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Mitochondria: Eubacteria Descendant, Cellular Dynamics, Interactions with Nuclear DNA, and Neurological Diseases John K. Grandy North Country Urgent Care, 21017 NYS Route 12f, Water town NY, 13601, USA. INTRODUCTION It is an amazing fact that almost every single cell in the human body possesses organelles that are descendant from ancient eubacteria. These organelles, specifically the mitochondria, are vital to the survival of all eukaryotic cells. This chapter is a brief review of how the symbiotic relationship between the ancient eubacteria and nucleated ancestral cells arose, the cellular dynamics of the mitochondria, the system of mitochondria- nuclear interactions, and mutations that affect this system which result in neurological disorders. Understanding this symbiotic relationship may enable humankind to cure disease inherent to this very complex system of gene- gene interactions. Mitochondria (singular mitochondrion) [mitos- warp or thread + khondros- grain or granule] are descendant from ancient eubacteria that, through endosymbiosis, formed a dynamic symbiotic relationship with nucleated ancestral cells. The endosymbiont hypothesis (also known as the endosymbiotic theory) maintains that all eukaryotic cells emerged as anaerobic organisms that possessed no mitochondria (or in the case of plant cells no chloroplast). These cells would undergo an endocytic event in where they would, by endocytosis, take up or engulf aerobic prokaryotic cells that produce energy from their oxidative phosphorylation systems. This new found source of cellular energy possessed the potential to allow these novel cells to perform more complex functions.This process eventually evolved into a stable symbiotic relationship and is presumed to have taken place when substantial amounts of oxygen entered the atmosphere 1.5 X 10 9 years Chapter 14 Book: New Dimensions in Microbiology Publisher: Lenin Media Private Limited, Delhi, India Editors: Khan, M.M.A.A. et al., 2015 ISBN: 978-93-85160-84-4 Mithochondria...........................Neurological Diseases John K. Grandy Received: 04/05/2015 Accepted: 09/08/2015 174 New Dimensions in Microbiology ISBN 978-93-85160-84-4

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Mitochondria: Eubacteria Descendant,Cellular Dynamics, Interactions with

Nuclear DNA, and Neurological DiseasesJohn K. Grandy

North Country Urgent Care, 21017 NYS Route 12f, Water town NY, 13601, USA.

INTRODUCTION

It is an amazing fact that almost every single cell in the human bodypossesses organelles that are descendant from ancient eubacteria. Theseorganelles, specifically the mitochondria, are vital to the survival of alleukaryotic cells. This chapter is a brief review of how the symbioticrelationship between the ancient eubacteria and nucleated ancestral cellsarose, the cellular dynamics of the mitochondria, the system of mitochondria-nuclear interactions, and mutations that affect this system which result inneurological disorders. Understanding this symbiotic relationship may enablehumankind to cure disease inherent to this very complex system of gene-gene interactions. Mitochondria (singular mitochondrion) [mitos- warp orthread + khondros- grain or granule] are descendant from ancient eubacteriathat, through endosymbiosis, formed a dynamic symbiotic relationship withnucleated ancestral cells. The endosymbiont hypothesis (also known as theendosymbiotic theory) maintains that all eukaryotic cells emerged as anaerobicorganisms that possessed no mitochondria (or in the case of plant cells nochloroplast). These cells would undergo an endocytic event in where theywould, by endocytosis, take up or engulf aerobic prokaryotic cells thatproduce energy from their oxidative phosphorylation systems. This newfound source of cellular energy possessed the potential to allow these novelcells to perform more complex functions.This process eventually evolvedinto a stable symbiotic relationship and is presumed to have taken placewhen substantial amounts of oxygen entered the atmosphere 1.5 X 109 years

Chapter 14

Book: New Dimensions in MicrobiologyPublisher: Lenin Media Private Limited, Delhi, IndiaEditors: Khan, M.M.A.A. et al., 2015ISBN: 978-93-85160-84-4

Mithochondria...........................Neurological Diseases John K. Grandy

Received: 04/05/2015 Accepted: 09/08/2015

174New Dimensions in Microbiology ISBN 978-93-85160-84-4

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ago.However, as time went on the interaction between the nuclear DNA(nDNA) of the cell and the mitochondrial DNA (mtDNA) evolved into adynamic and eloquent level of communication with in the novel eukaryoticcell. This endocytic event is an extremely significant point in time, from amicrobiological perspective, as the mitochondria nowprovide vital functions;e.g., metabolic, regulatory, and developmental, to many modern daymicroorganisms and has also fueled the evolution of cellular complexitythroughout the animal kingdom. In humans, the nDNA and mtDNAinteractions have profound effectsin maintaining the optimal functioning ofall the cells in every organ system (with the exception of red blood cells andthe lens in the eyes). Genetic mutations that affect this system of interactionscan have a negative impact on tissues and organs which are contingent onaerobic metabolism. Mitochondrial disorders have been shown to affectsingle organs, e.g., the eye or ear, but can also be involved in multiple organsystems as seen in several prominent neurological and myopathic disorders.Some of these disorders can affect the neurons, and subsequently, humanconsciousness. Several of these disorders will be discussed later in thischapter, but first let us start at the beginning.

The Origin of Mitochondria and Functional Gene Transfer

In the late 1990’s, the genetic sequencing of many mitochondrial,prokaryotic, and several nuclear genomes amassed significant evidence onthe origin and early evolution of mitochondria (Gray et al. 2001).

This evidence suggested that the early mitochondrial genome has its originswithin the eubacteria, specifically the subdivision alpha-proteobacteria whichcontains Rickettsia and other obligate intracellular parasites.

These are the closest known relatives of mitochondria. This is supportedby the comparison of the phylogenetic analyses of protein-coding genes (Grayet al. 1999; Lang et al. 1999) and the ribosomal RNA genes (Gray 1999) in themtDNA.

During the early development of the symbiotic relationship that evolvedbetween the eubacteria-descendant mitochondria and the pre-eukaryoticancestral nucleated cells, many genes were relocated from the ancestralorganelle genome to the nucleus of the host. This is sometimes referred toas mitochondrion-to-nucleus transfers. But how did this take place?

In prokaryotes the DNA is not encased in a nucleus, rather it is organizedinto plasmids. Amongst prokaryotes, copies of plasmids are transferredeasily from one cell to another. In fact this is how antibiotic resistance ispassed on among certain populations of bacteria after exposure to antibiotics,i.e., the plasmid-gene for antibiotic resistance is copied and transmitted to

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another bacterium after making cell-cell contact. It is believed that a similarschematic is responsible for mitochondrion-to-nucleus gene transfer.However, there is still no general consent and much debate as to how thisactually proceeded.

Modern day genome sequencing projects have discovered multipleexamples of organelle-to-nucleus gene transfer to forge eukaryoticchromosomes. This includes not only mitochondria, but also with chloroplastsin plant cells. This influx of organelle DNA transfer has, in many ways,obliterated organelle autonomy making the assimilated organelles nuclear-dependent; as is the case with mitochondria, while at the same timesignificantly increasing nuclear complexity.

In 1981, one of the earliest proposals suggesting that gene transfer fromancestral organelles to nucleus was made in plant cells in order to explainthe presence of plastid-specific isozymes that were coded by nDNA (Weeden1981). In 1994, a study utilizing pulse-field gel electrophoresis, copies ofmtDNA were discovered in the genomes of domestic cat populations andtermed nuclear integrants of mtDNA or NUMT (Lopez et al. 1994).

In 2000, NUMTs were discovered in many primates using DNA extraction,amplification, cloning, and sequencing (Mundy et. al 2000). Collectivelly,these experiments, and several others, used different scientific techniques toestablish the fact that mtDNA has been transferred to nDNA in several speciesincluding humans.

In 1985, hybridization experiments estimated that human nDNAcontained, at the very least, several hundred copies of mtDNA-like fragments(Fukuda et al. 1985). In 2001, an extensive analysis using a combination ofconventional BLAST alignment, DNA block signaling, and a search of thehuman genome project for NUMTs was completed(Mourier et al. 2001). Thisstudy revealed 296 NUMTs (~90% of the mitochondrial genome) that rangedfrom 106-14,654 base pairs in size existing in the human genome.

