In June 2015, she joined the faculty at Stanford University as an Institute Scholar at Sarafan ChEM-H. Prof. Bertozzi's research interests span the disciplines of chemistry and biology with an emphasis on studies of cell surface glycosylation pertinent to disease states. A strain-promoted [3+2] azide-alkyne cycloaddition for covalent modification of blomolecules in living systems. Here, we extend the IsoTaG approach with the use of alkynyl sugars as metabolic labels and employ new probes in analysis of the sialylated glycoproteome from PC-3 cells. This article contains raw and processed data related to research published in "Role of the polypeptide N-acetylgalactosaminyltransferase 3 in ovarian cancer progression: possible implications in abnormal mucin O-glycosylation" [1]. To understand the adaptation of Mycobacterium tuberculosis to the intracellular environment, we used comprehensive metabolite profiling to identify the biochemical pathways utilized during growth on cholesterol, a critical carbon source during chronic infection. Under these conditions, Nrf1 is inactive in regulating proteasome subunit gene expression in response to proteasome inhibition. View details for DOI 10.1016/j.jmb.2006.08.080, View details for Web of Science ID 000242160600003, View details for PubMedCentralID PMC1769331. In this study we demonstrate that polysialyltransferases are capable of accepting unnatural substrates in terminally differentiated human neurons. We further demonstrate that the efficacy of a clinically used compound, clofazimine, is augmented by pH-based partitioning in a macrophage infection model. The antibody-sialidase conjugate desialylated tumor cells in a HER2-dependent manner, reduced binding by natural killer (NK) cell inhibitory sialic acid-binding Ig-like lectin (Siglec) receptors, and enhanced binding to the NK-activating receptor natural killer group 2D (NKG2D). Jacobs, C. L., Goon, S., Yarema, K. J., Hinderlich, S., Hang, H. C., Chai, D. H., Bertozzi, C. R. Biosynthesis of sialylated lipooligosaccharides in Haemophilis ducreyi is dependent on exogenous sialic acid and not mannosamine. View details for DOI 10.1074/jbc.M204613200, View details for Web of Science ID 000177859000029. Kiick, K. L., Saxon, E., Tirrell, D. A., Bertozzi, C. R. An inhibitor of the human UDP-GlcNAc 4-epimerase identified from a uridine-based library: A strategy to inhibit O-linked glycosylation, Homogeneous glycopeptides and glycoproteins for biological investigation. View details for PubMedCentralID PMC5675001. Polysialyltransferases catalyze the glycosylation of the neural cell adhesion molecule (NCAM) with polysialic acid (PSA). Both the activity and specificity of the inducible enzymes were indistinguishable from their WT counterparts. Bertozzi completed her undergraduate degree in Chemistry at Harvard University and her Ph.D. at UC Berkeley, focusing on the chemical synthesis of oligosaccharide analogs. Type I sulfatases require an unusual co- or post-translational modification for their activity in hydrolyzing sulfate esters. Mucin-domain glycoproteins are known to be key players in a host of human diseases, especially cancer, wherein mucin expression and glycosylation patterns are altered. We chose to use a phosphine probe because, despite their slow reaction kinetics, they remain the best-performing reagents for tagging azidosugars in mice. [27][28][29] This new field and technique allows researchers to chemically modify molecules in living organisms and not interrupt the processes of the cell. View details for Web of Science ID 000185051300005. A. Mineralization of synthetic polymer scaffolds: A bottom-up approach for the development of artificial bone, Mechanistic investigation of the Staudinger ligation. Recent advances in our understanding of SL-1 biosynthesis will help elucidate the role of this curious metabolite in M. tb infection. Inducible genetic inhibition of angiogenesis and Vegf signaling during granuloma formation results in bacterial growth deficits. Fluorescent probes designed for activation by bioorthogonal chemistry have enabled the visualization of biomolecules in living systems. A., Sun, J., Iram, T., Bonanno, L., Li, L., Lee, D. P., Morgens, D. W., Yang, A. C., Shuken, S. R., Gate, D., Scott, M., Khatri, P., Luo, J., Bertozzi, C. R., Bassik, M. C., Wyss-Coray, T. Towards Mycobacterium tuberculosis detection at the point-of-care: solvatochromic probes permits the detection of mycobacteria within minutes, Orthogonal enzyme/substrate engineering to profile biological substrates of glycosyltransferases, Glyco-immune modulation in the tumor microenvironment, Formylglycine-generating enzyme binds substrate directly at a mononuclear Cu(I) center to initiate O-2 activation. Carolyn Bertozzi biography. In