Many gene families in higher plants have expanded in number, giving rise to diverse protein paralogs with specialized biochemical functions. For instance, plant general transcription factors such as TFIIB have expanded in number and in some cases perform specialized transcriptional functions in the plant cell. To date, no comprehensive genome-wide identification of the TFIIB gene family has been conducted in the plant kingdom. To determine the extent of TFIIB expansion in plants, I used the remote homology program HHPred to search for TFIIB homologs in the plant kingdom and performed a comprehensive analysis of eukaryotic TFIIB gene families. I discovered that higher plants encode more than 10 different TFIIB-like proteins. In particular, Arabidopsis thaliana encodes 14 different TFIIB-like proteins and predicted domain architectures of the newly identified TFIIB-like proteins revealed that they have unique modular domain structures that are divergent in sequence and size. Phylogenetic analysis of selected eukaryotic organisms showed that most life forms encode three major TFIIB subfamilies that include TFIIB, Brf, Rrn7/TAF1B/MEE12 subfamilies, while all plants and some algae species encode one or two additional TFIIB-related protein subfamilies. A subset of A. thaliana GTFs have also expanded in number, indicating that GTF diversification and expansion is a general phenomenon in higher plants. Together, these findings were used to generate a model for the evolutionary history of TFIIB-like proteins in eukaryotes.
Keywords: Arabidopsis thaliana; At; BRP; Brf1; C-terminal domain; CTD; Evolution; GTF; Gene family; JTT; Jones–Taylor–Thornton; Phylogenetics; Pol; RNA polymerase; TATA-binding protein; TBP; TFB; TFIIB-like protein; TFIIB-related factor 1; TSS; Transcription; general transcription factor; plant specific TFIIB-related protein; rRNA; ribosomal RNA; siRNA; small interfering RNA; small nuclear RNA; snRNA; tRNA; transcription start site; transfer RNA.
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