Plant spliceosomal introns: not only cut and paste

Abstract

Spliceosomal introns in higher eukaryotes are present in a high percentage of protein coding genes and represent a high proportion of transcribed nuclear DNA. In the last fifteen years, a growing mass of data concerning functional roles carried out by such intervening sequences elevated them from a selfish burden carried over by the nucleus to important active regulatory elements. Introns mediate complex gene regulation via alternative splicing; they may act in cis as expression enhancers through IME (intron-mediated enhancement of gene expression) and in trans as negative regulators through the generation of intronic microRNA. Furthermore, some introns also contain promoter sequences for alternative transcripts. Nevertheless, such regulatory roles do not require long conserved sequences, so that introns are relatively free to evolve faster than exons: this feature makes them important tools for evolutionary studies and provides the basis for the development of DNA molecular markers for polymorphisms detection. A survey of introns functions in the plant kingdom is presented.

Fig. (1)

A model illustrating Eukaryotes intron-mediated gene expression versatility. g stays for genes that code for proteins (p). r stays for regulatory elements. The n outside the bracket stays for node which means a DNA locus transcriptionally active. The node is part of a vast gene network, with multiple nodes, that may change anytime during cell life and metabolism. This model should make it appreciable that the presence of introns in Eukaryotes may contribute to the increase of products and regulatory factors without altering the number of the coding genes (four in this example). Eukaryotes versatile expression has been gained in the course of evolution through the occurrence of different events such as the inclusion in protein coding genes of intervening sequences capable of self-splicing (groupI and II introns), exon shuffling, reversal splicing and the entry of the nuclear spliceosome. This latter has contributed to release those sequence constraints present in self-splicing introns. As a consequence, spliceosomal introns increased their sequence variability and may have acquired novel trans-acting regulatory functions. On the opposite, Prokaryotes have maintained their linearity of expression, substantially supported by monocistronic RNAs and few products endowed with simple-circuited regulatory functions.

Fig. (2)

Schematic representation of the two mechanisms by which AFE- containing transcripts are generated (see text).