Research Products

Follow the links to see a list of posters, seminars, and conference presentations.

Protein Databank Depositions

• PDB ID 7KD3 Structure of an HxlR/DUF24 family transcription regulator, CdTR_3200 from hypervirulent Clostridioides difficile R20291
• PDB ID 5DYM Crystal structure of a PadR family transcription regulator from hypervirulent Clostridium difficile R20291 – CdPadR_0991 to 1.89 Angstrom resolution
• PDB ID 7SUB 3-oxoacyl-ACP reductase FabG from Syntrophus aciditrophicus
• PDB ID 5J6C FMN-dependent Nitroreductase (CDR20291_0767) from Clostridium difficile R20291
• PDB ID 5J62 FMN-dependent Nitroreductase (CDR20291_0684) from Clostridium difficile R20291

Publications in Preparation or Submitted

(*indicates the corresponding author)

• Chanderban, M. and E.A. Karr*. A two-component signaling system is essential for growth of Methanococcus maripaludis on formate.
• Isom, C.E., S.K. Menon, G.B. Richter-Addo, A.H. West, and E.A. Karr*. Crystal structure and DNA functional analysis of an HxlR/DUF24 family transcription regulator, CdTR_3200 from hypervirulent Clostridioides difficile R20291. Planned submission to Protein Science.  Product PDB ID 7KD3.
• Dinh, D., S. Yaghoubi, L.M. Thomas, N. Wofford, M.J. McInerney, E.A. Karr*. Functional and Structural Characterization of AMP-forming Acetyl-CoA Synthetase (Acs1) from Syntrophus aciditrophicus strain SB.

Publications

(*indicates the corresponding author)
Link to Pubmed list of publications, Karr EA

