Essentiality and dynamic expression of the human tRNA pool during viral infection [HCMVinfection_tRNAseq]

Human viruses rely on host translation resources, including the cellular tRNA pool, because they lack tRNA genes. Using tRNA sequencing, we profiled mature tRNAs during infections with human cytomegalovirus (HCMV) and SARS-CoV-2. HCMV-induced alterations in mature tRNA levels were predominantly virus-driven, with minimal influence from the cellular immune response. Certain post-transcriptional modifications correlated with tRNA stability and were actively manipulated by HCMV. By contrast, SARS-CoV-2 caused minimal changes in mature tRNA levels or modifications. Comparing viral codon usage with proliferation- versus differentiation-associated codon-usage signatures in human genes revealed striking divergence. HCMV genes aligned with differentiation codon usage, whereas SARS-CoV-2 genes matched proliferation codon usage. Structural and gene-expression genes in both viruses showed strong adaptation to host tRNA pools. Finally, a systematic CRISPR screen of human tRNA genes and tRNA-modifying enzymes identified specific tRNAs and enzymes that either enhanced or restricted HCMV infectivity and influenced cellular growth. Together, these data define a dynamic interplay between the host tRNA landscape and viral infection and illuminate mechanisms governing host–virus interactions. tRNA-seq profiling of HCMV infected HFF in various time points following infection, uninfected samples and two addition treatments- uninfectec with IFNα+β and HCMV-infected (24hpi) with Ruxolitinib.

人类病毒因自身缺乏tRNA基因，故而依赖宿主翻译资源，其中包括细胞tRNA池。本研究通过tRNA测序（tRNA sequencing）技术，对人类巨细胞病毒（human cytomegalovirus, HCMV）与严重急性呼吸综合征冠状病毒2（SARS-CoV-2）感染过程中的成熟tRNA进行了谱分析。HCMV诱导的成熟tRNA水平变化主要由病毒自身驱动，受细胞免疫应答的影响极小；部分与tRNA稳定性相关的转录后修饰，同样受到HCMV的主动调控。与之形成鲜明对比的是，SARS-CoV-2对成熟tRNA水平及转录后修饰的影响微乎其微。将病毒密码子使用偏好与人类基因中增殖、分化相关的密码子使用特征进行比对后发现，二者存在显著差异：HCMV基因的密码子使用偏好与分化相关特征一致，而SARS-CoV-2基因则匹配增殖相关的密码子使用模式。两种病毒的结构基因与基因表达相关基因均展现出对宿主tRNA池的高度适应性。最后，本研究通过对人类tRNA基因及tRNA修饰酶开展系统性CRISPR（成簇规律间隔短回文重复序列，CRISPR）筛选，鉴定出一批可增强或抑制HCMV感染性并影响细胞生长的特定tRNA与修饰酶。综上，本研究数据阐明了宿主tRNA全貌与病毒感染之间的动态互作关系，并揭示了调控宿主-病毒相互作用的分子机制。本数据集包含感染后不同时间点的HCMV感染人包皮成纤维细胞（human foreskin fibroblasts, HFF）样本、未感染对照样本，以及两组额外处理样本：未感染但经干扰素α+β（interferon α+β, IFNα+β）处理的样本，与感染HCMV 24小时（24hpi）后经芦可替尼（Ruxolitinib）处理的样本。