NutriCoRe · An RNA-based mechanism for the nutritional control of bacterial DNA replication initiation

An RNA-based mechanism for the nutritional control of bacterial DNA replication initiation

Bacteria form the largest part of the Earth’s biomass, playing essential roles in natural environments and performing important functions in industrial processes. Nevertheless, uncontrolled growth of bacteria remains a major threat to humankind, posing various problems in industry and public health, especially due to the constant rise of antibiotic resistance. Under optimal conditions, bacteria thrive and proliferate with an astonishing rate. On the other hand, in response to adverse conditions, including nutrient depletion or environmental stress, bacteria can reduce or completely arrest their growth and proliferation to ensure their survival. Indeed, entering a non-proliferating state has been demonstrated to enhance bacterial drug tolerance and intracellular persistence of pathogenic bacteria. Knowledge about the mechanisms that allow bacteria to adjust their own growth and proliferation in response to changing conditions is thus critically important for a better understanding of infectious diseases and antibiotic resistance. Growth arrest requires a decline in the production of cellular mass and the concomitant cessation of cell cycle processes, including DNA replication. DNA replication is the process enabling the transmission of genetic information to the progeny and it is followed by chromosome segregation and cell division. It has been observed that under nutrient-starvation conditions different bacteria arrest the cell cycle with a reduced number of fully replicated chromosomes indicating that DNA replication is blocked at the replication initiation step. However, a molecular mechanism by which DNA replication initiation is nutritionally controlled has never been reported. The initiation of DNA replication in nearly all bacteria requires the product of the gene dnaA, an enzyme that recognises and binds specific sequences present on the bacterial chromosome at the origin of replication. DnaA forms an oligomeric structure that unwinds DNA and recruits the DNA replication apparatus. Given its central role in timing the initiation of DNA replication, DnaA represents a strong candidate for transducing environmental information into the cell cycle. The NutriCoRe project aimed to elucidate the molecular mechanisms involved in the DNA replication arrest in response to nutrient-starvation in bacteria. To address this fundamental question, I used the model bacterium Caulobacter crescentus. Under carbon depletion conditions and during the transition to the stationary phase, DnaA levels rapidly drop in C. crescentus and DNA replication is arrested. By combining bioinformatics, classical biochemistry, genetics, and cutting-edge molecular biology techniques, this project led to an improved understanding of the mechanism of nutritional control of DNA replication. In particular, I discovered that under carbon-limiting conditions, DnaA translation ceases, likely through the nutrient-dependent pausing of the protein synthesis machinery (i.e. the ribosome) during the synthesis DnaA’s nascent chain (Nterm). I hypothesise that the complex formed by the ribosome and DnaA Nterm is able to sense the nutritional state of the cell, thus arresting the synthesis of new DnaA. Overall, this project sheds new light onto the mechanisms transducing nutritional information into bacterial cell cycle.

Data: CORDIS, © European Union