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Sci Rep. 2015 Jul 30;5:12561. doi: 10.1038/srep12561.

Comparative analysis of essential genes in prokaryotic genomic islands.

Author information

1
Department of Physics, Tianjin University, Tianjin 300072, China.
2
1] Department of Physics, Tianjin University, Tianjin 300072, China [2] Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China [3] SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, China.

Abstract

Essential genes are thought to encode proteins that carry out the basic functions to sustain a cellular life, and genomic islands (GIs) usually contain clusters of horizontally transferred genes. It has been assumed that essential genes are not likely to be located in GIs, but systematical analysis of essential genes in GIs has not been explored before. Here, we have analyzed the essential genes in 28 prokaryotes by statistical method and reached a conclusion that essential genes in GIs are significantly fewer than those outside GIs. The function of 362 essential genes found in GIs has been explored further by BLAST against the Virulence Factor Database (VFDB) and the phage/prophage sequence database of PHAge Search Tool (PHAST). Consequently, 64 and 60 eligible essential genes are found to share the sequence similarity with the virulence factors and phage/prophages-related genes, respectively. Meanwhile, we find several toxin-related proteins and repressors encoded by these essential genes in GIs. The comparative analysis of essential genes in genomic islands will not only shed new light on the development of the prediction algorithm of essential genes, but also give a clue to detect the functionality of essential genes in genomic islands.

PMID:
26223387
PMCID:
PMC4519734
DOI:
10.1038/srep12561
[Indexed for MEDLINE]
Free PMC Article

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