Predicting the subcellular localization of viral proteins within a mammalian host cell

Ms Scott,R Oomen,Mt Hallett,Dy Thomas

doi:10.1186/1743-422x-3-24

Abstract

BackgroundThe bioinformatic prediction of protein subcellular localization has been extensively studied for prokaryotic and eukaryotic organisms. However, this is not the case for viruses whose proteins are often involved in extensive interactions at various subcellular localizations with host proteins.ResultsHere, we investigate the extent of utilization of human cellular localization mechanisms by viral proteins and we demonstrate that appropriate eukaryotic subcellular localization predictors can be used to predict viral protein localization within the host cell.ConclusionSuch predictions provide a method to rapidly annotate viral proteomes with subcellular localization information. They are likely to have widespread applications both in the study of the functions of viral proteins in the host cell and in the design of antiviral drugs.

Highlights

The bioinformatic prediction of protein subcellular localization has been extensively studied for prokaryotic and eukaryotic organisms
Viral proteins have been shown experimentally to be localized in many different cellular compartments including the nucleus, the nucleolus, the cytosol, the endoplasmic reticulum (ER)/ Golgi apparatus, the plasma membrane and cell surface, and the mitochondria (M11L protein from the myxoma virus and several others, reviewed in [7,8])
Eukaryotic targeting signals and functional domains in specific viral proteomes In order to investigate the extent of eukaryotic targeting signal usage by the viral proteins considered, we scanned the human, vaccinia virus and cytomegalovirus proteomes using various bioinformatics predictors that identify these signals

Summary

Introduction

The bioinformatic prediction of protein subcellular localization has been extensively studied for prokaryotic and eukaryotic organisms. This is not the case for viruses whose proteins are often involved in extensive interactions at various subcellular localizations with host proteins. Viruses use the host synthetic machinery to replicate They have evolved mechanisms to exploit the host nucleic acid replication and protein translation apparatus and have developed strategies to evade humoral immune surveillance. Viral proteins require targeting to the appropriate subcellular compartments of the host cell to fulfill their roles. Available predictors differ in many aspects including the computational method used, the type and diversity of protein characteristics considered for the prediction, the localization coverage, the target organism(s) and the reliability. Predictors can be grouped into four general classes based upon the protein characteristics that are considered: amino acid (page number not for citation purposes)

Methods

Results

Discussion

Conclusion