Identification and Evolution of Transcription Factors in Stramenopiles

Transcription factors (TFs) regulate spatial and temporal gene expression by binding to DNA and either activating or repressing the action of RNA polymerases; in addition to TFs, other transcriptional regulators (TRs) participate in transcriptional modulation. With the availability of genome sequences for several organisms and computational strategies for gene functional annotation, the entire set of TFs and TRs can be identified, described, and compared between species and lineages. The diversity among Stramenopiles is striking; they range from large multicellular seaweeds to tiny unicellular species, they are present in freshwater, marine and terrestrial habitats and embrace many ecologically important algal (e.g. diatoms, brown algae, chrysophytes), and heterotrophic (e.g., Oomycetes) groups. In order to find TF and TR genes in the deduced proteomes of Stramenopiles, we followed and extended the approach developed in Perez et al. 2010. Briefly, it exploits the presence of protein domains and their combinations, in the form of boolean rules, that are specific for different families of TFs and TRs. We applied an enlarged set of rules to the deduced proteomes of 9 different Stramenopiles, identifying more than 400 different regulatory genes in each species belonging to up to 126 different gene families. The identification of this class of regulatory genes will constitute and important resource that could be exploited in gene functional characterization and evolutionary analyses. All TFs/TRs families found will be publicly released via a web database. References. Pérez-Rodríguez P, Riaño-Pachón DM, Corrêa LG, Rensing SA, Kersten B, Mueller-Roeber B. 2010. Nucleic Acids Res. 38(Database issue):D822-7