Mitochondria: Origin

Peter E Thorsness, University of Wyoming, Laramie, Wyoming, USA Theodor Hanekamp, University of Wyoming, Laramie, Wyoming, USA
Mitochondria are double-membrane cellular organelles containing their own genetic system and are found in nearly every eukaryotic cell. The endosymbiotic hypothesis postulates that a proto-mitochondrion, an ancestor of present-day bacteria, colonized a eukaryotic cell and established a symbiotic relationship to the mutual benefit of both organisms.

Secondary article
Article Contents
. Overview of Mitochondrial Structure . The Mitochondrial Genome: Size and Genome Maintenance . The Bacterial Origins of Mitochondria . Evidence of a Bacterial Origin for Mitochondria . Mitochondrial Evolution and Specialization

Overview of Mitochondrial Structure

Mitochondria can be fractionated into four components: outer membrane, intermembrane space, inner membrane and the matrix (Figure 1). These components have functional as well as structural relevance. The outer membrane serves as a semiporous barrier limiting diusion of intermembrane components away from mitochondria. The intermembrane components have important roles in electron transport and oxidative phosphorylation, and this space also serves at the destination for protons pumped from the mitochondrial matrix during the transfer of electrons to oxygen. The inner membrane serves as a tightly regulated barrier through which the ow of electrons and protons are coordinated in order to generate ATP. The inner membrane houses components of the electron transport chain and the F0 portion of the F1/F0 ATPase (also known as mitochondrial ATP synthase). This membrane contains many folds, termed cristae, which serve to increase the surface area of the membrane. The matrix houses the mitochondrial genome and the majority of gene products contained within the mitochondrial compartment. These gene products include various enzymes involved in intermediary metabolism, proteins
Outer membrane

necessary for the import of proteins into mitochondria, and proteins and nucleic acids required for the expression and propagation of the mitochondrial genome. The vast majority of the gene products contained within mitochondria are encoded by the nuclear genome and imported into mitochondria, subsequent to their synthesis in the cytoplasm. The organization of the mitochondrial compartment within the connes of the cell is highly variable depending upon cell type. Rather than static, sausage-shaped compartments, mitochondria are dynamic, plastic entities subject to frequent reorganization, depending upon the energetic or biosynthetic demands of the cell. During exponential growth, mitochondria in the yeast Saccharomyces cerevisiae are highly reticulated structures, largely positioned at the periphery of the cell. Often a single giant, reticulated mitochondrion is found under these conditions. When yeast cells reach stationary phase, mitochondria are found as many small, oval-shaped compartments, scattered throughout the cell volume. Mitochondria of more complex organisms also adapt their structure and change their position within the cell, depending on the needs of the particular cell type.

The Mitochondrial Genome: Size and Genome Maintenance

H+ H+ H2O ATP e O2

ADP + Pi Matrix

Size
In animals, the size of mitochondrial genomes range from about 14 kb to about 40 kb. Human mitochondrial DNA is a 16.5 kb circle. Fungal mitochondrial genomes exhibit a greater variance in size, ranging from the 19 kb of Schizosaccharomyces pombe to greater than the 75 kb of S. cerevisiae. Plant mitochondrial genomes are typically substantially larger and more complex than mitochondrial genomes found in all other eukaryotes. In the Cucurbitaceae family of plants, the mitochondrial genome is as large as 2400 kb, but land plants are more commonly found to have mitochondrial genomes of about 300 kb (366 kb in
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Mitochondrial DNA

Cytosol Inner membrane Intermembrane space

Figure 1 The salient features of a mitochondrion.

