A person in a suit and tie

Description generated with high confidenceGerald B. Koudelka

Professor of Biological Sciences

College of Arts & Sciences


DNA-Protein Interactions; DNA Structure, Transcriptional Regulation

Bacterial Pathogenesis



Ph.D. 1984 University at Buffalo

Postdoctoral work 1984-88 Harvard University

Address Information

Gerald B. Koudelka
Department of Biological Sciences
607 Cooke Hall
State University of New York at Buffalo
Buffalo, NY 14260

Phone: (716) 645-4940 (Research Office)

Click for Email


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


Mechanisms of Indirect Readout:

The mechanisms whereby regulatory proteins recognize 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, in the presence of an overwhelming number of potential non-specific binding sites. In our studies of direct readout of DNA sequence, we have uncovered the intimate details of how amino acids and base pairs can interact, and how these interactions can be regulated by both protein and DNA structure.  In indirect readout, sequence-dependent differences in the structure and flexibility of noncontacted bases in a DNA binding site regulate the stability and sequence-specificity of a protein-DNA complex. Despite the high prevalence and functional importance of indirect readout it is unclear how DNA sequence differences lead to changes in DNA structure and flexibility. We are determining the structural basis for, and functional implications of the indirect readout mechanism used by DNA binding proteins.


Evolution of Bacteriophage-encoded Exotoxins

Bacterially-derived exotoxins are among the most deadly substances known. The genes that encode these exotoxins are usually carried by bacterial viruses (bacteriophages) integrated into the bacterial host chromosome. It is generally assumed that the targets of these toxins are mammals. However, these phage-encoded exotoxin genes are widespread in the environment and are found with unexpectedly high frequency in regions that lack the presumed mammalian targets. These observations suggest that humans and other susceptible mammals are not the primary “targets” of these toxins. We are exploring the hypothesis that exotoxins are part of an antipredator defense mechanism.



A dna structure with different colored strands

Description generated with high confidenceIndirect Readout: DNA Structure Effects on Protein-DNA Interactions
 The binding of proteins to specific DNA sequences plays a central role in the regulation of gene expression in all organisms. These proteins regulate gene expression by binding DNA at specific sites and activating or repressing transcription. Structural and biochemical studies have provided a detailed insight into how the intimate contacts between proteins and DNA enable proteins to bind specifically and with high affinity only to their cognate DNA binding sites. One conclusion of these studies is that sequence specific DNA recognition involves both direct and indirect readout of the binding site sequence.


In indirect readout, the stability and specificity of a protein-DNA complex is regulated by the sequence of bases not in contact with the protein. These noncontacted bases can inhibit or prevent the contacted DNA from being properly juxtaposed with protein groups. DNA sequence-dependent differences in the structure and flexibility of noncontacted bases lead to alterations in the strength and/or ease of forming protein-DNA contacts. The DNA sequence-limited geometry changes thereby indirectly alter the affinity and/or specificity of a protein for its cognate binding site. Hence, indirect effects of DNA sequence on protein-DNA complex formation occur by a modulation of the structural complementarity between the interacting molecules.

While it is clear that indirect readout of DNA sequence is an important component of the DNA sequence recognition mechanisms of many proteins, until recently, it was unclear how DNA sequence directs changes in DNA structure and/or flexibility. Our current studies indicate that indirect readout by DNA binding proteins repressor is influenced by sequence-dependent interactions between the solvent and the unbound and/or protein-bound DNA. These data also show that manipulating the solvent environment inside cells leads to specific effects on gene regulation.

Hence, our ongoing studies are aimed at 1) providing a thermodynamic and structural framework to explain the mechanisms of solvent-dependent indirect readout of DNA sequence, and 2) understanding how these sequence- and solvent-dependent differences in DNA structure influence the stability and function of protein-DNA complexes.


A close-up of a plant

Description generated with very high confidenceEvolution of Bacteriophage-encoded Exotoxins
Phages encoding exotoxin genes are found ubiquitously as lysogens in environmental bacteria, but it is unclear what advantage there is to the bacteria to harbor phage that encode such toxic compounds. 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. Moreover, these phage-encoded exotoxin genes are found at high frequency in free phages and lysogenic bacteria isolated from environments where the corresponding human diseases are not prevalent. These observations suggest that mammals are neither the original nor primary “targets” of these toxins. The phage-encoded exotoxins like the well-studied Shiga toxin (Stx), kill eukaryotic cells by attacking features and pathways that are common to all eukaryotes both, uni- and multi-cellular. Thus the evolution of these toxins may have occurred before the appearance of multicellular organisms. Since predation by eukaryotic predators (e.g., ciliates and other protozoa), is a major source of bacterial mortality, these observations suggest that exotoxins may have arisen as part of an antipredator, (antiprotozoan) defense strategy. Hence humans may be innocent bystanders in the evolutionary battle between protozoans and their bacterial prey.

The environment in which microbes live is dynamic, changing as a consequence of anthropogenic, environmental and evolutionary processes. Rapid changes can also result from the activities of the microbes themselves when they respond to ecological pressures such as predation. Our published data indicate phage-encoded exotoxins (e.g., Shiga toxin, diphtheria toxin) evolved as a defense against bacterivorous predators. Our preliminary data indicate that the efficacy of an exotoxin’s antipredator activity may govern the environmental persistence of exotoxin-encoding bacteria and phages. By determining how biochemical, cell biological and population-based factors impact the persistence of an evolutionarily diverse set of Shiga toxin-encoding bacteria and phage in natural and artificial microcosms, we are attempting to 1) identify how the microbial responses to predation shape, and are shaped by, the microbial community and; 2) delineate how these responses impact microbial survival and success.



