Animal Mitochondrial Genome
One of the most essential organelles in the animal cell is the mitochondrion, as it is not only the center of ATP production, it also have a phylogenetic value that reveals taxonomic relationships among organisms. These are rod-shaped organelles convert oxygen and glucose into adenosine triphosphate (ATP), otherwise known as the chemical energy “currency” of the cell that powers the cell’s metabolic activities. This kind of respiration is termed aerobic and it supplies energy to most cellular activities.
This mode of respiration is more efficient than in the absence of oxygen as anaerobic respiration can only produce two ATPs, as opposed to the 36-38 ATPs produced by the aerobic mode. This is why higher life forms are adapted to utilize oxygen for their ATP production (Davidson, 2004). Mitochondria are hypothesized by scientist to have evolved from a symbiotic relationship between aerobic bacteria and primordial eukaryotic cells (Wallace, 2005), otherwise known as the endosymbiont theory. It functions in common physiological processes such as metabolism, apoptosis, disease, and aging. Being the primary site where oxidative phosphorylation occurs, these double-membrane organelles are efficient in aerobic respiration which allows eukaryotic cells to generate the necessary amount of ATP (Chan, 2006).
The mitochondrion maintains its own set of genes although most of its proteins (about 900) are synthesized within and imported from the nuclear genome necessary for its respiratory function (Wallace, 2005).The genome contained by this subcellular organelle separate from the nuclear chromatin is otherwise referred to as the mitochondrial DNA (mtDNA). Particularly in animals, mtDNAs commonly have a closed-circular molecule, with the exception of certain classes containing linear mtDNA chromosomes (Boore, 1998).
These extrachromosomal genomes contain 37 genes composed of 13 protein subunits for enzymes coding for oxidative phosphorylation, two ribosomal RNAs of mitochondrial ribosome, and 22 tRNAs for protein translation. Together with proteins and RNAS synthesized in the cytoplasm, products of these 37 genes allow the mitochondrion to possess its own system facilitating DNA transcription, translation, mRNA processing and protein translation. This circular genome is comprised of a mixture of covalently closed circular monomers and different amounts of concatenated dimers and higher oligomers (Burger et al., 2002).
Genes contained in the animal mitochondrion are usually encoded on both strands. The H-strand, or the heavy strand, and the L-strand, or the light strand, are these two mentioned strands that comprise the genome. Their names are derived from their molecular weight differences caused by their varying base compositions. 12 out of the 13 protein coding genes comprise the H-strand while only the single gene left belongs to the L-strand. The genome also contains noncoding regions which are restricted to certain areas known as the D-Loop (Shadel and Clayton 1997).
These two strands, the H-strand and the L-strand, originated within the D-Loop, or the displacement loop, region and within a cluster of five tRNA genes respectively. The entire replication process only commences in the initiation of the H-strand synthesis, while the L-strand lags behind. The L-strand synthesis can only begin when two-thirds of the H-strand synthesis across the circular genome is already completed. Therefore, only in the intiation of H-strand synthesis can mtDNA start replicating. Aside from its mentioned function, the D-Loop region is also the location of two transcriptional promoters (HSP and LSP), one for each strand of mtDNA. Synthesis of polycistronic transcripts for the expression of the majority or all of the genes encoded in each strand are directed by these promoters (Chang and Clayton, 1985).
Scientists have speculated that the mitochondria are derived from eubacterial endosymbionts. This is due to the possession of mitochondria their own genetic material (DNA) and their own system for genetic expression. Although mitochondria are contained in species belognoing to different kingdoms, they offer considerable differences and even reveal phylogenetic relationships and distances.
There are characteristic variations among the three major kingdoms Animalia, Eukaryomycota, and Plantae (including protests). Among animals, their mitochondrial genome is relatively small, having an approximate measurement between 16 and 19 kb, and are compactly arranged as they lack introns or spacer regions. Fungal mtDNAs are considerably larger that animal mtDNAs. Their size is within the range of 17-176 kb and they encode more gene sequences than those of animals.
It can be observed that the size range is quite vast, reflecting great variations in genome size. This is not due to coding capacities, instead it can be attributed to the presence of varying sizes of introns and spacer regions. In the case of plants, the genome size range is even more variable as it ps 16 to 2400 kb. Its mtDNA is distinctly characterized by a wide variety of gene content and molecular structure, and the variation of the length of spacer regions and introns (Ohta et al., 1998).
One of the most extensively studied group are those of the protists. Their mtDNAs are considered intermediate in size with a measurement range of 6 to 77 kb. Most of protist genomes are compact having little or no non-coding regions. Although present, intergenic spacers are sparse and are generally small, with some coding regions overlapping. There is an general high concentration of Adenine and Thymine that are particularly elevated in non-coding intergenic regions (Gray et al., 1997).
Mitochondrial genome composition in vertebrates predominantly includes a standard set of genes coding for 13 inner mitochondrial membrane proteins for electron transport and oxidative phosphorylation functions. Included genes for this function are nad1-6 and 4L, cob, cox1-3 and atp6 and 8. Genes for both large subunit (LSU) and small subunit (SSU) rRNAs are also contained within the animal mitochondrial genome.
The mentioned set of mtDNA-encoded genes (plus atp9) is also found in fungal organisms such as Allomyces macrogynus mtDNAs. However, particular ascomycete fungi such as Schizosaccharomyces pombe lack all nad genes. Both animal and fungal mtDNAs do not encode a 5S rRNA nor, with the exception of rps3 in A. macrogynus mtDNA, do they carry any ribosomal protein genes. Terrestrial plants contain mitochondrial genomes with a few extra respiratory chain protein genes such as nad9 and atp1 in M.polymorpha. But the most distinct variation of the plant mtDNA from the animal and fungal mtDNAs is the presence of both the 5S rRNA (Gray et al., 1997).
Animal mtDNA sequences are found to evolve rapidly however they maintain their genetic arrangements for long periods of evolutionary time. A notable example is the identical arrangement of humans and trouts. Although there are few exceptions, gene arrangements are considered stable within major taxonomic groups but are variable between them. We can potentially utilize these data comparisons in reconciling phylogenetic conflicts. Greater differences would entail divergence among the taxa. Comparisons of mitochondrial gene arrangements have provided convincing phylogenies in several cases where all other data were equivocal, including the relationships among major groups of echinoderms and arthropods (Burger et al., 2002).
Although studies in mitochondrial genomes of different taxonomic groups are still inconclusive, it still holds a large potential in revolutionizing the taxonomic field. It has opened avenue for prospective discoveries on the currently unknown areas of biological sciences. Therefore, mitochondrial genome research studies are yet to reach their pinnacle and would surely still be an essential focus of phylogenetic sciences.
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