RNA obelisks represent a newly identified group of genetic elements, challenging established biological classifications. These circular RNA elements have recently emerged from extensive genomic analyses, marking a significant biological discovery. Their identification suggests a new class of life-like entities, previously unnoticed within diverse biological systems. This discovery prompts a reconsideration of the full spectrum of genetic diversity across Earth’s ecosystems.
Discovery and Basic Structure
RNA obelisks were first identified through advanced metagenomic sequencing techniques, which involve analyzing genetic material directly from environmental samples. This approach allowed researchers to uncover unknown sequences from diverse biological samples, including the human gut and oral cavities. A specialized bioinformatics tool called Viroid Nominator (VNom) was instrumental in their detection from Human Microbiome Project data, enabling a more sensitive search for novel RNA elements.
These elements are characterized by their small, circular ribonucleic acid (RNA) genomes, typically around 1,000 nucleotides. Their structure often forms a rod-like secondary conformation due to extensive internal base pairing. Unlike conventional viruses, RNA obelisks do not possess a protein capsid or outer shell, distinguishing them structurally from many known viral agents.
Distinguishing Features
RNA obelisks are distinguished by their unique genetic content, particularly their ability to encode a novel class of proteins known as “obulins.” These obulin proteins have no detectable sequence or structural similarities to any known proteins in existing biological databases. This lack of homology suggests a distinct evolutionary lineage, indicating that obelisks are not closely related to previously characterized viruses or viroids.
Unlike viroids, which are non-coding circular RNAs that primarily infect plants, obelisks carry open reading frames that translate into proteins. Despite their protein-coding capacity, their small size and absence of a protein coat differentiate them from typical RNA viruses. Some obelisks also contain mutated hammerhead ribozyme sites, suggesting they may possess self-splicing capabilities, a feature seen in some other RNA-based organisms.
Interactions with Host Cells
RNA obelisks have been detected across a broad spectrum of eukaryotic organisms, indicating their widespread presence. They are found in human microbiomes, including the gut and oral cavity, and in global environmental samples such as ocean waters. Their detection in both prokaryotic and eukaryotic fractions within oceanic environments highlights their broad distribution.
These elements rely on the cellular machinery of their hosts for replication, though precise mechanisms are still under investigation. For example, Obelisk-S.s is highly abundant in Streptococcus sanguinis SK36, a common bacterium in the human oral microbiome. This suggests certain bacteria can serve as replicative hosts. The encoded obulin proteins are hypothesized to play a role in their replication or to modulate host cellular functions.
Broader Biological Implications
The discovery of RNA obelisks expands the known diversity of genetic elements and prompts a re-evaluation of “life-like” entities. They potentially represent an unrecognized component of the virosphere, the collective genetic material of all viruses and virus-like agents. This finding offers new insights into the diversity and evolution of genetic elements, suggesting that many such entities may remain undiscovered.
Obelisks could potentially bridge gaps in understanding early life forms, especially concerning the origins of genetic molecules. Their presence in human microbiomes also raises questions about their potential roles in human health or disease, although this area remains largely speculative and requires further research. This discovery opens up new avenues for exploring fundamental biological processes, host-microbe interactions, and the vast, hidden RNA biosphere.