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Okutman O, Gürbüz AS, Büyük U, Real E, Leconte R, Chennen K, Mayer C, Muller J, Le May N, Viville S. Pathogenic missense variation in PABPC1L/EPAB causes female infertility due to oocyte maturation arrest at the germinal vesicle stage. J Assist Reprod Genet 2024; 41:311-322. [PMID: 38177974 PMCID: PMC10894787 DOI: 10.1007/s10815-023-03009-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 12/13/2023] [Indexed: 01/06/2024] Open
Abstract
Women undergoing controlled ovarian hyperstimulation prior to in vitro fertilization (IVF) are treated using various protocols to induce multiple follicular growths. Complete failure of all oocytes to mature during IVF cycles is rare; however, it is a known cause of primary female infertility. Recently, pathogenic variations in a few genes have been identified in women with oocyte maturation defects; however, the underlying genetic causes remain largely unknown.This study included a Turkish family comprising three sisters with recurring oocyte maturation arrest at the germinal vesicle stage after multiple ovarian stimulations. Exome sequencing revealed a homozygous missense variant (c.1037C>T, p.Ala346Val) in the EPAB gene (also known as PABPC1L) in all three affected sisters, which was either absent or heterozygous in the unaffected family members. Functional experiments confirming the pathogenicity of the variant were performed by transfecting HEK293T cells and demonstrated the instability and increased rate of proteolysis of the mutated PABPC1L/EPAB protein. The identified variant, located in the well-conserved fourth RNA recognition motif (RRM4), in silico 3D modelling suggested changes in the physical properties of the pathogenic variant of PABPC1L/EPAB. Our findings validate PABPC1L/EPAB as an essential genetic contributor to the oocyte maturation process in humans and have direct implications for the genetic counselling of patients and their family members.
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Affiliation(s)
- O Okutman
- Université Libre de Bruxelles (ULB), Hôpital Universitaire de Bruxelles (H.U.B), Hôpital Erasme, Service de Gynécologie-Obstetrique, Clinique de Fertilité, Route de Lennik, 808, 1070, Brussels, Belgium
| | | | - U Büyük
- Department of Molecular Biology and Genetics, Institute of Graduate Studies in Sciences, Istanbul University, Istanbul, Turkey
| | - E Real
- Laboratoire de Génétique Médicale LGM, Institut de Génétique Médicale d'Alsace IGMA, INSERM UMR 1112, Université de Strasbourg, Strasbourg, France
| | - R Leconte
- Laboratoire de Génétique Médicale LGM, Institut de Génétique Médicale d'Alsace IGMA, INSERM UMR 1112, Université de Strasbourg, Strasbourg, France
| | - K Chennen
- Complex Systems and Translational Bioinformatics, ICube UMR 7357, Université de Strasbourg, 67000, Strasbourg, France
| | - C Mayer
- Complex Systems and Translational Bioinformatics, ICube UMR 7357, Université de Strasbourg, 67000, Strasbourg, France
- UFR Sciences de La Vie, Université Paris Cité, 75013, Paris, France
| | - J Muller
- Laboratoire de Génétique Médicale LGM, Institut de Génétique Médicale d'Alsace IGMA, INSERM UMR 1112, Université de Strasbourg, Strasbourg, France
- Unité Fonctionnelle de Bioinformatique Médicale Appliquée Au Diagnostic (UF7363), Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - N Le May
- Laboratoire de Génétique Médicale LGM, Institut de Génétique Médicale d'Alsace IGMA, INSERM UMR 1112, Université de Strasbourg, Strasbourg, France
| | - S Viville
- Laboratoire de Génétique Médicale LGM, Institut de Génétique Médicale d'Alsace IGMA, INSERM UMR 1112, Université de Strasbourg, Strasbourg, France.
- Laboratoire de Diagnostic Génétique, Unité de Génétique de L'infertilité (UF3472), Hôpitaux Universitaires de Strasbourg, 67091, Strasbourg, France.
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2
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Scalzitti N, Kress A, Orhand R, Weber T, Moulinier L, Jeannin-Girardon A, Collet P, Poch O, Thompson JD. Spliceator: multi-species splice site prediction using convolutional neural networks. BMC Bioinformatics 2021; 22:561. [PMID: 34814826 PMCID: PMC8609763 DOI: 10.1186/s12859-021-04471-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 11/09/2021] [Indexed: 12/14/2022] Open
Abstract
Background Ab initio prediction of splice sites is an essential step in eukaryotic genome annotation. Recent predictors have exploited Deep Learning algorithms and reliable gene structures from model organisms. However, Deep Learning methods for non-model organisms are lacking. Results We developed Spliceator to predict splice sites in a wide range of species, including model and non-model organisms. Spliceator uses a convolutional neural network and is trained on carefully validated data from over 100 organisms. We show that Spliceator achieves consistently high accuracy (89–92%) compared to existing methods on independent benchmarks from human, fish, fly, worm, plant and protist organisms. Conclusions Spliceator is a new Deep Learning method trained on high-quality data, which can be used to predict splice sites in diverse organisms, ranging from human to protists, with consistently high accuracy. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04471-3.
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Affiliation(s)
- Nicolas Scalzitti
- Complex Systems and Translational Bioinformatics (CSTB), ICube Laboratory, UMR7357, University of Strasbourg, 1 rue Eugène Boeckel, 67000, Strasbourg, France
| | - Arnaud Kress
- Complex Systems and Translational Bioinformatics (CSTB), ICube Laboratory, UMR7357, University of Strasbourg, 1 rue Eugène Boeckel, 67000, Strasbourg, France.,BiGEst-ICube Platform, ICube Laboratory, UMR7357, 1 rue Eugène Boeckel, 67000, Strasbourg, France
| | - Romain Orhand
- Complex Systems and Translational Bioinformatics (CSTB), ICube Laboratory, UMR7357, University of Strasbourg, 1 rue Eugène Boeckel, 67000, Strasbourg, France
| | - Thomas Weber
- Complex Systems and Translational Bioinformatics (CSTB), ICube Laboratory, UMR7357, University of Strasbourg, 1 rue Eugène Boeckel, 67000, Strasbourg, France
| | - Luc Moulinier
- Complex Systems and Translational Bioinformatics (CSTB), ICube Laboratory, UMR7357, University of Strasbourg, 1 rue Eugène Boeckel, 67000, Strasbourg, France.,BiGEst-ICube Platform, ICube Laboratory, UMR7357, 1 rue Eugène Boeckel, 67000, Strasbourg, France
| | - Anne Jeannin-Girardon
- Complex Systems and Translational Bioinformatics (CSTB), ICube Laboratory, UMR7357, University of Strasbourg, 1 rue Eugène Boeckel, 67000, Strasbourg, France
| | - Pierre Collet
- Complex Systems and Translational Bioinformatics (CSTB), ICube Laboratory, UMR7357, University of Strasbourg, 1 rue Eugène Boeckel, 67000, Strasbourg, France
| | - Olivier Poch
- Complex Systems and Translational Bioinformatics (CSTB), ICube Laboratory, UMR7357, University of Strasbourg, 1 rue Eugène Boeckel, 67000, Strasbourg, France
| | - Julie D Thompson
- Complex Systems and Translational Bioinformatics (CSTB), ICube Laboratory, UMR7357, University of Strasbourg, 1 rue Eugène Boeckel, 67000, Strasbourg, France.
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3
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Novel Approach Combining Transcriptional and Evolutionary Signatures to Identify New Multiciliation Genes. Genes (Basel) 2021; 12:genes12091452. [PMID: 34573434 PMCID: PMC8470418 DOI: 10.3390/genes12091452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 11/19/2022] Open
Abstract
Multiciliogenesis is a complex process that allows the generation of hundreds of motile cilia on the surface of specialized cells, to create fluid flow across epithelial surfaces. Dysfunction of human multiciliated cells is associated with diseases of the brain, airway and reproductive tracts. Despite recent efforts to characterize the transcriptional events responsible for the differentiation of multiciliated cells, a lot of actors remain to be identified. In this work, we capitalize on the ever-growing quantity of high-throughput data to search for new candidate genes involved in multiciliation. After performing a large-scale screening using 10 transcriptomics datasets dedicated to multiciliation, we established a specific evolutionary signature involving Otomorpha fish to use as a criterion to select the most likely targets. Combining both approaches highlighted a list of 114 potential multiciliated candidates. We characterized these genes first by generating protein interaction networks, which showed various clusters of ciliated and multiciliated genes, and then by computing phylogenetic profiles. In the end, we selected 11 poorly characterized genes that seem like particularly promising multiciliated candidates. By combining functional and comparative genomics methods, we developed a novel type of approach to study biological processes and identify new promising candidates linked to that process.
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4
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Schmitt E, Coureux PD, Kazan R, Bourgeois G, Lazennec-Schurdevin C, Mechulam Y. Recent Advances in Archaeal Translation Initiation. Front Microbiol 2020; 11:584152. [PMID: 33072057 PMCID: PMC7531240 DOI: 10.3389/fmicb.2020.584152] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 08/24/2020] [Indexed: 12/20/2022] Open
Abstract
Translation initiation (TI) allows accurate selection of the initiation codon on a messenger RNA (mRNA) and defines the reading frame. In all domains of life, translation initiation generally occurs within a macromolecular complex made up of the small ribosomal subunit, the mRNA, a specialized methionylated initiator tRNA, and translation initiation factors (IFs). Once the start codon is selected at the P site of the ribosome and the large subunit is associated, the IFs are released and a ribosome competent for elongation is formed. However, even if the general principles are the same in the three domains of life, the molecular mechanisms are different in bacteria, eukaryotes, and archaea and may also vary depending on the mRNA. Because TI mechanisms have evolved lately, their studies bring important information about the evolutionary relationships between extant organisms. In this context, recent structural data on ribosomal complexes and genome-wide studies are particularly valuable. This review focuses on archaeal translation initiation highlighting its relationships with either the eukaryotic or the bacterial world. Eukaryotic features of the archaeal small ribosomal subunit are presented. Ribosome evolution and TI mechanisms diversity in archaeal branches are discussed. Next, the use of leaderless mRNAs and that of leadered mRNAs having Shine-Dalgarno sequences is analyzed. Finally, the current knowledge on TI mechanisms of SD-leadered and leaderless mRNAs is detailed.
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Affiliation(s)
- Emmanuelle Schmitt
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole Polytechnique, CNRS-UMR7654, Institut Polytechnique de Paris, Palaiseau, France
| | - Pierre-Damien Coureux
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole Polytechnique, CNRS-UMR7654, Institut Polytechnique de Paris, Palaiseau, France
| | - Ramy Kazan
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole Polytechnique, CNRS-UMR7654, Institut Polytechnique de Paris, Palaiseau, France
| | - Gabrielle Bourgeois
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole Polytechnique, CNRS-UMR7654, Institut Polytechnique de Paris, Palaiseau, France
| | - Christine Lazennec-Schurdevin
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole Polytechnique, CNRS-UMR7654, Institut Polytechnique de Paris, Palaiseau, France
| | - Yves Mechulam
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole Polytechnique, CNRS-UMR7654, Institut Polytechnique de Paris, Palaiseau, France
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5
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Delfosse V, Bourguet W, Drin G. Structural and Functional Specialization of OSBP-Related Proteins. ACTA ACUST UNITED AC 2020. [DOI: 10.1177/2515256420946627] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Lipids are precisely distributed in the eukaryotic cell where they help to define organelle identity and function, in addition to their structural role. Once synthesized, many lipids must be delivered to other compartments by non-vesicular routes, a process that is undertaken by proteins called Lipid Transfer Proteins (LTPs). OSBP and the closely-related ORP and Osh proteins constitute a major, evolutionarily conserved family of LTPs in eukaryotes. Most of these target one or more subcellular regions, and membrane contact sites in particular, where two organelle membranes are in close proximity. It was initially thought that such proteins were strictly dedicated to sterol sensing or transport. However, over the last decade, numerous studies have revealed that these proteins have many more functions, and we have expanded our understanding of their mechanisms. In particular, many of them are lipid exchangers that exploit PI(4)P or possibly other phosphoinositide gradients to directionally transfer sterol or PS between two compartments. Importantly, these transfer activities are tightly coupled to processes such as lipid metabolism, cellular signalling and vesicular trafficking. This review describes the molecular architecture of OSBP/ORP/Osh proteins, showing how their specific structural features and internal configurations impart unique cellular functions.
