Comparative analysis of essential genes in prokaryotic genomic islands.

Xi Zhang,Chong Peng,Feng Gao,Ge Zhang

doi:10.1038/srep12561

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.

Highlights

If the evolutionary distance is too far, it can greatly decrease the number of shared genes identified by comparative genomics
It is a difficult and time consuming task to decide which of these identified genes are really required for growth or form the universal minimal genome, combining the reliable computational with experimental methods to determine essential genes between a huge set of species would open opportunities for better understanding the essence of life
We find several toxin-related proteins and repressors encoded by these essential genes in genomic islands (GIs)

Summary

Introduction

If the evolutionary distance is too far, it can greatly decrease the number of shared genes identified by comparative genomics. The essential genome of P. aeruginosa has been established with statistical precision by a Monte Carlo simulation method[13] It is a difficult and time consuming task to decide which of these identified genes are really required for growth or form the universal minimal genome, combining the reliable computational with experimental methods to determine essential genes between a huge set of species would open opportunities for better understanding the essence of life. Mobile elements are frequently found in GIs, such as integrases, transposases, insertion sequence elements and some particular genes which encode cell surface proteins, virulence factors, host interactions proteins, DNA-binding proteins and phage-related proteins[31,32,33]. Knowledge of essential genes in genomic islands is of great importance, because it gives a better understanding of what the gene set of universal minimal genome would be, and helps a lot in the recognition of new essential genes

Methods

Results

Conclusion