1
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Gaschignard G, Millet M, Bruley A, Benzerara K, Dezi M, Skouri-Panet F, Duprat E, Callebaut I. AlphaFold2-guided description of CoBaHMA, a novel family of bacterial domains within the heavy-metal-associated superfamily. Proteins 2024; 92:776-794. [PMID: 38258321 DOI: 10.1002/prot.26668] [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: 09/28/2023] [Revised: 12/22/2023] [Accepted: 01/01/2024] [Indexed: 01/24/2024]
Abstract
Three-dimensional (3D) structure information, now available at the proteome scale, may facilitate the detection of remote evolutionary relationships in protein superfamilies. Here, we illustrate this with the identification of a novel family of protein domains related to the ferredoxin-like superfold, by combining (i) transitive sequence similarity searches, (ii) clustering approaches, and (iii) the use of AlphaFold2 3D structure models. Domains of this family were initially identified in relation with the intracellular biomineralization of calcium carbonates by Cyanobacteria. They are part of the large heavy-metal-associated (HMA) superfamily, departing from the latter by specific sequence and structural features. In particular, most of them share conserved basic amino acids (hence their name CoBaHMA for Conserved Basic residues HMA), forming a positively charged surface, which is likely to interact with anionic partners. CoBaHMA domains are found in diverse modular organizations in bacteria, existing in the form of monodomain proteins or as part of larger proteins, some of which are membrane proteins involved in transport or lipid metabolism. This suggests that the CoBaHMA domains may exert a regulatory function, involving interactions with anionic lipids. This hypothesis might have a particular resonance in the context of the compartmentalization observed for cyanobacterial intracellular calcium carbonates.
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Affiliation(s)
- Geoffroy Gaschignard
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Maxime Millet
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Apolline Bruley
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Karim Benzerara
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Manuela Dezi
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Feriel Skouri-Panet
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Elodie Duprat
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Isabelle Callebaut
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
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2
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Bruley A, Bitard-Feildel T, Callebaut I, Duprat E. A sequence-based foldability score combined with AlphaFold2 predictions to disentangle the protein order/disorder continuum. Proteins 2023; 91:466-484. [PMID: 36306150 DOI: 10.1002/prot.26441] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/14/2022] [Accepted: 10/18/2022] [Indexed: 11/11/2022]
Abstract
Order and disorder govern protein functions, but there is a great diversity in disorder, from regions that are-and stay-fully disordered to conditional order. This diversity is still difficult to decipher even though it is encoded in the amino acid sequences. Here, we developed an analytic Python package, named pyHCA, to estimate the foldability of a protein segment from the only information of its amino acid sequence and based on a measure of its density in regular secondary structures associated with hydrophobic clusters, as defined by the hydrophobic cluster analysis (HCA) approach. The tool was designed by optimizing the separation between foldable segments from databases of disorder (DisProt) and order (SCOPe [soluble domains] and OPM [transmembrane domains]). It allows to specify the ratio between order, embodied by regular secondary structures (either participating in the hydrophobic core of well-folded 3D structures or conditionally formed in intrinsically disordered regions) and disorder. We illustrated the relevance of pyHCA with several examples and applied it to the sequences of the proteomes of 21 species ranging from prokaryotes and archaea to unicellular and multicellular eukaryotes, for which structure models are provided in the AlphaFold protein structure database. Cases of low-confidence scores related to disorder were distinguished from those of sequences that we identified as foldable but are still excluded from accurate modeling by AlphaFold2 due to a lack of sequence homologs or to compositional biases. Overall, our approach is complementary to AlphaFold2, providing guides to map structural innovations through evolutionary processes, at proteome and gene scales.
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Affiliation(s)
- Apolline Bruley
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Tristan Bitard-Feildel
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Isabelle Callebaut
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Elodie Duprat
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
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3
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Gaëtan J, Halary S, Millet M, Bernard C, Duval C, Hamlaoui S, Hecquet A, Gugger M, Marie B, Mehta N, Moreira D, Skouri-Panet F, Travert C, Duprat E, Leloup J, Benzerara K. Widespread formation of intracellular calcium carbonates by the bloom-forming cyanobacterium Microcystis. Environ Microbiol 2023; 25:751-765. [PMID: 36550062 DOI: 10.1111/1462-2920.16322] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
The formation of intracellular amorphous calcium carbonates (iACC) has been recently observed in a few cultured strains of Microcystis, a potentially toxic bloom-forming cyanobacterium found worldwide in freshwater ecosystems. If iACC-forming Microcystis are abundant within blooms, they may represent a significant amount of particulate Ca. Here, we investigate the significance of iACC biomineralization by Microcystis. First, the presence of iACC-forming Microcystis cells has been detected in several eutrophic lakes, indicating that this phenomenon occurs under environmental conditions. Second, some genotypic (presence/absence of ccyA, a marker gene of iACC biomineralization) and phenotypic (presence/absence of iACC) diversity have been detected within a collection of strains isolated from one single lake. This illustrates that this trait is frequent but also variable within Microcystis even at a single locality. Finally, one-third of publicly available genomes of Microcystis were shown to contain the ccyA gene, revealing a wide geographic and phylogenetic distribution within the genus. Overall, the present work shows that the formation of iACC by Microcystis is common under environmental conditions. While its biological function remains undetermined, this process should be further considered regarding the biology of Microcystis and implications on the Ca geochemical cycle in freshwater environments.
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Affiliation(s)
- Juliette Gaëtan
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS-SU-MNHN 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
- Sorbonne Université, UMR 7618 CNRS-INRA-IRD-Paris 7-UPEC, Institut d'Ecologie et des Sciences de l'Environnement de Paris (iEES-Paris), Paris, France
| | - Sébastien Halary
- Muséum National d'Histoire Naturelle, UMR 7245 CNRS-MNHN, Molécules de Communication et Adaptation des Microorganismes, Paris, France
| | - Maxime Millet
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS-SU-MNHN 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - Cécile Bernard
- Muséum National d'Histoire Naturelle, UMR 7245 CNRS-MNHN, Molécules de Communication et Adaptation des Microorganismes, Paris, France
| | - Charlotte Duval
- Muséum National d'Histoire Naturelle, UMR 7245 CNRS-MNHN, Molécules de Communication et Adaptation des Microorganismes, Paris, France
| | - Sahima Hamlaoui
- Muséum National d'Histoire Naturelle, UMR 7245 CNRS-MNHN, Molécules de Communication et Adaptation des Microorganismes, Paris, France
| | - Amandine Hecquet
- Sorbonne Université, UMR 7618 CNRS-INRA-IRD-Paris 7-UPEC, Institut d'Ecologie et des Sciences de l'Environnement de Paris (iEES-Paris), Paris, France
| | - Muriel Gugger
- Institut Pasteur, Université Paris Cité, Collection of Cyanobacteria, Paris, France
| | - Benjamin Marie
- Muséum National d'Histoire Naturelle, UMR 7245 CNRS-MNHN, Molécules de Communication et Adaptation des Microorganismes, Paris, France
| | - Neha Mehta
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS-SU-MNHN 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - David Moreira
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Fériel Skouri-Panet
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS-SU-MNHN 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - Cynthia Travert
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS-SU-MNHN 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - Elodie Duprat
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS-SU-MNHN 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - Julie Leloup
- Sorbonne Université, UMR 7618 CNRS-INRA-IRD-Paris 7-UPEC, Institut d'Ecologie et des Sciences de l'Environnement de Paris (iEES-Paris), Paris, France
| | - Karim Benzerara
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS-SU-MNHN 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
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Benzerara K, Duprat E, Tristan BF, Géraldine C, Corinne CC, Franck C, Manuela D, Issa DS, Geoffroy G, Sigrid G, Muriel G, Purificación LG, Maxime M, Fériel SP, David M, Isabelle C. A new gene family diagnostic for intracellular biomineralization of amorphous Ca-carbonates by cyanobacteria. Genome Biol Evol 2022; 14:6526398. [PMID: 35143662 PMCID: PMC8890360 DOI: 10.1093/gbe/evac026] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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] [Accepted: 01/29/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
Cyanobacteria have massively contributed to carbonate deposition over the geological history. They are traditionally thought to biomineralize CaCO3 extracellularly as an indirect byproduct of photosynthesis. However, the recent discovery of freshwater cyanobacteria forming intracellular amorphous calcium carbonates (iACC) challenges this view. Despite the geochemical interest of such a biomineralization process, its molecular mechanisms and evolutionary history remain elusive. Here, using comparative genomics, we identify a new gene (ccyA) and protein family (calcyanin) possibly associated with cyanobacterial iACC biomineralization. Proteins of the calcyanin family are composed of a conserved C-terminal domain, which likely adopts an original fold, and a variable N-terminal domain whose structure allows differentiating 4 major types among the 35 known calcyanin homologs. Calcyanin lacks detectable full-length homologs with known function. The overexpression of ccyA in iACC-lacking cyanobacteria resulted in an increased intracellular Ca content. Moreover, ccyA presence was correlated and/or co-localized with genes involved in Ca or HCO3- transport and homeostasis, supporting the hypothesis of a functional role of calcyanin in iACC biomineralization. Whatever its function, ccyA appears as diagnostic of intracellular calcification in cyanobacteria. By searching for ccyA in publicly available genomes, we identified 13 additional cyanobacterial strains forming iACC, as confirmed by microscopy. This extends our knowledge about the phylogenetic and environmental distribution of cyanobacterial iACC biomineralization, especially with the detection of multicellular genera as well as a marine species. Moreover, ccyA was probably present in ancient cyanobacteria, with independent losses in various lineages that resulted in a broad but patchy distribution across modern cyanobacteria.
