Tightly Regulated Expression of <i>Autographa californica</i> Multicapsid Nucleopolyhedrovirus Immediate Early Genes Emerges from Their Interactions and Possible Collective Behaviors

<div><p>To infect their hosts, DNA viruses must successfully initiate the expression of viral genes that control subsequent viral gene expression and manipulate the host environment. Viral genes that are immediately expressed upon infection play critical roles in the early infection process. In this study, we investigated the expression and regulation of five canonical regulatory immediate-early (IE) genes of <i>Autographa californica</i> multicapsid nucleopolyhedrovirus: <i>ie0</i>, <i>ie1</i>, <i>ie2</i>, <i>me53</i>, and <i>pe38</i>. A systematic transient gene-expression analysis revealed that these IE genes are generally transactivators, suggesting the existence of a highly interactive regulatory network. A genetic analysis using gene knockout viruses demonstrated that the expression of these IE genes was tolerant to the single deletions of activator IE genes in the early stage of infection. A network graph analysis on the regulatory relationships observed in the transient expression analysis suggested that the robustness of IE gene expression is due to the organization of the IE gene regulatory network and how each IE gene is activated. However, some regulatory relationships detected by the genetic analysis were contradictory to those observed in the transient expression analysis, especially for IE0-mediated regulation. Statistical modeling, combined with genetic analysis using knockout alleles for <i>ie0</i> and <i>ie1</i>, showed that the repressor function of <i>ie0</i> was due to the interaction between <i>ie0</i> and <i>ie1</i>, not <i>ie0</i> itself. Taken together, these systematic approaches provided insight into the topology and nature of the IE gene regulatory network.</p>