this work, we synthesized the first phosphine-luciferin probe for use in real-time BLI and demonstrated that azide-labeled cell-surface glycans can be imaged with 1 using concentrations as low as single digit nanomolar and times as little as 5 min, a feat that cannot be matched by any previous fluorescent phosphine probes. Sialic acid is a component of many tumor-associated oligosaccharide antigens. [reaction: see text] Nearly all known sulfatases share a common active site modification that is required for their activity: conversion of cysteine to alpha-formylglycine. Lastly, we show that sialic acid depletion enhances ADC lysosomal delivery and killing in diverse cancer cell types, including with FDA (US Food and Drug Administration)-approved trastuzumab emtansine (T-DM1) in Her2-positive breast cancer cells. Using sequence alignments with other carbohydrate and cytosolic sulfotransferases, we selected residues within the putative binding regions for 3'-phosphoadenosine 5'-phosphosulfate (PAPS) and the carbohydrate substrate for mutagenesis. Interactions of mucin glycoproteins with cognate receptors are dictated by the structures and spatial organization of glycans that decorate the mucin polypeptide backbone. Attachment via these "cell-adhesion barcodes" is rapid and specific, with close-packed arrays of cells forming within minutes. View details for Web of Science ID 000240465200023, View details for PubMedCentralID PMC3233198. Lu, L., Riley, N. M., Shortreed, M. R., Bertozzi, C. R., Smith, L. M. Targeted glycan degradation potentiates the anticancer immune response in vivo. While assays for specific glycosyltransferases exist, there is no generalizable method that can be applied across the enzyme superfamily. However, the estimated barrier is much smaller than expected for folding of isolated S-layer proteins, suggesting an energetic rationale for this multistage pathway. Glyco-seek combines chemoenzymatic labeling, proximity ligation, and quantitative polymerase chain reaction to detect O-GlcNAcylated proteins with ultrahigh sensitivity. A key feature of the synthesis was application of an intramolecular aglycon delivery reaction to join two differentially protected glucose monomers, one prepared with a novel alpha-selective glycosylation. Directed evolution was used to improve the activity of JamB, a membrane-bound bifunctional desaturase/acetylenase. Thus, to advance insight into the role of O-GlcNAc in T cell activation, we performed glycosite mapping studies via direct glycopeptide measurement on resting and activated primary human T cells with a technique termed Isotope Targeted Glycoproteomics. de Almeida, G., Sletten, E. M., Nakamura, H., Palaniappan, K. K., Bertozzi, C. R. Synthesis of Heterobifunctional Protein Fusions Using Copper-Free Click Chemistry and the Aldehyde Tag. A genome-wide CRISPR screen identifies novel ligands for the Siglec family of glyco-immune checkpoint receptors. Luchansky, S. J., Hang, H. C., Saxon, E., Grunwell, J. R., Danielle, C. Y., Dube, D. H., Bertozzi, C. R. Drug targeting Mycobacterium tuberculosis cell wall synthesis: Development of a microtiter plate-based screen for UDP-galactopyranose mutase and identification of an inhibitor from a uridine-based library. Single Jurkat cells exhibited an extracellular acidification rate of 11 milli-pH min(-1), while primary T cells exhibited only 2 milli-pH min(-1). Here, we show that Cu(I)-FGE is functional in O2 activation and reveal a high-resolution X-ray crystal structure of FGE in complex with its catalytic copper cofactor. Professor of Chemical & Systems Biology and Radiology By contrast, most bacteria use trehalose solely as a general osmoprotectant or thermoprotectant. This new protocol incorporates 12 known heparin disaccharides, including three sets of isomers. Exhaled air and bioaerosol volumes were estimated using continuous CO2 monitoring and airborne particle counting, respectively. Palaniappan, K. K., Hangauer, M. J., Smith, T. J., Smart, B. P., Pitcher, A. Investigators have developed tools including small molecule inhibitors, decoy substrates, and engineered proteins to modify cellular glycans. Methods capable of directing orientation, as well as an understanding of the underlying physical mechanisms are, however, lacking. Although the mechanisms of Golgi enzyme localisation are still under debate, the distribution of these enzymes among the Golgi cisternae can dictate the overall structures produced by the cell. In addition, we have redefined the substrate specificity of the B. subtilis CysH, formerly designated a PAPS reductase, as an APS reductase, based on its ability to complement a mutant E. coli strain deficient in APS kinase. Z. O-Pair Search with MetaMorpheus for O-glycopeptide