TFIIB is a component of the minimal eukaryotic as well as the archaeal transcriptional
machinery that is essential for promoter-directed transcription. The flexible linker
domain of the protein engages in an intimate association with the RNA polymerase
surface. Early structural data suggested that the linker forms a finger-like structure (the
‘B-finger’) within the RNA exit channel projecting into the active centre. Biochemical
data indicated a contribution of the archaeal ‘B-finger’ domain to the catalytic
mechanism by stimulating abortive transcription. The path of the linker within the RNA
polymerase catalytic centre has recently been re-assessed and residues of the original Bfinger
were re-assigned to structural elements named ‘B-reader helix’ and ‘B-reader
loop’.
Novel high-throughput tools, in combination with a comprehensive mutagenesis screen
of residues E78 to A95, facilitated the biochemical evaluation of structural-functional
relationships of the M. jannaschii TFIIB linker – RNAP interface at a single residue
resolution. The performance of such point mutants during abortive initiation and RNA
polymerase recruitment was interpreted in light of structural information.
The tip region of the ‘B-finger’ that was predicted to be closest to the active site was
insensitive to mutations in abortive initiation assays, thus disproving the original model.
Individual residues, forming part of the B-reader helix and the C-terminal half of the Breader
loop, were found to engage in abortive transcription. Three-residue deletions
within the N-terminal half of the B-reader loop resulted in super-stimulation of abortive
transcription. Individual point mutations within the B-reader loop led to enhanced
recruitment of RNA polymerase. A functional role of the loop in stabilizing TFIIBRNA
polymerase-DNA complexes in both the absence and presence of TBP seems
feasible.
The combined data provide a detailed view of biochemical functions of individual
residues of the TFIIB linker favouring the ‘B-reader’ model over the ‘B-finger’ model