Translation rate underpins specific targeting of N-terminal transmembrane proteins to mitochondria

Protein biogenesis is a complex process, and complexity is greatly increased in eukaryotic cells through specific targeting of proteins to different organelles. To direct targeting, organellar proteins carry an organelle-specific targeting signal for recognition by organelle-specific import machinery. However, the situation is confusing for transmembrane domain (TMD)-containing signal-anchored (SA) proteins of various organelles because TMDs function as an endoplasmic reticulum (ER) targeting signal. Although ER targeting of SA proteins is well understood, how they are targeted to mitochondria and chloroplasts remains elusive. Here, we investigated how the targeting specificity of SA proteins is determined for specific targeting to mitochondria and chloroplasts. Mitochondrial targeting requires multiple motifs around and within TMDs: a basic residue and an arginine-rich region flanking the N- and C-termini of TMDs, respectively, and an aromatic residue in the C-terminal side of the TMD that specify mitochondrial targeting in an additive manner. These motifs play a role in slowing down the elongation speed during translation, thereby ensuring mitochondrial targeting in a co-translational manner. By contrast, the absence of any of these motifs individually or together causes at varying degrees chloroplast targeting that occurs in a post-translational manner.

Automated summary

Protein biogenesis is a complex process in eukaryotic cells, and the targeting of proteins to different organelles involves organelle-specific import machinery and organelle-specific targeting signals. While the targeting of signal-anchored (SA) proteins to the endoplasmic reticulum (ER) is understood, the mechanisms for targeting SA proteins to mitochondria and chloroplasts are still unclear. This study investigated the targeting specificity of SA proteins for mitochondria and chloroplasts and found that multiple motifs surrounding and within the transmembrane domains (TMDs) play a role in mitochondrial targeting, whereas the absence of these motifs results in chloroplast targeting through a post-translational mechanism.