Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.
Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada.
Front Immunol. 2023 Aug 9;14:1220081. doi: 10.3389/fimmu.2023.1220081. eCollection 2023.
Tripartite motif (TRIM) proteins are involved in development, innate immunity, and viral restriction. TRIM gene repertoires vary between species, likely due to diversification caused by selective pressures from pathogens; however, this has not been explored in birds. We mined a assembled transcriptome for the TRIM gene repertoire of the domestic mallard duck (), a reservoir host of influenza A viruses. We found 57 TRIM genes in the duck, which represent all 12 subfamilies based on their C-terminal domains. Members of the C-IV subfamily with C-terminal PRY-SPRY domains are known to augment immune responses in mammals. We compared C-IV TRIM proteins between reptiles, birds, and mammals and show that many C-IV subfamily members have arisen independently in these lineages. A comparison of the MHC-linked C-IV TRIM genes reveals expansions in birds and reptiles. The TRIM25 locus with related innate receptor modifiers is adjacent to the MHC in reptile and marsupial genomes, suggesting the ancestral organization. Within the avian lineage, both the MHC and TRIM25 loci have undergone significant TRIM gene reorganizations and divergence, both hallmarks of pathogen-driven selection. To assess the expression of TRIM genes, we aligned RNA-seq reads from duck tissues. C-IV TRIMs had high relative expression in immune relevant sites such as the lung, spleen, kidney, and intestine, and low expression in immune privileged sites such as in the brain or gonads. Gene loss and gain in the evolution of the TRIM repertoire in birds suggests candidate immune genes and potential targets of viral subversion.
三基序蛋白（TRIM）参与发育、先天免疫和病毒限制。TRIM 基因库在物种之间存在差异，这可能是由于病原体的选择压力导致的多样化；然而，这在鸟类中尚未得到探索。我们从组装的转录组中挖掘了家鸭（一种流感 A 病毒的储存宿主）的 TRIM 基因库。我们在鸭子中发现了 57 个 TRIM 基因，它们基于 C 末端结构域代表所有 12 个亚家族。已知具有 C 末端 PRY-SPRY 结构域的 C-IV 亚家族成员可以增强哺乳动物的免疫反应。我们比较了爬行动物、鸟类和哺乳动物的 C-IV TRIM 蛋白，并表明许多 C-IV 亚家族成员在这些谱系中独立出现。比较 MHC 连锁的 C-IV TRIM 基因表明，鸟类和爬行动物都有扩展。与先天受体修饰物相关的 TRIM25 基因座与爬行动物和有袋动物基因组中的 MHC 相邻，表明存在祖先组织。在鸟类谱系中，MHC 和 TRIM25 基因座都经历了显著的 TRIM 基因重排和分化，这都是病原体驱动选择的标志。为了评估 TRIM 基因的表达，我们对鸭组织的 RNA-seq 读数进行了比对。C-IV TRIM 在免疫相关部位（如肺、脾、肾和肠）的相对表达较高，而在免疫特权部位（如大脑或性腺）的表达较低。TRIM 基因库在鸟类进化中的基因丢失和获得表明了候选免疫基因和潜在的病毒颠覆的目标。
