1. Volume 5, Issue 2, Pages 546-552 (October 2013)
A Chemical Glycoproteomics Platform Reveals O-GlcNAcylation of Mitochondrial Voltage-Dependent Anion Channel 2 
Krishnan K. Palaniappan, Matthew J. Hangauer, Timothy J. Smith, Brian P. Smart, Austin A. Pitcher, Emily H. Cheng, Carolyn R. Bertozzi, Michael Boyce 
Cell Reports 
Volume 5, Issue 2, Pages (October 2013)
DOI: /j.celrep
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2. Cell Reports 2013 5, 546-552DOI: (10.1016/j.celrep.2013.08.048)
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3. Figure 1 Glyco-DIGE System
(A) Endogenous O-GlcNAcylated proteins can be metabolically labeled by the conversion of GalNAz to UDP-GlcNAz, as described (Boyce et al., 2011). Such O-GlcNAzylated substrates can then be detected by chemical tagging with one of several azide-reactive probes. CuAAC is depicted here. The yellow stars represent a useful chemical moiety on the probe molecule, such as a fluorophore or affinity handle.
(B) Glyco-DIGE workflow is illustrated. First, protein extracts are made from two populations of cells (e.g., control and drug treated) that have been treated with GalNAz to metabolically label O-GlcNAc substrates with an azidoglycan (O-GlcNAz), as described (Boyce et al., 2011). The two protein samples are then labeled separately with azide-reactive Cy3- and Cy5-based dyes, mixed, and analyzed by 2D gel (horizontal dimension is for IEF; vertical dimension is for SDS-PAGE). When the gel is scanned, protein spots unchanged between samples appear as dual-color overlap (yellow), whereas proteins unique to one sample appear as single color spots (green indicates Cy3; red indicates Cy5), thereby permitting ready detection of sample-specific changes in O-GlcNAcylated proteins.
(C) Glyco-DIGE alkyne-functionalized fluorescent probes are shown.
(D) Glyco-DIGE probes specifically label azidosugar-tagged mammalian proteins. Jurkat cells were metabolically labeled with 100 μM peracetylated GalNAz (Ac4GalNAz) or vehicle only for 24 hr. Whole-cell lysates were reacted with 1 or 2 via CuAAC and analyzed by standard SDS-PAGE and fluorescence scanning.
(E) 1 and 2 do not differentially affect protein migration in 2D gels. Jurkat cells were metabolically labeled with 100 μM Ac4GalNAz for 24 hr. Then, mitochondria were purified and extracted into lysis buffer. Half the sample was labeled with 1 and half with 2, and labeled samples were analyzed by glyco-DIGE. 1 is indicated in green, 2 in red, and 1+2 overlap in yellow.
See also Figure S8.
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4. Figure 2 Glyco-DIGE Identifies VDAC2 as a Mitochondrial Glycoprotein
(A) Jurkat cells were metabolically labeled with 100 μM Ac4GalNAz for 24 hr, and mitochondrial and cytosolic extracts were prepared. Mitochondrial extracts were reacted with 1 (green), and cytosolic extracts with 2 (red). Then, the samples were mixed and analyzed by glyco-DIGE. 1+2 overlap is indicated in yellow. Arrows point to VDAC2 spots. The characteristic “charge train” pattern of VDAC2 spots likely reflects the presence of multiple phosphorylated forms of the protein.
(B) Wild-type and VDAC2−/− MEFs were metabolically labeled with 100 μM Ac4GalNAz for 24 hr. Mitochondrial extracts were prepared and labeled with 1 (wild-type is in green) or 2 (VDAC2−/− is in red) and then analyzed by glyco-DIGE. Arrows indicate VDAC2 spots.
(C) Wild-type (WT) and VDAC2−/− (ø) MEFs were metabolically labeled with 100 μM Ac4GalNAz or vehicle only for 24 hr, and mitochondrial extracts were prepared and reacted with phosphine-biotin. Then, biotin-tagged proteins were affinity purified essentially as described (Boyce et al., 2011) and analyzed by immunoblot. Left view shows affinity-purified material. Right view presents 3% total input of material (loading control). MnSOD serves as a loading control for total mitochondrial protein and demonstrates the removal of unglycosylated proteins during affinity purification.
See also Figures S1, S2, S3, and S4.
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5. Figure 3
Loss of VDAC2 Protects Cells from Mitochondrial Dysfunction and Cell Death Induced by Global O-GlcNAc Perturbation
(A) Wild-type or VDAC2−/− cells were treated with 10 μM Thiamet-G and 4 mM glucosamine or vehicle control for 26 or 50 hr and analyzed by MTS assay to measure mitochondrially produced reducing equivalents (i.e., NADH and NADPH). Treated samples were normalized to their corresponding vehicle-only controls. Error bars represent SDs.