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Affiliation(s)
- Vanessa Delfosse
- Centre de Biochimie Structurale, Inserm, CNRS, Univ Montpellier, Montpellier, France
| | - William Bourguet
- Centre de Biochimie Structurale, Inserm, CNRS, Univ Montpellier, Montpellier, France
| | - Guillaume Drin
- CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d’Azur, Valbonne, France
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6
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Huang Y, Zheng X, Pilgaard B, Holck J, Muschiol J, Li S, Lange L. Identification and characterization of GH11 xylanase and GH43 xylosidase from the chytridiomycetous fungus, Rhizophlyctis rosea. Appl Microbiol Biotechnol 2018; 103:777-791. [PMID: 30397764 PMCID: PMC6373445 DOI: 10.1007/s00253-018-9431-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 09/26/2018] [Accepted: 09/28/2018] [Indexed: 11/08/2022]
Abstract
The early-lineage, aerobic, zoosporic fungi from the Chytridiomycota constitute less than 1% of the described fungi and can use diverse sources of nutrition from plant or animal products. One of the ancestral sources of fungal nutrition could be products following enzymatic degradation of plant material. However, carbohydrate-active enzymes from these ancient fungi have been less studied. A GH11 xylanase (RrXyn11A) (EC 3.2.1.8) and a GH43 xylosidase (RrXyl43A) (EC 3.2.1.37) were identified from an early-lineage aerobic zoosporic fungus, Rhizophlyctis rosea NBRC 105426. Both genes were heterologously expressed in Pichia pastoris and the recombinant enzymes were purified and characterized. The optimal pH for recombinant RrXyn11A and RrXyl43A was pH 7. RrXyn11A had high stability over a wide range of pH (4–8) and temperature (25–70 °C). RrXyn11A also showed high substrate specificity on both azurine-cross-linked (AZCL) arabinoxylan and AZCL xylan. RrXyl43A had β-xylosidase and minor α-l-arabinofuranosidase activity. This enzyme showed low product inhibition and retained 51% activity in the presence of 100 mM xylose. A combination of RrXyn11A and RrXyl43A exhibited significantly higher hydrolytic and polymer degradation capability and xylose release on wheat bran and beechwood xylan compared to treatment with commercial enzymes. This study was the first to heterologously express and characterize the GH11 xylanase (RrXyn11A) and GH43 xylosidase (RrXyl43A) from the ancient fungus, R. rosea. Meanwhile, this study also demonstrated that the enzymes from the ancient fungus R. rosea can be easily handled and heterologously expressed in Pichia, which presents a promising path to a new source of enzymes for biomass degradation.
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Affiliation(s)
- Yuhong Huang
- Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Xianliang Zheng
- Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark.,Sino-Danish Center for Education and Research, Beijing, 100190, China.,The National Food Institute, Technical University of Denmark, Building 201, Søltofts Plads, 2800, Kongens Lyngby, Denmark.,Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Bo Pilgaard
- Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Jesper Holck
- Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Jan Muschiol
- Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Shengying Li
- Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark.,Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Lene Lange
- Chemical and Biochemical Engineering, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark.
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7
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Production of unstable proteins through the formation of stable core complexes. Nat Commun 2016; 7:10932. [PMID: 26983699 PMCID: PMC4800440 DOI: 10.1038/ncomms10932] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 02/02/2016] [Indexed: 11/30/2022] Open
Abstract
Purification of proteins that participate in large transient complexes is impeded by low amounts, heterogeneity, instability and poor solubility. To circumvent these difficulties we set up a methodology that enables the production of stable complexes for structural and functional studies. This procedure is benchmarked and applied to two challenging protein families: the human steroid nuclear receptors (SNR) and the HIV-1 pre-integration complex. In the context of transcriptional regulation studies, we produce and characterize the ligand-binding domains of the glucocorticoid nuclear receptor and the oestrogen receptor beta in complex with a TIF2 (transcriptional intermediary factor 2) domain containing the three SNR-binding motifs. In the context of retroviral integration, we demonstrate the stabilization of the HIV-1 integrase by formation of complexes with partner proteins and DNA. This procedure provides a powerful research tool for structural and functional studies of proteins participating in non-covalent macromolecular complexes. Flexible or disordered domains often hinder the purification of proteins involved in functional interactions. Here the authors describe an approach that enables the production of stable and functional complexes of otherwise unstable proteins in quantities sufficient for structural and functional studies.
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8
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Broadbent JA, Broszczak DA, Tennakoon IUK, Huygens F. Pan-proteomics, a concept for unifying quantitative proteome measurements when comparing closely-related bacterial strains. Expert Rev Proteomics 2016; 13:355-65. [PMID: 26889693 DOI: 10.1586/14789450.2016.1155986] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The comparison of proteomes between genetically heterogeneous bacterial strains may offer valuable insights into physiological diversity and function, particularly where such variation aids in the survival and virulence of clinically-relevant strains. However, reports of such comparisons frequently fail to account for underlying genetic variance. As a consequence, the current knowledge regarding bacterial physiological diversity at the protein level may be incomplete or inaccurate. To address this, greater consideration must be given to the impact of genetic heterogeneity on proteome comparisons. This may be possible through the use of pan-proteomics, an analytical concept that permits the ability to qualitatively and quantitatively compare the proteomes of genetically heterogeneous organisms. Limited examples of this emerging technology highlight currently unmet analytical challenges. In this article we define pan-proteomics, where its value lies in microbiology, and discuss the technical considerations critical to its successful execution and potential future application.
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Affiliation(s)
- James A Broadbent
- a Tissue Repair and Regeneration Program, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health , Queensland University of Technology , Brisbane , Australia.,b Molecular Microbiological Pathogenesis Group, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health , Queensland University of Technology , Brisbane , Australia
| | - Daniel A Broszczak
- a Tissue Repair and Regeneration Program, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health , Queensland University of Technology , Brisbane , Australia
| | - Imalka U K Tennakoon
- b Molecular Microbiological Pathogenesis Group, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health , Queensland University of Technology , Brisbane , Australia
| | - Flavia Huygens
- b Molecular Microbiological Pathogenesis Group, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health , Queensland University of Technology , Brisbane , Australia
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9
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D'Alessandro M, Hnia K, Gache V, Koch C, Gavriilidis C, Rodriguez D, Nicot AS, Romero NB, Schwab Y, Gomes E, Labouesse M, Laporte J. Amphiphysin 2 Orchestrates Nucleus Positioning and Shape by Linking the Nuclear Envelope to the Actin and Microtubule Cytoskeleton. Dev Cell 2016; 35:186-98. [PMID: 26506308 DOI: 10.1016/j.devcel.2015.09.018] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 07/31/2015] [Accepted: 09/23/2015] [Indexed: 12/31/2022]
Abstract
Nucleus positioning is key for intracellular organization, cell differentiation, and organ development and is affected in many diseases, including myopathies due to alteration in amphiphysin-2 (BIN1). The actin and microtubule cytoskeletons are essential for nucleus positioning, but their crosstalk in this process is sparsely characterized. Here, we report that impairment of amphiphysin/BIN1 in Caenorhabditis elegans, mammalian cells, or muscles from patients with centronuclear myopathy alters nuclear position and shape. We show that AMPH-1/BIN1 binds to nesprin and actin, as well as to the microtubule-binding protein CLIP170 in both species. Expression of the microtubule-anchoring CAP-GLY domain of CLIP170 fused to the nuclear-envelope-anchoring KASH domain of nesprin rescues nuclear positioning defects of amph-1 mutants. Amphiphysins thus play a central role in linking the nuclear envelope with the actin and microtubule cytoskeletons. We propose that BIN1 has a direct and evolutionarily conserved role in nuclear positioning, altered in myopathies.
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Affiliation(s)
- Manuela D'Alessandro
- IGBMC, INSERM U964, CNRS UMR7104, Strasbourg University, 67404 Illkirch, France; University Claude Bernard Lyon 1, CGphiMC UMR CNRS 5534, 69622 Villeurbanne, France.
| | - Karim Hnia
- IGBMC, INSERM U964, CNRS UMR7104, Strasbourg University, 67404 Illkirch, France
| | - Vincent Gache
- Myology Group, UMR S 787 INSERM, Université Pierre et Marie Curie Paris 6, 75634 Paris, France; CNRS UMR5239, Laboratoire de Biologie Moléculaire de la Cellule (LBMC), Ecole Normale Supérieure de Lyon, 69364 Lyon Cedex 07, France
| | - Catherine Koch
- IGBMC, INSERM U964, CNRS UMR7104, Strasbourg University, 67404 Illkirch, France
| | | | - David Rodriguez
- IGBMC, INSERM U964, CNRS UMR7104, Strasbourg University, 67404 Illkirch, France
| | - Anne-Sophie Nicot
- IGBMC, INSERM U964, CNRS UMR7104, Strasbourg University, 67404 Illkirch, France
| | - Norma B Romero
- Morphology Neuromuscular Unit of the Myology Institute, GHU Pitié-Salpêtrière, 75013 Paris, France
| | - Yannick Schwab
- IGBMC, INSERM U964, CNRS UMR7104, Strasbourg University, 67404 Illkirch, France; Cell Biology and Biophysics Unit, EMBL Heidelberg, 69117 Heidelberg, Germany
| | - Edgar Gomes
- Myology Group, UMR S 787 INSERM, Université Pierre et Marie Curie Paris 6, 75634 Paris, France; Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Michel Labouesse
- IGBMC, INSERM U964, CNRS UMR7104, Strasbourg University, 67404 Illkirch, France; UMR7622, IBPS, UPMC, 75252 Paris, France
| | - Jocelyn Laporte
- IGBMC, INSERM U964, CNRS UMR7104, Strasbourg University, 67404 Illkirch, France.
