Pan-modification profiling facilitates a cross-evolutionary dissection of the thermoregulated ribosomal epitranscriptome - HsapiScere

Over 170 modifications are deposited on RNA, across the tree of life. A major bottleneck to systematically dissecting RNA modifications has been the lack of methods allowing to acquire systematic, high-confidence maps of many RNA modifications and at scale. Here we have developed Pan-Mod-seq, which permits de-novo, sensitive and specific identification of 16 distinct modifications in dozens of samples in parallel. We applied Pan-Mod-seq to RNA from 14 different species from all 3 domains of life, most of which sampled under highly variable chemical/physical/biological gradients, aiming to systematically explore the plasticity of rRNA modifications. While dynamically modified sites are relatively rare in mesophiles, we find that these are widespread in hyperthermophiles, where ~50% of identified modifications were induced with temperature. We focused on dissection of three key dynamically induced modifications: m5C, ac4C and Ψ. We uncover an m5C program encompassing dozens of targets across both rRNA subunits, all of which are dramatically induced with growth temperature in two of the sampled hyperthermophiles. In both cases m5C is introduced at a single consensus motif, via a single enzyme which is essential for growth at higher temperatures. ac4C in turn is dynamically induced among all three sampled hyperthermophiles at hundreds of sites, also at a single consensus motif. Remarkably, the methylation and acetylation overlap, and together form a tandemly modified temperature induced G-m5C-ac4C-G sequence motif. Temperature-dependent induction of both enzymes can be recapitulated in vitro, establishing that it is an intrinsic property of the two enzymes rather than externally regulated. We obtain high-resolution cryoEM structures of ribosomes from WT strains at low and high temperatures and ones deleted of the methylating enzyme, and identify numerous mechanisms via which m5C confers structural stability. Finally, we also uncover a systematic induction in Ψ levels in T. kodakarensis, and reveal that it is largely coordinated by a single temperature-induced sRNA guiding pseudouridine formation at an unprecedented number of targets, whose loss results in growth deficiency at higher temperatures. Our findings offer a wide and systematic view of rRNA modification plasticity across representative species sampled from the tree of life, dissect the ability of different modifications to contribute to the stability of ribosomes at higher temperatures, and present a methodology allowing an unprecedented view on the the rRNA epitranscriptome in health and in disease.在整个生命之树中，RNA上已鉴定出超过170种修饰。长期以来，系统性解析RNA修饰的核心瓶颈在于缺乏能够大规模、系统性获取多种RNA修饰的高可信度图谱的方法。本研究开发了Pan-Mod-seq技术，可并行对数十个样本中的16种不同RNA修饰进行从头(de-novo)、灵敏且特异性的鉴定。我们将Pan-Mod-seq应用于覆盖生命三大域的14个不同物种的RNA样本，其中多数样本是在高度多变的化学、物理及生物学梯度条件下采集的，旨在系统性探究核糖体RNA(rRNA)修饰的可塑性。尽管在嗜温微生物中，动态修饰位点相对罕见，但我们发现这类位点在超嗜热微生物中广泛存在，其中约50%已鉴定的修饰会随温度诱导产生。本研究聚焦于解析三种关键的动态诱导修饰：5-甲基胞嘧啶(m5C)、N4-乙酰胞嘧啶(ac4C)与假尿嘧啶(Ψ)。我们发现了一个m5C修饰调控网络，覆盖两个核糖体RNA亚基中的数十个靶标位点，在两个采样的超嗜热微生物中，所有这些位点均会随生长温度升高而显著诱导产生。在这两种体系中，m5C修饰均通过单一酶在单一保守基序处引入，而该酶对微生物在高温下的生长至关重要。而ac4C修饰则在三个采样的超嗜热微生物中均有数百个位点被动态诱导，同样仅存在单一保守基序。值得注意的是，甲基化与乙酰化修饰存在重叠，二者共同形成了温度诱导的串联修饰序列基序G-m5C-ac4C-G。两种酶的温度依赖性诱导均可在体外重现，这表明该调控过程是两种酶的内在属性，而非受外部调控。我们解析了野生型(WT)菌株在低温和高温条件下，以及甲基化酶缺失菌株的核糖体高分辨率冷冻电镜(cryoEM)结构，并鉴定出m5C修饰赋予核糖体结构稳定性的多种机制。最后，我们还发现柯达热球菌(T. kodakarensis)中的Ψ修饰水平存在系统性诱导现象，并揭示该过程主要由单一温度诱导的小RNA(sRNA)所调控，该小RNA可指导前所未有的大量靶标位点形成假尿嘧啶修饰，其缺失会导致微生物在高温下生长缺陷。本研究的发现为源自生命之树的代表性物种的核糖体RNA修饰可塑性提供了全面且系统性的视角，解析了不同修饰在高温条件下对核糖体稳定性的贡献能力，并提出了一种能够前所未有地揭示健康与疾病状态下核糖体RNA表观转录组(epitranscriptome)的研究方法。