2017, Number 4
<< Back Next >>
Rev Educ Bioquimica 2017; 36 (4)
Los códigos genéticos mitocondriales: características, origen y evolución
Aguilar GK, Vilchis PA, Valdés LV
Language: Spanish
References: 57
Page: 129-140
PDF size: 638.45 Kb.
ABSTRACT
The mitochondrion is a highly specialized organelle, present in almost all eukaryotic
cells that carry out the energy production through oxidative phosphorylation and
also takes part in many cellular processes. Mitochondria has its own genome,
whose size, structure and genetic content varies in different organisms, Since the
first mitochondrial genome description, it was shown that many organisms exhibit
genetic code variants, which give different meanings to some codons. Nowadays, the
number of variants has increased. In this work we analyze the code variants that have
been found, focusing on mitochondrial variants and how they are recognized for the
translation systems in these organelles. We also analyzed the different hypothesis
on the origin of these variants.
REFERENCES
Osellame L, Blacker T, Duchen M (2012) Cellular and molecular mechanisms of mitochondrial function. Best Pract Res Clin Endocrinol Metab 26:711-723.
Chinnery P, Hudson G (2013) Mitochondrial genetics. Br Med Bull 106:135-159.
Kasiviswanathan R., Collins T, Copeland W (2012) The interface of transcription and DNA replication in the mitochondria. Biochim Biophys Acta 1819:970 - 978.
Gray M, Burger G, Lang B (2001) The origin and early evolution of mitochondria. Genome Biol 2: REVIEWS 1018.1- 1018.5.
Hirt R, Horner D (ed.) (2004) Organelles, Genomes and Eukaryote Phylogeny: An Evolutionary Synthesis in the Age of Genomics. CRC Press, New York, p 400.
Burger G, Gray M, Forget L, Lang B (2013) Strikingly bacteria-like and gene-rich mitochondrial genomes throughout jakobid protists. Genome Biol Evol 5:418-438.
Avila G, Tovar J (2004) Mitosomes of Entamoeba histolytica are abundant mitochondrion-related remnant organelles that lack a detectable organellar genome. Microbiol 150:1245–1250.
Van der Giezen M, Tovar J, Clark C (2005) Mitochondrion-derived organelles in protists and fungi. Int Rev Cytol 244:175–225.
Boxma B, de Graaf R, van der Staay G, van Alen T, Ricard G, Gabaldón T, van Hoek A, Moon-van der Staay S, Koopman W, van Hellemond J, Tielens A, Friedrich T, Veenhuis M, Huynen M, Hackstein J (2005) An anaerobic mitochondrion that produces hydrogen. Nature 434: 74 –79.
Barbrook A, Howe C, Kurniawan D, Tarr S (2010) Organization and expression of organellar genomes. Philos Trans R Soc Lond B Biol Sci 365:785-797.
Anderson S, Bankier A, Barrell B, de Bruijn M, Coulson A, Drouin J, Eperon I, Nierlich D, Roe B, Sanger F, Schreier P, Smith A, Staden R, Young I ( 1981) Sequence and organization of the human mitochondrial genome. Nature 290: 457–465.
Zhang J, Lin A, Powers J, Lam M, Lotz C, Liem D, Lau E, Wang D, Deng N, Korge P, Zong N, Cai H, Weiss J, Ping P (2012) Perspectives on: SGP symposium on mitochondrial physiology and medicine: mitochondrial proteome design: from molecular identity to pathophysiological regulation. J Gen Physiol 139:395-406.
Marshall W. Nirenberg - Nobel Lecture: The Genetic Code. Nobelprize.org.Nobel Media AB 2013. Web 1 Jun 2014. http://www.nobelprize.org/nobel_prizes/ medicine/laureates/1968/nirenberg-lecture. html
Freeland S, Hurst L (2004) Evolution encoded. Sci Am 290:84-91.
Koonin E, Novozhilov A (2009) Origin and evolution of the genetic code: the universal enigma. IUBMB Life 61, 99-111.
Woese C (1965) On the evolution of the genetic code. Proc Natl Acad Sci U S A 54: 1546-1552.
