Unique translation initiation at the second AUG codon determines mitochondrial localization of the phage-type RNA polymerases in the moss Physcomitrella patens

The nuclear genome of the moss Physcomitrella patens contains two genes encoding phage-type RNA polymerases (PpRPOT1 and PpRPOT2). Each of the PpRPOT1 and PpRPOT2 transcripts possesses two in-frame AUG codons at the 5' terminus that could act as a translational initiation site. Observation of transient and stable Physcomitrella transformants expressing the 5' terminus of each PpRPOT cDNA fused with the green fluorescent protein gene suggested that both PpRPOT1 and PpRPOT2 are not translated from the first (upstream) AUG codon in the natural context but translated from the second (downstream) one, and that these enzymes are targeted only to mitochondria, although they are potentially targeted to plastids when translation is forced to start from the first AUG codon. The influence of the 5'-upstream sequence on the translation efficiency of the two AUG codons in PpRPOT1 and PpRPOT2 was quantitatively assessed using a beta-glucuronidase reporter. The results further supported that the second AUG codon is the sole translation initiation site in Physcomitrella cells. An Arabidopsis (Arabidopsis thaliana) RPOT homolog AtRpoT;2 that possesses two initiation AUG codons in its transcripts, as do the RPOTs of P. patens, has been regarded as a dually targeted protein. When the localization of AtRpoT; 2 was tested using green fluorescent protein in a similar way, AtRpoT; 2 was also observed only in mitochondria in many Arabidopsis tissues. These results suggest that, despite the presence of two in-frame AUGs at the 5' termini of RPOTs in Physcomitrella and Arabidopsis, the second AUG is specifically recognized as the initiation site in these organisms, resulting in expression of a protein that is targeted to mitochondria. This finding may change the current framework of thinking about the transcription machinery of plastids in land plants.