The Complete Nucleotide Sequence, Gene Organization, and Genetic Code of the Mitochondrial Genome of Paracentrotus lividus

P Cantatore,M Roberti,G Rainaldi,M N Gadaleta,C Saccone

doi:10.1016/s0021-9258(18)60413-2

P Cantatore, M Roberti + Show 3 more

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https://doi.org/10.1016/s0021-9258(18)60413-2

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Abstract

The 15,697-nucleotide sequence of Paracentrotus lividus mitochondrial DNA is reported. This genome codes for 2 rRNAs, 22 tRNAs, and 12 mRNAs which specify 13 subunits of the mitochondrial inner membrane respiratory complexes. The gene arrangement differs from that of other animal species. The two ribosomal genes 16 S and 12 S are separated by a stretch of about 3.3 kilobase pairs which contains the ND1 and ND2 genes and a cluster of 15 tRNA genes. The ND4L coding sequence is not contained in the ND4 mRNA but has its own mRNA which maps between the tRNA(Arg) and the Co II genes. The main noncoding region, located in the tRNA gene cluster, is only 132 nucleotides long, but contains sequences homologous to the mammalian displacement loop. Other short noncoding sequences are interspersed in the genome: they contain a conserved AT consensus which probably has a role in transcription or RNA processing. As regards the mitochondrial genetic code, the codons AGA and AGG specify serine and are recognized by a tRNA with a GCU anticodon, whereas AUA and AAA code for isoleucine and asparagine rather than for methionine and lysine. Except for ND4L which starts with AUC and ATPase 8 which starts with GUG, AUG is used as the initiation codon. In 11 out of 13 cases the genes terminate with the canonical stop codons UAA or UAG. These observations suggest that during invertebrate evolution each lineage developed its own mechanism of mitochondrial DNA replication and transcription and of RNA processing and translation.

Highlights

The15,697-nucleotide sequence of Paracentrotus lividus mitochondrial DNA is reported
Vertebrate mgtene organization is a model of economy and compactness: few or no nucleotides separate individual genes, and the tRNA genes areinterspersed with almost absolute regularity between mRNA and rRNA coding sequences
Because most previously reported (Cantatore et al, 1987a) that thecodons of the genes have about the same size as in vertebrate mtDNA, AGA and AGG are notused as stopcodons but specify serine. the smaller size of P. lividus mtDNA can be accounted for Further analysis has shown that the codons AUA mostly by a reduction in size of the noncoding region

Summary

RESULTS

Genome Organization and Genetic Code-Fig. 2 reports the tRNAA'",tRNACYa"nd tRNA"", CoIII, and tRNASerUCNe,n15,697-nucleotidesequence of the P. lividus mtDNA. The The analysis of the codon usage of P. lividus mt protein largest noncoding sequence is 132-nt long and it is placed genes (Fig. 4) has revealed an unusual genetic code. The first AUG codon is separated from the 3' end of the tRNAArg by nt Were this the start codon it would make the sea urchin ND4L gene about 10% smaller than that of mammals, erasing a regionwhich retainsa highdegree of homology (64%)with its human counterpart (Cantatore et al, 1987a).This suggeststhat thegene really starts with AUC. The GUG codon has been reported to occur as the first in frame triplet both in prokaryotic genes (Storm0 et al, 1982) and in a number of mitochondrial genes such as the ND5 gene of D

5LbO szso

Paracentrotus lividus Mitochondrial Genome

CAC Clu GM

COI nucleotides