The Mourier et al. study also suggested that several NUMTs exceed thesize of the longest human NUMT, all parts of the mitochondrial genome arerepresented in the nDNA, and that the integration of mtDNA into the nDNAis an ongoing continuous evolutionary process. However, the Mourier et al.study met some criticism as it was speculated that the 296 NUMTs may nothave been an accurate approximation due the heteroplasmy and the fact thatthe entire human genome project was not completed until 2003 [for a goodreview of the development and completion of the human genome projectplease consult reference (Grandy 2006)].

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Heteroplasmy is a genetic phenomenon, particularly in human cells, inwhere mtDNA polyploidy is an intrinsic physiological trait, i.e., severaldifferent mtDNA genotypes of the same mtDNA gene co-exist in the samecell. This is the reason why certain mitochondrial mutations do not exert aphenotypic effect until a particular mutational load threshold is reachedbecause a good copy (or copies) of that gene still exist in the cell. The obstaclepresented by heteroplasmy was addressed in 2014, in a study utilizingcaptured human mtDNA sequences from the 1000 Genome Whole SequencingData (Abecasis et al. 2012) which targeted nuclear genes and recovered 1242assembled mtDNA (Diroma et al. 2014). The Diroma et al. study providedan extended population-scale mitochondrial genotyping in humans whichwas enriched with an estimation of heteroplasmies and reconstructed a vastnumber or human mitochondrial sequences from targeted exome data.

Several experiments and studies have been discussed demonstrating thatmitochondrion-to-nucleus gene transfer has taken place during the evolutionof eukaryotic cells. The functional transfer implicitly involves the relocationof a mitochondrial gene to the nucleus, the acquisition of a promoter, successfultargeting to the mitochondrial outer membrane for proper function, andsubsequently the loss of the gene from the mitochondrial genome(Brandvainand Wade 2009). The subsequent loss of mitochondrial genes after nucleartransfer may take place since endosymbiosis reduces the strength of selectionon genes especially now that there is a functional copy in the nucleus. Thesegenes may be lost in the mitochondrial genome by the neutral fixation of adeletion or other forms of loss-of-function mutations which could beaccomplished by mitochondrial fusion and fission. The functions of fusionand fission will be discussed in the next section. In conclusion, the availableevidence suggests, very lucidly, that the nDNA is likely to progress in aschematic that maintains nuclear-mitochondrial gene combinations after thisendosymbiotic event between nucleated cells and ancestral mitochondria.

General Concepts of the Cellular Dynamics of the Mitochondria

It has been briefly reviewed how the original eubacteria evolved into aeukaryotic cellular organelle, via an endosymbiotic event followed bymitochondria-to-nucleus gene transfer. This has resulted in what is presentlyacknowledged as the cellular organelle called the mitochondria. Now wewill survey some of the basic cellular dynamics of the mitochondria.

Mitochondria maintain a pivotal role in the host cell, i.e., the productionof adenosine triphosphate (ATP) by a process called oxidativephosphorylation. It is called oxidative phosphorylation because ATP isphosphorylated from ADP. This process utilizes the electron transport system(ETS); also called the electron transport chain (ETC), which is a series of

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enzymatic electron donors and acceptors that ultimately phosphorylates ADPto ATP. ATP provides available energy to the host cell. The enzymecomplexes of the ETS are embedded in the inner mitochondrial membraneand required for oxidative phosphorylation.

The mitochondria perform several other functions, e.g., the beta-oxidationof fatty acids, regulation of calcium homeostasis, the biosynthesis of aminoacids and steroids, and it is involved in apoptotic cell death (also known asapoptosis or programmed cell death). Additionally, as a vibrantorganelle,the mitochondria communicate with the nDNA, which will be discussed later.

Next, we will take a brief look at some important mitochondrial processes:fusion, fission, mitophagy, and mitochondrial interactions with cytoskeletalmicrotubules.

In addition, mutations that affect these cellular dynamics will be brieflymentioned. Keep in mind that mitochondria are inherited strictly from thecytoplasm of the ovum. This means that all mitochondrial disorders that arederived from mutations of the mtDNA are passed on from the mother to allof her children; as the mitochondria reproduce asexually (non-Mendelian).However, mitochondrial disorders that derive from the nDNA can be passedon from both the mother and the father, which typically abide by Mendel’slaws of inheritance [for a good review on the history of the discovery ofDNA underlying the laws of inheritance consult reference (Grandy 2010)].Finally, the acquisition of some mutations during the lifespan can becorrelated to the aging process or exposure to chemical mutagens andelectromagnetic radiation.

Mitochondrial Fusion and Fission

Mitochondrial continuously undergo the coordinated processes of fusionand fission. Because of these fluctuating phases between fusion and fission,continuous changes in the shape of the mitochondrion morphology are seen.This is referred to as mitochondrial plasticity, which is necessary forcytoskeleton-based transport along the microtubules. All of thisserves thepurpose of organelle maintenance andrequires the correct functioning of whatare known as mitochondria-shaping proteins. As we will see, mutations insome of the genes that underlay fusion and fission cause numerous humanneurological disorders.

During the process of mitochondrial fusion, two mitochondria mergetogether to form a morphologically bigger mitochondrion. This processinvolves the collision of two mitochondria at which time a contact point onboth outermembranes is established. Mitochondrial fusion requiresoutermembrane proteins mitofusin 1 (MFN1), mitofusin 2 (MFN2), and

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intermediate dynamic-related protein optic atrophy 1 (OPA1). Mitochondrialfusion is important because it allows defective or mutated mitochondria theopportunity to exchange healthy components of the respiratory chain and/or operationally healthy mtDNA (Milone and Benarroch 2012).

During the process of mitochondrial fission, one mitochondrion splitsinto two mitochondria, which is a postulated mechanism of mitochondrialproliferation. This process requires the dynamin-related protein 1 (DRP1;also known as DLP1 and as Dnm1 in yeast) and the collaboration of bothadaptor proteins FIS1 and mitochondrial fission factor (MFF), mitochondrialenlongation factor (MIEF; also known as MiD51), and ganglioside-induceddifferentiation-associated protein 1 (GDAP1). Mitochondrial fission isimportant because it facilitates apoptosis (by the release of intermediate-space proteins into the cytosol), removes dysfunctional mitochondria, and isrequired for proper mitochondrial transport (Otera, Ishihara, and Mihara2013; Milone and Benarroch 2012).

The processes of fusion and fission are important to the survival offunctional mitochondria. However, mutations can cause dysfunction in theprocesses ofmitochondrial fusion and fission, abnormalities in the cell, andcan result in many human neurological disorders:

Mutations in MFN2 have been correlated with Charcot-Marie-Toothdisease type 2 (CMT2A)(Chung et al. 2006). This condition is ademyelinating peripheral neuropathy that is characterized by muscleweakness, loss of reflexes, loss of sensation in the distal parts of thelimbs, and muscle wasting. Additionally, mutations in the GDAP1gene are associated with the autosomal recessive and dominant Charcot-Marie-Tooth disease (Zimon et al. 2011).

Mutations in OPA1 have been correlated with autosomal dominantoptic atrophy (Alexander et al. 2000). This condition is a childhooddisorder that results in an insidious progressive loss of bilateral vision,optic disc pallor, dyschromatopsia (a disorder of color vision), andcentrocecal scortoma (a region of decreased vision in the visual field).

DLP1 mutation has been found in a lethal infant neurological disorder.This condition is characterized by microcephaly, abnormal braindevelopment, optic atrophy, truncal hypotonia, dysmorphisms, lacticacidosis, and elevated very-long chain fatty acid concentration(Waterham et al. 2007). In addition, DLP1 mutations have alsodemonstrated a critical role in the pathogenesis of Huntington disease(Song et al. 2011; Wang et al. 2008). Huntington disease is aneurodegenerative disorder that is characterized by theloss of motorcontrol, cognitive impairment, and affective disturbances.

