Department of Molecular and Cellular Biology Faculty . Dr. Anthony Clarke

Dr. Anthony Clarke Professor, Assistant VP
(Graduate Studies & Program Quality Assurance)

Dr. Anthony Clarke


Office: SSC 3522
Ext: 54124
Lab: SSC 4204
Ext: 54902


My interest in microbiology began as an undergraduate student at the University of Waterloo. I was pursuing a double honours B.Sc. in chemistry and biology and during the third and fourth years of my program I focused my attention on microbiological systems. My fourth year honours research project concerned a study on the inhibition of β lactamase, the enzyme that renders the β-lactam antibiotics (penicillins, cephalosporins) ineffective and thus representing a major factor of antibiotic resistance. Through this experience, I developed a passion for research in enzymology and so I continued my studies at Waterloo for my doctorate in biochemistry. I was introduced to carbohydrate-active enzymes as a post-doctoral fellow at the Carlsberg Research Centre in Copenhagen, and then as a research associate at the National Research Council in Ottawa. On joining the University of Guelph, I established a research program that integrates biochemical, biophysical, microbiological, and molecular biological techniques to investigate the structure-function relationship of the enzymes that synthesize and lyse the essential bacterial cell wall polymer peptidoglycan and the plant cell wall polymer cellulose, with the major goals of identifying new targets for antibiotic development and the efficient production of cellulosic ethanol, respectively. This multi-disciplinary approach involves collaborations with colleagues at Guelph, across the country, and around the World. 


B.Sc. Waterloo
M.Sc. Waterloo
Ph.D. Waterloo


Research in my laboratory concerns investigating the structure and function relationship of enzymes involved in the metabolism of the bacterial cell wall polymer peptidoglycan, and the biodegradation of cellulose.  Peptidoglycan is a heteropolymer of both aminosugars and short peptides that completely surrounds bacterial cells as a single macromolecule to provide their rigidity and structure. Its biosynthesis occurs in three stages involving the cytoplasm, the cytoplasmic membrane, and the cell wall.  Specific reactions in each of these stages have proven to be effective targets for antibiotic therapy, including the inhibition of peptide crosslinking within the cell wall by the β-lactam class of drugs (penicillins and celphalosporins).  Our studies focus on the events within the cell wall with the aim to identify new potential targets for antibiotic development.

The biodegradation of the plant cell wall polymer cellulose involves the concerted action of three distinct enzymes. One field of biofuel production involves the application of these enzymes in the generation of cellulosic ethanol and other value-added products from waste plant matter.  To be economically viable, the efficiency of the cellulolytic enzymes needs to be enhanced and to this end, we combine protein engineering with the biophysical analyses of cellulose degradation.

Both the search for new antibiotic targets and enhancing the production of biofuels provide fascinating challenges for experimental research involving a wide range of experimental approaches that span the biochemistry, biophysics, microbiology, molecular biology, and structural biology.

Current areas of emphasis include:

  1. Structure and function of the lytic transglycosylases, endogenous 'autolysins' that are involved in the biosynthesis and turnover of peptidoglycan, and the insertion of multi-protein complexes through the cell wall, such as flagella, pili, and secretion systems.
  2. Characterization of the enzyme systems required for the O-acetylation of peptidoglycan in both Gram positive and Gram negative bacteria, using primarily Bacillus anthracis and Neisseria gonorrhoeae as model systems, respectively.
  3. Structural basis for substrate recognition and inhibition of O-acetylpeptidoglycan esterases by ABC transporters involved in the export of bacterial cell-surface polysaccharides.
  4. Localization and characterization of peptidoglycan metabolizing enzyme systems within bacterial cell walls.
  5. Engineering of cellulolytic enzymes to enhance their physico-chemical and catalytic properties.

Selected Publications

Herlihey, F.A., P.J. Moynihan, and A. J. Clarke (2104) The essential protein for bacterial flagella formation FlgJ functions as a β-N-acetylglucosaminidase. J. Biol. Chem. 289: 31029–31042.

Moynihan, P.J. and A.J. Clarke (2014) The mechanism of peptidoglycan O-acetyltransferase involves an Asp-His-Ser catalytic triad. Biochemistry 53: 6243-6251.