characterization. Gerling-Driessen, U. M., Tomlin, F. M., Cambier, C. J., Liu, Y., Bertozzi, C. R. A Model for Accelerating Patient-to-Bench Research. View details for DOI 10.1371/journal.pone.0029266, View details for Web of Science ID 000299771900011, View details for PubMedCentralID PMC3261144, View details for DOI 10.1002/anie.201106325, View details for Web of Science ID 000300934700029, View details for PubMedCentralID PMC3384729, View details for DOI 10.1002/anie.201108130, View details for Web of Science ID 000303001000032. Williams, S. J., Senaratne, R. H., Mougous, J. D., Riley, L. W., Bertozzi, C. R. A 96-well dot-blot assay for carbohydrate sulfotransferases, Sulfotransferases and sulfatases in mycobacteria. Flynn, R. A., Pedram, K., Malaker, S. A., Batista, P. J., Smith, B. We use this framework to assess existing data and to ask the question, "How many distinct primary structures of proteins (proteoforms) are created from the 20,300 human genes?" Here we describe the characterization and application of a synthetic riboswitch-based system, which comprises a mycobacterial promoter for transcriptional control and a riboswitch for translational control. Preliminary screening has identified compounds that inhibit estrogen sulfotransferase (EST), an enzyme relevant to breast cancer. Carolyn Bertozzi is a chemist who has made important contributions to understanding how cells interact. Whereas the former enzyme has been shown to direct metabolic flux toward sialic acid in vivo, the function of the latter enzyme is unclear. LC-MS/MS mass spectrometry analysis was then performed and the processed data related to the identified glycoproteins show that several hundred proteins are differentially expressed between control and GALNT3 KD A2780s cells. No BPAS is found inside the cells. We demonstrate a technique for detecting magnetically labeled Listeria monocytogenes and for measuring the binding rate between antibody-linked magnetic particles and bacteria. Surprisingly, for three of the enzymes, significant activity was observed with sialylated LacNAc, and two of the enzymes were capable of detectable sulfation of GlcNAc in the context of sialyl Lewis x. We determined the crystal structure of the apo Rv3406 sulfatase at 2.5 . Yap, M. C., Kostiuk, M. A., Martin, D. D., Perinpanayagam, M. A., Hak, P. G., Siddam, A., Majjigapu, J. R., Rajaiah, G., Keller, B. O., Prescher, J. The compounds did not inhibit other mammalian glycosyltransferases or nucleotide sugar utilizing enzymes, suggesting selectivity for the ppGalNAcTs. Subcellular Partitioning and Intramacrophage Selectivity of Antimicrobial Compounds against Mycobacterium tuberculosis. Tuberculosis (TB) disease is a global epidemic caused by the pathogenic Mycobacterium tuberculosis (Mtb). Employing the Huisgen 1,3-dipolar cycloaddition of azides and alkynes, we examined crosslinking of cognate NRPS modules within the tyrocidine pathway and demonstrated the sensitivity of our panel of crosslinking probes toward the selective protein interactions of compatible COM domains. View details for Web of Science ID 000245946400051, View details for PubMedCentralID PMC2535821. [40] It focuses on biotechnologies for at-home diagnoses for type 1 diabetes, HIV, and other diseases. She is an elected member of the Institute of Medicine, National Academy of Sciences, and American Academy of Arts and Sciences. Hudak, J. E., Belardi, B., Appel, M. J., Solania, A., Robinson, P. V., Bertozzi, C. R. Isotope-targeted glycoproteomics (IsoTaG) analysis of sialylated N- and O-glycopeptides on an Orbitrap Fusion Tribrid using azido and alkynyl sugars. This imaging approach should further our understanding of basic metabolic processes and pathological alterations in multiple disease models. In this work, we apply an aluminum "lift off" lithography method to allow the efficient generation of complex patterns comprising different DNA sequences. Oligosaccharides transact information exchange at the cell surface and modulate the activities and distribution of proteins within cells. View details for Web of Science ID 000177297600001. Cells adorned with longer glycopolymers showed increased metastatic potential, enhanced cell cycle progression, and greater levels of integrin-FAK mechanosignaling and Akt signaling in a syngeneic mouse model of metastasis. However, the complexities of glycan biosynthesis prevent the installation of nonnatural moieties at defined, predictable locations within glycoproteins at high levels of incorporation. We summarize developments in four key areas: enrichment of glycoproteins and glycopeptides from complex mixtures, emphasizing methods that exploit unique chemical properties of glycans or introduce unnatural functional groups through metabolic labeling and