Do N-glycoproteins have preference for specific sequons?

Abstract

Protein N-glycosylation requires the presence of asparagine (N) in the consensus tri-peptide NXS/T (where X is any amino acid, S is serine and T is threonine). Several factors affect the glycosylation potential of NXS/T sequons and one such factor is the type of amino acid at position X. While proline was shown to negatively affect N-glycosylation, the nature of other amino acids at this position is not clear. Using Markov chain analysis of tri-peptide NXS/T from viral, archaeal and eukaryotic proteins as well as experimentally confirmed N-glycosylated sequons from eukaryotic proteins, we show here that the occurrence of most sequon types differ significantly from the expected probability. Sequon types with F, G, I, S, T and V amino acids are consistently preferred while those with P and charged amino acids are under-represented in all four groups. Further, proteins contained far fewer number of possible sequon types (maximum 20 types for NXS or NXT taken separately) for any given number of sequons, which may be explained based on random sampling. Consistent with the present finding, majority of the over-represented sequons found in two important viral envelope glycoproteins (hemagglutinin of influenza A H3N2 and glycoprotein120 of HIV-1) are indeed preferred sequon types, which may provide a selective advantage. Accordingly, although there seems to be some preference for sequons, this preference may not be unique to N-glycosylation.

Comparative Glycomics Analysis of Influenza Hemagglutinin (H5N1) Produced in Vaccine Relevant Cell Platforms

“…Sequons with Ser in the third position are less likely to be filled than those with Thr in this position 51, 54, 58 . NetNGlyc gave a glycosylation potential score of 0.6024 for this site, which predicted a high probability of occupancy.…”

Glycosylation analysis of Chinese hamster ovary produced glycoproteins

“…Glycans are attached only to the asparagine at spe cific amino acid sequences or sequons, asparagineX threonine/serine (NxT/S), where X cannot be proline. OST preferentially attaches glycan to the NxT sequon over the NxS sequon [24], and other amino acids at the Xposition or near the sequon also affect OST efficiency [25][26][27][28]. This is where macroheterogeneity is introduced, as not all sequons are glycosylated, and variation in glycan attachment occurs [29,30].…”

Structural Biology of Glycoproteins

“…The occupancy of an N-glycosylation site depends upon the recognition sequon along with the structure of the protein in proximity to the glycosylation site. Some N-glycosylation sites have very low occupancy as a result of the local sequence composition, secondary structure and also distance to the C-terminus [67][68][69]. Bioinformatics programmes such as NetNGlyc and NetOGlyc (http://www.cbs.dtu.dk/services/NetNGlyc/ and http://www.cbs.dtu.dk/services /NetOGlyc/) [70][71] can predict occupancy of N-glycosylation and O-glycosylation sites respectively; however these are sequence based predictions and so need to be verified experimentally.…”