The Abundance of Viroid-Like RNA Obelisk-S.s in Streptococcus sanguinis SK36 May Suffice for Evolutionary Persistence

A new class of viroid-like RNAs, called Obelisks, was recently reported by Zheludev et al. (Cell 187:6521-6536.e6518, 2024). They found thousands of Obelisk sequences globally and identified a specific 1137 nt Obelisk, called Obelisk-S.s, in monoculture transcriptomes of Streptococcus sanguinis SK36, a commensal bacterium of the human oral microbiome. Here, we confirm that Obelisk-S.s is highly abundant in SK36, despite its absence from the SK36 genome (i.e., as DNA). In 11 out of 17 monoculture SK36 RNA-seq datasets examined, Obelisk-S.s is more abundant than any mRNA. Given its relative abundance, we hypothesized that multiple Obelisk-S.s variants could coexist within SK36. We found three Obelisk-S.s mutations at 5-10% allele frequency in some samples: a R162R synonymous mutation in one set of replicate transcriptomes, and an I48I synonymous mutation and an intergenic mutation in another set of replicate transcriptomes. A simple mathematical model shows how high Obelisk abundance can transiently stabilize intracellular Obelisk populations, and how extreme Obelisk abundances may stabilize intracellular Obelisk populations indefinitely. Evolution experiments with SK36 could test this theory and could shed light on how Obelisks function and evolve within their microbial hosts.