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Mutations in FIS1 have been shown to result in nonfunctional fission,impaired interactions with DRP1, and disruptions in mitochondrialmorphology (Hill et al. 2014). In yeast, FIS1 mutations result in theacquisition of secondary mutations that bestows sensitivity to cell deathand FIS1-knockout strains fail to suppress cell growth(Cheng et al.2008).

The down regulation of MFF has been shown to inhibit the recruitmentof DRP1 and induces mitochondrial enlongation; whereas the overexpression of MFF stimulates the recruitment of DRP1 and inducesmitochondrial fission (Otera et al. 2010). Therefore, the correct geneticexpression of MFF is essential for the recruitment of DRP1 duringmitochondrial fusion andfission.

Mitophagy

Mitophagy is a systematic mechanism of specific autophagic eliminationof “bad” mitochondria, i.e., mitophagy is a form ofmitochondrial qualitycontrol. This is based on the continuous activity of mitochondrial fissionand fusion.This system has the ability to distinguish between the “good”and “bad” mitochondria in the cell. Bad mitochondria typical have defectiveenzymatic cascades and/or mutations.

In order to prevent the buildup of bad mitochondria in the cell, the badmitochondria are eliminated by selective mitophagy. This process isdependent on an ubiquitin-proteasome system involving Parkin (encodedby the PARK2 gene) and PINK1 (Milone and Benarroch 2012). Mitophagy ofthe mitochondria is typically initiated by damage due to oxidative stress orfrom mutations in mtDNA.

As with mitochondrial fusion and fission, mitophagy, plays a pivotal rolein maintaining a healthy mitochondrial population in the cell. However,mutations in PARK2 (Kitada et al. 1998) and PINK1 (Valente et al. 2004) areassociated with familial and sporadic early-onset Parkinson disease (EOPD);as well as the adult-onset Parkinsonism (Youles and Narendra 2011; Klein etal. 2005).Parkinson disease is a degenerative disorder amongst the elderlypopulation, which is characterized by resting tremor, bradykinesia, rigidity,and impairment in the ability to initiate and sustain movements.

The progression of Parkinson disease results in a distinctive shufflinggait, impairment in balance, and greatly diminished facial movements thatproduce an expression less mask-like appearance.

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Mitochondrial Interactions with Cytoskeletal Microtubules

The mitochondria are not homogeneous in shape or morphology ratherthey are constantly fluctuating in shape and size due to the ongoing processesof fusion and fission. This gives the mitochondria an intrinsic motility.

In addition, they have a nonrandom distribution and can be restrained inpreferred positions in the cell(Scheffler 2008). Mitochondria can also berepositioned in the cell where mitochondrial output is required. This ismost notable in neurons, where the locations of the mitochondria areconcentrated at the synaptic terminal. This is accomplished, in all cells, bythe interactions of the mitochondria with the cytoskeletal array ofmicrotubules.

Some of the first evidence that mitochondria interacts with cytoskeletonmicrotubules in multiple cell types came from experiments utilizing indirectimmunofluorescence techniques(Heggeness et al. 1978)and fluorescent laserdye rhodamine 123 (Johnson et al. 1980). Both of these studies demonstratedthat mitochondria were arranged along the cytoplasmic microtubules.Microtubules are an essential component to the cytoskeleton and they arerequired for cell motility, cellular division, organelle transport, and the generalmorphology of the cell. In most mammals, there are at least six different formsof alpha and beta tubulin which are encoded by specific genes (Raff 1984). Later,it would be discovered that the mitochondria also interact with intermediatefilaments (Mose-Larsen et al. 1982; Toh et al. 1980). The intermediate filamentsare also important for the structure and function of the cell.

In order for the mitochondria to move along the microtubules andintermediate filaments, molecular motors provide the means to bindmitochondria (and other organelles) to the cytoskeletal fibers. Dynein,kinesins, and myosin are molecular motors that are critical to the binding ofmitochondria, as well as vesicles, to the cytoskeleton (Anesti and Scorrano2006). In addition, the mitochondrial-shaping proteins, which werementioned earlier in this section, control the shape of the mitochondria whiletraveling along the cytoskeleton.

This mitochondrial-cytoskeletal interaction is significant as it gives thehost cell sway, to a large extent, over the whereabouts of the mitochondriain the cytoplasm. Of course, nDNA encodes for the cytoskeleton material,the motor proteins, and the outer mitochondrial membrane proteins that allcontribute to this system of locomotion with in the cell.

This relationship evokes some interesting questions as to whether or notthis is truly a symbiotic relationship between the eukaryotic host cell and themitochondria and whom or what commands the mitochondria where to go?

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At present, with the available information at hand, it would appear that thenDNA conducts these events in a manner that implies intelligence, cognition,or perchance, a degree of consciousness.

The Translocation of Proteins into the Mitochondria

Human mtDNA was one of the first mitochondrial genomes to becompletely sequenced and is composed of 16,569 nucleotide bases whichcontain an essential subset of genesthat encode for 2 mitochondrial rRNAs(called mitoribosomes), 22 mitochondrial tRNAs, and the 13 proteins of theETS components (Anderson et al. 1981; Kang and Hamasaki 2005; Asin-Cayuela and Gustafsson 2007). This accounts for 37 coding mitochondrialgenes.

As mentioned earlier, the electron transport chain is pivotal for theproduction of ATP. However, in the process of producing this energy, themitochondria also produces free radicals, via oxidative stress, that can causemutations to its very own mtDNA.

It has been speculated by many scientists that the free radical productionin the mitochondria may have been one reason why the mitochondria-to-nucleus functional gene transfer took place after the endosymbiotic event.

The gene organization of mammalian mtDNA is highly conserved (Shadeland Clayton 1997). These genes are present on both strands of DNA whichare identified as heavy (H)-strand and light (L)-strand. It is the H-strandthat encodes for 2 rRNAs, 12 tRNAs, and 14 RNAs, whereas, the L-strandencodes for 1 mRNA and 8 tRNAs. The transcription of mtDNA is directedby a single-subunit RNA polymerase and POLRMT gene- which requiresprimary transcription factors TFB2M and TFAM in order to achieve basalregulation of the system (Bestwick and Shadel 2013).

As discussed earlier, during the course of eukaryotic cellular evolution,the vast majority of the mitochondrial genome was relocated from the ancestralversion of this organelle to the nuclear genome (Timmis et al. 2004).Consequently, the mitochondria in the eukaryotic cell are heavily dependenton proteins that are derived from the nucleus and receive/import a significantportion of their proteins from the cytoplasm.

In general, the nDNA produces mRNA from the translocated mtDNA,which is now part of the nuclear genome. Most mammalian genomes containthousands of copies on mtDNA and these are organized into what arereferred to as nucleoids (Chen and Butow 2005; Kucej and Butow 2007). Thismt-mRNA leaves the nucleus and enters the cytosol where ribosomes producepreproteins. These mitochondrial preproteins interact with cytosolic

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chaperones that induce a translocation-competent conformation. This nowmust pass through the mitochondrial outer membrane, the innermitochondrial space (an aqueous compartment), and some will pass into theinner mitochondrial membrane; in order to enter the mitochondrial matrix(a second aqueous compartment) for utilization by the mitochondrialorganelle.

The Outer Mitochondrial Membrane

The successful translocation of the mitochondrial precursor proteins intothe mitochondria is dependent on several assembled protein complexes, whichact as very specific and highly flexible molecular machines that, in collaborationwith molecular chaperones, actively drive protein transport (Pfanner andMeijer 1997).

The translocation-competent-cytosolic chaperone conformationis targetedby the preprotein translocase of the outer mitochondrial membrane (TOM),which is a multi-subunit protein. The TOM receptor complexes dynamicallyinteract with a general import pore and smaller proteins that modulate thedynamics of the translocase (Pfanner et al. 1996). Most mitochondrial proteinspass into the mitochondria through the outermembrane translocator calledthe TOM40 complex.Once these proteins have entered the intermembranespace various TOM subcomplexes promote the transfer and sorting of themitochondrial preproteins.

Protein-sorting pathways branch out into four different mitochondrialsubcompartments utilizing distinct sorting-specific import machineries (Endoet al. 2011):

1. TIM23 complex in the inner membrane mediates the sorting ofprecursor proteins that have an N-terminal cleavable presequence tothe inner membrane and matrix.

