Temporal proteomic analysis and label-free quantification of viral proteins of an invertebrate iridovirus

Abstract

Invertebrate iridescent virus 6 (IIV-6) is a nucleocytoplasmic virus with a~212 kb linear dsDNA genome that encodes 215 putative ORFs. The IIV-6 virion-associated proteins consist of at least 54 virally encoded proteins. One of our previous findings showed that most of these proteins are encoded by genes from the early transcriptional class. This indicated that these structural proteins may not only function in the formation of the virion, but also in the initial stage of viral infection. In the current study, we followed the protein expression profile of IIV-6 over time in Drosophila S2 cells by label-free quantification using a proteomic approach. A total of 95 virally encoded proteins were detected in infected cells, of which 37 were virion proteins. The expressed IIV-6 virion proteins could be categorized into three main clusters based on their expression profiles: proteins with stably low expression levels during infection, proteins with exponentially increasing expression levels during infection and proteins that were initially highly abundant, but showed slightly reduced levels after 48 h post-infection. We thus provided novel information on the kinetics of virion and infected cell-specific protein levels that assists in our understanding of gene regulation in this lesser-known DNA virus model.

Invertebrate Iridoviruses: A Glance over the Last Decade

“…Iridovirid genomes contain multiple genes coding for kinases and phosphatases that perform important post-translational modifications of proteins to help regulate protein activities over the course of the infection [ 127 ]. Active expression of these virus-encoded phosphatases and kinases involved in dephosphorylation and phosphorylation reactions was observed by proteomic analysis of infected cells.…”

“…However, the roles of several kinases have been elucidated. One putative serine/threonine kinase (380R) was present in high abundances in IIV-6 virions [ 127 ]. A purified serine/threonine protein kinase 389L (also called iridoptin) induced apoptosis in insect cells and was initially thought to be associated with the IIV-6 virion structure [ 137 ].…”

“…A purified serine/threonine protein kinase 389L (also called iridoptin) induced apoptosis in insect cells and was initially thought to be associated with the IIV-6 virion structure [ 137 ]. However, no peptides were identified from this protein in either the virion proteome or the proteome from infected cells [ 127 , 128 ]. Thus, it remains uncertain whether 389L is a virion associated protein or not.…”

“…Both cis -acting and trans -acting regulatory factors initiate the transcription that coincide with various stages of viral infection. However, some IE and DE transcripts are still present during the late phase of infection and no meaningful correlation has yet been identified between transcription and the prevalence of particular proteins during infection [ 127 , 143 ]. Overall, a previous study performed by northern blot analyses using putative gene-specific probes on total cellular RNA from IIV-6 infected IPRI-CF-124T cells confirmed the expression of 137 viral transcripts including, 38 IE, 34 DE and 65 L gene transcripts.…”

DNA repair genes in the Megavirales pangenome

“…Most of the key enzymes in these DNA repair pathways can be found in the genomes of Megavirales (Table S1). Transcriptomic ( [24,[28][29][30][31][32][33]) and proteomic ( [24,[34][35][36][37]) studies revealed that many of these DNA repair genes are transcriptionally active during infection and that gene products (i.e., enzymes) are packaged into Megavirales virions (Table S1). Individual Megavirales genomes encode 0 up to 15 of those genes (3.6 genes on average).…”