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Romei M, Carpentier M, Chomilier J, Lecointre G. Origins and Functional Significance of Eukaryotic Protein Folds. J Mol Evol 2023; 91:854-864. [PMID: 38060007 DOI: 10.1007/s00239-023-10136-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 10/03/2023] [Indexed: 12/08/2023]
Abstract
Folds are the architecture and topology of a protein domain. Categories of folds are very few compared to the astronomical number of sequences. Eukaryotes have more protein folds than Archaea and Bacteria. These folds are of two types: shared with Archaea and/or Bacteria on one hand and specific to eukaryotic clades on the other hand. The first kind of folds is inherited from the first endosymbiosis and confirms the mixed origin of eukaryotes. In a dataset of 1073 folds whose presence or absence has been evidenced among 210 species equally distributed in the three super-kingdoms, we have identified 28 eukaryotic folds unambiguously inherited from Bacteria and 40 eukaryotic folds unambiguously inherited from Archaea. Compared to previous studies, the repartition of informational function is higher than expected for folds originated from Bacteria and as high as expected for folds inherited from Archaea. The second type of folds is specifically eukaryotic and associated with an increase of new folds within eukaryotes distributed in particular clades. Reconstructed ancestral states coupled with dating of each node on the tree of life provided fold appearance rates. The rate is on average twice higher within Eukaryota than within Bacteria or Archaea. The highest rates are found in the origins of eukaryotes, holozoans, metazoans, metazoans stricto sensu, and vertebrates: the roots of these clades correspond to bursts of fold evolution. We could correlate the functions of some of the fold synapomorphies within eukaryotes with significant evolutionary events. Among them, we find evidence for the rise of multicellularity, adaptive immune system, or virus folds which could be linked to an ecological shift made by tetrapods.
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Affiliation(s)
- Martin Romei
- Institut Systématique Evolution Biodiversité (ISYEB UMR 7205), Sorbonne Université, MNHN, CNRS, EPHE, UA, Paris, France
- IMPMC (UMR 7590), BiBiP, Sorbonne Université, CNRS, MNHN, Paris, France
| | - Mathilde Carpentier
- Institut Systématique Evolution Biodiversité (ISYEB UMR 7205), Sorbonne Université, MNHN, CNRS, EPHE, UA, Paris, France.
| | - Jacques Chomilier
- IMPMC (UMR 7590), BiBiP, Sorbonne Université, CNRS, MNHN, Paris, France
| | - Guillaume Lecointre
- Institut Systématique Evolution Biodiversité (ISYEB UMR 7205), Sorbonne Université, MNHN, CNRS, EPHE, UA, Paris, France
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Romei M, Sapriel G, Imbert P, Jamay T, Chomilier J, Lecointre G, Carpentier M. Protein folds as synapomorphies of the tree of life. Evolution 2022; 76:1706-1719. [PMID: 35765784 PMCID: PMC9541633 DOI: 10.1111/evo.14550] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 05/17/2022] [Accepted: 05/31/2022] [Indexed: 01/22/2023]
Abstract
Several studies showed that folds (topology of protein secondary structures) distribution in proteomes may be a global proxy to build phylogeny. Then, some folds should be synapomorphies (derived characters exclusively shared among taxa). However, previous studies used methods that did not allow synapomorphy identification, which requires congruence analysis of folds as individual characters. Here, we map SCOP folds onto a sample of 210 species across the tree of life (TOL). Congruence is assessed using retention index of each fold for the TOL, and principal component analysis for deeper branches. Using a bicluster mapping approach, we define synapomorphic blocks of folds (SBF) sharing similar presence/absence patterns. Among the 1232 folds, 20% are universally present in our TOL, whereas 54% are reliable synapomorphies. These results are similar with CATH and ECOD databases. Eukaryotes are characterized by a large number of them, and several SBFs clearly support nested eukaryotic clades (divergence times from 1100 to 380 mya). Although clearly separated, the three superkingdoms reveal a strong mosaic pattern. This pattern is consistent with the dual origin of eukaryotes and witness secondary endosymbiosis in their phothosynthetic clades. Our study unveils direct analysis of folds synapomorphies as key characters to unravel evolutionary history of species.
