Figure 1.
Identification of putative chloroplast COPI and CCV transport components in Arabidopsis.
Schematic work flow of the bioinformatics methods used to find putative COPI- and CCV-related transport proteins in chloroplasts. Cytosolic COPI and CCV proteins were retrieved from the literature or Uniprot, and their characteristic domains were identified using Prosite or Pfam. Identified domains were used to search a database of chloroplast-localized proteins, and the localization of proteins found in the chloroplast with relevant domains was further checked using ARAMEMNON, SUBA and Chloroplast 2010. Finally, a list of chloroplast proteins with similarities to known COPI and CCV proteins was compiled.
Table 1.
Putative chloroplast localized CCV triskelion components identified using characteristic domains in searches of the TAIR chloroplast dataset.
Table 2.
Putative chloroplast localized CCV AP1 complex components identified using characteristic domains in searches of the TAIR chloroplast dataset.
Table 3.
Putative chloroplast localized CCV AP2 complex components identified using characteristic domains in searches of the TAIR chloroplast dataset.
Table 4.
Putative chloroplast-localized CCV AP3, AP4 and AP5 complex components identified using characteristic domains in searches of the TAIR chloroplast dataset.
Table 5.
Putative chloroplast localized B-COPI components identified using characteristic domains in searches of the TAIR chloroplast dataset.
Table 6.
Putative chloroplast localized F-COPI components identified using characteristic domains in searches of the TAIR chloroplast dataset.
Figure 2.
A model of putative CCV and COPI components in Arabidopsis chloroplasts.
The figure is based on homologies to components of cytosolic systems (http://www.endocytosis.org/Adaptors/index.html) [130], [131]. Red, no proteins with domains of interest detected in chloroplasts. Yellow, proteins with domains of interest identified in chloroplasts, but known to have other roles than vesicle transport and/or the proteins identified had commonly occurring domains, and thus predicted as different subunits in the chloroplasts, and unknown proteins. Green, proteins with domains of interest found in chloroplasts and previously known to have a vesicle transport role.
Table 7.
Putative chloroplast localized CCV and COPI Coat GTPase components identified using characteristic domains in searches of the TAIR chloroplast dataset.
Table 8.
Overview of putative chloroplast localized proteins in rice (subsp. Japonica) with characteristic domains of CCV and COPI subunit counterparts.
Table 9.
Overview of putative chloroplast-localized proteins with characteristic domains of CCV and COPI subunit counterparts.