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| Auteurs principaux: | , , , , , , , , , |
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| Format: | Artículo científico |
| Langue: | en |
| Publié: |
bioRxiv : the preprint server for biology
2025
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| Accès en ligne: | https://pubmed.ncbi.nlm.nih.gov/40970131/ |
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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 Obelisk-like covalently closed circular RNA replicon in hot springs by double-stranded RNA sequencing and expansion of the 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 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. |
| format | Artículo científico |
| id | pubmed_40970131 |
| institution | PubMed |
| language | en |
| publishDate | 2025 |
| publisher | bioRxiv : the preprint server for biology |
| record_format | pubmed |
| spellingShingle | 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. Urayama, Syun-Ichi Fukudome, Akihito Mutz, Pascal Matsushita, Yosuke Takaki, Yoshihiro Nishimura, Yosuke Medvedeva, Sofia Krupovic, Mart Koonin, Eugene V Nunoura, Takuro 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. Urayama, Syun-Ichi Fukudome, Akihito Mutz, Pascal Matsushita, Yosuke Takaki, Yoshihiro Nishimura, Yosuke Medvedeva, Sofia Krupovic, Mart Koonin, Eugene V Nunoura, Takuro 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. |
| 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. |
| url | https://pubmed.ncbi.nlm.nih.gov/40970131/ |