2. TIM22 complex, also in the inner membrane, facilitates insertion; incollaboration with TIM9-10-12, of polytopic membraneproteinswithout a presequence directly into the inner membrane.

3. The TOB/SAM complex (topogenesis of beta-barrel proteins/sortingand assembly machinery) in the outer membrane; in collaboration withTIM8-13 and TIM9-10, mediates the assembly and insertion of beta-barrel membrane proteins in the outer membrane. The significance ofbeta-barrel proteins will be discussed in the next section.

4. TIM40/Mia40 and Erv1 are collectively referred to as themitochondrial intermembrane space assembly (MIA). This complex

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constitutes a disulfide relay system in the inter membrane space whichserves to facilitate the import and oxidative folding of mostly smallsoluble proteins in the inter membrane space.

Thus, after the TOM complex brings precursor proteins past the outermembrane they are then designated to one of four locations; theoutermembrane, the intermembrane space, the inner membrane, ormitochondrial matrix.

The Significance of Beta-barrel Proteins

Beta-barrel proteins are found in the outer membrane of Gram-negativebacteria, mitochondria, and chloroplasts, which demonstrates an evolutionaryconservation and divergence between these respective cellular organellesand their distant ancestors (Walither and Rapaport 2009). In addition, thebeta-barrel proteins in Gram-negative bacteria, mitochondria, andchloroplasts clearly demonstrate overlapping and distinctive features (Misra2012). The function of beta-barrel proteins include operating as pore-formingproteins that allow the flux of metabolites across the membrane by passivediffusion, proceed as active transporters of siderophores (soluble iron-bindingagents),perform enzymatic functions, support the integrity of the outermembrane, and mediate protein translocation that transports proteins acrossthe membrane or inserts them into the membrane. The presence of beta-barrel proteins is significant because it reinforces the phylogenetic relationshipbetween bacterial and modern day eukaryotic cellular organelles.

The Inner Mitochondrial Membrane

The inner mitochondrial membrane is typically convoluted andconsequently forms series of infoldings that are called cristae.

These infoldings project into the mitochondrial matrix. After themitochondrial preproteins transverse the outer membrane of themitochondria, they undergo subsequent intramitochondrial sorting, and someof these are then translocated through the inner mitochondrial membrane.The transportation across the inner mitochondrial membrane is mediated bytranslocase of the inner mitochondrial membrane (TIM). The TIM complexis a collection of protein translocators in the mitochondrial inner membrane.Various TIM subcomplex proteins are exposed to the inter membrane space.These proteins are part of the translocation channel that allows the passageof the pre proteins into the matrix of the mitochondria.Most of the matrixproteins are synthesized as precursor proteins with an N-terminalpresequence. These pre sequences usually contain a mitochondrial-targetingsignal which is cleaved off by the processing peptidase in the matrix afterthey are imported (Endo and Kohda 2002).

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Another large protein complex, called the mitochondrial inner membraneorganizing system (MINOS) interacts with both TOM and SAMindependently, providing a critical role in the maintenance of inner membranearchitecture (Bohnert et al. 2012).

In the past decade and a half a significant amount of information on thestructural aspects of the mitochondrial import systems has been attained,specifically using high-resolution structures of many components of the thissystem (Endo et al. 2011).

This has contributed enormously to the understanding of the mechanismsof protein importing and sorting in the mitochondria.

At the end of the previous section, the idea was introduced that therelationship between the mitochondria and the nucleated cell may not beentirely symbiotic. This dynamic relationship is even more curious due tothe fact that the replication, transcription, translation, and repair of mtDNAis controlled by proteins that are encoded by nDNA (Shutt and Shadel 2010;Scarpulla 2008). But how does this bi-genomic relationship work?

nDNA and mtDNA Interactions: Gene-based Communications

At this juncture a brief survey of the emergence of mitochondria organellefrom an endosymbiotic event between ancient eubacteria and nucleatedancestral cells, organelle-to-nucleus gene transfer (functional gene transfer),the cellular dynamics of the mitochondria, and how the translocation ofproteins that- originate in the nDNA, then are pre-assembled in the cytosol,and final find their destination into the mitochondria, have all been completed.However, in order for this symbiotic arrangement to function properly asystem of communication must exist to orchestrate and control the correctexpression and timing of the nuclear- and mitochondrial-encoded genes.This presses the question as to how do the nucleus and the mitochondriacommunicate in order to ensure the functional collaboration that makes thissystem successful?

A study involving a type of yeast, Saccharomyces cervisiae, demonstratedan example of this DNA-based communication between loci on themitochondrial genome and nuclear loci (mito-nDNA). In this study, an inter-organelle DNA-based communication system was identified utilizing genomeconformation capture, which is a proximity-based ligation method that arrestsinter- and intra- chromosomal interactions (Rodley et al. 2012). This methodwas used to map a global network of mito-nDNA interactions. The resultsdemonstrated that interactions between mitochondrial genes COX1 andQ0182, and nuclear encoded loci MSY1 and RSM7, respectively are dependent

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on reverse-transcriptase (an enzyme that creates copies of DNA from anRNA template) which mediates inter-organelle DNA interactions.

This was supported by observed decreases in the mito-nDNA interactionfrequency seen between COX1-MSY1 and Q0182-RSM7 from the knockoutof mitochondrial reverse-transcriptase activity. The Rodley et al. study alsosuggests, that this DNA mediated communication system, which involvesthe reverse transcription of mitochondrial RNA, responds to metabolic statesin the cell that in turn regulate nuclear transcription levels.

DNA polymerase-gamma, which is encoded by nuclear gene polymerase-gamma (POLG- also called pol gamma), is involved in the replication ofmtDNA. The core replication apparatus consist of POLG, mtDNA helicase,Twinkle, and mitochondrial single-stranded binding protein (Lee et al. 2009).POLG comprises a catalytic core in the replication apparatus and it has beenproposed to be the lone polymerase accountable for mtDNA replication andrepair (Kaguni 2004).

Moreover, POLG has three main roles in mtDNA maintenance andmutagenesis; and as a consequence has a profound impact in health anddisease (Copeland 2010):

1. Spontaneous mutagenesis- POLG is the origin of most of thespontaneous mutations.

2. Nucleotide reverse transcriptase inhibitor induced mitochondrialtoxicity- POLG is sensitive to nucleoside analogs which are used totreat HIV patients. Consequently, patients taking this class of drugsmay develop mitochondrial-induced toxicity.

3. Mutations in the gene for POLG- over 150 gene mutations involvingthe POLG gene have been identified and associated with mitochondrialdiseases.

Nuclear gene POLG demonstrates control over the mitochondrial genomeby its pivotal role in replication and represents an extremely importantnDNA-mtDNA interaction. Associated mutations to the POLG gene accountfor several neurological disorders. For example, one study involving 30patients using single-strand conformational polymorphism analysisdemonstrated that 13% of patients with progressive external ophthalmoplegia(PEO) are associated with POLG mutations (Filosto et al. 2003). In addition,POLG recessive mutations have been linked to Alper-like encephalopathy(Alpers syndrome) which is characterized by early onset psychomotorregression, intractable seizures, liver failure, and sensory or cerebellar ataxia(Milone 2011).

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Nuclear gene-encoded protein, thymidine kinase 2 (TK2), catalyzes thephosphorylation of thymidine (dT) and deoxycytidine (dC) in themitochondrial matrix. Both dT and dC are deoxyribonucleosides, i.e., theyare components of the mtDNA. This give TK2 the ability to affect the relativeamounts of mtDNA produced by supplying deoxyribonucleotides and TK2-deficient mice have demonstrated a progressive loss of mtDNA (Zhou et al.2008). In humans, deficiency in TK2 due to mutations is associated withmtDNA depletion syndrome and mitochondrial myopathy (Sun and Wang2014; Behin 2012).

The nuclear gene TSFM encodes for mitochondrial translation elongationfactor Ts (EFTs). EFTs has been shown to be involved in catalyzing theelongation step of mitochondrial protein translation. Mutations in the TSFMgene have been associated with Leigh disease, ataxia, neuropathy, and opticatrophy (Ahola et al. 2014).

