{"doi":"10.1101/2025.09.03.673927","title":"Identification of Obelisk-like covalently closed circular RNA replicon in hot springs by double-stranded RNA sequencing and expansion of the diversity of the Obelisk superfamily","abstract":"Extensive metatranscriptome mining has recently vastly expanded the range of covalently closed circular (ccc) RNA replicons. A notable group of such replicons are Obelisks, cccRNAs of about 1 kilobase (kb) encoding a protein with a unique fold, Oblin-1, and detected in a broad variety of metatranscriptomes, in particular, those from the human gastrointestinal tract. We adopted Fragmented and primer-Ligated DsRNA Sequencing (FLDS) method to selectively sequence double-stranded (ds) RNAs, the replicative intermediates of RNA replicons, and to identify cccRNAs among the resulting sequences. From these data, we selected cccRNAs with predicted extensive intramolecular base-pairing, a hallmark of viroid-like elements. ch We employed FLDS to explore metatranscriptomes from acidic hot springs in Japan and discovered a distinct family of Obelisks probably associated with thermoacidophilic bacteria (Hot spring Obelisks, HsObs). The proteins encoded by HsObs, HsOblins, show no significant sequence similarity to previously identified Oblin-1 proteins, but are predicted to adopt a closely similar structure. A comprehensive search of metagenomes for Oblin-1 and HsOblin homologs substantially expanded this family of Obelisk-encoded proteins revealing several distinct subfamilies that share the same core fold. A cccRNA encoding an HsOblin homolog was also detected in a Yellowstone hot spring metatranscriptome. Apart from Oblin-1, some subfamilies of Obelisks were predicted to encode additional small proteins with simple alpha-helical folds.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2025,"id":555272,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":4,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9447,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":98682,"name":"Akihito Fukudome","orcid":"0000-0001-8924-1035","position":1,"is_corresponding":false},{"id":552369,"name":"Pascal Mutz","orcid":"0000-0002-0430-2095","position":2,"is_corresponding":false},{"id":1453562,"name":"Yosuke Matsushita","orcid":"0000-0002-1325-3125","position":3,"is_corresponding":false},{"id":1188592,"name":"Yoshihiro Takaki","orcid":"0000-0002-1247-4946","position":4,"is_corresponding":false},{"id":19121,"name":"Yosuke Nishimura","orcid":"0000-0002-8028-3228","position":5,"is_corresponding":false},{"id":484247,"name":"Sofia Medvedeva","orcid":"0000-0002-7841-0814","position":6,"is_corresponding":false},{"id":109878,"name":"Mart Krupovìč","orcid":"0000-0001-5486-0098","position":7,"is_corresponding":false},{"id":17837,"name":"Eugene V. Koonin","orcid":"0000-0003-3943-8299","position":8,"is_corresponding":false},{"id":814656,"name":"Takuro Nunoura","orcid":"0000-0003-2323-0880","position":9,"is_corresponding":false},{"id":1188589,"name":"Syun‐ichi Urayama","orcid":"0000-0001-5318-9212","position":0,"is_corresponding":true}],"reference_count":56,"raw_metadata":null,"created_at":"2026-07-19T02:54:59.329539Z","pmid":"40970131","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}