Replication Checkpoints and the Metabolic Response to Perturbations in DNA Replication

Stanford University, Stanford CA

Investigators

Abstract

All cells have mechanisms for delaying cell division until DNA replication and repair have been successfully completed. In the gram-positive bacterium Bacillus subtilis, three signaling pathways have been identified that delay cell division or shift the division site when DNA replication is inhibited. A fourth signaling pathway mediated by the checkpoint protein Sda delays sporulation, a developmental response to nutrient limitation, when DNA replication is perturbed. Preliminary data show that blocking replication elongation induces a starvation-like signal and that the Sda checkpoint prevents cells from inappropriately responding to replication stress as though they were starving. Hypothesis-based approaches are being used to identify the starvation-like signal and to determine how it is generated by replication stress. These studies will lay the foundation for asking if the physiological response occurs in other organisms and if checkpoints analogous to Sda are important for competitive fitness in stressful and changing environments. The second aim of this project is to identify genes that are required to prevent cells from dividing over unsegregated chromosomes ("nucleoid bisection") when DNA replication is inhibited. Mutant cells lacking the three known replication checkpoints often delay cell division or shift the division site when DNA replication is perturbed, suggesting that there is at least one more checkpoint pathway. Several new genes required to prevent nucleoid bisection during replication stress have been identified using genetic and bioinformatics approaches. Two encode enzymes, one of which directly or indirectly inhibits cell division in the presence but not the absence of replication stress. These early results suggest that cell cycle progression may be subject to metabolic regulation in ways that are only now being identified. Replication checkpoints and the cellular response to replication stress are often studied at the level of 'information processing', asking how cells monitor DNA replication to stably maintain genetic information. This project broadens the question and is aimed at developing an integrated view of how cellular information processing and metabolism are interconnected. The PI has developed a teaching program that synergizes well with the questions addressed in these studies, generating excitement and fresh ideas in both the classroom and the laboratory. The courses focus on student developing in the areas of problem solving skills, critical and independent thinking, and formulating clear arguments for presentation. The mentoring of undergraduate and Ph.D. students is a key component of the research program, and students have regular opportunities to present their work at seminars and meetings.