Several examples of nDNA-mtDNA gene interactions have been discussed.As it has been observed, optimal epistatic interactions between these bi-genomic relationships is required for transcription and translation of mtDNAand for the proper functioning of the oxidative phosphorylation system.Furthermore, mutations in some of these genes, as seen in POLG, can havecatastrophic results on human morbidity and mortality.

Mitochondria and Neurological Disorders

Mitochondrial dynamics regulate mitochondrial morphology, mitophagy,apoptosis, oxidative phosphorylation, Ca2+ signaling, mtDNA stability,mitochondrial quality, ROS generation, and cellular stress response (Babbarand Sheikh 2013). Hence, because mitochondria are implicitly involved in avariety of cellular functions, mitochondrial dysfunctions and ETS breakdownshave been linked to various metabolic and neurodegenerative disorders. Inthis section four disorders and some of the genetic underpinnings will bebriefly discussed.

MELAS: Mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes

Mutations can occur in the mtDNA or in the nDNA. Both can result indiseases know as mitochondrial encephalomyopathies which are brain-musclesyndromes that often have unpredictable clinical features.

Mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes(MELAS) is a mitochondrial disease that can affect multiple organ systems.This condition is characterized by progressive encephalopathy (a condition

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that affects the function and/or structure of the brain) and stroke-likeepisodes (Ciafaloni et al. 1992).

The most common mutation seen in MELAS is the mtDNA A-to-Gtransition located at nucleotide 3243. One 3-year follow-up study involvingm.3243 A>G mutation carriers demonstrated a profound increase in the globaldisease severity scale; including reductions in audiometry,electroencephalography, and electrocardiology (Majamaa-Voltti et al. 2006).A more recent study, involving 35 families with m.3243 A>G mutations anda 10.6 year follow-up, demonstrated progressive worsening in theneuropsychological global scores; as well as, measureable declines in clinicaland imaging outcomes (Kaufmann et al. 2011).

In individuals with MELAS there are varying cerebral metabolicabnormalities involving elevated lactate levels. This can contribute to theencephalopathy by causing cerebral edema which is a poor prognosticindicator for MELAS. However, it has been difficult to follow this objectivelywith prognostic biomarkers. A recent study, utilizing proton magneticresonance spectroscopic imaging (1H MRSI), demonstrated some promise asa surrogate biomarker to predict the risk of an asymptomatic or prodromalm.3243 A>G carriers of developing the MELAS phenotype (Weiduschat etal. 2014). Thus, this technique would give researchers another method toelucidate the disease progression in this particular genotype.

In addition to neurocognitive impairment, MELAS can manifestgastrointestinal involvement. Symptoms can include dysphagia, chronicdiarrhea, anorexia, abdomen pain, paralytic (commonly intractable) ileus,and delayed gastric emptying (Hom and Lavine 2004). A more recent casestudy reported a MELAS patient with chronic gastrointestinal dysmotility,and acute refractory intestinal pseudo-obstruction, which was responsive toprucalopride (Primiano et al. 2014). Hence, MELAS does not affect merelythe nervous system but other systems as well.

Parkinson disease

Parkinson disease (PD) is a progressive neurodegenerative diseasecharacterized by the decreased production of dopamine in the brain. This iscaused by a selective loss of dopaminergic neurons in the nigrostriatalpathway. Mitochondrial dysfunction and nuclear genes that are associatedwith the regulation of mitochondrial function have been implicated in PD(Gaweda-Walerych and Zekanowski 2015).

For example, the roles of some of these nuclear genes have been discussedalready in this chapter, e.g., POLG, TFAM, and transcription factor A. In

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addition, PARK2 and PINK1 mutations associated with PD were mentionedearlier in this chapter in the section on mitophagy.

Between the years 1989 and 1990, some of the first evidence emergedthat suggested that mitochondrial pathogenesis played a part inneurodegenerative processes. It became clear that complex I deficiency (orreductions) was detected in the substantia nigra and in platelet mitochondriain patients diagnosed with PD (Schapira et al. 1990; Parker et al. 1989).

Complex I (NADH: ubiquinone oxidoreductase), which consists of 7subunits (ND1, 2, 3, 4, 4L, 5, and 6) encoded by the mitochondrial genome,is of significance as it maintains a central role and is the first enzyme in themitochondrial respiratory chain (Smeitink et al 1998).

A more rigorous understanding of the bi-genomic relationship betweenmtDNA and nDNA may yield insight to therapeutic pathways for thetreatment of PD. One example is the use of a flavonoid called silibinin,which is found in milk thistle seeds.

In a recent study, using a mouse model, silibinin demonstrated protectionfrom the cell death of neurons and mitochondrial membrane disruption, via,stabilization of the mitochondrial membrane potential (Lee et al. 2015).

Alzheimer disease

Alzheimer disease (AD) is a neurodegenerative disorder that slowlyerodes some of thefacets of human consciousness. During the pathologicalcourse of AD beta-amyloid plaques and neural fibrillary tangles (NFTs) richin hyperphosphorylated tau protein form in the brain. This causes damageto neurons and results in the gross loss of brain volume. As a consequenceof AD, the afflicted individual develops decreases in cognitive/executivefunction, memory impairment/loss, and the inability to inhibit inappropriatebehaviors.

It has been proposed that mtDNA may not play a primary role in ADpathology. More recent research indicates that mtDNA is primarilyresponsible for aging phenotypes (Hroudova et al. 2014). However, severaldeficiencies in various mitochondrial ETC complexes have been discoveredin AD.

Early PET studies in AD patients have demonstrated reductions in brainglucose metabolism and blood flow in primary cortical regions(Chandrasekaran et al. 1996). This has been associated with down regulationof oxidative phosphorylation in the brain. Metabolism abnormalities implyinvolvement of the mitochondrial ETC dysfunction. Evidence of

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mitochondrial dysfunction and increased oxidative stress found in AD willbe briefly discussed.

Deficiencies in cytochrome c oxidase (COX) have been discovered inneuronal mitochondria in 9 postmortem AD patients (Parker et al. 1994).This may suggest that COX may represent a pathological center in the defectiveETC in the AD brain. In another study, COX-deficient hippocampal pyramidalneurons had an anatomically distinct distribution from the amyloid plaguesand neurons that contained NFTs were COX-positive (Cottrell et al. 2002).This suggests that mitochondrial defects are not directly involved in beta-amyloid and hyperphosphorylated tau accumulation, but rather, contributeto nervous system dysfuzction and neurodegeneration by mechanisms otherthat apoptosis.

Although COX-deficiencies have been found in some AD models, someother conflicting results have emerged. For example, COX-deficient (COX10knock out) mice exhibited fewer amyloid plaques in their brain and lowerlevels of oxidative damage (Fukui et al. 2007). These results suggest thatCOX-deficient states do not always increase oxidative damage or increasethe accumulation of beta-amyloid.

In the AD brain, it was found using northern blot, that the levels of sub-complex ND4 gene expression was decreased in the temporal cortex whencompared to non-AD brains (Fukuyama et al. 1996). This early findingsuggests that ND4-deficiency may promote a form of selective neuronalvulnerability.

Immunohistochemistry and quantitative autoradiographic techniques havedemonstrated that both subunits COX1 and COX4 levels were absent in ADtangle-bearing hippocampal neurons (Nayg et al. 1999). Furthermore, COX4levels were correlated with the amount of hyperphosphorylated tauaccumulation of the hippocampus. Another study demonstrated thatmitochondrial and nuclear genes encoding complex I subunits, e.g., ND4,showed decreased expression in the hippocampus and inferior parietal lobe(Aksenor et al. 1999).

In a study using immunofluorescence techniques, 11 mitochondrial-encoded genes where differentially expressed in AD patients (Manczak etal. 2004). The results demonstrated that down-regulation of complex I ofthe oxidative phosphorylation in early and definite AD brain samples. Inaddition, decreases were the highest in complex IV, which fortifies thatproposal that complex IV is critical for oxidative phosphorylation.Mitochondrial gene expression did vary in these AD patients, which suggeststhat mtDNA deficits may be in part accountable for the amounts ofheterogeneity of the AD phenotypes.

