Intron Conservation across the Prokaryote-Eukaryote Boundary: Structure of the Nuclear Gene for Chloroplast Glyceraldehyde-3-phosphate Dehydrogenase from Maize

The nuclear gene encoding chloroplast glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from maize has been cloned and sequenced. The gene is G + C rich in its coding sequences and, in addition, contains a CpG-rich region surrounding the promoter. Further upstream several enhancer-like repetitions have been identified that may control the light- and phytochrome-mediated expression of this gene. The gene is interrupted by three introns. Introns 1 and 2 are located within the sequence encoding the transit peptide, dividing it into three parts, each containing one of the three major homology blocks typical for transit peptides of nucleus-encoded chloroplast proteins. Intron 3 is located at codon 166 (glycine) at the same nucleotide position as intron 1 in the GAPDH gene from the nematode Caenorhabditis elegans, suggesting that this intron was present in the parental GAPDH gene from which these two modern descendants originated. Intron 3 divides the GAPDH protein into its two constituent domains, the NAD-binding and the catalytic domain, immediately after helix α 1 at a position homologous to that of intron 9 in the gene for maize alcohol dehydrogenase, thereby confirming the prediction of Brändén et al. on the basis of gene-protein structure correlations in maize alcohol dehydrogenase for the placement of introns in the GAPDH gene [Brändén, C.-I., Eklund, H., Cambillau, C. & Pryor, A. J. (1984) EMBO J. 3, 1307-1310]. These results suggest that intron 3 is an archetypical relic of early GAPDH and alcohol dehydrogenase evolution, whereas introns 1 and 2 were implicated in the evolution of chloroplast transit peptides.