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Three Computational Tools for Predicting Bacterial Essential Genes

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Book cover Gene Essentiality

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1279))

Abstract

Essential genes are those genes indispensable for the survival of any living cell. Bacterial essential genes constitute the cornerstones of synthetic biology and are often attractive targets in the development of antibiotics and vaccines. Because identification of essential genes with wet-lab ways often means expensive economic costs and tremendous labor, scientists changed to seek for alternative way of computational prediction. Aiming to help to solve this issue, our research group (CEFG: group of Computational, Comparative, Evolutionary and Functional Genomics, http://cefg.uestc.edu.cn) has constructed three online services to predict essential genes in bacterial genomes. These freely available tools are applicable for single gene sequences without annotated functions, single genes with definite names, and complete genomes of bacterial strains. To ensure reliable predictions, the investigated species should belong to the same family (for EGP) or phylum (for CEG_Match and Geptop) with one of the reference species, respectively. As the pilot software for the issue, predicting accuracies of them have been assessed and compared with existing algorithms, and note that all of other published algorithms have not any formed online services. We hope these services at CEFG will help scientists and researchers in the field of essential genes.

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References

  1. Zhang R, Ou HY, Zhang CT (2004) DEG: a database of essential genes. Nucleic Acids Res 32:D271–D272

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  2. Mushegian AR, Koonin EV (1996) A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc Natl Acad Sci U S A 93:10268–10273

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  3. Juhas M, Eberl L, Glass JI (2011) Essence of life: essential genes of minimal genomes. Trends Cell Biol 21:562–568

    Article  CAS  PubMed  Google Scholar 

  4. Read TD, Gill SR, Tettelin H, Dougherty BA (2001) Finding drug targets in microbial genomes. Drug Discov Today 6:887–892

    Article  CAS  PubMed  Google Scholar 

  5. Juhas M, Eberl L, Church GM (2012) Essential genes as antimicrobial targets and cornerstones of synthetic biology. Trends Biotechnol 30:601–607

    Article  CAS  PubMed  Google Scholar 

  6. Koonin EV (2003) Comparative genomics, minimal gene-sets and the last universal common ancestor. Nat Rev Microbiol 1:127–136

    Article  CAS  PubMed  Google Scholar 

  7. Deng J, Su S, Lin X, Hassett DJ, Lu LJ (2013) A statistical framework for improving genomic annotations of prokaryotic essential genes. PLoS One 8:e58178

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  8. Seringhaus M, Paccanaro A, Borneman A, Snyder M, Gerstein M (2006) Predicting essential genes in fungal genomes. Genome Res 16:1126–1135

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  9. Chen WH, Minguez P, Lercher MJ, Bork P (2012) OGEE: an online gene essentiality database. Nucleic Acids Res 40:D901–D906

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  10. Jeong H, Oltvai ZN, Barabási AL (2003) Prediction of protein essentiality based on genomic data. ComPlexUs 1:19–28

    Article  Google Scholar 

  11. Roberts SB, Mazurie AJ, Buck GA (2007) Integrating genome-scale data for gene essentiality prediction. Chem Biodivers 4:2618–2630

    Article  CAS  PubMed  Google Scholar 

  12. Chen Y, Xu D (2005) Understanding protein dispensability through machine-learning analysis of high-throughput data. Bioinformatics 21:575–581

    Article  CAS  PubMed  Google Scholar 

  13. Wang J, Peng W, Wu FX (2013) Computational approaches to predicting essential proteins: a survey. Proteomics Clin Appl 7:181–192

    Article  CAS  PubMed  Google Scholar 

  14. Singh NK, Selvam SM, Chakravarthy P (2006) T-iDT: tool for identification of drug target in bacteria and validation by Mycobacterium tuberculosis. In Silico Biol 6:485–493

    CAS  PubMed  Google Scholar 

  15. Jeong H, Mason SP, Barabasi AL, Oltvai ZN (2001) Lethality and centrality in protein networks. Nature 411:41–42

    Article  CAS  PubMed  Google Scholar 

  16. Acencio ML, Lemke N (2009) Towards the prediction of essential genes by integration of network topology, cellular localization and biological process information. BMC Bioinformatics 10:290

    Article  PubMed Central  PubMed  Google Scholar 

  17. Plaimas K, Eils R, Konig R (2010) Identifying essential genes in bacterial metabolic networks with machine learning methods. BMC Syst Biol 4:56

    Article  PubMed Central  PubMed  Google Scholar 

  18. Deng J, Deng L, Su S, Zhang M, Lin X, Wei L et al (2011) Investigating the predictability of essential genes across distantly related organisms using an integrative approach. Nucleic Acids Res 39:795–807

