The Mark Laboratory

Understanding the molecular basis of disease


Our Publications

Cabot G, Kim K, Mark BL, Oliver A, Khajehpour M. (2023) Biochemical Insights into Imipenem Collateral Susceptibility Driven by ampC Mutations Conferring Ceftolozane/Tazobactam Resistance in Pseudomonas aeruginosa. Antimicrob Agents Chemother. 16;67(2):e0140922.

van Vliet VJE, Huynh N, Palà J, Patel A, Singer A, Slater C, Chung J, van Huizen M, Teyra J, Miersch S, Luu GK, Ye W, Sharma N, Ganaie SS, Russell R, Chen C, Maynard M, Amarasinghe GK, Mark BL, Kikkert M, Sidhu SS. (2022) Ubiquitin variants potently inhibit SARS-CoV-2 PLpro and viral replication via a novel site distal to the protease active site. PLoS Pathog. 22;18(12):e1011065.

Benzie G, Bouma K, Battellino T, Cooper S, Hemming R, Kammouni W, Liu L, Do C, Khajehpour M, Perreault H, Kornfeld S, Triggs-Raine B, Mark BL (2022) Increased phosphorylation of HexM improves lysosomal uptake and potential for managing GM2 gangliosidoses BBA Advances 2, 100032

Patel A, McBride JAM and Mark BL (2021) The endopeptidase of the maize-affecting Marafivirus type member maize rayado fino virus doubles as a deubiquitinase. Journal of Biological Chemistry 297(2):100957. doi: 10.1016/j.jbc.2021.100957. Epub 2021 Jul 12

Kohlmeier MG, Bailey-Elkin BA, Mark BL and Oresnik IJ (2021) Characterization of the sorbitol dehydrogenase SmoS from Sinorhizobium meliloti 1021. Acta Crystallogr D Struct Biol 77(Pt 3):380-390. doi: 10.1107/S2059798321001017. Epub 2021 Feb 24.

Mark BL and Mahuran D (2021) Letter to the Editor of Molecular Therapy – The hexosaminidase system. Molecular Therapy 29 (1): 3

Russell R, Pelka P, Mark BL (2020) Frontrunners in the race to develop a SARS-CoV-2 vaccine. Canadian Journal of Microbiology PMID: 33264067. DOI: 10.1139/cjm-2020-0465

Patel A, Treffers EE, Meier M, Patel TR, Stetefeld J, Snijder EJ, Mark BL (2020) Molecular characterization of the RNA-protein complex directing -2/-1 programmed ribosomal frameshifting during arterivirus replicase expression. Journal of Biological Chemistry 295(52):17904-17921.

(Editor’s Pick in the November 2020 issue of the Journal of Biological Chemistry).

Slater CL, Winogrodzki J, Fraile-Ribot PA, Oliver A, Khajehpour M, and Mark BL. (2020) Adding Insult to Injury: Mechanistic Basis for How AmpC Mutations Allow Pseudomonas aeruginosa To Accelerate Cephalosporin Hydrolysis and Evade Avibactam. Antimicrobial Agents Chemotherapy 64(9): 1-17.

(Editor’s Pick in the September 2020 issue of Antimicrobial Agents and Chemotherapy.)

Tchesnokov, E. P., Bailey-Elkin, B. A., Mark, B. L., and Gotte, M. (2020) Independent inhibition of the polymerase and deubiquitinase activities of the Crimean-Congo Hemorrhagic Fever Virus full-length L-protein. PLoS Neglected Tropical Diseases 14, e0008283

Mangat CS, Vadlamani G, Larmour VLC, Chu M, Mulvey M and Mark BL (2019) Avibactam potently inhibits a novel Class A carbapenemase (VCC-1) from Vibrio cholera recently isolated from retail shrimp imported into Canada. Antimicrobial Agents and Chemotherapy 63(4). pii: e02112-18.

(ASM Press release (Washington, DC – February 19, 2019) “Investigators Figure Out How to Block New Antibiotic Resistance Gene”

Ho LA, Winogrodzki JL, Debowski AW, Madden Z, Vocadlo DJ, Mark BL, Stubbs KA (2018) A mechanism-based GlcNAc-inspired cyclophellitol inactivator of the peptidoglycan recycling enzyme NagZ reverses resistance to β-lactams in Pseudomonas aeruginosa. Chemical Communications (Camb) 54(75):10630-10633

Macdonald SS, Patel A, Larmour VLC, Morgan-Lang C, Hallam SJ, Mark BL and Withers SG (2018) Structural and mechanistic analysis of a β-glycoside phosphorylase identified by screening a metagenomic library. Journal of Biological Chemistry 293(9):3451-3467.

