Mitochondrial codons

Mitochondria of various organisms use different genetic code. Search the Internet site to obtain information for the mitochondrial codons from either vertebrates or invertebrates. Discuss usage differences between the standard codons and mitochondrial codons. 

Finally, fungi differ from other organisms in a range of biochemical and molecular features such as the regulation of some enzymes, some aspects of mitochondrial codon usage, etc. 

The I vaginalis hydrogenosomal presequences are generally short, ranging from 5 to 14 amino acid residues for those that have been proven experimentally, and up to 17 residues for the predicted presequences (Table 1). The presequences are enriched in the amino acid residues Ser (20%), Leu (14%), Arg (11%), Ala (8%), Phe (7%), Val (6%), Thr (6%) and Asn (5%). The other amino acids are significantly under-represented. Incidentally, or accidentally, the three amino acids most commonly found in these presequences, Ser, Leu and Arg, are the ones that are each encoded by six codons. This may have been relevant in the evolution of these presequences. The mitochondrial matrix N-terminal presequences are enriched in Arg (14%), Leu (12%), Ser (11%) and Ala (14%). On the other hand, chloroplast leader peptides have a different amino acid composition with 19% Ser and 9% Thr (von Heijne et al. 1989). Markedly under-represented in hydrogenosomal presequences are the acidic residues, as in the case of both mitochondrial and plastidic presequences (von Heijne et al. 1989). 

N indicates any nucleotide +, codon has the same meaning as in the normal code , codon not observed in this mitochondrial genome. 

Another peculiarity of the mitochondrial code emerged from a study of yeast codon usage. By comparing tables 29.3 and 29.1, you will see that the mitochondrial code has several differences in code word meaning. The codons beginning with CU represent Thr instead of Leu, the AUA codon represents Met instead of He, and the UGA codon represents Trp rather than a stop signal. 

The genetic code differs very little between species. By contrast, considerable differences occur between species in the anticodon translation system of tRNA, as evidenced by the mitochondrial tRNA system. In all systems the bases in the anticodon-codon complex run antiparallel, as in standard double-helix pairing, and in all cases only Watson-Cricklike base pairing occurs between the first two bases in the codon and the opposing bases in the anticodon segment of the tRNA. However, for the 3 base in the codon, the rules for pairing vary with the species and with the base in question. These rules, summarized in table 29.4, are as follows. 

Garey, J.R. and Wolstenholme, D.R. (1 989) PlatyheIminth mitochondrial DNA evidence for early evolutionary origin of a tRNA(ser AGN) that contains a dihydrouridine arm replacement loop, and of serine-specifying AGA and AGG codons. Journal of Molecular Evolution 28, 374-387. 

Le, T.H., McManus, D.P. and Blair, D. (2004) Codon usage and bias in mitochondrial genomes of parasitic platyhelminthes. Korean Journal of Parasitology 42, 159-167. 

Nakao, M., Sako, Y. and Ito, A. (2003) The mitochondrial genome of the tapeworm Taenia solium a finding of the abbreviated stop codon U. Journal of Parasitology 89, 633-635. 

Ohama, T., Osawa, S., Watanabe, K. and Jukes, T.H. (1990) Evolution of the mitochondrial genetic code. IV. AAA as an asparagine codon in some animal mitochondria. Journal of Molecular Evolution 30, 329-332. 

Y3. Yasukawa, T., Suzuki, T., Ishii, N., Ohta, S., and Watanabe, K., Wobble modification defect in tRNA disturbs codon-anticodon interaction in a mitochondrial disease. EMBO J. 20,4794-4802 (2001). 

The genetic code is not universal but is the same in most organisms. Exceptions are found in mitochondrial genomes where some codons specify different amino acids to that normally encoded by nuclear genes. In mitochondria, the UGA codon does not specify termination of translation but instead encodes for tryptophan. Similarly, in certain protozoa UAA and UAG encode glutamic acid instead of acting as termination codons. 

A surprise was encountered when the sequence of human mitochondrial DNA became known. Human mitochondria read UGA as a codon for tryptophan rather than as a stop signal (Table 5.5). Furthermore, AGA and AGG are read as stop signals rather than as codons for arginine, and AUA is read as a codon for methionine instead of isoleucine. 

Human mitochondrial DNA comprises 16,569 bp and encodes 13 respiratory-chain proteins as well as the small and large ribosomal RNAs and enough tRNAs to translate all codons. However, mitochondria also contain many proteins encoded by nuclear DNA. Cells that contain mitochondria depend on these organelles for oxidative phosphorylation, and the mitochondria in turn depend on the cell for their very existence. How did this intimate symbiotic relation come to exist ... 

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