chemoenzymatic tagging; identification of sites of protein glycosylation; targeted glycoproteomics; and functional glycoproteomics, with a focus on probing interactions between glycoproteins and glycan-binding proteins. Patterson, B. n., Dinkele, R. n., Gessner, S. n., Morrow, C. n., Kamariza, M. n., Bertozzi, C. R., Kamholz, A. n., Bryden, W. n., Call, C. n., Warner, D. F., Wood, R. n. Marschallinger, J. n., Iram, T. n., Zardeneta, M. n., Lee, S. E., Lehallier, B. n., Haney, M. S., Pluvinage, J. V., Mathur, V. n., Hahn, O. n., Morgens, D. W., Kim, J. n., Tevini, J. n., Felder, T. K., Wolinski, H. n., Bertozzi, C. R., Bassik, M. C., Aigner, L. n., Wyss-Coray, T. n. Updates to the Symbol Nomenclature for Glycans guidelines, Neelamegham, S., Aoki-Kinoshita, K., Bolton, E., Frank, M., Lisacek, F., Luetteke, T., O'Boyle, N., Packer, N. H., Stanley, P., Toukach, P., Varki, A., Woods, R. J., Darvill, A., Dell, A., Henrissat, B., Bertozzi, C., Hart, G., Narimatsu, H., Freeze, H., Yamada, I., Paulson, J., Prestegard, J., Marth, J., Vliegenthart, J. G., Etzler, M., Aebi, M., Kanehisa, M., Taniguchi, N., Edwards, N., Rudd, P., Seeberger, P., Mazumder, R., Ranzinger, R., Cummings, R., Schnaar, R., Perez, S., Kornfeld, S., Kinoshita, T., York, W., Knirel, Y., SNFG Discussion Grp, Engineering Orthogonal Polypeptide GalNAc-Transferase and UDP-Sugar Pairs. Together, these data suggest that the expressed levels of sialylated LOS glycoforms observed in H. ducreyi are in large part controlled by the exogenous concentrations of sialic acid and at levels one might expect in vivo. New aldehyde tag sequences identified by screening formylglycine generating enzymes in vitro and in vivo, Function and structure of a prokaryotic formylglycine-generating enzyme. in these pages has relative advantages and disadvantages. A., Bertozzi, C. R., Stout, C. D. A chemical reporter strategy to probe glycoprotein fucosylation. Sulfurcontaining molecules were initially identified by mass spectral analysis of cell extracts from bacteria labeled metabolically with a stable sulfur isotope (34SO 4 2-). Kamariza, M., Shieh, P., Ealand, C. S., Peters, J. S., Chu, B., Rodriguez-Rivera, F. P., Sait, M., Treuren, W. V., Martinson, N., Kalscheuer, R., Kana, B. D., Bertozzi, C. R. Antibody detection by agglutination-PCR (ADAP) enables early diagnosis of HIV infection by oral fluid analysis. We designed phosphine-luciferin reagent 1 to activate bioluminescence in response to Staudinger ligation with azide-labeled glycans. We also note that >200 illustrations in the second edition have already been published using our nomenclature and are available for download at PubMed. This technique, which is described in detail, provides a direct measurement of the energy that is released nonradiatively following photostimulation, and can therefore be used to indirectly determine the amount of energy released via luminescent pathways. This system enables the production of glycoproteins that are functionalized for specific chemical modifications at their glycosylation sites. She completed her undergraduate degree in Chemistry from Harvard University in 1988 and her Ph.D. in Chemistry from UC Berkeley in 1993. These modified GFPs were incorporated in supported lipid bilayers, and their mobilities were analyzed using fluorescence correlation spectroscopy. The d-alanine analogues were specifically incorporated into nascent PG of the intracellular pathogen Listeria monocytogenes both in vitro and during macrophage infection. Chp1 is fully active in vitro, but in M. tuberculosis, its function is potentiated by the previously identified sulfolipid transporter MmpL8. Gas-phase stability of the 4Fe-4S cluster was investigated using both in-source and collision induced dissociation, which provided information regarding the relative gas-phase binding strength of iron towards protein ligands and inorganic sulfides. Each enzyme preferred a terminal GlcNAc residue, and was impeded by the addition of a beta1,4-linked Gal residue (i.e., terminal LacNAc). These data suggest that chemical inhibition of OGT and perturbation of protein O-GlcNAcylation accelerate the differentiation of hESCs along the neuronal lineage, thus providing further insight into the dynamic molecular mechanisms involved in neuronal development. These improvements represent a lowering of the limit of detection in the RASC-2 platform to 0.9 Mtb bacilli per 100L of exhaled air from 3.3 Mtb bacilli per 100L (RASC-1).This study demonstrates that technical improvements in particle collection together with sensitive detection enable rapid quantitation of viable Mtb in bioaerosols of sputum positive TB cases. Unlike existing systems for controlling gene expression in Mtb, the riboswitch does not require the co-expression of