Metabolites production improvement by identifying minimal genomes and essential genes using flux balance analysis

Abdul Hakim Mohamed Salleh, Mohd Saberi Mohamad, Safaai Deris, Rosli Md Illias

Research output: Contribution to journalArticlepeer-review


With the advancement in metabolic engineering technologies, reconstruction of the genome of host organisms to achieve desired phenotypes can be made. However, due to the complexity and size of the genome scale metabolic network, significant components tend to be invisible. We proposed an approach to improve metabolite production that consists of two steps. First, we find the essential genes and identify the minimal genome by a single gene deletion process using Flux Balance Analysis (FBA) and second by identifying the significant pathway for the metabolite production using gene expression data. A genome scale model of Saccharomyces cerevisiae for production of vanillin and acetate is used to test this approach. The result has shown the reliability of this approach to find essential genes, reduce genome size and identify production pathway that can further optimise the production yield. The identified genes and pathways can be extendable to other applications especially in strain optimisation.

Original languageEnglish
Pages (from-to)85-99
Number of pages15
JournalInternational Journal of Data Mining and Bioinformatics
Issue number1
Publication statusPublished - 2015
Externally publishedYes


  • Bioinformatics
  • Essential genes
  • Flux balance analysis
  • Gene expression data
  • Metabolic engineering
  • Metabolic network
  • Metabolic reconstruction
  • Metabolites production
  • Minimal genome
  • Significant pathway

ASJC Scopus subject areas

  • Information Systems
  • General Biochemistry,Genetics and Molecular Biology
  • Library and Information Sciences


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