ENCYCLOPEDIA OF LIFE SCIENCES 2001, John Wiley & Sons, Ltd. www.els.net

Mitochondria: Origin

Arabidopsis thaliana). The mitochondrial genome of plants is sometimes present as a large circular genome known as the master circle, but the master circle is usually outnumbered by smaller circles containing a subset of the genome. This heterogeneous population of mitochondrial DNAs can intraconvert to larger forms via recombination. Protist mitochondrial genomes range in size from 6 kb in Plasmodium falciparum to 76 kb in Monosiga brevicollis. Variations in genome size are dependent upon a number of parameters. In general, however, the biggest impact on mitochondrial genome size is made by the amount of noncoding sequence in any given genome. For example, the human mitochondrial genome, 16.5 kb in size, uses 77% of this DNA to encode 37 genes (protein-encoding, tRNA and rRNA). In contrast, the mitochondrial genome of the land plant A. thaliana, 366.9 kb in size, uses 10% of this DNA to encode 57 genes. The bulk of the DNA in mitochondria of plants has no obvious function or derivation, with some of the noncoding DNA corresponding to introns, duplications and remnants of retrotransposons. Protein-coding genes in mitochondria are generally restricted to two groups: those involved in electron transport and oxidative phosphorylation, and those that encode ribosomal proteins. The human mitochondrial genome encodes 13 proteins, including subunits of NADH dehydrogenase, ATP synthase, cytochrome oxidase and cytochrome b. Plant mitochondrial genomes typically encode similar gene products, but also include a dozen or more genes that encode mitochondrial ribosomal proteins. Mitochondrial genomes from protists appear to resemble the protein-encoding characteristics of both animal and plant mitochondrial genomes, in some cases encoding ribosomal protein genes and in some cases not. Seemingly, all mitochondrial genomes encode large subunit and small subunit rRNAs. However, plants and most protists also encode a 5S rRNA gene. The mitochondrial genomes of animals typically encode sucient tRNAs to decode the mitochondrial protein-encoding genes. The human mitochondrial genome encodes 22 tRNAs. A number of plant and protist mitochondrial genomes do not encode a complete set of tRNAs and presumably, and in some cases demonstratively, import some tRNAs. It is also possible that some mitochondrial tRNA genes have not been recognized owing to the possibility that the primary transcript may be edited to create a functional tRNA. There are two noteworthy departures from the norm in terms of gene products encoded by mitochondria, and both formally belong to the protist group of eukaryotes. The malarial parasite Plasmodium falciparum has mitochondrial genome only 6 kb in size. Only three protein-encoding gene products, subunits I and II of cytochrome oxidase and cytochrome b, and the two invariant rRNA genes are found in the P. falciparum mitochondrial genome (Feagin et al., 1992). The mitochondrial genome of Reclinomonas americana, a heterotrophic agellate, seems to be most closely related to the ancestral proto-mitochondrial
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genome of any yet examined (Lang et al., 1997). In addition to encoding a homologue to every gene found in any other mitochondrial genome, R. americana also contains an additional 20 genes that have not been previously found in any other mitochondrial genome. These genes include those that encode additional mitochondrial ribosome subunits, an additional component of mitochondrial ATP synthase, a translation factor, a secretory pathway protein and four subunits of an eubacterial-type RNA polymerase.

Genome maintenance
Maintenance of the mitochondrial genome is dependent upon two general processes: replication and inheritance. Initiation of replication of each strand of the circular mitochondrial genome in vertebrates occurs at a distinct origin; hence, replication on each strand is unidirectional. The displacement loop region of vertebrate mitochondrial chromosomes has a dual role as both the origin of replication for heavy strand DNA synthesis and as the site of transcription promotion for both the heavy and light chains of mitochondrial DNA. The heavy strand replication origin coincides with, and utilizes, processed transcripts originating at the light strand transcription promoter. The origin of replication for the light strand of mammalian mitochondrial DNA is typically characterized by a stable stemloop that forms subsequent to the passage of the heavy strand DNA replication fork. This stemloop then serves as the site of synthesis of an RNA primer. As at the heavy chain origin of DNA replication, the RNA primer at the light chain origin is extended in a templatedependent manner by DNA polymerase g. Replication of mitochondrial DNA in the yeast S. cerevisiae has also been extensively studied. The mitochondrial genome of S. cerevisiae also has the distinction of being especially genetically malleable: strains containing mutant mitochondrial genomes are easy to isolate and analyse, and it is possible to introduce recombinant DNA into mitochondria to generate specic mutations, and even introduce novel genes. S. cerevisiae cells lacking mitochondrial DNA entirely can have their mitochondria transformed with small recombinant plasmids which can be faithfully replicated. Seemingly, any DNA sequence can be used as an origin of replication in S. cerevisiae, although there is evidence that certain sequences may be better origins than others. The replication of mitochondrial DNAs in fungi and plants is likely to occur by a rollingcircle mechanism. The appearance of s-shaped, linear and circular DNA molecules in electron micrographs taken of DNA prepared from mitochondria of plant and fungi support this model of replication. In general, there is a substantially higher rate of mutation of the mitochondrial mutation than of the nuclear genome, with point mutations occurring at a rate

