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Our lab uses a variety of cutting edge tools to study collisions between DNA replication forks and RNA polymerases. These include in vivo single molecule microscopy, deep sequencing, bioinformatics, and lab-based experimental evolution. We pair these new technologies with classical genetics and molecular biology techniques, typically using the model bacterium Bacillus subtilis. This naturally competent bacteria grows quickly and is genetically tractable making experiments fast and efficient. In recent years we have also begun studying DNA replication in pathogenic bacteria including Mycobacterium tuberculosisPseudomonas aeruginosa, and Salmonella enterica.

Replication-Transcription Conflicts

Bacteria (and most other organisms) have a common requirement for accurate, timely, and faithful DNA replication. Yet a wide variety natural impediments are known to
physically slow or stall DNA replication forks, reducing fitness and increasing mutation rates. Impediments include chemical lesions, broken DNA strands, and tightly bound proteins. Much of our interest lies in identifying such obstacles, and determining what happens when DNA replication forks encounter them. In particular, we have found that actively transcribing RNA polymerases represent the most significant impediment to DNA replication. Using single molecule analysis of DNA repliction fork dynamics, we have shown that transcription collapses the replication fork and the replisome multiple times per cell cycle, increasing mutation rates, causing DNA strand breakage, and cutting the overall rate of DNA replication in half. Hence replication-transcription conflicts are a major and fundamental problem for cells.

Bacterial genome organization

Replication-transcription conflicts are especially harmful when the two machineries meet head-on. This occurs when RNA polymerases transcribe genes on the lagging strand. Presumably to avoid these
encounters, bacteria have developed highly co-oriented genomes. While this greatly reduces the frequency of head-on conflicts, many lagging strand genes remain in every bacterial species. Our previous work (matching the work of other labs) shows that transcription dramatically increases the mutation rate of co-directional genes. In head-on genes, this increase is doubled. Consistent with their higher mutation rate, we also found that head-on genes evolve at an accelerated rate. In other words, our work shows that cells can customize mutation rates in a gene-specific (based on their orientation) and temporally controlled (based on transcriptional activation/repression) manner. As such, gene orientation and replication-transcription conflicts represent fundamental aspects of genomic architecture.

Though head-on conflicts are extremely harmful to the replication fork, our latest work shows that over evolutionary time scales new head-on genes are continually being created in every bacterial species we examined. This incredible finding suggests that head-on conflicts may actually be desirable for many genes — in particular, genes that need to evolve quickly. Our functional analyses show that genes with similar functions are enriched in the head-on orientation in species that diverged more than a billion years ago. These include virulence and antibiotic resistance functions. We are actively investigating these and other exciting findings at the intersection between repliction-transcription conflicts and the evolution of genomic architectures.

Blocking evolution to prevent antibiotic resistance

Our work shows that bacteria use active mechanims to increase the mutation rate of head-on genes, accelerating their evolution. We have characterized some of these pathways, and have identified a new class of proteins we are terming “evolvability factors”. Our newest data shows that when these evolvability factors are knocked out, cells can no longer adapt to environmental stresses including exposure to antibiotics. Using new state of the art high-throughput lab-based evolution experiments and bioinformatics analyses, we are currently investigating the molecular mechanisms underlying accelerated evolution and the development of antibiotic resistance.