Transcriptome Profiling and Deciphering the Regulatory Role of Global Transcription Factor fadR

fadR is a transcription factor which has a Helix-turn-Helix motif [5], one of most common prokaryotic transcription factor. It regulates metabolic pathway such as the fatty acid biosynthesis and degradation pathways, glyoxylate pathway and possible role in regulation of amino acid biosynthesis directly or indirectly [1, 2, 3, 4]. By use of cDNA microarray one can search for regulation of transcription factors and its impact on metabolism using microarray data analysis and sequence information. By comparing wild-type W3110 strain, fadR null mutant strain, subjecting them in various conditions (i.e., different carbon sources such as oleic acid), it is possible to identify the functional role of fadR [1, 3]. Also candidate genes that could possibly be regulated by fadR can be predicted using sequence information, which assist microarray data analysis. Expression profile of wild-type W3110 strain and fadR null mutant strain (WFR) was compared in LB media (peptone 10g/L, yeast extract 5g/L, NaCl 5g/L) using E. coli cDNA microarray with 2850 ORFs. Genes related to fatty acid biosynthesis of WFR, compared to W3110, was down-regulated and genes related to fatty acid degradation were up-regulated. Through analyzing the transcriptome of Escherichia coli, genetic regulation and physiology of the cell related to fadR regulation could be explained. Understanding of the cell physiology and genetic regulation through cDNA microarray analysis may find its use in metabolic engineering and deciphering genetic regulation in metabolism.