Unusual characteristics of amino-terminal and hydrophobic domains in nuclear-encoded thylakoid signal peptides

Eur J Biochem. 1997 Apr 15;245(2):340-8. doi: 10.1111/j.1432-1033.1997.00340.x.


Thylakoid transfer signals carry information specifying translocation by either a Sec- or delta pH-dependent protein translocator in the chloroplast thylakoid membrane, yet all resemble classical signal peptides in overall structural terms. Comparison of known transfer signals reveals two differences: (a) signals for the delta pH-driven system invariably contain a critical twin-arginine (Arg-Arg) motif prior to the hydrophobic (H) domain, whereas known Sec-dependent signals contain lysine, and (b) the H-domains of Sec-dependent signals are generally longer. Previous work has shown that a twin-Arg motif before the H-domain is critical for targeting by the delta pH-dependent pathway; in this report we show that the charge characteristics of this region are not important for sorting by the Sec pathway. Twin-Lys, twin-Arg or single Arg are all acceptable to the Sec system, although single Lys/Arg is preferred. The single Lys in pre-plastocyanin can even be replaced by an uncharged residue without apparent effect. We have also generated a pre-plastocyanin mutant containing an H-domain which, in terms of hydropathy profile, is identical to that of a delta pH-dependent protein. This mutant is also transported efficiently by the Sec system, demonstrating that hydrophobicity per se is not a key sorting determinant. However, the characteristics of the H-domain may be important in avoiding a different form of mis-targeting: to the endoplasmic reticulum. Thylakoid signal peptides have undergone substantial structural changes during the evolution of the chloroplast from endosymbiotic cyanobacterium: plastid-encoded and cyanobacterial signals contain H-domains that are highly hydrophobic and enriched in Leu and aromatic residues, whereas nuclear-encoded counterparts are Ala-rich and far less hydrophobic. We speculate that this trend may reflect a need to avoid mistargeting through recognition by cytosolic signal recognition particle, which preferentially interacts with more hydrophobic signal peptides.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Bacterial Proteins / chemistry*
  • Biological Transport, Active
  • Cell Nucleus / metabolism
  • Chlorophyta / chemistry
  • Chloroplasts / chemistry
  • Cyanobacteria / chemistry
  • Hydrogen Bonding
  • Molecular Sequence Data
  • Peptide Mapping
  • Plant Proteins / chemistry*
  • Plastids / chemistry
  • Plastocyanin / chemistry
  • Protein Sorting Signals / chemistry*
  • Structure-Activity Relationship


  • Bacterial Proteins
  • Plant Proteins
  • Protein Sorting Signals
  • Plastocyanin