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Research Article
Glycosylation of closely spaced acceptor sites in human glycoproteins
Shiteshu Shrimal, Reid Gilmore
Journal of Cell Science 2013 126: 5513-5523; doi: 10.1242/jcs.139584
Shiteshu Shrimal
Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
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Reid Gilmore
Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
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  • For correspondence: reid.gilmore@umassmed.edu
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  • Fig. 1.
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    Fig. 1.

    Bioinformatic analysis of closely spaced sequons and glycans. (A,B) The distribution of distances in amino acid residues between asparagines in N-x≠P-T/S sites in murine glycoproteins (A) or in murine cytoplasmic proteins (B) was determined (black circles) and is plotted on a wide (0–400 residues) or narrow scale (0–50 residues, inset plot). The glycoprotein sequon database consisted of 11,983 N-x-T/S sequons in 1902 proteins. The murine cytoplasmic protein database had 10614 N-x≠P-T/S sites in 2256 proteins. Color-coded symbols in the inset plot correspond to overlapping sites (NN-T/S-T/S, red square), adjacent sites (e.g. NxT/S-NxT/S, blue square) or gap-1 to gap-3 sites (NxT/S-Z1–3-NxT/S; cyan square, circle and triangle, respectively). The frequency distribution for distances between sites was fit to a log normal distribution (A, black line) or an exponential density function (B, red line). (A) The expected distribution for uniformly distributed sites in the mouse glycoproteins is shown in red. (C) The observed distribution for overlapping sequons, adjacent sequons (Gap0) and sequon pairs with small (NxT/S-Z1–10-NxT/S) or intermediate gaps (NxT/S-Z21–50-NxT/S) was compared with the observed distribution of all sequon pairs. A pairwise chi-square test of association was performed to identify values that deviated from the total sequon pair distribution (*P<0.05; **P<0.005). (D) The apparent frequency of diglycosylated closely spaced sequons compared to the total apparent modification frequency. Apparent modification frequencies underestimate the actual modification frequency as a result of incomplete detection of all glycopeptides by mass spectrometry. (E) The number of diglycosylated glycopeptides (cyan bars) and the percentage of di-glycosylated glycopeptides (NxT/S-Z0–2-NxT/S) that have paired NxT sites (black bars) was determined for adjacent, gap-1 and gap-2 sites. The glycopeptide database consisted of 14091 glycopeptides identified by mass spectrometry from M. musculus, S. cerevisiae, S. pombe, A. thaliana, C. elegans, D. melanogaster and D. rerio.

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    Fig. 2.

    STT3B-independent glycosylation of closely spaced sites in hemopexin. (A) Diagram of hemopexin (Hpx) showing the signal sequence (black), glycosylation sites, disulfide bonds (red lines) and DDK-His tag. The five sequons are numbered 1–5; Hpx mutants lacking one or more sequons are designated as Hpx-ΔXYZ, where XYZ is the list of mutated sequon(s). HeLa cells were treated with negative control (NC) siRNA or siRNAs specific for STT3A or STT3B as indicated (B–E) for 48 hours prior to transfection with Hpx expression vectors. Cells were pulse labeled for 4 minutes and chased for 20 minutes. EH designates digestion with endoglycosidase H. Hpx glycoforms (0–5 glycans) were immunoprecipitated with anti-DDK sera and resolved by SDS-PAGE. Quantified values below gel lanes are for the displayed image that is representative of two or more experiments.

  • Fig. 3.
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    Fig. 3.

    Sequon skipping of adjacent NxS sites. (A) Diagram of ZAG showing the signal sequence (black), glycosylation sites, disulfide bonds (red lines) and Myc-DDK tag. The four sequons are numbered 1–4; ZAG mutants lacking one or more sequons are designated as ZAG-ΔXYZ, where XYZ is the list of mutated sequon(s). (B) HeLa cells were treated with negative control (NC) siRNA or siRNAs specific for STT3A or STT3B for 48 hours prior to transfection with wild-type ZAG. Cells expressing wild-type ZAG (B), or various ZAG glycosylation site mutants (C) were pulse labeled for 4 minutes and chased for 20 minutes. ZAG glycoforms (0–3 glycans) were immunoprecipitated using anti-DDK antibody and resolved by SDS-PAGE. Arrowheads designate a transient form of ZAG (see supplementary material Fig. S1). EH designates digestion with endoglycosidase H. Quantified values below gel lanes are for the displayed image that is representative of two or more experiments.