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Studies involving cytoplastic hybrid (cybrid) models- in where mtDNAfrom AD patients was transferred into replicating human neural cells thatwere initially barren of endogenous mtDNA; revealed the following findings(Onyango et al. 2006):

1. Decreased cytochrome oxidase activity

2. Increased oxidative stress

3. Increased beta-amyloid production

4. Activation of detrimental intracellular signaling and caspases

5. Accelerated mtDNA proliferation

6. Abnormal mitochondrial morphology and transport

These findings seem to suggest that the contribution of altered mtDNAinvolved in AD progression and pathogenesis is likely heterogeneous.

Two nuclear-encoded mitochondrial genes, PGC-1alpha and TFAM, areimportant to mitochondrial biogenesis and function. A study using epistaticinteraction analysis and meta-analysis, demonstrated the mtDNAhaplogroups and subhaplogroupsboth contribute to the putative rolesinvolved in the partial uncoupling of oxidative phosphorylation and aresignificantly associated with a decreased risk in late-onset AD (LOAD)(Maruszak et al. 2011). It was discovered that haplogroup K exerted aneutralizing effect on APOE4+ status. In addition, Maruszak et al. furtherdemonstrated that synergistic interactions involving both subhaplogroupH5 and TFAM rs1937 with APOE+ status were also found to influence LOADrisk. Therefore, no interactions suggesting a dual mt-nDNA variation effecton LOAD occurrence was found.

Autism Spectrum Disorders

A reoccurring theme in this chapter is that impaired mitochondrial functioncan have a direct impact on cellular processes that are highly dependent onenergy productions. One such process is seen during neurodevelopment.Consequently, it has been proposed that impairment due to genetic perturbationsmay also contribute to disorders like autism spectrum disorders (ASD).

An observational study involving 10 children selected from theChildhood Autism Risk from Genes and Environment Study demonstratedthat children with ASD where more likely to encompass mitochondrialdysfunction, mtDNA over-replication, and mtDNA deletions (Giulivi et al.2010). More recently, single nucleotide polymorphisms rs2292813 andrs2056202, in the SLC25a12 gene have demonstrated an association with ASD

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(Aoki and Cortese 2015). This is significant as SLC25A12 is a nuclear-encodedmitochondrial gene that encodes the mitochondrial aspartate/glutamatecarrier across the mitochondrial inner membrane.

Nuclear-encoded mitochondrial gene, branched-chain ketoaciddehydrogenase (BCKDK) encodes for the branched-chain alpha-ketoaciddehydrogenase complex (BCKD). BCKD is found in the mitochondrion andis an important regulator of essential amino acids valine, isoleucine, andhomophobic amino acid leucine catabolic pathways. Mutations in this genehave been associated with a form of ASD associated with epilepsy, whichwas found to respond to dietary supplementation treatment with branched-chain amino acids (BCAAs) (Novarino et al. 2012). Support for the Novarinoet al. findings were established in a more recent study, which demonstratedtwo novel exonic BCKDK mutations that where identified in two unrelatedchildren (Garcia-Cazorla et al. 2014). These two children both demonstrateda reduction of BCAAs; in addition to developmental delay, microcephaly,and neurobehavioral abnormalities.

It was validated in this section that mutations in nDNA and mtDNA canresult in neurological disorders. In many ways researchers are merelyscratching the surface. However, many new breakthroughs continue toemerge, especially in the field of biomarkers [for a great updated review onbiomarkers please consult reference (Grandy 2015)].

Summary

The mitochondria produces ATP via oxidative phosphorylation utilizingthe ETS complexes embedded in the inner mitochondrial membrane.Additionally, the mitochondria perform various, but pivotal, functions inthe eukaryotic cell. The mitochondria are plastic and dynamic organellesthat utilize three important process, called fusion, fission, and mitophagy- inorder to maintain a functionally healthy population. Fusion and fission allowthe exchange of healthy mitochondrial proteins and the production of stablemitochondria. Selective mitophagy contributes to mitochondria qualitycontrol by autophagic elimination of unhealthy mitochondria.

Long ago an endosymbiotic event took place between ancient eubacteriaand nucleated ancestral cells. During the assimilation of this symbioticrelationship, a genetic process called mitochondrion-to-nucleus functionalgene transfer took place. In this process of organelle-to-nucleus gene transferthe apparent autonomy also shifted from mitochondria to nucleus, as underthe current paradigm the mitochondrial organelle is dependent on the nucleusfor the majority of its constituent components.

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Due to the loss of genetic content in the mitochondrial genome duringthe mitochondrion-to-nucleus gene transfer, most modern mitochondriacontain only an essential subset of genes called nucleoids (in prokaryotesthese are collectively referred to as a genophore). Consequently,mitochondria rely on the nDNA to produce mitochondrial proteins. Afterthe mt-mRNAis transcribed it exits the nucleus and is translated in the cytosolas a preprotein, which is then translocated into the mitochondria.

When these preproteins arrive at the mitochondria they may end up inthe outer mitochondrial membrane, the inter membrane space, the innermitochondrial membrane, or in the mitochondrial matrix. There are severalprotein complexes, e.g., the TOB/SAM, TOM, and TIM complexes- thatfacilitate the mitochondrial protein’s destination.

In order for the endosymbiotic event to have been successful, functionalgene transfer to have taken place, the mt-mRNA to be adequately producedin the nucleus, and the mitochondrial preproteins delivered to ensure thatthe cellular dynamics of the mitochondria function properly- a functionalcommunication system must be in place for this bi-genomic collaboration towork. Currently, this system is poorly understood.

However, some breakthroughs in research have shed light on threepathways in this communication system. First, this DNA-basedcommunication system, which appears to be dependent on reverse-transcriptase, has been identified utilizing a proximity-based ligation methodthat arrest chromosomal interactions between nDNA and mtDNA. Second,it was seen that POLG is produced in the nucleus and is the catalytic coreapparatus that controls mtDNA replication and repair. Third, TK2, a nuclear-encoded protein, has a profound effect on the relative amounts of mtDNAproduced.

Cells that are heavily dependent on ATP production, e.g., neurons andmuscle cells, are particularly sensitive to abnormalities in mitochondrialfunction. Thus, mutations that interfere with mitochondrial functions canhave profound effects on the viability of eukaryotic cells and consequentlyresult in human disease. Mutations involving mitochondria in MELAS, PD,AD, and ASD where briefly discussed at the end of this chapter; and severalother examples were discussed throughout the entire chapter. These fourneurological diseases demonstrate how very small aberrations in the nDNAor mtDNA can affect the functions of the human brain, including cognitionand consciousness.

