.S. Hannah, K.E. Lowe, A.W. Norman, H.L. Henry, Tissue-specic regulation by Vitamin D status of nuclear and mitochondrial gene expression in kidney and intestine, Endocrinology 136 (1995) 55205526. [68] G. Li, Y. Liu, S.S. Tsang, Expression of a retinoic acid-inducible mitochondrial ND5 gene is regulated by cell density in bovine papillomavirus DNA-transformed mouse C127 cells but not in revertant cells, Int. J. Oncol. 5 (1994) 301307. [69] I.C. Gaemers, A.M.M. Van Pelt, A.P.N. Themmen, D.G. De Rooij, Isolation and characterization of all-trans-retinoic acid-responsive genes in the rat testis, Mol. Reprod. Develop. 50 (1998) 16. [70] P. Ruiz-Lozano, S.M. Smith, G. Perkins, S.W. Kubalak, G.R. Boss, H.M. Sucov, R.M. Evans, K.R. Chien, Energy deprivation and a deciency in downstream metabolic target genes during the onset of embryonic heart failure in RXR embryos, Development 125 (1998) 533544. [71] H.B. Everts, C.D. Berdanier, Optimal mitochondrial function in mitochondrial diabetes depends on a three-fold increase in dietary Vitamin A, Diabetes 48 (1999) A6. [72] H. Everts, The effects of dietary Vitamin A on mitochondrial function and gene expression in diabetes-prone BHE/Cdb rats, Ph.D. dissertation, University of Georgia, 2000, 267 pp. [73] C.E. Mathews, R.A. Mcgraw, C.D. Berdanier, A point mutation in the mitochondrial DNA of diabetes-prone BHE/Cdb rats, FASEB J. 9 (1995) 16381642. [74] C.E. Mathews, R.A. McGraw, R. Dean, C.D. Berdanier, Inheritance of a mitochondrial DNA defect and impaired glucose tolerance in BHE/Cdb rats, Diabetologia 42 (1999) 3541. [75] X. Huang, K.F. Eriksson, A. Vaag, M. Lehtovirta, M. Hansson, E. Laurila, T. Kanninen, B.T. Olesen, L. Koranyi, L. Groop, Insulin regulated mitochondria gene expression is associated with glucose ux in human skeletal muscle, Diabetes 48 (1999) 15081514. [76] Y.L. Germanyuk, A.G. Minchenko, Effect of insulin on RNA and protein biosynthesis in liver mitochondria from normal and alloxan diabetic rats, Endocrinol. Exp. 12 (1978) 233243.

182

C.D. Berdanier, H.B. Everts / Mutation Research 475 (2001) 169184 Polonsky, P. Froguel, Clinical phenotypes, insulin secretion, and insulin sensitivity in kindreds with maternally inherited diabetes and deafness due to mitochondrial tRNALeu(UUR) gene mutation, Diabetes 45 (1996) 478487. C.B. Lucking, S. Kosel, P. Mehracin, M.B. Graeber, Absence of the mitochondrial A7237T mutation in Parkinsons disease, Biochem. Biophys. Res. Commun. 211 (1995) 700704. R.E. Davis, S. Miller, C. Herrnstadt, S. Ghosh, E. Fahy, L.A. Shinobu, D. Galasko, L.J. Thal, M.F. Beal, N. Howell, W.D. Parker, Mutations in cytochrome c oxidase genes segregate with late onset Alzheimer disease, Proc. Natl. Acad. Sci. U.S.A. 94 (1997) 45264531. T. Hutchin, G. Cortopassi, A mitochondrial DNA clone is associated with increased risk for Alzheimer disease, Proc. Natl. Acad. Sci. U.S.A. 92 (1995) 68926895. H. Schagger, T. Georg, Human diseases with defects in oxidative phosphorylation 2. F1 F0 ATP-synthase defects in Alzheimer disease revealed by blue native polyacrylamide gel electrophoresis, Eur. J. Biochem. 227 (1995) 916921. F. Degoul, I. Nelson, S. Amselem, N. Romero, B. Obermaier-Kusser, G. Ponsot, C. Marsac, P. Lestienne, Different mechanisms inferred from sequences of human mitochondrial DNA deletions in ocular myopathies, Nucl. Acids Res. 19 (1990) 493496. C.T. Moraes, F. Ciacci, E. Bonilla, C. Jansen, M. Hirano, N. Rao, R.E. Locelace, L.P. Rowland, E.A. Schon, S. DiMauro, Two novel pathogenic mitochondrial DNA mutations affecting organelle number and protein synthesis. Is the tRNA(Leu(UUR)) gene an etiologic hot spot? J. Clin. Invest. (1993). K.J. Morten, J.M. Cooper, G.K. Brown, B.D. Lake, D. Pike, J. Poulton, A new point mutation associated with mitochondrial encephalomyopathy, Hum. Mol. Genet. 2 (1993) 20812087. M. Zeviani, C. Gellera, C. Antozzi, M. Rimoldi, L. Morandi, F. Villani, V. Tiranti, S. DiDonato, Maternally inherited myopathy and cardiomyopathy: association with mutation in mitochondrial DNA tRNA(Leu)(UUR), Lancet 338 (1991) 143147. J.-I. Hiraoka, Y.-H. Hirao, Fate of sperm tail components after incorporation into the hampster egg, Gamete Res. 19 (1988) 369380. H. Kaneda, J.-I. Hayashi, S. Takahama, C. Taya, K.F. Lindahl, H. Yonekawa, Elimination of paternal mitochondrial DNA in intraspecic crosses during early mouse embryogenesis, Proc. Natl. Acad. Sci. U.S.A. 92 (1995) 45424546. P. Sutovsky, C.S. Navara, G. Schatten, Fate of the sperm mitochondria, and the incorporation, conversion, and disassembly of the sperm tail structures during bovine fertilization, Biol. Reproduction 55 (1996) 11951205. F. Ankel-Simons, J.M. Cummins, Misconceptions about mitochondria and mammalian fertilization: implications for theories on human evolution, Proc. Natl. Acad. Sci. U.S.A. 93 (1996) 1385913863.