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10
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Fischer MJC, Rustenhloz C, Leh-Louis V, Perrière G. Molecular and functional evolution of the fungal diterpene synthase genes. BMC Microbiol 2015; 15:221. [PMID: 26483054 PMCID: PMC4617483 DOI: 10.1186/s12866-015-0564-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 10/12/2015] [Indexed: 11/24/2022] Open
Abstract
Background Terpenes represent one of the largest and most diversified families of natural compounds and are used in numerous industrial applications. Terpene synthase (TPS) genes originated in bacteria as diterpene synthase (di-TPS) genes. They are also found in plant and fungal genomes. The recent availability of a large number of fungal genomes represents an opportunity to investigate how genes involved in diterpene synthesis were acquired by fungi, and to assess the consequences of this process on the fungal metabolism. Results In order to investigate the origin of fungal di-TPS, we implemented a search for potential fungal di-TPS genes and identified their presence in several unrelated Ascomycota and Basidiomycota species. The fungal di-TPS phylogenetic tree is function-related but is not associated with the phylogeny based on housekeeping genes. The lack of agreement between fungal and di-TPS-based phylogenies suggests the presence of Horizontal Gene Transfer (HGTs) events. Further evidence for HGT was provided by conservation of synteny of di-TPS and neighbouring genes in distantly related fungi. Conclusions The results obtained here suggest that fungal di-TPSs originated from an ancient HGT event of a single di-TPS gene from a plant to a fungus in Ascomycota. In fungi, these di-TPSs allowed for the formation of clusters consisting in di-TPS, GGPPS and P450 genes to create functional clusters that were transferred between fungal species, producing diterpenes acting as hormones or toxins, thus affecting fungal development and pathogenicity. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0564-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marc J C Fischer
- Université de Strasbourg, INRA, Inst Natl Recherche Agron, Métab Second Vigne, Unit Mixte Recherche Santé Vigne & Qual Vins, 28 rue de Herrlisheim, F-68021, Colmar, France.
| | - Camille Rustenhloz
- Université de Strasbourg, INRA, Inst Natl Recherche Agron, Métab Second Vigne, Unit Mixte Recherche Santé Vigne & Qual Vins, 28 rue de Herrlisheim, F-68021, Colmar, France.
| | - Véronique Leh-Louis
- Université de Strasbourg, CNRS, FRE 2326, Institut de Biologie Moléculaire et Cellulaire du CNRS, UPR 9002, 15 rue René Descartes, F-67084, Strasbourg, France.
| | - Guy Perrière
- Universite Claude Bernard - Lyon 1, 43 bd. du 11 Novembre 1918, Laboratoire de Biometrie et Biologie Evolutive, UMR CNRS 5558, F-69622, Villeurbanne, France.
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11
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Bianchetti L, Tarabay Y, Lecompte O, Stote R, Poch O, Dejaegere A, Viville S. Tex19 and Sectm1 concordant molecular phylogenies support co-evolution of both eutherian-specific genes. BMC Evol Biol 2015; 15:222. [PMID: 26459560 PMCID: PMC4603632 DOI: 10.1186/s12862-015-0506-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 10/01/2015] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Transposable elements (TE) have attracted much attention since they shape the genome and contribute to species evolution. Organisms have evolved mechanisms to control TE activity. Testis expressed 19 (Tex19) represses TE expression in mouse testis and placenta. In the human and mouse genomes, Tex19 and Secreted and transmembrane 1 (Sectm1) are neighbors but are not homologs. Sectm1 is involved in immunity and its molecular phylogeny is unknown. METHODS Using multiple alignments of complete protein sequences (MACS), we inferred Tex19 and Sectm1 molecular phylogenies. Protein conserved regions were identified and folds were predicted. Finally, expression patterns were studied across tissues and species using RNA-seq public data and RT-PCR. RESULTS We present 2 high quality alignments of 58 Tex19 and 58 Sectm1 protein sequences from 48 organisms. First, both genes are eutherian-specific, i.e., exclusively present in mammals except monotremes (platypus) and marsupials. Second, Tex19 and Sectm1 have both duplicated in Sciurognathi and Bovidae while they have remained as single copy genes in all further placental mammals. Phylogenetic concordance between both genes was significant (p-value < 0.05) and supported co-evolution and functional relationship. At the protein level, Tex19 exhibits 3 conserved regions and 4 invariant cysteines. In particular, a CXXC motif is present in the N-terminal conserved region. Sectm1 exhibits 2 invariant cysteines and an Ig-like domain. Strikingly, Tex19 C-terminal conserved region was lost in Haplorrhini primates while a Sectm1 C-terminal extra domain was acquired. Finally, we have determined that Tex19 and Sectm1 expression levels anti-correlate across the testis of several primates (ρ = -0.72) which supports anti-regulation. CONCLUSIONS Tex19 and Sectm1 co-evolution and anti-regulated expressions support a strong functional relationship between both genes. Since Tex19 operates a control on TE and Sectm1 plays a role in immunity, Tex19 might suppress an immune response directed against cells that show TE activity in eutherian reproductive tissues.
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Affiliation(s)
- Laurent Bianchetti
- Biocomputing and Molecular Modelling Laboratory, Integrated Structural Biology Department, Genetics institute of Molecular and Cellular Biology (IGBMC), INSERM U964/CNRS UMR 1704/Strasbourg University, 1 rue Laurent Fries, 67404, Illkirch, France.
| | - Yara Tarabay
- Primordial Germ Cells' Ontogeny and Pluripotency Laboratory, Functional Genomics and Cancer Department, Genetics Institute of Molecular and Cellular Biology (IGBMC), INSERM U964/CNRS UMR 1704/Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France. .,Present address: Institut de génétique humaine (IGH), 141 rue de la Cardonille, 34396, Montpellier, France.
| | - Odile Lecompte
- Bioinformatics and Integrated Genomics Laboratory (LBGI), ICube, CNRS UMR 7357/Université de Strasbourg, 11 rue Humann, 67085, Strasbourg, France.
| | - Roland Stote
- Biocomputing and Molecular Modelling Laboratory, Integrated Structural Biology Department, Genetics institute of Molecular and Cellular Biology (IGBMC), INSERM U964/CNRS UMR 1704/Strasbourg University, 1 rue Laurent Fries, 67404, Illkirch, France.
| | - Olivier Poch
- Bioinformatics and Integrated Genomics Laboratory (LBGI), ICube, CNRS UMR 7357/Université de Strasbourg, 11 rue Humann, 67085, Strasbourg, France.
| | - Annick Dejaegere
- Biocomputing and Molecular Modelling Laboratory, Integrated Structural Biology Department, Genetics institute of Molecular and Cellular Biology (IGBMC), INSERM U964/CNRS UMR 1704/Strasbourg University, 1 rue Laurent Fries, 67404, Illkirch, France.
| | - Stéphane Viville
- Primordial Germ Cells' Ontogeny and Pluripotency Laboratory, Functional Genomics and Cancer Department, Genetics Institute of Molecular and Cellular Biology (IGBMC), INSERM U964/CNRS UMR 1704/Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France. .,Centre Hospitalier Universitaire, 67000, Strasbourg, France.
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12
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Carroll AJ, Zhang P, Whitehead L, Kaines S, Tcherkez G, Badger MR. PhenoMeter: A Metabolome Database Search Tool Using Statistical Similarity Matching of Metabolic Phenotypes for High-Confidence Detection of Functional Links. Front Bioeng Biotechnol 2015; 3:106. [PMID: 26284240 PMCID: PMC4518198 DOI: 10.3389/fbioe.2015.00106] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 07/10/2015] [Indexed: 12/14/2022] Open
Abstract
This article describes PhenoMeter (PM), a new type of metabolomics database search that accepts metabolite response patterns as queries and searches the MetaPhen database of reference patterns for responses that are statistically significantly similar or inverse for the purposes of detecting functional links. To identify a similarity measure that would detect functional links as reliably as possible, we compared the performance of four statistics in correctly top-matching metabolic phenotypes of Arabidopsis thaliana metabolism mutants affected in different steps of the photorespiration metabolic pathway to reference phenotypes of mutants affected in the same enzymes by independent mutations. The best performing statistic, the PM score, was a function of both Pearson correlation and Fisher's Exact Test of directional overlap. This statistic outperformed Pearson correlation, biweight midcorrelation and Fisher's Exact Test used alone. To demonstrate general applicability, we show that the PM reliably retrieved the most closely functionally linked response in the database when queried with responses to a wide variety of environmental and genetic perturbations. Attempts to match metabolic phenotypes between independent studies were met with varying success and possible reasons for this are discussed. Overall, our results suggest that integration of pattern-based search tools into metabolomics databases will aid functional annotation of newly recorded metabolic phenotypes analogously to the way sequence similarity search algorithms have aided the functional annotation of genes and proteins. PM is freely available at MetabolomeExpress (https://www.metabolome-express.org/phenometer.php).
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Affiliation(s)
- Adam J. Carroll
- College of Medicine, Biology and Environment, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Peng Zhang
- College of Medicine, Biology and Environment, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Lynne Whitehead
- College of Medicine, Biology and Environment, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Sarah Kaines
- College of Medicine, Biology and Environment, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Guillaume Tcherkez
- College of Medicine, Biology and Environment, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Murray R. Badger
- College of Medicine, Biology and Environment, Research School of Biology, The Australian National University, Canberra, ACT, Australia
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Beinsteiner B, Michalon J, Klaholz BP. IBiSS, a versatile and interactive tool for integrated sequence and 3D structure analysis of large macromolecular complexes. Bioinformatics 2015; 31:3339-44. [DOI: 10.1093/bioinformatics/btv347] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 05/30/2015] [Indexed: 11/13/2022] Open
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14
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Marton L, Nagy GN, Ozohanics O, Lábas A, Krámos B, Oláh J, Vékey K, Vértessy BG. Molecular Mechanism for the Thermo-Sensitive Phenotype of CHO-MT58 Cell Line Harbouring a Mutant CTP:Phosphocholine Cytidylyltransferase. PLoS One 2015; 10:e0129632. [PMID: 26083347 PMCID: PMC4470507 DOI: 10.1371/journal.pone.0129632] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 05/10/2015] [Indexed: 01/27/2023] Open
Abstract
Control and elimination of malaria still represents a major public health challenge. Emerging parasite resistance to current therapies urges development of antimalarials with novel mechanism of action. Phospholipid biosynthesis of the Plasmodium parasite has been validated as promising candidate antimalarial target. The most prevalent de novo pathway for synthesis of phosphatidylcholine is the Kennedy pathway. Its regulatory and often also rate limiting step is catalyzed by CTP:phosphocholine cytidylyltransferase (CCT). The CHO-MT58 cell line expresses a mutant variant of CCT, and displays a thermo-sensitive phenotype. At non-permissive temperature (40°C), the endogenous CCT activity decreases dramatically, blocking membrane synthesis and ultimately leading to apoptosis. In the present study we investigated the impact of the analogous mutation in a catalytic domain construct of Plasmodium falciparum CCT in order to explore the underlying molecular mechanism that explains this phenotype. We used temperature dependent enzyme activity measurements and modeling to investigate the functionality of the mutant enzyme. Furthermore, MS measurements were performed to determine the oligomerization state of the protein, and MD simulations to assess the inter-subunit interactions in the dimer. Our results demonstrate that the R681H mutation does not directly influence enzyme catalytic activity. Instead, it provokes increased heat-sensitivity by destabilizing the CCT dimer. This can possibly explain the significance of the PfCCT pseudoheterodimer organization in ensuring proper enzymatic function. This also provide an explanation for the observed thermo-sensitive phenotype of CHO-MT58 cell line.
