The function annotations of ST3GAL4 in human LAMP1 and Lassa virus GP-C interaction from the perspective of systems virology

Abstract

Lassa virus (LASV) is a single-stranded RNA virus that has plagued the Sub-Saharan part of Africa, precisely Nigeria where various pathogenic strains with varied genomic isoforms have been identified. The human lysosomal-associated membrane protein 1 (LAMP1) is alternately required for the micropinocytosis of LASV. Therefore, it is of interest to understand the mechanism of action of the host LAMP1 with LASV protein during infection. The role of ST3 beta-galactoside alpha-2, 3-sialyltransferase 4 (ST3GAL4) in the interaction between LASV (glycoprotein) GP-C and the human LAMP1 is relevant in this context. Deposited curated protein sequences of both LAMP1 and LASV GP-C were retrieved for the study. The ST3GAL4 associated data was constructed and analysed from weighted network analysis to infer the function annotations and molecular mediators that characterize the LASV infection. The gene network shows that glycoprotein sialylation, sialyltransferase enzymatic activities and glycosphingolipid biosynthesis are linked with the ST3GAL4 function. However, the physical interaction of FAM 213A, CD8B molecule and proprotein convertase subtilisin/kexin type 1 inhibitor (PCSK1N) with ST3GAL4 is intriguing in this perspective. There are 11 glycosylated asparagine sequons of the human LAMP1 but only nine were assigned a sialylated glycan cap to mediate the LASV GP-C and LAMP1 interaction having exceeded a recommended glycosylation threshold of 0.5. Therefore, the sialylated glycans of the human LAMP1 are a total of nine and these sialylated glycans mediate the molecular recognition between LASV and LAMP1. This study therefore, predicts that there is a cellular interchange between N-linked glycosylation properties of the human LAMP1 and LASV glycoprotein, and sialylation functions of ST3GAL4 in LASV infectivity. Further studies and the clinical trial of this predictive model on the sialylated glycans of LAMP1 will facilitate the understanding of the LASV micropinocytosis process in host cells.

Keywords: Glycosylation; LAMP1; Lassa virus; Neural network; ST3GAL4; Sialylation.

Fig. 1.

Flow chart of the summarized methods and analysis conducted.

Fig. 2.

Concentric network visualization layout with annotated information for 20 important genes interacting with ST3GAL4. It also includes physical and genetic interactions, co-expression, shared pathways and protein structure domain represented by the edges between the nodes. Black nodes represent the 20 important genes, and the lines represent the different interactions of the genes. The different colour displayed in the nodes represents the annotated functions of the ST3GAL4 and also its specific pathway types with related genes.

Fig. 3.

Weighted network consisting of ST3GAL4, CD8B and PCSK1N query genes connected via a strong link (physical interactions). Genes with similar expression patterns were recruited in the network.

Fig. 4.

Graphical output of the thresholds and potentials of the N-glycosylated Lassa virus GP-C complex. The graph illustrates predicted N-glyc sites across the protein chain (X-axis represents protein length from N- to C- terminal). A position with a potential (vertical lines) crossing the threshold (horizontal lines at 0.5) is predicted glycosylated. All of the predicted potential residues exceeded the threshold of 0.5, as shown in the graph. The signal precursor had no glycosylated residue as N-glycosylation starts from the GP1 complex. LASV GP2 glycosylated residues starts from position 365 as graphically displayed.

Fig. 5.

The α2,3 anomeric linkage of the Neu5Ac and the galactose sugar catalysed by neuraminidase. The structural moiety of the α2,3 linkage Neu5Ac, which is the biologically relevant form relating to the Lassa virus infection and ST3GAL4, which is beta galactoside alpha 2,3 glycosidic bond.

Fig. 6.

The glycosylated peak of the human LAMP1 asparagine seqouns highly dominated with high mannosylation and exceeding the threshold of 0.5.

Fig. 7.

Sialylated glycans of the human LAMP1. The glycoconjugate of sialic acid and N-glycans (Neu5A(α2,3) Gal(b1-4)(Fuc(α1–3))GlcNAc) is recognized by the LASV GP-C complex facilitating its cell recognition and cellular entry through the host receptor. The virus-encoded neuraminidase protein catalyses removal of Neu5Ac from the cell surface and viral glycoproteins to release newly formed virions. The glycosylated Lassa virus protein mediates the attachment of the virus to the receptor.