[77] E.E. McKee, B.L. Grier, Insulin stimulates mitochondrial protein synthesis and respiration in isolated perfused heart, Am. J. Physiol. 259 (1990) E413E421. [78] T.M. Johnson, M.P. Rosenberg, M.H. Meisler, An insulin-responsive element in the pancreatic enhancer of the amylase gene, J. Biol. Chem. 268 (1993) 464468. [79] R.M. OBrien, E.L. Noisin, A. Suwanichkul, T. Yamasaki, P.C. Lucas, J.C. Wang, D.R. Powell, D.K. Granner, Hepatic nuclear factor 3- and hormone-regulated expression of the phophosenolpyruvate carboxykinase and insulin-like growth factor-binding protein 1 genes, Mol. Cell. Biol. 15 (1995) 17471758. [80] P. Lestienne, Mitochondrial DNA mutations in human diseases: a review, Biochimie 74 (1992) 123130. [81] E.A. Schon, M.H. Grossman, Mitochondrial diseases: genetics, Biofactors 7 (1998) 191195. [82] E.A. Shoubridge, Mitochondrial DNA diseases: histological and cellular studies, J. Bioenergetics Biomembranes 26 (1994) 301B310B. [83] K.D. Gerbitz, K. Gempel, D. Brdiczka, Mitochondria and diabetes. Genetic, biochemical, and clinical implications of the cellular energy circuit, Diabetes 45 (1996) 113126. [84] K.D. Gerbitz, A. Paprotta, M. Jaksch, S. Zierz, J. Drechsel, Diabetes mellitus is one of the heterogeneous phenotypic features of a mtDNA point mutation within the tRNA leu gene, FEBS Lett. 321 (1993) 194196. [85] W. Reardon, R.J. Ross, M.G. Sweeney, L.M. Luxon, M.E. Pembry, A.E. Harding, R.C. Trembath, Diabetes mellitus associated with a pathogenic point mutation in mitochondrial DNA, Lancet 340 (1992) 13761379. [86] M. Odowara, Involvement of mitochondrial gene abnormalities in the pathogenesis of diabetes mellitus, Ann. New York Acad. Sci. 865 (1996) 7281. [87] C.E. Mathews, C.D. Berdanier, Non-insulin dependent diabetes mellitus as a mitochondrial genomic disease, Proc. Soc. Exp. Biol. Med. 219 (1998) 97108. [88] H.H.P.J. Lempkes, M. de Vijlder, P.A.A. Struyvenberg, J.J.P. van de Kamp, M. Frolich, Maternal inherited diabetes deafness of the young (MIDDY), a new mitochondrial syndrome, Diabetologia 32 (1989) 509A. [89] J.M.W. van der Ouweland, H.H.P.J. Lemkes, W. Ruitenbeek, L.A. Sandkuijil, M.F. Vijlder, P.A.A. Struyvenberg, J.J.P. van de Kamp, J.A. Maassen, Mutantion in mitochondrial tRNALeu(UUR) gene in a large pedigree with maternally transmitted type II diabetes mellitus and deafness, Nature Genet. 1 (1992) 368371. [90] G. Velho, M.M. Byrne, K. Clement, J. Sturis, M.E. Pueyo, H. Blanche, N. Vionnet, J. Fiet, P. Passa, J.J. Robert, K.S. Polonsky, P. Froguel, Clinical phenotypes, insulin secretion, and insulin sensitivity in kindreds with maternally inherited diabetes and deafness due to mitochondrial tRNALeu(UUR) gene mutation, Diabetes 45 (1996) 478487. [91] J.C. Alcolado, A. Majid, M. Brockington, M.G. Sweeney, R. Morgan, A. Rees, A.E. Harding, A.H. Barnett, Mitochondrial gene defects in patients with NIDDM, Diabetologia 37 (1994) 372376. [92] G. Velho, M.M. Byrne, K. Clement, J. Sturis, M.E. Pueyo, H. Blanche, N. Vionnet, J. Fiet, P. Passa, J.J. Robert, K.S.

