{"@context":{"@vocab":"https://cir.nii.ac.jp/schema/1.0/","rdfs":"http://www.w3.org/2000/01/rdf-schema#","dc":"http://purl.org/dc/elements/1.1/","dcterms":"http://purl.org/dc/terms/","foaf":"http://xmlns.com/foaf/0.1/","prism":"http://prismstandard.org/namespaces/basic/2.0/","cinii":"http://ci.nii.ac.jp/ns/1.0/","datacite":"https://schema.datacite.org/meta/kernel-4/","ndl":"http://ndl.go.jp/dcndl/terms/","jpcoar":"https://github.com/JPCOAR/schema/blob/master/2.0/"},"@id":"https://cir.nii.ac.jp/crid/1360865816792598528.json","@type":"Article","productIdentifier":[{"identifier":{"@type":"DOI","@value":"10.1101/2023.07.05.547881"}},{"identifier":{"@type":"URI","@value":"https://syndication.highwire.org/content/doi/10.1101/2023.07.05.547881"}}],"resourceType":"preprint","dc:title":[{"@value":"Missing-link fold reveals the evolutionary pathway between RNA polymerase and ribosomal proteins"}],"description":[{"type":"abstract","notation":[{"@value":"<jats:title>Abstract</jats:title>\n                <jats:p>Numerous molecular machines are required to drive the central dogma of molecular biology. However, the means by which such numerous proteins emerged in the early evolutionary stage of life remains enigmatic. Many of them possess small β-barrel folds with different topologies, represented by DPBB conserved in DNA and RNA polymerases, and RIFT, OB, and SH3 in ribosomal proteins. Here, we discovered that the previously reconstructed ancient DPBB sequence could also adopt a novel β-barrel fold named DZBB, which shares similarities with RIFT and OB. Indeed, DZBB could be transformed into them through simple engineering experiments. Furthermore, the OB designs could be converted into SH3 by circular-permutation. These results indicate that these β-barrels diversified quickly from a common ancestor at the beginning of the central dogma evolution.</jats:p>"}]}],"creator":[{"@id":"https://cir.nii.ac.jp/crid/1420564276160050048","@type":"Researcher","personIdentifier":[{"@type":"KAKEN_RESEARCHERS","@value":"10779820"},{"@type":"NRID","@value":"1000010779820"},{"@type":"NRID","@value":"9000274309460"},{"@type":"NRID","@value":"9000383215312"},{"@type":"RESEARCHMAP","@value":"https://researchmap.jp/sota_yagi"}],"foaf:name":[{"@value":"Sota Yagi"}]},{"@id":"https://cir.nii.ac.jp/crid/1380865816792598400","@type":"Researcher","foaf:name":[{"@value":"Shunsuke Tagami"}]}],"publication":{"dc:publisher":[{"@value":"openRxiv"}],"prism:publicationDate":"2023-07-05"},"reviewed":"false","dcterms:accessRights":"http://purl.org/coar/access_right/c_abf2","url":[{"@id":"https://syndication.highwire.org/content/doi/10.1101/2023.07.05.547881"}],"createdAt":"2023-07-06","modifiedAt":"2026-01-15","project":[{"@id":"https://cir.nii.ac.jp/crid/1040848250658070272","@type":"Project","projectIdentifier":[{"@type":"KAKEN","@value":"20K15854"},{"@type":"JGN","@value":"JP20K15854"},{"@type":"URI","@value":"https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-20K15854/"}],"notation":[{"@language":"ja","@value":"単純なペプチドから汎用的な祖先タンパク質フォールドへの進化"},{"@language":"en","@value":"Protein evolution from simple peptide to versatile protein fold"}]}],"relatedProduct":[{"@id":"https://cir.nii.ac.jp/crid/1360011144908720640","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"The three-dimensional structure of the RNA-binding domain of ribosomal protein L2; a protein at the peptidyl transferase center of the ribosome"}]},{"@id":"https://cir.nii.ac.jp/crid/1360013171662116096","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Common Evolutionary Origin of Swapped-Hairpin and Double-Psi β Barrels"}]},{"@id":"https://cir.nii.ac.jp/crid/1360014417024915584","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Functional evolution of two subtly different (similar) folds"}]},{"@id":"https://cir.nii.ac.jp/crid/1360016866458571520","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Dali server: structural unification of protein families"}]},{"@id":"https://cir.nii.ac.jp/crid/1360021396345545984","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Recreating ancient metabolic pathways before enzymes"}]},{"@id":"https://cir.nii.ac.jp/crid/1360021396526016896","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Fold Evolution before LUCA: Common Ancestry of SH3 Domains and OB Domains"}]},{"@id":"https://cir.nii.ac.jp/crid/1360021396526624640","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Sources of Nitrogen-, Sulfur-, and Phosphorus-Containing Feedstocks for Prebiotic Chemistry in the Planetary Environment"}]},{"@id":"https://cir.nii.ac.jp/crid/1360292274168292992","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Highly accurate protein structure prediction with