Trends in Biochemical Sciences
Volume 24, Issue 9, 1 September 1999, Pages 335-339
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Talking Point
The TBP-like factor: an alternative transcription factor in Metazoa?

https://doi.org/10.1016/S0968-0004(99)01436-XGet rights and content

Abstract

Protein sequence analysis has revealed a family of TATA-binding-protein (TBP)-like factors (TLFs) in metazoan organisms. Modelling of the three-dimensional structure of these TLFs suggests that they form an asymmetric saddle-like structure and that, unlike TBP, TLFs might bind to DNA sequences other than classical TATA boxes. Thus, the existence of TLFs presents a challenge to the doctrine that TBP is a universal regulator of transcription in metazoans.

Section snippets

A new family of TBP-like factors (TLFs) found in metazoans

The emerging controversy in the literature about factors with homology to TBPs17, 18, 19, 20, 21 and the recent progress made in genome and cDNA sequencing prompted us to search more carefully for TBP homologues. We have used the core domain of human TBP as a query sequence in PSI-BLAST searches of GenBank, EMBL, DDBJ and Genome Sequencing Center databases. Surprisingly, in addition to the previously described TBPs, we found a set of factors with a significantly high similarity to TBPs (E

Conserved structural features of TBPs and TLFs

Several amino acid residues that fulfil important functions in the molecular structure of TBP are conserved among all TLFs (Fig. 1). This sequence conservation raises the interesting possibility that the molecular architecture of the TLF is similar to that of TBP and that TLFs also adopt a saddle-like structure. In the TBP–TATA box crystallographic structure the two asparagine residues (N167 and N257

Key amino acids of TLFs determine their DNA-binding specificity

The most impressive structural interaction between the side chains of TBP and the minor groove of the DNA is shown by the two pairs of phenylalanine residues (F197–F214 and F288–F305 in hsTBP, arrowheads in Fig. 1), one in each repeat, which insert into the DNA helix between T1 and A2 as well as between A7 and G8 bases of the TATA box25, kinking the DNA (Fig. 3a). In this respect, TBPs exhibit a symmetric interaction with the DNA, i.e. both repeats interact with DNA in a similar way. The first

Interactions of TLF with other components of the Pol II pre-initiation complex

Separate crystal structure complexes revealed the TBP residues that are involved in contacts with TFIIA (29, 30) and TFIIB (Ref. 31). The TLF residues corresponding to TBP residues that contact TFIIA and TFIIB are fairly well-conserved among all TLFs. TFIIA-binding residues in the N-terminal repeat of the different TLFs are about 40–75% identical to the corresponding TBP residues, whereas, strikingly, the TFIIB-binding 283YEPEL287 structural motif in the C-terminal repeat is 100% conserved

Conclusions and outlook

Taken together, the above observations suggest that the TLF will function in Pol II transcription but with a DNA-binding specificity different from TBP. As TLFs have been found in a large number of metazoans (in contrast to TRF), it is likely that Metazoa have developed a second factor to facilitate differential gene expression. Thus, the interpretation of the mechanisms responsible for mRNA production in Metazoa should be revised and the above-described alignments, structural similarities and

Acknowledgements

We thank the Filarial Genome Project (University of Edinburgh), the Resource Centre of the German Human Genome Project (Max Planck Institute) and the Berkeley Drosophila Genome Project for the different EST clones, the Genome Sequencing Center (Washington University, St Louis) for communication of DNA sequence data prior to publication, and Brendan Bell for critical reading of the manuscript. We apologize to colleagues whose work could only be cited indirectly in this review owing to space

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