Protein complex to die for
9 November 2017
Our hereditary material contains around 20.000 genes, which make our cells and organs function. The cell has put in place an elaborate control mechanism to ensure that the right genes are put to work at the right time. Otherwise, malfunction and disease occur. Short pieces of DNA, called promoters, are located in front of genes. These are recognized by specific regulatory proteins that switch the genes on and off.
The protein in humans at the core of this control mechanism is called TBP. TBP stands for TATA-box binding protein. The TATA-box, a short DNA segment, is a hallmark of human promoters. TBP comes in shape of a saddle as it straddles the DNA double helix in front of genes. Many other proteins, called transcription factors, then join TBP to activate a gene of choice.
At least this is how conventional thinking goes. An international research team lead by Bristol genome biologist Imre Berger now discovered an unforeseen twist to the story.
“The literature says that two transcription factors, called TAF11 and TAF13, would bind to TBP when it sits on promoter DNA, and hold TBP in place there.” recalls Kapil Gupta, post-doc in the Berger lab and first author of the study. “Our results, however, radically challenged this view.” Rather than helping TBP to bind DNA, the two transcription factors seemingly conspired to throw TBP off the promoter, by obstructing TBP’s DNA binding groove.
The scientists and their collaborators painstakingly scrutinized their findings until there remained no doubt. The structure of the TAF11/TAF13/TBP complex, backed up by a host of biochemical data, confirmed that the transcription factors effectively competed for promoter DNA when engaging TBP.
“We then wanted to know whether what we saw was real and not just some in vitro artefact” says Kapil. With expert help of their colleague, Anna Chambers, the scientists put to test their findings in baker’s yeast, a workhorse for genetic studies in higher organisms.
“Our structure helped us identify key amino acid residues that were crucial for the interaction of TAF11, TAF13 and TBP” recalls Kapil. Mutating these residues abolished the complex in the test tube, while leaving all other known functions of TBP, TAF11 and TAF13 unperturbed. When the same mutations were introduced in yeast, they had a profound effect – the yeast cells died.
“Evidently, this protein complex we discovered was not only entirely unexpected” concludes Kapil. “Our results also show that the complex is fundamentally important - it is required for survival”.
Gupta K, Watson AA, Baptista T, Scheer E, Chambers AL, Koehler C, Zou J, Obong-Ebong I, Kandiah E, Temblador A, Round A, Forest E, Man P, Bieniossek C, Laue ED, Lemke EA, Rappsilber J, Robinson CV, Devys D, Tora L, Berger I. Architecture of TAF11/TAF13/TBP complex suggests novel regulation properties of general transcription factor TFIID. Elife. 2017 Nov 7;6. pii: e30395.