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Protein localization analysis of essential genes in prokaryotes.

Peng C, Gao F - Sci Rep (2014)

Bottom Line: Both statistical analysis of localization information in these genomes and GO (Gene Ontology) terms enriched in the essential genes show that proteins encoded by essential genes are enriched in internal location sites, while exist in cell envelope with a lower proportion compared with non-essential ones.Meanwhile, there are few essential proteins in the external subcellular location sites such as flagellum and fimbrium, and proteins encoded by non-essential genes tend to have diverse localizations.These results would provide further insights into the understanding of fundamental functions needed to support a cellular life and improve gene essentiality prediction by taking the protein localization and enriched GO terms into consideration.

View Article: PubMed Central - PubMed

Affiliation: Department of Physics, Tianjin University, Tianjin 300072, China.

ABSTRACT
Essential genes, those critical for the survival of an organism under certain conditions, play a significant role in pharmaceutics and synthetic biology. Knowledge of protein localization is invaluable for understanding their function as well as the interaction of different proteins. However, systematical examination of essential genes from the aspect of the localizations of proteins they encode has not been explored before. Here, a comprehensive protein localization analysis of essential genes in 27 prokaryotes including 24 bacteria, 2 mycoplasmas and 1 archaeon has been performed. Both statistical analysis of localization information in these genomes and GO (Gene Ontology) terms enriched in the essential genes show that proteins encoded by essential genes are enriched in internal location sites, while exist in cell envelope with a lower proportion compared with non-essential ones. Meanwhile, there are few essential proteins in the external subcellular location sites such as flagellum and fimbrium, and proteins encoded by non-essential genes tend to have diverse localizations. These results would provide further insights into the understanding of fundamental functions needed to support a cellular life and improve gene essentiality prediction by taking the protein localization and enriched GO terms into consideration.

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(a) Percentages of proteins located in cytoplasm, cytoplasm membrane and extracellular for essential and non-essential genes in the 27 genomes. (b) Average percentages of proteins located in periplasm, outer membrane and cell wall for essential and non-essential genes in the related genomes.
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f2: (a) Percentages of proteins located in cytoplasm, cytoplasm membrane and extracellular for essential and non-essential genes in the 27 genomes. (b) Average percentages of proteins located in periplasm, outer membrane and cell wall for essential and non-essential genes in the related genomes.

Mentions: We first submitted the amino acid sequences of both essential and non-essential genes in the 27 organisms to PSORTb and obtained the protein localization records. With precision values >97% for both archaea and bacteria, PSORTb 3.0 is the most precise prokaryotic localization prediction tool available. Compared with other localization prediction tools, PSORTb is able to discriminate between Gram-positive and Gram-negative bacteria, which makes it a more suitable tool for the current study23. The final prediction includes five Gram-negative localization sites (cytoplasm, cytoplasmic membrane, periplasm, outer membrane and extracellular space) and four Gram-positive localization sites (cytoplasm, cytoplasmic membrane, cell wall and extracellular space)24. When a protein might have multiple localization sites, PSORTb will output the most possible localization site. Then we calculated the proportions of proteins located in the location sites for essential and non-essential genes respectively. The results are displayed in Figure 2. The average percentages of proteins located in cytoplasm are 64.40% and 43.88% for essential and non-essential genes, respectively. The Student's t test shows that the difference is statistically significant (p = 1.57 × 10−10). For all the organisms except Vibrio cholerae N16961, the percentages of proteins located in cytoplasm for essential genes are higher than those for non-essential genes (Figure 2a). The reason for the anomalous outcome in Vibrio cholerae N16961 may be the higher proportion of ‘unknown’ predicted results (43.13%) compared with the average percentage (16.43%). To test this hypothesis, we used another tool CELLO2526 to predict the protein localization in Vibrio cholerae N16961 again. Then the percentages become 71.08% and 54.31% for essential and non-essential genes respectively, which is in accordance with the results of the other 26 organisms. These results suggest that proteins encoded by essential genes are enriched in cytoplasm. The average percentages of proteins located in cytoplasm membrane are 16.73% and 23.35% for essential and non-essential genes, respectively. The Student's t test shows that the difference is statistically significant (p = 1.33 × 10−5). The bars in Figure 2a shows that in 23 (85.19%) of the 27 groups of data, the percentages of proteins located in cytoplasm membrane for non-essential genes are higher than those for essential genes. For both essential and non-essential proteins, the proportions of secreted proteins are quite low, just 0.50% essential proteins and 1.54% non-essential proteins are located in extracellular space. With Student's t test p = 1.95 × 10−4, it's credible that the proportion of non-essential proteins located in extracellular is significantly higher than that of essential ones (Figure 2a).


Protein localization analysis of essential genes in prokaryotes.

