title: N-glycan occupancy of Arabidopsis N-glycoproteins.
abstract: Most secreted proteins in eukaryotes are modified on the amino acid consensus sequence NxS/T by an N-glycan through the process of N-glycosylation. The N-glycans on glycoproteins are processed in the endoplasmic reticulum (ER) to different mannose-type N-glycans or, when the protein passes through the Golgi apparatus, to different complex glycan forms. Here we describe the capturing of N-glycopeptides from a trypsin digest of total protein extracts of Arabidopsis plants and release of these captured peptides following Peptide N-glycosidase (PNGase) treatment for analysis of N-glycan site-occupancy. The mixture of peptides released as a consequence of the PNGase treatment was analyzed by two dimensional nano-LC-MS. As the PNGase treatment of glycopeptides results in the deamidation of the asparagine (N) in the NxS/T site of the released peptide, this asparagine (N) to aspartic acid (D) conversion is used as a glycosylation 'signature'. The efficiency of PNGase F and PNGase A in peptide release is discussed. The identification of proteins with a single glycopeptide was limited by the used search algorithm but could be improved using a reference database including deamidated peptide sequences. Additional stringency settings were used for filtering results to minimize false discovery. This resulted in identification of 330 glycopeptides on 173 glycoproteins from Arabidopsis, of which 28 putative glycoproteins, that were previously not annotated as secreted protein in The Arabidopsis Information Resource database (TAIR). Furthermore, the identified glycosylation site occupancy helped to determine the correct topology for membrane proteins. A quantitative comparison of peptide signal was made between wild type and complex-glycan-less (cgl) mutant Arabidopsis from three replicate leaf samples using a label-free MS peak comparison. As an example, the identified membrane protein SKU5 (AT4G12420) showed differential glycopeptide intensity ratios between WT and cgl indicating heterogeneous glycan modification on single protein.
  
  
  CONCLUSIONS
  Proteins that enter the secretory pathway are mostly modified by N-glycans. The function of N-glycosylation has been well studied in mammals. However, in plants the function of N-glycosylation is still unclear, because glycosylation mutants in plants often do not have a clear phenotype. Here we analyzed which proteins are modified by N-glycans in plants by developing a glycopeptide enrichment method for plant proteins. Subsequently, label free comparative proteomics was employed using protein fractions from wild type and from a mutant which is blocked in modification of the N-glycan into complex glycans. The results provide new information on N-glycosylation sites on numerous secreted proteins. Results allow for specific mapping of multiple glycosylation site occupancy on proteins, which provides information on which glycosylation sites are protected or non-used from downstream processing and thus presumably are buried into the protein structure. Glycoproteomics can therefore contribute to protein structure analysis. Indeed, mapping the glycosylation sites on membrane proteins gives information on the topology of protein folds over the membrane. We thus were able to correct the topology prediction of three membrane proteins. Besides, these studies also identified limitations in the software that is used to identify single modified peptide per protein. This article is part of a Special Issue entitled: Translational Plant Proteomics.
authors.affiliation: Laboratory of Plant Physiology, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; Plant Research International, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
authors.forename: Wei
authors.initials: W
authors.lastname: Song
authors.forename: Remco A
authors.initials: RA
authors.lastname: Mentink
authors.forename: Maurice G L
authors.initials: MG
authors.lastname: Henquet
authors.forename: Jan H G
authors.initials: JH
authors.lastname: Cordewener
authors.forename: Aalt D J
authors.initials: AD
authors.lastname: van Dijk
authors.forename: Dirk
authors.initials: D
authors.lastname: Bosch
authors.forename: Antoine H P
authors.initials: AH
authors.lastname: America
authors.forename: Alexander R
authors.initials: AR
authors.lastname: van der Krol
mesh_terms: D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000737:chemistry* / Q000235:genetics; D029681:Arabidopsis Proteins / Q000737:chemistry; D006020:Glycopeptides / Q000302:isolation & purification; D006023:Glycoproteins / Q000737:chemistry*; D006031:Glycosylation; D008562:Membrane Glycoproteins / Q000737:chemistry; D043524:Peptide-N4-(N-acetyl-beta-glucosaminyl) Asparagine Amidase / Q000378:metabolism
chemical_list: D029681:Arabidopsis Proteins; D006020:Glycopeptides; D006023:Glycoproteins; D008562:Membrane Glycoproteins; C000589479:SKU5 protein, Arabidopsis; D043524:Peptide-N4-(N-acetyl-beta-glucosaminyl) Asparagine Amidase
keywords: ACN; Arabidopsis; DDA; DIA (MS(E)); Data independent acquisition (MS(E)); ER; Endoplasmatic Reticulum; GO; Gene Ontology; LC–MS; LC–MS/MS; MS/MS; N-glycoproteomics; N-glycosylation; OST; PAGE; PNGase; Q-TOF; TAIR; The Arabidopsis Information Resource database.; UPLC; Ultra performance liquid chromatography; acetonitrile; cgl; complex glycan less Arabidopsis mutant; data dependent acquisition; data independent acquisition; liquid chromatography tandem mass spectrometry; oligosaccharyltransferase; peptide-N-glycosidase; polyacrylamide gel electrophoresis; quadrupole time of flight