Research Focus

The Michener team studies and engineers proteins and bacteria to support a sustainable bioeconomy. These goals often require discovering new enzymes or metabolic pathways to enable targeted engineering. Enzymes may require additional engineering to enhance desired activities. Transfer of pathways into new hosts puts new stresses on the cell, and may require optimization to support heterologous activity. 

Much of the research on the team involves genetic modification of non-model microbes. We use high-throughput screens and selections for untargeted discovery, combined with lower-throughput validation of particular genetic modifications and biochemical predictions. We frequently collaborate with computational biologists to develop models that guide our discovery and engineering efforts.

Gene Discovery:
In many cases, the phenotypes that we wish to study have no known genetic basis, which limits our ability to transfer or optimize that phenotype. In these situations, we must first identify the genes that are required for the phenotype, potentially uncovering new biology. We have developed a novel technique for bacterial quantitative trait-locus mapping that provides new opportunities for genetic mapping of complex traits. Phenotypes of interest include lignin valorization and ecologically-relevant population-scale behaviors such as biofilm formation.

Relevant publications:

  • Vasileva DP†, Streich JC†, Burdick LH†, Klingeman DM, Chhetri HB, Brelsford CM, Ellis JC, Close DM, Jacobson DA, and Michener JK*. Protoplast fusion in Bacillus
    species produces frequent, unbiased, genome-wide homologous recombination. Nucleic Acids Res 2022. Link.
  • Bleem A†, Kuatsjah E†, Presley GN†, et al.,  Discovery, characterization, and metabolic engineering of Rieske non-heme iron monooxygenases for guaiacol O-demethylation. Chem Cat 2022. Link. 
  • Presley GN†, Werner AZ†, et al., Pathway discovery and engineering for cleavage of a β-1 lignin-derived biaryl compound. Metab Eng 2021. Link. 

Enzyme Characterization and Engineering:
We are currently expanding our enzymatic biochemistry efforts to characterize newly-discovered enzymes and engineer them to enhance desirable activities. Targets of interest include enzymes for lignin catabolism and polymer degradation/upcycling.

Pathway Transfer:

Once we identify a pathway of interested, we typically reconstruct that pathway in a new host to verify that we have all the necessary genetic elements and to determine the range of organisms in which the pathway functions. From an engineering perspective, knowing when you can reuse a particular pathway in a new strain simplifies the design process. In nature, understanding the genetic and physiological factors that limit post-transfer pathway function helps us to understand and predict horizontal gene transfers.

Relevant publications: 

  • Michener JK, et al., Transfer of a catabolic pathway for chloromethane in Methylobacterium strains highlights different limitations for growth with chloromethane or with dichloromethane. Front Microbiol 2016. Link
  • Michener JK, et al., Phylogeny poorly predicts the utility of a challenging horizontally-transferred gene in Methylobacterium strains. J Bacteriol 2014. Link.

Host/Pathway Optimization:
Pathways frequently function poorly after transfer into a new host or environment. In these cases, we identify mutations that improve pathway activity, and then work backwards from those mutations to uncover the deleterious interactions that were previously limiting pathway activity. Once we know the interactions between host and pathway, we can design pathways and select hosts to minimize these interactions. We are additionally using directed evolution to optimize enzymes for new reactions and environments.

Relevant publications:

  • Millet L, et al., Genetic selection for small molecule production in competitive microfluidic droplets. ACS Synth Biol 2019. Link.
  • Close D, et al., Horizontal transfer of a pathway for coumarate catabolism unexpectedly inhibits purine nucleotide biosynthesis. Mol Microbiol 2019. Link
  • Clarkson SM, et al., Construction and optimization of a heterologous pathway for protocatechuate catabolism in Escherichia coli enables bioconversion of model aromatic compounds. Appl Env Microbiol 2017. Link.
  • Michener JK, et al., Effective use of a horizontally-transferred pathway for dichloromethane catabolism requires post-transfer refinement. eLife 2014. Link.
 
 

Project funding:

Center for Bioenergy Innovation (CBI):
In CBI, we are developing tools for quantitative trait-locus mapping in C. thermocellum for gene functional annotation.

Secure Ecosystem Engineering Design (SEED):
In SEED, we are investigating the genetic determinants of establishment and HGT in environmental strains of Bacillus. We wish to enhance or limit these processes when new strains are introduced into managed ecosystems such as biofuels plantations.

Center for Plastic Innovation (CPI):
Working with CPI, we are engineering enzymes to convert depolymerized plastic waste to new value-added polymer precursors.

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