any accessory proteins: all of the regulatory machinery is encoded by a short DNA segment directly upstream of the target gene. The efficacy of these drugs is frequently undermined by acquired resistance. Using a panel of sulfated lactose (Galbeta1-->4Glc) neoglycolipids as substrates in direct binding assays, we found that 6',6-disulfolactose was the preferred structure for L-selectin, although significant binding to 6'- and 6-sulfolactose was observed as well. To this end, we generated the first high-density library of transposon insertion mutants in the model organism C. glutamicum. Furthermore, we developed a biomemetic coating strategy to interface BNNTs with proteins and cells. Hudak, J. E., Barfield, R. M., de Hart, G. W., Grob, P., Nogales, E., Bertozzi, C. R., Rabuka, D. Synthesis of a Fluorogenic Cyclooctyne Activated by Cu-Free Click Chemistry, Protein Glycoengineering Enabled by the Versatile Synthesis of Aminooxy Glycans and the Genetically Encoded Aldehyde Tag, Cell surface glycoproteomic analysis of prostate cancer-derived PC-3 cells. This enzyme transfers sialic acid residues from the host's sialylglycoconjugates to the parasite's galactosylglycoconjugates. Our editors will review what youve submitted and determine whether to revise the article. We find that emergence of this supermolecular architecture is the outcome of hierarchical processes; the proteins condense in solution to form 2-D crystals, which then stack parallel to one another to create isotropic bilayered assemblies. While this method is highly effective for cultured mammalian cells, we report here a significant improvement of this technique that allows the direct modification of cell surfaces with NHS-DNA conjugates. To accomplish this goal, we took advantage of the bioorthogonal chemical reporter technique. View details for Web of Science ID 000171204900005. We present the development of NIR fluorogenic azide probes based on the Si-rhodamine scaffold that undergo a fluorescence enhancement of up to 48-fold upon reaction with terminal or strained alkynes. VIDEO ABSTRACT. The IsoTaG platform is broadly applicable to the discovery of PTM sites that are amenable to chemical labeling, as well as previously unknown protein isoforms including pSPs. [6], She received the MacArthur "genius" award at age 33. Activation of SFKs requires depletion of tyrosine phosphatases from the area of particle engagement. Finally, we demonstrate that the cell-surface Staudinger ligation is compatible with hydrazone formation from metabolically introduced ketones. Here we describe a strategy for exploiting trehalose metabolic pathways to label glycolipids in mycobacteria with azide-modified trehalose (TreAz) analogues. Diboron reagents display minimal cell toxicity at millimolar concentrations, penetrate cell membranes, and effectively reduce N-oxides inside mammalian cells. As part of the quest for new gold drugs, we have explored the efficacy of three gold complexes derived from the tuberculosis drug pyrazinamide (PZA), namely, the gold(I) complex [Au(PPh3)(PZA)]OTf (1, OTf = trifluoromethanesulfonate) and two gold(III) complexes [Au(PZA)Cl2] (2) and [Au(PZO)Cl2] (3, PZO = pyrazinoic acid, the metabolic product of PZA) against two mycobacteria, Mycobacterium tuberculosis and Mycobacterium smegmatis. Second messengers generated by Fc receptors activated integrins, which formed an actin-tethered diffusion barrier that excluded CD45. A., Bertozzi, C. R. Synthesis of mono- and dideoxygenated alpha,alpha-trehalose analogs. Among the EMBs loci were genes encoding RipC and the FtsEX complex, a PG cleaving enzyme required for proper cell division and its predicted regulator, respectively. Myristoylation is the attachment of the 14-carbon fatty acid myristate to the N-terminal glycine residue of proteins. This tutorial review focuses on recent applications of homogeneous synthetic glycopeptides and glycoproteins for studies of structure and function. Carroll, K. S., Gao, H., Chen, H. Y., Leary, J. Parthasarathy, R., Rabuka, D., Bertozzi, C. R., Groves, J. T. Copper-free click chemistry for dynamic in vivo imaging. Second, we evaluated a panel of five different cyclooctyne structures and found that fluorophore conjugates to aza-dibenzocyclooctyne (ADIBO) gave the highest and most specific derivatization of azide-conjugated LAP in cells. DMN-Tre labeling enabled the rapid, no-wash visualization of mycobacterial and corynebacterial species without nonspecific labeling of Gram-positive or Gram-negative bacteria. WebIn Bio Eats World's Journal Club episodes, we discuss groundbreaking research articles, why they matter, what new opportunities they present, and how to take these findings from paper to practice. 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