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Mutagenesis and Functional Selection Protocols for Directed Evolution of Proteins in E. coli

Mutagenesis and Functional Selection Protocols for Directed Evolution of Proteins in E. coli

Published on: March 16, 2011

Genes under positive selection in Escherichia coli.

Lise Petersen¹, Jonathan P Bollback, Matt Dimmic

¹Bioinformatics Centre, University of Copenhagen, Copenhagen DK-2200, Denmark. lpe@binf.ku.dk

Genome Research

|August 7, 2007

Summary

Comparative genomics reveals genes under positive selection in Escherichia coli and Shigella flexneri. This includes cell surface proteins and transposases, suggesting evolutionary arms races and genomic conflicts.

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Area of Science:

Microbiology
Evolutionary Biology
Genomics

Background:

Escherichia coli and Shigella flexneri are significant bacterial pathogens.
Understanding the evolutionary pressures driving bacterial adaptation is crucial for public health.

Purpose of the Study:

To identify genes under positive selection in pathogenic strains of E. coli and S. flexneri.
To investigate the functional categories and potential evolutionary drivers of positive selection in these bacteria.

Main Methods:

Comparative genomics approach applied to six strains of E. coli and S. flexneri.
Structural mapping of positively selected sites on beta barrel porins.

Main Results:

Positive selection identified across diverse gene functions, including cell surface proteins (beta barrel porins) and enigmatic rhs elements.
Positively selected residues on porins are located in extracellular regions targeted by phages, colicins, and the host immune system.
Transposases also show strong evidence of positive selection, potentially linked to host-transposable element genomic conflict.

Conclusions:

Cell surface proteins are under selection due to interactions with external agents like phages, colicins, and host immunity.
Transposases may be subject to positive selection driven by intragenomic conflict with the host genome.
Positive selection plays a significant role in the adaptation and evolution of E. coli and S. flexneri pathogens.