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  19. Ning LW, Lin H, Ding H, Huang J, Rao N, Guo FB (2014) Predict essential genes using only sequence composition information. Genet Mol Res 13:4564–4572

    Article  CAS  PubMed  Google Scholar 

  20. Guo FB, Ning LW, Huang J, Lin H, Zhang HX (2010) Chromosome translocation and its consequence in the genome of Burkholderia cenocepacia AU-1054. Biochem Biophys Res Commun 403:375–379

    Article  CAS  PubMed  Google Scholar 

  21. Ye YN, Hua ZG, Huang J, Rao N, Guo FB (2013) CEG: a database of essential gene clusters. BMC Genomics 14:769

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  22. Wei W, Ning LW, Ye YN, Guo FB (2013) Geptop: a gene essentiality prediction tool for sequenced bacterial genomes based on orthology and phylogeny. PLoS One 8:e72343

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  23. Chang CC, Lin CJ (2011) LIBSVM: a library for support vector machines. ACM Trans Intell Syst Technol 2:27

    Article  Google Scholar 

  24. Li W, Godzik A (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22:1658–1659

    Article  CAS  PubMed  Google Scholar 

  25. Gustafson AM, Snitkin ES, Parker SC, Delisi C, Kasif S (2006) Towards the identification of essential genes using targeted genome sequencing and comparative analysis. BMC Genomics 7:265

    Article  PubMed Central  PubMed  Google Scholar 

  26. Kobayashi K, Ehrlich SD, Albertini A, Amati G, Andersen KK, Arnaud M et al (2003) Essential Bacillus subtilis genes. Proc Natl Acad Sci U S A 100:4678–4683

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  27. Peterson SN, Fraser CM (2001) The complexity of simplicity. Genome Biol 2:Comment2002

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  28. Zhang CT, Zhang R (2008) Gene essentiality analysis based on DEG, a database of essential genes. Methods Mol Biol 416:391–400

    Article  CAS  PubMed  Google Scholar 

  29. Zhang R, Lin Y (2009) DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes. Nucleic Acids Res 37:D455–D458

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  30. Xu Z, Hao B (2009) CVTree update: a newly designed phylogenetic study platform using composition vectors and whole genomes. Nucleic Acids Res 37:W174–W178

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  31. Jordan IK, Rogozin IB, Wolf YI, Koonin EV (2002) Essential genes are more evolutionarily conserved than are nonessential genes in bacteria. Genome Res 12:962–968

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  32. Gong X, Fan S, Bilderbeck A, Li M, Pang H, Tao S (2008) Comparative analysis of essential genes and nonessential genes in Escherichia coli K12. Mol Genet Genomics 279:87–94

    Article  CAS  PubMed  Google Scholar 

  33. Fang G, Rocha E, Danchin A (2005) How essential are nonessential genes? Mol Biol Evol 22:2147–2156

    Article  CAS  PubMed  Google Scholar 

  34. Wei W, Ye YN, Luo S, Deng YY, Lin D, Guo FB (2014) IFIM: a database of integrated fitness information for microbial genes. Database (Oxford). pii bau052

    Google Scholar 

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Acknowledgements

We thank the book editor for his encouragement and advice. This work was supported by the National Natural Science Foundation of China (grant number 31470068), Sichuan Youth Science and Technology Foundation of China (grant number 2014JQ0051) and the Fundamental Research Funds for the Central Universities of China (grant number ZYGX2013J101).

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Authors and Affiliations

  1. Computational, Comparative, Evolutionary and Functional Genomics Group (CEFG), School of Life Science and Technology, University of Electronic Science and Technology of China, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, China

    Feng-Biao Guo, Yuan-Nong Ye, Lu-Wen Ning & Wen Wei

Authors
  1. Feng-Biao Guo
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  2. Yuan-Nong Ye
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  3. Lu-Wen Ning
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  4. Wen Wei
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Corresponding author

Correspondence to Feng-Biao Guo .

Editor information

Editors and Affiliations

  1. Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA

    Long Jason Lu

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Guo, FB., Ye, YN., Ning, LW., Wei, W. (2015). Three Computational Tools for Predicting Bacterial Essential Genes. In: Lu, L. (eds) Gene Essentiality. Methods in Molecular Biology, vol 1279. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2398-4_13

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  • DOI: https://doi.org/10.1007/978-1-4939-2398-4_13

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-2397-7

  • Online ISBN: 978-1-4939-2398-4

  • eBook Packages: Springer Protocols

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