The mitochondrial atpA/atp9 co-transcript in wheat and triticale: RNA processing depends on the nuclear genotype

The gene region coding for subunits alpha and 9 of the mitochondrial ATP synthase exhibit an identical DNA sequence in wheat, rye, and the intergeneric hybrid triticale (xTriticosecale Wittmack). However, co-transcripts containing both genes show different sizes depending on the nuclear genotype. To investigate nuclear-mitochondrial interactions leading to this variation, we performed a comparative transcript analysis with various lines carrying defined nuclear and cytoplasmic genotypes. Northern analyses showed that all wheat lines investigated possess a single atpA/atp9 mRNA of 2.6kb, whereas in rye and five independent triticale lines an additional transcript of 2.35kb appeared. Primer-extension and RNase-protection analyses indicate that the co-transcripts of this gene have staggered 5' termini in some lines, whereas the 3' termini seem to be similar in wheat, rye, and triticale. Transcription is initiated at position -338/-339 upstream of the atpA gene in all lines investigated, giving rise to a 2.6-kb mRNA. In rye and triticale, staggered 5' termini were observed closer to the translational start. The DNA sequences upstream of these termini exhibit homology to plant mitochondrial-processing sites, therefore the proximal 5' ends are most probably generated by RNA processing. As the processing event occurs more frequently in triticale carrying the Triticum timopheevi cytoplasm, trans-acting factors from rye are likely to interact with other cytoplasmic factors resulting in the observed RNA modification. Most interestingly, the T. timopheevi cytoplasm inducing male sterility in alloplasmic wheat, fails to generate the CMS phenotype in triticale. The data support our hypothesis that nuclear factors affect mitochondrial gene expression and thus control sexual fertility in wheat and triticale.