University of Otago

Cook Lab Research

Research Overview

Research in my laboratory focuses on how both pathogenic (Mycobacterium tuberculosis) and environmental (polyextremophiles) bacteria adapt to different environments. The molecular mechanisms involved in this adaptation and how they control the physiological response of a particular bacterium to environmental signals is a major theme.

Research Projects

These projects utilize modern technologies (e.g. proteomics, transcriptomics, molecular biology and structural biology) to address important questions in bacterial adaptation to environment.

Group members:

Nicola Marechal, Lab manager, nicola.marechal@otago.ac.nz , +64 3 4797733

Dr Jennifer Robson, jenrobson1@gmail.com

Dr Adam Heikal, adam.heikal@otago.ac.nz

Dr Idiko Pecsi, ildiko.pecsi@otago.ac.nz

Marion Weimar, marion.weimar@otago.ac.nz

Lara Pfister, larapfister@gmx.ch

Kiel Hards, harki408@student.otago.ac.nz

 

Htin Aung, PhD candidate, htinlinaung@gmail.com

Shaaly Aishath, PhD candidate, shaaly@gmail.com

Marina Iglesias Cans, PhD candidate, miglesiascans@gmail.com

Chris Greening, PhD Candiate, chrisgreening1987@gmail.com

Elyse Dunn, PhD candidate, elyse.a.dunn@gmail.com

Michael Petridu, PhD candidate, michaelpetridu@gmail.com

Kieran Jongerius, BSc(Hons) student, jonki313@student.otago.ac.nz

Adrian Patterson, BSc(Hons) student, patad124@student.otago.ac.nz

Jessica Petri, Summer student, jessi@kleinvolk.de

 

Recent publications

2013

Berney, M. and Cook, G.M. Respiration and Oxidative Phosphorylation in Mycobacteria. In Advances in Photosynthesis and Respiration volume 29. Springer, Dordrecht, The Netherlands ISSN 1572-0233 (2013)

Shaaly, A., Kalamorz, F., Gebhard, S. and Cook, G.M. Undecaprenyl pyrophosphate phosphatase confers low-level resistance to bacitracin in Enterococcus faecalis. Journal of Antimicrobial Chemotherapy doi: 10.1093/jac/dkt048 (2013)

Cook, G.M., Robson, J.R., Frampton, R.A., McKenzie, J., Przybilski, R., Fineran, P.C. and Arcus, V.L. Ribonucleases in bacterial toxin-antitoxin systems. Biochimica et Biophysica Acta- Gene Regulatory Mechanisms 1829:523–531 (2013)

Wilson, J.L., Jesse, H.E., Hughes, B., Lund, V., Naylor, K., Davidge, K.S., Cook, G.M., Mann, B.E. and Poole, R.K. Ru(CO)3Cl(glycinate) (CORM-3): a CO-releasing molecule with broad-spectrum antimicrobial and photosensitive activities against respiration and cation transport in Escherichia coli. Antioxidants and Redox Signaling Nov 27. [Epub ahead of print] (2013)

Arcus, V.L. and Cook, G.M. Type II Toxin-Antitoxins: Structural and Functional Aspects of Type II Loci in Mycobacteria. In Prokaryotic Toxin-Antitoxins, Gerdes, K (Ed) Springer-Verlag Berlin Heidelberg (2013) ISBN 978-3-642-33252-4.

2012

Cook, G.M. and Heikal, A. Bridging the gap between a TB drug and its target. Science Translational Medicine 4, 150fs33 (2012)

Berney, M.*, Weimar, M.R., Heikal, A. and Cook, G.M. Regulation of proline metabolism in mycobacteria and its role in carbon metabolism under hypoxia. Molecular Microbiology 84:664–681 (2012)

McKenzie, J.L., Duyvestyn, J.M., Smith, T., Bendak, K., Mackay, J., Cursons, R., Cook, G.M. and Arcus, V.L. Determination of ribonuclease sequence-specificity using pentaprobes and mass spectrometry. RNA 18:1267-1278 (2012)