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Affiliation(s)
- Lívia Marton
- Institute of Enzymology, Research Centre for National Sciences, HAS, Budapest Hungary
- Doctoral School of Multidisciplinary Medical Science, University of Szeged, Szeged, Hungary
| | - Gergely N. Nagy
- Institute of Enzymology, Research Centre for National Sciences, HAS, Budapest Hungary
- Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Budapest, Hungary
| | - Olivér Ozohanics
- Institute of Organic Chemistry, Research Centre for National Sciences, HAS, Budapest, Hungary
| | - Anikó Lábas
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Budapest, Hungary
| | - Balázs Krámos
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Budapest, Hungary
| | - Julianna Oláh
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Budapest, Hungary
| | - Károly Vékey
- Institute of Organic Chemistry, Research Centre for National Sciences, HAS, Budapest, Hungary
| | - Beáta G. Vértessy
- Institute of Enzymology, Research Centre for National Sciences, HAS, Budapest Hungary
- Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Budapest, Hungary
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Comparison of structural architecture of HCV NS3 genotype 1 versus Pakistani genotype 3a. BIOMED RESEARCH INTERNATIONAL 2014; 2014:749254. [PMID: 25401105 PMCID: PMC4221965 DOI: 10.1155/2014/749254] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Revised: 08/10/2014] [Accepted: 08/19/2014] [Indexed: 11/17/2022]
Abstract
This study described the structural characterization of Pakistani HCV NS3 GT3a in parallel with genotypes 1a and 1b NS3. We investigated the role of amino acids and their interaction patterns in different HCV genotypes by crystallographic modeling. Different softwares were used to study the interaction pattern, for example, CLCBIO sequence viewer, MODELLER, NMRCLUST, ERRAT score, and MODELLER. Sixty models were produced and clustered into groups and the best model of PK-NCVI/Pk3a NS3 was selected and studied further to check the variability with other HCV NS3 genotypes. This study will help in future to understand the structural architecture of HCV genome variability and to further define the conserved targets for antiviral agents.
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16
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Gadelle D, Krupovic M, Raymann K, Mayer C, Forterre P. DNA topoisomerase VIII: a novel subfamily of type IIB topoisomerases encoded by free or integrated plasmids in Archaea and Bacteria. Nucleic Acids Res 2014; 42:8578-91. [PMID: 24990376 PMCID: PMC4117785 DOI: 10.1093/nar/gku568] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 06/10/2014] [Accepted: 06/11/2014] [Indexed: 11/14/2022] Open
Abstract
Type II DNA topoisomerases are divided into two families, IIA and IIB. Types IIA and IIB enzymes share homologous B subunits encompassing the ATP-binding site, but have non-homologous A subunits catalyzing DNA cleavage. Type IIA topoisomerases are ubiquitous in Bacteria and Eukarya, whereas members of the IIB family are mostly present in Archaea and plants. Here, we report the detection of genes encoding type IIB enzymes in which the A and B subunits are fused into a single polypeptide. These proteins are encoded in several bacterial genomes, two bacterial plasmids and one archaeal plasmid. They form a monophyletic group that is very divergent from archaeal and eukaryotic type IIB enzymes (DNA topoisomerase VI). We propose to classify them into a new subfamily, denoted DNA topoisomerase VIII. Bacterial genes encoding a topoisomerase VIII are present within integrated mobile elements, most likely derived from conjugative plasmids. Purified topoisomerase VIII encoded by the plasmid pPPM1a from Paenibacillus polymyxa M1 had ATP-dependent relaxation and decatenation activities. In contrast, the enzyme encoded by mobile elements integrated into the genome of Ammonifex degensii exhibited DNA cleavage activity producing a full-length linear plasmid and that from Microscilla marina exhibited ATP-independent relaxation activity. Topoisomerases VIII, the smallest known type IIB enzymes, could be new promising models for structural and mechanistic studies.
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Affiliation(s)
- Danièle Gadelle
- Université Paris-Sud, CNRS UMR8621, Institut de Génétique Microbiologie, 91405 Orsay Cedex, France
| | - Mart Krupovic
- Institut Pasteur, Unité de Biologie moléculaire du gène chez les extrêmophiles, Département de Microbiologie, F-75015 Paris, France
| | - Kasie Raymann
- Institut Pasteur, Unité de Biologie moléculaire du gène chez les extrêmophiles, Département de Microbiologie, F-75015 Paris, France
| | - Claudine Mayer
- Institut Pasteur, Unité de Microbiologie structurale, Département de Biologie structurale et Chimie, F-75015 Paris, France CNRS, UMR3528, F-75015 Paris, France Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, rue du Dr Roux 75015 Paris, France
| | - Patrick Forterre
- Université Paris-Sud, CNRS UMR8621, Institut de Génétique Microbiologie, 91405 Orsay Cedex, France Institut Pasteur, Unité de Biologie moléculaire du gène chez les extrêmophiles, Département de Microbiologie, F-75015 Paris, France
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17
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Huet T, Miannay FA, Patton JR, Thore S. Steroid receptor RNA activator (SRA) modification by the human pseudouridine synthase 1 (hPus1p): RNA binding, activity, and atomic model. PLoS One 2014; 9:e94610. [PMID: 24722331 PMCID: PMC3983220 DOI: 10.1371/journal.pone.0094610] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 03/18/2014] [Indexed: 11/23/2022] Open
Abstract
The most abundant of the modified nucleosides, and once considered as the “fifth” nucleotide in RNA, is pseudouridine, which results from the action of pseudouridine synthases. Recently, the mammalian pseudouridine synthase 1 (hPus1p) has been reported to modulate class I and class II nuclear receptor responses through its ability to modify the Steroid receptor RNA Activator (SRA). These findings highlight a new level of regulation in nuclear receptor (NR)-mediated transcriptional responses. We have characterised the RNA association and activity of the human Pus1p enzyme with its unusual SRA substrate. We validate that the minimal RNA fragment within SRA, named H7, is necessary for both the association and modification by hPus1p. Furthermore, we have determined the crystal structure of the catalytic domain of hPus1p at 2.0 Å resolution, alone and in a complex with several molecules present during crystallisation. This model shows an extended C-terminal helix specifically found in the eukaryotic protein, which may prevent the enzyme from forming a homodimer, both in the crystal lattice and in solution. Our biochemical and structural data help to understand the hPus1p active site architecture, and detail its particular requirements with regard to one of its nuclear substrates, the non-coding RNA SRA.
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Affiliation(s)
- Tiphaine Huet
- Department of Molecular Biology, University of Geneva, Sciences III, Geneva, Switzerland
| | | | - Jeffrey R. Patton
- Department of Pathology, Microbiology and Immunology, University of South Carolina, School of Medicine, Columbia, South Carolina, United States of America
| | - Stéphane Thore
- Department of Molecular Biology, University of Geneva, Sciences III, Geneva, Switzerland
- * E-mail:
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18
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Larousse M, Govetto B, Séassau A, Etienne C, Industri B, Theodorakopoulos N, Deleury E, Ponchet M, Panabières F, Galiana E. Characterization of PPMUCL1/2/3, three members of a new oomycete-specific mucin-like protein family residing in Phytophthora parasitica biofilm. Protist 2014; 165:275-92. [PMID: 24739437 DOI: 10.1016/j.protis.2014.03.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 02/21/2014] [Accepted: 03/10/2014] [Indexed: 11/28/2022]
Abstract
The plant pathogen Phytophthora parasitica forms a biofilm on the host surface. The biofilm transcriptome is characterized by the expression of PPMUCL1/2/3 (PHYTOPHTHORA PARASITICA MUCIN-LIKE) genes, which we report here to be members of a new, large mucin-like gene family restricted to the oomycete lineage. These genes encode secreted proteins organized into two domains. The NH2-terminal domain is highly conserved, but of unknown function. The second domain is a mucin-like domain enriched in threonine and serine residues, with a large number of putative O-glycosylation sites and a repeated motif defining 15 subgroups among the 315 members of the family. The second domain was found to be glycosylated in the recombinant rPPMUCL1 and rPPMUCL2 proteins. An analysis of PPMUCL1/2/3 gene expression indicated that these genes were expressed in a specific and coordinated manner in the biofilm. A novel cis-motif (R) bound to nuclear proteins, suggesting a possible role in PPMUCL1/2/3 gene regulation. Immunohistochemical staining revealed that the PPMUCL1/2 proteins were secreted and accumulated on the surface of the biofilm. Our data demonstrate that PPMUCL1/2/3 belong to a new oomycete-specific family of mucin-like proteins playing a structural role in the biofilm extracellular matrix.
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Affiliation(s)
- Marie Larousse
- INRA, UMR1355 Institut Sophia Agrobiotech, F-06903 Sophia Antipolis, France; University Nice Sophia Antipolis, ISA, UMR 1355, 06900 Sophia Antipolis, France; CNRS, UMR 7254, Institut Sophia Agrobiotech, F-06903 Sophia Antipolis, France
| | - Benjamin Govetto
- INRA, UMR1355 Institut Sophia Agrobiotech, F-06903 Sophia Antipolis, France; University Nice Sophia Antipolis, ISA, UMR 1355, 06900 Sophia Antipolis, France; CNRS, UMR 7254, Institut Sophia Agrobiotech, F-06903 Sophia Antipolis, France
| | - Aurélie Séassau
- INRA, UMR1355 Institut Sophia Agrobiotech, F-06903 Sophia Antipolis, France; University Nice Sophia Antipolis, ISA, UMR 1355, 06900 Sophia Antipolis, France; CNRS, UMR 7254, Institut Sophia Agrobiotech, F-06903 Sophia Antipolis, France
| | - Catherine Etienne
- INRA, UMR1355 Institut Sophia Agrobiotech, F-06903 Sophia Antipolis, France; University Nice Sophia Antipolis, ISA, UMR 1355, 06900 Sophia Antipolis, France; CNRS, UMR 7254, Institut Sophia Agrobiotech, F-06903 Sophia Antipolis, France
| | - Benoit Industri
- INRA, UMR1355 Institut Sophia Agrobiotech, F-06903 Sophia Antipolis, France; University Nice Sophia Antipolis, ISA, UMR 1355, 06900 Sophia Antipolis, France; CNRS, UMR 7254, Institut Sophia Agrobiotech, F-06903 Sophia Antipolis, France
| | - Nicolas Theodorakopoulos
- INRA, UMR1355 Institut Sophia Agrobiotech, F-06903 Sophia Antipolis, France; University Nice Sophia Antipolis, ISA, UMR 1355, 06900 Sophia Antipolis, France; CNRS, UMR 7254, Institut Sophia Agrobiotech, F-06903 Sophia Antipolis, France
| | - Emeline Deleury
- INRA, UMR1355 Institut Sophia Agrobiotech, F-06903 Sophia Antipolis, France; University Nice Sophia Antipolis, ISA, UMR 1355, 06900 Sophia Antipolis, France; CNRS, UMR 7254, Institut Sophia Agrobiotech, F-06903 Sophia Antipolis, France
| | - Michel Ponchet
- INRA, UMR1355 Institut Sophia Agrobiotech, F-06903 Sophia Antipolis, France; University Nice Sophia Antipolis, ISA, UMR 1355, 06900 Sophia Antipolis, France; CNRS, UMR 7254, Institut Sophia Agrobiotech, F-06903 Sophia Antipolis, France
| | - Franck Panabières
- INRA, UMR1355 Institut Sophia Agrobiotech, F-06903 Sophia Antipolis, France; University Nice Sophia Antipolis, ISA, UMR 1355, 06900 Sophia Antipolis, France; CNRS, UMR 7254, Institut Sophia Agrobiotech, F-06903 Sophia Antipolis, France
| | - Eric Galiana
- INRA, UMR1355 Institut Sophia Agrobiotech, F-06903 Sophia Antipolis, France; University Nice Sophia Antipolis, ISA, UMR 1355, 06900 Sophia Antipolis, France; CNRS, UMR 7254, Institut Sophia Agrobiotech, F-06903 Sophia Antipolis, France.
