Development of an In vitro, coupled transcription-to-translation system for analysis of the interactions between the ribosome and RNA polymerase

PhD ThesisThe various properties of actively transcribing RNA polymerase (RNAP) complexes with nucleic acids during different stages involve various types of regulation and different cross-talk with other cellular entities and with RNAP itself. For instance, transcription and translation are coupled in bacteria, meaning that translation takes place co-transcriptionally. The interactions of transcriptional apparatus with the translational machinery have been focused mainly in terms of gene expression, whereas the study of the physical interaction of the ribosome and the RNA polymerase remains obscure due to the lack of a system which allows such observations. In this study we have developed a pure, transcription-coupled-to-translation system in which the translocation of the ribosome can be performed in a step-wise manner towards RNAP allowing the observation of the outcomes of the interactions between the two machineries at colliding and non-colliding distances; the system also allows the positioning of RNAP in any desired elongation complex such as paused, roadblocked, backtracked, etc. We show the study of the interactions of the ribosome on different aspects of transcription elongation and also the effects on translation caused by RNAP