[93]

[94]

[95]

[96]

[97]

[98]

[99]

[100]

[101]

[102]

[103]

[104]

C.D. Berdanier, H.B. Everts / Mutation Research 475 (2001) 169184 [105] C. Yen, C.Y. Pang, R.H. Hsieh, C.H. Su, K.L. King, Y.H. Wei, Age dependent 6 kb deletion in human mitochondrial DNA, Biochem. Int. 26 (1992) 457468. [106] T.C. Yen, H.H. Su, K.L. King, Y.H. Wei, Aging associated 5 kb deletion in human liver mitochondrial DNA, Biochem. Biophys. Res. Commun. 178 (1991) 124131. [107] S. Simonetti, X. Chen, S. DiMauro, E.A. Schon, Accumulation of deletions in human mitochondria during normal aging: analysis by quantitative PCR, Biochem. Biophys. Acta 1180 (1992) 113122. [108] K. Asano, M. Nakamura, T. Sato, H. Tauchi, A. Asano, Age dependency of mtDNA decrease differs in different tissues of rat, J. Biochem. 114 (1993) 303306. [109] Y.-H. Wei, S.-H. Kao, Mitochondrial DNA mutations and lipid peroxidation in human aging, in: C.D. Berdanier (Ed.), Nutrients and Gene Expression, CRC Press, Boca Raton, FL, 1996, pp. 165188. [110] Y.-H. Wei, C.Y. Pang, B.-J. You, H.-C. Lee, Tandem duplications and large scale deletions of mitochondrial DNA are early molecular events of human aging process, Ann. New York Acad. Sci. 786 (1996) 82101. [111] Y.-H. Wei, Oxidative stress and mitochondrial DNA mutations in human aging, Proc. Soc. Exp. Biol. Med. 217 (1998) 5363. [112] B.P. Yu, J.J. Chen, C.M. Kang, M. Choe, Y.S. Maeng, B.S. Kristal, Mitochondrial aging and lipoperoxidative products, Ann. New York Acad. Sci. 786 (1996) 4456. [113] R.S. Sohal, A. Dubey, Mitochondrial oxidative damage, hydrogen peroxide release and aging, Free Rad. Biol. Med. 16 (1994) 621626. [114] H. Jaeschke, Mechanisms of oxidant stress-induced acute tissue injury, Proc. Soc. Exp. Biol. Med. 209 (1995) 104111. [115] R.S. Sohal, Mitochondria generate superoxide anion radicals and hydrogen peroxide, FASEB J. 11 (1997) 12691270. [116] B.S. Kristal, J. Chen, B.P. Yu, Sensitivity of mitochondrial transcription to different free radical species, Free Rad. Biol. Med. 16 (1994) 323329. [117] J.G. de la Asuncion, M.L. del Olmo, J. Saste, A. Millan, A. Pellin, F.V. Pallardo, J. Vina, AZT treatment induces molecular and ultrastructural damage to muscle mitochondria, J. Clin. Invest. 102 (1998) 49. [118] J.G. de la Asuncion, M.L. del Olmo, J. Sastre, F.V. Pallardo, J. Vina, Zidovudine (AZT) causes oxidation of mitochondrial DNA in mouse liver, Hepatology 29 (1999) 985987. [119] C.C. Pettepher, S.P. LeDoux, V.A. Bohr, G.L. Wilson, Repair of alkali-labile sites within mitochondrial DNA of RINr cells after exposure to nitrosourea streptozotocin, J. Biol. Chem. 266 (1991) 31133117. [120] W.J. Driggers, S.P. LeDoux, G.L. Wilson, Repair of oxidative damage within the mitochondrial DNA of RINr 38 cells, J. Biol. Chem. 268 (1993) 2204222045. [121] D. Demple, L. Harrison, Repair of oxidative damage to DNA, Ann. Rev. Biochem. 63 (1994) 915948. [122] E.A. Schon, R. Rizzuto, C.T. Moraes, H. Nakase, M. Zevaiani, S. DiMauro, A direct repeat is a hot spot for large scale deletion of human mitochondrial DNA, Science 244 (1989) 346349.