(B) Wild-type or VDAC2−/− cells were treated as in (A), and whole-cell lysates were prepared and analyzed by immunoblot as indicated.
See also Figures S5 and S6.
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6. Figure S1
Verification of Subcellular Fractionation, Related to Figure 2
Wild-type MEFs were fractionated as described (Frezza et al., 2007) and successful enrichment in mitochondrial and nuclear/cytoplasmic fractions was verified by immunoblot for known mitochondrial (MnSOD), nuclear (Ezh2) and cytoplasmic (tubulin) marker proteins. Similar results were obtained with Jurkat cells (not shown).
Cell Reports 2013 5, DOI: ( /j.celrep )
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7. Figure S2
VDAC2 Is Identified in a Glyco-DIGE Experiment, Related to Figure 2
Protein spots corresponding to those in Figure 2A were excised from preparative glyco-DIGE gels and analyzed by mass spectrometry. Reported are the merged tryptic peptides and their statistical indicators of quality from two proteomics experiments that identified VDAC2 as the major protein.
Cell Reports 2013 5, DOI: ( /j.celrep )
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8. Figure S3
VDAC2 Immunoreactivity Corresponds to VDAC2 Glyco-DIGE Spots, Related to Figure 2
Mitochondrial extracts were prepared from wild-type MEFs and analyzed by 2D immunoblot as indicated. The anti-VDAC2 immunoreactive spots correspond to the fluorescent spots identified as VDAC2 in glyco-DIGE experiments (Figures 2A and 2B). Proteins were separated between pI 3 (left) and 11 (right) in the horizontal dimension and between MW ∼115 kDa (top) and ∼19 kDa (bottom) in the vertical dimension.
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9. Figure S4
VDAC2 Is Specifically Enriched from Mitochondrial Extracts Prepared from Ac4GalNAz-Treated Cells, Related to Figure 2
Jurkat cells were treated with 100 μM Ac4GalNAz or vehicle-only control for 24 hr. Mitochondrial extracts (Frezza et al., 2007) were made and reacted with phosphine-biotin, and samples were subjected to anti-biotin affinity purification. Reported are the merged tryptic peptides and their statistical indicators of quality from two Ac4GalNAz-treated samples that identified VDAC2. In the vehicle-only (i.e., no Ac4GalNAz) negative control sample, avidin was the only protein identified (not shown).
Cell Reports 2013 5, DOI: ( /j.celrep )
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10. Figure S5
MEFs Downregulate OGT and Upregulate OGA in Response to Thiamet-G and Glucosamine Treatment, Related to Figure 3
Wild-type (“WT”) or VDAC2−/− (“ø”) MEFs were treated with 10 μM Thiamet-G and 4 mM glucosamine or vehicle control for 26 or 50 hr and whole-cell lysates were prepared and analyzed by immunoblot as indicated. Tubulin serves as a loading control.
Cell Reports 2013 5, DOI: ( /j.celrep )
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11. Figure S6
Stable Re-Expression of VDAC2 in VDAC−/− MEFs Restores Sensitivity to Perturbation of Global O-GlcNAc, Related to Figure 3
(A) VDAC2−/− MEFs were stably transduced with vector only or HA-tagged VDAC2. Expression was verified by immunoblot of whole-cell lysate for HA, MnSOD (mitochondrial protein loading control) and tubulin (cytoplasmic protein loading control).
(B) VDAC2−/− MEFs stably transduced with vector or HA-VDAC2 were treated with vehicle only or 10 μM Thiamet-G and 4 mM glucosamine for 24 hr and analyzed by caspase-3/7 activity assay to measure apoptotic protease activation. Treated samples were normalized to their corresponding vehicle-only controls. Error bars represent standard deviations.
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12. Figure S7
Glyco-DIGE Detects DNA Damage-Dependent Changes in O-GlcNAcylated Nuclear Proteins Conserved across Disparate Human Cell Lines, Related to Discussion
HT1080 (left) or Jurkat (right) cells were treated with 100 μM Ac4GalNAz and either 1 μg/ml doxorubicin or vehicle-only control for 24 hr. Nuclear extracts were made and reacted with 1 (vehicle-only, green) or 2 (+doxorubicin, red) and analyzed by glyco-DIGE. Arrows indicate candidate DNA damage-specific changes in O-GlcNAcylated proteins. Proteins were separated between pI 3 (left) and 11 (right) in the horizontal dimension and between MW ∼190 kDa (top) and ∼19 kDa (bottom) in the vertical dimension.
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13. Figure S8
Analytical HPLC Traces for Compounds 1 and 2, Related to Figure 1 and Experimental Procedures
Analytical HPLC traces are provided for 1 (A, top) and 2 (B, bottom).
Cell Reports 2013 5, DOI: ( /j.celrep )
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