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koudelkaDr. Gerald B. Koudelka

Office: Cooke 607
Office Hours: Monday and Thursday 2:00-3:00 PM (or by appointment)
Phone: (716) 645-4940 (Cooke 607)


Ph.D. University at Buffalo
Postdoctoral Research at Harvard University

Laboratory webpage

Research Summary

The research in the Koudelka lab is focused around two central themes:

Mechanisms of DNA Sequence Recognition:

Understanding the mechanisms used by regulatory proteins in recognizing specific DNA sequences remains one of the most important areas of study in biology. This process requires that the protein be able to seek out and recognize its particular binding sequence amidst the presence of an overwhelming number of potential non-specific binding sites. We seek to uncover the intimate biochemical and thermodynamic underpinnings of DNA sequence recognition.

Evolution of Bacteriophage-encoded Exotoxins

Phages encoding exotoxin genes are found ubiquitously within bacteria isolated from the environment. In the context of humans, these exotoxins cause diseases ranging from cholera to diphtheria to enterohemorrhagic diarrhea. However, the frequency of occurrence of the genes encoding any particular exotoxin gene in bacteriophage and/or lysogens far exceeds the number of potential animal hosts. These observations suggest that humans and other susceptible mammals are not the primary “targets” of these toxins. We are exploring the hypothesis that exotoxins arose in bacteria as part of an antipredator defense mechanism.

Selected Publications

  • Aijaz I, Koudelka GB. (2017) Tetrahymena phagocytic vesicles as ecological micro-niches of phage transfer. FEMS Microbiol Ecol. 93,  doi: 10.1093/femsec/fix030 (Full text).
  • Colon, M.P., Chakraborty D., Pevzner, Y., Koudelka. G.B. (2016) Mechanisms determining the differential stability of of Stx+ and Stx- lysogens, Toxins 8, 96 doi:10.3390/toxins8040096 (Full text).
  • Arnold, J.W., Spacht, D., Koudelka, G.B., (2016) Molecular determinants governing the recognition and uptake of E. coli O157:H7 by Acanthamoeba castellanii, Cellular Microbiology, 18(10), 1459–1470 (Full text).
  • Samorodnitsky, D., Szyjka, C., Koudelka, G.B., (2015) A Role for Autoinhibition in Preventing Dimerization of the Transcription Factor ETS1 Journal of Biological Chemistry 290, 22101-22110 (Full text)
  • Arnold, J.W, Koudelka, G.B. (2014) The Trojan horse of the microbiological arms race: Phage encoded bacterial toxins as a weapon against eukaryotic predators, Env. Micro. 16, 454-466 (Full text).
  • Mauro, S.A., Opalka, H., Lindsay, K., Colon, M.P., Koudelka, G.B. (2013) The microcosm mediates the persistence of Shiga toxin producing E. coli (STEC) in freshwater ecosystems. Applied and Env. Microbiology, 79, 4821-4842 (Full text).
  • Shkilnyj, P., Colon, M.P., and Koudelka, G.B., (2013) Bacteriophage 434 Hex protein prevents RecA-mediated repressor autocleavage Viruses 5, 111-126 (Full text)
  • Stolfa, G., and Koudelka, G.B., (2013) Entry and Killing of Tetrahymena by Bacterially Produced Shiga toxin, mBio, 4 e00416-12; doi:10.1128/mBio.00416-12. (Full text)
  • Harris, L.A., Watkins, D., Williams, L.D., and Koudelka G. B. (2013) Indirect Readout of DNA Sequence by P22 Repressor: Roles of DNA and Protein Functional Groups in modulating DNA Conformation, J. Mol. Biol 425, 133-143.,
  • Bullwinkle, T.J., Samorodnitsky, D., Rosati, R.C. and Koudelka, G.B., (2012) DNA binding specificity determinants of 933W repressorPLOS One, 7: e34563. doi:10.1371/journal.pone.0034563
  • Pawlowski , D.R., Raslawsky, A., Siebert, G., Metzger, D.J., Koudelka, G.B.., Karalus, R.J. (2011) Identification of Hylemonella gracilis as an antagonist of Yersinia pestis persistenceJournal of Bioterrorism & Biodefense, S3:004. doi:10.4172/2157-2526.S3-004.
  • Mauro S.A. and Koudelka, G.B, (2011) Shiga Toxin: Expression, Distribution, and Its Role in the Environment Toxins 3, 608-625; doi:10.3390/toxins3060608
  • Bullwinkle, T.J., and Koudelka, G.B., (2011) The Lysis-Lysogeny Decision of Bacteriophage 933W: A 933W Repressor-Mediated Long Distance Loop Has No Role in Regulating 933W PRM ActivityJ. Bacteriol, 193, 3313-3323 (Full text)
  • Watkins, D., Mohan, S., Koudelka, G.B., Williams, L.D., (2010) Sequence Recognition of DNA by Protein-Induced Conformational TransitionsJ. Mol. Biol. 396, 1145-64. (Full text)
  • Lainhart, W, Stolfa, G. and Koudelka, G.B. (2009) Shiga Toxin as a Bacterial Defense against a Eukaryotic Predator, Tetrahymena thermophilaJ. Bacteriol. 191 5116-5122 (Full text)
  • Watkins, D., Hsiao, C., Woods, K.K., Koudelka, G.B., Williams, L.D., (2008) P22 c2 Repressor-Operator Complex: Mechanisms of Direct and Indirect Readout. Biochemistry 47, 2325-2338 (Full text).

[Complete list of publications is here]