ELUCIDATING THE ESSENTIALITY OF ESSENTIAL GENES IN E COLI

721 FEEDBACK TEXT AND PICTURES ELUCIDATING PROCESS ORIENTED
ELUCIDATING THE ESSENTIALITY OF ESSENTIAL GENES IN E COLI



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Elucidating the essentiality of essential genes in E. coli K-12


Yue-Yang Bow1,#, Jen-Yun Chang1,#, Hsueh-Fen Juan2, Hirotada Mori3,
Hsuan-Cheng Huang1

1Institute of Bioinformatics, National Yang-Ming University, Taipei 112, Taiwan, 2Department of Life Science, National Taiwan University, Taipei 106, Taiwan,
3Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayama, Ikoma, Nara 630-0101, Japan,
#These authors contributed equally to this work.

We recently established single-gene deletion library for all of the predicted genes of E. coli K-12 by Wanner’s method [1] and simultaneously 303 genes have been predicted as essential genes in LB medium [2]. Elucidating the essentiality of these essential genes is a key to understand the system level organization of living cells. Here we present our analysis to address this issue from the perspectives of protein-protein interaction and metabolic networks.

We have performed a comparison between essential and non-essential genes within an interaction network of E. coli and found that essential genes have significantly more links than the non-essential genes, validating earlier findings in budding yeast [3]. Furthermore, other topological features are investigated to find their correlation with essential genes.

Based on the known metabolic reactions of E. coli collected from the KEGG (Kyoto Encyclopedia of Genes and Genomes) [4] and EcoCyc [5] databases, a simple metabolic simulator is developed to reconstruct and navigate all the possible pathways and participated metabolites. In-silico gene deletion is performed to obtain the variation of metabolite distributions and examine the effect of missing links. Our results indicate that the average number of affected metabolites and reactions by deletion of essential genes are significantly higher than non-essential genes. The predicted results are validated by DNA microarray experiments with deletion mutatant and phenotype microarray data [6].


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  2. Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y. and Hattori, M. (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res, 32, D277-280.

  3. Keseler, I.M., Collado-Vides, J., Gama-Castro, S., Ingraham, J., Paley, S., Paulsen, I.T., Peralta-Gil, M. and Karp, P.D. (2005) EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Res, 33, D334-337.

  4. Bochner, B.R. (2003) New technologies to assess genotype-phenotype relationships. Nat Rev Genet, 4, 309-314.






Tags: elucidating the, [2]. elucidating, essentiality, elucidating, essential, genes