AlphaFold"}]},{"@id":"https://cir.nii.ac.jp/crid/1360292620540017920","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Shared active site architecture between archaeal PolD and multi-subunit RNA polymerases revealed by X-ray crystallography"}]},{"@id":"https://cir.nii.ac.jp/crid/1360302867630822016","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Creative destruction: New protein folds from old"}]},{"@id":"https://cir.nii.ac.jp/crid/1360302867630979840","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"RNA binding in an Sm core domain: X-ray structure and functional analysis of an archaeal Sm protein complex"}]},{"@id":"https://cir.nii.ac.jp/crid/1360302868283150080","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Unfolding the Mysteries of Protein Metamorphosis"}]},{"@id":"https://cir.nii.ac.jp/crid/1360302868284122624","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Protein Assistants of Small Ribosomal Subunit Biogenesis in Bacteria"}]},{"@id":"https://cir.nii.ac.jp/crid/1360574093482827648","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"RNA binding strategies of ribosomal proteins"}]},{"@id":"https://cir.nii.ac.jp/crid/1360855570245798656","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Molecular Evolution of Multisubunit RNA Polymerases: Structural Analysis"}]},{"@id":"https://cir.nii.ac.jp/crid/1360857593678721408","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Seven Amino Acid Types Suffice to Create the Core Fold of RNA Polymerase"}]},{"@id":"https://cir.nii.ac.jp/crid/1360857596536484992","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Linked cycles of oxidative decarboxylation of glyoxylate as protometabolic analogs of the citric acid cycle"}]},{"@id":"https://cir.nii.ac.jp/crid/1360861291391561600","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Prebiotic photoredox synthesis from carbon dioxide and sulfite"}]},{"@id":"https://cir.nii.ac.jp/crid/1360861712130772096","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Root of the Tree: The Significance, Evolution, and Origins of the Ribosome"}]},{"@id":"https://cir.nii.ac.jp/crid/1361137045544910208","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"ECOD: An Evolutionary Classification of Protein Domains"}]},{"@id":"https://cir.nii.ac.jp/crid/1361137045925550464","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Cradle-loop barrels and the concept of metafolds in protein classification by natural descent"}]},{"@id":"https://cir.nii.ac.jp/crid/1361137046124763264","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"A model for genesis of transcription systems"}]},{"@id":"https://cir.nii.ac.jp/crid/1361699995106192512","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Metamorphic proteins mediate evolutionary transitions of structure"}]},{"@id":"https://cir.nii.ac.jp/crid/1361699996117324800","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Archaeal chromatin and transcription"}]},{"@id":"https://cir.nii.ac.jp/crid/1362262943328267776","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"SCOPe: Structural Classification of Proteins—extended, integrating SCOP and ASTRAL data and classification of new structures"}]},{"@id":"https://cir.nii.ac.jp/crid/1362544419848694272","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"SCOP2 prototype: a new approach to protein structure mining"}]},{"@id":"https://cir.nii.ac.jp/crid/1363107368823145344","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Control over overall shape and size in de novo designed proteins"}]},{"@id":"https://cir.nii.ac.jp/crid/1363388845485560832","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Evolutionary Origins of Two-Barrel RNA Polymerases and Site-Specific Transcription Initiation"}]},{"@id":"https://cir.nii.ac.jp/crid/1363670320952285440","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Archaeal Genome Guardians Give Insights into Eukaryotic DNA Replication and Damage Response Proteins"}]},{"@id":"https://cir.nii.ac.jp/crid/1363951793958757632","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Nucleic Acid Recognition by OB-Fold Proteins"}]},{"@id":"https://cir.nii.ac.jp/crid/1364233268159685376","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"CATH: expanding the horizons of structure-based functional annotations for genome sequences"}]},{"@id":"https://cir.nii.ac.jp/crid/1370865816792598403","@type":"Product","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Why we are made of proteins and nucleic acids: Structural biology views on extraterrestrial life"}]}],"dataSourceIdentifier":[{"@type":"CROSSREF","@value":"10.1101/2023.07.05.547881"},{"@type":"KAKEN","@value":"PRODUCT-25050350"}]}