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REFERENCES

Abecasis, G. R., et al. (2012). An integrated map of genetic variation from 1,092 humangenomes.Nature 491 (7422): 56-65.Ahola, Sofia et al. (2014). Mitochondrial EFTs defects in juvenile-onset Leigh disease,ataxia, neuropathy, and optic atrophy. Neurology 83 (8): 743-751.Aksenov, M. Y., et al. (1999). The expression of several mitochondrial and nuclear genesencoding the subunits of electron transport chain enzyme complexes, cytochrome coxidase, and NADH dehydrogenase, in different brain regions in Alzheimer’s disease.Neurochem Res 24 (6): 767-774.Alexander, C., Votruba, M., Pesch, U.E., et al. (2000). OPA1, encoding a dynamin-relatedGTPase, is mutated in autosomal dominant optic atrophy linked to chromosome 3q28.Nat Genet 26:211-215.Anderson, S., et al. (1981). Sequence and organization of the human mitochondrialgenome.Nature 290: 457-465.Anesti, Vasiliki, and Luca Scorrano (2006). The relationship between mitochondrial shapeand function and the cytoskeleton.Biochimica et BiophysicaActa1757: 692-699.Aoki, Y., and Cortese, S. (2015). Mitochondrial Aspartate/Glutamate Carrier SLC25A12and Autism Spectrum Disorder: a Meta-Analysis. MolNeurobiol[Epub ahead of print].Asin-Cayuela, J. and Gustafsson, C. M. (2007). Mitochondrial transcription and itsregulation in mammalian cells.Trends Biochem. Sci. 32: 111-117.Babbar, Mansi, and M. Saeed Sheikh (2013). Metabolic Stress and Disorders Related toAlterations in Mitochondrial Fission or Fusion. Mol Cell Pharmacol.5 (3): 109-133.Behin A. et al. (2012). Adult cases of mitochondrial DNA depletion due to TK2 defect.Neurology 78 (9): 644-648.Bestwick, Megan, L., and Gerald, S. Shadel. (2013). Accessorizing the human mitochondrialtranscription machinery. Trends Biochem Sci. 38 (6): 283-291.Brandvain, Yaniv et al. (2009). The Functional Transfer of Genes from the Mitochondriato the Nucleus: The Effect of Selection, Mutation, Population Size and Rate of Self-Fertilization. Genetics 180: 1129-1139.Chandrasekaran, K. et al. (1996). Evidence for physiological down-regulation of brainoxidative phosphorylation in Alzheimer’s disease.ExpNeurol142 (1): 80-88.Chen, X. J. and Butow, R. A. (2005). The organization and inheritance of the mitochondrialgenome.Nat. Rev. Genet. 6: 815-825.Cheng, W.C., et al. (2008). Fis1 deficiency selects for compensatory mutations responsiblefor cell death and growth control defects. Cell Death Differ 15 (12): 1838-1846.Chung, K.W., Kim, S.B., Park, K.D., et al. (2006). Early onset severe and late-onset mildCharcot-Marie-Tooth disease with mitofusion 2 (MFN2) mutations. Brain 129:2103-2118.Ciafaloni, E. et al. (1992). MELAS: clinical features, biochemistry, and molecular genetics.Ann Neurol 31: 391-398.Copeland, William, C. (2010). The Mitochondrial DNA Polymerase in Health and Disease.Subcell Biochem, 50: 211-222.Cottrell, D. A. et al. (2002). The role of cytochrome c oxidase deficient hippocampalneurons in Alzheimer’s disease. Neuropathol Appl Neurobiol, 28 (5): 390-396.Diroma, Marie Angela (2014). Extraction and annotation of human mitochondrial genomesfrom 1000 Genomes Whole Exome Sequencing data. BMC Genomics 14 (supplement 3): 52.

Mithochondria...........................Neurological Diseases John K. Grandy

Page 22: Mitochondria: Eubacteria Descendant, Cellular Dynamics ...publicationslist.org/data/john.grandy/ref-46... · Mitochondria: Eubacteria Descendant, Cellular Dynamics, Interactions with

195New Dimensions in Microbiology ISBN 978-93-85160-84-4

Endo, Toshiya and D. Kohda (2002). Functions of outer membrane receptors inmitochondrial protein import. Biochim. Biophys. Acta 1592: 3–14.Endo, Toshiya, Koji Yamano, and Shin Kawano (2011). Structural insight into themitochondrial protein import system. Biochimic et Biophysica Acta 1808: 955-970.Fukuda, M. et al. (1985). Mitochondrial DNA-like sequences in the human nucleargenome.Characterization and implications in the evolution of mitochondrial DNA. J.Mol. Biol. 186 (2): 257-266.Fukuyama, R. et al. (1996). Gene expression of ND4, a subunit of complex I of oxidativephosphorylation in mitochondria, is decreased in temporal cortex of brains of Alzheimer’sdisease patients. Brain Research 713 (1-2): 290-293.Garcia-Cazorla, A. et al. (2014). Two novel mutations in the BCKDK (branched-chainketo-acid dehydrogenase kinase) gene are responsible for a neurobehavioral deficit intwo pediatric unrelated patients. Human Mutations 35 (4): 470-477.Gaweda-Walerych, Katarzyna, and Cezary Zekanowski (2013). The Impact of MtochondrialDNA and Nuclear Genes Related to Mitochondrial Functioning on the Risk of Parkinson’sDisease. Current Genomics 14 (8): 543-559.Giulivi, Cecilia et al. (2010). Mitochondrial Dysfunction in Autism. JAMA 304 (21): 2389Grandy, John (2015). The 2014 European Summit on Biomarkers: Biomarkers inDiagnostics. Journal of Biological and Chemical Research 32 (1): 198-210.Grandy, John (2010). DNA and Genetic Engineering. In: 21st Century Anthropology. SagePublications, Inc. Thousand Oaks, California. Volume 1: pp 76-90.Grandy, John (2006). The Human Genome Project. In: The Encyclopedia of Anthropology.Vol. 3 pp 1223-1226. Sage Publications, Inc. Thousand Oaks, California.Gray, Michael W. (1999). Evolution of organellar genomes. Current Opinion in Genetics 9:678-687.Gray, Michael W., Gertraud Burger, and B. Franz Lang (1999). Mitochondrial evolution.Science 283: 1476-1481.Gray, Michael W., Gertraud Burger, and B. Franz Lang (2001). The origin and earlyevolution of mitochondria. Genome Biology 2 (6): 1018.1-1018.5.Heggeness, Michael, Melvin Simon, and S. J. Singer. (1978). Association of mitochondriawith microtubules in cultured cells. PNAS 75 (8): 3863-3866.Hill, Blake, et al. (2014). Fis1 and Drp1 cooperate in mitochondrial homeostasis. FASEBJournal, 28 (1): Supplement 756.8.Hirokazu, Fukui, et al. (2007). Cytochrome c oxidase deficiency in neurons decreases bothoxidative stress and amyloid formation in a mouse model of Alzheimer’s disease. PNAS104 (35): 14163-14168.Hom, X.B., and Lavine J.E. (2004). Gastrointestinal complications of mitochondrial disease.Mitochondrion 4: 601-607.Hroudova, Jana, et al. (2014). Mitochondrial Dysfunction in Neurodegenerative Diseases:Relevance to Alzheimer’s Disease. BioMed Research International Article ID: 175062Johnson, L. V., Walsh, M. L., and Chen L. B. (1980). Localization of mitochondria in livingcells with rhodamine 123. PNAS 77 (2): 990-994.Kaguni, L.S. (2004). DNA polymerase gamma, the mitochondrial replicase.Annu RevBiochem73: 293-320.

Mithochondria...........................Neurological Diseases John K. Grandy

Page 23: Mitochondria: Eubacteria Descendant, Cellular Dynamics ...publicationslist.org/data/john.grandy/ref-46... · Mitochondria: Eubacteria Descendant, Cellular Dynamics, Interactions with

