Professor of Functional Genomics

550A Thomas Hall
North Carolina State University
Raleigh, NC 27695-7615
919.513.4295 (office)
919.515.7136 (lab)
919.515.7867 (fax)

Biographical Sketch

Amy Grunden was born in Lakeland, Florida. As the daughter of an active-duty serviceman, she lived in a number of places during her childhood including El Paso (Texas), Omaha (Nebraska), Leominster (Massachusetts), Sierra Vista (Arizona), Fort Meade (Maryland) and Munich (Germany). Even as a child in grammar school, Amy had a keen interest in the biological sciences. She went on to pursue this interest in college, majoring in microbiology and cell sciences at the University of Florida. As an undergraduate, Amy became interested in academic research and undertook undergraduate research studies on the genetic and biochemical characterization of the regulation molybdate uptake by the bacterium Escherichia coli. After graduating with her B.S. in 1993, she continued her former undergraduate research project at the University of Florida, and eventually graduated with a Ph.D. in 1996. Amy next served as a post-doctoral research associate in the Department of Biochemistry and Molecular Biology at the University of Georgia. While at Georgia, she began working with microorganisms known as hyperthermophiles, which grow at temperatures ranging from 80C to 113C and became very interested in the mechanisms and adaptations which allow these unique organisms to thrive at such high temperatures. In July, 2000, Amy joined the faculty in the Department of Microbiology at North Carolina State University as an assistant professor and she is currently developing a research program to further investigate the physiology of hyperthermophilic microorganisms using a thermal-vent archaeon Pyrococcus furiosus as the primary research organism.

Research Brief


Hyperthermophiles, which are microorganisms that have an optimum growth temperature of at least 80C and a maximum growth temperature of 90C or above, were first isolated from hydrothermal vents (image at left) in the early 1980s. At present, more than 20 different genera of hyperthermophiles are known with two of these classified as bacteria and the rest as archaea. Archaea, which are known to constitute a third domain of life based on 16S rRNA analysis, are prokaryotes that have some eukaryotic features such as a similar mechanism of transcription. The discovery of hyperthermophilic archaea immediately engendered a great deal of research interest in several areas such as the potential biotechnological applications of purified thermostable enzymes, the identification of thermoprotection mechanisms that enable growth at high temperatures, and the characterization of the basic biochemistry and physiology of hyperthermophiles. Additionally, their discovery prompted studies focusing on the evolutionary significance of hyperthermophilic archaea, which are considered the extant microbes most closely related to the universal common ancestor from which both prokaryotic and eukaryotic cells arose.


While much progress has been made in these areas, especially with regard to the biochemistry and physiology of these organisms, very little is known about the actual regulation of their metabolic processes. My primary research interest is to investigate the mechanisms of metabolic regulation, particularly transcriptional regulatory mechanisms, utilized by hyperthermophilic archaea. The hyperthermophilic archaeon, Pyrococcus furiosus, an obligately anaerobic, fermentative heterotroph, growing optimally at 98C, serves as the primary research organism for these studies since its genome has been recently sequenced and because there already exists a sizeable body of literature describing the biochemistry and physiology of P. furiosus (image at right).

Currently my laboratory is investigating the regulation of two different critical metabolic systems in P. furiosus: the regulation of the utilization of phosphate and the regulation of the uptake and processing of tungsten. The methods that we are using to characterize the regulation of these two systems are DNA array analysis (below, left) and differential proteomic analysis (below, right). By using these methods, we will be able to determine how P. furiosus genes are regulated in response to a host of different growth conditions including growth with varying phosphate and tungsten availability, growth on different carbon and nitrogen sources, and growth under conditions of heat and cold shock. From the analysis of regulated genes, regulatory DNA-binding motifs can be identified which will ultimately enable the identification of the responsible transcriptional regulatory genes. The subsequent biochemical and genomic analysis of identified transcriptional regulators will substantially expand our currently limited understanding of transcriptional regulation of metabolic pathways in hyperthermophilic archaea.


1: Mathews SL, Pawlak JJ, Grunden AM. Isolation of Paenibacillus glucanolyticusfrom pulp mill sources with potential to deconstruct pulping waste. BioresourTechnol. 2014 Jul;164:100-5. doi: 10.1016/j.biortech.2014.04.093. Epub 2014 May5. PubMed PMID: 24841577.

2: Mathews SL, Ayoub AS, Pawlak J, Grunden AM. Methods for facilitating microbialgrowth on pulp mill waste streams and characterization of the biodegradationpotential of cultured microbes. J Vis Exp. 2013 Dec 12;(82):e51373. doi:10.3791/51373. PubMed PMID: 24378616.

3: Schreck SD, Grunden AM. Biotechnological applications of halophilic lipasesand thioesterases. Appl Microbiol Biotechnol. 2014 Feb;98(3):1011-21. doi:10.1007/s00253-013-5417-5. Epub 2013 Dec 7. Review. PubMed PMID: 24318008.

4: Bruno-Barcena JM, Chinn MS, Grunden AM. Genome Sequence of the AutotrophicAcetogen Clostridium autoethanogenum JA1-1 Strain DSM 10061, a Producer ofEthanol from Carbon Monoxide. Genome Announc. 2013 Aug 15;1(4). pii: e00628-13.doi: 10.1128/genomeA.00628-13. PubMed PMID: 23950130; PubMed Central PMCID:PMC3744686.