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Affiliation(s)
- Karim Benzerara
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 4 Place Jussieu, 75005 Paris, France
| | - Elodie Duprat
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 4 Place Jussieu, 75005 Paris, France
| | - Bitard-Feildel Tristan
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 4 Place Jussieu, 75005 Paris, France
| | - Caumes Géraldine
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 4 Place Jussieu, 75005 Paris, France
| | - Cassier-Chauvat Corinne
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Chauvat Franck
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Dezi Manuela
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 4 Place Jussieu, 75005 Paris, France
| | - Diop Seydina Issa
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 4 Place Jussieu, 75005 Paris, France
| | - Gaschignard Geoffroy
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 4 Place Jussieu, 75005 Paris, France
| | - Görgen Sigrid
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 4 Place Jussieu, 75005 Paris, France
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Gugger Muriel
- Institut Pasteur, Université de Paris, Collection of Cyanobacteria, F-75015 Paris, France
| | - López-García Purificación
- Unité d’Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Millet Maxime
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 4 Place Jussieu, 75005 Paris, France
| | - Skouri-Panet Fériel
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 4 Place Jussieu, 75005 Paris, France
| | - Moreira David
- Unité d’Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Callebaut Isabelle
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 4 Place Jussieu, 75005 Paris, France
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5
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Busigny V, Mathon FP, Jézéquel D, Bidaud CC, Viollier E, Bardoux G, Bourrand JJ, Benzerara K, Duprat E, Menguy N, Monteil CL, Lefevre CT. Mass collection of magnetotactic bacteria from the permanently stratified ferruginous Lake Pavin, France. Environ Microbiol 2021; 24:721-736. [PMID: 33687779 DOI: 10.1111/1462-2920.15458] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/04/2021] [Accepted: 03/07/2021] [Indexed: 01/16/2023]
Abstract
Obtaining high biomass yields of specific microorganisms for culture-independent approaches is a challenge faced by scientists studying organism's recalcitrant to laboratory conditions and culture. This difficulty is highly decreased when studying magnetotactic bacteria (MTB) since their unique behaviour allows their enrichment and purification from other microorganisms present in aquatic environments. Here, we use Lake Pavin, a permanently stratified lake in the French Massif Central, as a natural laboratory to optimize collection and concentration of MTB that thrive in the water column and sediments. A method is presented to separate MTB from highly abundant abiotic magnetic particles in the sediment of this crater lake. For the water column, different sampling approaches are compared such as in situ collection using a Niskin bottle and online pumping. By monitoring several physicochemical parameters of the water column, we identify the ecological niche where MTB live. Then, by focusing our sampling at the peak of MTB abundance, we show that the online pumping system is the most efficient for fast recovering of large volumes of water at a high spatial resolution, which is necessary considering the sharp physicochemical gradients observed in the water column. Taking advantage of aerotactic and magnetic MTB properties, we present an efficient method for MTB concentration from large volumes of water. Our methodology represents a first step for further multidisciplinary investigations of the diversity, metagenomic and ecology of MTB populations in Lake Pavin and elsewhere, as well as chemical and isotopic analyses of their magnetosomes.
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Affiliation(s)
- Vincent Busigny
- Université de Paris, Institut de Physique du Globe de Paris, CNRS, Paris, F-75005, France.,Institut Universitaire de France, Paris, 75005, France
| | - François P Mathon
- Université de Paris, Institut de Physique du Globe de Paris, CNRS, Paris, F-75005, France.,Aix-Marseille University, CNRS, CEA, UMR7265 Institute of Biosciences and Biotechnologies of Aix-Marseille, CEA Cadarache, Saint-Paul-lez-Durance, F-13108, France
| | - Didier Jézéquel
- Université de Paris, Institut de Physique du Globe de Paris, CNRS, Paris, F-75005, France.,INRAE & Université Savoie Mont Blanc, UMR CARRTEL, Thonon-les-Bains, 74200, France
| | - Cécile C Bidaud
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - Eric Viollier
- Université de Paris, Institut de Physique du Globe de Paris, CNRS, Paris, F-75005, France
| | - Gérard Bardoux
- Université de Paris, Institut de Physique du Globe de Paris, CNRS, Paris, F-75005, France
| | - Jean-Jacques Bourrand
- Université de Paris, Institut de Physique du Globe de Paris, CNRS, Paris, F-75005, France
| | - Karim Benzerara
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - Elodie Duprat
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - Nicolas Menguy
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - Caroline L Monteil
- Aix-Marseille University, CNRS, CEA, UMR7265 Institute of Biosciences and Biotechnologies of Aix-Marseille, CEA Cadarache, Saint-Paul-lez-Durance, F-13108, France
| | - Christopher T Lefevre
- Aix-Marseille University, CNRS, CEA, UMR7265 Institute of Biosciences and Biotechnologies of Aix-Marseille, CEA Cadarache, Saint-Paul-lez-Durance, F-13108, France
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6
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Delestrain C, Aissat A, Simon S, Tarze A, Duprat E, Nattes E, Costes B, Delattre V, Finet S, Fanen P, Epaud R. Methylprednisolone pulse treatment improves ProSP-C trafficking in twins with SFTPC mutation: An isoform story? Br J Clin Pharmacol 2021; 87:2361-2373. [PMID: 33179299 DOI: 10.1111/bcp.14645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/29/2020] [Accepted: 10/20/2020] [Indexed: 11/28/2022] Open
Abstract
Mutations in the gene encoding surfactant protein C (SP-C) cause interstitial lung disease (ILD), and glucocorticosteroid (GC) treatment is the most recognized therapy in children. We aimed to decipher the mechanisms behind successful GC treatment in twins carrying a BRICHOS c.566G > A (p.Cys189Tyr) mutation in the SP-C gene (SFTPC). METHODS: The twins underwent bronchoscopy before and after GC treatment and immunoblotting analysis of SP-C proprotein (proSP-C) and SP-C mature in bronchoalveolar fluid (BALF). Total RNA was extracted and analysed using quantitative real-time PCR assays. In A549 cells, the processing of mutated protein C189Y was studied by immunofluorescence and immunoblotting after heterologous expression of eukaryotic vectors containing wild type or C189Y mutant cDNA. RESULTS: Before treatment, BALF analysis identified an alteration of the proSP-C maturation process. Functional study of C189Y mutation in alveolar A549 cells showed that pro-SP-CC189Y was retained within the endoplasmic reticulum together with ABCA3. After 5 months of GC treatment with clinical benefit, the BALF analysis showed an improvement of proSP-C processing. SFTPC mRNA analysis in twins revealed a decrease in the expression of total SFTPC mRNA and a change in its splicing, leading to the expression of a second shorter proSP-C isoform. In A549 cells, the processing and the stability of this shorter wild-type proSP-C isoform was similar to that of the longer isoform, but the half-life of the mutated shorter isoform was decreased. These results suggest a direct effect of GC on proSP-C metabolism through reducing the SFTPC mRNA level and favouring the expression of a less stable protein isoform.