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De Craene JO, Courte F, Rinaldi B, Fitterer C, Herranz MC, Schmitt-Keichinger C, Ritzenthaler C, Friant S. Study of the plant COPII vesicle coat subunits by functional complementation of yeast Saccharomyces cerevisiae mutants. PLoS One 2014; 9:e90072. [PMID: 24587212 PMCID: PMC3934973 DOI: 10.1371/journal.pone.0090072] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 01/29/2014] [Indexed: 11/29/2022] Open
Abstract
The formation and budding of endoplasmic reticulum ER-derived vesicles depends on the COPII coat protein complex that was first identified in yeast Saccharomyces cerevisiae. The ER-associated Sec12 and the Sar1 GTPase initiate the COPII coat formation by recruiting the Sec23–Sec24 heterodimer following the subsequent recruitment of the Sec13–Sec31 heterotetramer. In yeast, there is usually one gene encoding each COPII protein and these proteins are essential for yeast viability, whereas the plant genome encodes multiple isoforms of all COPII subunits. Here, we used a systematic yeast complementation assay to assess the functionality of Arabidopsis thaliana COPII proteins. In this study, the different plant COPII subunits were expressed in their corresponding temperature-sensitive yeast mutant strain to complement their thermosensitivity and secretion phenotypes. Secretion was assessed using two different yeast cargos: the soluble α-factor pheromone and the membranous v-SNARE (vesicle-soluble NSF (N-ethylmaleimide-sensitive factor) attachment protein receptor) Snc1 involved in the fusion of the secretory vesicles with the plasma membrane. This complementation study allowed the identification of functional A. thaliana COPII proteins for the Sec12, Sar1, Sec24 and Sec13 subunits that could represent an active COPII complex in plant cells. Moreover, we found that AtSec12 and AtSec23 were co-immunoprecipitated with AtSar1 in total cell extract of 15 day-old seedlings of A. thaliana. This demonstrates that AtSar1, AtSec12 and AtSec23 can form a protein complex that might represent an active COPII complex in plant cells.
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Affiliation(s)
- Johan-Owen De Craene
- Department of Molecular and Cellular Genetics, UMR7156, Université de Strasbourg and CNRS, Strasbourg, France
| | - Fanny Courte
- Department of Molecular and Cellular Genetics, UMR7156, Université de Strasbourg and CNRS, Strasbourg, France
- Institut de Biologie Moléculaire des Plantes (IBMP), UPR2357 CNRS, Université de Strasbourg, Strasbourg, France
| | - Bruno Rinaldi
- Department of Molecular and Cellular Genetics, UMR7156, Université de Strasbourg and CNRS, Strasbourg, France
| | - Chantal Fitterer
- Institut de Biologie Moléculaire des Plantes (IBMP), UPR2357 CNRS, Université de Strasbourg, Strasbourg, France
| | - Mari Carmen Herranz
- Institut de Biologie Moléculaire des Plantes (IBMP), UPR2357 CNRS, Université de Strasbourg, Strasbourg, France
| | - Corinne Schmitt-Keichinger
- Institut de Biologie Moléculaire des Plantes (IBMP), UPR2357 CNRS, Université de Strasbourg, Strasbourg, France
| | - Christophe Ritzenthaler
- Institut de Biologie Moléculaire des Plantes (IBMP), UPR2357 CNRS, Université de Strasbourg, Strasbourg, France
| | - Sylvie Friant
- Department of Molecular and Cellular Genetics, UMR7156, Université de Strasbourg and CNRS, Strasbourg, France
- * E-mail:
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Abstract
In contrast with most bacteria which possess two type II topoisomerases (topoisomerase IV and DNA gyrase), Mycobacterium tuberculosis possesses only one, DNA gyrase, which is functionally a hybrid enzyme. Functional differences between the two type IIA topoisomerases are thought to be specified by a CTD (C-terminal DNA-binding domain), which controls DNA recognition. To explore the molecular mechanism responsible for the hybrid functions of the M. tuberculosis DNA gyrase, we conducted a series of sequence analyses and structural and biochemical experiments with the isolated GyrA CTD and the holoenzyme. Although the CTD displayed a global structure similar to that of bona fide GyrA and ParC paralogues, it harbours a second key motif similar in all respects to that of the conserved GyrA-box sequence motif. Biochemical assays showed that the GyrA-box is responsible for DNA supercoiling, whereas the second GyrA-box-l (GyrA-box-like motif) is responsible for the enhanced decatenation activity, suggesting that the mechanistic originality of M. tuberculosis DNA gyrase depends largely on the particular DNA path around the CTD allowed for by the presence of GyrA-box-l. The results of the present study also provide, through phylogenetic exploration of the entire Corynebacterineae suborder, a new and broader insight into the functional diversity of bacterial type IIA topoisomerases.
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Schwenzer H, Scheper GC, Zorn N, Moulinier L, Gaudry A, Leize E, Martin F, Florentz C, Poch O, Sissler M. Released selective pressure on a structural domain gives new insights on the functional relaxation of mitochondrial aspartyl-tRNA synthetase. Biochimie 2013; 100:18-26. [PMID: 24120687 DOI: 10.1016/j.biochi.2013.09.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 09/30/2013] [Indexed: 10/26/2022]
Abstract
Mammalian mitochondrial aminoacyl-tRNA synthetases are nuclear-encoded enzymes that are essential for mitochondrial protein synthesis. Due to an endosymbiotic origin of the mitochondria, many of them share structural domains with homologous bacterial enzymes of same specificity. This is also the case for human mitochondrial aspartyl-tRNA synthetase (AspRS) that shares the so-called bacterial insertion domain with bacterial homologs. The function of this domain in the mitochondrial proteins is unclear. Here, we show by bioinformatic analyses that the sequences coding for the bacterial insertion domain are less conserved in opisthokont and protist than in bacteria and viridiplantae. The divergence suggests a loss of evolutionary pressure on this domain for non-plant mitochondrial AspRSs. This discovery is further connected with the herein described occurrence of alternatively spliced transcripts of the mRNAs coding for some mammalian mitochondrial AspRSs. Interestingly, the spliced transcripts alternately lack one of the four exons that code for the bacterial insertion domain. Although we showed that the human alternative transcript is present in all tested tissues; co-exists with the full-length form, possesses 5'- and 3'-UTRs, a poly-A tail and is bound to polysomes, we were unable to detect the corresponding protein. The relaxed selective pressure combined with the occurrence of alternative splicing, involving a single structural sub-domain, favors the hypothesis of the loss of function of this domain for AspRSs of mitochondrial location. This evolutionary divergence is in line with other characteristics, established for the human mt-AspRS, that indicate a functional relaxation of non-viridiplantae mt-AspRSs when compared to bacterial and plant ones, despite their common ancestry.
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Affiliation(s)
- Hagen Schwenzer
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, IBMC - 15 rue René Descartes, F-67084 Strasbourg Cedex, France
| | - Gert C Scheper
- Department of Pediatrics and Child Neurology, VU University Medical Center, 1081 HV Amsterdam, The Netherlands
| | - Nathalie Zorn
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes, Chimie de la Matière Complexe, 1 rue Blaise Pascal, F-67008 Strasbourg Cedex, France
| | - Luc Moulinier
- Laboratoire de Bioinformatique et de Génomique Intégratives, IGBMC, 1 rue Laurent Fries BP-10142, F-67404 Illkirch Cedex, France
| | - Agnès Gaudry
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, IBMC - 15 rue René Descartes, F-67084 Strasbourg Cedex, France
| | - Emmanuelle Leize
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes, Chimie de la Matière Complexe, 1 rue Blaise Pascal, F-67008 Strasbourg Cedex, France
| | - Franck Martin
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, IBMC - 15 rue René Descartes, F-67084 Strasbourg Cedex, France
| | - Catherine Florentz
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, IBMC - 15 rue René Descartes, F-67084 Strasbourg Cedex, France
| | - Olivier Poch
- Laboratoire de Bioinformatique et de Génomique Intégratives, IGBMC, 1 rue Laurent Fries BP-10142, F-67404 Illkirch Cedex, France
| | - Marie Sissler
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, IBMC - 15 rue René Descartes, F-67084 Strasbourg Cedex, France.
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Involvement of protein IF2 N domain in ribosomal subunit joining revealed from architecture and function of the full-length initiation factor. Proc Natl Acad Sci U S A 2013; 110:15656-61. [PMID: 24029017 DOI: 10.1073/pnas.1309578110] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Translation initiation factor 2 (IF2) promotes 30S initiation complex (IC) formation and 50S subunit joining, which produces the 70S IC. The architecture of full-length IF2, determined by small angle X-ray diffraction and cryo electron microscopy, reveals a more extended conformation of IF2 in solution and on the ribosome than in the crystal. The N-terminal domain is only partially visible in the 30S IC, but in the 70S IC, it stabilizes interactions between IF2 and the L7/L12 stalk of the 50S, and on its deletion, proper N-formyl-methionyl(fMet)-tRNA(fMet) positioning and efficient transpeptidation are affected. Accordingly, fast kinetics and single-molecule fluorescence data indicate that the N terminus promotes 70S IC formation by stabilizing the productive sampling of the 50S subunit during 30S IC joining. Together, our data highlight the dynamics of IF2-dependent ribosomal subunit joining and the role played by the N terminus of IF2 in this process.
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Maillot B, Lévy N, Eiler S, Crucifix C, Granger F, Richert L, Didier P, Godet J, Pradeau-Aubreton K, Emiliani S, Nazabal A, Lesbats P, Parissi V, Mely Y, Moras D, Schultz P, Ruff M. Structural and functional role of INI1 and LEDGF in the HIV-1 preintegration complex. PLoS One 2013; 8:e60734. [PMID: 23593299 PMCID: PMC3623958 DOI: 10.1371/journal.pone.0060734] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 03/01/2013] [Indexed: 02/07/2023] Open
Abstract
Integration of the HIV-1 cDNA into the human genome is catalyzed by the viral integrase (IN) protein. Several studies have shown the importance of cellular cofactors that interact with integrase and affect viral integration and infectivity. In this study, we produced a stable complex between HIV-1 integrase, viral U5 DNA, the cellular cofactor LEDGF/p75 and the integrase binding domain of INI1 (INI1-IBD), a subunit of the SWI/SNF chromatin remodeling factor. The stoichiometry of the IN/LEDGF/INI1-IBD/DNA complex components was found to be 4/2/2/2 by mass spectrometry and Fluorescence Correlation Spectroscopy. Functional assays showed that INI1-IBD inhibits the 3′ processing reaction but does not interfere with specific viral DNA binding. Integration assays demonstrate that INI1-IBD decreases the amount of integration events but inhibits by-product formation such as donor/donor or linear full site integration molecules. Cryo-electron microscopy locates INI1-IBD within the cellular DNA binding site of the IN/LEDGF complex, constraining the highly flexible integrase in a stable conformation. Taken together, our results suggest that INI1 could stabilize the PIC in the host cell, by maintaining integrase in a stable constrained conformation which prevents non-specific interactions and auto integration on the route to its integration site within nucleosomes, while LEDGF organizes and stabilizes an active integrase tetramer suitable for specific vDNA integration. Moreover, our results provide the basis for a novel type of integrase inhibitor (conformational inhibitor) representing a potential new strategy for use in human therapy.
