CRISPR-like properties of eukaryotic ribosomal 45S RNA gene clusters

As viruses lack their own ribosomes, they have evolved various strategies of cellular mimicry and deception to usurp and repurpose host cell ribosomes toward viral protein production 1. This omnipresent challenge posed by viruses results in virus-host coevolution, with ribosomes and ribosomal RNA (rRNA) gene clusters locked in genetic conflict with viral genomes. In addition to their tandem repeat redundancy, eukaryotic 45S rRNA gene clusters have a number of striking, CRISPR-like features, such as palindromic organization 2 of highly conserved sequences (18S, 5.8S, and 28S rDNA) separated by unique, internal transcribed spacers 1 (ITS1) and 2 (ITS2). ITS sequences are highly dissimilar between species but tend to preserve RNA secondary structure that includes a stem-loop 3,4. We discovered that, not unlike bacterial and archaeal CRISPRs 5, eukaryotic ITS regions contain ancient fragments of integrated virus-like sequences, predominantly homologous to DNA viruses, such as herpesviruses in vertebrates. Human ITS2 sequences not only exhibit homologies to herpesvirus sequences but also exert potent immunostimulatory and antiviral properties against herpesvirus infection. These findings will help establish the groundwork for a new paradigm in antiviral immunity and treatment.

由于病毒自身不拥有核糖体，因此进化出多种细胞模拟与欺骗策略，以篡夺并重新利用宿主细胞核糖体来合成病毒蛋白¹。病毒所带来的这一普遍挑战引发了病毒-宿主共进化过程，使得核糖体与核糖体RNA（ribosomal RNA，rRNA）基因簇与病毒基因组陷入遗传冲突。除了具备串联重复冗余特性外，真核生物45S rRNA基因簇还拥有多项类似成簇规律间隔短回文重复序列（CRISPR）的显著特征，例如由独特的内部转录间隔区1（internal transcribed spacer 1，ITS1）与内部转录间隔区2（internal transcribed spacer 2，ITS2）分隔的高度保守序列（18S、5.8S及28S rDNA）的回文排布²。ITS序列在不同物种间差异极大，但通常会保留包含茎环结构的RNA二级结构³,⁴。我们的研究发现，与细菌和古菌的CRISPR类似⁵，真核生物的ITS区域中存在整合的类病毒序列古片段，这些序列主要与DNA病毒同源，例如脊椎动物中的疱疹病毒。人类ITS2序列不仅与疱疹病毒序列存在同源性，还能对疱疹病毒感染产生强效的免疫刺激与抗病毒活性。本研究结果将为抗病毒免疫与治疗领域的全新范式奠定基础。