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Redalyc.Structure of the Mitochondrial Control Region and Flanking Trna Hidrobiológica ISSN: 0188-8897 [email protected] Universidad Autónoma Metropolitana Unidad Iztapalapa México Rocha Olivares, Axayácatl; Garber, Nikola M.; Garber, Amber F.; Stuck, Kenneth C. Structure of the mitochondrial control region and flanking tRNA genes of Mugil cephalus Hidrobiológica, vol. 15, núm. 2, agosto, 2005, pp. 139-149 Universidad Autónoma Metropolitana Unidad Iztapalapa Distrito Federal, México Available in: http://www.redalyc.org/articulo.oa?id=57815205 How to cite Complete issue Scientific Information System More information about this article Network of Scientific Journals from Latin America, the Caribbean, Spain and Portugal Journal's homepage in redalyc.org Non-profit academic project, developed under the open access initiative Hidrobiológica 2005, 15 (2 Especial): 139-149 Structure of the mitochondrial control region and flanking tRNA genes of Mugil cephalus Estructura de la región control mitocondrial y genes ARNt adyacentes de Mugil cephalus Axayácatl Rocha-Olivares1, Nikola M. Garber2, Amber F. Garber3, and Kenneth C. Stuck4 1 Department of Biological Oceanography, CICESE, km 107 Carretera Tijuana-Ensenada, Ensenada B. C. 22860 2 NOAA Sea Grant, 1315 East West Highway, R/SG, Rm 11718, Silver Spring, Maryland 20910 3 North Carolina State University, Department of Zoology, Campus Box 7617, Raleigh, North Carolina 27695-7617 4 Gulf Coast Research Laboratory, University of Southern Mississippi, PO Box 7000, Ocean Springs, Mississippi 39566-7000 Dr. Axayácatl Rocha-Olivares CICESE-Department of Biological Oceanography Tel: (646) 175-0500 x 24240 Fax: (646) 175-0545 E. mail: [email protected] Rocha-Olivares, A., N. M. Garber, A. F. Garber and K. C. Stuck. 2005. Structure of the mitochondrial control region and flanking tRNA genes of Mugil cephalus. Hidrobiológica 15 (2 Especial): 139-149. ABSTRACT We cloned and sequenced the mitochondrial (mt) control region (CR) and flanking transfer RNA genes (T, P, and F) of the striped mullet, Mugil cephalus and designed species-specific primers to amplify the entire CR in specimens from the Pacific (Hawaii), the Gulf of Mexico, and the Atlantic. We verified the absence of heteroplasmy and nuclear mtDNA duplications of this region in the organisms sampled, finding an extraordinary level of sequence divergence (mean 38-75% Tamura & Nei distance- L ) between fish from both Oceans, including Japan. The CR of the mullet was variable in length (845-930 bp) and contained structural elements in common with other CRs, including a central conserved segment flanked by hypervariable regions and smaller conserved sequence blocks. Termination associated sequences, however, were not found. The CR of the striped mullet was rich in AT (~67%) and poor in GC. Key words: Mitochondrial DNA, cloning, molecular divergence, mullet, control region. RESUMEN Se clonó y secuenció la región control (RC) mitocondrial (mt) y los genes de ARNt adyacentes (T, P, y F) de la lisa rayada, Mugil cephalus y se diseñaron cebadores especie-específicos para amplificar la RC en su totalidad en organismos del Pacífico (Hawai), el Golfo de México y el Atlántico. Se verificó la ausencia de heteroplasmia y de duplicaciones nucleares del ADN mt de esta región en los peces analizados, encontrándose una divergencia genética extraordinaria (38-75% distancia Tamura & Nei- L ) entre las lisas de ambos océanos, incluyendo a Japón. La longitud de la RC fue variable en la lisa (845-930 pb) y presenta elementos estructurales en común con otras RC, incluyendo un segmento central conservado rodeado por dos regiones hipervariables y además bloques de secuencias conservadas más pequeños. No se encontraron secuencias asociadas a la terminación en la RC de la lisa, que se caracterizó por ser rica en AT (~67%) y pobre en GC. Palabras clave : ADN mitocondrial, clonación, divergencia molecular, lisa, región de control 140 Rocha-Olivares, A., et al. INTRODUCTION vares & Vetter, 1999; Rocha-Olivares & Sandoval-Castillo, 2003). The vertebrate mitochondrial (mt) genome shows an ex- treme structural economy with circa 16,000 base pairs (bp) Mugil cephalus Linnaeus 1758, known as striped, grey, or coding for 37 compactly packed genes: two rRNAs, 13 protein black mullet, or “lisa rayada” (Nelson et al., 2004), is a cosmo- open reading frames, and 22 tRNAs (Boore, 1999). Two impor- politan species inhabiting tropical and subtropical regions of the tant structural and functional features of animal mtDNA are world between 42ºN and 42ºS (Gilbert, 1993). The species is of the absence of introns (but see Beagley et al., 1998) and of re- commercial importance in most countries including Mexico combination (but see Smith & Smith, 2002). However, the mole- (v.gr., Ibañez-Aguirre & Gallardo-Cabello, 1996) and the cule does contain a non-coding region of varying size known United States of America (Leber et al., 1996). In part because as the "control region" (CR), "Displacement-loop containing of the economic relevance, but also because its morphologi- region", or just "D-loop" (Brown et al., 1986). This non-coding cal conservatism and challenging systematics, this species segment contains conserved motifs, the origin of heavy- has motivated several genetic studies that have brought to strand replication, and both heavy- and light-strand transcrip- light unsuspected levels of genetic differentiation using bio- tion initiation sites (Clayton, 1991). In vertebrates, this region chemical markers and mitochondrial DNA (Tsvetnenko, 1991; is flanked by the genes coding for tRNA-threonine (tRNA-T), Crosetti et al., 1993; Crosetti et al., 1994; Rossi et al., 1998; tRNA-proline (tRNA-P) at the 5' end of the light strand and for Rocha-Olivares et al., 2000; Garber et al., 2001; see also Miya the tRNA-phenylalanine (tRNA-F) at the 3' end (Meyer, 1993). et al., 2001 for the complete mitochondrial genome). Here, we During the evolution of mitochondria from hypothesized ␣- report the sequence and structure of the complete CR and proteobacteria several genes were completely translocated flanking tRNA genes of M. cephalus from the Pacific (Hawaii to the eukaryotic nucleus (Gray et al., 1999). Data are accu- and Japan) and the Atlantic (Gulf of Mexico and Northwest mulating showing mitochondrial duplications (known as nu- Atlantic) Oceans to establish base line levels of geographic clear mitochondrial or numt DNA) that have also been copied variation in the structure of this important region of the mito- to the nucleus in several taxa, with the potential confounding chondrial genome in the context of vertebrate control region and misleading effects on the interpretation of the data if they evolution. go unrecognized as pseudogenes (Richly & Leister, 2004). The rapid evolution of mitochondrial protein coding genes compared to nuclear genes has long been established MATERIALS AND METHODS (Brown et al., 1979) and within the mtDNA, the CR has been Mugil cephalus were collected from the Atlantic coast estimated to evolve 2-5 times faster than protein coding (North Carolina) and the Gulf of Mexico (Florida, Mississippi, genes (Meyer, 1993). Due to its elevated evolutionary rate, the Louisiana, and Texas) (n = 96) and from the Pacific Ocean CR has been the marker of choice to address a variety of (Island of Oahu, Hawaii) (n = 19), as reported in Rocha- intra-specific genetic questions in a wide range of taxa (v.gr., Olivares et al. (2000). Total genomic DNA was isolated by phe- Taberlet, 1996). Comparative studies of the animal CR have nol-chloroform extraction from white muscle tissue and revealed a structure consisting of a central conserved region quantified using fluorescence spectrophotometry (Sambrook flanked by two hypervariable sections; as well as the exis- & Russell, 2001). tence of conserved sequence blocks (CSB, < 30 bp), which may be found near the heavy strand origin of replication A segment containing the 3’ end of the cytochrome b (Walberg & Clayton, 1981) but also several hundred gene, tRNA-T, tRNA-P, control region, tRNA-F, and the 5’ end nucleotides downstream from it (Doda et al., 1981). The latter of the 12S rRNA was amplified by PCR using universal primers have not been documented in the species of fish examined to CB3 (Palumbi, 1996) and 12SAR (Martin et al., 1992) in repli- date, although some CSBs are conserved from fish to mam- cate 25 µl reactions (100 ng template DNA, 1.5 mM MgCl2, 200 mals (v. gr., Lee et al., 1995; Liu et al., 2002). Other structural µM dNTPs, 0.3 µM of each primer, 1.75 units of Taq DNA poly- features of the piscine CR are the termination associated merase, 1X PCR buffer Amersham Life Science). Cycling sequences (TAS) (Liu et al., 2002). The 5' hypervariable region parameters were 3 min at 94ºC, followed by 35 cycles of 45 of the CR adjacent to tRNA-P is characterized by high levels sec at 94ºC, 1 min at 55ºC, and 2 min at 72ºC, with a final elon- of nucleotide substitution and, due in part to historical cir- gation of 7 min at 72ºC. After visualization on a 1% agarose cumstances (since universal primers were first designed for gel, the appropriate PCR product was excised, purified using it, Kocher et al., 1989), it has been the most widely used in fish the QIAquick Gel Extraction Kit (QIAGEN, Inc.), quantified, and micro- and macroevolutionary genetic research (e.g. Rocha- direct sequenced. Species specific primers (MulPro and Olivares et al., 1999a; Rocha-Olivares et al., 1999b; Rocha-Oli- Mul12S) were designed from this product (Fig. 1). Hidrobiológica Mitochondrial control region of Mugil cephalus 141 Figure 1. Map of the mtDNA control region and adjacent genes constructed from mullet mitochondrial genome (Genebank NC003182) indicating the position and sequence of the primers used in this study relative to the first base of the cytochrome b gene. The 3’ end of RNA genes and primers is indicated by arrows, tRNA genes are named after IUPAC single letter amino acid codes. PCR products obtained with species-specific primers DNA sequences were aligned using CLUSTAL-W with were purified and cloned using the pGEM®-T Easy Vector the default settings and verified by eye.
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