Transcriptomic and epigenomic dynamics of honey bees in response to lethal IAPV viral infection

Abstract

Honey bees (Apis mellifera L) suffer from many brood pathogens, including viruses. Despite considerable research, the molecular responses and dynamics of honey bee pupae to viral pathogens remain poorly understood. Israeli Acute Paralysis Virus (IAPV) is emerging as a model virus since its association with severe colony losses. Using worker pupae, we studied the transcriptomic and methylomic consequences of IAPV infection over three distinct time points after inoculation. Contrasts of gene expression and 5mC DNA methylation profiles between IAPV-infected and control individuals at these time points--corresponding to the pre-replicative (5 hr), replicative (20 hr), and terminal (48 hr) phase of infection--indicate that profound immune responses and distinct manipulation of host molecular processes accompany the lethal progression of this virus. We identify the temporal dynamics of the transcriptomic response to with more genes differentially expressed in the replicative and terminal phases than in the pre-replicative phase. However, the number of differentially methylated regions decreased dramatically from the pre-replicative to the replicative and terminal phase. Several cellular pathways experienced hyper- and hypo-methylation in the pre-replicative phase and later dramatically increased in gene expression at the terminal phase, including the MAPK, Jak-STAT, Hippo, mTOR, TGF-beta signaling pathways, ubiquitin mediated proteolysis, and spliceosome. These affected biological functions suggest that adaptive host responses to combat the virus are mixed with viral manipulations of the host to increase its own reproduction, all of which are involved in anti-viral immune response, cell growth, and proliferation. Comparative genomic analyses with other studies of viral infections of honey bees and fruit flies indicated that similar immune pathways are shared. Our results further suggest that dynamic DNA methylation responds to viral infections quickly, regulating subsequent gene activities. Our study provides new insights of molecular mechanisms involved in epigenetic that can serve as foundation for the long-term goal to develop anti-viral strategies for honey bees, the most important commercial pollinator. Author SummaryHoney bees, the most important managed pollinators, are experiencing unsustainable mortality. Israeli Acute Paralysis Virus (IAPV) causes economically important disease in honey bees, and it is emerging as a model system to study viral pathogen-host interactions in pollinators. The pupation stage is important for bee development but individuals are particularly vulnerable for parasitic mite infestations and viral infections. Currently, it is unclear how honey bee pupae respond to this virus. However, these responses, including gene expression and DNA methylomic changes, are critical to understand so that anti-viral genes can be identified and new anti-viral strategies be developed. Here, we use next-generation sequencing tools to reveal the dynamic changes of gene expression and DNA methylation as pupae succumb to IAPV infections after 5, 20, and 48 hours. We found that IAPV causes changes in regions of DNA methylation more at the beginning of infection than later. The activity of several common insect immune pathways are affected by the IAPV infections, as are some other fundamental biological processes. Expression of critical enzymes in DNA methylation are also induced by IAPV in a temporal manner. By comparing our results to other virus studies of honey bees and fruit flies, we identified common anti-viral immune responses. Thus, our study provides new insight on the genome responses of honey bees over the course of a fatal virus infection with theoretical and practical implications.