Amy K. Schmid

Assistant Professor of Biology

Office: 
125 Science Dr, French Family Science Center 4105, Durham, NC 27708
Campus Box: 
90338
Phone: 
(919) 613-4464

Lab Site: http://www.biology.duke.edu/schmidlab

Research Interests: 

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.

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.

Education

  • Ph.D. 2004, University of Washington

  • B.S. 1997, Marquette University

Papers Published

Growth-Phase-Specific Modulation of Cell Morphology and Gene Expression by an Archaeal Histone Protein., 1, 2015
Dulmage, KA; Todor, H; Schmid, AK, mBio. 6 vol. (5); pp. e00649-e00615

Dynamic Metabolite Profiling in an Archaeon Connects Transcriptional Regulation to Metabolic Consequences., 1, 2015
Todor, H; Gooding, J; Ilkayeva, OR; Schmid, AK, PloS one. 10 vol. (8); pp. e0135693

A regulatory hierarchy controls the dynamic transcriptional response to extreme oxidative stress in archaea., 1, 2015
Tonner, PD; Pittman, AMC; Gulli, JG; Sharma, K; Schmid, AK, PLoS genetics. 11 vol. (1); pp. e1004912

A transcription factor links growth rate and metabolism in the hypersaline adapted archaeon Halobacterium salinarum., 9, 2014
Todor, H; Dulmage, K; Gillum, N; Bain, JR; Muehlbauer, MJ; Schmid, AK, Molecular Microbiology. 93 vol. (6); pp. 1172-1182

Protein-DNA binding dynamics predict transcriptional response to nutrients in archaea., 10, 2013
Todor, H; Sharma, K; Pittman, AMC; Schmid, AK, Nucleic Acids Res. 41 vol. (18); pp. 8546-8558

The RosR transcription factor is required for gene expression dynamics in response to extreme oxidative stress in a hypersaline-adapted archaeon, July, 2012
Sharma, K; Gillum, N; Boyd, JL; Schmid, A, BMC Genomics. (July, 2012) 13 vol. (1); pp. 351

Two transcription factors are necessary for iron homeostasis in a salt-dwelling archaeon., April, 2011
Schmid, AK; Pan, M; Sharma, K; Baliga, NS, Nucleic Acids Res. (April, 2011) 39 vol. (7); pp. 2519-2533

Prevalence of transcription promoters within archaeal operons and coding sequences, 0, 2009
Koide, T; Reiss, DJ; Bare, JC; Pang, WL; Facciotti, MT; Schmid, AK; Pan, M; Marzolf, B; Van, PT; Lo, F-Y; Pratap, A; Deutsch, EW; Peterson, A; Martin, D; Baliga, NS, Mol Syst Biol. 5 pp. 285

A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability, 0, 2009
Schmid, AK; Reiss, DJ; Pan, M; Koide, T; Baliga, NS, Molecular systems biology. 5 pp. 282

Halobacterium salinarum NRC-1 peptideAtlas: Toward strategies for targeted proteomics and improved proteome coverage, 0, 2008
Phu, TV; Schmid, AK; King, NL; Kaur, A; Pan, M; Whitehead, K; Koide, T; Facciotti, MT; Goo, YA; Deutsch, EW; Reiss, DJ; Mallick, P; Baliga, NS, J Proteome Res. 7 vol. (9); pp. 3755-3764

The firegoose: Two-way integration of diverse data from different bioinformatics web resources with desktop applications, 0, 2007
Bare, JC; Shannon, PT; Schmid, AK; Baliga, NS, BMC Bioinformatics. 8 pp. 456

The anatomy of microbial cell state transitions in response to oxygen, 0, 2007
Schmid, AK; Reiss, DJ; Kaur, A; Pan, M; King, N; Van, PT; Hohmann, L; Martin, DB; Baliga, NS, Genome research. 17 vol. (10); pp. 1399-1413

A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell, 0, 2007
Bonneau, R; Facciotti, MT; Reiss, DJ; Schmid, AK; Pan, M; Kaur, A; Thorsson, V; Shannon, P; Johnson, MH; Bare, JC; Longabaugh, W; Vuthoori, M; Whitehead, K; Madar, A; Suzuki, L; Mori, T; Chang, D-E; DiRuggiero, J; Johnson, CH; Hood, L; Baliga, NS, Cell. 131 vol. (7); pp. 1354-1365

Involvement of the S-layer proteins Hpi and SlpA in the maintenance of cell envelope integrity in Deinococcus radiodurans R1., 9, 2006
Rothfuss, H; Lara, JC; Schmid, AK; Lidstrom, ME, Microbiology (Reading, England). 152 vol. (Pt 9); pp. 2779-2787

Prokaryotic Systems Biology, 2006
Schmid, AK; Baliga, NS, (2006) 5 pp. 395-423

Involvement of the S-layer proteins Hpi and SlpA in the maintenance of cell envelope integrity in Deinococcus radiodurans R1, 0, 2006
Rothfuss, H; Lara, JC; Schmid, AK; Lidstrom, ME, Microbiology (Reading, England). 152 vol. (9); pp. 2779-2787

Global whole-cell FTICR mass spectrometric proteomics analysis of the heat shock response in the radioresistant bacterium Deinococcus radiodurans, 2005
Schmid, AK; Lipton, MS; Mottaz, H; Monroe, ME; Smith, RD; Lidstrom, ME, Journal of Proteome Research. (2005) 4 vol. (3); pp. 709-718

HspR is a global negative regulator of heat shock gene expression in Deinococcus radiodurans, 0, 2005
Schmid, AK; Howell, HA; Battista, JR; Peterson, SN; Lidstrom, ME, Molecular Microbiology. 55 vol. (5); pp. 1579-1590

Global transcriptional and proteomic analysis of the Sig1 heat shock regulon of Deinococcus radiodurans, 0, 2005
Schmid, AK; Howell, HA; Battista, JR; Peterson, SN; Lidstrom, ME, Journal of Bacteriology. 187 vol. (10); pp. 3339-3351

Involvement of two putative alternative sigma factors in stress response of the radioresistant bacterium Deinococcus radiodurans, 0, 2002
Schmid, AK; Lidstrom, ME, Journal of Bacteriology. 184 vol. (22); pp. 6182-6189

Papers Submitted

Genome-Wide Assessment of Outer Membrane Vesicle Production in Escherichia coli. in PloS one 1, 2015
Kulp, AJ; Sun, B; Ai, T; Manning, AJ; Orench-Rivera, N; Schmid, AK; Kuehn, MJ

Awards

  • 2011 Biology Award for Distinguished Teaching and Service, Unknown