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Affiliation(s)
- Céline Delestrain
- Université Paris Est Creteil, INSERM, IMRB, F-94010 Creteil, France.,Centre Hospitalier Intercommunal de Créteil, Service de Pédiatrie Générale, Créteil, 94000, France.,FHU SENEC, Créteil, France
| | - Abdel Aissat
- Université Paris Est Creteil, INSERM, IMRB, F-94010 Creteil, France.,FHU SENEC, Créteil, France.,AP-HP, Hôpital Henri Mondor, Pôle de Biologie-Pathologie, Département de Génétique, Créteil, 94000, France
| | - Stéphanie Simon
- Université Paris Est Creteil, INSERM, IMRB, F-94010 Creteil, France
| | - Agathe Tarze
- Université Paris Est Creteil, INSERM, IMRB, F-94010 Creteil, France
| | - Elodie Duprat
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, CNRS, Sorbonne Université, Muséum National d'Histoire Naturelle, Paris, France
| | - Elodie Nattes
- Université Paris Est Creteil, INSERM, IMRB, F-94010 Creteil, France.,Centre Hospitalier Intercommunal de Créteil, Service de Pédiatrie Générale, Créteil, 94000, France.,FHU SENEC, Créteil, France
| | - Bruno Costes
- Université Paris Est Creteil, INSERM, IMRB, F-94010 Creteil, France.,FHU SENEC, Créteil, France.,AP-HP, Hôpital Henri Mondor, Pôle de Biologie-Pathologie, Département de Génétique, Créteil, 94000, France
| | - Valérie Delattre
- AP-HP, Hôpital Henri Mondor, Pôle de Biologie-Pathologie, Département de Génétique, Créteil, 94000, France
| | - Stéphanie Finet
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, CNRS, Sorbonne Université, Muséum National d'Histoire Naturelle, Paris, France
| | - Pascale Fanen
- Université Paris Est Creteil, INSERM, IMRB, F-94010 Creteil, France.,FHU SENEC, Créteil, France.,AP-HP, Hôpital Henri Mondor, Pôle de Biologie-Pathologie, Département de Génétique, Créteil, 94000, France
| | - Ralph Epaud
- Université Paris Est Creteil, INSERM, IMRB, F-94010 Creteil, France.,Centre Hospitalier Intercommunal de Créteil, Service de Pédiatrie Générale, Créteil, 94000, France.,FHU SENEC, Créteil, France
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Morlet E, Costemale-Lacoste JF, Poulet E, McMahon K, Hoertel N, Limosin F, Alezrah C, Amado I, Amar G, Andréi O, Arbault D, Archambault G, Aurifeuille G, Barrière S, Béra-Potelle C, Blumenstock Y, Bardou H, Bareil-Guérin M, Barrau P, Barrouillet C, Baup E, Bazin N, Beaufils B, Ben Ayed J, Benoit M, Benyacoub K, Bichet T, Blanadet F, Blanc O, Blanc-Comiti J, Boussiron D, Bouysse AM, Brochard A, Brochart O, Bucheron B, Cabot M, Camus V, Chabannes JM, Charlot V, Charpeaud T, Clad-Mor C, Combes C, Comisu M, Cordier B, Costi F, Courcelles JP, Creixell M, Cuche H, Cuervo-Lombard C, Dammak A, Da Rin D, Denis JB, Denizot H, Deperthuis A, Diers E, Dirami S, Donneau D, Dreano P, Dubertret C, Duprat E, Duthoit D, Fernandez C, Fonfrede P, Freitas N, Gasnier P, Gauillard J, Getten F, Gierski F, Godart F, Gourevitch R, Grassin Delyle A, Gremion J, Gres H, Griner V, Guerin-Langlois C, Guggiari C, Guillin O, Hadaoui H, Haffen E, Hanon C, Haouzir S, Hazif-Thomas C, Heron A, Hubsch B, Jalenques I, Januel D, Kaladjian A, Karnycheff JF, Kebir O, Krebs MO, Lajugie C, Leboyer M, Legrand P, Lejoyeux M, Lemaire V, Leroy E, Levy-Chavagnat D, Leydier A, Liling C, Llorca PM, Loeffel P, Louville P, Lucas Navarro S, Mages N, Mahi M, Maillet O, Manetti A, Martelli C, Martin P, Masson M, Maurs-Ferrer I, Mauvieux J, Mazmanian S, Mechin E, Mekaoui L, Meniai M, Metton A, Mihoubi A, Miron M, Mora G, Niro Adès V, Nubukpo P, Omnes C, Papin S, Paris P, Passerieux C, Pellerin J, Perlbarg J, Perron S, Petit A, Petitjean F, Portefaix C, Pringuey D, Radtchenko A, Rahiou H, Raucher-Chéné D, Rauzy A, Reinheimer L, Renard M, René M, Rengade CE, Reynaud P, Robin D, Rodrigues C, Rollet A, Rondepierre F, Rousselot B, Rubingher S, Saba G, Salvarelli JP, Samuelian JC, Scemama-Ammar C, Schurhoff F, Schuster JP, Sechter D, Segalas B, Seguret T, Seigneurie AS, Semmak A, Slama F, Taisne S, Taleb M, Terra JL, Thefenne D, Tran E, Tourtauchaux R, Vacheron MN, Vandel P, Vanhoucke V, Venet E, Verdoux H, Viala A, Vidon G, Vitre M, Vurpas JL, Wagermez C, Walter M, Yon L, Zendjidjian X. Psychiatric and physical outcomes of long-term use of lithium in older adults with bipolar disorder and major depressive disorder: A cross-sectional multicenter study. J Affect Disord 2019; 259:210-217. [PMID: 31446382 DOI: 10.1016/j.jad.2019.08.056] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 07/11/2019] [Accepted: 08/18/2019] [Indexed: 12/19/2022]
Abstract
OBJECTIVE Although lithium is widely used in current practice to treat bipolar disorder (BD) and treatment-resistant major depressive disorder (MDD) among older adults, little is known about its efficacy and tolerability in this population, which is generally excluded from randomized clinical trials. The objective of this study was to evaluate the efficacy and tolerability of long-term use of lithium among older adults with BD and MDD. METHOD Data from the Cohort of individuals with Schizophrenia and mood disorders Aged 55 years or more (CSA) were used. Two groups of patients with BD and MDD were compared: those who were currently receiving lithium versus those who were not. The effects of lithium on psychiatric (i.e., depressive symptoms severity, perceived clinical severity, rates of psychiatric admissions in the past-year), geriatric (overall and cognitive functioning) and physical outcomes (i.e., rates of non-psychiatric medical comorbidities and general hospital admissions in the past-year) were evaluated. All analyses were adjusted for age, sex, duration of disorder, diagnosis, smoking status, alcohol use, and use of antipsychotics, antiepileptics or antidepressants. RESULTS Among the 281 older participants with BD or MDD, 15.7% were taking lithium for a mean duration of 12.5(SD = 11.6) years. Lithium use was associated with lower intensity of depressive symptoms, reduced perceived clinical global severity and lower benzodiazepine use (all p < 0.05), without being linked to greater rates of medical comorbidities, except for hypothyroidism. LIMITATIONS Data were cross-sectional and data on lifetime history of psychotropic medications was not assessed. CONCLUSION Our results suggest that long-term lithium use may be efficient and relatively well-tolerated in older adults with BD or treatment-resistant MDD.
