RNASEDYNAMICS · Spatial organization and dynamics of Escherichia coli RNA degradation machinery

The aim of this research proposal is to investigate in detail the location and mobility of RNA degradation machinery in E. coli. RNA decay has been widely studied in bacteria but continues to reveal subtle secrets [1,2]. Recent research demonstrates that the degradosome complex forms cytoskeletal-like structures linked with the inner cell membrane [3]. Preliminary results from Cecilia Arraiano’s laboratory (host laboratory) have shown that RNase R colocalises with the bacterial nucleoid, whereas RNase II is exclusively a cytoplasmic protein. Consequently, the main bacterial nucleases may have different cellular locations. After developing a system for in vivo localisation of RNases I will investigate their dynamics, likely factors that influence their mobility, and consequences of differential location. Because environmental stresses alter levels of RNases, I will check whether rearrangement of the degradation machinery is connected to changes in its cell location, and/or is linked to the formation of degradation foci analogous to eukaryotic processing/degradation P-bodies. This year it was reported in Science that abortive E. coli polymerase transcripts are produced in vivo during transcription initiation [4]. I will therefore investigate whether RNase R location in the nucleoid is functionally connected to degradation of these newly discovered small RNAs.