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Plazzi F, Le Cras Y, Formaggioni A, Passamonti M. Mitochondrially mediated RNA interference, a retrograde signaling system affecting nuclear gene expression. Heredity (Edinb) 2024; 132:156-161. [PMID: 37714959 PMCID: PMC10923801 DOI: 10.1038/s41437-023-00650-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/30/2023] [Accepted: 08/31/2023] [Indexed: 09/17/2023] Open
Abstract
Several functional classes of short noncoding RNAs are involved in manifold regulatory processes in eukaryotes, including, among the best characterized, miRNAs. One of the most intriguing regulatory networks in the eukaryotic cell is the mito-nuclear crosstalk: recently, miRNA-like elements of mitochondrial origin, called smithRNAs, were detected in a bivalve species, Ruditapes philippinarum. These RNA molecules originate in the organelle but were shown in vivo to regulate nuclear genes. Since miRNA genes evolve easily de novo with respect to protein-coding genes, in the present work we estimate the probability with which a newly arisen smithRNA finds a suitable target in the nuclear transcriptome. Simulations with transcriptomes of 12 bivalve species suggest that this probability is high and not species specific: one in a hundred million (1 × 10-8) if five mismatches between the smithRNA and the 3' mRNA are allowed, yet many more are allowed in animals. We propose that novel smithRNAs may easily evolve as exaptation of the pre-existing mitochondrial RNAs. In turn, the ability of evolving novel smithRNAs may have played a pivotal role in mito-nuclear interactions during animal evolution, including the intriguing possibility of acting as speciation trigger.
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Affiliation(s)
- Federico Plazzi
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi, 3 - 40126, Bologna, BO, Italy.
| | - Youn Le Cras
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi, 3 - 40126, Bologna, BO, Italy
- Magistère Européen de Génétique, Université Paris Cité, 85 Boulevard Saint Germain, 75006, Paris, Italy
| | - Alessandro Formaggioni
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi, 3 - 40126, Bologna, BO, Italy
| | - Marco Passamonti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi, 3 - 40126, Bologna, BO, Italy
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Bongiovanni TR, Latario CJ, Le Cras Y, Trus E, Robitaille S, Swartz K, Schmidtke D, Vincent M, Kosta A, Orth J, Stengel F, Pellarin R, Rocha EPC, Ross BD, Durand E. Assembly of a unique membrane complex in type VI secretion systems of Bacteroidota. Nat Commun 2024; 15:429. [PMID: 38200008 PMCID: PMC10781749 DOI: 10.1038/s41467-023-44426-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 12/13/2023] [Indexed: 01/12/2024] Open
Abstract
The type VI secretion system (T6SS) of Gram-negative bacteria inhibits competitor cells through contact-dependent translocation of toxic effector proteins. In Proteobacteria, the T6SS is anchored to the cell envelope through a megadalton-sized membrane complex (MC). However, the genomes of Bacteroidota with T6SSs appear to lack genes encoding homologs of canonical MC components. Here, we identify five genes in Bacteroides fragilis (tssNQOPR) that are essential for T6SS function and encode a Bacteroidota-specific MC. We purify this complex, reveal its dimensions using electron microscopy, and identify a protein-protein interaction network underlying the assembly of the MC including the stoichiometry of the five TssNQOPR components. Protein TssN mediates the connection between the Bacteroidota MC and the conserved baseplate. Although MC gene content and organization varies across the phylum Bacteroidota, no MC homologs are detected outside of T6SS loci, suggesting ancient co-option and functional convergence with the non-homologous MC of Pseudomonadota.
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Affiliation(s)
- Thibault R Bongiovanni
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 7255, Institut national de la santé et de la recherche médicale (INSERM), Marseille, France
- Laboratoire de Chimie Bactérienne (LCB), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 7255, Institut national de la santé et de la recherche médicale (INSERM), Marseille, France
| | - Casey J Latario
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
| | - Youn Le Cras
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Evan Trus
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
| | - Sophie Robitaille
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
| | - Kerry Swartz
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
| | - Danica Schmidtke
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
- Department of Microbiology, University of Washington, Seattle, WA, 98109, USA
| | - Maxence Vincent
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 7255, Institut national de la santé et de la recherche médicale (INSERM), Marseille, France
- Laboratoire de Chimie Bactérienne (LCB), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 7255, Institut national de la santé et de la recherche médicale (INSERM), Marseille, France
| | - Artemis Kosta
- Microscopy Core Facility, Institut de Microbiologie de la Méditerranée (IMM), FR3479, CNRS, Aix-Marseille University, Marseille, France
| | - Jan Orth
- Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Florian Stengel
- Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Riccardo Pellarin
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS & University of Lyon, 7 Passage du Vercors, 69007, Lyon, France
| | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Benjamin D Ross
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA.
