Why is the bacterial mRNA degradation machinery membrane associated?

A defining characteristic of living cells is the process in which genetic information encoded on DNA is transcribed into a mobile information carrier (mRNA) which, in turn, guides protein biosynthesis. In order to respond to environmental changes, and to induce developmental processes, cells can regulate their protein production. This process relies on high turnover of mRNA, which enables the control of protein biosynthesis by regulating gene expression. In eukaryotic cells, these processes are spatially separated into different cellular compartments (nucleus and cytoplasm), thus providing protection and control over the potentially deleterious RNA-degradation process. By contrast, bacterial cells are not compartmentalised and other means are required to protect the synthesised mRNA from premature degradation, while still providing high enough mRNA turnover for the gene regulation mechanisms to work.
In bacteria, the main proteins providing high mRNA turnover assemble into a large protein complex termed the RNA degradosome. This protein complex is assembled around conserved endoribonucleases RNase E (Gram-negative bacteria) or RNase Y (Gram-positive bacteria). While these protein are not homologs, they exhibit an astonishing level of convergent evolution with respect to their role as the central scaffold for the degradosome formation, and with respect to the cellular spatial organisation. By using a different mode of membrane attachment (periferal membrane binding and transmembrane domain, respectively), both ribonucleases tether the corresponding mRNA degrading machineries to the cytoplasmic membrane. The biological reason for the conserved membrane association has so far remained elusive. By restricting mRNA degradation to the cell periphery, mRNA synthesised within the mid-cell localised nucleoid needs to diffuse through the ribosome-rich cytoplasm before reaching the membrane-bound RNA degradosome. This spatial separation could, thus, provide the cell with the necessary means to protect mRNA from pre-translational degradation while still allowing high enough turnover required for efficient regulation of protein synthesis.
In this PhD project, we will combine cell biology with next generation sequencing techniques to analyse the biological reason for the surprising membrane association of the RNA degradation. To answer this fundamental research question, we will use an unbiased genetic suppressor screen combined with next generation genome sequencing to identify mutations that supress the acute toxicity of the RNA degradosome upon release to the cytoplasm. This approach allows us to gain insight into the poorly understood regulatory mechanism governing the cellular mRNA turnover. We will also analyse the consequences of the cytoplasmic release of the RNA degradosome on the global mRNA pool by RNA-sequencing, thus providing crucial information about the biological benefits of tethering the mRNA degradation machinery to the cell periphery. At last, we will analyse the clustering of the mRNA degradation machinery induced by certain environmental conditions; a recently discovered phenomenon which points towards a so far unrecognised layer of global regulation affecting the cellular mRNA pool.
The proposed research programme combines two powerful but rarely integrated approaches to obtain insight into the fundamental cell function: bioimaging data providing information of the cellular spatial organisation, and RNA-sequencing providing an unprecedented level of insight into the transcriptome. The spatial aspect of cellular biology is currently overlooked in most systems modelling approaches. The proposed project, thus, paves the way to the integration of spatial data with computational models of living cells.