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Amy Schmid

Assistant Professor
Research Interest: 
Microbiology and virology
Research Summary: 
Systems biology of archaea: understanding regulatory network responses to environmental extremes
Research Description: 

Although life science research has entered the post-genomic era, we still understand little about the diversity of microbial life on earth. Information is particularly lacking on microbial extremophiles, which thrive at the limits of life. Extremophiles can be found in deep-sea hydrothermal vents under high pressure and temperature, saturated salt lakes, and polar icecaps. Many of these organisms are members of the third domain of life, the archaea. How do these microorganisms cope with an extreme and changing environment? How do they alter their genetic programs and metabolic pathways to adapt and survive changes in their unique habitats on earth? Central to this process are gene regulatory networks (GRNs) composed of groups of regulatory proteins that switch genes on and off in response to environmental stimuli. Upon sensing a change in the environment, the GRN increases the production of genes encoding proteins that repair damage, restore the cell to a healthy state and prepare for future stress. The organism studied in the current research, called Halobacterium salinarum, thrives in high salt environments. The long-term aim of our work is to determine the underlying mechanisms by which regulatory factors interact in the GRN of H. salinarum enable survival during environmental perturbations. We are using a systems biology approach, which combines cutting-edge high throughput experimental techniques with computational or statistical modeling. Research toward these goals will lay the foundation for rational re-engineering of cellular physiology for desired outcomes such as targeted industrial, environmental and medical purposes.

Protein-DNA binding dynamics predict transcriptional response to nutrients in archaea.
Todor H, Sharma K, Pittman AM, Schmid AK.
Nucleic Acids Res. 2013. 41:8546-58.

The RosR transcription factor is required for gene expression dynamics in response to extreme oxidative stress in a hypersaline-adapted archaeon.
Sharma K, Gillum N, Boyd JL, Schmid A.
BMC Genomics. 2012. 13:351.

Two transcription factors are necessary for iron homeostasis in a salt-dwelling archaeon.
Schmid AK, Pan M, Sharma K, Baliga NS.
Nucleic Acids Res. 2011. 39:2519-33.

A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability.
Schmid AK, Reiss DJ, Pan M, Koide T, Baliga NS.
Mol Syst Biol. 2009. 5:282.

Prevalence of transcription promoters within archaeal operons and coding sequences.
Koide T, Reiss DJ, Bare JC, Pang WL, Facciotti MT, Schmid AK, Pan M, Marzolf B, Van PT, Lo FY, Pratap A, Deutsch EW, Peterson A, Martin D, Baliga NS.
Mol Syst Biol. 2009. 5:285.