Wong J (1975) A co-evolution theory of the genetic code. Proc Natl Acad Sci U S A 72:1909-1912.
Baranov P, Gesteland R, Atkins J (2002) Recoding: Translational Bifurcations in Gene Expression. Gene 286: 187–201.
Srinivasan G, James C, Krzycki J (2002) Pyrrolysine encoded by UAG in Archaea: charging of a UAG-decoding specialized tRNA. Science 296:1459–1462.
Bender A, Hajieva P, Moosmann B (2008) Adaptive antioxidant methionine accumulation in respiratory chain complexes explains the use of a deviant genetic code in mitochondria. Proc Natl Acad Sci U S A 105:16496-16501.
Barrell B, Bankier A, Drouin J (1979) A different genetic code in human mitochondria. Nature 282:189-194.
Vallabhaneni H, Fan-Minogue H, Bedwell DM, Farabaugh PJ (2009) Connection between stop codon reassignment and frequent use of shifty stop frameshifting. RNA 15:889-897.
Knight R, Freeland S, Landweber L (2001) Rewiring the keyboard: evolvability of the genetic code. Nat Rev Genet 2:49-58.
McCutcheon J, McDonald B, Moran N (2009) Origin of an alternative genetic code in the extremely small and GC-rich genome of a bacterial symbiont. PLoS Genet 5, e1000565.
Elzanowski A, Ostell J. The Genetic Codes. National Center for Biotechnology. 18 Nov 2016. Web. 05 Jun 2017. http://www. ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc. cgi?mode=c
Santos M, Moura G, Massey S, Tuite M (2004) Driving change: the evolution of alternative genetic codes. Trends Genet 20:95-102.
Lekomtsev S (2007) Non-standard genetic codes and translation termination. Mol Biol (Mosk) 41:964-972.
Parker J (1989) Errors and alternatives in reading the universal genetic code. Microbiol Rev 53:273-298.
Lobanov A, Turanov A, Hatfield D, Gladyshev V (2010) Dual functions of codons in the genetic code. Crit Rev Biochem Mol Biol 45:257-265.
Sakurai M, Ohtsuki T, Suzuki T, Watanabe K (2005) Unusual usage of wobble modifications in mitochondrial tRNAs of the nematode Ascaris suum. FEBS Lett 579:2767-2772.
Martin RP, Sibler A, Gehrke C, Kuo K, Edmonds C, McCloskey J, Dirheimer G (1990) 5-[[(carboxymethyl)amino]methyl]uridine is found in the anticodon of yeast mitochondrial tRNAs recognizing two-codon families ending in a purine. Biochemistry 29:956-959.
Hekele A, Beier H (1991) Nucleotide sequence and functional characterization of a mitochondrial tRNA(Trp) from Tetrahymena thermophila. Nucleic Acids Res 19:1941.
Suzuki T, Miyauchi K, Suzuki T, Yokobori S, Shigi N, Kondow A, Takeuchi N, Yamagishi A, Watanabe K (2011) Taurine-containing uridine modifications in tRNA anticodons are required to decipher non-universal genetic codes in ascidian mitochondria. J Biol Chem 286:35494-35498.
Alfonzo J, Blanc V, Estevez A, Rubio M, Simpson L (1999) C to U editing of the anticodon of imported mitochondrial tRNA(Trp) allows decoding of the UGA stop codon in Leishmania tarentolae. Embo J 18:7056-7062.
Simpson L, Thiemann O, Savill N, Alfonzo J, Maslov D (2000) Evolution of RNA editing in trypanosome mitochondria. Proc Natl Acad Sci U S A 97:6986-6993.
Jackman J, Alfonzo J (2013) Transfer RNA modifications: nature’s combinatorial chemistry playground. Wiley Interdiscip Rev RNA 4:35-48.
Agris P. (2004) Decoding the genome: a modified view. Nucleic Acids Res 32:223-38.
Christian B, Spremulli L (2012) Mechanism of protein biosynthesis in mammalian mitochondria. Biochim Biophys Acta 1819, 1035-1054.
Tomita K, Ueda T, Watanabe K (1998) 7-Methylguanosine at the anticodon wobble position of squid mitochondrial tRNA(Ser)GCU: molecular basis for assignment of AGA/AGG codons as serine in invertebrate mitochondria. Biochim Biophys Acta 1399:78-82.