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Affiliation(s)
- Martin Romei
- Institut Systématique Evolution Biodiversité (ISYEB UMR 7205)Sorbonne Université, MNHN, CNRS, EPHE, UAParisFrance,IMPMC (UMR 7590), BiBiP, Sorbonne Université, CNRS, MNHNParisFrance
| | - Guillaume Sapriel
- Institut Systématique Evolution Biodiversité (ISYEB UMR 7205)Sorbonne Université, MNHN, CNRS, EPHE, UAParisFrance,UFR des sciences de la santéUniversité Versailles‐St‐QuentinVersaillesFrance
| | - Pierre Imbert
- Institut Systématique Evolution Biodiversité (ISYEB UMR 7205)Sorbonne Université, MNHN, CNRS, EPHE, UAParisFrance
| | - Théo Jamay
- Institut Systématique Evolution Biodiversité (ISYEB UMR 7205)Sorbonne Université, MNHN, CNRS, EPHE, UAParisFrance
| | | | - Guillaume Lecointre
- Institut Systématique Evolution Biodiversité (ISYEB UMR 7205)Sorbonne Université, MNHN, CNRS, EPHE, UAParisFrance
| | - Mathilde Carpentier
- Institut Systématique Evolution Biodiversité (ISYEB UMR 7205)Sorbonne Université, MNHN, CNRS, EPHE, UAParisFrance
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Summer S, Smirnova A, Gabriele A, Toth U, Fasemore AM, Förstner KU, Kuhn L, Chicher J, Hammann P, Mitulović G, Entelis N, Tarassov I, Rossmanith W, Smirnov A. YBEY is an essential biogenesis factor for mitochondrial ribosomes. Nucleic Acids Res 2020; 48:9762-9786. [PMID: 32182356 PMCID: PMC7515705 DOI: 10.1093/nar/gkaa148] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 02/24/2020] [Accepted: 02/26/2020] [Indexed: 12/11/2022] Open
Abstract
Ribosome biogenesis requires numerous trans-acting factors, some of which are deeply conserved. In Bacteria, the endoribonuclease YbeY is believed to be involved in 16S rRNA 3′-end processing and its loss was associated with ribosomal abnormalities. In Eukarya, YBEY appears to generally localize to mitochondria (or chloroplasts). Here we show that the deletion of human YBEY results in a severe respiratory deficiency and morphologically abnormal mitochondria as an apparent consequence of impaired mitochondrial translation. Reduced stability of 12S rRNA and the deficiency of several proteins of the small ribosomal subunit in YBEY knockout cells pointed towards a defect in mitochondrial ribosome biogenesis. The specific interaction of mitoribosomal protein uS11m with YBEY suggests that the latter helps to properly incorporate uS11m into the nascent small subunit in its late assembly stage. This scenario shows similarities with final stages of cytosolic ribosome biogenesis, and may represent a late checkpoint before the mitoribosome engages in translation.
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Affiliation(s)
- Sabrina Summer
- Center for Anatomy & Cell Biology, Medical University of Vienna, Vienna A-1090, Austria
| | - Anna Smirnova
- UMR7156 - Molecular Genetics, Genomics, Microbiology, University of Strasbourg, CNRS, Strasbourg F-67000, France
| | - Alessandro Gabriele
- UMR7156 - Molecular Genetics, Genomics, Microbiology, University of Strasbourg, CNRS, Strasbourg F-67000, France
| | - Ursula Toth
- Center for Anatomy & Cell Biology, Medical University of Vienna, Vienna A-1090, Austria
| | | | - Konrad U Förstner
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg 97080, Germany.,TH Köln - University of Applied Sciences, Faculty of Information Science and Communication Studies, Institute of Information Science, Cologne D-50678, Germany.,ZB MED - Information Centre for Life Sciences, Cologne D-50931, Germany
| | - Lauriane Kuhn
- Proteomics Platform Strasbourg-Esplanade, FRC1589, IBMC, CNRS, Strasbourg F-67000, France
| | - Johana Chicher
- Proteomics Platform Strasbourg-Esplanade, FRC1589, IBMC, CNRS, Strasbourg F-67000, France
| | - Philippe Hammann
- Proteomics Platform Strasbourg-Esplanade, FRC1589, IBMC, CNRS, Strasbourg F-67000, France
| | - Goran Mitulović
- Proteomics Core Facility, Clinical Department for Laboratory Medicine, Medical University of Vienna, Vienna A-1090, Austria
| | - Nina Entelis
- UMR7156 - Molecular Genetics, Genomics, Microbiology, University of Strasbourg, CNRS, Strasbourg F-67000, France
| | - Ivan Tarassov
- UMR7156 - Molecular Genetics, Genomics, Microbiology, University of Strasbourg, CNRS, Strasbourg F-67000, France
| | - Walter Rossmanith
