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Luo Y, Wang Y, Tian Y, Zhou H, Wen L. "Two Birds One Stone" Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation. Journal of the American Chemical Society 2023 37340703
Abstract:
Core fucosylation and O-GlcNAcylation are the two most famous protein glycosylation modifications that regulate diverse physiological and pathological processes in living organisms. Here, a "two birds one stone" strategy has been described for the site-specific analysis of core fucosylation and O-GlcNAcylation. Taking advantage of two mutant endoglycosidases (EndoF3-D165A and EndoCC-N180H), which efficiently and specifically recognize core fucose and O-GlcNAc, glycopeptides can be labeled using a biantennary N-glycan probe bearing azido and oxazoline groups. Then, a temperature-sensitive poly(N-isopropylacrylamide) polymer functionalized with dibenzocyclooctyne was introduced to facilitate the enrichment of the labeled glycopeptides from the complex mixture. The captured glycopeptides can be further released enzymatically by wild-type endoglycosidases (EndoF3 and EndoCC) in a traceless manner for mass spectrometry (MS) analysis. The described strategy allows simultaneous profiling of core-fucosylated glycoproteome and O-GlcNAcylated glycoproteome from one complex sample by MS technology and searching the database using different variable modifications.
O-GlcNAc proteins:
LCE6A, RBM47, HFM1, SMCO3, SBNO1, ODAD3, CNOT1, RCCD1, GLTD2, AGAP5, CX049, PDLI1, TAF4, ABLM1, DVL1, HGS, SC16A, NPC1, LAMA5, TET3, IF4G3, E41L2, AKAP8, PLIN3, MAFK, OPHN1, MITF, OBSL1, ANR17, ENTP6, NCOR1, ERLN1, JERKY, MYCB2, WDHD1, CBPD, TOX4, AGFG2, SC24B, PCNT, BAG3, DDAH2, CLPT1, AACT, LMNA, FINC, FETUA, GCR, KITH, HSPB1, RPN1, RLA2, ITB1, K1C18, ENOA, CATD, TBB5, TACD2, LYAG, BIP, LAMC1, HSP7C, DMD, MPRI, SKI, GILT, GLU2B, ENPL, RSMB, PO2F1, PVR, ZEP1, DPEP1, CBPE, ATF7, SON, ATF1, ITIH2, FST, ICAL, FGF7, CD9, CBL, ITA6, PTPRB, COF1, GATA3, PSA4, PEBP1, CLIP1, ZEP2, GLPK, ELF1, CD68, GPC1, HRH1, IRS1, NU214, SRP14, NUP62, ETFB, LICH, TXLNA, STAT3, MATR3, SSRA, GATA4, MMP13, 5HT3A, NOTC1, YAP1, RFX5, FAS, CDK8, CENPF, NU153, SEPP1, EMD, BCAM, HCFC1, SPHM, ARSD, AGFG1, NUP98, PTTG, RAD, AF17, DSRAD, ITA1, IF6, STAR6, ACTB, HNRPK, H4, RL40, CXAR, GPC5, FOXK1, PGBM, SPTB2, FOXK2, IF4G1, NOTC2, TLE3, PTN12, MTG8, ZO1, LRP1, RGS1, CD47, EP300, AHNK, TROAP, BPTF, NFIA, HYAL2, LMAN2, FOXC1, MB211, OS9, TUSC3, ROCK1, ASAH1, RIPK1, ASPP2, CDK13, SCRB2, VEZF1, DSG2, UBP2L, GIT2, PUM1, RRP1B, NCOA6, MEF2D, CHD4, NUMA1, R3HD1, RCN1, RBMS2, TAF1C, SF01, JHD2C, ELF2, TAB1, HERC1, ZFHX3, ZYX, ADRM1, CCDC6, SNPC1, MA2A1, YC018, QSER1, AAK1, P3H1, GNPTA, RABL6, TB10B, LUZP6, PRC2B, WIPI1, DCA10, HP1B3, ZN362, ZEP3, ZC3HD, UBR4, RHG21, UBAP2, RPRD2, DNAI4, TASO2, RN123, PCX4, ARID2, FTM, BICRL, SCAR3, GRHL2, NIPBL, LIN54, NFRKB, ZC3HE, LCN15, CREL2, IGS10, GGYF2, NBEL2, SRCAP, K0408, UBN2, BACHL, KDM3B, PARPT, RGPD4, POGZ, MAVS, EMSY, RAI1, I2BP2, ABCAC, ZFHX4, LUZP1, FRAS1, RB6I2, AHNK2, S22A9, TEX2, MGAP, SULF2, ANKH1, SUGP1, HYCC2, MILK2, CC116, PHAR4, K319L, ASPM, RPTOR, SYNPO, GALT4, MFSD9, SLAI1, CC168, TNR6A, PHC3, VP37A, SYNE1, PLBL2, TIP, CC110, TEX47, TBC15, STT3B, SPP2B, MAGC3, DYH5, PO210, GEMI5, PIGO, F222B, F151A, LMO7, P66B, MYO3B, GBF1, NICA, TM131, ZN592, LAR4B, GSLG1, GPKOW, LPP, TTC28, PF21A, RBM33, GWL, TONSL, PDLI5, VCIP1, ZFR, EP400, CH048, CI072, NOL4L, RBM14, GBP4, CDK15, PHF12, CIC, MED15, G3ST4, FNBP1, MINT, HTF4, EYA3, ARI3A, H2A1J, GDF15, DPH2, BCL7B, TM2D3, PELO, DIDO1, TRAIP, RBM4, CLC7A, UBE2O, PEG3, SP130, BRD8, I2BPL, EPC1, ADNP, RM46, NELFA, WNK1, ZHX3, SDS3, MLXIP, RC3H2, MUC5B, TANC2, CHD8, CELR2, APMAP, PDLI7, RBM12, STAU2, GPTC2, TAB2, CDK12, PTTG3, FLRT1, CRIM1, DAPLE, IBTK, RBM27, KANL3, RERE, SE1L1, LIMD1, TCF20, DPP2, BAP29, S30BP, LCAP, BTNL2, SIX4, POMT2, INT6, MRTFB, NOTC3, ATS5, BSN, SCAF8, ANR26, SHAN2, SRRM2, CTND2, SCML2, ZN652, ZN281, STRAP, VPP2, PRC2C, NCOR2, DC1L1, STON1, S23IP
Species: Homo sapiens
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Jackson EG, Cutolo G, Yang B, Yarravarapu N, Burns MWN, Bineva-Todd G, Roustan C, Thoden JB, Lin-Jones HM, van Kuppevelt TH, Holden HM, Schumann B, Kohler JJ, Woo CM, Pratt MR. 4-Deoxy-4-fluoro-GalNAz (4FGalNAz) Is a Metabolic Chemical Reporter of O-GlcNAc Modifications, Highlighting the Notable Substrate Flexibility of O-GlcNAc Transferase. ACS chemical biology 2022 17(1) 34931806
Abstract:
Bio-orthogonal chemistries have revolutionized many fields. For example, metabolic chemical reporters (MCRs) of glycosylation are analogues of monosaccharides that contain a bio-orthogonal functionality, such as azides or alkynes. MCRs are metabolically incorporated into glycoproteins by living systems, and bio-orthogonal reactions can be subsequently employed to install visualization and enrichment tags. Unfortunately, most MCRs are not selective for one class of glycosylation (e.g., N-linked vs O-linked), complicating the types of information that can be gleaned. We and others have successfully created MCRs that are selective for intracellular O-GlcNAc modification by altering the structure of the MCR and thus biasing it to certain metabolic pathways and/or O-GlcNAc transferase (OGT). Here, we attempt to do the same for the core GalNAc residue of mucin O-linked glycosylation. The most widely applied MCR for mucin O-linked glycosylation, GalNAz, can be enzymatically epimerized at the 4-hydroxyl to give GlcNAz. This results in a mixture of cell-surface and O-GlcNAc labeling. We reasoned that replacing the 4-hydroxyl of GalNAz with a fluorine would lock the stereochemistry of this position in place, causing the MCR to be more selective. After synthesis, we found that 4FGalNAz labels a variety of proteins in mammalian cells and does not perturb endogenous glycosylation pathways unlike 4FGalNAc. However, through subsequent proteomic and biochemical characterization, we found that 4FGalNAz does not widely label cell-surface glycoproteins but instead is primarily a substrate for OGT. Although these results are somewhat unexpected, they once again highlight the large substrate flexibility of OGT, with interesting and important implications for intracellular protein modification by a potential range of abiotic and native monosaccharides.
