SummaryPublicly available microarray experiments were used to analyze Arabidopsis thaliana genes whose expression is correlated with that of nuclear genes encoding components of the oxidative phosphorylation machinery (OxPhos genes). This analysis indicated the existence of coordination in the expression of genes encoding components of the five respiratory complexes. For these genes, preferential expression was observed in anthers and roots, especially in the elongation zone, while reduced or very low relative expression was evident in leaves and mature pollen grains. A global induction of OxPhos genes by carbohydrates, photo-destruction of chloroplasts, inhibition of cellulose synthesis, release from dormancy and germination, among other conditions, was also observed. Cluster analysis of the response of Arabidopsis genes to a set of 15 treatments allowed the identification of DNA motifs, known as site II, that are frequently present in the upstream regions of genes with responses like those of OxPhos genes. Mutagenic analysis of site II motifs in several genes encoding respiratory chain components showed that they actively participate in transcription of these genes. We conclude that an important number of nuclear genes encoding components of the five respiratory complexes show coordinated expression under various circumstances, and that site II elements and the putative proteins that interact with them are, together with as yet unidentified factors, important actors in this coordinated response.

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The exon junction complex (EJC) is deposited on mRNA after splicing and participates in several aspects of RNA metabolism, from intracellular transport to translation. In this work, the functional and molecular interactions of Arabidopsis homologues of Mago, Y14, and PYM, three EJC components that participate in intron-mediated enhancement of gene expression in animals, have been analysed. AtMago, AtY14, and AtPYM are encoded by single genes that show similar expression patterns and contain common regulatory elements, known as site II, that are required for expression. AtPYM and AtY14 are phosphorylated by plant extracts and this modification regulates complex formation between both proteins. In addition, overexpression of AtMago and AtY14 in plants produces an increase in AtPYM protein levels, while overexpression of AtPYM results in increased formation of a complex that contains the three proteins. The effect of AtMago and AtY14 on AtPYM expression is most likely to be due to intron-mediated enhacement of AtPYM expression, since the AtPYM gene contains a leader intron that is required for expression. Indeed, transient transformation asssays indicated that the three proteins are able to increase expression from reporter constructs that contain leader introns required for the expression of different genes. The results indicate that the plant homologues of Mago, Y14, and PYM are closely interconnected, not only through their function as EJC components but also at different steps of their own gene expression mechanisms, probably reflecting the importance of their interaction for the correct expression of plant genes.

The promoters of the three Arabidopsis nuclear genes encoding mitochondrial cytochrome c oxidase subunit 6b (AtCOX6b) have similar expression patterns, with preferential expression in anthers and meristems, and are induced by sucrose and etiolation. Additionally, induction of AtCOX6b-1 by GA(3) and AtCOX6b-3 by 6-benzylaminopurine was observed. Site II elements (TGGGCC/T) present in the three promoters bind common nuclear proteins and are important for basal and induced expression. Induction by sucrose requires, in addition, the integrity of elements with the sequence TACTAA. The results imply the participation of common regulatory factors in the expression of the three Arabidopsis COX6b genes.

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