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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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Related in: MedlinePlus

The plot of statistically significant GO terms in the category of cellular component incorporating the phylogenetic information.Every GO term with p value less than 0.05 in over two organisms according to the results of Fisher's exact tests is listed in the vertical axis. If the GO term is over-represented in the organism listed in the horizontal axis, the cell at the crossing of the row and column is red. Blue boxes represent that the GO term is under-represented in the organism of the column. If the GO term is not statistically significant in the organism, the box is white. The lines at the top of the figure are the phylogenetic tree of the organisms used in the current study.
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f1: The plot of statistically significant GO terms in the category of cellular component incorporating the phylogenetic information.Every GO term with p value less than 0.05 in over two organisms according to the results of Fisher's exact tests is listed in the vertical axis. If the GO term is over-represented in the organism listed in the horizontal axis, the cell at the crossing of the row and column is red. Blue boxes represent that the GO term is under-represented in the organism of the column. If the GO term is not statistically significant in the organism, the box is white. The lines at the top of the figure are the phylogenetic tree of the organisms used in the current study.

Mentions: We selected 27 prokaryotic organisms to analyze the protein location of the essential and non-essential genes. The data used in the current study are obtained from DEG (a database of essential genes, available at http://www.essentialgene.org/)21 and are displayed in Table 1. To elucidate the evolutionary relationship among the organisms, the phylogenetic tree was constructed. The lines at the top of Figure 1 are the phylogenetic tree of the organisms used in the current study. The tree was constructed using the MEGA6 program (Statistical Method: Maximum Likelihood, Test of Phylogeny: Bootstrap method, No. of Bootstrap Replications: 1000)22 with the sequences of 16S ribosomal RNA of the 27 organisms downloaded from the NCBI FTP site (ftp://ftp.ncbi.nih.gov/genomes/Bacteria). Based on the clades of the tree, the organisms can be divided into 4 groups: 20 Gram-negative bacteria (pink clades in Figure 1), 4 Gram-positive bacteria (purple clades), 2 mycoplasmas (blue clades) and 1 archaeon (green clades). To which group Mycobacterium tuberculosis H37Rv should be classified is disputable. We treated it as Gram-negative bacterium due to its cell structure.


Protein localization analysis of essential genes in prokaryotes.

Peng C, Gao F - Sci Rep (2014)

The plot of statistically significant GO terms in the category of cellular component incorporating the phylogenetic information.Every GO term with p value less than 0.05 in over two organisms according to the results of Fisher's exact tests is listed in the vertical axis. If the GO term is over-represented in the organism listed in the horizontal axis, the cell at the crossing of the row and column is red. Blue boxes represent that the GO term is under-represented in the organism of the column. If the GO term is not statistically significant in the organism, the box is white. The lines at the top of the figure are the phylogenetic tree of the organisms used in the current study.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f1: The plot of statistically significant GO terms in the category of cellular component incorporating the phylogenetic information.Every GO term with p value less than 0.05 in over two organisms according to the results of Fisher's exact tests is listed in the vertical axis. If the GO term is over-represented in the organism listed in the horizontal axis, the cell at the crossing of the row and column is red. Blue boxes represent that the GO term is under-represented in the organism of the column. If the GO term is not statistically significant in the organism, the box is white. The lines at the top of the figure are the phylogenetic tree of the organisms used in the current study.
Mentions: We selected 27 prokaryotic organisms to analyze the protein location of the essential and non-essential genes. The data used in the current study are obtained from DEG (a database of essential genes, available at http://www.essentialgene.org/)21 and are displayed in Table 1. To elucidate the evolutionary relationship among the organisms, the phylogenetic tree was constructed. The lines at the top of Figure 1 are the phylogenetic tree of the organisms used in the current study. The tree was constructed using the MEGA6 program (Statistical Method: Maximum Likelihood, Test of Phylogeny: Bootstrap method, No. of Bootstrap Replications: 1000)22 with the sequences of 16S ribosomal RNA of the 27 organisms downloaded from the NCBI FTP site (ftp://ftp.ncbi.nih.gov/genomes/Bacteria). Based on the clades of the tree, the organisms can be divided into 4 groups: 20 Gram-negative bacteria (pink clades in Figure 1), 4 Gram-positive bacteria (purple clades), 2 mycoplasmas (blue clades) and 1 archaeon (green clades). To which group Mycobacterium tuberculosis H37Rv should be classified is disputable. We treated it as Gram-negative bacterium due to its cell structure.

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