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Affiliation(s)
- Elise Morlet
- Department of Psychiatry, Corentin Celton Hospital, 4 Parvis Corentin Celton, 92130 Issy-les-Moulineaux, France
| | - Jean-François Costemale-Lacoste
- Department of Psychiatry, Corentin Celton Hospital, 4 Parvis Corentin Celton, 92130 Issy-les-Moulineaux, France; INSERM UMRS 1178, CESP, Le Kremlin Bicêtre, France.
| | - Emmanuel Poulet
- INSERM, U1028, CNRS, UMR5292, Lyon Neuroscience Research Center, PSY-R2 Team, Lyon F-69000, France
| | - Kibby McMahon
- Department of Psychology & Neuroscience, Duke University, 2213 Elba Street, Durham, NC 27710, United States
| | - Nicolas Hoertel
- Department of Psychiatry, Corentin Celton Hospital, 4 Parvis Corentin Celton, 92130 Issy-les-Moulineaux, France; INSERM UMR 894, Psychiatry and Neurosciences Center, Paris, France; Paris Descartes University, Sorbonne Paris Cité, Paris, France
| | - Frédéric Limosin
- Department of Psychiatry, Corentin Celton Hospital, 4 Parvis Corentin Celton, 92130 Issy-les-Moulineaux, France; INSERM UMR 894, Psychiatry and Neurosciences Center, Paris, France; Paris Descartes University, Sorbonne Paris Cité, Paris, France
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De Wever A, Benzerara K, Coutaud M, Caumes G, Poinsot M, Skouri-Panet F, Laurent T, Duprat E, Gugger M. Evidence of high Ca uptake by cyanobacteria forming intracellular CaCO 3 and impact on their growth. Geobiology 2019; 17:676-690. [PMID: 31347755 DOI: 10.1111/gbi.12358] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 06/15/2019] [Accepted: 07/04/2019] [Indexed: 06/10/2023]
Abstract
Several species of cyanobacteria biomineralizing intracellular amorphous calcium carbonates (ACC) were recently discovered. However, the mechanisms involved in this biomineralization process and the determinants discriminating species forming intracellular ACC from those not forming intracellular ACC remain unknown. Recently, it was hypothesized that the intensity of Ca uptake (i.e., how much Ca was scavenged from the extracellular solution) might be a major parameter controlling the capability of a cyanobacterium to form intracellular ACC. Here, we tested this hypothesis by systematically measuring the Ca uptake by a set of 52 cyanobacterial strains cultured in the same growth medium. The results evidenced a dichotomy among cyanobacteria regarding Ca sequestration capabilities, with all strains forming intracellular ACC incorporating significantly more calcium than strains not forming ACC. Moreover, Ca provided at a concentration of 50 μM in BG-11 was shown to be limiting for the growth of some of the strains forming intracellular ACC, suggesting an overlooked quantitative role of Ca for these strains. All cyanobacteria forming intracellular ACC contained at least one gene coding for a mechanosensitive channel, which might be involved in Ca influx, as well as at least one gene coding for a Ca2+ /H+ exchanger and membrane proteins of the UPF0016 family, which might be involved in active Ca transport either from the cytosol to the extracellular solution or the cytosol toward an intracellular compartment. Overall, massive Ca sequestration may have an indirect role by allowing the formation of intracellular ACC. The latter may be beneficial to the growth of the cells as a storage of inorganic C and/or a buffer of intracellular pH. Moreover, high Ca scavenging by cyanobacteria biomineralizing intracellular ACC, a trait shared with endolithic cyanobacteria, suggests that these cyanobacteria should be considered as potentially significant geochemical reservoirs of Ca.
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Affiliation(s)
- Alexis De Wever
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR CNRS 7590, Sorbonne Université, Muséum National d'Histoire Naturelle, Paris, France
| | - Karim Benzerara
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR CNRS 7590, Sorbonne Université, Muséum National d'Histoire Naturelle, Paris, France
| | - Margot Coutaud
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR CNRS 7590, Sorbonne Université, Muséum National d'Histoire Naturelle, Paris, France
| | - Géraldine Caumes
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR CNRS 7590, Sorbonne Université, Muséum National d'Histoire Naturelle, Paris, France
| | - Mélanie Poinsot
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR CNRS 7590, Sorbonne Université, Muséum National d'Histoire Naturelle, Paris, France
| | - Fériel Skouri-Panet
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR CNRS 7590, Sorbonne Université, Muséum National d'Histoire Naturelle, Paris, France
| | - Thierry Laurent
- Collection des Cyanobactéries, Institut Pasteur, Paris Cedex 15, France
| | - Elodie Duprat
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR CNRS 7590, Sorbonne Université, Muséum National d'Histoire Naturelle, Paris, France
| | - Muriel Gugger
- Collection des Cyanobactéries, Institut Pasteur, Paris Cedex 15, France
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Chandramohan A, Duprat E, Remusat L, Zirah S, Lombard C, Kish A. Novel Mechanism for Surface Layer Shedding and Regenerating in Bacteria Exposed to Metal-Contaminated Conditions. Front Microbiol 2019; 9:3210. [PMID: 30697196 PMCID: PMC6341005 DOI: 10.3389/fmicb.2018.03210] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 12/11/2018] [Indexed: 12/17/2022] Open
Abstract
Surface layers (S-layers) are components of the cell walls throughout the Bacteria and the Archaea that provide protection for microorganisms against diverse environmental stresses, including metal stress. We have previously characterized the process by which S-layers serve as a nucleation site for metal mineralization in an archaeon for which the S-layer represents the only cell wall component. Here, we test the hypothesis originally proposed in cyanobacteria that a “shedding” mechanism exists for replacing S-layers that have become mineral-encrusted, using Lysinibacillus sp. TchIII 20n38, metallotolerant gram-positive bacterium, as a model organism. We characterize for the first time a mechanism for resistance to metals through S-layer shedding and regeneration. S-layers nucleate the formation of Fe-mineral on the cell surface, depending on physiological state of the cells and metal exposure times, leading to the encrustation of the S-layer and changes in the cell morphology as observed by scanning electron microscopy. Using Nanoscale Secondary Ion Mass Spectrometry, we show that mineral-encrusted S-layers are shed by the bacterial cells after a period of latency (2 days under the conditions tested) in a heterogeneous fashion likely reflecting natural variations in metal stress resistance. The emerging cells regenerate new S-layers as part of their cell wall structure. Given the wide diversity of S-layer bearing prokaryotes, S-layer shedding may represent an important mechanism for microbial survival in metal-contaminated environments.
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Affiliation(s)
- Archjana Chandramohan
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d'Histoire Naturelle, CNRS UMR 7245, Paris, France
| | - Elodie Duprat
- Institut de Minéralogie, Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Université, Muséum National d'Histoire Naturelle, CNRS UMR 7590, IRD UMR 206, Paris, France
| | - Laurent Remusat
- Institut de Minéralogie, Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Université, Muséum National d'Histoire Naturelle, CNRS UMR 7590, IRD UMR 206, Paris, France
| | - Severine Zirah
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d'Histoire Naturelle, CNRS UMR 7245, Paris, France
| | - Carine Lombard
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d'Histoire Naturelle, CNRS UMR 7245, Paris, France
| | - Adrienne Kish
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d'Histoire Naturelle, CNRS UMR 7245, Paris, France
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Rodriguez PM, Stratmann D, Duprat E, Papandreou N, Acuna R, Lacroix Z, Chomilier J. Correlating topology and thermodynamics to predict protein structure sensitivity to point mutations. Bio-Algorithms and Med-Systems 2018. [DOI: 10.1515/bams-2018-0026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractThe relation between distribution of hydrophobic amino acids along with protein chains and their structure is far from being completely understood. No reliable method allowsab initioprediction of the folded structure from this distribution of physicochemical properties, even when they are highly degenerated by considering only two classes: hydrophobic and polar. Establishment of long-range hydrophobic three dimension (3D) contacts is essential for the formation of the nucleus, a key process in the early steps of protein folding. Thus, a large number of 3D simulation studies were developed to challenge this issue. They are nowadays evaluated in a specific chapter of the molecular modeling competition, Critical Assessment of Protein Structure Prediction. We present here a simulation of the early steps of the folding process for 850 proteins, performed in a discrete 3D space, which results in peaks in the predicted distribution of intra-chain noncovalent contacts. The residues located at these peak positions tend to be buried in the core of the protein and are expected to correspond to critical positions in the sequence, important both for folding and structural (or similarly, energetic in the thermodynamic hypothesis) stability. The degree of stabilization or destabilization due to a point mutation at the critical positions involved in numerous contacts is estimated from the calculated folding free energy difference between mutated and native structures. The results show that these critical positions are not tolerant towards mutation. This simulation of the noncovalent contacts only needs a sequence as input, and this paper proposes a validation of the method by comparison with the prediction of stability by well-established programs.