Hammann, E., Zappe, A., Keis, S., Ernst, S., Matthies, D., Meier, T., Cook, G.M. and Börsch, M. Step size of the rotary proton motor in single FoF1-ATP synthase from a thermoalkaliphilic bacterium by DCO-ALEX FRET. Quantitative Biology - Biomolecules arXiv:1202.1007v1 (2012)

McKenzie, J.L., Robson, J.R., Berney, M., Smith, T., Ruthe, A., Arcus, V.L. and Cook, G.M. A VapBC toxin-antitoxin module is a post-transcriptional regulator of metabolic flux in mycobacteria. Journal of Bacteriology 194:2189-2204 (2012)

Zhang, X.-X., Chang, H., Tran, S.L., Gauntlett, J.C., Cook, G.M. and Rainey, P.B. Variation in transport explains polymorphism of histidine and urocanate utilization in a natural Pseudomonas population. Environmental Microbiology Jan 9. doi: 10.1111/j.1462-2920.2011.02692.x. [Epub ahead of print] (2012)

Frampton R.A., Aggio, R.B., Villas-Boas, S.G., Arcus, V.L. and Cook G.M. Toxin-antitoxin systems of Mycobacterium smegmatis are essential for cell survival. Journal of Biological Chemistry 287:5340-5356 (2012)

Tannock, G.W., Wilson, C.M, Loach, D., Cook, G., Eason, J., O’Toole, P.W., Holtrop, G. and Lawley, B. Resource partitioning in relation to cohabitation of Lactobacillus species in the mouse forestomach. The ISME Journal 6:927-938 (2012)

2011

McMillan, D.G.G., Ferguson, S.A., Dey, D., Schröder, K., Aung, H.L., Vince Carbone, V., Attwood, G.T., Ronimus, R.S., Meier, T., Janssen, P.H. and Cook, G.M. A1Ao-ATP synthase of Methanobrevibacter ruminantium couples sodium ions for ATP synthesis under physiological conditions. Journal of Biological Chemistry 286:39882-39892 (2011)

Kalamorz, F., Keis, S., McMillan, D.G.G., Olsson, K., Stanton, J.A., Stockwell, P., Black, M.A., Klingeman, D.M., Land, M.L., Han, C.S., Martin, S.L., Becher, S.A., Peddie, C.J., Morgan, H.W., Matthies, D., Preiß, L., Meier, T., Brown, S.D. and Cook, G.M.Draft genome sequence of thermoalkaliphilic Caldalkalibacillus thermarum strain TA2.A1. Journal of Bacteriology 193:4290–4291 (2011)

Taniguchi, N., Toshiharu, S., Berney, M., Yoshida, M. and Cook, G.M. The regulatory C-terminal domain of subunit epsilon of FoF1 ATP synthase is dispensable for growth and survival of Escherichia coli. Journal of Bacteriology 193:2046-2052 (2011)

Sims, I.M., Frese, S.A., Walter, J., Loach, D., Wilson, M., Appleyard, K., Eason, J., Livingston, M., Baird, M., Cook, G. and Tannock, G.W. Structure and functions of exopolysaccharide produced by gut commensal Lactobacillus reuteri 100-23. The ISME Journal 5:1115-1124 (2011)

Yu, Z., Bekker, M., Tramonti, A., Cook, G.M., van Ulsen, P., Scheffers, D.J., Teixeira de Mattos, J.T., De Biase, D. and Luirink, J. Activators of glutamate-dependent acid resistance system alleviate deleterious effects of YidC depletion in Escherichia coli. Journal of Bacteriology 193:1308-1316 (2011)

2010

Swe, P., Heng, N.C.K., Cook, G.M., Tagg, J. and Jack, R.W. Identification of DysI, the immunity factor of the streptococcal bacteriocin dysgalacticin. Applied and Environmental Microbiology 76:7885-7889 (2010)

McMillan, D.G.G., Velasquez, I., Nunn, B.L., Goodlett, D.R., Hunter, K.A., Lamont, I., Sander, S.G. and Cook, G.M. Acquisition of iron by alkaliphilic Bacillus species. Applied and Environmental Microbiology 76:6955–6961 (2010)

