Evolution and Design Principles of the Diverse Chloroplast Transit Peptides

  • Lee, Dong Wook (Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology) ;
  • Hwang, Inhwan (Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology)
  • Received : 2018.01.19
  • Accepted : 2018.02.06
  • Published : 2018.03.31


Chloroplasts are present in organisms belonging to the kingdom Plantae. These organelles are thought to have originated from photosynthetic cyanobacteria through endosymbiosis. During endosymbiosis, most cyanobacterial genes were transferred to the host nucleus. Therefore, most chloroplast proteins became encoded in the nuclear genome and must return to the chloroplast after translation. The N-terminal cleavable transit peptide (TP) is necessary and sufficient for the import of nucleus-encoded interior chloroplast proteins. Over the past decade, extensive research on the TP has revealed many important characteristic features of TPs. These studies have also shed light on the question of how the many diverse TPs could have evolved to target specific proteins to the chloroplast. In this review, we summarize the characteristic features of TPs. We also highlight recent advances in our understanding of TP evolution and provide future perspectives about this important research area.


Grant : Cooperative Research Program for Agriculture Science and Technology Development

Supported by : Rural Development Administration, National Research Foundation


  1. Abe, Y., Shodai, T., Muto, T., Mihara, K., Torii, H., Nishikawa, S., Endo, T., and Kohda, D. (2000). Structural basis of presequence recognition by the mitochondrial protein import receptor Tom20. Cell 100, 551-560.
  2. Bhushan, S., Kuhn, C., Berglund, A.K., Roth, C., and Glaser, E. (2006). The role of the N-terminal domain of chloroplast targeting peptides in organellar protein import and miss-sorting. FEBS Lett. 580, 3966-3972.
  3. Bruce, B.D. (2000). Chloroplast transit peptides: structure, function and evolution. Trends Cell Biol. 10, 440-447.
  4. Chotewutmontri, P., and Bruce, B.D. (2015). Non-native, N-terminal Hsp70 molecular motor recognition elements in transit peptides support plastid protein translocation. J. Biol. Chem. 290, 7602-7621.
  5. Chotewutmontri, P., Reddick, L.E., McWilliams, D.R., Campbell, I.M., and Bruce, B.D. (2012). Differential transit peptide recognition during preprotein binding and translocation into flowering plant plastids. Plant Cell 24, 3040-3059.
  6. Chotewutmontri, P., Holbrook, K., and Bruce, B.D. (2017). Plastid Protein Targeting: Preprotein Recognition and Translocation. Int. Rev. Cell Mol. Biol. 330, 227-294.
  7. Constan, D., Patel, R., Keegstra, K., and Jarvis, P. (2004). An outer envelope membrane component of the plastid protein import apparatus plays an essential role in Arabidopsis. Plant J. 38, 93-106.
  8. de Vries, J., Sousa, F.L., Bolter, B., Soll, J., and Gould, S.B. (2015). YCF1: A Green TIC? Plant Cell 27, 1827-1833.
  9. Dempsey, D.A., Vlot, A.C., Wildermuth, M.C., and Klessig, D.F. (2011). Salicylic Acid biosynthesis and metabolism. Arabidopsis Book 9, e0156.
  10. Facchinelli, F., and Weber, A.P. (2011). The metabolite transporters of the plastid envelope: an update. Front. Plant Sci. 2, 50.
  11. Garg, S.G., and Gould, S.B. (2016). The role of charge in protein targeting evolution. Trends Cell Biol. 26, 894-905.
  12. Gould, S.B., Waller, R.F., and McFadden, G.I. (2008). Plastid evolution. Annu. Rev. Plant Biol. 59, 491-517.
  13. Holbrook, K., Subramanian, C., Chotewutmontri, P., Reddick, L.E., Wright, S., Zhang, H., Moncrief, L., and Bruce, B.D. (2016). Functional analysis of semi-conserved transit peptide motifs and mechanistic implications in precursor targeting and recognition. Mol. Plant 9, 1286-1301.
  14. Inoue, H., Li, M., and Schnell, D.J. (2013). An essential role for chloroplast heat shock protein 90 (Hsp90C) in protein import into chloroplasts. Pro. Natl. Acad. Sci. USA 110, 3173-3178.
