The system comprised of the bacterium Escherichia coli and its virus, bacteriophage lambda, serves as the basic paradigm for many aspects of gene regulation, ranging in scale from the molecular to the organismic level. Questions asked within the lambda system often yield insights relevant to "higher" eukaryotic systems. The lambda system has been extensively characterized using the traditional tools of genetics and biochemistry, enabling the formation of an elegant and seemingly complete narrative of the observed phenomenology in terms of the microscopic interactions in the cell. However, from the point of view of a quantitative scientist there is an immense gap of understanding between the genetic and biochemical knowledge on the one hand, and the observed population phenotype on the other. This gap manifests itself in the poor predictive powers of mathematical models of the system. To try and bridge the knowledge gap it is required to "deconstruct" the life cycle of bacteriophage lambda by studying the events comprising this life cycle in real-time, in individual living cells, quantifying the intracellular dynamics with sufficient resolution to describe individual events in space and time. In this proposal we suggest to characterize gene regulation during the lambda life cycle, concentrating on the following aims: (1) Characterizing the function of the lysis/lysogeny switch during the maintenance of the lysogenic (dormant) state as well as the induction of the lytic (virulent) pathway following cell damage. (2) Elucidating spatiotemporal aspects affecting the life cycle, for example how the different stages of the lytic pathway genome replication, gene expression, capsid self-assembly and lysis are organized in space and time. (3) Distinguishing precision versus stochasticity in the lambda life cycle, by separating "real" stochasticity one resulting from actual sources of uncontrolled variability from "apparent" stochasticity, resulting from our own inability to detect and measure differences in physiological parameters between individual cells.

Public Health Relevance

Filling the knowledge gap at the single-event level will in turn bring us closer to a quantitative understanding of whole-system (organism) characteristics in terms of the microscopic constituents, in the vain of "systems biology". Achieving this goal in a simple model system such as lambda can then be followed by similar endeavors in higher organisms.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM082837-05
Application #
8313930
Study Section
Modeling and Analysis of Biological Systems Study Section (MABS)
Program Officer
Lyster, Peter
Project Start
2008-08-04
Project End
2013-07-31
Budget Start
2012-08-01
Budget End
2013-07-31
Support Year
5
Fiscal Year
2012
Total Cost
$306,771
Indirect Cost
$110,751
Name
Baylor College of Medicine
Department
Biochemistry
Type
Schools of Medicine
DUNS #
051113330
City
Houston
State
TX
Country
United States
Zip Code
77030
Gordon, Alasdair J E; Satory, Dominik; Wang, Mengyu et al. (2014) Removal of 8-oxo-GTP by MutT hydrolase is not a major contributor to transcriptional fidelity. Nucleic Acids Res 42:12015-26
Koirala, Santosh; Mears, Patrick; Sim, Martin et al. (2014) A nutrient-tunable bistable switch controls motility in Salmonella enterica serovar Typhimurium. MBio 5:e01611-14
Bednarz, Michael; Halliday, Jennifer A; Herman, Christophe et al. (2014) Revisiting bistability in the lysis/lysogeny circuit of bacteriophage lambda. PLoS One 9:e100876
Mears, Patrick J; Koirala, Santosh; Rao, Chris V et al. (2014) Escherichia coli swimming is robust against variations in flagellar number. Elife 3:e01916
Zheng, Liuliu; Sepulveda, Leonardo A; Lua, Rhonald C et al. (2013) The maternal-to-zygotic transition targets actin to promote robustness during morphogenesis. PLoS Genet 9:e1003901
Skinner, Samuel O; SepĂșlveda, Leonardo A; Xu, Heng et al. (2013) Measuring mRNA copy number in individual Escherichia coli cells using single-molecule fluorescent in situ hybridization. Nat Protoc 8:1100-13
Sanchez, Alvaro; Golding, Ido (2013) Genetic determinants and cellular constraints in noisy gene expression. Science 342:1188-93
Figard, Lauren; Xu, Heng; Garcia, Hernan G et al. (2013) The plasma membrane flattens out to fuel cell-surface growth during Drosophila cellularization. Dev Cell 27:648-55
Kessler, Jessica D; Kahle, Kristopher T; Sun, Tingting et al. (2012) A SUMOylation-dependent transcriptional subprogram is required for Myc-driven tumorigenesis. Science 335:348-53
Zhang, Ruobing; Rothenberg, Eli; Fruhwirth, Gilbert et al. (2011) Two-photon 3D FIONA of individual quantum dots in an aqueous environment. Nano Lett 11:4074-8

Showing the most recent 10 out of 18 publications