Comparative Analysis of Predicted Plastid-Targeted Proteomes of Sequenced Higher Plant Genomes

Abstract

Plastids are actively involved in numerous plant processes critical to growth, development and adaptation. They play a primary role in photosynthesis, pigment and monoterpene synthesis, gravity sensing, starch and fatty acid synthesis, as well as oil, and protein storage. We applied two complementary methods to analyze the recently published apple genome (Malus × domestica) to identify putative plastid-targeted proteins, the first using TargetP and the second using a custom workflow utilizing a set of predictive programs. Apple shares roughly 40% of its 10,492 putative plastid-targeted proteins with that of the Arabidopsis (Arabidopsis thaliana) plastid-targeted proteome as identified by the Chloroplast 2010 project and ∼57% of its entire proteome with Arabidopsis. This suggests that the plastid-targeted proteomes between apple and Arabidopsis are different, and interestingly alludes to the presence of differential targeting of homologs between the two species. Co-expression analysis of 2,224 genes encoding putative plastid-targeted apple proteins suggests that they play a role in plant developmental and intermediary metabolism. Further, an inter-specific comparison of Arabidopsis, Prunus persica (Peach), Malus × domestica (Apple), Populus trichocarpa (Black cottonwood), Fragaria vesca (Woodland Strawberry), Solanum lycopersicum (Tomato) and Vitis vinifera (Grapevine) also identified a large number of novel species-specific plastid-targeted proteins. This analysis also revealed the presence of alternatively targeted homologs across species. Two separate analyses revealed that a small subset of proteins, one representing 289 protein clusters and the other 737 unique protein sequences, are conserved between seven plastid-targeted angiosperm proteomes. Majority of the novel proteins were annotated to play roles in stress response, transport, catabolic processes, and cellular component organization. Our results suggest that the current state of knowledge regarding plastid biology, preferentially based on model systems is deficient. New plant genomes are expected to enable the identification of potentially new plastid-targeted proteins that will aid in studying novel roles of plastids.

Comparative ultrastructure of fruit plastids in three genetically diverse genotypes of apple (Malus × domestica Borkh.) during development

“…Recently, we reported a comparative analysis of the predicted plastid-targeted proteomes from seven plant species and identified a large number of novel, species-specific plastid-targeted proteins along with alternatively targeted homologs across the analyzed species (Schaeffer et al 2014). Interestingly, out of the seven species, Malus × domestica Borkh., with 10,492 proteins, possessed the largest number of predicted plastid-targeted proteins.…”

“…Interestingly, out of the seven species, Malus × domestica Borkh., with 10,492 proteins, possessed the largest number of predicted plastid-targeted proteins. Only 40% of these proteins were homologous to members of the Arabidopsis plastid-targeted proteome and 57% of the apple proteins shared a homolog with the Arabidopsis total proteome (Schaeffer et al 2014). There is a strong indication that plastids in perennial, fruit bearing species such as apple have far more complex and specialized functions compared to model systems such as Arabidopsis and tomato.…”

“…There is extensive information regarding the ripening physiology (Bulens et al 2014) due to its biological, nutritional, and economical value. Except for a recent report on its predicted plastid proteome (Schaeffer et al 2014), not much is known about the novel proteomic or metabolomic constitution of apple plastids, which carry out important biochemical processes. To further this field, a thorough characterization of apple fruit plastid development is needed.…”

Differential Chloroplast Proteomics of Temperature Adaptation in Apple (Malus x domestica Borkh.) Microshoots

“…The subcellular localization of proteins can be predicted in silico from known transit peptide sequences and sequence similarity to model species such as Arabidopsis thaliana . However, there are species‐specific plastid targeted proteins, that have homology to proteins that are not predicted to be plastid proteins in Arabidopsis …”

“…[15] However, there are species-specific plastid targeted proteins, that have homology to proteins that are not predicted to be plastid proteins in Arabidopsis. [16] We purified chloroplasts by centrifugation in Percoll gradient [17] from low temperature (4°C), control (22°C), and high temperature (30°C) grown Malus x domestica microshoots. The purity of the chloroplast fractions was evaluated by marker proteins as well as by using subcellular localization prediction software.…”