(For complete list see here)

Gong, C, Chakraborty D., Koudelka, G.B. (2023)

A prophage encoded ribosomal RNA methyltransferase regulates the virulence of Shiga-toxin-producing Escherichia coli (STEC) Nucleic Acids Res. 2023 Dec 12:gkad1150. doi: 10.1093/nar/gkad1150 https://doi.org/10.1093/nar/gkad1150.


Gong, C., Koudelka, G.B. (2023)

The Shiga toxin (Stx)-Phage Encoded Ribosomal RNA Methyltransferase Regulates Stx-producing Escherichia coli (STEC) Virulence by Blocking Stx-Mediated Inactivation of Bacterial Ribosomes (2023) bioRxiv.09.20.558713; doi: https://doi.org/10.1101/2023.09.20.558713


Liu, Y., Koudelka, G.B. (2023)

O-polysaccharides of LPS modulate E. coli uptake by Acanthamoeba. castellanii Microorganisms, 11, 1377  https://doi.org/10.3390/microorganisms11061377 .


Liu, Y., Koudelka, G.B. (2023)

The oligosaccharide region of LPS governs predation of E. coli by the bacterivorous protist, Acanthamoeba castellanii Microbiology Spectrum, 11  e02930-22 https://journals.asm.org/doi/10.1128/spectrum.02930-22


Peng, L.; Dumevi, R.M.; Chitto, M.; Haarmann, N.; Berger, P.; Koudelka, G.; Schmidt, H.; Mellmann, A.; Dobrindt, U.; Berger, M. A (2022)

Robust One-Step Recombineering System for Enterohemorrhagic Escherichia coli. Microorganisms, 10, 1689. https://doi.org/10.3390/microorganisms10091689


Lama, R., Xu, C., Galster, S.L., Querol-García, J., Portwood, S., Mavis, C.K., Ruiz, F.M., Martin, D., Wu, J., Giorgi, M.C., Bargonetti, J., Wang, E.S., Hernandez-Ilizaliturri, F.J., Koudelka, G.B., Chemler, S.R., Muñoz,  Wang, X. (2022)

Small Molecule MMRi62 Targets MDM4 for Degradation and Induces Leukemic Cell Apoptosis Regardless of p53 Status Front. Oncol. https://doi.org/10.3389/fonc.2022.933446.


Berger, M., Aijaz, I., Berger, P., Dobrindt, U., Koudelka, G.B. (2019)

Transcriptional and Translational Inhibitors Block SOS Response and Shiga Toxin Expression in Enterohemorrhagic Escherichia coli.

Sci Rep 9, 18777. https://doi.org/10.1038/s41598-019-55332-2.


Berger, P., Kouzel, I.U., Berger, M., Haarmann, N., Dobrindt, U., Koudelka, G.B., Mellmann, A. (2019)

Carriage of Shiga toxin phage profoundly affects Escherichia coli gene expression and carbon source utilization.

BMC Genomics 20:504. doi.org/10.1186/s12864-019-5892-x.


Koudelka G.B., Arnold J.W., Chakraborty, D. (2018)

 Evolution of STEC virulence: Insights from the antipredator activities of Shiga toxin producing E. coli.

Int J Med Microbiol. 308 956-961. doi: 10.1016/j.ijmm.2018.07.001


Chakraborty, D., Clark, E., Mauro, S.A., Koudelka, G.B. (2018)

Molecular Mechanisms Governing "Hair-Trigger" Induction of Shiga Toxin-Encoding Prophages.

Viruses 10 pii: E228. doi: 10.3390/v10050228.


Aijaz, I., Koudelka, G.B. (2018).

Cheating, facilitation and cooperation regulate the effectiveness of phage-encoded exotoxins as antipredator molecules

Microbiologyopen e00636. doi: 10.1002/mbo3.636.


Aijaz, I., Koudelka, G.B. (2017)

Tetrahymena phagocytic vesicles as ecological micro-niches of phage transfer

FEMS Microbiology Ecology, 93, Issue 4, fix030, doi: 10.1093/femsec/fix030


Colon, M.P., Chakraborty D., Pevzner, Y., Koudelka. GB (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)

Determinants that govern the recognition and uptake of E. coli O157:H7 by Acanthamoeba castellanii

Cellular Microbiology, (2016) 18, 1459–1470 (Full text)


Samorodnitsky, D., Szyjka, C., Koudelka, G.B., (2015)

A Role for Autoinhibition in Preventing Dimerization of the Transcription Factor ETS1

J. Biol. Chem. 290, 22101-22110 (Full text)


Harris, L.A., Williams, L.D., and Koudelka G. B. (2014)

Specific minor groove solvation is a crucial determinant of DNA binding site recognition.

Nucl. Acids Res. doi: 10.1093/nar/gku1259 (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., http://dx.doi.org/10.1016/j.jmb.2012.10.008.


Bullwinkle, T.J., Samorodnitsky, D., Rosati, R.C. and Koudelka, G.B. (2012)

DNA binding specificity determinants of 933W repressor,

PLOS 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 persistence.

Journal 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 (2011)

The Lysis-Lysogeny Decision of Bacteriophage 933W: A 933W Repressor-Mediated Long Distance Loop Has No Role in Regulating 933W PRM Activity,

J. 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 Transitions.

J. 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 thermophila,

 J. Bacteriol. 191 5116-5122 (Full text)




Page last modified: 03/21/2024 by G. Koudelka


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