183

[123] J. Poulton, M.E. Deadman, L. Bendoff, K. Morten, J. Land, G. Brown, Families of mitochondrial DNA re-arrangements can be detected in patients with mitochondrial deletions: duplications may be a transient intermediate form, Hum. Mol. Genet. 2 (1993) 2330. [124] J. Poulton, M.E. Deadman, S. Raamacharan, R.M. Gardiner, Germ line deletions of mitochondrial DNA in mitochondrial myopathy, Am. J. Hum. Genet. 48 (1991) 649653. [125] N.G. Larsson, E. Holme, B. Kristianson, A. Oldfors, M. Rtulinius, Progressive increase of the mutated mitochcondrial fraction in KearnsSayre syndrome, Ped. Res. 28 (1990) 131136. [126] E.A. Shubridge, G. Karpati, K.E. Hasting, Deletion mutants are functionally dominent over wild type mitochondrial genomes in skeletal muscle ber segments in mitochondrial disease, Cell 62 (1990) 4349. [127] J.I. Hayashi, S. Ohta, A. Kikuchi, M. Takemitsu, Y.-I. Goto, I. Nonaka, Introduction of disease related mitochondrial DNA deletions in HeLa cells lacking mitochondrial DNA results in mitochondrial dysfunction, Proc. Natl. Acad. Sci. U.S.A. 88 (1991) 1061410618. [128] J.M. Collombet, G. Mandon, R. Dumoulin, B. Mousson, G. Stepien, Accumulations of mitochondrial DNA deletions in myotubules cultured from muscles of patients with mitochondrial myopathies, Mol. Gen. Genet. 253 (1996) 182188. [129] S. Mita, B. Schmidt, E.A. Schon, S. Dimauro, E. Bonilla, Detection of deleted mitochondrial genomes in cytochrome oxidase decient bers of a patient with KearnsSayre syndrome, Proc. Natl. Acad. Sci. U.S.A. 86 (1989) 9509 9513. [130] D.C. Wallace, Report of the Committee on human mitochondrial DNA, Cytogenet. Cell Genet. 51 (1989) 612621. [131] P.M. Eimon, S.S. Chung, C.M. Lee, R. Weindruch, J.M. Aiken, Age associated mitochondrial deletions in mouse skeletal muscle: comparison of different regions of the mitochondrial genome, Develop. Genet. 18 (1996) 107113. [132] Z. Djuric, D. Kritschevsky, Modulation of oxidative DNA damage levels by dietary fat and calories, Nutr. Res. 295 (1993) 181190. [133] D. Harmon, Free radical theory of aging. Consequences of mitochondrial aging, Age 6 (1983) 8694. [134] F.M. Yakes, B. Van Houten, Mitochondrial DNA damage is more extensive and persists longer than nuclear DNA damage in human cells following oxidative stress, Proc. Natl. Acad. Sci. U.S.A. 94 (1997) 514519. [135] C. Richter, Oxidative damage to the mitochondrial DNA and its relationship to aging, Int. J. Biochem. Cell Biol. 27 (1995) 647653. [136] D. Harmon, Free radical involvement in aging. Pathophysiology and therapeutic implications, Drugs Aging 3 (1993) 6080. [137] C. Zhang, V.W.S. Liu, C.L. Addessi, D.A. Shefeld, A.W. Linnane, P. Nagley, Differential occurrence of mutations in mitochondrial DNA of human skeletal muscle during aging, Hum. Mutat. 11 (1998) 360371.

