A chloroplast-localized vesicular transport system: a bio-informatics approach

Abstract

Background: The thylakoid membrane of higher plant chloroplasts is made of membrane lipids synthesized in the chloroplast envelope. As the inner envelope membrane and the thylakoid are separated by the aqueous stroma, a system for transporting newly synthesized lipids from the inner envelope membrane to the thylakoid is required. Ultrastructural as well as biochemical studies have indicated that lipid transport inside the chloroplast could be mediated by a system similar in characteristics to vesicular trafficking in the cytosol. If indeed the chloroplast system is related to cytosolic vesicular trafficking systems, a certain degree of sequence conservation between components of the chloroplast and the cytosolic systems could be expected. We used the Arabidopsis thaliana genome and web-based subcellular localization prediction tools to search for chloroplast-localized homologues of cytosolic vesicular trafficking components.

Results: Out of the 28952 hypothetical proteins in the A. thaliana genome sequence, 1947 were predicted to be chloroplast-localized by two different subcellular localization predictors. In this chloroplast protein dataset, strong homologues for the main coat proteins of COPII coated cytosolic vesicles were found. Homologues of the small GTPases ARF1 and Sar1 were also found in the chloroplast protein dataset.

Conclusion: Our database search approach gives further support to that a system similar to cytosolic vesicular trafficking is operational inside the chloroplast. However, solid biochemical data is needed to support the chloroplast localization of the identified proteins as well as their involvement in intra-chloroplast lipid trafficking.

Figure 1

Multiple alignment of the yeast Sec23, the best match in the whole A. thaliana proteome At4g14160.2 and the best match in the predicted chloroplast proteome At4g01810.1. Identical residues are shown in black and conserved residues are shown in gray.

Figure 2

Multiple alignment of the yeast Sec24, the best match in the whole A. thaliana proteome At3g07100.1 and the two best matches in the predicted chloroplast proteome At3g44340.1 and At4g32640.1. Identical residues are shown in black and conserved residues are shown in gray.

Figure 3

Multiple alignment of the yeast Sar1, the best match in the whole A. thaliana proteome At1g56330.1 and the best match in the predicted chloroplast proteome At5g18570.1. Identical residues are shown in black and conserved residues are shown in gray.

Figure 4

Multiple alignment of the yeast Arf1, the best match in the whole A. thaliana proteome At3g62290.1 and the best match in the predicted chloroplast proteome At1g05810.1. Identical residues are shown in black and conserved residues are shown in gray.