Emergence and expansion of TFIIB-like factors in the plant kingdom

Abstract

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.

A Genetic Screen for Pre-mRNA Splicing Mutants of Arabidopsis thaliana Identifies Putative U1 snRNP Components RBM25 and PRP39a

“…Promoter recognition and transcription initiation by RNAP II requires up to seven general transcription factors (GTFs), including TATA binding protein (TBP), TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIIH. Two of the best-studied GTFs are TBP and TFIIB, which have key roles at multiple steps of the RNAP II transcription cycle ( Knutson 2013 ). Arabidopsis encodes two distinct TBPs ( Lawit et al 2007 ) and eight TFIIB-like proteins ( Knutson 2013 ).…”

“…Two of the best-studied GTFs are TBP and TFIIB, which have key roles at multiple steps of the RNAP II transcription cycle ( Knutson 2013 ). Arabidopsis encodes two distinct TBPs ( Lawit et al 2007 ) and eight TFIIB-like proteins ( Knutson 2013 ). We identified both TBP genes and TFIIB1 in our analysis of alternative splicing in prp39a mutants.…”

Arabidopsis CBP1 Is a Novel Regulator of Transcription Initiation in Central Cell-Mediated Pollen Tube Guidance

“…The TFIIB family consists of 14 members in Arabidopsis (Knutson, 2013). In contrast to TFIIB1 and TFIIB2 containing an N-terminal zinc ribbon domain, a linker domain, and two cyclin fold repeats, CCG contains an extended C-terminal domain ( Figure 1A).…”

“…Phylogenic analysis classifies CCG as the RNA polymerase I (Pol I) TFIIB-like transcription factor by sequence homology with the yeast and human counterpart Rrn7 and TAF1B (Knutson and Hahn, 2011;Naidu et al, 2011;Knutson, 2013). Pol I transcribes the ribosomal DNA into rRNA precursor, which is essential for cell viability.…”

“…Immunostaining analysis showed that Arabidopsis LURE1 peptides are not detected in myb98, maa3, and ccg ovules (Takeuchi and Higashiyama, 2012), suggesting that there might be intercellular interactions between the central cell and the synergids to coordinate LURE1 production. CCG encodes a nuclear protein with a conserved N-terminal zinc ribbon domain that is typical for the transcription factor TFIIB family (Knutson, 2013). It has been proposed that CCG plays a role in transcription initiation, but the underlying mechanism remains unclear.…”