Mitochondria: Origin

about 10-fold higher for mitochondrial DNA than for nuclear DNA. The biochemical processes carried out in mitochondria have the ability to generate reactive oxygen species, thus accounting for some of the increased mutation rate in mitochondria. Mutation rates are also a function of processes involved in the repair of DNA adducts. Biochemical products and enzymatic activities consistent with various pathways for DNA repair have been observed in animal and yeast mitochondria. It has also been suggested the propensity of recombinational events in the mitochondria of plants and fungi serve as a mechanism for DNA repair, presuming a selective advantage for mitochondrial compartments and cells that maintain a nominally wild-type mitochondrial genome. Interestingly, mitochondrial DNA in vertebrate cells do not undergo homologous recombination, or at least do so very rarely. The inheritance of mitochondrial genomes during cell division is nonmendelian in nature. In any given eukaryotic cell there are anywhere from 50 to 10 000 more mitochondrial genomes than nuclear genomes, and the mitochondrial genomes are generally dispersed throughout the cytoplasm within mitochondria. Hence, many of the issues of mitochondrial genome inheritance during cell division are aected by the stochastic distribution of mitochondrial genomes within the cell. There are also inuences on mitochondrial genome distribution, and subsequently inheritance, within mitochondria. Mitochondrial DNA, while commonly placed in the matrix, also can be cofractionated with protein complexes that are tightly associated with the inner membrane of mitochondria. Mitochondrial DNA distribution within mitochondria can also be aected by the extent to which a given mitochondrial genome is replicated. In both animals and yeast, preferential replication of certain mitochondrial DNA molecules has been proposed as the basis for selective inheritance of certain mitochondrial genomes during cell division and growth of the organism. The dynamics of mitochondrial genome distribution in animal cells can be studied by introducing into cells, or even animals, mitochondrial genomes that exhibit mutant phenotypes and/or restriction length polymorphisms that serve as functional or physical markers. It is clear that inheritance and selective propagation of mitochondrial genomes in animals are complex issues that likely reect aspects of mitochondrial DNA replication and genetic status of the mitochondrial genome, mitochondrial compartment fusion, localization and turnover, as well as the genetic makeup of the nucleus. In mitochondria of plants, with their complex genome usually represented by topologically interconvertible subgenomic fragments, recombination is an essential feature of genome maintenance owing to its inuence on the copy number of the individual subgenomic elements, their topological position, and rate of mutation.

The Bacterial Origins of Mitochondria

The endosymbiotic hypothesis proposes that a protoeukaryote survived the colonization of its cytoplasm by a bacterium, termed the proto-mitochondrion. Subsequently, a mutually benecial system was established whereby the proto-mitochondrion was provided the appropriately reduced carbon molecules by the host cell in return for ATP. While the original proposal was perhaps motivated by an eerie resemblance of mitochondria to bacterial cells, there is ample evidence for a bacterial origin, some of which is described below. There is now a general consensus that the endosymbiont that has given us presentday mitochondria was an organism related to a-proteobacteria. The nature of the proto-eukaryote is perhaps more controversial than is the identity of the closest present-day bacterial relative of mitochondria. The proto-eukaryote has been presumed to already possess a nucleus and additional intracellular membrane systems before the capture of the proto-mitochondrion. Protists are candidates for the closest present-day relative of the protoeukaryote. It has recently been speculated that perhaps the acquisition of the proto-mitochondrion was the seminal event in the evolution of eukaryotic cells, instigating an increase in the size and complexity of the proto-eukaryotes genome as a direct result of an increased level of tness (Vellai et al., 1998). In this model, nuclear and secretory membranes arose subsequent to establishment of the proto-mitochondrial symbiont.

Evidence of a Bacterial Origin for Mitochondria

Mitochondrially encoded gene products can be placed in phylogenetic trees with related bacterial gene products more readily than they can with equivalent eukaryotic homologues (e.g. nuclear-encoded gene products that are not localized to mitochondria). These include both gene products encoded by the mitochondrial genome and a subset of the gene products found in mitochondria that are encoded by the nuclear genome and subsequently imported into mitochondria. Phylogenies based upon 16S rRNA genes indicate that mitochondria are closely related to eubacteria, even suggesting that they share a common ancestor with Rickettsia (Yang et al., 1985). Bacteria from the rickettsial group are obligate intracellular parasites, and the lifestyle of these organisms is consistent with the postulated ancestral relationship with the proto-mitochondrion (Andersson, 1998). Phylogenies have also been constructed based upon the sequences of the heat-shock proteins (Gupta, 1995), superoxide dismutase (Grace, 1990), and proteins involved in electron transport in mitochondria
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Mitochondria: Origin

(Paquin et al., 1995); all support a monophylogenetic origin for mitochondria. Hence, all mitochondria derive from the same eubacterial lineage and the same endosymbiotic event. Additionally, the mitochondrial genome of R. americana has features that are very reminiscent of an eubacterial genome, including a multisubunit, eubacterialtype RNA polymerase (Lang et al., 1997).

