Polymorphism in rRNA Operon of the Hyperthermophilic Archaeon Aeropyrum pernix, Implying the Presence of Hot Spots for Intron-insertion
Yoshihiko SAKO*, Norimichi NOMURA, Taeko KOGISHI, and Aritsune UCHIDA
Laboratory of Marine Microbiology, Division of Applied Bioscience, Graduate School of Agriculture, Kyoto University, Kyoto 606-01, Japan
Reflecting the scope of their early paradigm, introns and RNA splicing have been considered as characteristics that distinguish eukaryote from prokaryote (bacteria and archaea). However, studies in the last decade elucidated that prokaryotic genes encoding stable RNAs such as rRNAs and tRNAs are scattered with introns, despite of low frequency. Molecular approaches to prokaryotic introns might provide some valuable implication on the evolution of genome organization and gene expression system.
Our previous work showed a novel aerobic hyperthermophilic archaeon Aeropyrum pernix K1 isolated from a coastal solfataric vent in Japan (1), which can grow optimally at temperatures above 90℃. In the process of the phylogenetic analysis of A. pernix K 1, we obtained a nearly complete nucleotide sequence of the 16S rRNA gene retrieved from the chromosomal DNA by PCR and found an intron of 699nt, designated as Iα. This observation promoted us to conduct an extensive investigation of the rRNA operon in Aeropyrum pernix.
We have cloned and sequenced ca. 10.7-kb locus containing the single rRNA operon (16S-23S) of A. pernix K1. The resulting sequence reveals that two distinct introns are also inserted within the 23S rRNA gene (Iβ, 202nt; Iγ, 575nt). The additional sequence analyses of the single rRNA operon in several isolates of Aeropyrum pernix from various marine hydrothermal sources demonstrate that four distinct genotypes (K1, OH2, TB 1, and TB7) based on the introns present within this region harbor a total of 10 introns. All of them possess the typical or aberrant bulge- helix-bulge structures at intron/exon junctions. Based on the sequence differences observed in the introns, we have assigned these introns into six types (Iα; Iβ; Iγ; Iδ, 62nt; Iε, 122nt; and Iζ, 56nt). Interestingly, Iα and Iδ precisely occupy the same insertion sites in the 16S rRNA genes, although they differ in length and primary structure. As is the case observed between Iγ and Iζ in the 23S rRNA genes. These results lead us to suppose the presence of at least four hot spots (Iα/Iδ, Iβ, Iγ/Iζ, and Iε) for intron-insertion within the rRNA coding region of Aeropyrum, pernix.
1. Sako, Y., Nomura, N., Uchida, A., Ishida,Y., Morii, H., Koga, Y., Hoaki, T., and Maruyama, T.(1996) Int. J. Syst. Bacteriol., 46, 1070-1077.