O-GlcNAc proteins:
MYO1G, HAT1, ZN207, NPA1P, HNRPQ, MAFK, SC31A, G3P, NPM, PTPRC, MPRI, 1433T, APEX1, CALR, CALX, HNRH1, NU214, VDAC2, NU153, RBP2, HCFC1, NUP98, RD23B, BPTF, VEZF1, DPYL2, RPRD2, KDM3B, HUWE1, PRRC1, RCC2, VDAC3, NOP58, PRC2C, SRPRB
Species: Homo sapiens
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Xu S, Zheng J, Xiao H, Wu R. Simultaneously Identifying and Distinguishing Glycoproteins with O-GlcNAc and O-GalNAc (the Tn Antigen) in Human Cancer Cells. Analytical chemistry 2022 94(7) 35132862
Abstract:
Glycoproteins with diverse glycans are essential to human cells, and subtle differences in glycan structures may result in entirely different functions. One typical example is proteins modified with O-linked β-N-acetylglucosamine (O-GlcNAc) and O-linked α-N-acetylgalactosamine (O-GalNAc) (the Tn antigen), in which the two glycans have very similar structures and identical chemical compositions, making them extraordinarily challenging to be distinguished. Here, we developed an effective method benefiting from selective enrichment and the enzymatic specificity to simultaneously identify and distinguish glycoproteins with O-GlcNAc and O-GalNAc. Metabolic labeling was combined with bioorthogonal chemistry for enriching glycoproteins modified with O-GlcNAc and O-GalNAc. Then, the enzymatic reaction with galactose oxidase was utilized to specifically oxidize O-GalNAc, but not O-GlcNAc, generating the different tags between glycopeptides with O-GlcNAc and O-GalNAc that can be easily distinguishable by mass spectrometry (MS). Among O-GlcNAcylated proteins commonly identified in three types of human cells, those related to transcription and RNA binding are highly enriched. Cell-specific features are also revealed. Among glycoproteins exclusively in Jurkat cells, those involved in human T-lymphotropic virus type 1 (HTLV-1) infection are overrepresented, which is consistent with the cell line source and suggests that protein O-GlcNAcylation participated in the response to the virus infection. Furthermore, glycoproteins with the Tn antigen have different subcellular distributions in different cells, which may be attributed to the distinct mechanisms for the formation of protein O-GalNAcylation.
O-GlcNAc proteins:
RBM47, E2F8, SBNO1, CNOT1, HMX3, ABTB3, RHG32, P121C, PDLI1, SNP23, PSMD9, TAF4, ARI1A, ABLM1, STX16, HGS, MYPT1, SC16A, SR140, SET1A, FYB1, TIF1A, PPM1G, SHIP2, EIF3D, NUP42, KDM6A, TET3, SI1L1, DC1L2, HNRPR, PRPF3, TPD54, E41L2, ZN207, BUB3, AKAP8, ZNRD2, MYPT2, GANP, HNRPQ, DIAP1, PLIN3, MAFK, TBL1X, MITF, N4BP1, ZC11A, T22D2, PP6R2, ANR17, BCAS1, NCOR1, SPAG7, TIPRL, SPF30, TOX4, TOX, PCF11, AGFG2, ZFPL1, KIF4A, SC24A, SC24B, CNOT4, ASML, M4K4, BPNT1, PX11B, CHK2, LMNA, GLPA, TFR1, ALDOA, GCR, HSPB1, GNAI2, RLA1, RLA2, RLA0, K1C18, K2C8, RB, CATD, SYEP, PTPRC, VIME, GSTP1, HMGB1, ROA1, ATX1L, DERPC, ZN865, TPR, LAMP2, EF2, PLSL, PLST, GLU2B, HCLS1, PO2F1, RAC2, ATF2, ZEP1, TFE2, MUC1, CREB1, JUNB, ATF7, PTN2, DDX5, SON, ATF1, CSK22, NFKB1, FLNA, PUR2, RFX1, CBL, COF1, PTBP1, ARNT, DCK, PYR1, MAP4, CALX, 