Mitochondrial Evolution and Specialization

Despite the wide variations in size, gene order, and modes of replication and maintenance, mitochondrial genomes have all undergone a large-scale transfer of genetic information to the nuclear genome. Presumably, much of the transfer and outright loss of genetic material occurred prior to any evolutionary branches in the eukaryotic lineage. However, the escape and transfer of genetic material from mitochondria to the nucleus is an on-going process, and the extent and nature of the actual material transferred varies depending on the organism and the particular selective pressures to which that organism is subjected. The basis for the selective pressures experienced by dierent organisms and the evolutionary responses of the mitochondrial genome to those pressures are largely speculative. One pressure that surely aects mitochondrial genomes is the continual generation of reactive oxygen species as an undesirable byproduct of electron transport and oxidative phosphorylation. In the face of this selective pressure, mitochondrial genomes of animal cells have evolved an exceedingly compact genome, with a relatively high rate of silent mutations. Plant cells have evolved larger genomes with a comparatively low rate of mutation. It has been suggested that these two eukaryotic lineages have evolved two separate means for dealing with frequent encounters with reactive oxygen species (Atlan and Couvet, 1993). Animal cells have responded by decreasing the size of the mitochondrial genome, consequently xing mutations that do not cause a selective disadvantage by virtue of a higher rate of replication. The mitochondria of plant cells defend themselves through a high rate of recombination and gene conversion, which prevents the accumulation of deleterious mutations. As a consequence, mitochondrial DNA sequences in plants expand due to duplication and rearrangement of DNA. An extremely interesting adaptation of mitochondrial gene expression is the editing of RNA transcripts in plant and kinetoplast mitochondria. Many primary transcripts in plants are subject to C to U conversions, and even a few U to C conversions. These changes most often occur in structural genes and can result in a dierent amino acid being expressed than was encoded by the DNA. These edits can also occur in regions of transcripts corresponding to
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start and stop codons, introns and structural RNAs. The mitochondria of kinetoplastid protozoa, of which the causative agent of malaria, Trypanosoma brucei, is a representative, have their mitochondrial genome encoded on many small circular DNAs, termed maxicircles (20 40 kb in size) and minicircles (0.82.5 kb in size). These DNAs form a nucleoid of catenated molecules in the single mitochondrion adjacent to the basal body of the organisms agellum. RNA transcripts derived from cryptogenes encoded on the maxicircles are modied by the insertion and deletion of U residues. The extent of editing ranges from only a few insertions or deletions in a transcript to the addition and elimination of hundreds of U residues throughout the transcript. Guide RNAs, usually encoded by the minicircle portion of the mitochondrial genome, catalyses this editing process. The evolutionary basis of these editing processes is unknown. Changes and attenuation of mitochondrial functions have accompanied the evolution of eukaryotes. Whereas the relationship established at the time of symbiosis was presumably predicated around energy metabolism, mitochondria clearly have been adapted by the host during evolution of eukaryotes to serve biosynthetic and developmental roles. Mitochondria are often found localized at sites within the cell where energy requirements are likely to be high. For instance, mitochondria are found wound around the agellar axoneme of sperm and localized between layers of myobrils in cardiac muscle. Mitochondria are also enriched in certain types of epithelial cells that are involved in the acidication of various biological uids. The classic alteration of mitochondrial function due to an alteration of the organelle itself occurs in the specialized adipose cells termed brown fat. The majority of the energy generated by oxidation in mitochondria of these cells is released as heat rather than being coupled to the synthesis of ATP. The presence of a specic proton transporter in the inner membrane of brown fat cells bypasses the mitochondrial ATP synthase. In mammals, a developmental programme regulates many aspects of mitochondrial activity. Changes in the array and amount of proteins involved in electron transport and oxidative phosphorylation occur upon birth and allow adaptation of the fetus to an extrauterine environment. Recently, the mitochondrion has been identied as an important component in the pathway of programmed cell death, apoptosis. In response to certain signals, mitochondria swell and release cytochrome c, which in turn serves as a coactivator of additional signalling molecules in the apoptotic pathway. It also likely those mitochondria serve as a source for reactive oxygen species that contribute to cell death during apoptosis. Perhaps the most extensive modication of a mitochondrion is the conversion of that organelle into a hydrogenosome. The hydrogenosome is found in facultative anaerobic protists that lack mitochondria. These doublemembrane organelles resemble mitochondria and are used

