Bioinformatic Indications That COPI- and Clathrin-Based Transport Systems Are Not Present in Chloroplasts: An Arabidopsis Model

Abstract

Coated vesicle transport occurs in the cytosol of yeast, mammals and plants. It consists of three different transport systems, the COPI, COPII and clathrin coated vesicles (CCV), all of which participate in the transfer of proteins and lipids between different cytosolic compartments. There are also indications that chloroplasts have a vesicle transport system. Several putative chloroplast-localized proteins, including CPSAR1 and CPRabA5e with similarities to cytosolic COPII transport-related proteins, were detected in previous experimental and bioinformatics studies. These indications raised the hypothesis that a COPI- and/or CCV-related system may be present in chloroplasts, in addition to a COPII-related system. To test this hypothesis we bioinformatically searched for chloroplast proteins that may have similar functions to known cytosolic COPI and CCV components in the model plants Arabidopsis thaliana and Oryza sativa (subsp. japonica) (rice). We found 29 such proteins, based on domain similarity, in Arabidopsis, and 14 in rice. However, many components could not be identified and among the identified most have assigned roles that are not related to either COPI or CCV transport. We conclude that COPII is probably the only active vesicle system in chloroplasts, at least in the model plants. The evolutionary implications of the findings are discussed.

Chloroplast vesicle transport

“…If the chloroplast vesicle system has similarities with cytosolic systems, proteins that maintain cytosolic vesicle transport could be expected to have homologs in chloroplasts, with similar functions and a degree of sequence conservation (Andersson and Sandelius 2004 ). Using bioinformatics with Arabidopsis as model plant revealed that most cytosolic COPII proteins had putative homologs in the chloroplast, whereas only a few potential COPI and CCV homologs were found (Khan et al 2013 ; Lindquist et al 2014 ). Moreover, analysis of motifs for cytosolic cargo proteins identified several putative cargo proteins destined for the thylakoids.…”

Vesicles Are Persistent Features of Different Plastids

“…Interestingly, attempts to identify COPI or CCV systems in the chloroplast failed, as not enough putative components were found to claim the presence of such systems. This indicates that a vesicle system in chloroplasts is likely to be more similar to the COPII system than the COPI and CCV systems, with regard to the components involved . The identification of protein components as such further supports vesicles as internal structures of the stroma.…”

“…The identification of protein components as such further supports vesicles as internal structures of the stroma. However, it is important to note that not all COPII components had chloroplast homologues, implying that the system in chloroplast resembles COPII but could be unique to this organelle .…”

Biogenesis of thylakoid membranes

“…More recently, comprehensive bioinformatic studies have provided evidence for chloroplast localization for several proteins that share high sequence similarity with known components of the vesicle-based secretory pathway in the cytoplasm [43][44][45]. Based on these analyses, it seems likely that a complete vesicle transport system which resembles the cytosolic COPII system is active in the chloroplast, whereas COPI and clathrincoated vesicles are probably absent from plastids [45,46]. However, in the case of most components of the putative chloroplast vesicle transport system, unequivocal experimental validation of their localization and function is still missing.…”