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Sandoz PA, Tremblay C, van der Goot FG, Frechin M. Image-based analysis of living mammalian cells using label-free 3D refractive index maps reveals new organelle dynamics and dry mass flux. PLoS Biol 2019; 17:e3000553. [PMID: 31856161 PMCID: PMC6922317 DOI: 10.1371/journal.pbio.3000553] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 11/15/2019] [Indexed: 12/22/2022] Open
Abstract
Holo-tomographic microscopy (HTM) is a label-free microscopy method reporting the fine changes of a cell's refractive indices (RIs) in three dimensions at high spatial and temporal resolution. By combining HTM with epifluorescence, we demonstrate that mammalian cellular organelles such as lipid droplets (LDs) and mitochondria show specific RI 3D patterns. To go further, we developed a computer-vision strategy using FIJI, CellProfiler3 (CP3), and custom code that allows us to use the fine images obtained by HTM in quantitative approaches. We could observe the shape and dry mass dynamics of LDs, endocytic structures, and entire cells' division that have so far, to the best of our knowledge, been out of reach. We finally took advantage of the capacity of HTM to capture the motion of many organelles at the same time to report a multiorganelle spinning phenomenon and study its dynamic properties using pattern matching and homography analysis. This work demonstrates that HTM gives access to an uncharted field of biological dynamics and describes a unique set of simple computer-vision strategies that can be broadly used to quantify HTM images.
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Affiliation(s)
- Patrick A. Sandoz
- Global Health Institute, Life Sciences Faculty, EPFL, Lausanne, Switzerland
| | - Christopher Tremblay
- Global Health Institute, Life Sciences Faculty, EPFL, Lausanne, Switzerland
- Nanolive SA, EPFL Innovation Park, Ecublens, Switzerland
| | - F. Gisou van der Goot
- Global Health Institute, Life Sciences Faculty, EPFL, Lausanne, Switzerland
- * E-mail: (GvdG); (MF)
| | - Mathieu Frechin
- Nanolive SA, EPFL Innovation Park, Ecublens, Switzerland
- * E-mail: (GvdG); (MF)
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Frechin M, Enkler L, Tetaud E, Laporte D, Senger B, Blancard C, Hammann P, Bader G, Clauder-Münster S, Steinmetz L, Martin R, di Rago JP, Becker H. Expression of Nuclear and Mitochondrial Genes Encoding ATP Synthase Is Synchronized by Disassembly of a Multisynthetase Complex. Mol Cell 2014; 56:763-76. [DOI: 10.1016/j.molcel.2014.10.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 09/04/2014] [Accepted: 10/16/2014] [Indexed: 10/24/2022]
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Araiso Y, Huot JL, Sekiguchi T, Frechin M, Fischer F, Enkler L, Senger B, Ishitani R, Becker HD, Nureki O. Crystal structure of Saccharomyces cerevisiae mitochondrial GatFAB reveals a novel subunit assembly in tRNA-dependent amidotransferases. Nucleic Acids Res 2014; 42:6052-63. [PMID: 24692665 PMCID: PMC4027206 DOI: 10.1093/nar/gku234] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Yeast mitochondrial Gln-mtRNAGln is synthesized by the transamidation of mischarged Glu-mtRNAGln by a non-canonical heterotrimeric tRNA-dependent amidotransferase (AdT). The GatA and GatB subunits of the yeast AdT (GatFAB) are well conserved among bacteria and eukaryota, but the GatF subunit is a fungi-specific ortholog of the GatC subunit found in all other known heterotrimeric AdTs (GatCAB). Here we report the crystal structure of yeast mitochondrial GatFAB at 2.0 Å resolution. The C-terminal region of GatF encircles the GatA–GatB interface in the same manner as GatC, but the N-terminal extension domain (NTD) of GatF forms several additional hydrophobic and hydrophilic interactions with GatA. NTD-deletion mutants displayed growth defects, but retained the ability to respire. Truncation of the NTD in purified mutants reduced glutaminase and transamidase activities when glutamine was used as the ammonia donor, but increased transamidase activity relative to the full-length enzyme when the donor was ammonium chloride. Our structure-based functional analyses suggest the NTD is a trans-acting scaffolding peptide for the GatA glutaminase active site. The positive surface charge and novel fold of the GatF–GatA interface, shown in this first crystal structure of an organellar AdT, stand in contrast with the more conventional, negatively charged bacterial AdTs described previously.
