Limits...
dbPSP: a curated database for protein phosphorylation sites in prokaryotes.

Pan Z, Wang B, Zhang Y, Wang Y, Ullah S, Jian R, Liu Z, Xue Y - Database (Oxford) (2015)

Bottom Line: With the dataset, the sequence preferences of the phosphorylation sites and functional annotations of the phosphoproteins were analyzed, while the results shows that there were obvious differences among the phosphorylation in bacteria, archaea and eukaryotes.All the phosphorylation sites were annotated with original references and other descriptions in the database, which could be easily accessed through user-friendly website interface including various search and browse options.Taken together, the dbPSP database provides a comprehensive data resource for further studies of protein phosphorylation in prokaryotes.

View Article: PubMed Central - PubMed

Affiliation: School of Life Sciences, University of Science and Technology of China, Hefei 230027, China, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China, and State Key Laboratory of Biocontrol, School of Life Sciences, School of Advanced Computing, Sun Yat-sen University, Guangzhou 510275, China School of Life Sciences, University of Science and Technology of China, Hefei 230027, China, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China, and State Key Laboratory of Biocontrol, School of Life Sciences, School of Advanced Computing, Sun Yat-sen University, Guangzhou 510275, China.

Show MeSH
Statistical analyses of GO annotation for phosphoproteins in E. Coli k12 and S. acidocaldarius. (A) The enriched GO terms for phosphoproteins in E. Coli k12. (B) The enriched GO terms for phosphoproteins in S. acidocaldarius.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4385273&req=5

bav031-F6: Statistical analyses of GO annotation for phosphoproteins in E. Coli k12 and S. acidocaldarius. (A) The enriched GO terms for phosphoproteins in E. Coli k12. (B) The enriched GO terms for phosphoproteins in S. acidocaldarius.

Mentions: Furthermore, with the comprehensive phosphorylation datasets in the dbPSP database, we tried to analyze the functional annotations of phosphoproteins in prokaryotes with the examples of E.coli (strain K12) (E. Coli k12) and Sulfolobus acidocaldarius, which contained the most identified phosphoproteins and sites in bacteria and archaea, respectively. The gene ontology (GO) (31 March 2012) association files were downloaded from the The Gene Ontology Annotation (GOA) database at the European Bioinformatics Institute (EBI) (http://www.ebi.ac.uk/goa) (34) and the complete proteomes were retrieved from AmiPro Database (26). With hypergeometric distribution (35), we statistically analysed the enriched biological processes, molecular functions and cellular components for phosphoproteins in E. Coli k12 (Figure 6A, P-value < 10−9) and S. acidocaldarius (Figure 6B, P-value < 10−2). It was observed that translation (GO:0006412) was the intensively enriched biological process in phosphoproteins from E. Coli k12 (Figure 6A), while translation-related annotations of tRNA aminoacylation for protein translation (GO:0006418) and regulation of translational fidelity (GO:0006450) were also over-presented in phosphoproteins from S. acidocaldarius (Figure 6). For molecular functions, phosphoproteins from E. Coli k12 and S. acidocaldarius both enriched annotations of nucleotide binding (GO:0000166) (Figure 6). Furthermore, phosphoproteins from E. Coli k12 over-presented other molecular functions including structural constituent of ribosome (GO:0003735), rRNA binding (GO:0019843), protein binding (GO:0005515), magnesium ion binding (GO:0000287), identical protein binding (GO:0042802) and RNA binding (GO:0003723) (Figure 6A), while phosphoproteins from S. acidocaldarius enriched aminoacyl-tRNA ligase activity (GO:0004812), ligase activity (GO:0016874), aminoacyl-tRNA editing activity (GO:0002161), nucleic acid binding (GO:0003676) and ATP binding (GO:0005524) (Figure 6B). In addition, a handful of cellular components were over-presented in phosphoproteins from E. Coli k12 (Figure 6A), while no enrichment was observed in for S. acidocaldarius.Figure 6.


dbPSP: a curated database for protein phosphorylation sites in prokaryotes.

