Co-expression and regulation of photorespiratory genes in Arabidopsis thaliana: A bioinformatic approach

Abstract

Being a pathway tightly linked to photosynthesis, photorespiration is regulated by light, but also by both nutrients and metabolites on transcriptional level. However, only little is known about the signals and how they are integrated on promoter level to coordinate the whole pathway. Using a bioinformatic approach we analyzed the co-expression patterns of photorespiratory genes, the predicted cis-regulatory elements in their 5′ upstream regions and the existence of introns in their 5′UTRs. We found that there are groups of photorespiratory genes that are strongly co-expressed among each other. The analysis showed a high co-expression between photorespiration and ammonia re-fixation. However, a strong co-regulation between two genes, like GDCH1 and GDCH2, did not necessarily mean that these genes share common cis-element in their 5′ upstream regions. TATA-box, MYB1AT, and MYB4 binding site motifs occurred in 16 out of 20 genes. Furthermore, photorespiratory genes are subjected to alternative splicing. We discuss the presence of cis-elements in the context of both stress responses and development. A genome wide analysis of Arabidopsis 5′UTRs revealed that 5′UTRs introns are overrepresented in photorespiratory genes. Promoter:gusA studies indicated that photorespiratory gene expression is also regulated by intron-mediated enhancement (IME). As already shown for glutamate: glyoxylate aminotransferase, transcript abundance of serine: glyoxylate aminotransferase was affected by IME on mRNA level. IME of gene expression of glycolate oxidase was shown to act on translational level. Keywords: Photorespiration, Co-expression, Gene regulation, Promoter, cis-Regulatory elements, Intron-mediated enhancement