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Mol Biol Rep (2008) 35:239249 DOI 10.1007/s11033-007-9076-4
Group I introns and gnra tetraloops: remnants of The RNA world?
J. Prathiba R. Malathi
Received: 10 January 2007 / Accepted: 26 February 2007 / Published online: 17 April 2007 Springer Science+Business Media B.V. 2007
Abstract GNRA tetraloops, found in high frequency in natural RNAs, make loop-receptor interactions, stabilizing the tertiary structure of Group I introns, a class of small RNAs. Analyzing 230 Group I introns, to study the distribution and sequence pattern of the GNRA tetraloops, we suggest that these features reect the ancestral nature of these catalytic molecules, in a prebiotic RNA world. The adeno-sine rich GNRA tetraloops would have interacted with each other through long range RNARNA interactions to form higher order structures forming potential sites that render the propensity for the short RNAs to bind to metal ions from the prebiotic pool, aiding them to act as metalloenzymes.
Keywords RNA world GNRA tetraloops Group I
intron Metalloenzymes
Introduction
RNA is a versatile molecule capable of self-folding and can bring about long-range and short-range interactions. The existence of a self-replicating RNA entity was suspected to have formed a part of a RNA world and led to the proposal of existence of an RNA world about around 4.2 billion years ago (Joyce 1991). The breakthrough discovery of catalytic RNAs, the autocatalytic group I introns in the ciliated protozoan Tetrahymena thermophila by Prof. Thomas Cech and the catalytic role of RNA in RNase P RNAs in E. coli (Kruger et al. 1982; Guerrier Takada et al. 1983) added further credence to this concept.
Self-splicing Group I introns have been found to occur in rRNA, tRNA and mRNA genes of diverse group of organisms including Cyanobacteria, Protozoa, lower eukaryotes like fungi and in chloroplasts of plants. The mechanism of self-splicing of these Group I introns is also conserved and occurs through a two-step transesterication reaction in the presence of a divalent metal ion (preferably Mg2+): (1) Cleavage of 5 splice site and addition of a guanosine substrate to the intron. (2) Cleavage of 3-splice site and ligation of the exons. An external guanosine attacks the phosphorous atom at the 5 splice site and forms a 3, 5-phosphodiester bond to the rst nucleotide of the intron. The 5 exon,...