184

C.D. Berdanier, H.B. Everts / Mutation Research 475 (2001) 169184 [148] C.M. Lee, R. Weindruch, J.M. Aiken, Age associated alterations of the mitochondrial genome, Free Rad. Biol. Med. 22 (1997) 12591269. [149] M.K. Shigenaga, T.M. Hagen, B.N. Ames, Oxidative damage and mitochondrial decay in aging, Proc. Natl. Acad. Sci. U.S.A. 91 (1994) 1077110778. [150] M. Corral-Debrinski, G. Stepien, J.M. Shoffner, M.T. Lott, K. Kanter, D.C. Wallace, Hypoxemia is associated with mtDNA damage and gene induction. Implications for cardiac disease, JAMA 266 (1991) 18121816. [151] M.S. Bianchi, N.O. Bianchi, G. Baillet, Mitochondrial DNA mutations in normal and tumor tissues from breast cancer patients, Cytogenet. Cell Genet. 71 (1995) 99103. [152] G. Cortopassi, Y. Liu, Genotype selection of mitochondrial and oncogenic mutations in human tissues suggests mechanisms of age related pathophysiology, Mutat. Res. 338 (1995) 151159. [153] C.M. Kang, B.S. Kristal, B.P. Yu, Age related mitochondrial DNA deletions: Effect of dietary restriction, Free Rad. Biol. Med. 24 (1998) 148154. [154] V. Haley-Zitlin, A. Richardson, Effect of dietary restriction on DNA repair and DNA damage, Nutr. Res. 295 (1993) 237245. [155] K. Randerath, R.W. Hart, G.D. Zhou, R. Reddy, T.F. Danna, E. Randerath, Enhancement of age related increases in DNA-I compound levels by calorie restriction: comparison of male B-N and F344 rats, Mutat. Res. 295 (1993) 3146. [156] G. DeBenedictus, G. Rose, G. Carrieri, M. LeLuca, E. Falcone, G. Passarino, G. Passarino, M. Bonafe, D. Monti, G. Baggio, S. Bertolini, D. Mari, R. Mattace, C. Franceschi, Mitochondrial DNA inherited variants are associated with successful aging and longevity in humans, FASEB J. 13 (1999) 15321536.

[138] M. Hayakawa, K. Torii, S. Sugiyama, M. Tanaka, T. Ozawa, Age associated accumulation of 8-hydroxyguanosine in mitochondrial DNA of human diaphragm, Biochem. Biophys. Res. Commun. 179 (1991) 10231029. [139] R.B. Blok, D.A. Gook, D.R. Thorburn, H.-H.M. Dahl, Skewed segregation of the mtDNA mt 8993 (T G) mutation in human oocytes, Am. J. Hum. Genet. 60 (1997) 1495 1501. [140] D.R. Marchington, V. Macaulay, G.M. Hartshorne, B. Barlow, J. Pouton, Evidence from human oocytes for a genetic bottleneck in an mtDNA disease, Am. J. Hum. Genet. 63 (1998) 769775. [141] J. Poulton, V. Macaulay, D.R. Marchington, Mitochondrial genetics98. Is the bottleneck cracked? Am. J. Hum. Genet. 62 (1998) 752757. [142] B.S. Kristal, B.-J. Park, B.P. Yu, Antioxidants reduce peroxyl-mediated inhibition of mitochondrial transcription, Free Rad. Biol. Med. 16 (1994) 653660. [143] C.K. Chow, W. Ibrahim, Z. Wei, A.C. Chan, Vitamin E regulates mitochondrial hydrogen peroxide generation, Free Rad. Biol. Med. 27 (1999) 580587. [144] H. Isliker, H. Weiser, U. Moser, Stabilization of rat heart mitochondria by -tocopherol in rats, Int. J. Vit. Nutr. Res. 67 (1997) 9194. [145] K. Wickwire, K. Kras, C. Gunnett, D. Hartle, C.D. Berdanier, Menhaden oil feeding increases potential for renal free radical production in BHE/Cdb rats, P.S.E.B.M. 209 (1995) 397402. [146] M.J. Kullen, C.D. Berdanier, Inuence of sh oil feeding on the Vitamin E requirement of BHE/Cdb rats, Biochem. Arch. 8 (1992) 247257. [147] H.M.A. Cacciultolo, L. Trinh, J.A. Lumpkin, G. Rao, Hypoxia induces DNA damage in mammalian cells, Free Rad. Biol. Med. 14 (1993) 267276.