A general O-glycosylation system important to the physiology of a major human intestinal symbiont

Abstract

The Bacteroides are a numerically dominant genus of the human intestinal microbiota. These organisms harbor a rare bacterial pathway for incorporation of exogenous fucose into capsular polysaccharides and glycoproteins. The infrequency of glycoprotein synthesis by bacteria prompted a more detailed analysis of this process. Here, we demonstrate that Bacteroides fragilis has a general O-glycosylation system. The proteins targeted for glycosylation include those predicted to be involved in protein folding, protein-protein interactions, peptide degradation as well as surface lipoproteins. Protein glycosylation is central to the physiology of B. fragilis and is necessary for the organism to competitively colonize the mammalian intestine. We provide evidence that general O-glycosylation systems are conserved among intestinal Bacteroides species and likely contribute to the predominance of Bacteroides in the human intestine.

Figure 1. Identification of Eight Glycoproteins

(A) 2D gel of AAL-purified proteins obtained from B. fragilis whole cell lysate. Gene numbers indicate proteins that were unequivocally identified by MS analysis. (B) Whole cell lysates of wild-type (WT) and Δgmd-fclΔfkp (ΔΔ), separated by SDS-PAGE, blotted and probed with antiserum to BF2494-His or BF3567-His purified from E. coli. (C) Whole cell lysates of wild-type (WT) and Δgmd-fclΔfkp (ΔΔ) expressing His-tagged glycoprotein candidates, separated by SDS-PAGE, blotted and probed with antibody to the His-tag. BF3810 is an example of a negative result. (D) BF2494-His purified from B. fragilis (Bf) or E. coli (Ec), separated by SDS-PAGE and stained with Coomassie Blue or Pro-Q Emerald Glycostain (first two panels), or blotted and probed with AAL, antiserum to the glycan of BF2494, antibody to the His-tag, or anti-BF2494-His purified from E. coli. (E) Six additional His-tagged glycoproteins purified from B. fragilis and analyzed as in panel D.

Figure 2. Subcellular Localization of the Glycoproteins

(A) Cytoplasmic and periplasmic fractions of wild-type B. fragilis, separated by SDS-PAGE, blotted and probed with antiserum to BF2494-His purified from E. coli. (B) Cytoplasmic and periplasmic fractions from B. fragilis expressing His-tagged BF2494, BF0447, BF0935 or BF2334, separated by SDS-PAGE, blotted and probed with anti-His-tag. (C) Intact B. fragilis Δtsr15M8 cells were incubated with proteinase K for the indicated times and the lysate separated by SDS-PAGE, blotted and probed with antisera to His-tagged BF3567, AapA, or BF2494 purified from E. coli. BF2494 and AapA are controls located in the periplasm or on the surface of the cell, respectively. (D) Wild-type B. fragilis expressing BF0522-His or BF3918-His were incubated with proteinase K for the indicated times, lysed, separated by SDS-PAGE, blotted and probed with anti-His-tag.

Figure 3. Site-Directed Mutagenesis of BF2494

(A) Amino acid sequence of BF2494. The signal peptide is underlined. Segments in upper case and bolded are S/T-containing tryptic peptides that were not detected in at least 2 of 6 MS analyses of purified BF2494-His (excluding the signal peptide). Boxed or underlined residues in these segments were mutated to alanine to determine whether they are glycosylated; boxed residues were found to be glycosylated and underlined residues were not. (B) Wild-type (WT) and mutant BF2494-His proteins purified from B. fragilis, separated by SDS-PAGE, blotted and probed with antiserum to BF2494-His purified from E. coli or stained with Coomassie Blue. (C) Same as panel B except that the gel was either stained with Pro-Q Emerald Glycostain, or blotted and probed with AAL or the antiserum to the glycan of BF2494. (D) Cytoplasmic and periplasmic fractions of B. fragilis expressing His-tagged BF2494 Δ(2-18), separated by SDS-PAGE, blotted and probed with anti-His-tag. The periplasmic fraction is significantly contaminated with cytoplasmic material but the His-tagged protein is partitioned between the fractions in the proportions expected for a cytoplasmic molecule (Table S2). (E) Same as panel D except that the protein is the triple T→A BF2494-His molecule. (F) Alignment of protein sequences surrounding the three glycosylation sites of BF2494. Glycosylated residues are underlined and conserved or similar residues are bold. (G) Whole cell lysates of B. fragilis expressing wild-type and various mutant BF2494-His proteins, separated by SDS-PAGE, blotted and probed with antibody to the His-tag.

Figure 4. A Genomic Region Involved in Protein Glycosylation

(A) The region of the B. fragilis genome containing metG and genes BF4298-4306. Putative glycosyltransferase genes are hatched. (B) Phosphoimager scan of SDS-PAGE-separated whole cell lysates of wild-type, Δgmd-fclΔfkp, and Δ(BF4298-4306) grown in a medium containing ³H-fucose. (C) Whole cell lysates of wild-type and mutants separated by SDS-PAGE, blotted and probed with antiserum to BF2494-His purified from E. coli. (D) Whole cell lysates of wild-type and mutant B. fragilis expressing BF0447-His or BF0522-His, separated by SDS-PAGE, blotted and probed with anti-His-tag. (E) RT-PCR amplification of a 1142 bp region including portions of the coding regions of metG and wzx, as indicated in panel A. Reactions were performed with and without reverse transcriptase (RT).

Figure 5. Conservation of Protein Glycosylation in the Intestinal Bacteroides

(A) The lfg region of B. fragilis and the corresponding regions downstream of metG in other intestinal Bacteroides species. Putative glycosyltransferases are hatched. (B) Whole cell lysates of various Bacteroides species separated by SDS-PAGE, blotted and probed with antiserum to the glycan of BF2494. (C) Same as panel B except that the blot was probed with antiserum to BF2494 purified from E. coli, which recognizes the protein component of the molecule. (D) Alignment of segments of BF2494 and its orthologs demonstrating conservation of the glycosylation motif (bolded). The three residues that are glycosylated in B. fragilis (T87, T178 and T231), and its counterparts in the orthologous proteins are underlined. (E) Western blot analysis of whole cell lysates of various Bacteroides species expressing the B. fragilis wild-type BF2494-His protein (WT), or the B. fragilis BF2494-His triple glycosylation site mutant (T87A.T178A.T231A), probed with anti-His-tag.