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Genetics, Vol. 179, 31-39, May 2008, Copyright © 2008
doi:10.1534/genetics.107.086090
Green Transcription Factors: A Chlamydomonas Overview
Diego Mauricio Riaño-Pachón*,
,1,
Luiz Gustavo Guedes Corrêa*,
,1,
Raúl Trejos-Espinosa*, and
Bernd Mueller-Roeber*,,2
* Department of Molecular Biology, University of Potsdam, 14476 Potsdam-Golm, Germany, Bioinformatics Research Group, Max-Planck Institute of Molecular Plant Physiology, GabiPD Team, 14476 Potsdam-Golm, Germany and Cooperative Research Group, Max-Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
2 Corresponding author: Department of Molecular Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, Haus 20, 14476 Potsdam-Golm, Germany.
E-mail: bmr{at}uni-potsdam.de
Transcription factors (TFs) control gene expression by interacting with cis-elements in target gene promoters. Transcription regulators (TRs) assist in controlling gene expression through interaction with TFs, chromatin remodeling, or other mechanisms. Both types of proteins thus constitute master controllers of dynamic transcriptional networks. To uncover such control elements in the photosynthetic green alga Chlamydomonas reinhardtii, we performed a comprehensive analysis of its genome sequence. In total, we identified 234 genes encoding 147 TFs and 87 TRs of 
40 families. The set of putative TFs and TRs, including their transcript and protein sequences, domain architectures, and supporting information about putative orthologs, is available at http://plntfdb.bio.uni-potsdam.de/v2.0/. Twelve of 34 plant-specific TF families were found in at least one algal species, indicating their early evolutionary origin. Twenty-two plant-specific TF families and one plant-specific TR family were not observed in algae, suggesting their specific association with developmental or physiological processes characteristic to multicellular plants. We also analyzed the occurrence of proteins that constitute the light-regulated transcriptional network in angiosperms and found putative algal orthologs for most of them. Our analysis provides a solid ground for future experimental studies aiming at deciphering the transcriptional regulatory networks in green algae.
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