MINING THE TRANSCRIPTION FACTOR FAMILIES FROM PLANT EST DATABASES

¹ Department of Biology and the Institute of Molecular Evolutionary Genetics, Penn State University, 208 Mueller Lab, University Park, PA 16802, USA

² Bioinformatics and Molecular Evolution, CEH Oxford,Mansfield Road, Oxford OX1 3SR, UK

Transcription factors(TFs) are important regulators of gene expression in eukaryotes. Plant transcription factors play key roles in metabolism regulation, development, reproduction and stress responses. The vast amount of EST sequences generated from specific plant tissues provide unique resources to estimate the distribution and expression level of such TF families. We surveyed all 12 (super)families of plant TFs in the the InterPro database and EST from numerous plant species. The data from various tomato tissue displays a high diversity of TFs in the early flower buds compared to later developing stages and non-reproductive tissues. The expression level of these putative developmental regulators is low when evaluated by the EST counts from non-normalized libraries. To validate the observation across species, we selected early flower and inflorescence libraries from Arabidopsis, tomato and rice, each with about 3,000 ESTs. BLAST searches identified 66~134 EST hits to transcription factor proteins. Mapping the ESTs onto contigs assembled from large pooled EST datasets yielded about 60~80 non-redundant putative genes. All TF families are represented and each species displays a comparable number of the members in a family. This is an integrated approach using EST data to identify homologs of transcription factors and to estimate the expression level in different tissues. We are expecting to combine the EST analysis results with gene-specific microarray data when the data become available. The research is supported by NSF Plant Genome Grant DBI-0115684.