Strong functional GC pressure in a light-regulated maize gene encoding subunit GAPA of chloroplast glyceraldehyde-3-phosphate dehydrogenase: implications for the evolution of GAPA pseudogenes.

The light-regulated nuclear gene encoding subunit A of chloroplast glyceraldehyde-3-phosphate dehydrogenase (subunit GAPA, gene Gpa1) from maize is extremely G + C rich (67% in codons). The genomic surroundings of this gene have been characterized together with the sequences of two strongly conserved Gpa pseudogenes isolated from a genomic maize library by differential cDNA hybridization. The comparisons show that the high G + C content of the maize gene is maintained independently of the surrounding noncoding sequences, which are G + C poor (42%), and only as long as the gene encodes a functional protein. After nonfunctionalization, Gpa pseudogenes rapidly loose G + C mainly due to enhanced turnover of CpG and CpXpG methylation sites. These results suggest that the maize Gpa1 gene is under strong functional GC pressure, due to constraints (CpG island) probably exerted at the transcriptional level. They also indicate that Gpa pseudogenes are methylated and that methylation was either the cause or the immediate consequence of their nonfunctionalization. It can be concluded further that the progenitor of pseudogenes 1 and 2 was a second functional Gpa gene (Gpa'), which, after duplication, accelerated in evolutionary rate due to relaxation of selective constraints. This is in agreement with the neutral theory of evolution. Comparison of Gpa intron sequences reveals a gradient of divergence: the more 3' the position of an intron the more its sequence has diverged between the three Gpa genes. A speculative model is presented explaining these observations in terms of a homologous recombination of genes with their reverse-transcribed pre-mRNAs.