Modern systems biology and synthetic bioengineering face a grand challenge in relating the genetic components of a natural or engineered system to its integrated behavior;this is often referred to as the genotype to phenotype challenge. It involves the fundamental unsolved problem of relating the genotype-- which has a well-defined, generic, digital representation -- to the phenotype- which has a poorly-defined, ad hoc, analog representation. Without a rigorous generic definition of phenotype to provide the context for a deep understanding of the relation between genotype and phenotype, we are at a loss to know how many qualitatively distinct phenotypes are in an organism's repertoire or the relative fitness of the phenotypes in different environments. These are practical challenges for clinicians attempting to develop therapeutic strategies to treat pathology and bioengineers wishing to redirect normal cellular functions for biotechnological purposes. The projects of this proposal have been specifically selected to address this fundamental problem in two ways. First, they will serve as a test of the general applicability of a newly developed approach for relating genotype to phenotype that involves the first-of-its-kind generic characterization of a systems phenotypic repertoire. With this approach, phenotypes are identified and enumerated, their relative fitness compared, and their tolerance to phenotypic change measured. Although proof of concept has been established, the systems to which the method has been applied are few. Thus, applications to a very diverse selection of systems are needed to demonstrate the general utility of this innovative methodology.
The specific aims of this proposal, which have been selected with this goal in mind, are to: (1) relate hemolytic anemia in diabetics with variants of the glucose-6-phosphate dehydrogenase enzyme to levels of oxidative stress, (2) uncover design principles for reversible pathways, (3) model a global transcription factor network implicated in growth-phase progression of bacteria, and (4) compare alternative gene circuitry for toxin-antitoxin and restriction-modification systems. Second, the characterization of their phenotypic repertoire will reveal underlying system design principles and improve basic understanding for general classes of gene circuitry and biochemical networks that are found in all organisms from bacteria to humans. The outline for the treatment in each case is as follows: Specific kinetic models are formulated based on known or suspected molecular elements and interactions;several criteria for functional effectiveness are identified that are relevant for the system in question;the complex nonlinear models are decomposed into a set of simpler submodels, each manifesting a qualitatively-distinct phenotype;the integrated behavior of each submodel is exhaustively analyzed and evaluated according to the criteria for functional effectiveness;the relative fitness of the phenotypes is established by quantitative comparison;results are interpreted in terms of effective design for specific functions;and, finally, physiological and pathological significance are addressed and predictions are made for experimental testing. PHS 398/2590 (Rev. 06/09) Page Continuation Format Page

Public Health Relevance

This project is focused on the fundamental unsolved problem of relating the genotype -- which has a well- defined, generic, digital representation -- to the phenotype- which has a poorly-defined, ad hoc, analog representation. The subprojects have been selected specifically to represent widely different classes of gene circuitry and biochemical networks found in organisms from microbes to humans in order (a) to test the general applicability of a newly developed approach that involves the first-of-its-kind generic characterization of a systems phenotypic repertoire, and (b), by characterizing their phenotypic repertoire, to improve basic understanding of microbes that manifest the persistent phenotype resulting in antibiotic resistance and those that rapidly spread infectious disease by the transfer of multiple drug-resistance genes. Moreover, the subprojects selected include primitive and highly conserved mechanisms that are implicated in human diseases from cancer and diabetes to birth defects and ageing. PHS 398/2590 (Rev. 06/09) Page Continuation Format Page

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM030054-28
Application #
8468711
Study Section
Modeling and Analysis of Biological Systems Study Section (MABS)
Program Officer
Brazhnik, Paul
Project Start
1982-04-01
Project End
2016-04-30
Budget Start
2013-05-01
Budget End
2014-04-30
Support Year
28
Fiscal Year
2013
Total Cost
$279,033
Indirect Cost
$88,445
Name
University of California Davis
Department
Biomedical Engineering
Type
Schools of Engineering
DUNS #
047120084
City
Davis
State
CA
Country
United States
Zip Code
95618
Lomnitz, Jason G; Savageau, Michael A (2014) Strategy revealing phenotypic differences among synthetic oscillator designs. ACS Synth Biol 3:686-701
Fasani, Rick A; Savageau, Michael A (2014) Evolution of a genome-encoded bias in amino acid biosynthetic pathways is a potential indicator of amino acid dynamics in the environment. Mol Biol Evol 31:2865-78
Williams, Kristen; Savageau, Michael A; Blumenthal, Robert M (2013) A bistable hysteretic switch in an activator-repressor regulated restriction-modification system. Nucleic Acids Res 41:6045-57
Balderas-Martinez, Yalbi Itzel; Savageau, Michael; Salgado, Heladia et al. (2013) Transcription factors in Escherichia coli prefer the holo conformation. PLoS One 8:e65723
Lomnitz, Jason G; Savageau, Michael A (2013) Phenotypic deconstruction of gene circuitry. Chaos 23:025108
Fasani, Rick A; Savageau, Michael A (2013) Molecular mechanisms of multiple toxin-antitoxin systems are coordinated to govern the persister phenotype. Proc Natl Acad Sci U S A 110:E2528-37
Martinez-Antonio, Agustino; Lomnitz, Jason G; Sandoval, Santiago et al. (2012) Regulatory design governing progression of population growth phases in bacteria. PLoS One 7:e30654
Savageau, Michael A (2011) Design of the lac gene circuit revisited. Math Biosci 231:19-38
Savageau, Michael A (2011) Biomedical engineering strategies in system design space. Ann Biomed Eng 39:1278-95
Tolla, Dean A; Savageau, Michael A (2011) Phenotypic repertoire of the FNR regulatory network in Escherichia coli. Mol Microbiol 79:149-65

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