The long temi goals of this proposal are to understand the control of bacterial DNA replication and the connections between replication and gene expression. Cell growth and propagation require duplication and segregation of chromosomal DNA. Cells have multiple mechanisms for regulating the initiation of replication and many have regulatory responses to perturbations in replication, often called checkpoints, which control cell cycle progression. Coupling gene expression and cell cycle progression to chromosome replication and integrity helps prevent the generation of cells with defective chromosomes. The coordination of genome duplication with cell cycle progression is also important for cellular differentiation and preventing uncontrolled cell growth. Many diseases, including cancers, result from aberrant regulation of replication and cell growth, in addition, microbial pathogenesis often depends on normal bacterial replication and growth in the host. This proposal focuses on several aspects of chromosome dynamics and gene expression in the Gram- positive bacterium Bacillus subtilis. We will use a variety of approaches and methodologies, both in vivo and in vitro, to characterize genes controlled in response to replication fork arrest, the role of DnaA, the replication initiator protein, in the transcriptional response to replication fork arrest, and the control of replication initiation and assembly of the replisome at an origin of replication in vivo. The fundamental principles and mechanisms controlling these processes are easily studied in B. subtilis using a combination of cell biological, genetic, molecular, physiological, biochemical, and bioinformatic approaches. Because many of the proteins involved in these processes are highly conserved, insights gained from our work with this relatively simple, experimentally accessible microbe, are likely to provide information regarding similar processes and homologous proteins in a wide variety of organisms, including many of the important Gram-positive pathogens. Learning more about the essential mechanisms governing chromosome replication and its effects on gene expression could lead to the identification of targets for the development of new antibiotics.

Public Health Relevance

Many diseases result from aberrant replication and microbial pathogenesis often depends on normal bacterial replication and growth, making these processes potentially useful antibiotic targets. This project investigates several conserved aspects of replication control in the bacterium Bacillus subtilis, a harmless yet useful organism representative of several bacterial species that cause serious human disease. L

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Method to Extend Research in Time (MERIT) Award (R37)
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Special Emphasis Panel (NSS)
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Reddy, Michael K
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Massachusetts Institute of Technology
Schools of Arts and Sciences
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Seid, Charlotte A; Smith, Janet L; Grossman, Alan D (2017) Genetic and biochemical interactions between the bacterial replication initiator DnaA and the nucleoid-associated protein Rok in Bacillus subtilis. Mol Microbiol 103:798-817
Washington, Tracy A; Smith, Janet L; Grossman, Alan D (2017) Genetic networks controlled by the bacterial replication initiator and transcription factor DnaA in Bacillus subtilis. Mol Microbiol 106:109-128
Schons-Fonseca, Luciane; da Silva, Josefa B; Milanez, Juliana S et al. (2016) Analysis of LexA binding sites and transcriptomics in response to genotoxic stress in Leptospira interrogans. Nucleic Acids Res 44:1179-91
Smith, Janet L; Grossman, Alan D (2015) In Vitro Whole Genome DNA Binding Analysis of the Bacterial Replication Initiator and Transcription Factor DnaA. PLoS Genet 11:e1005258
Bonilla, Carla Y; Grossman, Alan D (2012) The primosomal protein DnaD inhibits cooperative DNA binding by the replication initiator DnaA in Bacillus subtilis. J Bacteriol 194:5110-7
Merrikh, Houra; Zhang, Yan; Grossman, Alan D et al. (2012) Replication-transcription conflicts in bacteria. Nat Rev Microbiol 10:449-58
Merrikh, Houra; Grossman, Alan D (2011) Control of the replication initiator DnaA by an anti-cooperativity factor. Mol Microbiol 82:434-46
Merrikh, Houra; Machón, Cristina; Grainger, William H et al. (2011) Co-directional replication-transcription conflicts lead to replication restart. Nature 470:554-7
Rahn-Lee, Lilah; Merrikh, Houra; Grossman, Alan D et al. (2011) The sporulation protein SirA inhibits the binding of DnaA to the origin of replication by contacting a patch of clustered amino acids. J Bacteriol 193:1302-7
Smits, Wiep Klaas; Merrikh, Houra; Bonilla, Carla Yaneth et al. (2011) Primosomal proteins DnaD and DnaB are recruited to chromosomal regions bound by DnaA in Bacillus subtilis. J Bacteriol 193:640-8

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