Mitochondria: Origin

to generate ATP using pyruvate. Hydrogenosomes, unlike mitochondria, do not contain DNA, cytochromes, or enzymes used in the TCA cycle. Instead, these organelles contain enzymes that are also found in anaerobic bacteria that are capable of producing hydrogen. It has been demonstrated, using phylogenetic analysis of heat-shock proteins contained within the hydrogenosome, that these organelles share the same lineage as mitochondria (Bui et al., 1996). Hence, the most likely explanation for the origin of hydrogenosomes is that they evolved from the proto-mitochondrion soon after symbiosis.

Paquin B, Forget L, Roewer I and Lang BF (1995) Molecular phylogeny of Allomyces macrogynus: congruency between nuclear ribosomal RNA- and mitochondrial protein-based trees. Journal of Molecular Evolution 41: 657665. Vellai T, Takacs K and Vida G (1998) A new aspect to the origin and evolution of eukaryotes. Journal of Molecular Evolution 46: 499507. Yang D, Oyaizu Y, Oyaizu H, Olsen GJ and Woese CR (1985) Mitochondrial origins. Proceedings of the National Academy of Sciences of the USA 82: 44434447.

Further Reading
Alfonzo JD, Thiemann O and Simpson L (1997) The mechanism of U insertion/deletion RNA editing in kinetoplastid mitochondria. Nucleic Acids Research 25: 37513759. Gray MW, Lang BF, Cedergren R et al. (1998) Genome structure and gene content in protist mitochondrial DNAs. Nucleic Acids Research 26: 865878. Leblanc C, Richard O, Kloareg B et al. (1997) Origin and evolution of mitochondria: what have we learnt from red algae? Current Genetics 31: 193207. Maier RM, Zeltz P, Kossel H et al. (1996) RNA editing in plant mitochondria and chloroplasts. Plant Molecular Biology 32: 343365. Margulis L (1981) Symbiosis in Cell Evolution: Life and its Environment on the Early Earth. San Francisco: WH Freeman. Moyes CD, Battersby BJ and Leary SC (1998) Regulation of muscle mitochondrial design. Journal of Experimental Biology 201: 299307. Paquin B, Laforest MJ, Forget L et al. (1997) The fungal mitochondrial genome project: evolution of fungal mitochondrial genomes and their gene expression. Current Genetics 31: 380395. Shadel GS and Clayton DA (1997) Mitochondrial DNA maintenance in vertebrates. Annual Review of Biochemistry 66: 409435. Thorsness PE and Weber ER (1996) Escape and migration of nucleic acids between chloroplasts, mitochondria, and the nucleus. International Review of Cytology 165: 207234.

References
Andersson SG (1998) Bioenergetics of the obligate intracellular parasite Rickettsia prowazekii. Biochimica et Biophysica Acta 1365: 105111. Atlan A and Couvet D (1993) A model simulating the dynamics of plant mitochondrial genomes. Genetics 135: 213222. Bui ET, Bradley PJ and Johnson PJ (1996) A common evolutionary origin for mitochondria and hydrogenosomes. Proceedings of the National Academy of Sciences of the USA 93: 96519656. Feagin JE, Werner E, Gardner MJ, Williamson DH and Wilson RJ (1992) Homologies between the contiguous and fragmented rRNAs of the two Plasmodium falciparum extrachromosomal DNAs are limited to core sequences. Nucleic Acids Research 20: 879887. Grace SC (1990) Phylogenetic distribution of superoxide dismutase supports an endosymbiotic origin for chloroplasts and mitochondria. Life Sciences 47: 18751886. Gupta RS (1995) Evolution of the chaperonin families (Hsp60, Hsp10 and Tcp-1) of proteins and the origin of eukaryotic cells. Molecular Microbiology 15: 111. Lang BF, Burger G, OKelly CJ et al. (1997) An ancestral mitochondrial DNA resembling a eubacterial genome in miniature. Nature 387: 493 497.