Pan Z, Wang B, Zhang Y, Wang Y, Ullah S, Jian R, Liu Z, Xue Y - Database (Oxford) (2015)

Statistical analyses of GO annotation for phosphoproteins in E. Coli k12 and S. acidocaldarius. (A) The enriched GO terms for phosphoproteins in E. Coli k12. (B) The enriched GO terms for phosphoproteins in S. acidocaldarius.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4385273&req=5

bav031-F6: Statistical analyses of GO annotation for phosphoproteins in E. Coli k12 and S. acidocaldarius. (A) The enriched GO terms for phosphoproteins in E. Coli k12. (B) The enriched GO terms for phosphoproteins in S. acidocaldarius.
Mentions: Furthermore, with the comprehensive phosphorylation datasets in the dbPSP database, we tried to analyze the functional annotations of phosphoproteins in prokaryotes with the examples of E.coli (strain K12) (E. Coli k12) and Sulfolobus acidocaldarius, which contained the most identified phosphoproteins and sites in bacteria and archaea, respectively. The gene ontology (GO) (31 March 2012) association files were downloaded from the The Gene Ontology Annotation (GOA) database at the European Bioinformatics Institute (EBI) (http://www.ebi.ac.uk/goa) (34) and the complete proteomes were retrieved from AmiPro Database (26). With hypergeometric distribution (35), we statistically analysed the enriched biological processes, molecular functions and cellular components for phosphoproteins in E. Coli k12 (Figure 6A, P-value < 10−9) and S. acidocaldarius (Figure 6B, P-value < 10−2). It was observed that translation (GO:0006412) was the intensively enriched biological process in phosphoproteins from E. Coli k12 (Figure 6A), while translation-related annotations of tRNA aminoacylation for protein translation (GO:0006418) and regulation of translational fidelity (GO:0006450) were also over-presented in phosphoproteins from S. acidocaldarius (Figure 6). For molecular functions, phosphoproteins from E. Coli k12 and S. acidocaldarius both enriched annotations of nucleotide binding (GO:0000166) (Figure 6). Furthermore, phosphoproteins from E. Coli k12 over-presented other molecular functions including structural constituent of ribosome (GO:0003735), rRNA binding (GO:0019843), protein binding (GO:0005515), magnesium ion binding (GO:0000287), identical protein binding (GO:0042802) and RNA binding (GO:0003723) (Figure 6A), while phosphoproteins from S. acidocaldarius enriched aminoacyl-tRNA ligase activity (GO:0004812), ligase activity (GO:0016874), aminoacyl-tRNA editing activity (GO:0002161), nucleic acid binding (GO:0003676) and ATP binding (GO:0005524) (Figure 6B). In addition, a handful of cellular components were over-presented in phosphoproteins from E. Coli k12 (Figure 6A), while no enrichment was observed in for S. acidocaldarius.Figure 6.

Bottom Line: With the dataset, the sequence preferences of the phosphorylation sites and functional annotations of the phosphoproteins were analyzed, while the results shows that there were obvious differences among the phosphorylation in bacteria, archaea and eukaryotes.All the phosphorylation sites were annotated with original references and other descriptions in the database, which could be easily accessed through user-friendly website interface including various search and browse options.Taken together, the dbPSP database provides a comprehensive data resource for further studies of protein phosphorylation in prokaryotes.

View Article: PubMed Central - PubMed

Affiliation: School of Life Sciences, University of Science and Technology of China, Hefei 230027, China, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China, and State Key Laboratory of Biocontrol, School of Life Sciences, School of Advanced Computing, Sun Yat-sen University, Guangzhou 510275, China School of Life Sciences, University of Science and Technology of China, Hefei 230027, China, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China, and State Key Laboratory of Biocontrol, School of Life Sciences, School of Advanced Computing, Sun Yat-sen University, Guangzhou 510275, China.

Show MeSH