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Affiliation(s)
- Yuhei Araiso
- Unité Mixte de Recherche 7156 Génétique Moléculaire Génomique Microbiologie, Centre National de la Recherche Scientifique, Université de Strasbourg, F-67084 Strasbourg, France
| | - Jonathan L Huot
- Unité Mixte de Recherche 7156 Génétique Moléculaire Génomique Microbiologie, Centre National de la Recherche Scientifique, Université de Strasbourg, F-67084 Strasbourg, France
| | - Takuya Sekiguchi
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, 113-0033 Tokyo, Japan
| | - Mathieu Frechin
- Institute of Molecular Life Sciences, University of Zurich, CH-8057 Zurich, Switzerland
| | - Frédéric Fischer
- Unité Propre de Recherche Architecture et Réactivité de l'ARN, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, F-67084 Strasbourg, France
| | - Ludovic Enkler
- Unité Mixte de Recherche 7156 Génétique Moléculaire Génomique Microbiologie, Centre National de la Recherche Scientifique, Université de Strasbourg, F-67084 Strasbourg, France
| | - Bruno Senger
- Unité Mixte de Recherche 7156 Génétique Moléculaire Génomique Microbiologie, Centre National de la Recherche Scientifique, Université de Strasbourg, F-67084 Strasbourg, France
| | - Ryuichiro Ishitani
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, 113-0033 Tokyo, Japan
| | - Hubert D Becker
- Unité Mixte de Recherche 7156 Génétique Moléculaire Génomique Microbiologie, Centre National de la Recherche Scientifique, Université de Strasbourg, F-67084 Strasbourg, France
| | - Osamu Nureki
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, 113-0033 Tokyo, Japan
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Snijder B, Liberali P, Frechin M, Stoeger T, Pelkmans L. Predicting functional gene interactions with the hierarchical interaction score. Nat Methods 2013; 10:1089-92. [PMID: 24097268 DOI: 10.1038/nmeth.2655] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 08/06/2013] [Indexed: 12/18/2022]
Abstract
Systems biology aims to unravel the vast network of functional interactions that govern biological systems. To date, the inference of gene interactions from large-scale 'omics data is typically achieved using correlations. We present the hierarchical interaction score (HIS) and show that the HIS outperforms commonly used methods in the inference of functional interactions between genes measured in large-scale experiments, making it a valuable statistic for systems biology.
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Affiliation(s)
- Berend Snijder
- 1] Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland. [2]
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Frechin M, Kern D, Martin RP, Becker HD, Senger B. Arc1p: Anchoring, routing, coordinating. FEBS Lett 2009; 584:427-33. [DOI: 10.1016/j.febslet.2009.11.037] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2009] [Revised: 11/09/2009] [Accepted: 11/09/2009] [Indexed: 10/20/2022]
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Frechin M, Senger B, Brayé M, Kern D, Martin RP, Becker HD. Yeast mitochondrial Gln-tRNA(Gln) is generated by a GatFAB-mediated transamidation pathway involving Arc1p-controlled subcellular sorting of cytosolic GluRS. Genes Dev 2009; 23:1119-30. [PMID: 19417106 DOI: 10.1101/gad.518109] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
It is impossible to predict which pathway, direct glutaminylation of tRNA(Gln) or tRNA-dependent transamidation of glutamyl-tRNA(Gln), generates mitochondrial glutaminyl-tRNA(Gln) for protein synthesis in a given species. The report that yeast mitochondria import both cytosolic glutaminyl-tRNA synthetase and tRNA(Gln) has challenged the widespread use of the transamidation pathway in organelles. Here we demonstrate that yeast mitochondrial glutaminyl-tRNA(Gln) is in fact generated by a transamidation pathway involving a novel type of trimeric tRNA-dependent amidotransferase (AdT). More surprising is the fact that cytosolic glutamyl-tRNA synthetase ((c)ERS) is imported into mitochondria, where it constitutes the mitochondrial nondiscriminating ERS that generates the mitochondrial mischarged glutamyl-tRNA(Gln) substrate for the AdT. We show that dual localization of (c)ERS is controlled by binding to Arc1p, a tRNA nuclear export cofactor that behaves as a cytosolic anchoring platform for (c)ERS. Expression of Arc1p is down-regulated when yeast cells are switched from fermentation to respiratory metabolism, thus allowing increased import of (c)ERS to satisfy a higher demand of mitochondrial glutaminyl-tRNA(Gln) for mitochondrial protein synthesis. This novel strategy that enables a single protein to be localized in both the cytosol and mitochondria provides a new paradigm for regulation of the dynamic subcellular distribution of proteins between membrane-separated compartments.
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Affiliation(s)
- Mathieu Frechin
- UPR 9002, Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
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Abstract
Aminoacyl-tRNAs are generally formed by direct attachment of an amino acid to tRNAs by aminoacyl-tRNA synthetases, but glutaminyl-tRNA (Q-tRNA) is an exception to this rule. Glutaminyl-tRNA(Gln) (Q-tRNA(Q)) is formed by this direct pathway in the eukaryotic cytosol and in a small subset of bacteria, but is formed by an indirect transamidation pathway in most bacteria and archaea. To date it is almost impossible to predict what pathway generates organellar Q-tRNA(Q) in a given eukaryote. All eukaryotic genomes sequenced so far, display a single glutaminyl-tRNA synthetase (QRS) gene which is at least responsible for the cytosolic QRS activity, as well as a gene coding for a mitochondrial ortholog of the essential GatB subunit of the tRNA-dependent amidotransferase (AdT). Indeed, QRS activity was found in protozoan mitochondria while AdT activity was characterized in plant organelles. The pathway for Q-tRNA(Q) synthesis in yeast and mammals mitochondria is still questionable.
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Affiliation(s)
- Mathieu Frechin
- UPR Architecture et Réactivité de l'ARN, Université Louis Pasteur de Strasbourg, Strasbourg, France
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Wayoff M, Labaeye P, Frechin M. [Pre- and postoperative audionystagmographic correlations in otospongiosis]. Ann Otolaryngol Chir Cervicofac 1970; 87:65-76. [PMID: 5435040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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