Transcriptome responses of the host Trichoplusia ni to infection by the baculovirus Autographa californica multiple nucleopolyhedrovirus

Abstract

Productive infection of Trichoplusia ni cells by the baculovirus Autographa californica multiple nucleopolyhedrovirus (AcMNPV) leads to expression of ~156 viral genes and results in dramatic cell remodeling. How the cell transcriptome responds to viral infection was unknown due to the lack of a reference genome and transcriptome for T. ni. We used an ~60-Gb RNA sequencing (RNA-seq) data set from infected and uninfected T. ni cells to generate and annotate a de novo transcriptome assembly of approximately 70,322 T. ni unigenes (assembled transcripts), representing the 48-h infection cycle. Using differential gene expression analysis, we found that the majority of host transcripts were downregulated after 6 h postinfection (p.i.) and throughout the remainder of the infection. In contrast, 5.7% (4,028) of the T. ni unigenes were upregulated during the early period (0 to 6 h p.i.), followed by a decrease through the remainder of the infection cycle. Also, a small subset of genes related to metabolism and stress response showed a significant elevation of transcript levels at 18 and 24 h p.i. but a decrease thereafter. We also examined the responses of genes belonging to a number of specific pathways of interest, including stress responses, apoptosis, immunity, and protein trafficking. We identified specific pathway members that were upregulated during the early phase of the infection. Combined with the parallel analysis of AcMNPV expression, these results provide both a broad and a detailed view of how baculovirus infection impacts the host cell transcriptome to evade cellular defensive responses, to modify cellular biosynthetic pathways, and to remodel cell structure.

Importance: Baculoviruses are insect-specific DNA viruses that are highly pathogenic to their insect hosts. In addition to their use for biological control of certain insects, baculoviruses also serve as viral vectors for numerous biotechnological applications, such as mammalian cell transduction and protein expression for vaccine production. While there is considerable information regarding viral gene expression in infected cells, little is known regarding responses of the host cell to baculovirus infection. In these studies, we assembled a cell transcriptome from the host Trichoplusia ni and used that transcriptome to analyze changes in host cell gene expression throughout the infection cycle. The study was performed in parallel with a prior study of changes in viral gene expression. Combined, these studies provide an unprecedented new level of detail and an overview of events in the infection cycle, and they will stimulate new experimental approaches to understand, modify, and utilize baculoviruses for a variety of applications.

FIG 1

(A) Transcript profile of AcMNPV mRNA versus T. ni Tnms42 mRNA by comparison of Illumina RNA-seq reads. Each data point represents Illumina reads as a percentage of total reads. (B) Proportions of unigenes up- or downregulated at various times postinfection. For each time point, the proportion of upregulated unigenes, downregulated unigenes, and unigenes with no significant change or for which data are indeterminate are shown as a combined single bar equal to 100%. (C) The numbers of unigenes up- and downregulated are indicated above and below the horizontal line, respectively. Upregulated unigenes are subdivided into those that are induced (unigenes with RPKM values of <5 for uninfected controls) and those that are upregulated (unigenes with RPKM values of ≥5 for uninfected controls). Downregulated unigenes are also subdivided into those that are repressed (unigenes with RPKM values of <5 for the specified time point postinfection) and those that are downregulated (unigenes with RPKM values of ≥5 for the specified time point postinfection).

FIG 2

Differentially expressed transcripts among different biological processes. (Top) Distributions of upregulated unigenes at 6 h p.i.; (B) distributions of downregulated unigenes at 6 h p.i. Gene ontology (GO) analysis of differentially expressed T. ni transcripts was performed as described in Materials and Methods.

FIG 3

Cluster analysis of T. ni Tnms42 gene expression patterns throughout the 48-h AcMNPV infection cycle. A heat map of normalized gene expression levels from 0 to 48 h p.i. shows each gene as a single horizontal line. Relative expression levels are represented as high (red), intermediate (black), and low (green). Based on gene expression levels and patterns of expression, unigenes were clustered into groups G1 to G9 (indicated on the left).