20. Correlation between mRNA Structure of the Coding Region and Translational Pauses: Spider Silk Fibroin Spidroin 2

Mitsuo Zama

Keywords: mRNA structure, translational pauses, spider silk fibroin

Transient accumulations of discrete size nascent polypeptide chains during translational elongation have been observed for some proteins. This is due to pauses or discontinuities in the translational process, which may occur at specific sites in mRNA templates. In a series of studies for such proteins, silkworm fibroin, type I collagen, colicin A, chloroplast photosystem II reaction center protein D1 and globin, we have so far presented evidence to support the view that the pauses may be attributable to the mRNA secndary structure of the protein-coding region.

Discontinuous translational elongation of polypeptides is observed during spider dragline silk fibroin synthesis. The spider major ampullate (dragline) silk of Nephila clavipes consists of the two subunit proteins, Spidroin 1 and Spidroin 2. In the present study, we tried to analyze Spidroin 2, which exhibits an entirely different repetitive amino acid sequence motif than Spidroin 1, to examine the possible correlation between mRNA structure and translational pauses for this protein.

The repeating segment of Spidroin 2 consists of alternate alanine-rich and proline-rich regions. It was found that the calculated free energy of the secondary structure of Spidroin 2 mRNA per nucleotide for the alanine-rich region is about the same as that for the successive proline-rich region. The small stability changes of local mRNA secondary structures along the mRNA chain suggest that the translational pauses observed for dragline silk fibroin synthesis may not be correlated with Spidroin 2 mRNA structure, in contrast to Spidroin 1 mRNA structure which may explain the translational pauses as has been suggested in our preceding study.