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Skouri-Panet F, Benzerara K, Cosmidis J, Férard C, Caumes G, De Luca G, Heulin T, Duprat E. In Vitro and in Silico Evidence of Phosphatase Diversity in the Biomineralizing Bacterium Ramlibacter tataouinensis. Front Microbiol 2018; 8:2592. [PMID: 29375498 PMCID: PMC5768637 DOI: 10.3389/fmicb.2017.02592] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 12/12/2017] [Indexed: 11/13/2022] Open
Abstract
Microbial phosphatase activity can trigger the precipitation of metal-phosphate minerals, a process called phosphatogenesis with global geochemical and environmental implications. An increasing diversity of phosphatases expressed by diverse microorganisms has been evidenced in various environments. However, it is challenging to link the functional properties of genomic repertoires of phosphatases with the phosphatogenesis capabilities of microorganisms. Here, we studied the betaproteobacterium Ramlibacter tataouinensis (Rta), known to biomineralize Ca-phosphates in the environment and the laboratory. We investigated the functional repertoire of this biomineralization process at the cell, genome and molecular level. Based on a mineralization assay, Rta is shown to hydrolyse the phosphoester bonds of a wide range of organic P molecules. Accordingly, its genome has an unusually high diversity of phosphatases: five genes belonging to two non-homologous families, phoD and phoX, were detected. These genes showed diverse predicted cis-regulatory elements. Moreover, they encoded proteins with diverse structural properties according to molecular models. Heterologously expressed PhoD and PhoX in Escherichia coli had different profiles of substrate hydrolysis. As evidenced for Rta cells, recombinant E. coli cells induced the precipitation of Ca-phosphate mineral phases, identified as poorly crystalline hydroxyapatite. The phosphatase genomic repertoire of Rta (containing phosphatases of both the PhoD and PhoX families) was previously evidenced as prevalent in marine oligotrophic environments. Interestingly, the Tataouine sand from which Rta was isolated showed similar P-depleted, but Ca-rich conditions. Overall, the diversity of phosphatases in Rta allows the hydrolysis of a broad range of organic P substrates and therefore the release of orthophosphates (inorganic phosphate) under diverse trophic conditions. Since the release of orthophosphates is key to the achievement of high saturation levels with respect to hydroxyapatite and the induction of phosphatogenesis, Rta appears as a particularly efficient driver of this process as shown experimentally.
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Affiliation(s)
- Fériel Skouri-Panet
- Centre National de la Recherche Scientifique, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Universités, UMR 7590, Muséum National d'Histoire Naturelle, Université Pierre et Marie Curie, IRD 206, Paris, France
| | - Karim Benzerara
- Centre National de la Recherche Scientifique, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Universités, UMR 7590, Muséum National d'Histoire Naturelle, Université Pierre et Marie Curie, IRD 206, Paris, France
| | - Julie Cosmidis
- Department of Geological Sciences, University of Colorado, Boulder, CO, United States
| | - Céline Férard
- Centre National de la Recherche Scientifique, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Universités, UMR 7590, Muséum National d'Histoire Naturelle, Université Pierre et Marie Curie, IRD 206, Paris, France
| | - Géraldine Caumes
- Centre National de la Recherche Scientifique, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Universités, UMR 7590, Muséum National d'Histoire Naturelle, Université Pierre et Marie Curie, IRD 206, Paris, France
| | - Gilles De Luca
- Laboratoire d'Écologie Microbienne de la Rhizosphère et Environnements Extrêmes, UMR 7265, Aix Marseille Univ, Centre National de la Recherche Scientifique, Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Saint-Paul-lez-Durance, France
| | - Thierry Heulin
- Laboratoire d'Écologie Microbienne de la Rhizosphère et Environnements Extrêmes, UMR 7265, Aix Marseille Univ, Centre National de la Recherche Scientifique, Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Saint-Paul-lez-Durance, France
| | - Elodie Duprat
- Centre National de la Recherche Scientifique, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Universités, UMR 7590, Muséum National d'Histoire Naturelle, Université Pierre et Marie Curie, IRD 206, Paris, France
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Miot J, Remusat L, Duprat E, Gonzalez A, Pont S, Poinsot M. Fe biomineralization mirrors individual metabolic activity in a nitrate-dependent Fe(II)-oxidizer. Front Microbiol 2015; 6:879. [PMID: 26441847 PMCID: PMC4562303 DOI: 10.3389/fmicb.2015.00879] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 08/10/2015] [Indexed: 12/15/2022] Open
Abstract
Microbial biomineralization sometimes leads to periplasmic encrustation, which is predicted to enhance microorganism preservation in the fossil record. Mineral precipitation within the periplasm is, however, thought to induce death, as a result of permeability loss preventing nutrient and waste transit across the cell wall. This hypothesis had, however, never been investigated down to the single cell level. Here, we cultured the nitrate reducing Fe(II) oxidizing bacteria Acidovorax sp. strain BoFeN1 that have been previously shown to promote the precipitation of a diversity of Fe minerals (lepidocrocite, goethite, Fe phosphate) encrusting the periplasm. We investigated the connection of Fe biomineralization with carbon assimilation at the single cell level, using a combination of electron microscopy and Nano-Secondary Ion Mass Spectrometry. Our analyses revealed strong individual heterogeneities of Fe biomineralization. Noteworthy, a small proportion of cells remaining free of any precipitate persisted even at advanced stages of biomineralization. Using pulse chase experiments with (13)C-acetate, we provide evidence of individual phenotypic heterogeneities of carbon assimilation, correlated with the level of Fe biomineralization. Whereas non- and moderately encrusted cells were able to assimilate acetate, higher levels of periplasmic encrustation prevented any carbon incorporation. Carbon assimilation only depended on the level of Fe encrustation and not on the nature of Fe minerals precipitated in the cell wall. Carbon assimilation decreased exponentially with increasing cell-associated Fe content. Persistence of a small proportion of non-mineralized and metabolically active cells might constitute a survival strategy in highly ferruginous environments. Eventually, our results suggest that periplasmic Fe biomineralization may provide a signature of individual metabolic status, which could be looked for in the fossil record and in modern environmental samples.
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Affiliation(s)
- Jennyfer Miot
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Muséum National d’Histoire Naturelle, Université Pierre et Marie Curie – Sorbonne Universités, CNRS UMR 7590, IRD 206Paris, France
| | - Laurent Remusat
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Muséum National d’Histoire Naturelle, Université Pierre et Marie Curie – Sorbonne Universités, CNRS UMR 7590, IRD 206Paris, France
| | - Elodie Duprat
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Muséum National d’Histoire Naturelle, Université Pierre et Marie Curie – Sorbonne Universités, CNRS UMR 7590, IRD 206Paris, France
| | - Adriana Gonzalez
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Muséum National d’Histoire Naturelle, Université Pierre et Marie Curie – Sorbonne Universités, CNRS UMR 7590, IRD 206Paris, France
| | - Sylvain Pont
- Département des Collections, Muséum National d’Histoire NaturelleParis, France
| | - Mélanie Poinsot
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Muséum National d’Histoire Naturelle, Université Pierre et Marie Curie – Sorbonne Universités, CNRS UMR 7590, IRD 206Paris, France
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Banach M, Prudhomme N, Carpentier M, Duprat E, Papandreou N, Kalinowska B, Chomilier J, Roterman I. Contribution to the prediction of the fold code: application to immunoglobulin and flavodoxin cases. PLoS One 2015; 10:e0125098. [PMID: 25915049 PMCID: PMC4411048 DOI: 10.1371/journal.pone.0125098] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [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: 12/16/2014] [Accepted: 03/20/2015] [Indexed: 12/19/2022] Open
Abstract
Background Folding nucleus of globular proteins formation starts by the mutual interaction of a group of hydrophobic amino acids whose close contacts allow subsequent formation and stability of the 3D structure. These early steps can be predicted by simulation of the folding process through a Monte Carlo (MC) coarse grain model in a discrete space. We previously defined MIRs (Most Interacting Residues), as the set of residues presenting a large number of non-covalent neighbour interactions during such simulation. MIRs are good candidates to define the minimal number of residues giving rise to a given fold instead of another one, although their proportion is rather high, typically [15-20]% of the sequences. Having in mind experiments with two sequences of very high levels of sequence identity (up to 90%) but different folds, we combined the MIR method, which takes sequence as single input, with the “fuzzy oil drop” (FOD) model that requires a 3D structure, in order to estimate the residues coding for the fold. FOD assumes that a globular protein follows an idealised 3D Gaussian distribution of hydrophobicity density, with the maximum in the centre and minima at the surface of the “drop”. If the actual local density of hydrophobicity around a given amino acid is as high as the ideal one, then this amino acid is assigned to the core of the globular protein, and it is assumed to follow the FOD model. Therefore one obtains a distribution of the amino acids of a protein according to their agreement or rejection with the FOD model. Results We compared and combined MIR and FOD methods to define the minimal nucleus, or keystone, of two populated folds: immunoglobulin-like (Ig) and flavodoxins (Flav). The combination of these two approaches defines some positions both predicted as a MIR and assigned as accordant with the FOD model. It is shown here that for these two folds, the intersection of the predicted sets of residues significantly differs from random selection. It reduces the number of selected residues by each individual method and allows a reasonable agreement with experimentally determined key residues coding for the particular fold. In addition, the intersection of the two methods significantly increases the specificity of the prediction, providing a robust set of residues that constitute the folding nucleus.
