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Eukaryotic transcription factors

DOI: 10.1186/gb-2001-2-2-reports0004

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Abstract:

Within the Arabidopsis genome, 1,533 genes were found to encode members of known transcription factor families, 45% of which are from families specific for plants. The fraction of transcription factor genes among all genes is slightly higher in Arabidopsis (5.9%) compared with Drosophila, C. elegans and yeast (4.5, 3.5 and 3.5%, respectively). A variety of prominent transcription factor families are present in all four species, including Myb, basic helix-loop-helix, basic leucine zipper, C2H2 zinc finger and homeodomain transcription factors. Except for the conserved DNA-binding domains, however, there are no significant similarities between members of the same transcription factor family from different kingdoms.Three types of evolutionary process appear to be mainly responsible for the observed differences in transcription factor complements: the generation of completely novel families; the specific amplification of families common to all three eukaryotic kingdoms; and domain shuffling, leading to new combinations of common transcription factor domains. As well as several small families, the large families of AP2/EREBP, NAC and WRKY transcription factors, consisting of 144, 109 and 72 members, respectively, are found exclusively in plants. In contrast, nuclear hormone receptors and GAL4-like C6 zinc finger proteins, which are strongly represented in animals and yeast, respectively, appear to be absent from plants. In plants, the Myb superfamily is strongly amplified, comprising 190 members. These regulators, which constitute the largest class of plant transcription factors, are only weakly represented in the other eukaryotic kingdoms. Exon shuffling has led to transcription factors unique to plants that contain both homeodomains and leucine zippers. In addition to these HD-ZIP proteins, leucine zippers can be found in the plant-specific WRKY factors as well as in basic leucine zippers, which are present in all three eukaryotic kingdoms.Supplementary data to Science

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