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Affiliation(s)
- Benoit Maillot
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Département de Biologie Structurale intégrative, Université de Strasbourg, U596 INSERM, UMR7104 CNRS, Illkirch, France
| | - Nicolas Lévy
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Département de Biologie Structurale intégrative, Université de Strasbourg, U596 INSERM, UMR7104 CNRS, Illkirch, France
| | - Sylvia Eiler
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Département de Biologie Structurale intégrative, Université de Strasbourg, U596 INSERM, UMR7104 CNRS, Illkirch, France
| | - Corinne Crucifix
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Département de Biologie Structurale intégrative, Université de Strasbourg, U596 INSERM, UMR7104 CNRS, Illkirch, France
| | - Florence Granger
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Département de Biologie Structurale intégrative, Université de Strasbourg, U596 INSERM, UMR7104 CNRS, Illkirch, France
| | - Ludovic Richert
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, UDS, Faculté de Pharmacie, Illkirch, France
| | - Pascal Didier
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, UDS, Faculté de Pharmacie, Illkirch, France
| | - Julien Godet
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, UDS, Faculté de Pharmacie, Illkirch, France
| | - Karine Pradeau-Aubreton
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Département de Biologie Structurale intégrative, Université de Strasbourg, U596 INSERM, UMR7104 CNRS, Illkirch, France
| | - Stéphane Emiliani
- Institut Cochin, Université Paris Descartes, CNRS (UMR8104), INSERM (U567), Paris, France
| | | | - Paul Lesbats
- Laboratoire de Microbiologie Fondamentale et Pathogénicité, CNRS (UMR5234), Université de Bordeaux 2, Bordeaux, France
| | - Vincent Parissi
- Laboratoire de Microbiologie Fondamentale et Pathogénicité, CNRS (UMR5234), Université de Bordeaux 2, Bordeaux, France
| | - Yves Mely
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, UDS, Faculté de Pharmacie, Illkirch, France
| | - Dino Moras
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Département de Biologie Structurale intégrative, Université de Strasbourg, U596 INSERM, UMR7104 CNRS, Illkirch, France
| | - Patrick Schultz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Département de Biologie Structurale intégrative, Université de Strasbourg, U596 INSERM, UMR7104 CNRS, Illkirch, France
| | - Marc Ruff
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Département de Biologie Structurale intégrative, Université de Strasbourg, U596 INSERM, UMR7104 CNRS, Illkirch, France
- * E-mail:
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Brants J, Semenchenko K, Wasylyk C, Robert A, Carles A, Zambrano A, Pradeau-Aubreton K, Birck C, Schalken JA, Poch O, de Mey J, Wasylyk B. Tubulin tyrosine ligase like 12, a TTLL family member with SET- and TTL-like domains and roles in histone and tubulin modifications and mitosis. PLoS One 2012; 7:e51258. [PMID: 23251473 PMCID: PMC3520985 DOI: 10.1371/journal.pone.0051258] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 10/30/2012] [Indexed: 01/15/2023] Open
Abstract
hTTLL12 is a member of the tubulin tyrosine ligase (TTL) family that is highly conserved in phylogeny. It has both SET-like and TTL-like domains, suggesting that it could have histone methylation and tubulin tyrosine ligase activities. Altered expression of hTTLL12 in human cells leads to specific changes in H4K20 trimethylation, and tubulin detyrosination, hTTLL12 does not catalyse histone methylation or tubulin tyrosination in vitro, as might be expected from the lack of critical amino acids in its SET-like and TTLL-like domains. hTTLL12 misexpression increases mitotic duration and chromosome numbers. These results suggest that hTTLL12 has non-catalytic functions related to tubulin and histone modification, which could be linked to its effects on mitosis and chromosome number stability.
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Affiliation(s)
- Jan Brants
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, UMR 7104 CNRS UDS - U 964 INSERM , Illkirch, France
| | - Kostyantyn Semenchenko
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, UMR 7104 CNRS UDS - U 964 INSERM , Illkirch, France
| | - Christine Wasylyk
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, UMR 7104 CNRS UDS - U 964 INSERM , Illkirch, France
| | - Aude Robert
- Université de Strasbourg, Ecole Supérieure de Biotechnologie de Strasbourg C.N.R.S. - U.M.R.7100, Equipe “Microtubules et Morphogenèse”, Parc d'Innovation, Illkirch, France
| | - Annaick Carles
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, UMR 7104 CNRS UDS - U 964 INSERM , Illkirch, France
| | - Alberto Zambrano
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, UMR 7104 CNRS UDS - U 964 INSERM , Illkirch, France
| | - Karine Pradeau-Aubreton
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, UMR 7104 CNRS UDS - U 964 INSERM , Illkirch, France
| | - Catherine Birck
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, UMR 7104 CNRS UDS - U 964 INSERM , Illkirch, France
| | - Jack A. Schalken
- Department of Urology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Olivier Poch
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, UMR 7104 CNRS UDS - U 964 INSERM , Illkirch, France
| | - Jan de Mey
- Université de Strasbourg, Ecole Supérieure de Biotechnologie de Strasbourg C.N.R.S. - U.M.R.7100, Equipe “Microtubules et Morphogenèse”, Parc d'Innovation, Illkirch, France
| | - Bohdan Wasylyk
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, UMR 7104 CNRS UDS - U 964 INSERM , Illkirch, France
- * E-mail:
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Bedez F, Linard B, Brochet X, Ripp R, Thompson JD, Moras D, Lecompte O, Poch O. Functional insights into the core-TFIIH from a comparative survey. Genomics 2012; 101:178-86. [PMID: 23147676 DOI: 10.1016/j.ygeno.2012.11.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 10/31/2012] [Accepted: 11/02/2012] [Indexed: 10/27/2022]
Abstract
TFIIH is a eukaryotic complex composed of two subcomplexes, the CAK (Cdk activating kinase) and the core-TFIIH. The core-TFIIH, composed of seven subunits (XPB, XPD, P62, P52, P44, P34, and P8), plays a crucial role in transcription and repair. Here, we performed an extended sequence analysis to establish the accurate phylogenetic distribution of the core-TFIIH in 63 eukaryotic organisms. In spite of the high conservation of the seven subunits at the sequence and genomic levels, the non-enzymatic P8, P34, P52 and P62 are absent from one or a few unicellular species. To gain insight into their respective roles, we undertook a comparative genomic analysis of the whole proteome to identify the gene sets sharing similar presence/absence patterns. While little information was inferred for P8 and P62, our studies confirm the known role of P52 in repair and suggest for the first time the implication of the core TFIIH in mRNA splicing via P34.
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Affiliation(s)
- Florence Bedez
- Laboratoire de Bioinformatique et Génomique Intégratives, Institut de Génétique et de Biologie Moléculaire et Cellulaire (CNRS, INSERM, UDS), BP163, 67404 Illkirch Cedex, France
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De Craene JO, Ripp R, Lecompte O, Thompson JD, Poch O, Friant S. Evolutionary analysis of the ENTH/ANTH/VHS protein superfamily reveals a coevolution between membrane trafficking and metabolism. BMC Genomics 2012; 13:297. [PMID: 22748146 PMCID: PMC3473312 DOI: 10.1186/1471-2164-13-297] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 06/22/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Membrane trafficking involves the complex regulation of proteins and lipids intracellular localization and is required for metabolic uptake, cell growth and development. Different trafficking pathways passing through the endosomes are coordinated by the ENTH/ANTH/VHS adaptor protein superfamily. The endosomes are crucial for eukaryotes since the acquisition of the endomembrane system was a central process in eukaryogenesis. RESULTS Our in silico analysis of this ENTH/ANTH/VHS superfamily, consisting of proteins gathered from 84 complete genomes representative of the different eukaryotic taxa, revealed that genomic distribution of this superfamily allows to discriminate Fungi and Metazoa from Plantae and Protists. Next, in a four way genome wide comparison, we showed that this discriminative feature is observed not only for other membrane trafficking effectors, but also for proteins involved in metabolism and in cytokinesis, suggesting that metabolism, cytokinesis and intracellular trafficking pathways co-evolved. Moreover, some of the proteins identified were implicated in multiple functions, in either trafficking and metabolism or trafficking and cytokinesis, suggesting that membrane trafficking is central to this co-evolution process. CONCLUSIONS Our study suggests that membrane trafficking and compartmentalization were not only key features for the emergence of eukaryotic cells but also drove the separation of the eukaryotes in the different taxa.
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Affiliation(s)
- Johan-Owen De Craene
- Department of Molecular and Cellular Genetics, UMR7156 CNRS/Université de Strasbourg, 21 rue Descartes, 67084, Strasbourg, France
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Luu TD, Rusu A, Walter V, Linard B, Poidevin L, Ripp R, Moulinier L, Muller J, Raffelsberger W, Wicker N, Lecompte O, Thompson JD, Poch O, Nguyen H. KD4v: Comprehensible Knowledge Discovery System for Missense Variant. Nucleic Acids Res 2012; 40:W71-5. [PMID: 22641855 PMCID: PMC3394327 DOI: 10.1093/nar/gks474] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
A major challenge in the post-genomic era is a better understanding of how human genetic alterations involved in disease affect the gene products. The KD4v (Comprehensible Knowledge Discovery System for Missense Variant) server allows to characterize and predict the phenotypic effects (deleterious/neutral) of missense variants. The server provides a set of rules learned by Induction Logic Programming (ILP) on a set of missense variants described by conservation, physico-chemical, functional and 3D structure predicates. These rules are interpretable by non-expert humans and are used to accurately predict the deleterious/neutral status of an unknown mutation. The web server is available at http://decrypthon.igbmc.fr/kd4v.
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Affiliation(s)
- Tien-Dao Luu
- Laboratoire de Bioinformatique et Génomique Intégratives, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
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Delavat F, Phalip V, Forster A, Plewniak F, Lett MC, Lièvremont D. Amylases without known homologues discovered in an acid mine drainage: significance and impact. Sci Rep 2012; 2:354. [PMID: 22482035 PMCID: PMC3319935 DOI: 10.1038/srep00354] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 03/08/2012] [Indexed: 12/25/2022] Open
Abstract
Acid Mine Drainages (AMDs) are extreme environments characterized by acidic and oligotrophic conditions and by metal contaminations. A function-based screening of an AMD-derived metagenomic library led to the discovery and partial characterization of two non-homologous endo-acting amylases sharing no sequence similarity with any known amylase nor glycosidase. None carried known amylolytic domains, nor could be assigned to any GH-family. One amylase displayed no similarity with any known protein, whereas the second one was similar to TraC proteins involved in the bacterial type IV secretion system. According to the scarce similarities with known proteins, 3D-structure modelling using I-TASSER was unsuccessful. This study underlined the utility of a function-driven metagenomic approach to obtain a clearer image of the bacterial community enzymatic landscape. More generally, this work points out that screening for microorganisms or biomolecules in a priori incongruous environments could provide unconventional and new exciting ways for bioprospecting.
