Distinctive origins of group I introns found in the COXI genes of three green algae

• Published in: Gene Vol. 213; no. 1; pp. 1 - 7
• Main Authors: Watanabe, Kazuo I, Ehara, Megumi, Inagaki, Yuji, Ohama, Takeshi
• Format: Journal Article
• Language: English
• Published: Elsevier B.V 15.06.1998
• Subjects: Chlorella vulgaris; Cytochrome c oxidase subunit I; Frameshift; Group I intron; Intron homing; Protosiphon botryoides; Scenedesmus quadricauda; aa, amino acid(s); Pb, Protosiphon botryoides; Chlorella vulgaris; ORF, open reading frame; Protosiphon botryoides; bp, base pair(s); rRNA, ribosomal RNA; Cytochrome c oxidase subunit I; Sq, Scenedesmus quadricauda; Cv, Chlorella vulgaris; LSU, large subunit; Frameshift; nc, nuclear; cp, chloroplast(s); nt, nucleotide(s); SSU, small-subunit; mt, mitochondria(l); Intron homing; PCR, polymerase chain reaction; COXI, cytochrome c oxidase subunit I; Group I intron; Pw, Prototheca wickerhamii; Scenedesmus quadricauda
• ISSN: 0378-1119; 1879-0038
• DOI: 10.1016/S0378-1119(98)00235-2

Upon surveying the cytochrome c oxidase subunit I (COXI) gene of green algae, we found group I introns in three species of algae, Chlorella vulgaris ( Cv), Scenedesmus quadricauda ( Sq) and Protosiphon botryoides ( Pb). The comparative analysis of these nucleotide sequences and their secondary structures revealed that the introns of Cv, Sq, and Pb belong to groups IB1, ID, and IB2, respectively. Each of the three introns contained an open reading frame (ORF) that showed a similarity to the sequence of the LAGLIDADG endonuclease family. However, each of the intronic ORFs in Sq and Pb had a discontinuity in the middle of the sequences coding for the LAGLIDADG endonuclease. Either of the two ORFs could be restored to a sequence homologous to the LAGLIDADG endonuclease by the insertion of a nucleotide in the appropriate position. In Sq, a putative pseudo-knot structure was detected in the intronic ORF. This suggests the occurrence of a ribosomal frameshift in the translation of the ORF, because such pseudo-knot structures are common in viral ORFs employing a (−1) ribosomal frameshift. In the phylogenetic tree that was inferred from the amino acid sequences of algal and non-algal intronic ORFs, the three algal ORFs did not make a cluster, but were scattered throughout the tree. In addition, each of the three algal ORFs showed a close relationship to the ORFs of non-algal introns that were inserted at the corresponding site of the COXI gene, suggesting distinctive origins of the three algal introns via independent horizontal transfers.