  15. Ivanova, Y., Smith, M.D., Chen, K., and Schnell, D.J. (2004). Members of the Toc159 import receptor family represent distinct pathways for protein targeting to plastids. Mol. Biol. Cell 15, 3379- 3392.
  16. Jarvis, P. (2008). Targeting of nucleus-encoded proteins to chloroplasts in plants. New Phytol. 179, 257-285.
  17. Kikuchi, S., Oishi, M., Hirabayashi, Y., Lee, D.W., Hwang, I., and Nakai, M. (2009). A 1-megadalton translocation complex containing Tic20 and Tic21 mediates chloroplast protein import at the inner envelope membrane. Plant Cell 21, 1781-1797.
  18. Kikuchi, S., Bedard, J., Hirano, M., Hirabayashi, Y., Oishi, M., Imai, M., Takase, M., Ide, T., and Nakai, M. (2013). Uncovering the protein translocon at the chloroplast inner envelope membrane. Science 339, 571-574.
  19. Kim, C., Lee, K.P., Baruah, A., Nater, M., Gobel, C., Feussner, I., and Apel, K. (2009). (1)O2-mediated retrograde signaling during late embryogenesis predetermines plastid differentiation in seedlings by recruiting abscisic acid. Proc. Natl. Acad. Sci. USA 106, 9920-9924.
  20. Kobayashi, K., and Wada, H. (2016). Role of lipids in chloroplast biogenesis. Subcell Biochem. 86, 103-125.
  21. Kubis, S., Patel, R., Combe, J., Bedard, J., Kovacheva, S., Lilley, K., Biehl, A., Leister, D., Rios, G., Koncz, C., et al. (2004). Functional specialization amongst the Arabidopsis Toc159 family of chloroplast protein import receptors. Plant Cell 16, 2059-2077.
  22. Lee, D.W., Lee, S., Lee, G.J., Lee, K.H., Kim, S., Cheong, G.W., and Hwang, I. (2006). Functional characterization of sequence motifs in the transit peptide of Arabidopsis small subunit of rubisco. Plant Physiol. 140, 466-483.
  23. Lee, D.W., Kim, J.K., Lee, S., Choi, S., Kim, S., and Hwang, I. (2008). Arabidopsis nuclear-encoded plastid transit peptides contain multiple sequence subgroups with distinctive chloroplast-targeting sequence motifs. Plant Cell 20, 1603-1622.
  24. Lee, D.W., Lee, S., Oh, Y.J., and Hwang, I. (2009a). Multiple sequence motifs in the Rubisco small subunit transit peptide independently contribute to Toc159-dependent import of proteins into chloroplasts. Plant Physiol. 151, 129-141.
  25. Lee, S., Lee, D.W., Lee, Y., Mayer, U., Stierhof, Y.D., Lee, S., Jurgens, G., and Hwang, I. (2009b). Heat shock protein cognate 70-4 and an E3 ubiquitin ligase, CHIP, mediate plastid-destined precursor degradation through the ubiquitin-26S proteasome system in Arabidopsis. Plant Cell 21, 3984-4001.
  26. Lee, S., Lee, D.W., Yoo, Y.J., Duncan, O., Oh, Y.J., Lee, Y.J., Lee, G., Whelan, J., and Hwang, I. (2012). Mitochondrial targeting of the Arabidopsis F1-ATPase gamma-subunit via multiple compensatory and synergistic presequence motifs. Plant Cell 24, 5037-5057.
  27. Lee, D.W., Jung, C., and Hwang, I. (2013). Cytosolic events involved in chloroplast protein targeting. Biochim. Biophys. Acta 1833, 245-252.
  28. Lee, D.W., Woo, S., Geem, K.R., and Hwang, I. (2015). Sequence motifs in transit peptides act as independent functional units and can be transferred to new sequence contexts. Plant Physiol 169, 471-484.
  29. Lee, D.W., Kim, S.J., Oh, Y.J., Choi, B., Lee, J., and Hwang, I. (2016). Arabidopsis BAG1 functions as a cofactor in Hsc70-mediated proteasomal degradation of unimported plastid proteins. Mol. Plant 9, 1428-1431.
  30. Lee, D.W., Lee, J., and Hwang, I. (2017). Sorting of nuclear-encoded chloroplast membrane proteins. Curr. Opin. Plant Biol. 40, 1-7.
  31. Lee, D.W., Yoo, Y.J., Razzak, M.A., and Hwang, I. (2018). Prolines in transit peptides Are crucial for efficient preprotein translocation into chloroplasts. Plant Physiol. 176, 663-677.
  32. Leister, D. (2003). Chloroplast research in the genomic age. Trends Genet. 19, 47-56.
  33. Li, H.M., and Chiu, C.C. (2010). Protein Transport into Chloroplasts. Ann. Rev. Plant Biol. 61, 157-180.
  34. Li, H.M., and Teng, Y.S. (2013). Transit peptide design and plastid import regulation. Trends Plant Sci. 18, 360-366.
  35. Liu, L., McNeilage, R.T., Shi, L.X., and Theg, S.M. (2014). ATP Requirement for Chloroplast Protein Import Is Set by the K-m for ATP Hydrolysis of Stromal Hsp70 in Physcomitrella patens. Plant Cell 26, 1246-1255.