Bailey-Elkin BA, Knaap RCM, Kikkert M and Mark BL (2017) Structure and function of viral deubiquitinating enzymes. Journal of Molecular Biology S0022-2836(17)30310-8.

Zhang W#, Bailey-Elkin BA#, Knaap, RCM#, Khare B, Dalebout TJ, Johnson GG, van Kasteren PB, McLeish NJ, Gu J, Hen W, Kikkert M, Mark BL, Sidhu SS* (2017) Potent and selective inhibition of pathogenic viruses by engineered ubiquitin variants. PLoS Pathogens 13(5):e1006372. #co-first authors, *corresponding authors

Bouquet J, King DT, Vadlamani G, Benzie GR, Iorga B, Ide D, Adachi I, Kato A, Vocadlo DJ, Mark BL, Blériot Y, Désiré J. (2017) Selective trihydroxylated azepane inhibitors of NagZ, a glycosidase involved in Pseudomonas aeruginosa resistance to β-lactam antibiotics. Organic & Biomolecular Chemistry. 15: 4609 – 4619.

Vadlamani G, Stubbs KA, Désiré J, Blériot Y, Vocadlo DJ, Mark BL (2017) Conformational flexibility of the glycosidase NagZ allows it to bind structurally diverse inhibitors to suppress beta-lactam antibiotic resistance. Protein Science 26(6):1161-1170.

Muggenthaler MM, Chowdhury B, Hasan SN, Cross HE, Mark B, Harlalka GV, Patton MA, Ishida M, Behr ER, Sharma S, Zahka K, Faqeih E, Blakley B, Jackson M, Lees M, Dolinsky V, Cross L, Stanier P, Salter C, Baple EL, Alkuraya FS, Crosby AH, Triggs-Raine B, Chioza BA. (2017) Mutations in HYAL2, Encoding Hyaluronidase 2, Cause a Syndrome of Orofacial Clefting and Cor Triatriatum Sinister in Humans and Mice. PLoS Genetics. 13(1):e1006470. doi: 10.1371/journal.pgen.1006470.

Hamou-Segarra M, Zamorano L, Vadlamani G, Chu M, Sánchez-Diener I, Juan C, Blázquez J, Stubbs KA, Mark BL, Oliver A (2017) Synergistic activity of fosfomycin, β-lactams and peptidoglycan recycling inhibition against Pseudomonas aeruginosa. Journal of Antimicrobial Chemotherapy 72(2):448-454

Perley-Robertson GE, Yadav AK, Winogrodzki JL, Stubbs KA, Mark BL and Vocadlo DJ (2016) Design of a Fluorescent Substrate and Transport Assayto Probe the Membrane Permease AmpG and its Role in Antibiotic Resistance. ACS Chemical Biology 11(9):2626-35.

Karumuthil-Melethil S, Kalburgi SN, Thompson P, Tropak M, Mark BL, Mahuran D,Walia J and Gray SJ (2016) Novel AAV vector design and Hexosaminidase variant to utilize self-complementary AAV for the treatment of Tay-Sachs disease. Human Gene Therapy27(7):509-21.

Osman KJL, Woodley E, Thompson P, Ong K, Karumuthil-Melethil S, Keimel JG, Mark BL, Mahuran D, Gray SJ and Walia JS (2016) Systemic Gene Transfer of a Hexosaminidase Variant Using a scAAV9.47 Vector Corrects GM2 Gangliosidosis Onset in Sandhoff Mice. Human Gene Therapy 27(7):497-508.

Santana AG, Vadlamani G, Mark BL and Withers SG (2016) N-Acetyl glycals are tight-binding and environmentally insensitive inhibitors of hexosaminidases. Chemical Communications (Cambridge) 52(51):7943-6.

