Bacteria achieve directed motion through their environments by integrating propulsion with chemical detection in the process of chemotaxis. Central to this process are the macromolecular protein structures of the flagellar motor and the chemoreceptor arrays, which are responsible for motility and chemical sensing, respectively. These protein complexes localise to different discrete subcellular positions in different bacterial species, and their correct subcellular localisation is often essential to their function. In the monotrichous α‐proteobacterium Rhodobacter sphaeroides, the flagellum is subpolar and two distinct sets of chemotaxis proteins localise to discrete polar and cytoplasmic positions within the cell. In this study, the development of software for the analysis of fluorescent microscopy images allowed cellular morphologies and the localisation and distribution of the chemoreceptor arrays of R.sphaeroides to be characterised in detail, showing that protein partitioning at cell division results in an asymmetric separation of both cytoplasmic and membrane‐bound protein components between daughter cells. The design of a fluorescence‐based assay for the analysis of gene expression assisted in demonstrating that expression of both the chemotaxis and motor genes of R.sphaeroides is regulated by the sigma factor, FliA, and its inhibitor, FlgM. FliA was then used to achieve varying expression of the chemotaxis genes, and the concentration dependence of array clustering was explored in microscopy images, revealing important differences between cluster formation in R.sphaeroides and other species. Additionally, FliA was identified as a regulator of flagellar number in R.sphaeroides, controlling a negative feedback‐loop in the hierarchy of flagellar assembly that represses flagellar formation upon secretion of FlgM. The complex regulatory pathway controlling R.sphaeroides flagellar assembly is the first identified system where completion of a single flagellum directly inhibits the production of a second, a mechanism that may be important to many monotrichous bacterial species.

Cells sense the properties of the surrounding environment and convert this information into changes in gene expression. Bacteria are, in contrast to many multi-cellular eukaryotes, remarkable in their ability to cope with rapid environmental changes and to endure harsh and extreme milieus. Previously, control of gene expression was thought to be carried out exclusively by proteins. However, it is now clear that small regulatory RNAs (sRNA) also carry out gene regulatory functions. Bacteria such as E. coli harbor a large class of sRNAs that bind to mRNAs to alter translation and/or mRNA stability. By identifying mRNAs that are targeted by sRNAs, my studies have broadened the understanding of the mechanisms that underlie sRNA-dependent gene regulation, and have shed light on the impact that this type of regulation has on bacterial physiology. Control of gene expression often relies on the interplay of many regulators. This interplay is exemplified by our discovery of mutual regulation between the sRNA MicF and the globally acting transcription factor Lrp. Through double negative feedback, these two regulators respond to nutrient availability in the environment which results in reprogramming of downstream gene expression. We have also shown that both the transcription factor CsgD, and the anti-sigma factor FlgM, are repressed by the two sRNAs OmrA and OmrB, suggesting that these sRNAs are important players in the complex regulation that allow bacteria to switch between motility and sessility. Bacterial populations of genetically identical individuals show phenotypic variations when switching to the sessile state due to bistability in gene expression. While bistability has previously been demonstrated to arise from stochastic fluctuations in transcription, our results suggest that bistability possibly may arise from sRNA-dependent regulatory events also on the post-transcriptional level.