Discontinuous translation and mRNA secondary structure.

It has recently been reported that ribosomes pause at specific sites during translation of the chloroplast photosystem II reaction center protein D1(1). We have obtained the stability map of local secondary structure of the mRNA of psbA gene, encoding for D1, by plotting the free energy of the optimal secondary structure of the local segment of the mRNA against the segment position along a base sequence of the mRNA. It was found that the positions of minima or lower free energy in the map coincide with the positions of the pausing sites during synthesis of D1. The result suggests that synthesis pauses of D1 could-be induced by the mRNA secondary structure.