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Affiliation(s)
- Mateusz Banach
- Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, Krakow, Poland
| | - Nicolas Prudhomme
- Protein Structure Prediction group, IMPMC, UPMC & CNRS, Paris, France
| | - Mathilde Carpentier
- Protein Structure Prediction group, IMPMC, UPMC & CNRS, Paris, France
- RPBS, 35 rue Hélène Brion, 75013, Paris, France
| | - Elodie Duprat
- Protein Structure Prediction group, IMPMC, UPMC & CNRS, Paris, France
- RPBS, 35 rue Hélène Brion, 75013, Paris, France
| | - Nikolaos Papandreou
- Genetics Department, Agricultural University of Athens, Iera Odos 75, Athens, Greece
| | - Barbara Kalinowska
- Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, Krakow, Poland
| | - Jacques Chomilier
- Protein Structure Prediction group, IMPMC, UPMC & CNRS, Paris, France
- RPBS, 35 rue Hélène Brion, 75013, Paris, France
- * E-mail: (JC); (IR)
| | - Irena Roterman
- Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, Krakow, Poland
- * E-mail: (JC); (IR)
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Skouri-Panet F, Michiel M, Férard C, Duprat E, Finet S. Structural and functional specificity of small heat shock protein HspB1 and HspB4, two cellular partners of HspB5: Role of the in vitro hetero-complex formation in chaperone activity. Biochimie 2012; 94:975-84. [DOI: 10.1016/j.biochi.2011.12.018] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 12/20/2011] [Indexed: 11/16/2022]
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Flutre T, Duprat E, Feuillet C, Quesneville H. Considering transposable element diversification in de novo annotation approaches. PLoS One 2011; 6:e16526. [PMID: 21304975 PMCID: PMC3031573 DOI: 10.1371/journal.pone.0016526] [Citation(s) in RCA: 322] [Impact Index Per Article: 24.8] [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: 08/31/2010] [Accepted: 01/04/2011] [Indexed: 01/24/2023] Open
Abstract
Transposable elements (TEs) are mobile, repetitive DNA sequences that are almost ubiquitous in prokaryotic and eukaryotic genomes. They have a large impact on genome structure, function and evolution. With the recent development of high-throughput sequencing methods, many genome sequences have become available, making possible comparative studies of TE dynamics at an unprecedented scale. Several methods have been proposed for the de novo identification of TEs in sequenced genomes. Most begin with the detection of genomic repeats, but the subsequent steps for defining TE families differ. High-quality TE annotations are available for the Drosophila melanogaster and Arabidopsis thaliana genome sequences, providing a solid basis for the benchmarking of such methods. We compared the performance of specific algorithms for the clustering of interspersed repeats and found that only a particular combination of algorithms detected TE families with good recovery of the reference sequences. We then applied a new procedure for reconciling the different clustering results and classifying TE sequences. The whole approach was implemented in a pipeline using the REPET package. Finally, we show that our combined approach highlights the dynamics of well defined TE families by making it possible to identify structural variations among their copies. This approach makes it possible to annotate TE families and to study their diversification in a single analysis, improving our understanding of TE dynamics at the whole-genome scale and for diverse species.
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Affiliation(s)
- Timothée Flutre
- Unité de Recherche en Génomique-Info, UR 1164, INRA Centre de Versailles-Grignon, Versailles, France
| | - Elodie Duprat
- Institut de Minéralogie et de Physique des Milieux Condensés, UMR 7590, CNRS-UPMC-IPGP-Université Paris Diderot, Paris, France
| | - Catherine Feuillet
- Génétique, Diversité et Ecophysiologie des Céréales, UMR 1095, INRA Domaine du Crouël, Clermont-Ferrand, France
| | - Hadi Quesneville
- Unité de Recherche en Génomique-Info, UR 1164, INRA Centre de Versailles-Grignon, Versailles, France
- * E-mail:
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Michiel M, Duprat E, Skouri-Panet F, Lampi JA, Tardieu A, Lampi KJ, Finet S. Aggregation of deamidated human betaB2-crystallin and incomplete rescue by alpha-crystallin chaperone. Exp Eye Res 2010; 90:688-98. [PMID: 20188088 DOI: 10.1016/j.exer.2010.02.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2009] [Revised: 02/02/2010] [Accepted: 02/16/2010] [Indexed: 11/16/2022]
Abstract
Aging of the lens is accompanied by extensive deamidation of the lens specific proteins, the crystallins. Deamidated crystallins are increased in the insoluble proteins and may contribute to cataracts. Deamidation has been shown in vitro to alter the structure and decrease the stability of human lens betaB1, betaB2 and betaA3-crystallin. Of particular interest, betaB2 mutants were constructed to mimic the effect of in vivo deamidations at the interacting interface between domains, at Q70 in the N terminal domain and at Q162, its C-terminal homologue. The double mutant was also constructed. We previously reported that deamidation at the critical interface sites decreased stability, while preserving the dimeric 3D structure. In the present study, dynamic light scattering, differential scanning calorimetry and small angle X-ray scattering were used to investigate the effect of deamidation on stability, thermal unfolding and aggregation. The bovine betaLb fraction was used for comparative analysis. The chaperone requirements of the various samples were determined using bovine alpha-crystallins as the chaperone. Deamidation at both interface Gln residues or at Q70, but not Q162, significantly lowered the temperature for unfolding and aggregation, which was rapidly followed by precipitation. This deamidation-induced aggregation and precipitation was not completely prevented by alpha-crystallin chaperone. A potential mechanism for cataract formation in vivo involving accumulation of deamidated beta-crystallin aggregates is discussed.
