Connecting viral with cellular interactomes

Abstract

Genome-scale screens for intraviral and virus-host protein interactions and the analysis of literature-curated datasets are able to provide a novel, comprehensive perspective of viruses, and virus-infected cells. Until now, large-scale interaction screens were predominantly performed with the yeast-two-hybrid (Y2H) system; however, alternative high-throughput technologies detecting binary protein interactions or protein complexes have been developed. Although many of the previous studies suffer from a rather poor validation of the results and few biological implications, these technologies potentially lead to a plethora of novel hypotheses. Here, we will give an overview of current approaches and their technical limitations, present recent examples and novel developments.

Figure 1

High-throughput technologies to detect protein interactions. Graphic depiction of several approaches for the detection of binary protein interaction including the yeast-two-hybrid (Y2H) system, the nucleic acid programmable protein array (NAPPA), the LUMIER (luminescence-based mammalian interactome mapping), the protein fragment complementation assay (PCA), and the MAPPIT (mammalian protein–protein interaction trap). Multicomponent protein interactions can be analyzed by the TAP (tandem affinity purification) of ProtA-tagged bait proteins followed by mass spectrometry of associated proteins. Bait (x) and prey (y) proteins are indicated, fusion tags are shown in orange (AD: activation domain; DBD: DNA binding protein; ATG: start codon).

Figure 2

Scheme of HSV-1 virus particle with protein interactions detected in a genome-wide Y2H screen. Capsid, tegument, and glycoproteins are indicated depending on their localization in the virus particle. Proteins are colored according to their conservation, purple: conserved in all herpesviruses, red: in alpha herpesviruses, grey: in Herpes simplex virus, pink: in alpha and gamma herpesviruses.

Figure 3

Global view of the interaction of two herpesviruses, VZV and KSHV, with the human proteome. Two experimental Y2H datasets were used to connect the two viral interactomes of VZV (red) and KSHV (pink) into a predicted high-confidence human interaction network consisting of 10 636 edges between 3169 nodes. Interactions between viral proteins are depicted in red or orange, interactions to cellular proteins in blue.

Figure 4

Nuclear egress of HSV-1 capsids. Herpesviral capsids are formed in the host nucleus and released to the cytoplasm by budding through the nuclear envelope. Primary envelopment at the inner nuclear membrane (INM) requires the membrane anchored UL34/UL31 family of proteins. The UL33 protein family interacts with this nuclear egress complex and may connect capsid packaging and nuclear egress (ER: endoplasmic reticulum; INM: inner nuclear membrane; ONM: outer nuclear membrane; NPC: nuclear pore complex).