Location: Bowdoin / Danielle H. Dube

Chemistry

Danielle Dube

Assistant Professor of Chemistry and Biochemistry

Contact Information

ddube@bowdoin.edu
207-798-4326
Chemistry
BIOCHEMISTRY
255 Druckenmiller Hall



Spring 2014

  • Biochemistry (CHEM 2320)
  • Chemical Biology (CHEM 3310)


Danielle Dube

Education

  • A.B., Cornell University, 2000
  • Ph.D., University of California, Berkeley, 2005
  • Postdoctoral, Stanford University, 2005-2007


Chemical tools to target, alter and understand glycosylation
Glycans, the oligosaccharide chains of sugars attached to many proteins and lipids, cover the surfaces of all cells, where they are crucial for myriad biological functions. In some pathogenic bacteria, glycans are essential for locomotion, and without the appropriate sugars on flagella these bacteria cannot colonize the gastrointestinal tract of their hosts. In pathogenic fungi, glycans are essential components of the cell wall, which provides a primary mode of defense against host immune recognition. Finally, in humans, glycans are responsible for mediating protein-protein interactions, and aberrant protein glycosylation often tracks closely with disease. Glycans are thus interesting targets for selective perturbation and analysis. Because glycans are refractory to study by most conventional methods (e.g. genetics), the use of chemical approaches with small molecule inhibitors and chemical reporters, in combination with other technologies, is necessary to perturb and analyze these biomolecules. The broad goals of the Dube lab are to chemically target unique glycans found on opportunistic pathogens for therapeutic and diagnostic purposes, and to create tools to better understand the role of glycosylation in human disease.

Students who conduct research in the Dube lab will be exposed to a variety of extremely powerful chemical and biological techniques, including organic synthesis, molecular cloning, protein expression and purification, and in vitro kinetics. If you’re interested in conducting research in the Dube lab, please set up an appointment with Professor Dube to discuss this possibility. Current projects in the lab are outlined below.

I.  Chemical tools to understand and target Helicobacter pylori glycosylation.  The pathogenic bacterium Helicobacter pylori is the leading cause of duodenal ulcers and gastric cancer worldwide.  Unfortunately, existing antibiotics no longer effectively eradicate H. pylori infection and cure these ailments.  The development of new treatments will be greatly aided by insights into the pathogenesis of H. pylori.  Virulence of H. pylori appears to be directly linked to the pathogen's ability to glycosylate proteins: H. pylori's flagellin proteins are heavily glycosylated with the unusual nine-carbon sugar pseudaminic acid, and this modification is absolutely essential for H. pylori to synthesize functional flagella and colonize the host's stomach.  Although H. pylori's glycans are linked to pathogenesis and are targets of therapeutic intervention, H. pylori's glycome remains poorly understood.  We are taking a metabolic labeling-based approach to discover novel H. pylori glycoproteins and to target H. pylori based on its unique glycans.

II. Utilizing the Golgi two-hybrid assay to detect the interactions of glycosylated proteins. During her postdoctoral work with Dr. Jennifer Kohler, Prof. Dube developed a two-hybrid assay that is capable of analyzing glycosylated proteins. We are using this assay to study glycoproteins of interest, in particular those associated with human diseases.  Current efforts are focused on delineating the interactions of a glycan-processing enzyme implicated in breast cancer.

V. Tra* and D. H. Dube, "Glycans in pathogenic bacteria -- potential for targeted covalent therapeutics and imaging agents," Chem. Commun., 2014, DOI: 10.1039/C4CC00660G

K. Champasa*, S. A. Longwell*, A. M. Eldridge, E. A. Stemmler and D. H. Dube, "Targeted identification of glycosylated proteins in the gastric pathogen Helicobacter pylori", Mol. Cell. Proteomics, 2013, 12, 2588-2586.
 
P. Kaewsapsak*, O. Esonu*, and D. H. Dube, "Recruiting the host's immune system to target Helicobacter pylori's surface glycans", ChemBioChem, 2013, 14, 721-726
 
S. A. Longwell* and D. H. Dube, "Deciphering the bacterial glycocode: recent advances in bacterial glycoproteomics", Curr. Opin. Chem. Biol., 2013, 17, 41-48

D. H. Dube. "Metabolic labeling of bacterial glycans with chemical reporters." In Bacterial glycomics:  Current research, technology, and applications.  Twine, S. M., ed. Horizon Scientific Press, Norfolk (UK), 2012

D. H. Dube†, B. Li†, E. J. Greenblatt, S. Nimer, A. K. Raymond* and J. J. Kohler, "A two-hybrid assay to study interactions within the secretory pathway", PLOS One, 20105, e15648. [† These authors contributed equally to this work.]

D. H. Dube, K. Champasa* and B. Wang*, "Chemical tools to discover and target bacterial glycoproteins",Chem. Commun., 201147, 87-101.

P. V. Chang, D. H. Dube and C. R. Bertozzi, "A strategy for the selective imaging of glycans using caged metabolic precursors", J. Am. Chem. Soc., 2010132, 9516-9518.

M. B. Koenigs*, E. A. Richardson* and D. H. Dube, "Metabolic profiling of Helicobacter pylori glycosylation",Mol. BioSyst., 20095, 909-912.

D. H. Dube, C. L. De Graffenried and J. J. Kohler, “Regulating cell surface glycosylation with a small-molecule switch”, Meth. Enzymol., 2006415, 213-229.

D. H. Dube†, J. A. Prescher†, C. N. Quang* and C. R. Bertozzi, “Probing mucin-type O-linked glycosylation in living animals”, Proc. Nat’l Acad. Sci. USA2006103, 4819-4824. [†These authors contributed equally to this work.]

D. H. Dube and C. R. Bertozzi, “Glycans in cancer and inflammation: potential for therapeutics and diagnostics”, Nat. Rev. Drug Disc., 20054, 477-488.

J. A. Prescher†, D. H. Dube†, and C. R. Bertozzi, “Chemical remodeling of cell surfaces in living animals”Nature2004430, 873-877. [†These authors contributed equally to this work.]

D. H. Dube and C. R. Bertozzi, “Metabolic oligosaccharide engineering as a tool for glycobiology”, Curr. Opin. Chem. Biol., 20037, 1-10.

S. J. Luchansky, H. C. Hang, E. Saxon, J. R. Grunwell, C. Yu, D. H. Dube and C. R. Bertozzi, “Constructing azide-labeled cell surfaces using polysaccharide biosynthetic pathways”, Meth. Enzymol., 2003362, 249-272.

*indicates undergraduate co-author

When she is not trying to “cure cancer” (as her Mom proudly broadcasts to the world), she spends as much time playing outdoors as possible. You can often find her rock climbing, backpacking, skiing, or running, all on the same day. On special occasions, you can find her underwater exploring a coral reef. Danielle is hugely fond of coral reefs, as they were both her first outdoor playground and the first place that she discovered her passion for science.

Danielle and Callie at Acadia National Park
Danielle and Callie at Acadia National Park