Modeling Glycan Processing Reveals Golgi-Enzyme Homeostasis upon Trafficking Defects and Cellular Differentiation

Peter Fisher,Hannah Spencer,Jane Thomas-Oates,A Jamie Wood,Daniel Ungar

doi:10.1016/j.celrep.2019.03.107

Abstract

SummaryThe decoration of proteins by carbohydrates is essential for eukaryotic life yet heterogeneous due to a lack of biosynthetic templates. This complex carbohydrate mixture—the glycan profile—is generated in the compartmentalized Golgi, in which level and localization of glycosylation enzymes are key determinants. Here, we develop and validate a computational model for glycan biosynthesis to probe how the biosynthetic machinery creates different glycan profiles. We combined stochastic modeling with Bayesian fitting that enables rigorous comparison to experimental data despite starting with uncertain initial parameters. This is an important development in the field of glycan modeling, which revealed biological insights about the glycosylation machinery in altered cellular states. We experimentally validated changes in N-linked glycan-modifying enzymes in cells with perturbed intra-Golgi-enzyme sorting and the predicted glycan-branching activity during osteogenesis. Our model can provide detailed information on altered biosynthetic paths, with potential for advancing treatments for glycosylation-related diseases and glyco-engineering of cells.

Highlights

Glycosylation is a ubiquitous post-translational modification in eukaryotes
The stochastic simulation algorithm (SSA) captures all possible reactions as discrete events, determined by a set of rules for each enzyme (Table S1) that dictate which substrates it is converting to which products
These reactions happen at random times and in a random order depending on the enzymatic rate and amount of each enzyme but independent of how the glycan substrate was generated

Summary

Introduction

Glycosylation is a ubiquitous post-translational modification in eukaryotes It plays roles ranging from protein stability (Waetzig et al, 2010) through cell adhesion (Zhao et al, 2008) to complex physiological traits like antibody-dependent cellular cytotoxicity (Ferrara et al, 2006; Shields et al, 2002). The GlcNAc-seeded antennae in complex glycans can be extended through galactosylation and capped by the often-functional sialic acid (Christie et al, 2008; Scott and Panin, 2014). Another functionally important modification is fucosylation, which can occur on the chain-initiating GlcNAc (core fucosylation) or the antennae (Hemmerich et al, 1994). In the absence of a template, and due to the limited time spent in the Golgi, competition among enzymatic modifications generates a heterogeneous glycan mixture (Stanley and Sudo, 1981)

Methods

Results

Discussion

Conclusion