5: Gosse JL, Chinn MS, Grunden AM, Bernal OI, Jenkins JS, Yeager C, Kosourov S,Seibert M, Flickinger MC. A versatile method for preparation of hydratedmicrobial-latex biocatalytic coatings for gas absorption and gas evolution. J IndMicrobiol Biotechnol. 2012 Sep;39(9):1269-78. doi: 10.1007/s10295-012-1135-8.Epub 2012 May 17. PubMed PMID: 22592947.

6: Kitchener RL, Grunden AM. Prolidase function in proline metabolism and itsmedical and biotechnological applications. J Appl Microbiol. 2012Aug;113(2):233-47. doi: 10.1111/j.1365-2672.2012.05310.x. Epub 2012 May 10.Review. PubMed PMID: 22512465.

7: McMahan L, Grunden AM, Devine AA, Sobsey MD. Evaluation of a quantitative H2S MPN test for fecal microbes analysis of water using biochemical and molecularidentification. Water Res. 2012 Apr 15;46(6):1693-704. doi:10.1016/j.watres.2011.12.037. Epub 2012 Jan 5. PubMed PMID: 22244995.

8: Theriot CM, Semcer RL, Shah SS, Grunden AM. Improving the catalytic activityof hyperthermophilic Pyrococcus horikoshii prolidase for detoxification oforganophosphorus nerve agents over a broad range of temperatures. Archaea.2011;2011:565127. doi: 10.1155/2011/565127. Epub 2011 Nov 28. PubMed PMID:22162664; PubMed Central PMCID: PMC3227228.

9: McMahan L, Devine AA, Grunden AM, Sobsey MD. Validation of the H2S method todetect bacteria of fecal origin by cultured and molecular methods. Appl MicrobiolBiotechnol. 2011 Dec;92(6):1287-95. doi: 10.1007/s00253-011-3520-z. Epub 2011 Oct26. PubMed PMID: 22038242.

10: Boss WF, Sederoff HW, Im YJ, Moran N, Grunden AM, Perera IY. Basal signaling regulates plant growth and development. Plant Physiol. 2010 Oct;154(2):439-43.doi: 10.1104/pp.110.161232. PubMed PMID: 20921159; PubMed Central PMCID:PMC2948987.

11: Theriot CM, Grunden AM. Hydrolysis of organophosphorus compounds by microbialenzymes. Appl Microbiol Biotechnol. 2011 Jan;89(1):35-43. doi:10.1007/s00253-010-2807-9. Epub 2010 Oct 2. Review. PubMed PMID: 20890601.

12: Theriot CM, Du X, Tove SR, Grunden AM. Improving the catalytic activity ofhyperthermophilic Pyrococcus prolidases for detoxification of organophosphorusnerve agents over a broad range of temperatures. Appl Microbiol Biotechnol. 2010 Aug;87(5):1715-26. doi: 10.1007/s00253-010-2614-3. Epub 2010 Apr 27. PubMed PMID:20422176.

13: Tirado-Acevedo O, Chinn MS, Grunden AM. Production of biofuels from synthesisgas using microbial catalysts. Adv Appl Microbiol. 2010;70:57-92. doi:10.1016/S0065-2164(10)70002-2. Epub 2010 Mar 6. Review. PubMed PMID: 20359454.

14: Theriot CM, Tove SR, Grunden AM. Characterization of two proline dipeptidases(prolidases) from the hyperthermophilic archaeon Pyrococcus horikoshii. ApplMicrobiol Biotechnol. 2010 Mar;86(1):177-88. doi: 10.1007/s00253-009-2235-x. Epub2009 Sep 26. Erratum in: Appl Microbiol Biotechnol. 2010 Mar;86(1):393. PubMedPMID: 19784642.

15: Johnson MC, Devine AA, Ellis JC, Grunden AM, Fellner V. Effects ofantibiotics and oil on microbial profiles and fermentation in mixed cultures ofruminal microorganisms. J Dairy Sci. 2009 Sep;92(9):4467-80. doi:10.3168/jds.2008-1841. PubMed PMID: 19700708.

16: Im YJ, Ji M, Lee A, Killens R, Grunden AM, Boss WF. Expression of Pyrococcus furiosus superoxide reductase in Arabidopsis enhances heat tolerance. PlantPhysiol. 2009 Oct;151(2):893-904. doi: 10.1104/pp.109.145409. Epub 2009 Aug 14.PubMed PMID: 19684226; PubMed Central PMCID: PMC2754621.

17: Theriot CM, Tove SR, Grunden AM. Biotechnological applications of recombinantmicrobial prolidases. Adv Appl Microbiol. 2009;68:99-132. doi:10.1016/S0065-2164(09)01203-9. Review. PubMed PMID: 19426854.

18: Lee AM, Sevinsky JR, Bundy JL, Grunden AM, Stephenson JL Jr. Proteomics ofPyrococcus furiosus, a hyperthermophilic archaeon refractory to traditionalmethods. J Proteome Res. 2009 Aug;8(8):3844-51. doi: 10.1021/pr801119h. PubMedPMID: 19425607.

19: Ying X, Grunden AM, Nie L, Adams MW, Ma K. Molecular characterization of the recombinant iron-containing alcohol dehydrogenase from the hyperthermophilicArchaeon, Thermococcus strain ES1. Extremophiles. 2009 Mar;13(2):299-311. doi:10.1007/s00792-008-0217-z. Epub 2008 Dec 25. PubMed PMID: 19115036.

20: Cotter JL, Chinn MS, Grunden AM. Ethanol and acetate production byClostridium ljungdahlii and Clostridium autoethanogenum using resting cells.Bioprocess Biosyst Eng. 2009 Apr;32(3):369-80. doi: 10.1007/s00449-008-0256-y.Epub 2008 Aug 26. PubMed PMID: 18726618.