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Luu TD, Rusu AM, Walter V, Ripp R, Moulinier L, Muller J, Toursel T, Thompson JD, Poch O, Nguyen H. MSV3d: database of human MisSense Variants mapped to 3D protein structure. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2012; 2012:bas018. [PMID: 22491796 PMCID: PMC3317913 DOI: 10.1093/database/bas018] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The elucidation of the complex relationships linking genotypic and phenotypic variations to protein structure is a major challenge in the post-genomic era. We present MSV3d (Database of human MisSense Variants mapped to 3D protein structure), a new database that contains detailed annotation of missense variants of all human proteins (20 199 proteins). The multi-level characterization includes details of the physico-chemical changes induced by amino acid modification, as well as information related to the conservation of the mutated residue and its position relative to functional features in the available or predicted 3D model. Major releases of the database are automatically generated and updated regularly in line with the dbSNP (database of Single Nucleotide Polymorphism) and SwissVar releases, by exploiting the extensive Décrypthon computational grid resources. The database (http://decrypthon.igbmc.fr/msv3d) is easily accessible through a simple web interface coupled to a powerful query engine and a standard web service. The content is completely or partially downloadable in XML or flat file formats. Database URL:http://decrypthon.igbmc.fr/msv3d
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Affiliation(s)
- Tien-Dao Luu
- Laboratoire de Bioinformatique et Génomique Intégratives, Institut de Génétique et de Biologie Moléculaire et Cellulaire (UMR7104), 67404 Illkirch
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Audo I, Bujakowska K, Orhan E, Poloschek C, Defoort-Dhellemmes S, Drumare I, Kohl S, Luu T, Lecompte O, Zrenner E, Lancelot ME, Antonio A, Germain A, Michiels C, Audier C, Letexier M, Saraiva JP, Leroy B, Munier F, Mohand-Saïd S, Lorenz B, Friedburg C, Preising M, Kellner U, Renner A, Moskova-Doumanova V, Berger W, Wissinger B, Hamel C, Schorderet D, De Baere E, Sharon D, Banin E, Jacobson S, Bonneau D, Zanlonghi X, Le Meur G, Casteels I, Koenekoop R, Long V, Meire F, Prescott K, de Ravel T, Simmons I, Nguyen H, Dollfus H, Poch O, Léveillard T, Nguyen-Ba-Charvet K, Sahel JA, Bhattacharya S, Zeitz C. Whole-exome sequencing identifies mutations in GPR179 leading to autosomal-recessive complete congenital stationary night blindness. Am J Hum Genet 2012; 90:321-30. [PMID: 22325361 DOI: 10.1016/j.ajhg.2011.12.007] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Revised: 11/18/2011] [Accepted: 12/08/2011] [Indexed: 10/14/2022] Open
Abstract
Congenital stationary night blindness (CSNB) is a heterogeneous retinal disorder characterized by visual impairment under low light conditions. This disorder is due to a signal transmission defect from rod photoreceptors to adjacent bipolar cells in the retina. Two forms can be distinguished clinically, complete CSNB (cCSNB) or incomplete CSNB; the two forms are distinguished on the basis of the affected signaling pathway. Mutations in NYX, GRM6, and TRPM1, expressed in the outer plexiform layer (OPL) lead to disruption of the ON-bipolar cell response and have been seen in patients with cCSNB. Whole-exome sequencing in cCSNB patients lacking mutations in the known genes led to the identification of a homozygous missense mutation (c.1807C>T [p.His603Tyr]) in one consanguineous autosomal-recessive cCSNB family and a homozygous frameshift mutation in GPR179 (c.278delC [p.Pro93Glnfs(∗)57]) in a simplex male cCSNB patient. Additional screening with Sanger sequencing of 40 patients identified three other cCSNB patients harboring additional allelic mutations in GPR179. Although, immunhistological studies revealed Gpr179 in the OPL in wild-type mouse retina, Gpr179 did not colocalize with specific ON-bipolar markers. Interestingly, Gpr179 was highly concentrated in horizontal cells and Müller cell endfeet. The involvement of these cells in cCSNB and the specific function of GPR179 remain to be elucidated.
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A functional variant of lipopolysaccharide binding protein predisposes to sepsis and organ dysfunction in patients with major trauma. Ann Surg 2012; 255:147-57. [PMID: 22167001 DOI: 10.1097/sla.0b013e3182389515] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
OBJECTIVE To determine the hypothesis that genetic variations of the lipopolysaccharide-binding protein (LBP) gene influence risk for the development of sepsis and multiple organ dysfunction (MOD) in patients with major trauma. BACKGROUND Lipopolysaccharide-binding protein plays a central role in innate immune response as the first line of defense and directing the microbial-induced activation of the inflammatory host response. Although a total of 112 single nucleotide polymorphisms (SNPs) have been identified so far within the entire LBP gene, only a few SNPs have been studied. METHODS Nine haplotype tagging SNPs (htSNPs) were selected from 51 SNPs with a minor allele frequency of ≥5% using the HapMap database for the Chinese Han population. Two independent cohorts of major trauma patients were recruited. The 9 htSNPs were genotyped using pyrosequencing method and analyzed in relation to the risk of development of sepsis and MOD, LBP production, and lipopolysaccharide (LPS)-induced activation of peripheral blood leukocytes. Moreover, the functionality of the rs2232618 polymorphism was assessed by the observation of its effects on the binding and activation of LPS and the LBP-CD14 interaction. RESULTS Among the 9 htSNPs, only the rs2232618 was significantly associated with higher susceptibility to sepsis and MOD in the 2 independent cohorts of major trauma patients recruited from southwest and eastern China. This SNP was also significantly associated with LPS-induced activation of peripheral blood leukocytes. In addition, the rs2232618 polymorphism could enhance LBP protein activities, showing significant increases in LPS binding to macrophages, LPS-induced cellular activation, and LBP-CD14 interaction at the presence of the variant LBP protein. CONCLUSIONS The rs2232618 polymorphism is a functional SNP and confers host susceptibility to sepsis and multiple organ dysfunction in patients with major trauma.
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Linard B, Nguyen NH, Prosdocimi F, Poch O, Thompson JD. EvoluCode: Evolutionary Barcodes as a Unifying Framework for Multilevel Evolutionary Data. Evol Bioinform Online 2011; 8:61-77. [PMID: 22267905 PMCID: PMC3256995 DOI: 10.4137/ebo.s8814] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Evolutionary systems biology aims to uncover the general trends and principles governing the evolution of biological networks. An essential part of this process is the reconstruction and analysis of the evolutionary histories of these complex, dynamic networks. Unfortunately, the methodologies for representing and exploiting such complex evolutionary histories in large scale studies are currently limited. Here, we propose a new formalism, called EvoluCode (Evolutionary barCode), which allows the integration of different evolutionary parameters (eg, sequence conservation, orthology, synteny …) in a unifying format and facilitates the multilevel analysis and visualization of complex evolutionary histories at the genome scale. The advantages of the approach are demonstrated by constructing barcodes representing the evolution of the complete human proteome. Two large-scale studies are then described: (i) the mapping and visualization of the barcodes on the human chromosomes and (ii) automatic clustering of the barcodes to highlight protein subsets sharing similar evolutionary histories and their functional analysis. The methodologies developed here open the way to the efficient application of other data mining and knowledge extraction techniques in evolutionary systems biology studies. A database containing all EvoluCode data is available at: http://lbgi.igbmc.fr/barcodes.
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Affiliation(s)
- Benjamin Linard
- Laboratoire De Bioinformatique Et Génomique Intégratives, Institut de Génétique et de Biologie Moléculaire et Cellulaire CNRS/INSERM/UDS, Illkirch, France
| | - Ngoc Hoan Nguyen
- Laboratoire De Bioinformatique Et Génomique Intégratives, Institut de Génétique et de Biologie Moléculaire et Cellulaire CNRS/INSERM/UDS, Illkirch, France
| | | | - Olivier Poch
- Laboratoire De Bioinformatique Et Génomique Intégratives, Institut de Génétique et de Biologie Moléculaire et Cellulaire CNRS/INSERM/UDS, Illkirch, France
| | - Julie D. Thompson
- Laboratoire De Bioinformatique Et Génomique Intégratives, Institut de Génétique et de Biologie Moléculaire et Cellulaire CNRS/INSERM/UDS, Illkirch, France
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Vaidya AT, Chen CH, Dunlap JC, Loros JJ, Crane BR. Structure of a light-activated LOV protein dimer that regulates transcription. Sci Signal 2011; 4:ra50. [PMID: 21868352 DOI: 10.1126/scisignal.2001945] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Light, oxygen, or voltage (LOV) protein domains are present in many signaling proteins in bacteria, archaea, protists, plants, and fungi. The LOV protein VIVID (VVD) of the filamentous fungus Neurospora crassa enables the organism to adapt to constant or increasing amounts of light and facilitates proper entrainment of circadian rhythms. Here, we determined the crystal structure of the fully light-adapted VVD dimer and reveal the mechanism by which light-driven conformational change alters the oligomeric state of the protein. Light-induced formation of a cysteinyl-flavin adduct generated a new hydrogen bond network that released the amino (N) terminus from the protein core and restructured an acceptor pocket for binding of the N terminus on the opposite subunit of the dimer. Substitution of residues critical for the switch between the monomeric and the dimeric states of the protein had profound effects on light adaptation in Neurospora. The mechanism of dimerization of VVD provides molecular details that explain how members of a large family of photoreceptors convert light responses to alterations in protein-protein interactions.
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Affiliation(s)
- Anand T Vaidya
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
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Boutet I, Ripp R, Lecompte O, Dossat C, Corre E, Tanguy A, Lallier FH. Conjugating effects of symbionts and environmental factors on gene expression in deep-sea hydrothermal vent mussels. BMC Genomics 2011; 12:530. [PMID: 22034982 PMCID: PMC3218092 DOI: 10.1186/1471-2164-12-530] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Accepted: 10/28/2011] [Indexed: 11/17/2022] Open
Abstract
Background The deep-sea hydrothermal vent mussel Bathymodiolus azoricus harbors thiotrophic and methanotrophic symbiotic bacteria in its gills. While the symbiotic relationship between this hydrothermal mussel and these chemoautotrophic bacteria has been described, the molecular processes involved in the cross-talking between symbionts and host, in the maintenance of the symbiois, in the influence of environmental parameters on gene expression, and in transcriptome variation across individuals remain poorly understood. In an attempt to understand how, and to what extent, this double symbiosis affects host gene expression, we used a transcriptomic approach to identify genes potentially regulated by symbiont characteristics, environmental conditions or both. This study was done on mussels from two contrasting populations. Results Subtractive libraries allowed the identification of about 1000 genes putatively regulated by symbiosis and/or environmental factors. Microarray analysis showed that 120 genes (3.5% of all genes) were differentially expressed between the Menez Gwen (MG) and Rainbow (Rb) vent fields. The total number of regulated genes in mussels harboring a high versus a low symbiont content did not differ significantly. With regard to the impact of symbiont content, only 1% of all genes were regulated by thiotrophic (SOX) and methanotrophic (MOX) bacteria content in MG mussels whereas 5.6% were regulated in mussels collected at Rb. MOX symbionts also impacted a higher proportion of genes than SOX in both vent fields. When host transcriptome expression was analyzed with respect to symbiont gene expression, it was related to symbiont quantity in each field. Conclusions Our study has produced a preliminary description of a transcriptomic response in a hydrothermal vent mussel host of both thiotrophic and methanotrophic symbiotic bacteria. This model can help to identify genes involved in the maintenance of symbiosis or regulated by environmental parameters. Our results provide evidence of symbiont effect on transcriptome regulation, with differences related to type of symbiont, even though the relative percentage of genes involved remains limited. Differences observed between the vent site indicate that environment strongly influences transcriptome regulation and impacts both activity and relative abundance of each symbiont. Among all these genes, those participating in recognition, the immune system, oxidative stress, and energy metabolism constitute new promising targets for extended studies on symbiosis and the effect of environmental parameters on the symbiotic relationships in B. azoricus.
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Affiliation(s)
- Isabelle Boutet
- CNRS, UMR 7144, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, 29682 Roscoff, France.
