The long-term objective of this research is to understand the mechanisms responsible for insertion and removal of ribonucleoside monophosphates (rNMPs) from chromosomal DNA. The accurate duplication of genetic material is essential for all living cells. Recently, it has become apparent that DNA polymerases directly incorporate ribose sugars into DNA as rNMPs. A hallmark of DNA is that it is chemically stable and much less reactive than RNA. The 2'hydroxyl on the ribose sugar causes rNMPs to be 100,000 fold more reactive resulting in hydrolysis and DNA breaks under normal physiological conditions. Furthermore, the intracellular concentration of rNTPs far exceeds that of dNTPs contributing to their misinsertion into chromosomal DNA during replication. Error rates for rNMP incorporation suggest misincorporation occurs every ~103 correctly paired bases making rNMP errors far exceed that of any type of replication error or damaged base in vivo. We have found that the replicative DNA polymerases in bacteria frequently incorporation rNMPs into DNA. In this work, we will elucidate the mechanisms of insertion, removal, and the consequences to genome integrity when rNMPs are left unrepaired. Moreover, we have found a novel protein that links rNMP removal to genome integrity providing an evolutionary benefit for rNMP errors. Incorporated rNMPs have profound effects on human health. Ribonucleoside monophosphates slow DNA synthesis and rNMPs have mutagenic potential. Furthermore, RNase H2 the enzyme responsible for removing single rNMPs from DNA is essential in mice and mutations in human RNase H2 results in a neurological disorder known as Aicardi-Goutieres syndrome. Thus, our studies of rNMP insertion and removal have practical implication for human health.
Our specific aims are: 1) to determine the rate of rNMP incorporation in vitro;2) determine the mechanisms of rNMP removal;3) determine the evolutionary benefit of rNMP removal to genome integrity.

Public Health Relevance

Defects in rNMP repair causes genome instability and a neurological disorder. Furthermore, processes that affect genome stability are linked to the development of several cancers and embryonic lethality. Studies of rNMP insertion and repair will allow for the elucidation of conserved mechanisms that are important for understanding DNA polymerase fidelity and mutagenesis. PUBLIC HEALTH RELEVANCE: This work investigates replication errors caused by misinsertion of ribonucleoside triphosphates (rNTPs) into genomic DNA. It is becoming clear that replicative DNA polymerases frequently incorporate rNMPs into DNA. The mechanisms of insertion, removal and the potential benefit of these errors are not well understood. Our investigation of replication errors and the effects on genome stability will allow for the elucidaton of conserved mechanisms that are important for understanding the development of genome instability and genetic diseases in humans.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Prokaryotic Cell and Molecular Biology Study Section (PCMB)
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Janes, Daniel E
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University of Michigan Ann Arbor
Schools of Arts and Sciences
Ann Arbor
United States
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Matthews, Lindsay A; Simmons, Lyle A (2018) Cryptic protein interactions regulate DNA replication initiation. Mol Microbiol :
Burby, Peter E; Simmons, Zackary W; Schroeder, Jeremy W et al. (2018) Discovery of a dual protease mechanism that promotes DNA damage checkpoint recovery. PLoS Genet 14:e1007512
Li, Yilai; Schroeder, Jeremy W; Simmons, Lyle A et al. (2018) Visualizing bacterial DNA replication and repair with molecular resolution. Curr Opin Microbiol 43:38-45
Schroeder, Jeremy W; Yeesin, Ponlkrit; Simmons, Lyle A et al. (2018) Sources of spontaneous mutagenesis in bacteria. Crit Rev Biochem Mol Biol 53:29-48
Burby, Peter E; Simmons, Zackary W; Simmons, Lyle A (2018) DdcA antagonizes a bacterial DNA damage checkpoint. Mol Microbiol :
Burby, Peter E; Simmons, Lyle A (2018) A bacterial DNA repair pathway specific to a natural antibiotic. Mol Microbiol :
Waack, Ursula; Johnson, Tanya L; Chedid, Khalil et al. (2017) Targeting the Type II Secretion System: Development, Optimization, and Validation of a High-Throughput Screen for the Identification of Small Molecule Inhibitors. Front Cell Infect Microbiol 7:380
Burby, Peter E; Nye, Taylor M; Schroeder, Jeremy W et al. (2017) Implementation and Data Analysis of Tn-seq, Whole-Genome Resequencing, and Single-Molecule Real-Time Sequencing for Bacterial Genetics. J Bacteriol 199:
Randall, Justin R; Hirst, William G; Simmons, Lyle A (2017) Substrate specificity for bacterial RNase HII and HIII is influenced by metal availability. J Bacteriol :
Schroeder, Jeremy W; Randall, Justin R; Hirst, William G et al. (2017) Mutagenic cost of ribonucleotides in bacterial DNA. Proc Natl Acad Sci U S A 114:11733-11738

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