  • Fig. 4.
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    Fig. 4.

    Glycosylation of haptoglobin. (A) Diagram of the haptoglobin precursor (Hp) showing the signal sequence (black), protease processing site at the α-β junction (arrow), glycosylation sites, disulfide bonds (red lines), cysteine residues that form interchain disulfides to link two α-subunits (elongated diamonds) and a DDK-His tag. The four sequons are numbered 1–4; Hp mutants lacking one or more sequons are designated as HpΔXYZ, where XYZ is the list of mutated sequon(s). (B,D) HeLa cells were treated with negative control (NC) siRNA or siRNAs specific for STT3A or STT3B as indicated for 48 hours prior to transfection with Hp expression constructs. Cells were then pulsed for 4 minutes and chased for 20 minutes. (C) Cells expressing Hp-wt were pulse labeled for 4 minutes and chased as indicated. Hp glycoforms were precipitated with anti-DDK sera and resolved by SDS-PAGE. EH designates digestion with endoglycosidase H. Quantified values below gel lanes are for the displayed image that is representative of two or more experiments.

  • Fig. 5.
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    Fig. 5.

    Sequence and gap-length dependence of sequon skipping. HeLa cells were treated with negative control (NC) siRNA or siRNAs specific for STT3A or STT3B as indicated for 48 hours prior to transfection with Hp expression constructs. The HpΔ14 derivatives had closely spaced NxT sites (A) or NxS sites (B) separated by 0–2 alanine residues. HeLa cells expressing Hp glycosylation site mutants were pulsed for 4 minutes and chased for 20 minutes. EH designates digestion with endoglycosidase H. Quantified values below gel lanes are for the displayed image that is representative of two or more experiments.

  • Fig. 6.
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    Fig. 6.

    Glycosylation of consecutive gap-1 sequons. (A) The sequences of HpΔ14 derivatives that have two to five closely spaced sites. (B–D) HeLa cells expressing Hp glycosylation site mutants were pulsed for 4 minutes and chased for 20 minutes. (C) Limited digestion of anti-DDK immunoprecipitates with endoglycosidase H (EH, 0–15 minutes). (D) HeLa cells were treated with negative control (NC) siRNA or siRNAs specific for STT3A or STT3B as indicated for 48 hours prior to transfection with Hp expression constructs. Quantified values below gel lanes are for the displayed image that is representative of two or more experiments.

  • Fig. 7.
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    Fig. 7.

    Glycosylation of extreme C-terminal closely spaced sites. (A) The C-terminal segment of sex hormone binding globulin (SHBG) and glycosylation site mutants. The asterisk designates the C-terminus. HeLa cells that were untreated (B) or treated with negative control (NC) siRNA or siRNAs specific for STT3A or STT3B for 48 hours (C) were transfected with SHBG expression vectors and radiolabeled 24 hours later using a 4 minute pulse label followed by a 20 minute chase. SHBG glycoforms (0–2 glycans) were immunoprecipitated with anti-SHBG and resolved by SDS-PAGE. EH designates digestion with endoglycosidase H. Quantified values below gel lanes are for the displayed image that is representative of two or more experiments.

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Keywords

  • Asparagine-linked glycosylation
  • Oligosaccharyltransferase
  • Endoplasmic reticulum

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Research Article
Glycosylation of closely spaced acceptor sites in human glycoproteins
Shiteshu Shrimal, Reid Gilmore
Journal of Cell Science 2013 126: 5513-5523; doi: 10.1242/jcs.139584
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Research Article
Glycosylation of closely spaced acceptor sites in human glycoproteins
Shiteshu Shrimal, Reid Gilmore
Journal of Cell Science 2013 126: 5513-5523; doi: 10.1242/jcs.139584

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