Negative regulatory proteins bind to operator sequences in the DNA and prevent or weaken RNA polymerase binding

Most prokaryotic mRNA molecules are polycistronic, they encode multiple genes. These genes are usually involved in the same biochemical event. A single promoter controls the expression of these genes. This functional unit of DNA is called an operon.

A classical example of transcriptional regulation is lactose metabolism in E. coli. Proteins required for lactose metabolism in E. coli are encoded by the lac operon.

The E. coli lac operon lacI – encodes the Lac repressor protein lacZ – encodes  -galactosidase lacY – encodes galactose permease lacA – encodes transacetylase O 2 and O 3 are pseudooperators

The Lac repressor protein is thought to bind to the main operator and one of the pseudooperators, forming a loop in the DNA.

When lactose is present in high concentrations, the lactose metabolism gene products are needed in a cell. In the absence of lactose, the Lac repressor protein binds to the operator in the DNA, repressing transcription. The Lac repressor, however, binds to allolactose, a metabolite of lactose, inducing a conformational change that abolishes binding to the DNA operator sequence. Transcription is no longer repressed. - allolactose  transparent + allolactose  bold

DNA binding proteins contain amino acids that hydrogen bond to functional groups in the major groove of DNA.

DNA sequences recognized by regulatory proteins are often inverted repeats of a short DNA sequence. These repeats form a palindrome with two-fold symmetry about a central axis. Regulatory proteins are often dimeric. Each subunit binds to one strand of the DNA. 5’-TACGGTACTGTGCTCGAGCACTGCTGTACT-3’ 3’-ATGCCATGACACGAGCTCGTGACGACATGA-5’ central axis

The Lac repressor protein The Lac repressor is a tetramer of four identical protein subunits. There are DNA-binding domains on each subunit shown in blue. The allolactose binding domain (green) is connected to the DNA binding domain through linker helices (yellow). Tetramerization domains (red) form contacts between subunits.

The Lac repressor protein The Lac repressor is a tetramer of four identical protein subunits. There are DNA-binding domains on each subunit shown in blue. The allolactose binding domain (green) is connected to the DNA binding domain through linker helices (yellow). Tetramerization domains (red) form contacts between subunits.

The DNA binding domains of the Lac repressor contain a helix-turn-helix motif, a structure critical for the interaction of many proteins with DNA. helix turn helix

Lac repressor protein (lacI)

Lac repressor bound to DNA