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Affiliation(s)
- Magalie Michiel
- Protéines, Biochimie Structurale et Fonctionnelle, CNRS-UPMC, case 29, 7 quai St Bernard, 75252 Paris Cedex 5, France
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Michiel M, Skouri-Panet F, Duprat E, Simon S, Férard C, Tardieu A, Finet S. Abnormal Assemblies and Subunit Exchange of αB-Crystallin R120 Mutants Could Be Associated with Destabilization of the Dimeric Substructure. Biochemistry 2008; 48:442-53. [DOI: 10.1021/bi8014967] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Magalie Michiel
- PBSF, CNRS-UPMC, case 29, 7 quai St. Bernard, 75252 Paris CEDEX 5, France, IMPMC, CNRS-IPGP-UPMC-Université Paris Diderot, 140 rue de Lourmel 75015 Paris, France, and CGMC, UMR5534, CNRS-Université Lyon 1, Bâtiment G. Mendel, 43 Bd du 11 Novembre 1918, 69622 Villeurbanne CEDEX, France
| | - Fériel Skouri-Panet
- PBSF, CNRS-UPMC, case 29, 7 quai St. Bernard, 75252 Paris CEDEX 5, France, IMPMC, CNRS-IPGP-UPMC-Université Paris Diderot, 140 rue de Lourmel 75015 Paris, France, and CGMC, UMR5534, CNRS-Université Lyon 1, Bâtiment G. Mendel, 43 Bd du 11 Novembre 1918, 69622 Villeurbanne CEDEX, France
| | - Elodie Duprat
- PBSF, CNRS-UPMC, case 29, 7 quai St. Bernard, 75252 Paris CEDEX 5, France, IMPMC, CNRS-IPGP-UPMC-Université Paris Diderot, 140 rue de Lourmel 75015 Paris, France, and CGMC, UMR5534, CNRS-Université Lyon 1, Bâtiment G. Mendel, 43 Bd du 11 Novembre 1918, 69622 Villeurbanne CEDEX, France
| | - Stéphanie Simon
- PBSF, CNRS-UPMC, case 29, 7 quai St. Bernard, 75252 Paris CEDEX 5, France, IMPMC, CNRS-IPGP-UPMC-Université Paris Diderot, 140 rue de Lourmel 75015 Paris, France, and CGMC, UMR5534, CNRS-Université Lyon 1, Bâtiment G. Mendel, 43 Bd du 11 Novembre 1918, 69622 Villeurbanne CEDEX, France
| | - Céline Férard
- PBSF, CNRS-UPMC, case 29, 7 quai St. Bernard, 75252 Paris CEDEX 5, France, IMPMC, CNRS-IPGP-UPMC-Université Paris Diderot, 140 rue de Lourmel 75015 Paris, France, and CGMC, UMR5534, CNRS-Université Lyon 1, Bâtiment G. Mendel, 43 Bd du 11 Novembre 1918, 69622 Villeurbanne CEDEX, France
| | - Annette Tardieu
- PBSF, CNRS-UPMC, case 29, 7 quai St. Bernard, 75252 Paris CEDEX 5, France, IMPMC, CNRS-IPGP-UPMC-Université Paris Diderot, 140 rue de Lourmel 75015 Paris, France, and CGMC, UMR5534, CNRS-Université Lyon 1, Bâtiment G. Mendel, 43 Bd du 11 Novembre 1918, 69622 Villeurbanne CEDEX, France
| | - Stéphanie Finet
- PBSF, CNRS-UPMC, case 29, 7 quai St. Bernard, 75252 Paris CEDEX 5, France, IMPMC, CNRS-IPGP-UPMC-Université Paris Diderot, 140 rue de Lourmel 75015 Paris, France, and CGMC, UMR5534, CNRS-Université Lyon 1, Bâtiment G. Mendel, 43 Bd du 11 Novembre 1918, 69622 Villeurbanne CEDEX, France
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Duprat E, Lefranc MP, Gascuel O. A simple method to predict protein-binding from aligned sequences--application to MHC superfamily and beta2-microglobulin. Bioinformatics 2005; 22:453-9. [PMID: 16352655 DOI: 10.1093/bioinformatics/bti826] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION The MHC superfamily (MhcSF) consists of immune system MHC class I (MHC-I) proteins, along with proteins with a MHC-I-like structure that are involved in a large variety of biological processes. beta2-Microglobulin (B2M) non-covalent binding to MHC-I proteins is required for their surface expression and function, whereas MHC-I-like proteins interact, or not, with B2M. This study was designed to predict B2M binding (or non-binding) of newly identified MhcSF proteins, in order to decipher their function, understand the molecular recognition mechanisms and identify deleterious mutations. IMGT standardization of MhcSF protein domains provides a unique numbering of the multiple alignment positions, and conditions to develop such predictive tool. METHOD We combine a simple-Bayes classifier with IMGT unique numbering. Our method involves two steps: (1) selection of discriminant binary features, which associate an alignment position with an amino acid group; and (2) learning of the classifier by estimating the frequencies of selected features, conditionally to the B2M binding property. RESULTS Our dataset contains aligned sequences of 806 allelic forms of 47 MhcSF proteins, corresponding to 9 receptor types and 4 mammalian species. Eighteen discriminant features are selected, belonging to B2M contact sites, or stabilizing the molecular structure required for this contact. Three leave-one-out procedures are used to assess classifier performance, which corresponds to B2M binding prediction for: (1) new proteins, (2) species not represented in the dataset and (3) new receptor types. The prediction accuracy is high, i.e. 98, 94 and 70%, respectively. Application of our classifier to lower vertebrate MHC-I proteins indicates that these proteins bind to B2M and should then be expressed on the cellular surface by a process similar to that of mammalian MHC-I proteins. These results demonstrate the usefulness and accuracy of our (simple) approach, which should apply to other function or interaction prediction problems.
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Affiliation(s)
- Elodie Duprat
- Laboratoire d'ImmunoGénétique Moléculaire IGH (UPR CNRS 1142), 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France
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Lefranc MP, Giudicelli V, Kaas Q, Duprat E, Jabado-Michaloud J, Scaviner D, Ginestoux C, Clément O, Chaume D, Lefranc G. IMGT, the international ImMunoGeneTics information system. Nucleic Acids Res 2005; 33:D593-7. [PMID: 15608269 PMCID: PMC540019 DOI: 10.1093/nar/gki065] [Citation(s) in RCA: 231] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The international ImMunoGeneTics information system® (IMGT) (http://imgt.cines.fr), created in 1989, by the Laboratoire d'ImmunoGénétique Moléculaire LIGM (Université Montpellier II and CNRS) at Montpellier, France, is a high-quality integrated knowledge resource specializing in the immunoglobulins (IGs), T cell receptors (TRs), major histocompatibility complex (MHC) of human and other vertebrates, and related proteins of the immune systems (RPI) that belong to the immunoglobulin superfamily (IgSF) and to the MHC superfamily (MhcSF). IMGT includes several sequence databases (IMGT/LIGM-DB, IMGT/PRIMER-DB, IMGT/PROTEIN-DB and IMGT/MHC-DB), one genome database (IMGT/GENE-DB) and one three-dimensional (3D) structure database (IMGT/3Dstructure-DB), Web resources comprising 8000 HTML pages (IMGT Marie-Paule page), and interactive tools. IMGT data are expertly annotated according to the rules of the IMGT Scientific chart, based on the IMGT-ONTOLOGY concepts. IMGT tools are particularly useful for the analysis of the IG and TR repertoires in normal physiological and pathological situations. IMGT is used in medical research (autoimmune diseases, infectious diseases, AIDS, leukemias, lymphomas, myelomas), veterinary research, biotechnology related to antibody engineering (phage displays, combinatorial libraries, chimeric, humanized and human antibodies), diagnostics (clonalities, detection and follow up of residual diseases) and therapeutical approaches (graft, immunotherapy and vaccinology). IMGT is freely available at http://imgt.cines.fr.
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Affiliation(s)
- Marie-Paule Lefranc
- IMGT, the international ImMunoGeneTics information system Université Montpellier II, Laboratoire d'ImmunoGénétique Moléculaire LIGM, UPR CNRS 1142, Institut de Génétique Humaine IGH, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France
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Lefranc MP, Duprat E, Kaas Q, Tranne M, Thiriot A, Lefranc G. IMGT unique numbering for MHC groove G-DOMAIN and MHC superfamily (MhcSF) G-LIKE-DOMAIN. Dev Comp Immunol 2005; 29:917-38. [PMID: 15936075 DOI: 10.1016/j.dci.2005.03.003] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2005] [Accepted: 03/10/2005] [Indexed: 05/02/2023]
Abstract
IMGT, the international ImMunoGeneTics information system (http://imgt.cines.fr) provides a common access to expertly annotated data on the genome, proteome, genetics and structure of immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC), and related proteins of the immune system (RPI) of human and other vertebrates. The NUMEROTATION concept of IMGT-ONTOLOGY has allowed to define a unique numbering for the variable domains (V-DOMAINs) and constant domains (C-DOMAINs) of the IG and TR, which has been extended to the V-LIKE-DOMAINs and C-LIKE-DOMAINs of the immunoglobulin superfamily (IgSF) proteins other than the IG and TR (Dev Comp Immunol 27:55--77, 2003; 29:185--203, 2005). In this paper, we describe the IMGT unique numbering for the groove domains (G-DOMAINs) of the MHC and for the G-LIKE-DOMAINs of the MHC superfamily (MhcSF) proteins other than MHC. This IMGT unique numbering leads, for the first time, to the standardized description of the mutations, allelic polymorphisms, two-dimensional (2D) representations and three-dimensional (3D) structures of the G-DOMAINs and G-LIKE-DOMAINs in any species, and therefore, is highly valuable for their comparative, structural, functional and evolutionary studies.
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Affiliation(s)
- Marie-Paule Lefranc
- IMGT, the international ImMunoGeneTics information system, Laboratoire d'ImmunoGénétique Moléculaire, LIGM, Université Montpellier II, Institut de Génétique Humaine, IGH UPR CNRS 1142, 34396 Montpellier cedex 5, France.
