Specificity of chloroplast-localized peptide deformylases as determined with peptide analogs of chloroplast-translated proteins

Peptide deformylase (DEF; EC 3.5.1.88) removes the N-formyl group from nascent polypeptides. Two nuclear-encoded DEFs in Arabidopsis thaliana (At) are localized to chloroplasts, and thus, the N-termini of chloroplast-translated proteins may be a consequence of AtDEFs’ substrate specificity. Using peptide analogs of select chloroplast-translated proteins, AtDEF1 activity was as much as 100-fold lower than AtDEF2 activity and showed little variance with peptide sequence. However, AtDEF2 activity was significantly influenced by peptide sequence, with the most efficiently processed substrate mimicking the N-terminus of the nascent D1 polypeptide, a core protein of photosystem II. Though AtDEF2’s specificity was predictive of N-formyl retention for some chloroplast proteins, exceptions suggests that additional factors in vivo aid in determining the retention of an N-formyl group.