Predicted Cellular Interactors of the Endogenous Retrovirus-K Integrase Enzyme

Abstract

Integrase (IN) enzymes are found in all retroviruses and are crucial in the retroviral integration process. Many studies have revealed how exogenous IN enzymes, such as the human immunodeficiency virus (HIV) IN, contribute to altered cellular function. However, the same consideration has not been given to viral IN originating from symbionts within our own DNA. Endogenous retrovirus-K (ERVK) is pathologically associated with neurological and inflammatory diseases along with several cancers. The ERVK IN interactome is unknown, and the question of how conserved the ERVK IN protein-protein interaction motifs are as compared to other retroviral integrases is addressed in this paper. The ERVK IN protein sequence was analyzed using the Eukaryotic Linear Motif (ELM) database, and the results are compared to ELMs of other betaretroviral INs and similar eukaryotic INs. A list of putative ERVK IN cellular protein interactors was curated from the ELM list and submitted for STRING analysis to generate an ERVK IN interactome. KEGG analysis was used to identify key pathways potentially influenced by ERVK IN. It was determined that the ERVK IN potentially interacts with cellular proteins involved in the DNA damage response (DDR), cell cycle, immunity, inflammation, cell signaling, selective autophagy, and intracellular trafficking. The most prominent pathway identified was viral carcinogenesis, in addition to select cancers, neurological diseases, and diabetic complications. This potentiates the role of ERVK IN in these pathologies via protein-protein interactions facilitating alterations in key disease pathways.

Keywords: DNA damage response; amyotrophic lateral sclerosis; cancer; diabetes; endogenous retrovirus; eukaryotic linear motif; integrase; interactome; model organisms; viral carcinogenesis.

Figure 1

ERVK integrase and exogenous betaretrovirus integrases share common eukaryotic linear motifs. In silico examination of the conserved and differential eukaryotic linear motifs (ELMs) within Endogenous retrovirus-K (ERVK) and similar betaretroviral integrases. A betaretroviral integrase consensus sequence was constructed using GenBank sequences as follows: Endogenous retrovirus-K (ERVK; P10266.2), Exogenous mouse mammary tumor virus (MMTV; AAF31469.1), Mason–Pfizer monkey virus 5 (M-PMV; BBG56792.1), Enzootic nasal tumor virus (ENTV; ANG58699.1) and Jaagsiekte sheep retrovirus (JSRV; NP_041186.1). The HHCC region and DDE active site motif (gray, with key aa. in black) was positioned based on Conserved Domains annotations. ELMs were grouped based on related pathways: DNA damage response (dark blue), cell cycle (cyan), cell signaling (green), cell trafficking (magenta), autophagy (mauve), and glycosylation (red). ELM abbreviations used include: 14-3-3 = 14-3-3 protein interaction site, BRCT = BRCA1 C-terminus domain interaction site, CK1-P = casein kinase 1 phosphorylation site, Cyclin = cyclin docking site, EBH = end binding homology domain interaction site, ERK/p38 = ERK1/2 and p38 MAP kinase docking site, FHA = Forkhead-associated domain interaction site, GlyNH = glycosaminoglycan attachment site, GSK3-P = GSK3 phosphorylation site, IAP = inhibitor of apoptosis protein interaction site, ITIM = immunoreceptor tyrosine-based inhibitory motif, LIR = site that interacts with Atg8 protein family members, NEK2-P = NEK2 phosphorylation site, p38-P = p38 phosphorylation site, Pex14 = peroxisomal membrane docking via Pex14, PIKK-P = PIKK family phosphorylation site, Pin1 = docking site for Pin1 via WW domain interaction, PKA-P = PKA phosphorylation site, PLK-P = polo-like kinase phosphorylation site, PP1c = protein phosphatase 1 catalytic subunit docking motif, SH2 = Src homology 2 domain interaction motif, SH3 = interaction site for non-canonical class I recognition specificity SH3 domains, STAT3 = STAT3 SH2 domain binding motif, STAT5 = STAT5 SH2 domain binding motif, TRAF2 = major TRAF2 binding consensus motif, USP7 = USP7 MATH (M) or UBL2 (U) domain interaction sites, WDR5 = interaction motif for WDR5 via WW domain interaction. Asterisks indicate ELMs unique to ERVK. Sequence alignment and annotation were performed using Geneious Prime software.

Figure 2

ERVK integrase and similar endogenous integrases share eukaryotic linear motifs patterns. Modified OneZoom image illustrating the conservation of ELM motifs in integrases from eukaryotic organisms (Homo sapiens, Macaca fasicicularis, Fukomys damarensis, Ochotona princeps, Equis asinus, and Capra hircus). Motifs are color-grouped according to function; DDR (blue), cell cycle (cyan), cell signaling (green), and intracellular trafficking (magenta). The number in each colored shape refers to the number of motifs with the respective integrase enzyme.

Figure 3

Predicted ERVK integrase interactome. Cellular proteins containing complementary interaction motifs for ELMs identified in Endogenous retrovirus-K (ERVK) integrase were listed as query proteins for STRING network analysis. Only query proteins with a minimum interaction score of 0.9 based on experiments and databases as interaction sources are indicated. Edges indicate both functional and physical protein associations. A payload list was generated to color nodes and hubs related to dominant pathways: DNA damage response (dark blue), cell cycle (cyan), apoptosis (black), cell signaling (green), and cell transport (magenta).

Figure 4

KEGG pathways associated with ERVK integrase interactome. Predicted interacting partners were curated based on ERVK IN ELM motifs and submitted to STRING network analysis software. Enriched KEGG pathways are reported along with significance scores (−log10 p value). ERVK IN is predicted to interact with cellular pathways involved in the cell cycle, cell signaling, immunity, and inflammation, as well as disease pathways associated with several cancers, the nervous system, and diabetes.