- Department of Microbiology, University of Washington, Seattle, WA, 98109, USA.
| | - Eric Durand
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 7255, Institut national de la santé et de la recherche médicale (INSERM), Marseille, France.
- Laboratoire de Chimie Bactérienne (LCB), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 7255, Institut national de la santé et de la recherche médicale (INSERM), Marseille, France.
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Vogg MC, Ferenc J, Buzgariu WC, Perruchoud C, Sanchez PGL, Beccari L, Nuninger C, Le Cras Y, Delucinge-Vivier C, Papasaikas P, Vincent S, Galliot B, Tsiairis CD. The transcription factor Zic4 promotes tentacle formation and prevents epithelial transdifferentiation in Hydra. Sci Adv 2022; 8:eabo0694. [PMID: 36563144 PMCID: PMC9788771 DOI: 10.1126/sciadv.abo0694] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The molecular mechanisms that maintain cellular identities and prevent dedifferentiation or transdifferentiation remain mysterious. However, both processes are transiently used during animal regeneration. Therefore, organisms that regenerate their organs, appendages, or even their whole body offer a fruitful paradigm to investigate the regulation of cell fate stability. Here, we used Hydra as a model system and show that Zic4, whose expression is controlled by Wnt3/β-catenin signaling and the Sp5 transcription factor, plays a key role in tentacle formation and tentacle maintenance. Reducing Zic4 expression suffices to induce transdifferentiation of tentacle epithelial cells into foot epithelial cells. This switch requires the reentry of tentacle battery cells into the cell cycle without cell division and is accompanied by degeneration of nematocytes embedded in these cells. These results indicate that maintenance of cell fate by a Wnt-controlled mechanism is a key process both during homeostasis and during regeneration.
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Affiliation(s)
- Matthias Christian Vogg
- Department of Genetics and Evolution, Institute of Genetics and Genomics (iGE3), Faculty of Sciences, University of Geneva, 30 Quai Ernest Ansermet, Geneva 4 1211, Switzerland
| | - Jaroslav Ferenc
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, Basel 4058, Switzerland
- University of Basel, Petersplatz 1, Basel 4001, Switzerland
| | - Wanda Christa Buzgariu
- Department of Genetics and Evolution, Institute of Genetics and Genomics (iGE3), Faculty of Sciences, University of Geneva, 30 Quai Ernest Ansermet, Geneva 4 1211, Switzerland
| | - Chrystelle Perruchoud
- Department of Genetics and Evolution, Institute of Genetics and Genomics (iGE3), Faculty of Sciences, University of Geneva, 30 Quai Ernest Ansermet, Geneva 4 1211, Switzerland
| | - Paul Gerald Layague Sanchez
- Department of Genetics and Evolution, Institute of Genetics and Genomics (iGE3), Faculty of Sciences, University of Geneva, 30 Quai Ernest Ansermet, Geneva 4 1211, Switzerland
| | - Leonardo Beccari
- Institut NeuroMyoGène, CNRS UMR 5310, INSERM U1217, University Claude Bernard Lyon 1, Lyon, France
| | - Clara Nuninger
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, Basel 4058, Switzerland
- University of Basel, Petersplatz 1, Basel 4001, Switzerland
| | - Youn Le Cras
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, Basel 4058, Switzerland
| | - Céline Delucinge-Vivier
- iGE3 Genomics Platform, University of Geneva, 1 Rue Michel-Servet, Geneva 4 1211, Switzerland
| | - Panagiotis Papasaikas
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, Basel 4058, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel 4058, Switzerland
| | - Stéphane Vincent
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, 46 allée d’Italie, Lyon F-69364, France
| | - Brigitte Galliot
- Department of Genetics and Evolution, Institute of Genetics and Genomics (iGE3), Faculty of Sciences, University of Geneva, 30 Quai Ernest Ansermet, Geneva 4 1211, Switzerland
- Corresponding author. (B.G.); (C.D.T.)
| | - Charisios D. Tsiairis
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, Basel 4058, Switzerland
- Corresponding author. (B.G.); (C.D.T.)
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