Baker, P., T. Ricer, P.J. Moynihan, E. Kitova, M.T.C. Walvoort, D.J. Little, J.C. Whitney, K. Dawson, J.T. Weadge, H. Robinson, D.E. Ohman, P. Tipton, J.D.C. Codee, J.S. Klassen, A.J. Clarke, and P. L. Howell (2014) P. aeruginosa SGNH hydrolase-like proteins AlgJ and AlgX have similar topology but separate and distinct roles in alginate acetylation. PLOS Pathogens 10: e1004334

Moynihan, P.J. and A.J. Clarke (2014) Substrate specificity and kinetic characterization of peptidoglycan O-acetyltransferase B from Neisseria gonorrhoeae. J. Biol. Chem. 289: 16748- 16760.

Moynihan, P.J., D. Sychantha, and A.J. Clarke (2014) Chemical biology of peptidoglycan acetylation and deacetylation. Bioorganic Chemistry 54: 44-50.

Raegen, A.N., K. Reiter, K. Dion, A. J. Clarke, J. Lipkowski, and J. R. Dutcher (2014) Advances in surface plasmon resonance imaging enable quantitative tracking of thickness and roughness changes on the nanoscale. Anal. Chem. 86: 3346-3354.

Wang, J., A. Quirk, J. Lipkowski, J. Dutcher, and A.J. Clarke. (2013) Direct in situ observation of synergism between cellulolytic enzymes during biodegradation of crystalline cellulose fibers. Langmuir 29: 14997 - 15005.

Moynihan, P.J. and A.J. Clarke (2013) Assay for peptidoglycan O-acetyltransferase: A potential new antibacterial target. Analytical Biochemistry 439: 73-79

Pfeffer, J.M., J.T. Weadge, and A.J. Clarke (2013) Mechanism of action of Neisseria gonorrhoeae O-acetylpeptidoglycan esterase, an SGNH serine esterase. J. Biol. Chem. 288: 2605-2612

Allen, S.G., O.M. Tanchak, A. Quirk, A. N. Raegen, K. Reiter, R. Whitney, A.J. Clarke, J. Lipkowski and J.R. Dutcher. (2012) Surface plasmon resonance imaging of the enzymatic degradation of cellulose microfibrils. Analytical Methods 4: 3238-3245 

Wang, J., A. Quirk, J. Lipkowski, J. R. Dutcher, C. Hill, A. Mark, and A. J. Clarke. (2012) Real-time observation of swelling and hydrolysis of a single crystalline cellulose fiber catalyzed by cellulase 7B from Trichoderma reesei. Langmuir  28: 9664-9672.

Pfeffer, J. M., and A. J. Clarke (2012) Identification of first-known inhibitors of O-acetylpeptidoglycan esterase: A potential new antibacterial target. ChemBioChem. 13: 722-731

Laaberki, M.-H., J. Pfeffer, A. J. Clarke, and J. Dworkin (2011) O-Acetylation of peptidoglycan is required for proper cell separation and S-layer anchoring in Bacillus anthracis. J. Biol. Chem. 286: 5278-5288.  

Clarke, C.A., E. M. Scheurwater and A. J. Clarke (2010) The vertebrate lysozyme inhibitor Ivy functions to inhibit the activity of lytic transglycosylase . J. Biol. Chem. 285: 14843-14847.

Moynihan, P. J., and A. J. Clarke (2010) O-Acetylation of peptidoglycan in Gram-negative bacteria: Identification and characterization of peptidoglycan O-acetyltransferase in Neisseria gonorrhoeae. J. Biol. Chem. 285: 13264-13273.
Ruiloba de León, S., K. Daniels, and A. J. Clarke (2010) Production and purification of the penicillin-binding protein 3 from Pseudomonas aeruginosa. Prot. Express. Purif.  73: 177-183.

Quirk, A., Lipkowski, J., Vandenende, C., Cockburn, D., Clarke, A. J., Dutcher, J., Roscoe, S.G.  (2010) Direct visualization of enzymatic digestion of a single fiber of native cellulose in aqueous environment by atomic force microscopy. Langmuir 26: 5007-5013.

Cockburn, D. W., Vandenende, C., and A. J. Clarke (2010) Modulating the pH-activity profile of cellulase by substitution: replacing the general base catalyst aspartate with cysteinesulfinate in cellulase A from Cellulomonas fimi. Biochemistry 49: 2042-2050.


MCB*4500 - Research Project in Molecular & Cellular Biology I (S, F, W)
MCB*4510 - Research Project in Molecular & Cellular Biology II (S, F, W)

Lab Members

Chris Vandenende - Technician

Graduate Students

Francesca Herlihey (PhD)
David Sychantha (PhD)
Laura Kell (MSc)
Ashley Brott (MSc)
Mark Ecclestone (MSc)

Clarke Lab 2012

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