The bacterial RNA polymerase (RNAP) requires an additional type of subunit called the σ factor to recognise the promoter element of the gene and to form the holoenzyme that is capable of transcription initiation. The sigma factor within the core enzyme separates the double-stranded DNA that helps to initiate the transcription in the active channel of the holoenzyme. As each of the sigma factors binds at the specific promoter region upstream of the gene, it can guide the assembly of the holoenzyme and consequently regulates the transcription of the gene. The different types of σ factor that bind to the RNAP core enzyme can regulate the transcription of different sets of genes, should the bacteria require to survive through the change in the environment. The σ factor can be regulated, and the proteins that regulate the sigma factor are therefore essential in the survival of the bacteria.

The thesis includes two parts. The first part of the thesis describes the NMR assignments and the solution structure of the receiver domain of RssB, a σS regulator that plays an essential role in the regulated proteolysis of the σS. Additionally, the NMR titration of one of the anti-adapter protein IraD with the receiver domain of RssB helps to understand the binding interface of the complex. This solution structure provided the basis for future studies on the regulation of the
σS.

The second part of the thesis describes the characterisation of the N-terminal CARF domain of RtcR, a transcriptional regulator of the RNA repairing system Rtc that interacts with σN . In this study, the protein was found to form a protein-RNA-protein complex with the 16S rRNA and the RNA cyclase protein RtcA. This finding provided the basis for further studies on this protein-RNA complex and its biological significance in the regulation of σN-dependent genes.