Cellular processes are controlled by gene regulatory circuits that are comprised of interactions among genes and proteins. One such process common to organisms ranging from bacteria to mammalian stem cells is pluripotent differentiation, where cells can differentiate into one of several possible fates. We propose to investigate how interactions at the molecular level within and across genetic circuits determine pluripotent differentiation at the cellular level. We will study pluripotent differentiation in Bacillus subtilis, a simple, well characterized and experimentally accessible system as a model for genetic control of cell fate choice. Environmental stress induces B. subtilis cells to undergo sporulation or differentiate into the competence state and take up extracellular DNA and incorporate it into their chromosome. We have recently identified the core competence circuit and showed that it exhibits excitable dynamics triggered by noise. Many of the molecular components that regulate competence and sporulation in B. subtilis are known. How interactions within and across competence and sporulation circuits regulate the choice and execution of appropriate differentiation programs is, however, poorly understood. We will study this problem using quantitative fluorescence time- lapse microscopy at the single-cell level to establish how the dynamics of molecular interactions regulate this process. Exploiting genetic manipulation techniques available for B. subtilis, we will measure how systematic re-engineering of circuit interactions control differentiation. Utilizing established connectivity maps of competence and sporulation circuits, we will also construct mathematical frameworks to generate predictions and analyze results. Specifically, we will apply these methods to: (1) Determine the functional importance of competence circuit architecture by comparing it to engineered alternative topologies in silico and in vivo. (2) Determine the functional importance of cross-regulation in cell fate choice. (3) Determine how the transient activity of the competence circuit alters the progression and execution of sporulation. This integrative research is necessary to determine how molecular interactions within and across genetic circuits control pluripotent differentiation at the cellular level. Identification of the mechanics that dictate the choice and execution of cell fate in this model organism are likely to be relevant to pluripotent differentiation in diverse organisms including mammalian systems.

Public Health Relevance

This proposal will establish a comprehensive description of how bacteria undergo differentiation. The resulting data will be relevant to: 1) Controlling differentiation in bacteria to prevent bacterial spore formation in foods. 2) Preventing the ability of bacteria to naturally become resistant to antibiotics. 3) Developing new techniques to control how cells differentiate, which can be applied in the future to control differentiation of mammalian stem cell to substitute for any missing or diseased cell types.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Modeling and Analysis of Biological Systems Study Section (MABS)
Program Officer
Brazhnik, Paul
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of California San Diego
Schools of Arts and Sciences
La Jolla
United States
Zip Code
Espinar, Lorena; Dies, Marta; Cagatay, Tolga et al. (2013) Circuit-level input integration in bacterial gene regulation. Proc Natl Acad Sci U S A 110:7091-6
Orchard, Robert C; Kittisopikul, Mark; Altschuler, Steven J et al. (2012) Identification of F-actin as the dynamic hub in a microbial-induced GTPase polarity circuit. Cell 148:803-15
Kuchina, Anna; Espinar, Lorena; Garcia-Ojalvo, Jordi et al. (2011) Reversible and noisy progression towards a commitment point enables adaptable and reliable cellular decision-making. PLoS Comput Biol 7:e1002273
Kuchina, Anna; Espinar, Lorena; Cagatay, Tolga et al. (2011) Temporal competition between differentiation programs determines cell fate choice. Mol Syst Biol 7:557
Rue, Pau; Suel, Gurol M; Garcia-Ojalvo, Jordi (2011) Optimizing periodicity and polymodality in noise-induced genetic oscillators. Phys Rev E Stat Nonlin Soft Matter Phys 83:061904
Kittisopikul, Mark; Suel, Gurol M (2010) Biological role of noise encoded in a genetic network motif. Proc Natl Acad Sci U S A 107:13300-5