International network for natural sciences – research journal
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Comparative microarray data analysis of Arabidopsis genome during interaction with a mutualistic and a pathogenic bacteria

By: Nazeer Ahmed, Shahjahan Shabbir Ahmed, Fazalur Rehman, Muhammad Naeem Shahwani, Muhammad Saeed, Imran Ali Sani, Muhammad Naseem

Key Words: Microarray, Mutualism, Pathogenesis, Expression profiling.

Int. J. Biosci. 9(4), 281-291, October 2016.



Plants are in continuous interaction with both mutualistic and pathogenic microorganisms, particularly in the rhizosphere. Arabidopsis has served as an excellent model plant in a variety of experiments to determine the details and nature of such relationships. Studies involving transcriptome profiling of Arabidopsis thaliana in response to pathogenic and beneficial bacterial infection are available, each focusing primarily on defense related and plant growth promotion related genetic component respectively. In an attempt to decipher the difference in responses of plants to these two types of bacteria, we resorted to genome wide comparative analysis both when it was exposed to a foe and a friend. Publically accessible web based array data emanating from Arabidopsis responses to Pseudomonas syringae pv. tomato DC 3000 (Pst) a virulent pathogen that causes disease on tomato and Arabidopsis and Burkholderia phytofirmans Ps JN, a growth promoting rhizobacteria were used for the comparative approach using bioinformatics tools including GEO 2R, TAIR etc. The results, although, contained regulated genes common in both treatments, the differentially regulated genes unique to each data set predominated the common genes. The results clearly indicated that different sets of Arabidopsis genes were regulated when treated with pathogenic and mutualistic bacteria. Differences were also evident at pathways, cellular processes and the molecular function level. The findings call for a comprehensive and detailed analysis of those genes showing a dissimilar trend as far as changes in their expression pattern is concerned.


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