Research

IMG_7444

Working hard: minds full and glasses empty.

Our lab works on questions at the intersection of physiology and evolutionary biology, and we integrate systems-level, mathematical models to generate quantitative predictions that linking genotype to phenotype. Nearly all of our work has refocused upon using Methylobacterium extorquens as a model system.

The laboratory currently tackles the following areas:

(1.) Exploring a novel stress response that directly links accumulation of the toxic intermediate formaldehyde to translational inhibition. This project ranges from structure-function analysis of the regulatory protein, EfgA, to unexpected population heterogeneity in the ability to handle formaldehyde stress.

(2.) Using in vivo gene editing, deep-sequencing, and kinetic models to uncover the epistatic interactions that constrain evolvability or biotechnological applications of synthetic metabolic pathways.

(3.) Predicting microbial interactions within synthetic, plant-associated communities. This includes the role of methylotrophs in aiding in the demethoxylation of lignin monomers and interactions between Methylobacterium strains.

Funding Resources:

  • 2018-2022       National Science Foundation: “Dimensions: An inordinate fondness for Methylobacterium– roles of phylogeny, genome content, and functional performance traits in the evolution and assembly of a diverse plant-associated community” (Co-PIs: James A. Foster, John M. (Jack) Sullivan; N. Cecilia Martinez-Gomez, Michigan State; Jessica A. Lee, Global Viral; Collaborators: Sergey Stolyar; Steven W. Kembel, B. Jesse Shapiro, U. Québec, Montréal, Canada; DEB-1831838).

 

  • Department of Energy: “Using gene editing and an accumulated bioproduct as a reporter for genotypic to phenotypic heterogeneity in growth-vs-production for Methylobacterium extorquens conversion of lignin-derived aromatics to butanol” (Co-PIs: Sergey Stolyar, Andreas E. Vasdekis; Ankur B. Dalia, Indiana U.; DE-SC0019436).

 

  • 2017-2020       National Science Foundation: “Collaborative Research: Deep-sequencing analysis of edited metabolic pathways to uncover, model, and overcome epistatic constraints upon optimization” (other PIs: Jeremy A. Draghi, CUNY Brooklyn College; N. Cecilia Martinez-Gomez, Michigan State; co-PIs: Sergey Stolyar, Ankur B. Dalia, Indiana U.; MCB-1714949)

 

  • 2017-2021       National Science Foundation (EPSCoR): “RII Track-2 FEC: Using biophysical protein models to map genetic variation to phenotypes” (PI: Frederick M. Ytreberg; co-PIs Craig R. Miller; Brandon Ogbunugafor, U. Vermont; Daniel M. Weinreich, Brown; OIA-1736253).

 

  • 2017-2020       National Science Foundation: “Collaborative Research: Deep-sequencing analysis of edited metabolic pathways to uncover, model, and overcome epistatic constraints upon optimization” (other PIs: Jeremy A. Draghi, CUNY Brooklyn College; N. Cecilia Martinez-Gomez, Michigan State; co-PIs: Sergey Stolyar, Ankur B. Dalia, Indiana U.; MCB-1714949).

 

  • 2018-2019       BEACON NSF Center for the Study of Evolution in Action: “Going Global: Applying Tn-Seq technology to address pleiotropy and evolvability on a genomic scale” (PI: Eric L. Bruger; other co-PIs: Jannell V. Bazurto, Craig R. Miller; N. Cecilia Martinez-Gomez, Michigan State).

 

  • 2018-2019       BEACON NSF Center for the Study of Evolution in Action: “Do you have to crawl before you walk?: Stepwise evolution of growth on lignin-derived substrates by the biotechnological platform organism Methylobacterium extorquensPA1” (PI: Tomislav Ticak; other co-PIs: Sergey Stolyar; N. Cecilia Martinez-Gomez, Michigan State).

 

  • 2018-2019       BEACON NSF Center for the Study of Evolution in Action: “Pleiotropy vs. evolvability within an enzyme: deep mutational scanning, molecular modeling, and experimental evolution to address constraints in a promiscuous enzyme” (PI: N. Cecilia Martinez-Gomez, Michigan State; other co-PIs: Jagdish S. Patel, Craig R. Miller, Sergey Stolyar,).

 

  • 2018-2019       BEACON NSF Center for the Study of Evolution in Action: “Sizing up the competition: does selection for increased competitive ability result in bigger cells?” (PI: Katrina van Raay, U. Washington; other co-PIs: Ben Kerr, U. Washington; Richard E. Lenski, Nkrumah Grant (Michigan State); Sergey Stolyar, U. Idaho).
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