Unmasking the Obelisk: A New Enigma in the Microbial World
- Ray Sullivan
- Jul 18
- 3 min read
Imagine a mysterious genetic element, smaller than viruses, yet incredibly abundant within its host, even though it's not part of the host's own genome. Obelisks are a newly discovered class of viroid-like RNAs that are changing our understanding of microbial life. A recent study authored by Rohan Maddamsetti, newly appointed assistant professor in the Department of Biochemistry & Microbiology, Rutgers, delves deeper into one such Obelisk. Obelisk-S.s, is found within Streptococcus sanguinis SK36, a common bacterium in the human oral microbiome.
The journey to uncover Obelisks began with Zheludev et al. (2024), who first reported these approximately 1000 nucleotide-long RNAs that fold into hairpin structures and encode one or two proteins called Oblins, whose functions remain unknown. They found thousands of Obelisk sequences globally, including Obelisk-S.s in Streptococcus sanguinis SK36 transcriptomes.
Maddamsetti and his former postdoc advisor, Lingchong You at Duke University, set out to confirm these observations using independent data. And confirm them they did! A crucial finding is that Obelisk-S.s is highly abundant in S. sanguinis SK36 transcriptomes despite being absent from the SK36 genome. This means Obelisk-S.s exists as an intracellular population of small, viroid-like RNAs within the SK36 cells. Researchers used various bioinformatic tools, including NCBI BLAST and resequencing data, and found no significant similarity or mapped reads to Obelisk-S.s in the SK36 genomic data. This reinforces previous experimental confirmation via DNA PCR.
On the other hand, analyzing 17 independent SK36 RNA-seq datasets revealed the astounding abundance of Obelisk-S.s in the transcriptome. In 11 out of 17 NCBI SRA datasets, Obelisk-S.s was more abundant than any mRNA, ranking as the top RNA among 2271 protein-coding genes and Obelisk-S.s itself. Even in the remaining datasets, it ranked no lower than 16th. Furthermore, despite Obelisk-S.s being less than 0.1% the size of the SK36 genome, at least 1% of all RNA-seq reads consistently mapped to Obelisk-S.s across all samples. This extreme relative abundance suggests Obelisk-S.s exists at very high copy numbers within SK36 cells.
This begs the question: how do these Obelisks persist without being encoded in the host genome, especially given they might even impose a fitness cost? The study explored this using a straightforward mathematical model. The model proposes that high Obelisk abundance can transiently stabilize intracellular Obelisk populations, even if they offer no fitness benefit to the host. The core idea is that a large number of Obelisks reduces the probability of a daughter cell losing all Obelisks during cell division. The model even suggests that extreme copy numbers, around 1100 Obelisks per cell, could theoretically stabilize these populations indefinitely because the chance of generating an Obelisk-free cell becomes negligible.
While the model offers a compelling explanation, many mysteries remain. The exact function of Obelisks and their encoded Oblins is still unknown. It's unclear if the low-frequency polymorphisms observed in Obelisk-S.s have any functional significance or are driven by selection. Although Obelisk-S.s appears to impose a negligible fitness burden in replete conditions, alternative mechanisms like encoding beneficial functions or post-segregational killing systems (similar to those stabilizing plasmids) could also contribute to their persistence. The possibility of horizontal gene transfer, perhaps via extracellular membrane vesicles produced by S. sanguinis, is another intriguing avenue for their spread and persistence.
This research highlights the fascinating complexity of the microbial world and opens up exciting new frontiers in understanding viroid-like RNAs, their evolutionary dynamics, and their potential interactions within their hosts.
Maddamsetti R, You L. The Abundance of Viroid-Like RNA Obelisk-S.s in Streptococcus sanguinis SK36 May Suffice for Evolutionary Persistence. J Mol Evol. 2025 Jun;93(3):370-378. doi: 10.1007/s00239-025-10250-y. Epub 2025 May 9. PMID: 40346363; PMCID: PMC12198308.