- Center for Anatomy & Cell Biology, Medical University of Vienna, Vienna A-1090, Austria
| | - Alexandre Smirnov
- UMR7156 - Molecular Genetics, Genomics, Microbiology, University of Strasbourg, CNRS, Strasbourg F-67000, France
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Rabl J. BRCA1-A and BRISC: Multifunctional Molecular Machines for Ubiquitin Signaling. Biomolecules 2020; 10:biom10111503. [PMID: 33142801 PMCID: PMC7692841 DOI: 10.3390/biom10111503] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/26/2020] [Accepted: 10/28/2020] [Indexed: 12/12/2022] Open
Abstract
The K63-linkage specific deubiquitinase BRCC36 forms the core of two multi-subunit deubiquitination complexes: BRCA1-A and BRISC. BRCA1-A is recruited to DNA repair foci, edits ubiquitin signals on chromatin, and sequesters BRCA1 away from the site of damage, suppressing homologous recombination by limiting resection. BRISC forms a complex with metabolic enzyme SHMT2 and regulates the immune response, mitosis, and hematopoiesis. Almost two decades of research have revealed how BRCA1-A and BRISC use the same core of subunits to perform very distinct biological tasks.
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Affiliation(s)
- Julius Rabl
- Cryo-EM Knowledge Hub, ETH Zürich, Otto-Stern-Weg 3, HPM C51, 8093 Zürich, Switzerland
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Neveu E, Khalifeh D, Salamin N, Fasshauer D. Prototypic SNARE Proteins Are Encoded in the Genomes of Heimdallarchaeota, Potentially Bridging the Gap between the Prokaryotes and Eukaryotes. Curr Biol 2020; 30:2468-2480.e5. [PMID: 32442459 DOI: 10.1016/j.cub.2020.04.060] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 04/05/2020] [Accepted: 04/23/2020] [Indexed: 12/15/2022]
Abstract
A defining feature of eukaryotic cells is the presence of numerous membrane-bound organelles that subdivide the intracellular space into distinct compartments. How the eukaryotic cell acquired its internal complexity is still poorly understood. Material exchange among most organelles occurs via vesicles that bud off from a source and specifically fuse with a target compartment. Central players in the vesicle fusion process are the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins. These small tail-anchored (TA) membrane proteins zipper into elongated four-helix bundles that pull membranes together. SNARE proteins are highly conserved among eukaryotes but are thought to be absent in prokaryotes. Here, we identified SNARE-like factors in the genomes of uncultured organisms of Asgard archaea of the Heimdallarchaeota clade, which are thought to be the closest living relatives of eukaryotes. Biochemical experiments show that the archaeal SNARE-like proteins can interact with eukaryotic SNARE proteins. We did not detect SNAREs in α-proteobacteria, the closest relatives of mitochondria, but identified several genes encoding for SNARE proteins in γ-proteobacteria of the order Legionellales, pathogens that live inside eukaryotic cells. Very probably, their SNAREs stem from lateral gene transfer from eukaryotes. Together, this suggests that the diverse set of eukaryotic SNAREs evolved from an archaeal precursor. However, whether Heimdallarchaeota actually have a simplified endomembrane system will only be seen when we succeed studying these organisms under the microscope.
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Affiliation(s)
- Emilie Neveu
- Department of Fundamental Neurosciences, University of Lausanne, Rue du Bugnon 9, 1005 Lausanne, Switzerland; Department of Computational Biology, University of Lausanne, Génopode, 1015 Lausanne, Switzerland
| | - Dany Khalifeh
- Department of Fundamental Neurosciences, University of Lausanne, Rue du Bugnon 9, 1005 Lausanne, Switzerland; Department of Computational Biology, University of Lausanne, Génopode, 1015 Lausanne, Switzerland
| | - Nicolas Salamin
- Department of Computational Biology, University of Lausanne, Génopode, 1015 Lausanne, Switzerland
| | - Dirk Fasshauer
- Department of Fundamental Neurosciences, University of Lausanne, Rue du Bugnon 9, 1005 Lausanne, Switzerland; Department of Computational Biology, University of Lausanne, Génopode, 1015 Lausanne, Switzerland.
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