Zaloba P, Bailey-Elkin BA, Derksen M and Mark BL (2016) Structural and biochemical insights into the peptidoglycan hydrolase domain of FlgJ from Salmonella typhimurium. PLoS One 11(2): e0149204

Tropak MB, Yonekawa S, Karumuthil-Melethil S, Thompson P, Wakarchuk W, Gray SJ, Walia JS, Mark BL, Mahuran D (2016) Construction of a Hybrid β-Hexosaminidase Subunit Capable of Forming Stable Homodimers that Hydrolyze GM2 Ganglioside in vivo. Molecular Therapy - Methods & Clinical Development (Nature Publishing Group) 3, 15057; doi:10.1038/mtm.2015.57 (*co-senior authors)

The editor-in-chief of Molecular Therapy - Methods & Clinical Development, Roland Herzog, featured the molecular model of HexM on journal homepage (

Bacik JP, Klesmith JR, Whitehead TA, Jarboe LR, Unkefer CJ, Mark BL and Michalczyk R (2015) Producing Glucose 6-Phosphate from Cellulosic Biomass: Structural insights into levoglucosan bioconversion. Journal of Biological Chemistry 290(44):26638-48.

Vadlamani G, Thomas MD, Patel TR, Donald LJ, Reeve TM, Stetefeld J, Standing KG, Vocadlo DJ, Mark BL. (2015) The β-lactamase Gene Regulator AmpR is a Tetramer that Recognizes and Binds the D-Ala-D-Ala Motif of its Repressor UDP-MurNAc-pentapeptide. Journal of Biological Chemistry 290(5):2630-43

Bailey-Elkin BA, Knaap RC, Johnson GG, Dalebout TJ, Ninaber DK, van Kasteren PB, Bredenbeek PJ, Snijder EJ, Kikkert M, Mark BL (2014) Crystal Structure of the MERS Coronavirus Papain-Like Protease Bound to Ubiquitin Facilitates Targeted Disruption of Deubiquitinating Activity to Demonstrate its Role in Innate Immune Suppression. Journal of Biological Chemistry 289(50): 34667-82.

Li Y, Treffers EE, Napthine S, Tas A, Zhu L, Sun Z, Bell S, Mark BL, van Veelen PA, van Hemert MJ, Firth AE, Brierley I, Snijder EJ and Fang Y. (2014) Trans-activation of programmed ribosomal frameshifting by a viral protein. Proceedings of the National Academy of Sciences U S A. 111(21):E2172-81.

Bailey-Elkin BA, van Kasteren PB, Snijder EJ, Kikkert M and Mark BL (2014) Viral OTU Deubiquitinases: a Structural and Functional Comparison. PLoS Pathogens. 10(3):e1003894.

Bacik JP, Tavassoli M, Patel TR, McKenna SA, Vocadlo DJ, Khajehpour M, Mark BL. (2014) Conformational itinerary of Pseudomonas aeruginosa 1,6-Anhydro-N-acetylmuramic acid kinase during its catalytic cycle. Journal of Biological Chemistry 289(7):4504-14.

Mondon M, Hur S, Vadlamani G, Rodrigues P, Madden Z, Oliver A, Mark BL, Vocadlo DJ, and Blériot Y (2013) Selective trihydroxyazepane NagZ inhibitors increase sensitivity of Pseudomonas aeruginosa to β-lactams. Chemical Communications (Cambridge) 49: 10983-10985.

Stubbs KA, Bacik JP, Perley-Robertson GE, Whitworth GE, Gloster TM, Vocadlo DJ and Mark BL (2013) The Development of Selective Inhibitors of NagZ: Increased Susceptibility of Gram-Negative Bacteria to beta-Lactams. ChemBioChem. 14(15):1973-81.

Sinici I, Yonekawa S, Tkachyova I, Gray SJ, Samulski RJ, Wakarchuk W, Mark BL and Mahuran DJ (2013) In cellulo examination of a beta-alpha Hybrid construct of beta- hexosaminidase A subunits, reported to interact with the GM2 activator protein and hydrolyze GM2 ganglioside. PLoS One 8(3):e57908.

van Kasteren PB, Bailey-Elkin BA, James TW, Ninabera DK, Beugelinga C, Khajehpour M, Snijder EJ, Mark BL* and Kikkert M* (2013) The deubiquitinase function of arterivirus papain-like protease 2 suppresses the innate immune response in infected host cells. Proceedings of the National Academy of Sciences U S A 110(9): E838-47. *corresponding authors

Bacik JP, Whitworth GE, Stubbs KA, Vocadlo DJ, Mark BL. (2012) Active site plasticity within the glycoside hydrolase NagZ underlies a dynamic mechanism of substrate distortion. Chemistry & Biology (Cell Press) 19(11):1471-82.