Peng C, Gao F - Sci Rep (2014)

(a) Percentages of proteins located in cytoplasm, cytoplasm membrane and extracellular for essential and non-essential genes in the 27 genomes. (b) Average percentages of proteins located in periplasm, outer membrane and cell wall for essential and non-essential genes in the related genomes.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4126397&req=5

f2: (a) Percentages of proteins located in cytoplasm, cytoplasm membrane and extracellular for essential and non-essential genes in the 27 genomes. (b) Average percentages of proteins located in periplasm, outer membrane and cell wall for essential and non-essential genes in the related genomes.
Mentions: We first submitted the amino acid sequences of both essential and non-essential genes in the 27 organisms to PSORTb and obtained the protein localization records. With precision values >97% for both archaea and bacteria, PSORTb 3.0 is the most precise prokaryotic localization prediction tool available. Compared with other localization prediction tools, PSORTb is able to discriminate between Gram-positive and Gram-negative bacteria, which makes it a more suitable tool for the current study23. The final prediction includes five Gram-negative localization sites (cytoplasm, cytoplasmic membrane, periplasm, outer membrane and extracellular space) and four Gram-positive localization sites (cytoplasm, cytoplasmic membrane, cell wall and extracellular space)24. When a protein might have multiple localization sites, PSORTb will output the most possible localization site. Then we calculated the proportions of proteins located in the location sites for essential and non-essential genes respectively. The results are displayed in Figure 2. The average percentages of proteins located in cytoplasm are 64.40% and 43.88% for essential and non-essential genes, respectively. The Student's t test shows that the difference is statistically significant (p = 1.57 × 10−10). For all the organisms except Vibrio cholerae N16961, the percentages of proteins located in cytoplasm for essential genes are higher than those for non-essential genes (Figure 2a). The reason for the anomalous outcome in Vibrio cholerae N16961 may be the higher proportion of ‘unknown’ predicted results (43.13%) compared with the average percentage (16.43%). To test this hypothesis, we used another tool CELLO2526 to predict the protein localization in Vibrio cholerae N16961 again. Then the percentages become 71.08% and 54.31% for essential and non-essential genes respectively, which is in accordance with the results of the other 26 organisms. These results suggest that proteins encoded by essential genes are enriched in cytoplasm. The average percentages of proteins located in cytoplasm membrane are 16.73% and 23.35% for essential and non-essential genes, respectively. The Student's t test shows that the difference is statistically significant (p = 1.33 × 10−5). The bars in Figure 2a shows that in 23 (85.19%) of the 27 groups of data, the percentages of proteins located in cytoplasm membrane for non-essential genes are higher than those for essential genes. For both essential and non-essential proteins, the proportions of secreted proteins are quite low, just 0.50% essential proteins and 1.54% non-essential proteins are located in extracellular space. With Student's t test p = 1.95 × 10−4, it's credible that the proportion of non-essential proteins located in extracellular is significantly higher than that of essential ones (Figure 2a).

Bottom Line: Both statistical analysis of localization information in these genomes and GO (Gene Ontology) terms enriched in the essential genes show that proteins encoded by essential genes are enriched in internal location sites, while exist in cell envelope with a lower proportion compared with non-essential ones.Meanwhile, there are few essential proteins in the external subcellular location sites such as flagellum and fimbrium, and proteins encoded by non-essential genes tend to have diverse localizations.These results would provide further insights into the understanding of fundamental functions needed to support a cellular life and improve gene essentiality prediction by taking the protein localization and enriched GO terms into consideration.

View Article: PubMed Central - PubMed

Affiliation: Department of Physics, Tianjin University, Tianjin 300072, China.

ABSTRACT
Essential genes, those critical for the survival of an organism under certain conditions, play a significant role in pharmaceutics and synthetic biology. Knowledge of protein localization is invaluable for understanding their function as well as the interaction of different proteins. However, systematical examination of essential genes from the aspect of the localizations of proteins they encode has not been explored before. Here, a comprehensive protein localization analysis of essential genes in 27 prokaryotes including 24 bacteria, 2 mycoplasmas and 1 archaeon has been performed. Both statistical analysis of localization information in these genomes and GO (Gene Ontology) terms enriched in the essential genes show that proteins encoded by essential genes are enriched in internal location sites, while exist in cell envelope with a lower proportion compared with non-essential ones. Meanwhile, there are few essential proteins in the external subcellular location sites such as flagellum and fimbrium, and proteins encoded by non-essential genes tend to have diverse localizations. These results would provide further insights into the understanding of fundamental functions needed to support a cellular life and improve gene essentiality prediction by taking the protein localization and enriched GO terms into consideration.

Show MeSH
Related in: MedlinePlus