Shepherd, M., Sanguinetti, G., Cook, G.M. and Poole, R.K. Compensations for diminished terminal oxidase activity in Escherichia coli: cytochrome bd-ii mediated respiration and glutamate metabolism. Journal of Biological Chemistry 285:18464-18472 (2010)

Hümpel, A., Gebhard, S., Cook, G. M. and Berney, M. The SigF Regulon in Mycobacterium smegmatis reveals roles in adaptation to stationary phase, heat and oxidative stress. Journal of Bacteriology 192:2491-2502 (2010)

Berney, M. and Cook, G.M. Unique flexibility in energy metabolism allows mycobacteria to combat starvation and hypoxia. PLoS ONE Jan 7;5(1):e8614 (2010)

2009

Gebhard, S., Ekanayaka, N. and Cook, G.M. The low-affinity phosphate transporter PitA is dispensable for in vitro growth of Mycobacterium smegmatis. BMC Microbiology 9:254 (2009)


McMillan, D.G.G., Berney, M., Keis, S. and Cook, G.M. Non-fermentative thermoalkaliphilic growth is restricted to alkaline environments. Applied and Environmental Microbiology 75:7649–7654 (2009)

Mesbah, N.M., Cook, G.M. and Wiegel, J. The halophilic alkalithermophile Natranaerobius thermophilus adapts to multiple environmental extremes using a large repertoire of Na+(K+)/H+ antiporters. Molecular Microbiology 74:270–281 (2009) MicroCommentary on paper in same issue pages 257–260

Gebhard, S., Gaballa, A., Helmann, J.D. and Cook, G.M.* Direct stimulus perception and transcription activation by a membrane-bound DNA binding protein. Molecular Microbiology 73:482-491 (2009)

Robson, J., McKenzie, J.L., Cursons, R., Cook, G.M. and Arcus, V.L. The vapBC operon from Mycobacterium smegmatis is an autoregulated toxin-antitoxin module which controls growth via inhibition of translation. Journal of Molecular Biology 390:353-367 (2009)

Matthies, D., Preiß, L., Klyszejko, A.L., Muller, D.J., Cook, G.M., Vonck, J. and Meier, T. The c13 ring from a thermoalkaliphilic ATP synthase reveals an extended diameter due to a special structural region. Journal of Molecular Biology 388:611-618 (2009) Cover of Journal

Swe, P., Cook, G.M., Tagg, J. and Jack, R. Mode of action of dysgalacticin, a large heat-labile bacteriocin. Journal of Antimicrobial Chemotherapy 63:679-686 (2009)

 

Previous group members

Postdoctoral or Research Fellows

Dr Michael Berney, 2007-2012
Dr Naohiro Taniguichi, 2009-2012
Dr Falk Kalamorz, 2009-2011
Dr Jonathan Gauntlett, 2008
Dr Duncan McMillan, 2008-2009
Dr Scott Ferguson, 2007-2008
Dr Susanne Gebhard, 2006 – 2009
Dr Sunil Ratnayake, 2003
Dr Stefanie Keis, 2001 – 2008
Sieu Tran, 2000-2007

PhD students

Nandula Ekanayaka, 2008-2012
Rebekah Frampton, 2008-2011
Jennifer Robson, 2005-2010
Anja Humpel, 2005-2010
Sui Mae Lee, 2004-2009 
Pearl Swe, 2004-2008 
Duncan McMillan, 2004-2008
Jonathan Gauntlett, 2004-2008 
Rebecca McDougal, 2003-2007 
Scott Ferguson, 2003-2007 
Susanne Gebhard, 2003-2006
Matthew James Shirley, 1999-2006
Rajan Prasad Adhikari, 2000-2004
Karen Olsson, 2001-2004 
Janet Manson, 2000-2004
 

MSc students

Lisa Shaw, 2008-2010
Marion R. Weimar, 2009
Faith Cox, 2004-2006
Pearl Swe, 2001-2003
Cameron Simmers, 2001-2003
Ian Monk, 2001-2003
Richard Udy, 1999-2001
Connor Wright, 2000-2002
Rebecca McDougal, 2000-2002
Craig Anderson, 1999-2001
Katherine A. Young 1998-2000
Kere R. Kobayashi, 1998-1999

 

Lab photo (2011)

Cooklab2010/