Schreiber-Agus N, Nakagawa S, Zhan J, Sun W, Ferreira JC, Keiles S, Hambuch T, Kammesheidt, Mark BL, Schneider A and Gross S. (2012) Platelet Hexosaminidase A enzyme assay effectively detects carriers missed by targeted DNA mutation analysis. Journal of Inherited Metabolic Disease Reports 6:1-6.

Mark BL, Vocadlo DJ, OliverA (2011) Providing β-lactams a helping hand: targeting the AmpC β-lactamase induction pathway. Future Microbiology 6:1415-27.

Pédelacq JD, Nguyen H, Cabantous S, Mark BL, Listwan P, Bell C, Friedland N, Lockard M, Faille A, Mourey L, Terwilliger TC and Waldo GS (2011) Experimental mapping of soluble protein domains using a hierarchical approach. Nucleic Acids Research 39(18): e125.

Yudistira H, McClarty L, Bloodworth RAM, Hammond SA, Butcher H, Mark BL and Cardona ST. (2011) Phenylalanine Induces Burkholderia cenocepacia Phenylacetic Acid Catabolism Through Degradation To Phenylacetyl-CoA In Synthetic Cystic Fibrosis Sputum Medium. Microbial Pathogenesis 51(3):186-93.

Zamorano L., Reeve TM, Juan C., Moyá B, Gabriel Cabot G, Vocadlo DJ, Mark BL and Oliver A. (2011) AmpG Inactivation Restores Susceptibility of Pan-β-lactam Resistant Pseudomonas aeruginosa Clinical Strains. Antimicrobial Agents and Chemotherapy 55(5):1990-6.

Bacik JP, Whitworth GE, Stubbs KA, Martin D, Bailey-Elkin BA, Vocadlo DJ, Mark BL (2011) Molecular basis of 1,6-anhydro bond cleavage and phosphoryl transfer by Pseudomonas aeruginosa 1,6-anhydro-N-acetylmuramic acid kinase. Journal of Biological Chemistry 286(14):12283-91.

James TW, Frias-Staheli N, Bacik JP, Levingston Macleod JM, Khajehpour M, Garcia-Sastre A and Mark BL (2011) Structural basis for the removal of ubiquitin and interferon-stimulated gene 15 by a viral ovarian tumor domain-containing protease. Proceedings of the National Academy of Sciences U S A 108(6):2222-7.

Zamorano L, Reeve TM, Deng L, Juan C, Moyá B, Cabot G, Vocadlo DJ, Mark BL and Oliver A (2010). NagZ inactivation prevents and reverts β-lactam resistance, driven by AmpD and PBP4 mutations, in Pseudomonas aeruginosa. Antimicrobial Agents and Chemotherapy 54(9):3557-63.

Balcewich MD, Reeve TM, Orlikow EA, Donald LJ, Vocadlo DJ and Mark BL (2010) Crystal structure of the AmpR ligand-binding domain provides insight into the molecular regulation of inducible AmpC β-lactamase gene expression. Journal of Molecular Biology 400(5):998-1010.

Balcewich M, Stubbs KA, He Y, James T, Davies GJ, Vocadlo DJ, Mark BL (2009) Insight into a strategy for attenuating AmpC-mediated β-lactam resistance: structural basis for selective inhibition of the glycoside hydrolase NagZ. Protein Science. 18(7):1541-51.

Armistead J, Khatkar S, Meyer B, Mark BL, Patel N, Coghlan G, Lamont RE, Liu S, Wiechert J, Cattini PA, Koetter P, Wrogemann K, Greenberg CR, Entian KD, Zelinski T, Triggs-Raine B. (2009) Mutation of a Gene Essential for Ribosome Biogenesis, EMG1, Causes Bowen-Conradi Syndrome. American Journal of Human Genetics 84(6):728-39.