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Lefranc MP, Clement O, Kaas Q, Duprat E, Chastellan P, Coelho I, Combres K, Ginestoux C, Giudicelli V, Chaume D, Lefranc G. IMGT-Choreography for immunogenetics and immunoinformatics. In Silico Biol 2005; 5:45-60. [PMID: 15972004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
IMGT, the international ImMunoGeneTics information system (http://imgt.cines.fr), was created in 1989 at Montpellier, France. IMGT is a high quality integrated knowledge resource specialized in immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrates, and related proteins of the immune system (RPI) which belong to the immunoglobulin superfamily (IgSF) and MHC superfamily (MhcSF). IMGT provides a common access to standardized data from genome, proteome, genetics and three-dimensional structures. The accuracy and the consistency of IMGT data are based on IMGT-ONTOLOGY, a semantic specification of terms to be used in immunogenetics and immunoinformatics. IMGT-ONTOLOGY has been formalized using XML Schema (IMGT-ML) for interoperability with other information systems. We are developing Web services to automatically query IMGT databases and tools. This is the first step towards IMGT-Choreography which will trigger and coordinate dynamic interactions between IMGT Web services to process complex significant biological and clinical requests. IMGT-Choreography will further increase the IMGT leadership in immunogenetics and immunoinformatics for medical research (repertoire analysis of the IG antibody sites and of the TR recognition sites in autoimmune and infectious diseases, AIDS, leukemias, lymphomas, myelomas), veterinary research (IG and TR repertoires in farm and wild life species), genome diversity and genome evolution studies of the adaptive immune responses, biotechnology related to antibody engineering (single chain Fragment variable (scFv), phage displays, combinatorial libraries, chimeric, humanized and human antibodies), diagnostics (detection and follow up of residual diseases) and therapeutical approaches (grafts, immunotherapy, vaccinology). IMGT is freely available at http://imgt.cines.fr.
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Affiliation(s)
- Marie-Paule Lefranc
- Universite Montpellier II, Laboratoire d'ImmunoGenetique Moleculaire LIGM, UPR CNRS 1142, Institut de Genetique Humaine IGH, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France.
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Lefranc MP, Pommié C, Kaas Q, Duprat E, Bosc N, Guiraudou D, Jean C, Ruiz M, Da Piédade I, Rouard M, Foulquier E, Thouvenin V, Lefranc G. IMGT unique numbering for immunoglobulin and T cell receptor constant domains and Ig superfamily C-like domains. Dev Comp Immunol 2005; 29:185-203. [PMID: 15572068 DOI: 10.1016/j.dci.2004.07.003] [Citation(s) in RCA: 186] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2004] [Accepted: 07/16/2004] [Indexed: 05/24/2023]
Abstract
IMGT, the international ImMunoGeneTics information system (http://imgt.cines.fr) provides a common access to expertly annotated data on the genome, proteome, genetics and structure of immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC), and related proteins of the immune system (RPI) of human and other vertebrates. The NUMEROTATION concept of IMGT-ONTOLOGY has allowed to define a unique numbering for the variable domains (V-DOMAINs) and for the V-LIKE-DOMAINs. In this paper, this standardized characterization is extended to the constant domains (C-DOMAINs), and to the C-LIKE-DOMAINs, leading, for the first time, to their standardized description of mutations, allelic polymorphisms, two-dimensional (2D) representations and tridimensional (3D) structures. The IMGT unique numbering is, therefore, highly valuable for the comparative, structural or evolutionary studies of the immunoglobulin superfamily (IgSF) domains, V-DOMAINs and C-DOMAINs of IG and TR in vertebrates, and V-LIKE-DOMAINs and C-LIKE-DOMAINs of proteins other than IG and TR, in any species.
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Affiliation(s)
- Marie-Paule Lefranc
- IMGT, the International ImMunoGeneTics Information System, LIGM, Laboratoire d'ImmunoGénétique Moléculaire, Université Montpellier II, UPR CNRS 1142, IGH, 141 rue de la Cardonille, 34396 Montpellier cedex 5, France.
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Bertrand G, Duprat E, Lefranc MP, Marti J, Coste J. Characterization of human FCGR3B*02 (HNA-1b, NA2) cDNAs and IMGT standardized description of FCGR3B alleles. ACTA ACUST UNITED AC 2004; 64:119-31. [PMID: 15245367 DOI: 10.1111/j.1399-0039.2004.00259.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The low-affinity Fc gamma receptor IIIb (Fc gamma RIIIb and CD16b) is constituted by a unique FCGR3B polypeptide chain that comprises two extracellular immunoglobulin-like domains, and is expressed as a glycosylphosphatidyl inositol-anchored receptor on the neutrophils. The FCGR3B chain bears allotypes that define the human neutrophil antigen-1 (HNA-1 and NA) system involved in major post-transfusional reactions. FCGR3B is highly homologous to FCGR3A, which is expressed as a transmembrane receptor on natural killer cells and monocytes/macrophages. Its transcription products were not yet fully characterized. In the present work, we sequenced FCGR3B cDNAs with complete 3' untranslated region from purified granulocytes of HNA-1b/HNA-1b (NA2/NA2) genotyped donors. We characterized two FCGR3B cDNAs of different lengths corresponding to two polyadenylation sites. This result was corroborated by data raised by serial analysis of gene expression (SAGE). FCGR3B allele polymorphisms, from this article [FCGR3B*02 (HNA-1b, NA2)] and from the literature, are described for the first time according to the IMGT standardized nomenclature and to the IMGT unique numbering for C-LIKE-DOMAIN (http://imgt.cines.fr). These rules, described in the IMGT Scientific chart, are based on the IMGT-ONTOLOGY concepts. IMGT allele alignments and IMGT Collier de Perles graphical two-dimensional representations are provided for the two Ig-like domains (or C-LIKE-DOMAINs) [D1] and [D2] of FCGR3B*02. The standardized description of FCGR3B allele polymorphisms was approved by the IMGT Nomenclature Committee (IMGT-NC) and is freely available in IMGT repertoire at IMGT, http://imgt.cines.fr.
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Affiliation(s)
- G Bertrand
- Laboratoire R & D, Agents Transmissibles par transfusion, Etablissement Français du Sang Pyrénées-Méditerranée, Montpellier, France
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Lefranc MP, Giudicelli V, Ginestoux C, Bosc N, Folch G, Guiraudou D, Jabado-Michaloud J, Magris S, Scaviner D, Thouvenin V, Combres K, Girod D, Jeanjean S, Protat C, Yousfi-Monod M, Duprat E, Kaas Q, Pommié C, Chaume D, Lefranc G. IMGT-ONTOLOGY for immunogenetics and immunoinformatics. In Silico Biol 2004; 4:17-29. [PMID: 15089751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
IMGT, the international ImMunoGeneTics information system(R) (http://imgt.cines.fr), is a high quality integrated knowledge resource specializing in immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC) and related proteins of the immune system (RPI) of human and other vertebrates, created in 1989, by the Laboratoire d'ImmunoGenetique Moleculaire LIGM. IMGT provides a common access to standardized data which include nucleotide and protein sequences, oligonucleotide primers, gene maps, genetic polymorphisms, specificities, 2D and 3D structures. IMGT consists of several sequence databases (IMGT/LIGM-DB, IMGT/MHC-DB, IMGT/PRIMER-DB), one genome database (IMGT/GENE-DB) and one three-dimensional structure database (IMGT/3Dstructure-DB), interactive tools for sequence analysis (IMGT/V-QUEST, IMGT/JunctionAnalysis, IMGT/PhyloGene, IMGT/Allele-Align), for genome analysis (IMGT/GeneSearch, IMGT/GeneView, IMGT/LocusView) and for 3D structure analysis (IMGT/StructuralQuery), and Web resources ("IMGT Marie-Paule page") comprising 8000 HTML pages. IMGT other accesses include SRS, FTP, search by BLAST, etc. By its high quality and its easy data distribution, IMGT has important implications in medical research (repertoire in autoimmune diseases, AIDS, leukemias, lymphomas, myelomas), veterinary research, genome diversity and genome evolution studies of the adaptive immune responses, biotechnology related to antibody engineering (scFv, phage displays, combinatorial libraries) and therapeutical approaches (grafts, immunotherapy). IMGT is freely available at http://imgt.cines.fr.
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Affiliation(s)
- Marie-Paule Lefranc
- IMGT, the international ImMunoGeneTics information system. Universite Montpellier II, Laboratoire d'ImmunoGenetique Moleculaire LIGM UPR CNRS 1142, Institut de Genetique Humaine IGH, Montpellier Cedex 5, France.
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Wickerham LJ, Duprat E. A Remarkable Fission Yeast, Schizosaccharomyces versatilis NOV. SP. J Bacteriol 1945; 50:597-607. [PMID: 16561035 PMCID: PMC374175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023] Open
Affiliation(s)
- L J Wickerham
- Fermentation Division, Northern Regional Research Laboratory, Peoria, Illinois
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