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Kang, D. and Hamasaki, N. (2005). Mitochondrial transcription factor A in the maintenanceof mitochondrial DNA: overview of its multiple roles. Ann N.Y. Acad. Sci. 1042: 101-108.Kaufmann, P. et al. (2011). Natural history of MELAS associated with mitochondrial DNAm.3243A>G genotype. Neurology 77 (22): 1965-1971.Kitada, T., Asakawa, S., Hattori, N., et al. (1998). Mutations in the parkin gene causeautosomal recessive juvenile parkinsonism. Nature, 392: 605-608.Klein, C., Djarmti, A., Hedrich, K., et al. (2005). PINK1, Parkin, and DJ-1 mutations inItalian patients with early-onset parkinsonism. Eur J Hum Genet 13: 1086-1093.Kucej, M. and Butow, R. A. (2007). Evolutionary tinkering with mitochondrial nucleoids.Trends in Cell Biology 17: 586-592.Lang, B.F., Gray, M.W., and Burger, G. (1999). Mitochondrial genome evolution and theorigin of eukaryotes. Annual Review of Genetics 33: 351-397.Lee, Y.S., et al. (2015). Silibinin prevents dopaminergic neuronal loss in a mouse model ofParkinson’s disease via mitochondrial stabilization. J Neurosci Res [Epub ahead of print].Lee, Y.S., Kennedy, W.D., and Yin, Y.W. (2009). Structural insight into processive humanmitochondrial DNA synthesis and disease-related polymerase mutations. Cell 139: 312-324.Lopez, J. V., et al. (1994). Numt, a recent transfer and tandem amplification ofmitochondrial DNA to the nuclear genome of the domestic cat. J. Mol. Evol. 39 (2): 174-190.Majamaa-Voltti, K.A., et al. (2006). A 3-year clinical follow-up of adult patients withm.3243A>G in mitochondrial DNA. Neurology 66: 1470-1475.Manczak, M., Park, B. S., and P. H. Reddy. (2004). Differential expression of oxidativephosphorylation genes in patients with Alzheimer’s disease: implications for earlymitochondrial dysfunction and oxidative damage. Neuromolecular Medicine 5 (2): 147-162.Maruszak, A. et al. (2011). The impact of mitochondrial and nuclear DNA variants on late-onset Alzheimer’s disease risk.Journal of Alzheimer’s Disease 27 (1): 197-210.Milone, Margherita, and Eduardo E. Benarroch (2012). Mitochondrial dynamics: Generalconcepts and clinical implications. Neurology 78 (20): 1612-1619.Milone, Margherita, Eduardo E. Benarroch, and Lee-Jun Wong (2011). POLG-relateddisorders: Defects of the nuclear and mitochondrial genome interaction.Neurology 77 (20):1847-1852.Misra, Rajeev (2012). Assembly of the beta-barrel outer membrane proteins in Gram-negative bacteria, mitochondria, and chloroplasts. ISNR Molecular Biology 2012: 708203.Mose-Larsen, P. et al. (1982). Putative association of mitochondria with a subpopulationof intermediate-sized filaments in cultured human skin fibroblast. Cell, 31: 681.Mourier, Tobias et al. (2001). The Human Genome Project Reveals a Continuous Transferof Large Mitochondrial Fragments to the Nucleus. Mol. Biol. Evol. 18 (9): 1833-1837.Mundy, Nicholas, Alcides Pissinatti, and David S. Woodruff (2000). Multiple NuclearInsertions of Mitochondrial Cytochrome b Sequences in Callitrichine Primates. Mol. Biol.& Evol.17 (7): 1075-80.Nagy, Z. et al. (1999). Mitochondrial enzyme expression in the hippocampus in relationto Alzheimer-type pathology. Acta Neuropathol 97 (4): 346-354.Novarino, Gaia et al. (2012). Mutations in BCKD-kinase Lead to a Potentially TreatableForm of Autism with Epilepsy. Science 338: 394-397.

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Onyango, I. et al. (2006). Mitochondrial genomic contribution to mitochondrialdysfunction in Alzheimer’s disease. Journal of Alzheimer’s Disease 9 (2): 183-193.Otera, Hidenori, Naotada Ishihara, and Katsuyoshi Mihare (2013). New insights into thefunction and regulation of mitochondrial fission. Biochimica et Biophysica Acta 1833: 1256-1268.Otera, Hidenori, et al. (2010). Mff is an essential factor for mitochondrial recruitment ofDrp1 during mitochondrial fission in mammalian cells. Journal of Cell Biology 191 (6): 1141-1158.Parker, W.D. Jr. et al. (1994). Electron transport chain defects in Alzheimer’s diseasebrain. Neurology 44 (6): 1090-1096.Parker, W.D. Jr. et al. (1989). Abnormalities of the electron transport chain in idiopathicParkinson’s disease. Annals of Neurology 26 (6): 719-723.Pfanner, Nickolaus, et al. (1996). Uniform nomenclature for the protein transportmachinery of the mitochondrial membranes. Trends Biochem Sci, 21: 51-52.Pfanner, Nickolaus, and Michiel Meijer (1997). Mitochondrial biogenesis: The Tom andTim machine. Current Biology 7 (2): R100-R103.Primiano, Guido, et al. (2014). Acute refractory intestinal pseudo-obstruction in MELAS:efficacy of Prucalopride. Neurology, 82 (21): 1932-1934.Raff, E. C. (1984). Genetics of microtubule systems. J. Cell Biol. 99: 1.Rodley, C.D.M., Grand, R.S., Lutz, R.G., et al. (2012). Mitochondrial-Nuclear DNAInteractions Contribute to the Regulation of Nuclear Transcript Levels as Part of theInter-Organelle Communication System. PLoS ONE 7 (1): e30943.Scarpulla, Richard C. (2008). Transcriptional Paradigms in Mammalian MitochondrialBiogenesis and Function.Physiol Rev 88: 611-638.Schapira A. H., et al. (1990). Mitochondria complex I deficiency in Parkinson’s disease. JNeurochem 54 (3): 823-827.Scheffler, Immo E. (2008). Mitochondria.Second edition, John Wiley and Sons Inc.Hoboken, New Jersey.Shadel, G.S. and Clayton, D.A. (1997). Mitochondrial DNA maintenance in vertebrates.Annu Rev Biochem. 66:409–435.Shutt, Timothy E., and Gerald, S. Shadel (2010). Inventory of the Human MitochondrialGene Expression Machinery with Links to Disease. Environ Mol Mutagen 51 (5): 360-379.Smeitink, J. A. M. et al. (1998). Nuclear genes of human complex I of the mitochondrialelectron transport chain: state of the art. Human Molecular Genetics 7 (10): 1573-1579.Song, W., Chen, J., Petrilli, A., et al. (2011). Mutant huntingtin binds the mitochondrialfission GTPase dynamin-related protein-1 and increases its enzymatic activity. Nat Med17: 377-382.Sun, R. and L. Wang (2014). Thymidine kinase 2 enzyme kinetics elucidate the mechanismof thymidine-induced mitochondrial DNA depletion. Biochemistry 53 (39): 6142-6150.Timmis, J.N., Ayliffe, M., Huang, C.Y., and William Martin (2004). Endosymbiotic genetransfer: organelle genomes forge eukaryotic chromosomes. Nature Reviews Genetics 5:123-135.Toh, B. H. et al. (1980). Association of mitochondria with intermediate filaments and ofpolyribosomes with cytoplastic actin. Cell Tissue Res 211: 163.

Mithochondria...........................Neurological Diseases John K. Grandy

Page 25: Mitochondria: Eubacteria Descendant, Cellular Dynamics ...publicationslist.org/data/john.grandy/ref-46... · Mitochondria: Eubacteria Descendant, Cellular Dynamics, Interactions with

198New Dimensions in Microbiology ISBN 978-93-85160-84-4

Valente, E.M., Salvi, S., Lalongo, T., et al. (2004). PINK1 mutations are associated withsporadic early-onset parkinsonism. Annals of Neurology 56: 336-341.Walther, Dirk, M., Daron Rapaport, and Jan Tommassen (2009). Biogenesis of beta-barrel membrane proteins in bacteria and eukaryotes: evolutionary conservation anddivergence. Cell. Mol. Life Sci. 66: 2789-2804.Wang, H. et al. (2008). Effects of overexpression of huntingtin proteins on mitochondrialintegrity.Human Molecular Genetics 18 (4): 737-752.Waterham, H.R., Koster, J., Van Roermund, C.W., et al. (2007). A lethal defect ofmitochondrial and peroxisomal fission. N Engl J Med 356: 1736-1741.Weeden, N. F. (1981). Genetic and biochemical implications of the endosymbiotic originof the chloroplast. J. Mol. Evol. 17 (3): 133-9.Weiduschat, Nora, et al. (2014). Cerebral metabolic abnormalities in A3243G mitochondrialDNA mutation carriers.Neurology 82 (9): 798-805.Youle, Richard J., and Derek, P. Narendra (2011). Mechanisms of mitophagy.Nature ReviewsMolecular Cell Biology 12: 9-14.Zhou Xiaoshan et al. (2008). Progressive loss of mitochondrial DNA in thymidine kinase2-deficient mice. Human Molecular Genetics 17 (15): 2329-2335.Zimon, M., J. Baets, G. M. Fabrizi, et al. (2011). Dominant GDAP1 mutations causepredominantly mild CMT phenotypes. Neurology 77 (6): 540-548.

Corresponding author: Dr. John K. Grandy, Senior Editor (Foreign), North CountryUrgent Care ,21017 NYS Route 12f, Water town NY, 13601, USA.Email: [email protected]

Mithochondria...........................Neurological Diseases John K. Grandy