The Chubiz Lab at UMSL

Molecular mechanisms driving the evolution of phenotypic drug resistance

A question that has interested me for several years relates to the intrinsic levels of drug resistance found in numerous bacterial pathogens. Specifically, resistance that has nothing to do with acquired plasmids, phages, transposon, integrons, and the like. How do bacteria sense and respond to antibiotic stress? How are different cellular responses integrated into large-scale changes in cellular physiology to acclimate to antibiotic stress? A model system for studying these questions is the mar-sox-rob system found in E. coli and related bacterial pathogens. With regards to this system, I have previously explored the transcriptional inter-connections between its members, its role in outer membrane permeability, and how intracellular metabolites act as inducers of intrinsic resistance.

Genetic robustness of microbe-microbe interactions

Given the myriad of microbes co-existing in nearly all environments on Earth, we have a limited picture of how microbes function in the context of a community. IN particular, how sensitive are microbial relationships to loss-of-function or gain-of-function mutatations? Does the poly-microbial environment select for genetic robustness? I try and explore these questions using model systems of bacterial cooperation and antagonism. For instance, in a recent study we found that different types of interactions (cooperation, unidirectional crossfeeding, and competition) result in different patterns of sensitivity to metabolic loss-of-function. Interestingly, competition appears to be most senstitive to loss-of-function, despite the perceived delicacy of mutualistic behavior.

Physiology and molecular genetics of Acidobacteria

Acidobacteria are an understudied bacterial phyla, despite their ubiquity and abundant in soil environments. In large part, this is due to the difficulty in isolating and cultivating these bacteria under laboratory. My lab is engaged in an effort to develop genetic tools study the physiology of Acidobacteria. Likewise, we are actively sequencing numerous Acidobacteria genomes in an effort to understand the genetic and catabolic diversity of the Acidobacteria phylum.

Current Lab Members

  • Lon Chubiz, Ph.D. - Principal Investigator
  • Silpi Thota - Ph.D. Student
  • Marisa Yoder - Ph.D. Student
  • Yu Liu - Research Associate
  • Michelle Fritsche - Undergraduate

Former Lab Members

  • Nick Dubina, 2017 - Undergraduate
  • Venkata Jonnalagadda, M.S. 2017 - Research Technician, Washington University School of Medicine
  • Safia Madani, M.S. 2016 - Biomerieux
  • Victoria Anderson, M.S. 2016 - MilliporeSigma
  • Christine Noto, B.S. 2016 - Ph.D. Student, St. Louis University
  • Timothy Kuensting, B.S. 2016 - Research Assistant, Washington University School of Medicine

Interested students and post-doctoral researchers

I am always keen to provide opportunities for students at the graduate and undergraduate levels. If you are interested in my research program, and would like training microbiology, molecular biology, and microbial evolution please contact me.

For students interested in performing their Ph.D. graduate work in my lab, please refer to graduate admissions policies found on the Department of Biology website. Students entering into the Cellular and Molecular Biology track wil be expected to perform laboratory rotations as part of the degree program - my lab is always open to rotators. Those entering the Evolution, Ecology and Systematics track must contact me prior to applying for me to confirm your application. I look forward to hearing from you.

For post-doctoral researchers, space is available but I currently do not have expressed funding for a post-doc position. However, I am always eager to see what can be worked out so please reach out and contact me if you are interested.

Publications

At UMSL

  • Douglas, S.M., Chubiz, L.M., Harcombe, W.R., and Marx, C.J., Identification of the potentiating mutations and synergistic epistasis that enabled the evolution of inter-species cooperation, PLoS One, 2017
  • Chubiz, L.M. 1 and Marx, C.J., Growth tradeoffs accompany the emergence of glycolytic metabolism in Shewanella oneidensis MR-1, J. Bacteriol., 2017
  • Douglas, S.M., Chubiz, L.M., Harcombe, W.R., Ytreberg, F.M., and Marx, C.J., Parallel Mutations Result in a Wide Range of Cooperation and Community Consequences in a Two-Species Bacterial Consortium, PLoS One, 2016
  • Agashe, D., Sane, M., Phalnikar, K., Diwan, G.D., Habibullah, A., Martinez-Gomez, N.C., Sahasrabuddhe, V., Polachek, W., Wang, J., Chubiz, L.M., and Marx, C.J., Large-Effect Beneficial Synonymous Mutations Mediate Rapid and Parallel Adaptation in a Bacterium, Mol. Biol. Evol., 2016
  • Chubiz, L.M. 1, Granger, B.R., Segrè, D., and Harcombe, W.R., Species interactions differ in their genetic robustness, Front Microbiol, 2015
  • Carroll, S.M., Chubiz, L.M., Agashe, D., and Marx C.J., Parallel and Divergent Evolutionary Solutions for the Optimization of an Engineered Central Metabolism in Methylobacterium extorquens AM1, Microorganisms, 2015

Elsewhere

  • Chubiz, L.M., Purswani, J., Carroll, S.M., and Marx, C.J., A novel pair of inducible expression vectors for use in Methylobacterium extorquens, BMC Res Notes, 2014
  • Chubiz, L.M., Lee, M.C., Delaney, N.F., and Marx, C.J., FREQ-Seq: a rapid, cost-effective, sequencing-based method to determine allele frequencies directly from mixed populations, PLoS One, 2012
  • Chubiz, L.M., Glekas, G.D., and Rao, C.V., Transcriptional cross talk within the mar-sox-rob regulon in Escherichia coli is limited to the rob and marRAB operons, J Bacteriol, 2012
  • Chubiz, L.M. and Rao, C.V., Role of the mar-sox-rob regulon in regulating outer membrane porin expression, J Bacteriol, 2011
  • Chubiz, L.M. and Rao, C.V., Aromatic acid metabolites of Escherichia coli K-12 can induce the marRAB operon., J Bacteriol, 2010
  • Min, T.L., Mears, P.J., Chubiz, L.M., Rao, C.V., Golding, I., Chemla, Y.R., High-resolution, long-term characterization of bacterial motility using optical tweezers, Nat Methods, 2009
  • Chubiz, L.M. and Rao, C.V., Computational design of orthogonal ribosomes, Nucleic Acids Res, 2008
  1. Indicates corresponding author  2