Asgarali A, Stubbs KA, Oliver A, Vocadlo DJ, Mark BL (2009) Inactivation of the glycoside hydrolase NagZ attenuates antipseudomonal beta-lactam resistance in Pseudomonas aeruginosa. Antimicrobial Agents and Chemotherapy 53(6):2274-82.

Stubbs KA, Scaffidi A, Debowski AW, Mark BL, Stick RV, Vocadlo DJ. (2008) Synthesis and use of mechanism-based protein-profiling probes for retaining beta-D-glucosaminidases facilitate identification of Pseudomonas aeruginosa NagZ. Journal of the American Chemical Society 130(1):327-35.

Stubbs KA, Balcewich M, Mark BL, Vocadlo, DJ (2007). Small molecule inhibitors of a glycoside hydrolase attenuate inducible AmpC-mediated beta-lactam resistance Journal of Biological Chemistry 282:21382-91.

Martin DC, Mark BL, Triggs-Raine BL and Natowicz MR (2007) Evaluation of the Risk for Tay-Sachs Disease in Individuals of French Canadian Ancestry Living in New England. Clinical Chemistry, 53(3):392-8.

Lemieux JM, Mark BL, Cherney M, Knapp S, Mahuran DL and James MN (2006) Understanding Tay-Sachs and Sandoff disease from the X-ray structure of human beta-Hexosaminidase A. Journal of Molecular Biology 359(4):913-29.

Cabantous S, Pédelacq J-D, Mark BL, Naranjo C, Terwilliger TC and Waldo GS (2005) Recent advances in GFP folding reporter and split-GFP solubility reporter technologies. Application for improving the folding and solubility of recalcitrant proteins from Mycobacterium tuberculosis. Journal of Structural and Functional Genomics 6(2-3):113- 9.

Mark BL, Mahuran DJ, Cherney MM, Zhao D, Knapp S and James MNG (2003) Crystal structure of human -hexosaminidase B: Understanding the molecular basis of Sandhoff and Tay-Sachs disease. Journal of Molecular Biology 327(5): 1093-1109.

Barrette-Ng IH, Ng KK, Mark BL, van Aken D, Cherney MM, Garen C, Kolodenko Y, Gorbalenya AE, Snijder EJ and James MNG (2002) Structure of arterivirus nsp4. The smallest chymotrypsin-like proteinase with an alpha/beta C-terminal extension and alternate conformations of the oxyanion hole. Journal of Biological Chemistry 277(42): 39960-6.

Williams SJ, Mark BL, Vocadlo DJ, James MNG and Withers SG (2002) The catalytic role of aspartate 313 in the Streptomyces plicatus hexosaminidase: Implications from kinetic and structural analysis. Journal of Biological Chemistry 277(42): 40055-65. These authors contributed equally to this work.

Mark BL and James MNG (2002) Anchimeric assistance in Hexosaminidases. Canadian Journal of Chemistry 80(8): 1064-1074.

Mark BL, Vocadlo DJ, Zhao D, Knapp S, Withers SG and James MNG (2001) Biochemical and structural assessment of the 1-N-azasugar GalNAc-isofagomine as a potent family 20 beta-N-acetyl-hexosaminidase inhibitor. Journal of Biological Chemistry 276(45): 42131-42137.

Mark BL, Parrish JC, Wang Z-X, Wiebe LI, Knaus E & James MNG (2001) (E)-1-(2’-deoxy-beta-D-ribofuranosyl)-2,4-difluoro-5-(2-iodovinyl) benzene. Acta Crystallographica Section C C57: 758-760.

Mark BL, Vocadlo DJ, Triggs-Raine BL, Withers SG & James MNG (2001) Crystallographic evidence for substrate-assisted catalysis in a bacterial beta-hexosamnindase. Journal of Biological Chemistry 276(13): 10330-37.

Mark BL, Wasney GA, Salo T, Khan AR, Cao Z, Robbins PW, James MNG and Triggs-Raine BL (1998) Structural and functional characterization of Streptomyces plicatus beta-N-acetylhexosaminidase by comparative molecular modelling and site directed mutagenesis. Journal of Biological Chemistry 273(31): 19618-24.

Mark BL, Jikina O, Bhullar RP (1996) Association of Ral GTP Binding proteins with platelet dense granules. Biochemical and Biophysical Research Communications 225(1): 40-46.