Table_2_Transcriptomic and Epigenomic Dynamics of Honey Bees in Response to Lethal Viral Infection.XLSX

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 5 mC DNA methylation profiles between IAPV-infected and control individuals at these time points – corresponding to the pre-replicative (5 h), replicative (20 h), and terminal (48 h) 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.

西方蜜蜂（Apis mellifera L.）会遭受多种侵染其未成熟个体的病原体侵害，其中包括各类病毒。尽管学界已开展大量相关研究，但蜜蜂蛹对病毒性病原体的分子应答及其动态变化仍未得到充分解析。以色列急性麻痹病毒（Israeli Acute Paralysis Virus, IAPV）因与蜂群大规模死亡存在明确关联，逐渐成为研究蜜蜂-病毒互作的模式病毒。本研究以工蜂蛹为实验材料，对接种IAPV后的三个不同时间节点开展转录组与甲基化组分析，这三个时间点分别对应病毒感染的前复制期（接种后5小时）、复制期（接种后20小时）以及终末期（接种后48小时）。通过对比感染组与对照组个体在上述时间点的基因表达谱与5-甲基胞嘧啶（5 mC）DNA甲基化谱，研究发现该病毒的致死性侵染过程伴随显著的宿主免疫应答，以及宿主分子进程被病毒精准操控的现象。本研究解析了转录组应答的时间动态特征：在复制期与终末期，差异表达基因的数量远多于前复制期。然而，差异甲基化区域的数量从前复制期到复制期、终末期出现了大幅下降。多个细胞通路在前复制期呈现高甲基化或低甲基化特征，并在终末期出现基因表达量的显著上调，其中包括丝裂原活化蛋白激酶（MAPK）通路、Jak-STAT通路、Hippo通路、mTOR通路、转化生长因子-β（TGF-beta）信号通路、泛素介导的蛋白水解通路以及剪接体通路。这些受影响的生物学功能提示，宿主对抗病毒的适应性应答与病毒操控宿主以提升自身增殖的过程相互交织，二者均参与抗病毒免疫应答、细胞生长与增殖过程。通过与其他针对蜜蜂及果蝇的病毒感染研究开展基因组比较分析，本研究发现二者共享相似的免疫通路。本研究进一步表明，动态DNA甲基化可快速响应病毒感染，并调控后续的基因活性。本研究为解析蜜蜂抗病毒相关的分子表观调控机制提供了新见解，可为开发针对这一最重要的商业授粉昆虫的抗病毒策略奠定长期研究基础。