Jeffrey A. Lewis
J. William Fulbright College of Arts & Sciences
All organisms must endure diverse environmental stresses during their lifetime. Our lab seeks to understand how cells adapt and even thrive in the face of various environmental assaults. Cellular stress responses are remarkably complex, coordinating multiple levels of sensing, signal transduction, and global regulatory networks. Thus, stress research feeds into nearly all aspects of cell biology, with implications for human disease, microbial pathogenesis, and the evolution of regulatory networks.
Our group is interested in both the function and regulation of stress defenses. On the functional level, we are interested in the coordination and logic of stress-responsive regulatory networks, and how stress defense genes allow cells to maintain homeostasis. We are also interested in how natural variation shapes differences in how individuals perceive and respond to stress. We frequently turn to nature to understand aspects of stress defense that are absent in laboratory strains. We are leveraging this approach to generate novel insights into the regulatory logic and function of stress signaling and defense.
More details about our research group can be found on our lab website.
General Genetics, Biological Regulation and Subcellular Communication, Laboratory in Microbial Fermentation
Ph.D. University of Wisconsin, 2007
B.S. University of California, Santa Barbara, 2001
- Scholes AN, Lewis JA. 2019. Comparison of RNA Isolation Methods on RNA-Seq: Implications for Differential Expression and Meta-Analyses. bioRxiv (preprint). doi:10.1101/728014
- Scholes AN, Pollock ED, Lewis JA. 2019. A Wild Yeast Laboratory Activity: From Isolation to Brewing. bioRxiv (preprint). doi:10.1101/698589
- Storey AJ, Hardman RE, Byrum SD, Mackintosh SG, Edmondson RD, Wahls WP, Tackett AJ, Lewis JA. 2019. Accurate and Sensitive Quantitation of the Dynamic Heat Shock Proteome using Tandem Mass Tags. bioRxiv (preprint). doi:10.1101/696641
- McDaniel EM, Stuecker TN, Veluvolu M, Gasch AP, Lewis JA. 2018. Independent mechanisms for acquired salt tolerance versus growth resumption induced by mild ethanol pretreatment in Saccharomyces cerevisiae. mSphere 3:e00574-18
- Stuecker TN, Scholes AN, Lewis JA. 2018. Linkage mapping of yeast cross protection connects gene expression variation to a higher-order organismal trait. PLoS Genetics 14(4):e100733
- Nguyen K, Marray S, Lewis JA, Kumar P. 2017. Morphology, cell division, and viability of Saccharomyces cerevisiae at high hydrostatic pressure. arXiv.
- Johnson WH, Douglas MR, Lewis JA, Stuecker TN, Carbonero FG, Austin BJ, Evans-White MA, Entrekin SA, Douglas ME. 2017. Do biofilm communities respond to the chemical signatures of fracking? A test involving streams in North-central Arkansas. BMC Microbiology. 17(1):29
- Lewis JA, Broman AT, Will J, Gasch AP. 2014. Genetic Architecture of Ethanol-Responsive Transcriptome Variation in Saccharomyces cerevisiae Strains. Genetics. 198(1):369-382 PMC4174948
- Wohlbach DJ, Rovinskiy N, Lewis JA, Sardi M, Schackwitz WS, Martin JA, Deshpande S, Daum CG, Lipzen A, Sato TK, Gasch AP. 2014. Comparative genomics of Saccharomyces cerevisiae natural isolates for bioenergy production. Genome Biol. Evol. 6(9):2557-2566 PMC4202335
- Gonçalves A, Ong I, Lewis JA, Costa VS. 2014. Towards using probabilities and logic to model regulatory networks. 2014 IEEE 27th International Symposium on Computer-Based Medical Systems: 239-242
- Gonçalves A, Ong I, Lewis JA, Costa VS. 2014. Discovering differentially expressed genes in yeast stress data. 2014 IEEE 27th International Symposium on Computer-Based Medical Systems: 537-538
- Lewis JA, Gasch AP. 2012. Natural variation in the yeast glucose-signaling network reveals a new role for the Mig3p transcription factor. G3 (Bethesda). 2(12):1607-1612 PMC3516482
- Gonçalves A, Ong I, Lewis JA, Costa VS. 2012. A ProbLog model for analyzing gene regulatory networks. 22nd International Conference on Inductive Logic Programming: 38-43
- Lewis JA, Elkon IM, McGee MA, Higbee AJ, Gasch AP. 2010. Exploiting natural variation in Saccharomyces cerevisiae to identify genes for increased ethanol resistance. Genetics. 186(4):1197-1205 PMC2998304
- Lewis JA, Stamper LW, Escalante-Semerena JC. 2009. Regulation of expression of the tricarballylate utilization operon (tcuABC) of Salmonella enterica. Res. Microbiol. 160(3):179-186 PMC2692759
- Lewis JA, Boyd JM, Downs DM, Escalante-Semerena JC. 2009. Involvement of the Cra global regulatory protein in the expression of the iscRSUA operon, revealed during studies of tricarballylate catabolism in Salmonella enterica J. Bacteriol. 191(7):2069-2076 PMC2655522
- Boyd JM, Lewis JA, Escalante-Semerena JC, Downs DM. 2008. Salmonella enterica requires ApbC function for growth on tricarballylate: Evidence of functional redundancy between ApbC and IscU J. Bacteriol. 190(13):4596-4602 PMC2446783
- Lewis JA, Escalante-Semerena JC. 2007. Tricarballylate catabolism in Salmonella enterica. The TcuB protein uses 4Fe-4S clusters and heme to transfer electrons from FADH2 in the tricarballylate dehydrogenase (TcuA) enzyme to electron acceptors in the cell membrane. Biochemistry 46(31):9107-9115
- Lewis JA, Escalante-Semerena JC. 2006. The FAD-dependent tricarballylate dehydrogenase (TcuA) enzyme of Salmonella enterica converts tricarballylate into cis-aconitate. J. Bacteriol. 188(15):5479-5486 PMC1540016
- Lewis JA, Horswill AR, Schwem BE, Escalante-Semerena JC. 2004. The Tricarballylate utilization (tcuRABC) genes of Salmonella enterica serovar Typhimurium LT2. J. Bacteriol. 186(6):1629-1637 PMC355976