Genomic instability drives cancers, adaptation of pathogens to hosts, and evolution of resistance to anti- pathogen and anti-cancer drugs. In contrast with classical assumptions that mutations occur purely stochastically with constant and gradual rates, microbes, plants, flies and human cancer cells possess mechanisms of mutagenesis upregulated by stress responses. Discovered in bacteria and similar across the tree of life, these mechanisms generate transient bursts of genetic diversity that can propel evolution specifically when cells are poorly adapted to their environments?when stressed. Stress-induced-mutation mechanisms may provide superior models for genetic changes that drive pathogen-host adaptation, antibiotic resistance, aging, cancer progression and therapy-resistance mechanisms, and possibly much of evolution generally. This proposal addresses how stress responses upregulate mutagenesis, and how to stop them: fundamental and medically urgent problems. We propose to investigate two stress-induced-mutation mechanisms in E. coli: mutagenic DNA break repair (MBR), and mutagenesis induced by antibiotics: models for mutagenesis in many medically critical contexts. Both require the general, stringent, and DNA-damage stress responses, which allow error-prone DNA polymerases to promote mutations. Our approach will integrate experimental genomic, genetic, synthetic and single-cell strategies with engineered proteins that trap DNA reaction intermediates, all in living cells. We will address regulated mutagenesis from four directions: Discovery of how cells regulate MBR in time. Which gene(s) up- or down-regulated by the general stress-response throw the switch to mutagenic break repair? By what mechanism? How does the stringent stress response independently promote starvation- and antibiotic-induced MBR? Discovery of MBR regulation in single cells. Four stress responses promote MBR, some activated in cell subpopulations. We will determine which subpopulations undergo mutagenesis and illuminate differentiation into a mutable state?a possible evolutionary ?bet hedging? strategy. Discovery of how cells restrict mutations in genomic space. We will map spontaneous DNA breaks in genomes, and unravel their causes. We will discover whether more breaks, more break-repair, or other causes target specific large genomic regions for multiple mutation hotspots. Antibiotic-induced mutagenesis. We will dissect a molecular mechanism of antibiotic-induced mutagenesis similar to MBR. We will develop novel drugs to target mutagenesis as possible antibiotic adjuncts, to slow evolution of pathogens, and as a model anti-cancer strategy. This project includes collaborations with pioneering chemists, physicists, bioinformaticians, biochemists, and molecular biologists. Our shared goal is to provide both important models for understanding of and intervention in the medical problems listed above and specific tools for combating antibiotic resistance.
This project will provide new ways to approach and combat problems of microbial pathogenesis and antibiotic resistance, development of cancers, evolution of cancer- chemotherapy resistance, and aging among other serious problems in human health.
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