Ohira T, Suzuki T, Miyauchi K, Suzuki T, Yokobori S, Yamagishi A, Watanabe K (2013) Decoding mechanism of non-universal genetic codes in Loligo bleekeri mitochondria. J Biol Chem 288:7645-7652.
Matsuyama S, Ueda T, Crain P, McCloskey J, Watanabe K (1998) A novel wobble rule found in starfish mitochondria. Presence of 7-methylguanosine at the anticodon wobble position expands decoding capability of tRNA. J Biol Chem 273:3363-3368.
Tomita K, Ueda T, Watanabe K (1999) The presence of pseudouridine in the anticodon alters the genetic code: a possible mechanism for assignment of the AAA lysine codon as asparagine in echinoderm mitochondria. Nucleic Acids Res 27:1683-1689.
Watanabe K, Yokobori S (2011) tRNA Modification and Genetic Code Variations in Animal Mitochondria. J Nucleic Acids 623095.
Su D, Lieberman A, Lang B, Simonovic M, Söll D, Ling J (2011) An unusual tRNAThr derived from tRNAHis reassigns in yeast mitochondria the CUN codons to threonine. Nucleic Acids Res 39:4866-4874.
Garey J, Wolstenholme D (1989) Platyhelminth mitochondrial DNA: evidence for early evolutionary origin of a tRNA(serAGN) that contains a dihydrouridine arm replacement loop, and of serine-specifying AGA and AGG codons. J Mol Evol 28:374-387.
Yu H, Li Q (2011) Mutation and selection on the wobble nucleotide in tRNA anticodons in marine bivalve mitochondrial genomes. PLoS One 6, e16147.
Crick FH (1966) Codon--anticodon pairing: the wobble hypothesis. J Mol Biol 19:548-555.
Alkatib S, Sharff L, Rogalski M, Fleischmann T, Matthes A, Seeger S, Schöttler M, Ruf S, Bock R (2012) The contributions of wobbling and superwobbling to the reading of the genetic code. PLoS Genet 8, e1003076.
Bilbille Y, Gustillo E, Harris K, Jones C, Lusic H, Kaiser R, Delaney M, Spremulli L, Deiters A, Agris P (2011) The human mitochondrial tRNAMet: structure/function relationship of a unique modification in the decoding of unconventional codons. J Mol Biol 406:257- 274.
Rubio M, Rinehart J, Krett B, Duvezin – Caubet S, Reichert A, Söll D, Alfonzo J (2008) Mammalian mitochondria have the innate ability to import tRNAs by a mechanism distinct from protein import. Proc Natl Acad Sci U S A 105, 9186-9191.
Watanabe, K. (2010) Unique features of animal mitochondrial translation systems. The nonuniversal genetic code, unusual features of the translational apparatus and their relevance to human mitochondrial diseases. Proc Jpn Acad Ser B Phys Biol Sci 86, 11-39.
Lightowlers R, Chranowska-Lightowlers Z (2010) Terminating human mitochondrial protein synthesis. A shift in our thinking. RNA Biol 7:282-286.
Lind C, Sund J Åqvist J (2013) Codon-reading specificities of mitochondrial release factors and translation termination at non-standard stop codons. Nat Commun 4:1-8.
Lang B, Burger G. Thraustochytrium aureum. Mitochondrial genome organization, gene content, genetic code. OGMP. 23-Oct-2007. Web. 1-Jun-2014. http://megasun.bch.umontreal.ca/ogmp/ projects/taure/gen.html
Osawa S, Jukes T, Watanabe K, Muto A (1992) Recent Evidence for Evolution of the Genetic Code. Microbiol Rev 56:229-264.
Cantatore P, Roberti M, Rainaldi G, Gadaleta M, Saccone C (1989) The complete nucleotide sequence, gene organization, and genetic code of the mitochondrial genome of Paracentrotus lividus. J Biol Chem 264:10965-10975.
Sengupta S, Yang X, Higgs P (2007) The mechanisms of codon reassignments in mitochondrial genetic codes. J Mol Evol 64:662-688.