Response: DNA Looping and Lac Repressor--CAP Interaction

Allosteric modulation as a unifying mechanism for receptor function and regulation

Four major receptor families enable cells to respond to chemical and physical signals from their proximal environment. The ligand- and voltage-gated ion channels, G-protein-coupled receptors, nuclear hormone receptors and receptor tyrosine kinases are all allosteric proteins that carry multiple, spatially distinct, yet conformationally linked ligand-binding sites. Recent studies point to common mechanisms governing the allosteric transitions of these receptors, including the impact of oligomerization, pre-existing and functionally distinct conformational ensembles, intrinsically disordered regions, and the occurrence of allosteric modulatory sites. Importantly, synthetic allosteric modulators are being discovered for these receptors, providing an enriched, yet challenging, landscape for novel therapeutics.

Transcriptional repression: conserved and evolved features

The regulation of gene expression by transcriptional repression is an ancient and conserved mechanism that manifests itself in diverse ways. Here we summarize conserved pathways for transcriptional repression prevalent throughout all forms of life, as well as indirect mechanisms that appear to have originated in eukaryotes, consistent with the unique chromatin environment of eukaryotic genes. The direct interactions between transcriptional repressors and the core transcriptional machinery in bacteria and archaea are sufficient to generate a sophisticated suite of mechanisms that provide flexible control. These direct interactions contrast with the activity of corepressors, which provide an additional regulatory control in eukaryotes. Their modulation of chromatin structure represents an indirect pathway to downregulate transcription, and their diversity and modulation provide additional complexity suited to the requirements of elaborate eukaryotic repression patterns. New findings indicate that corepressors are not necessarily restricted to generating a single stereotypic output, but can rather exhibit diverse functional responses depending on the context in which they are recruited, providing a hitherto unsuspected additional source of diversity in transcriptional control. Mechanisms within eukaryotes appear to be highly conserved, with novel aspects chiefly represented by addition of lineage-specific corepressor scaffolds that provide additional opportunities for recruiting the same core machinery.

Efficient control of raf gene expression by CAP and two Raf repressors that bend DNA in opposite directions

The plasmid-borne raf operon of Escherichia coli encodes proteins involved in the uptake and utilisation of the trisaccharide raffinose. The operon is subject to dual regulation; to negative control by the binding of RafR repressor to twin operators, O1 and O2, and to positive control by the cAMP-binding protein, CAP. We have identified the CAP binding site (CBS) as a 22 bp palindromic sequence with incomplete dyad symmetry by deletion analysis, DNasel footprinting and electrophoretic mobility shift assays (EMSA) of CAP-DNA complexes. The CBS is centred 60.5 bp upstream of the transcription start point and partially overlaps O1. In vivo, CAP increases rafA (alpha-galactosidase) gene expression up to 50-fold. The 28 bp spacing between the centres of CBS and the - 35 box is essential, since insertions of 4, 8, 12 or 16 bp completely eliminated rafA gene expression. In vitro binding studies revealed that the CBS, O1 and O2 sites, can be simultaneously occupied by their cognate proteins. However, no cooperativity between binding of CAP and RafR was detected. EMSA with circularly permuted DNA fragments demonstrated that CAP and RafR proteins bend raf promoter (rafP) DNA by 75 degrees +/- 5 degrees and 95 degrees +/- 5 degrees, respectively, in opposite directions. Among sugar catabolic operons, the compact arrangement of three protein-binding sites, a CBS and two operators bounding the - 35 promoter box, is unique and provides a sensitive and highly efficient device for transcriptional control.

Some repressors of bacterial transcription

For a long time, repression of transcription in Escherichia coli was thought to be generally caused by one repressor binding to one operator. Recent work has indicated the frequent presence of auxiliary operators and helper proteins. The recent solution of the X-ray structures of Lac and Pur repressors were breakthroughs; yet, it has become painfully clear that important aspects of repression are still not understood.