Is it possible to predict both the potential for selection and epistatic interactions across a biological network? Here we propose to quantitatively address the physiological basis of adaptation through the integration of experimental and computational approaches. Our model system is one in which the central, essential and highly interconnected metabolic pathway of Methylobacterium has been disabled and replaced with a foreign, unrelated pathway. The unique advantage of this engineered system is that this replacement specifically results in a 3-fold reduction in fitness, growth rate and metabolic flux, as well as 2.5-fold lower yield and a 30-fold redistribution of flux within the central metabolic hub. Because this alteration directly causes sub-optimal performance, we hypothesize that this will focus selection upon this subsystem during experimental evolution such that adaptation will largely proceed through mutations in the substituted pathway and/or those that it physiologically interacts with. Furthermore, we suggest that increasingly extended and verified mathematical models of this metabolic subsystem and its connections to the metabolic network will allow us to make testable predictions of the fitness effects of altering the activity of individual system components, as well as epistatic interactions between enzymes. Our preliminary results support both our model's predictions and the assertion that adaptation will strike this central metabolic hub.
Our specific aims are to 1.) explore the potential for selection with metabolic models and directly test predictions by modulating expression levels of enzymes, 2.) evolve replicate populations of the ancestral strain and examine phenotypic and genetic changes throughout the course of adaptation and 3.) test the role of epistasis in the adaptive trajectories observed or synthesized. The result of this project will be a novel model system and conceptual framework to apply a comprehensive, systems biology approach to understanding the physiological basis of selection and epistasis in adaptation. It also represents the opportunity to address adaptation occurring after introduction of new genetic material via horizontal gene transfer. We anticipate that placing selection and epistasis into a quantitative framework will have public health impacts ranging from the adaptation of pathogens, the modeling of metabolic diseases, to prognostic predictions of the 'adaptive'fate of a population of cancer cells with mutated oncogenes and tumor suppressors.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM078209-04
Application #
7848915
Study Section
Genetic Variation and Evolution Study Section (GVE)
Program Officer
Eckstrand, Irene A
Project Start
2007-07-10
Project End
2012-05-31
Budget Start
2010-06-01
Budget End
2011-05-31
Support Year
4
Fiscal Year
2010
Total Cost
$282,431
Indirect Cost
Name
Harvard University
Department
Biology
Type
Schools of Arts and Sciences
DUNS #
082359691
City
Cambridge
State
MA
Country
United States
Zip Code
02138
Agashe, Deepa; Sane, Mrudula; Phalnikar, Kruttika et al. (2016) Large-Effect Beneficial Synonymous Mutations Mediate Rapid and Parallel Adaptation in a Bacterium. Mol Biol Evol 33:1542-53
Nayak, Dipti D; Marx, Christopher J (2015) Experimental Horizontal Gene Transfer of Methylamine Dehydrogenase Mimics Prevalent Exchange in Nature and Overcomes the Methylamine Growth Constraints Posed by the Sub-Optimal N-Methylglutamate Pathway. Microorganisms 3:60-79
Carroll, Sean Michael; Chubiz, Lon M; Agashe, Deepa et al. (2015) Parallel and Divergent Evolutionary Solutions for the Optimization of an Engineered Central Metabolism in Methylobacterium extorquens AM1. Microorganisms 3:152-74
Chou, Hsin-Hung; Delaney, Nigel F; Draghi, Jeremy A et al. (2014) Mapping the fitness landscape of gene expression uncovers the cause of antagonism and sign epistasis between adaptive mutations. PLoS Genet 10:e1004149
Nayak, Dipti D; Marx, Christopher J (2014) Genetic and phenotypic comparison of facultative methylotrophy between Methylobacterium extorquens strains PA1 and AM1. PLoS One 9:e107887
Nayak, Dipti D; Marx, Christopher J (2014) Methylamine utilization via the N-methylglutamate pathway in Methylobacterium extorquens PA1 involves a novel flow of carbon through C1 assimilation and dissimilation pathways. J Bacteriol 196:4130-9
Carroll, Sean Michael; Marx, Christopher J (2013) Evolution after introduction of a novel metabolic pathway consistently leads to restoration of wild-type physiology. PLoS Genet 9:e1003427
Lee, Ming-Chun; Marx, Christopher J (2013) Synchronous waves of failed soft sweeps in the laboratory: remarkably rampant clonal interference of alleles at a single locus. Genetics 193:943-52
Chubiz, Lon M; Purswani, Jessica; Carroll, Sean Michael et al. (2013) A novel pair of inducible expression vectors for use in Methylobacterium extorquens. BMC Res Notes 6:183
Delaney, Nigel F; Rojas Echenique, José I; Marx, Christopher J (2013) Clarity: an open-source manager for laboratory automation. J Lab Autom 18:171-7

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