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Comparative analysis of essential genes and nonessential genes in Escherichia coli K12

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Abstract

Genes can be classified as essential or nonessential based on their indispensability for a living organism. Previous researches have suggested that essential genes evolve more slowly than nonessential genes and the impact of gene dispensability on a gene’s evolutionary rate is not as strong as expected. However, findings have not been consistent and evidence is controversial regarding the relationship between the gene indispensability and the rate of gene evolution. Understanding how different classes of genes evolve is essential for a full understanding of evolutionary biology, and may have medical relevance in the design of new antibacterial agents. We therefore performed an investigation into the properties of essential and nonessential genes. Analysis of evolutionary conservation, protein length distribution and amino acid usage between essential and nonessential genes in Escherichia coli K12 demonstrated that essential genes are relatively preserved throughout the bacterial kingdom when compared to nonessential genes. Furthermore, results show that essential genes, compared to nonessential genes, have a significantly higher proportion of large (>534 amino acids) and small proteins (<139 amino acids) relative to medium-sized proteins. The pattern of amino acids usage shows a similar trend for essential and nonessential genes, although some notable exceptions are observed. These findings help to clarify our understanding of the evolutionary mechanisms of essential and nonessential genes, relevant to the study of mutagenesis and possibly allowing prediction of gene properties in other poorly understood organisms.

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Acknowledgments

We are grateful to N.G.C. Smith and E.V. Koonin for critical reading and constructive comments. We would also like to thank all the members in the Bioinformatics Center in Northwest A&F University for the daily useful discussions.

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Authors and Affiliations

  1. Bioinformatics Center, Northwest A&F University, 712100, Yangling, Shaanxi, China

    Xiaodong Gong, Shaohua Fan, Mingkun Li, Hongxia Pang & Shiheng Tao

  2. College of Life Science, Northwest A&F University, 712100, Yangling, Shaanxi, China

    Shaohua Fan, Mingkun Li, Hongxia Pang & Shiheng Tao

  3. College of Science, Northwest A&F University, 712100, Yangling, Shaanxi, China

    Xiaodong Gong

  4. College of Life Science, Agricultural University of Hebei, 071001, Baoding, Hebei, China

    Xiaodong Gong

  5. Department of Experimental Psychology, University of Oxford, Oxford, England

    Amy Bilderbeck

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  1. Xiaodong Gong
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  2. Shaohua Fan
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  3. Amy Bilderbeck
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  4. Mingkun Li
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  5. Hongxia Pang
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  6. Shiheng Tao
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Correspondence to Shiheng Tao.

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Communicated by D. Ussery.

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Gong, X., Fan, S., Bilderbeck, A. et al. Comparative analysis of essential genes and nonessential genes in Escherichia coli K12 . Mol Genet Genomics 279, 87–94 (2008). https://doi.org/10.1007/s00438-007-0298-x

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  • DOI: https://doi.org/10.1007/s00438-007-0298-x

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