3MG, PRDX6, CDC27, AMRP, CLIP1, ZEP2, HNRH1, 1433S, ELF1, LSP1, PTN7, IRS1, ADDA, NU214, CUX1, TXLNA, MLH1, ECHA, IF2G, HNF4A, LAP2B, GPDM, RANG, KI67, CRKL, CAPZB, RFX5, SOX2, CAMLG, NASP, FAS, CDK8, SRP09, YLPM1, NU153, RBP2, TAF6, EMD, LRBA, PAPOA, HCFC1, HDGF, AGFG1, HNRPF, HXK2, NUP98, ATX1, RD23B, AF10, AF17, DSRAD, FOXA1, HNRH2, NU107, TPIS, PSME3, TPM4, F193A, GTF2I, PHC1, PRKDC, MAP1A, SARNP, FOXK1, FBLN2, FAM3A, EM55, NFKB2, HNRPU, SPTB2, FOXK2, RUNX1, FLI1, SATB1, SP2, MP2K1, NUCB1, KMT2A, IF4G1, TLE3, TLE4, KPCT, PSME1, GABPA, PRDX1, ACK1, AHNK, IFFO1, GALT2, SRBP2, TROAP, BPTF, TP53B, CBX3, NFAC2, PICAL, CUL4B, ASPP2, NFYC, CDK13, VEZF1, UBP2L, SRC8, CAPR1, LAGE3, PUM1, MDC1, EPN4, RRP1B, NCOA6, GSE1, UBP10, 2A5D, MEF2D, LASP1, NUMA1, CND1, TEBP, PCBP1, RBMS2, SF3A1, TSN, SF01, MED1, TRIP6, ELF2, TAB1, ZFHX3, ZYX, ADRM1, DPYL2, TAF9, MAPK3, CSPP1, PDS5A, QSER1, AAK1, LRRF1, VP26B, ACSF3, TPRN, CRTC2, PAN3, YIF1B, PRC2B, CEP78, ZN362, FKB15, LRIF1, CAF17, UBAP2, NT5D1, AHDC1, LYRM7, RPRD2, ZN318, TASO2, TBC9B, ARID2, C19L1, ABLM2, TWF2, GRHL2, CPZIP, NIPBL, LIN54, ZCHC8, C2D1A, SCYL2, NFRKB, RSBNL, MDEAS, ZC3HE, LARP1, SAMD1, FIP1, CRTC3, SAS6, MCAF1, BCOR, GGYF2, NBEL2, CO039, SRCAP, UBN2, TM1L2, ASXL2, SPT6H, MEPCE, BOP, KDM3B, ERMP1, TRM1L, ZCCHV, KANL1, POGZ, ZFY16, NUFP2, MAVS, EMSY, RAI1, I2BP2, SRGP1, RHG30, SH3R1, HUWE1, YTHD3, GALT7, LYRIC, BCL9L, CASZ1, TSYL5, DDX42, CACL1, P66A, I2BP1, VRK3, FOXP4, ARI3B, TEX2, MGAP, ANKH1, SUGP1, MILK2, ERF3B, K2013, PHAR4, XRN1, ZN687, FNBP4, ARFG1, ENAH, NHLC2, AVL9, XXLT1, GOLM1, TXND5, SERB1, CHSTE, SLAI1, TNR6A, PHC3, SP20H, VP37A, KMT2C, ARI1B, KNL1, NEDD1, ALMS1, PREX1, DLG5, GEMI5, PIGO, UBS3B, WIPF2, FRS2, PDC6I, ZFN2B, TPC12, SEN15, PCNP, LMO7, ATX2L, CSKI2, PSPC1, P66B, GBF1, SMG7, RTF1, TOPB1, PHF3, MAML1, TTC9A, PRCC, RREB1, CBP, DDX17, SEM4D, ARHG1, GPKOW, FUBP2, LPP, TTC28, PF21A, FAF2, ESS2, EDC3, A7L3B, P121A, PDLI5, FUBP3, VCIP1, PDLI2, Z512B, ZFR, EP400, PRRC1, NOL4L, RBM14, PURB, NACC1, CIC, MED15, NUDC1, SIN3A, AEDO, MINT, HTF4, CNN2, RGPD5, ATX2, HCD2, S29A1, ARI3A, SH3G1, TRIR, DPH2, MGME1, ERP44, ESYT1, CCM2, CNPY3, WAC, DIDO1, HGH1, MMTA2, PAXX, NTM1A, RBM4, SGPP1, HEMGN, HDHD5, YTHD1, FTO, CEP44, BC11B, PITH1, SP130, BRD8, RGAP1, I2BPL, ADNP, DHX36, FOXP1, CENPH, WNK1, E41L1, ZHX3, YTDC2, RANB3, PHAX, ECT2, CNO10, MLXIP, PKHA5, PKHA1, RC3H2, LY9, RDH14, TAF9B, NCOA5, TANC2, TNR6C, CHD8, SDF2L, ARFG3, UBN1, RTN4, PDLI7, CHSTC, STRN4, PNO1, BMP2K, RBM12, STAU2, TXLNG, PNPO, CARF, TAB2, TMOD3, CDK12, F120A, HPBP1, ITSN2, CNOT2, CHMP5, VAPA, CAMP3, RBM27, KANL3, RERE, ZN219, SE1L1, STAP2, LIMD1, TCF20, SEPT9, UBQL2, TRPS1, S30BP, NRBP, EI2BD, SIX4, APC7, TASOR, GMEB2, PARP4, MA1B1, ACINU, ZHX1, CDV3, MRTFB, ZBT21, YETS2, HECD1, ZMYD8, SCAF8, PP6R1, TRI33, TNR6B, ZC3H4, SHAN2, SRRM2, CTND2, SCML2, ZN148, T3JAM, VDAC3, AKAP2, DDX52, NOP58, GIT1, ZN281, SIT1, SALL2, ARIP4, CRBG1, HYOU1, KLF12, PRC2C, YTHD2, CD2AP, TNPO3, SRPRB, TSSC4, NUBP2, HCFC2, FHOD1, NCOR2, GMEB1, NCOA3,