  36. May, T., and Soll, J. (2000). 14-3-3 proteins form a guidance complex with chloroplast precursor proteins in plants. Plant Cell 12, 53-64.
  37. McFadden, G.I. (2014). Origin and evolution of plastids and photosynthesis in eukaryotes. Cold Spring Harb. Perspect Biol. 6, a016105.
  38. Nakai, M. (2015). YCF1: A green TIC: response to the de Vries et al. Commentary. Plant Cell 27, 1834-1838.
  39. Nouet, C., Motte, P., and Hanikenne, M. (2011). Chloroplastic and mitochondrial metal homeostasis. Trends Plant Sci. 16, 395-404.
  40. Okawa, K., Inoue, H., Adachi, F., Nakayama, K., Ito-Inaba, Y., Schnell, D.J., Uehara, S., and Inaba, T. (2014). Targeting of a polytopic membrane protein to the inner envelope membrane of chloroplasts in vivo involves multiple transmembrane segments. J. Exp. Bot. 65, 5257-5265.
  41. Paila, Y.D., Richardson, L.G.L., and Schnell, D.J. (2015). New insights into the mechanism of chloroplast protein import and its integration with protein quality control, organelle biogenesis and development. J. Mol. Biol. 427, 1038-1060.
  42. Paila, Y.D., Richardson, L.G., Inoue, H., Parks, E.S., McMahon, J., Inoue, K., and Schnell, D.J. (2016). Multi-functional roles for the polypeptide transport associated domains of Toc75 in chloroplast protein import. Elife 5, pii: e12631.
  43. Qbadou, S., Becker, T., Mirus, O., Tews, I., Soll, J., and Schleiff, E. (2006). The molecular chaperone Hsp90 delivers precursor proteins to the chloroplast import receptor Toc64. EMBO J. 25, 1836-1847.
  44. Razzak, M.A., Lee, D.W., Yoo, Y.J., and Hwang, I. (2017). Evolution of rubisco complex small subunit transit peptides from algae to plants. Sci. Rep. 7.
  45. Rensink, W.A., Schnell, D.J., and Weisbeek, P.J. (2000). The transit sequence of ferredoxin contains different domains for translocation across the outer and inner membrane of the chloroplast envelope. J. Biol. Chem. 275, 10265-10271.
  46. Richter, S., and Lamppa, G.K. (1999). Stromal processing peptidase binds transit peptides and initiates their ATP-dependent turnover in chloroplasts. J. Cell Biol. 147, 33-43.
  47. Schaller, A., and Stintzi, A. (2009). Enzymes in jasmonate biosynthesis - structure, function, regulation. Phytochem 70, 1532-1538.
  48. Schleiff, E., and Becker, T. (2011). Common ground for protein translocation: access control for mitochondria and chloroplasts. Nat. Rev. Mol. Cell Biol. 12, 48-59.
  49. Shapiguzov, A., Vainonen, J.P., Wrzaczek, M., and Kangasjarvi, J. (2012). ROS-talk - how the apoplast, the chloroplast, and the nucleus get the message through. Front Plant Sci. 3.
  50. Shi, L.X., and Theg, S.M. (2013). The chloroplast protein import system: from algae to trees. Biochim. Biophys. Acta 1833, 314-331.
  51. Su, P.H., and Li, H.M. (2010). Stromal Hsp70 Is Important for Protein Translocation into Pea and Arabidopsis Chloroplasts. Plant Cell 22, 1516-1531.
  52. Teng, Y.S., Chan, P.T., and Li, H.M. (2012) D.ifferential age-dependent import regulation by signal peptides. Plos Biol. 10. e1001416.
  53. Trosch, R., and Jarvis, P. (2011). The stromal processing peptidase of chloroplasts is essential in Arabidopsis, with knockout mutations causing embryo arrest after the 16-cell stage. PLoS One 6, e23039.
  54. Viana, A.A., Li, M., and Schnell, D.J. (2010). Determinants for stoptransfer and post-import pathways for protein targeting to the chloroplast inner envelope membrane. J. Biol. Chem. 285, 12948-12960.
  55. Yagi, Y., and Shiina, T. (2014). Recent advances in the study of chloroplast gene expression and its evolution. Front Plant Sci. 5, 61.
  56. Zimorski, V., Ku, C., Martin, W.F., and Gould, S.B. (2014). Endosymbiotic theory for organelle origins. Curr. Opin. Microbiol. 22, 38-48.
  57. Zybailov, B., Rutschow, H., Friso, G., Rudella, A., Emanuelsson, O., Sun, Q., and van Wijk, K.J. (2008). Sorting signals, N-terminal modifications and abundance of the chloroplast proteome. PLoS One 3, e1994.

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