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Comparative analysis of predicted plastid-targeted proteomes of sequenced higher plant genomes.

Schaeffer S, Harper A, Raja R, Jaiswal P, Dhingra A - PLoS ONE (2014)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Horticulture, Washington State University, Pullman, WA, United States of America; Molecular Plant Science Graduate Program, Washington State University, Pullman, WA, United States of America.

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.

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Molecular Function GO term composition of proteins shared between the 7 investigated plastid-targeted proteomes using two separate techniques.Two separate analyses were performed to identify proteins within the predicted plastid-targeted proteomes of seven species. The first, UCLUST with 50% identity, generated 15,750 clusters, 289 of which contained a member from all 7 species. USEARCH comparison performed at 40% identity and 40% coverage identified 737 sequences in the Arabidopsis thaliana putative plastid-targeted dataset which had a match in a protein sequence from the plastid-targeted sequences from all of the other 6 species. Sequences were analyzed via Blast2GO to determine the molecular functions of proteins at level 3.
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pone-0112870-g005: Molecular Function GO term composition of proteins shared between the 7 investigated plastid-targeted proteomes using two separate techniques.Two separate analyses were performed to identify proteins within the predicted plastid-targeted proteomes of seven species. The first, UCLUST with 50% identity, generated 15,750 clusters, 289 of which contained a member from all 7 species. USEARCH comparison performed at 40% identity and 40% coverage identified 737 sequences in the Arabidopsis thaliana putative plastid-targeted dataset which had a match in a protein sequence from the plastid-targeted sequences from all of the other 6 species. Sequences were analyzed via Blast2GO to determine the molecular functions of proteins at level 3.

Mentions: The first analysis using UCLUST at 50% identity identified 289 clusters of proteins which had at least one member from all seven species. These 289 clusters contain 497 unique sequences from Arabidopsis thaliana, 773 from Malus × domestica, 384 from Vitis vinifera, 392 from Fragaria vesca, 545 from Populus trichocarpa, 439 from Prunus persica, and 478 from Solanum lycopersicum. Blast2GO analysis reveals that these proteins are involved in a large number of biological processes (Figure 4) with the most populous being cellular component organization (GO:0016043, 109 proteins), carbohydrate metabolic process (GO:0005975, 98 proteins), and response to stress (GO:0006950, 95 proteins). The electron transport chain-related molecular functions for this data set reveals that the majority of proteins fit into six main categories; organic cyclic compound binding (GO:0097159 109 proteins), small molecule binding (GO:0036094 78 proteins), transferase activity (GO:0016740 68 proteins), protein binding (GO:0005515 68 proteins), hydrolase activity (GO:0016787 50 proteins), and nucleic acid binding (GO:0003676 40 proteins) (Figure 5). GO term enrichment was performed by selecting a single Arabidopsis thaliana protein sequence and utilizing agriGO to compare with those GO terms from the entire Arabidopsis thaliana predicted plastid-targeted proteome. This dataset contains 56 GO terms which were enriched with a p-value cut-off of 0.01 (Table 9). The lowest p-values are associated with the GO terms photosynthesis (GO:0015979), carbohydrate metabolic process (GO:0005975), macromolecule modification (GO:0043412), protein modification process (GO:0006464) and thylakoid (GO:0009579) respectively.


Comparative analysis of predicted plastid-targeted proteomes of sequenced higher plant genomes.

Schaeffer S, Harper A, Raja R, Jaiswal P, Dhingra A - PLoS ONE (2014)

Molecular Function GO term composition of proteins shared between the 7 investigated plastid-targeted proteomes using two separate techniques.Two separate analyses were performed to identify proteins within the predicted plastid-targeted proteomes of seven species. The first, UCLUST with 50% identity, generated 15,750 clusters, 289 of which contained a member from all 7 species. USEARCH comparison performed at 40% identity and 40% coverage identified 737 sequences in the Arabidopsis thaliana putative plastid-targeted dataset which had a match in a protein sequence from the plastid-targeted sequences from all of the other 6 species. Sequences were analyzed via Blast2GO to determine the molecular functions of proteins at level 3.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4231079&req=5

pone-0112870-g005: Molecular Function GO term composition of proteins shared between the 7 investigated plastid-targeted proteomes using two separate techniques.Two separate analyses were performed to identify proteins within the predicted plastid-targeted proteomes of seven species. The first, UCLUST with 50% identity, generated 15,750 clusters, 289 of which contained a member from all 7 species. USEARCH comparison performed at 40% identity and 40% coverage identified 737 sequences in the Arabidopsis thaliana putative plastid-targeted dataset which had a match in a protein sequence from the plastid-targeted sequences from all of the other 6 species. Sequences were analyzed via Blast2GO to determine the molecular functions of proteins at level 3.
Mentions: The first analysis using UCLUST at 50% identity identified 289 clusters of proteins which had at least one member from all seven species. These 289 clusters contain 497 unique sequences from Arabidopsis thaliana, 773 from Malus × domestica, 384 from Vitis vinifera, 392 from Fragaria vesca, 545 from Populus trichocarpa, 439 from Prunus persica, and 478 from Solanum lycopersicum. Blast2GO analysis reveals that these proteins are involved in a large number of biological processes (Figure 4) with the most populous being cellular component organization (GO:0016043, 109 proteins), carbohydrate metabolic process (GO:0005975, 98 proteins), and response to stress (GO:0006950, 95 proteins). The electron transport chain-related molecular functions for this data set reveals that the majority of proteins fit into six main categories; organic cyclic compound binding (GO:0097159 109 proteins), small molecule binding (GO:0036094 78 proteins), transferase activity (GO:0016740 68 proteins), protein binding (GO:0005515 68 proteins), hydrolase activity (GO:0016787 50 proteins), and nucleic acid binding (GO:0003676 40 proteins) (Figure 5). GO term enrichment was performed by selecting a single Arabidopsis thaliana protein sequence and utilizing agriGO to compare with those GO terms from the entire Arabidopsis thaliana predicted plastid-targeted proteome. This dataset contains 56 GO terms which were enriched with a p-value cut-off of 0.01 (Table 9). The lowest p-values are associated with the GO terms photosynthesis (GO:0015979), carbohydrate metabolic process (GO:0005975), macromolecule modification (GO:0043412), protein modification process (GO:0006464) and thylakoid (GO:0009579) respectively.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Horticulture, Washington State University, Pullman, WA, United States of America; Molecular Plant Science Graduate Program, Washington State University, Pullman, WA, United States of America.

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.

Show MeSH
Related in: MedlinePlus