Chris Todd Hittinger

Position title: Associate Professor


Evolution of carbon-responsive gene networks, yeast biodiversity, industrial brewing and biofuel applications

1552 University Avenue, Wisconsin Energy Institute 4129
PhD, University of Wisconsin-Madison (2007), Postdoctoral Fellow, Washington University in St. Louis, University of Colorado School of Medicine (2007-2011)
Lab Website
Research Interests
We study the evolution of the gene networks that regulate yeast carbon metabolism, yeast biodiversity, and applications in the brewing and biofuel industries.
Research Fields
Computational, Systems & Synthetic Biology, Evolutionary & Population Genetics, Gene Expression, Genomics & Proteomics, Fungi

Research Description:
Carbon metabolism is the energy superhighway of life. We study the diversity and evolution of yeast carbon metabolism, which is controlled by a complex system of interacting genes that respond to different carbon sources and determine the organism’s energy-use strategy. Some yeasts readily ferment sugars into ethanol, even in the presence of oxygen, but most organisms (including many yeast species) prefer respiration. The biofuel industry currently exploits the highly refined trait of aerobic fermentation or Crabtree-Warburg Effect in Saccharomyces cerevisiae to produce ethanol. However, the yeasts currently in use are not able to convert some common sugars like xylose into ethanol efficiently enough to compete in the energy market. By understanding how evolution has sculpted and rewired yeast gene networks to meet their different ecological needs, we can better determine how to engineer complex biological systems to meet our energy needs.

Since carbon-utilization traits are highly variable in yeast, both within and between species, they make an excellent model for understanding how the gene networks that control them have changed in response to recent selection and over the long arc of evolution. Our research uses next-generation sequencing, precise manipulation of yeast gene networks, functional genomics, and evolutionary genomics to study:

1. Evolution of aerobic fermentation (an unusual, derived trait that Saccharomyces yeasts share with some cancer cells and that is exploited by the brewing, wine, and biofuel industries).
2. Utilization of alternative and novel carbon sources (like galactose and xylose).
3. Rewiring of transcriptional regulatory networks.
4. How variation in gene networks is maintained and evolves.
5. Yeast biodiversity, ecology, and evolution.
6. Developing next-generation sequencing methods for non-model systems.

Representative Publications:
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RESEARCH PUBLICATIONS (& equal contributions, @corresponding author)

Libkind D &, Hittinger CT &, Valério E, Gonçalves C, Dover J, Johnston M, Gonçalves P, Sampaio JP. Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast. Proc Natl Acad Sci USA 108: 14539-44.

Scannell DR&, Zill OA&@, Rokas A, Payen C, Dunham MJ, Eisen MB, Rine J, Johnston M, Hittinger CT@. 2011. The awesome power of yeast evolutionary genetics: New genome sequences and strain resources for the Saccharomyces sensu stricto genus. G3 Genes Genomes Genet 1: 11-25.

Hittinger CT, Gonçalves P, Sampaio JP, Dover J, Johnston M, Rokas A. 2010. Remarkably ancient balanced polymorphisms in a multi-locus gene network. Nature 464: 54-8.

Hittinger CT, Johnston M, Tossberg JT, Rokas A. 2010. Leveraging skewed transcript abundance by RNA-Seq to increase the genomic depth of the tree of life. Proc Natl Acad Sci USA 107: 1476-81.

Gibbons JG, Janson EM, Hittinger CT, Johnston M, Abbot P, Rokas A. 2009. Benchmarking next-generation transcriptome sequencing for functional and evolutionary genomics. Mol Biol Evol 26: 2731-44.

Hittinger CT@, Carroll SB@. 2007. Gene duplication and the adaptive evolution of a classic genetic switch. Nature 449: 677-81.

Hittinger CT, Rokas A, Carroll SB. 2004. Parallel inactivation of multiple GAL pathway genes and ecological diversification in yeasts. Proc Natl Acad Sci USA 101: 14144-9.

REVIEWS/COMMENTARY (&equal contributions, @corresponding author)

Hittinger CT@. 2013. Saccharomyces diversity and evolution: a budding model genus. Trends Genet in press.

Hittinger CT@. 2012. Endless rots most beautiful. Science 336: 1649-50.

Hittinger CT@, Hesselberth JR. 2010. Nucleosome patterning evolution: steady aim despite moving targets. Mol Syst Biol 6: 376.

Rokas A, Hittinger CT. 2007. Galactose metabolism evolution: the proof is in the eating. Curr Biol 17: R626-8.