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| Main Authors: | , , , , , , , , , |
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| Format: | Artículo científico |
| Language: | en |
| Published: |
Nature communications
2026
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| Subjects: | |
| Online Access: | https://pubmed.ncbi.nlm.nih.gov/42010269/ |
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| author | Urayama, Syun-Ichi Fukudome, Akihito Mutz, Pascal Matsushita, Yosuke Takaki, Yoshihiro Nishimura, Yosuke Medvedeva, Sofia Krupovic, Mart Koonin, Eugene V Nunoura, Takuro |
| author_facet | Urayama, Syun-Ichi Fukudome, Akihito Mutz, Pascal Matsushita, Yosuke Takaki, Yoshihiro Nishimura, Yosuke Medvedeva, Sofia Krupovic, Mart Koonin, Eugene V Nunoura, Takuro Urayama, Syun-Ichi Fukudome, Akihito Mutz, Pascal Matsushita, Yosuke Takaki, Yoshihiro Nishimura, Yosuke Medvedeva, Sofia Krupovic, Mart Koonin, Eugene V Nunoura, Takuro |
| collection | PubMed - marine biology |
| contents | Identification of hot spring Obelisk-like RNA replicons and expanded diversity of the Obelisk superfamily. Urayama, Syun-Ichi Fukudome, Akihito Mutz, Pascal Matsushita, Yosuke Takaki, Yoshihiro Nishimura, Yosuke Medvedeva, Sofia Krupovic, Mart Koonin, Eugene V Nunoura, Takuro Replicon Hot Springs RNA Nucleic Acid Conformation Viroids Japan Molecular Sequence Data Phylogeny Base Sequence RNA, Double-Stranded Recent extensive metatranscriptome mining vastly expanded the range of apparently covalently closed circular (ccc) RNA replicons. A notable family of such replicons is Obelisks, ~1 kilobase (kb) cccRNAs encoding a protein with a unique fold, Oblin-1, and detected in diverse metatranscriptomes. To identify potential cccRNAs in a sequence similarity-independent manner, we adopt the Fragmented and primer-Ligated DsRNA Sequencing (FLDS) method to selectively sequence double-stranded (ds) RNAs, replicative intermediates of RNA replicons. We focus on candidates with predicted extensive intramolecular base-pairing, a hallmark of viroid-like elements. Using FLDS, we explore metatranscriptomes from acidic hot springs in Japan and discover a distinct family of Obelisks apparently associated with thermoacidophilic bacteria (Hot spring Obelisks, HsObs). Despite lacking sequence similarity to known Oblins, HsObs share key features, including ~1 kb genome size, rod-like RNA secondary structure, and the predicted fold of the encoded protein, HsOblin. A comprehensive metatranscriptome search for Oblin-1 and HsOblin homologs expands Obelisk diversity about two-fold, revealing multiple subfamilies sharing the same core fold,. some of which are also predicted to encode additional small proteins with simple alpha-helical folds. These findings highlight Obelisks as widespread and overlooked components of microbial ecosystems, expanding understanding of viroid-like RNA replicon diversity and evolution. |
| format | Artículo científico |
| id | pubmed_42010269 |
| institution | PubMed |
| language | en |
| publishDate | 2026 |
| publisher | Nature communications |
| record_format | pubmed |
| spellingShingle | Identification of hot spring Obelisk-like RNA replicons and expanded diversity of the Obelisk superfamily. Urayama, Syun-Ichi Fukudome, Akihito Mutz, Pascal Matsushita, Yosuke Takaki, Yoshihiro Nishimura, Yosuke Medvedeva, Sofia Krupovic, Mart Koonin, Eugene V Nunoura, Takuro Replicon Hot Springs RNA Nucleic Acid Conformation Viroids Japan Molecular Sequence Data Phylogeny Base Sequence RNA, Double-Stranded Identification of hot spring Obelisk-like RNA replicons and expanded diversity of the Obelisk superfamily. Urayama, Syun-Ichi Fukudome, Akihito Mutz, Pascal Matsushita, Yosuke Takaki, Yoshihiro Nishimura, Yosuke Medvedeva, Sofia Krupovic, Mart Koonin, Eugene V Nunoura, Takuro Replicon Hot Springs RNA Nucleic Acid Conformation Viroids Japan Molecular Sequence Data Phylogeny Base Sequence RNA, Double-Stranded Recent extensive metatranscriptome mining vastly expanded the range of apparently covalently closed circular (ccc) RNA replicons. A notable family of such replicons is Obelisks, ~1 kilobase (kb) cccRNAs encoding a protein with a unique fold, Oblin-1, and detected in diverse metatranscriptomes. To identify potential cccRNAs in a sequence similarity-independent manner, we adopt the Fragmented and primer-Ligated DsRNA Sequencing (FLDS) method to selectively sequence double-stranded (ds) RNAs, replicative intermediates of RNA replicons. We focus on candidates with predicted extensive intramolecular base-pairing, a hallmark of viroid-like elements. Using FLDS, we explore metatranscriptomes from acidic hot springs in Japan and discover a distinct family of Obelisks apparently associated with thermoacidophilic bacteria (Hot spring Obelisks, HsObs). Despite lacking sequence similarity to known Oblins, HsObs share key features, including ~1 kb genome size, rod-like RNA secondary structure, and the predicted fold of the encoded protein, HsOblin. A comprehensive metatranscriptome search for Oblin-1 and HsOblin homologs expands Obelisk diversity about two-fold, revealing multiple subfamilies sharing the same core fold,. some of which are also predicted to encode additional small proteins with simple alpha-helical folds. These findings highlight Obelisks as widespread and overlooked components of microbial ecosystems, expanding understanding of viroid-like RNA replicon diversity and evolution. |
| title | Identification of hot spring Obelisk-like RNA replicons and expanded diversity of the Obelisk superfamily. |
| topic | Replicon Hot Springs RNA Nucleic Acid Conformation Viroids Japan Molecular Sequence Data Phylogeny Base Sequence RNA, Double-Stranded |
| url | https://pubmed.ncbi.nlm.nih.gov/42010269/ |