• Dinh, D.M., L.M. Thomas, E. A. Karr*. 2023.  Crystal structure of putative 3-hydroxypimelyl-CoA dehydrogenase, Hcd1, at 1.78 Å resolution from Syntrophus aciditrophicus strain SB. Acta Cryst. F79, https://doi.org/10.1107/S2053230X23004399.
• James, K.L., J.W. Kung, B.R. Crable, H. Mouttaki, J.R. Sieber, H.N. Nguyen, Y. Yang, Y. Xie, J. Erde, N.Q. Wofford, E.A. Karr, J.A. Loo, R.R. Ogorzalek Loo, R.P. Gunsalus and M.J. McInerney*. 2019.  Syntrophus aciditrophicus uses the same enzymes in a reversible manner to degrade and synthesize aromatic and alicyclic acids.  Environ Microbiol, 21: 1833-1846. doi:10.1111/1462-2920.14601
• Hebdon, S., S.K. Menon, E.A. Karr, G.B. Richter-Addo, A.W. West*. 2018. Regulatory targets of the response regulator RR_1586 from Clostridioides difficile identified using a bacterial one-hybrid screen.  J. Bacteriol.  Vol 200.  DOI:  10.1128/JB.00351-18.
• Jennings, M.E., F.H. Lessner, E.A. Karr, D.J. Lessner*. 2017.  The [4Fe-4S] clusters of Rpo3 are key determinants in the post Rpo3/Rpo11 heterodimer formation of RNA polymerase in Methanosarcina acetivorans.  Microbiol. Open.  DOI: 10.1002/mbo3.399.
• Karr, E.A., C.E. Isom, V. Trinh and E. Peeters. 2017. Transcription factor-mediated gene regulation in Archaea.  In:  Nucleic Acids and Molecular Biology, Vol. RNA metabolism and gene expression in Archaea, Béatrice Clouet-d’Orval (ed).  Vol. 32, Spring, Cham, pp 27-69.
• Isom, C.E., S.K. Menon, L.M. Thomas, A.H. West, G.B. Richter-Addo and E.A. Karr*. 2016. Crystal structure of a PadR family transcription regulator from hypervirulent Clostridium difficile R20291. BMC Microbiol. 16:231.
• Wang, B., S.M. Powell, N. Hessami, F.Z. Najar, L.M. Thomas, E. A. Karr, A.H. West, G.B. Richter-Addo*. 2016. Crystal structures of two nitroreductases from hypervirulent Clostridium difficile and functionally related interactions with the antibiotic metronidazole.  Nitric Oxide: Biol. Chem.  60:32-39.
• James, K.L., L.A. Ríos-Hernández, N.Q. Wofford, H. Mouttaki, J.R. Sieber, C.S. Sheik, H.N. Nguyen, Y.Yang, Y. Xie, J. Erde, L. Rohlin, E.A. Karr, J.A. Loo, R.R. Ogorzalek-Loo, G.B. Hurst, R.P. Gunsalus, L.I. Szweda, and M.J. McInerney*. 2016.  Pyrophosphate-Dependent ATP Formation from Acetyl Coenzyme A in Syntrophus aciditrophicus, a New Twist on ATP Formation.  mBio 7.
• Karr, E.A.* Transcription Regulation in the Third Domain.  Adv. Appl. Microbiol.  Chapter 3, Vol 89:101-133.
• Isom, C.E.,  J.L. Turner, D.J. Lessner, E.A. Karr*. 2013.  Characterization of the Methanosarcina acetivorans C2A MsvR homologue reveals functional diversity of MsvR within methanogens.  BMC Microbiol. 13:163.
• Islam, S., E.A. Karr.* 2013.  Examination of Metal Corrosion by Desulfomicrobium thermophilum, Archaeoglobus fulgidus, and Methanothermobacter thermautotrophicus.  BIOS, 84.
• Cafasso, J., B.A. Manjasetty, E.A. Karr, K. Sandman, M.R. Chance and J.N. Reeve.  2010.  Preliminary crystallography confirms that the archaeal DNA-binding and tryptophan-sensing regulator, TrpY, is a dimer.  Acta Cryst. F66, 1493-1495.
• Karr, E.A.* The methanogen-specific transcription factor MsvR regulates the adjacent fpaA-rlp-rub oxidative stress operon in Methanothermobacter thermautotrophicus.  J. Bacteriol. 192 5914-5922.
• Dunn, A.K.*, E.A. Karr, Y. Wang, A. Batton, E. Ruby, and E. Stabb.  2010.  The alternative oxidase (AOX) gene in Vibrio fischeri is controlled by NsrR and upregulated in response to nitric oxide stress.  Mol. Microbiol.  77: 44-55.
• Walker, C., J. de la Torre, M. Klotz, H. Urakawa, N.  Pinel, D. Arp, C.  Brochier-Armanet, P. Chan, A.  Golabgir-Anbarani, J. Hemp, M. Hügler, E.A. Karr, M. Könneke, M. Shin, T. Lowe, W. Martens-Habena, L. Sayavedra-Soto, D. Lang, S. Sievert, A. Rosenzweig, G. Manning, and D. Stahl. 2010.  The Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine Archaea. Proc. Natl. Acad. Sci. U. S. A. 107: 8818-8823.
• Karr, E.A., Sandman, R. Lurz, and J.N. Reeve. 2008. TrpY Regulation of trpB2 Transcription in Methanothermobacter thermautotrophicus. J. Bacteriol. 190: 2637-2641.
• Cubonova, L., K. Sandman, E.A. Karr, A. Cochran, and J.N. Reeve. 2007.  Mutational Analysis of the archaeal regulator TrpY.  J. Bacteriol. 189:  4338-4342.
• Karr, E.A., M. Sattley, S.M. Belchik, M.T. Madigan, and L.A. Achenbach. 2006. Biodiversity of methanogenic and other Archaea in the permanently frozen Lake Fryxell, Antarctica. Appl. Environ. Microbiol. 72:  1663-1666.
• Madigan, M.T., D.O. Jung, E.A. Karr, W.M. Sattley, L.A. Achenbach, and M. van der Meer. 2005. Diversity of anoxygenic phototrophs in contrasting extreme environments. In: Geothermal Biology and Geochemistry in Yellowstone National Park. W. Inskeep (ed). Thermal Biology Institute, Montana State University.
• Karr, E.A., M. Sattley, M.R. Rice, D.O. Jung, M.T. Madigan, and L.A. Achenbach. 2005. Diversity and distribution of sulfate-reducing bacteria in the permanently frozen Lake Fryxell, McMurdo Dry Valleys, Antarctica. Appl. Environ. Microbiol. 71:  6353-6359.
• Jung, D.O., L.A. Achenbach, E.A. Karr, S. Takaichi, and M.T. Madigan. 2004.  A gas vesiculate planktonic strain of the purple nonsulfur bacterium Rhodoferax antarcticus isolated from Lake Fryxell, Dry Valleys, Antarctica.  Arch. Microbiol.  182:  236-243.
• Karr, E.A., M. Sattley, D.O. Jung, M.T. Madigan, and L.A. Achenbach. 2003.  Remarkable diversity of phototrophic purple bacteria in a permanently frozen Antarctic lake.  Appl. Environ. Microbiol. 69:  4910-4914.