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Masuda S, Harada J, Yokono M, Yuzawa Y, Shimojima M, Murofushi K, Tanaka H, Masuda H, Murakawa M, Haraguchi T, Kondo M, Nishimura M, Yuasa H, Noguchi M, Oh-Oka H, Tanaka A, Tamiaki H, Ohta H. A monogalactosyldiacylglycerol synthase found in the green sulfur bacterium Chlorobaculum tepidum reveals important roles for galactolipids in photosynthesis. THE PLANT CELL 2011; 23:2644-58. [PMID: 21764989 PMCID: PMC3226221 DOI: 10.1105/tpc.111.085357] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Monogalactosyldiacylglycerol (MGDG), which is conserved in almost all photosynthetic organisms, is the most abundant natural polar lipid on Earth. In plants, MGDG is highly accumulated in the chloroplast membranes and is an important bulk constituent of thylakoid membranes. However, precise functions of MGDG in photosynthesis have not been well understood. Here, we report a novel MGDG synthase from the green sulfur bacterium Chlorobaculum tepidum. This enzyme, MgdA, catalyzes MGDG synthesis using UDP-Gal as a substrate. The gene encoding MgdA was essential for this bacterium; only heterozygous mgdA mutants could be isolated. An mgdA knockdown mutation affected in vivo assembly of bacteriochlorophyll c aggregates, suggesting the involvement of MGDG in the construction of the light-harvesting complex called chlorosome. These results indicate that MGDG biosynthesis has been independently established in each photosynthetic organism to perform photosynthesis under different environmental conditions. We complemented an Arabidopsis thaliana MGDG synthase mutant by heterologous expression of MgdA. The complemented plants showed almost normal levels of MGDG, although they also had abnormal morphological phenotypes, including reduced chlorophyll content, no apical dominance in shoot growth, atypical flower development, and infertility. These observations provide new insights regarding the importance of regulated MGDG synthesis in the physiology of higher plants.
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Affiliation(s)
- Shinji Masuda
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, Yokohama 226-8501, Japan.
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Champion MD. Host-pathogen o-methyltransferase similarity and its specific presence in highly virulent strains of Francisella tularensis suggests molecular mimicry. PLoS One 2011; 6:e20295. [PMID: 21637805 PMCID: PMC3102702 DOI: 10.1371/journal.pone.0020295] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Accepted: 04/28/2011] [Indexed: 12/28/2022] Open
Abstract
Whole genome comparative studies of many bacterial pathogens have shown an overall high similarity of gene content (>95%) between phylogenetically distinct subspecies. In highly clonal species that share the bulk of their genomes subtle changes in gene content and small-scale polymorphisms, especially those that may alter gene expression and protein-protein interactions, are more likely to have a significant effect on the pathogen's biology. In order to better understand molecular attributes that may mediate the adaptation of virulence in infectious bacteria, a comparative study was done to further analyze the evolution of a gene encoding an o-methyltransferase that was previously identified as a candidate virulence factor due to its conservation specifically in highly pathogenic Francisella tularensis subsp. tularensis strains. The o-methyltransferase gene is located in the genomic neighborhood of a known pathogenicity island and predicted site of rearrangement. Distinct o-methyltransferase subtypes are present in different Francisella tularensis subspecies. Related protein families were identified in several host species as well as species of pathogenic bacteria that are otherwise very distant phylogenetically from Francisella, including species of Mycobacterium. A conserved sequence motif profile is present in the mammalian host and pathogen protein sequences, and sites of non-synonymous variation conserved in Francisella subspecies specific o-methyltransferases map proximally to the predicted active site of the orthologous human protein structure. Altogether, evidence suggests a role of the F. t. subsp. tularensis protein in a mechanism of molecular mimicry, similar perhaps to Legionella and Coxiella. These findings therefore provide insights into the evolution of niche-restriction and virulence in Francisella, and have broader implications regarding the molecular mechanisms that mediate host-pathogen relationships.
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Affiliation(s)
- Mia D Champion
- Division of Pathogen Genomics, Translational Genomics Research Institute, Arizona, United States of America.
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37
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Enabling high-throughput ligation-independent cloning and protein expression for the family of ubiquitin specific proteases. J Struct Biol 2011; 175:113-9. [PMID: 21453775 DOI: 10.1016/j.jsb.2011.03.017] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Revised: 03/11/2011] [Accepted: 03/19/2011] [Indexed: 11/23/2022]
Abstract
High-throughput methods to produce a large number of soluble recombinant protein variants are particularly important in the process of determining the three-dimensional structure of proteins and their complexes. Here, we describe a collection of protein expression vectors for ligation-independent cloning, which allow co-expression strategies by implementing different affinity tags and antibiotic resistances. Since the same PCR product can be inserted in all but one of the vectors, this allows efficiency in versatility while screening for optimal expression strategies. We first demonstrate the use of these vectors for protein expression in Escherichia coli, on a set of proteins belonging to the ubiquitin specific protease (USP) Family. We have selected 35 USPs, created 145 different expression constructs into the pETNKI-His-3C-LIC-kan vector, and obtained 38 soluble recombinant proteins for 21 different USPs. Finally, we exemplify the use of our vectors for bacterial co-expression and for expression in insect cells, with USP4 and USP7 respectively. We conclude that our ligation-independent cloning strategy allows for high-throughput screening for the expression of soluble proteins in a variety of vectors in E. coli and in insect cells. In addition, the same vectors can be used for co-expression studies, at least for simple binary complexes. Application in the family of ubiquitin specific proteases led to a number of soluble USPs that are used for functional and crystallization studies.
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Fischer MJC, Meyer S, Claudel P, Bergdoll M, Karst F. Metabolic engineering of monoterpene synthesis in yeast. Biotechnol Bioeng 2011; 108:1883-92. [PMID: 21391209 DOI: 10.1002/bit.23129] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2010] [Revised: 02/08/2011] [Accepted: 03/03/2011] [Indexed: 11/08/2022]
Abstract
Terpenoids are one of the largest and most diverse families of natural compounds. They are heavily used in industry, and the trend is toward engineering modified microorganisms that produce high levels of specific terpenoids. Most studies have focused on creating specific heterologous pathways for sesquiterpenes in Escherichia coli or yeast. We subjected the Saccharomyces cerevisiae ERG20 gene (encoding farnesyl diphosphate synthase) to a set of amino acid mutations in the catalytic site at position K197. Mutated strains have been shown to exhibit various growth rate, sterol amount, and monoterpenol-producing capacities. These results are discussed in the context of the potential use of these mutated strains for heterologous expression of monoterpenoid synthases, which was investigated using Ocimum basilicum geraniol synthase. The results obtained with up to 5 mg/L geraniol suggest a major improvement compared with previous available expression systems like Escherichia coli or yeast strains with an unmodified ERG20 gene that respectively delivered amounts in the 10 and 500 µg/L range or even a previously characterized K197E mutation that delivered amounts in the 1 mg/L range.
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Affiliation(s)
- Marc J C Fischer
- Univ Strasbourg, INRA, Inst Natl Recherche Agron, Métab Second Vigne, Unit Mixte Recherche Santé Vigne & Qual Vins, 28 rue de Herrlisheim, F-68021Colmar, France.
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Chouquet A, Païdassi H, Ling WL, Frachet P, Houen G, Arlaud GJ, Gaboriaud C. X-ray structure of the human calreticulin globular domain reveals a peptide-binding area and suggests a multi-molecular mechanism. PLoS One 2011; 6:e17886. [PMID: 21423620 PMCID: PMC3057994 DOI: 10.1371/journal.pone.0017886] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Accepted: 02/15/2011] [Indexed: 11/23/2022] Open
Abstract
In the endoplasmic reticulum, calreticulin acts as a chaperone and a
Ca2+-signalling protein. At the cell surface, it mediates
numerous important biological effects. The crystal structure of the human
calreticulin globular domain was solved at 1.55 Å resolution. Interactions
of the flexible N-terminal extension with the edge of the lectin site are
consistently observed, revealing a hitherto unidentified peptide-binding site. A
calreticulin molecular zipper, observed in all crystal lattices, could further
extend this site by creating a binding cavity lined by hydrophobic residues.
These data thus provide a first structural insight into the lectin-independent
binding properties of calreticulin and suggest new working hypotheses, including
that of a multi-molecular mechanism.
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Affiliation(s)
- Anne Chouquet
- Institut de Biologie Structurale Jean-Pierre
Ebel, CEA, Grenoble, France
| | - Helena Païdassi
- Institut de Biologie Structurale Jean-Pierre
Ebel, CEA, Grenoble, France
| | - Wai Li Ling
- Institut de Biologie Structurale Jean-Pierre
Ebel, CEA, Grenoble, France
| | - Philippe Frachet
- Institut de Biologie Structurale Jean-Pierre
Ebel, UJF Grenoble 1, Grenoble, France
| | - Gunnar Houen
- Department of Clinical Biochemistry and
Immunology, Statens Serum Institut, Copenhagen, Denmark
| | - Gérard J. Arlaud
- Institut de Biologie Structurale Jean-Pierre
Ebel, CNRS, Grenoble, France
| | - Christine Gaboriaud
- Institut de Biologie Structurale Jean-Pierre
Ebel, CEA, Grenoble, France
- * E-mail:
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Moreno-Morcillo M, Minvielle-Sébastia L, Mackereth C, Fribourg S. Hexameric architecture of CstF supported by CstF-50 homodimerization domain structure. RNA (NEW YORK, N.Y.) 2011; 17:412-418. [PMID: 21233223 PMCID: PMC3039141 DOI: 10.1261/rna.2481011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Accepted: 12/08/2010] [Indexed: 05/30/2023]
Abstract
The Cleavage stimulation Factor (CstF) complex is composed of three subunits and is essential for pre-mRNA 3'-end processing. CstF recognizes U and G/U-rich cis-acting RNA sequence elements and helps stabilize the Cleavage and Polyadenylation Specificity Factor (CPSF) at the polyadenylation site as required for productive RNA cleavage. Here, we describe the crystal structure of the N-terminal domain of Drosophila CstF-50 subunit. It forms a compact homodimer that exposes two geometrically opposite, identical, and conserved surfaces that may serve as binding platform. Together with previous data on the structure of CstF-77, homodimerization of CstF-50 N-terminal domain supports the model in which the functional state of CstF is a heterohexamer.
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Affiliation(s)
- María Moreno-Morcillo
- Institut Européen de Chimie et Biologie, Institut National de la Santé et de la Recherche Médicale (INSERM) U869, Pessac, France
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Nian Chua H. Prediction of Protein Function. Genomics 2010. [DOI: 10.1002/9780470711675.ch9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Gagnière N, Jollivet D, Boutet I, Brélivet Y, Busso D, Da Silva C, Gaill F, Higuet D, Hourdez S, Knoops B, Lallier F, Leize-Wagner E, Mary J, Moras D, Perrodou E, Rees JF, Segurens B, Shillito B, Tanguy A, Thierry JC, Weissenbach J, Wincker P, Zal F, Poch O, Lecompte O. Insights into metazoan evolution from Alvinella pompejana cDNAs. BMC Genomics 2010; 11:634. [PMID: 21080938 PMCID: PMC3018142 DOI: 10.1186/1471-2164-11-634] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2010] [Accepted: 11/16/2010] [Indexed: 11/29/2022] Open
Abstract
Background Alvinella pompejana is a representative of Annelids, a key phylum for evo-devo studies that is still poorly studied at the sequence level. A. pompejana inhabits deep-sea hydrothermal vents and is currently known as one of the most thermotolerant Eukaryotes in marine environments, withstanding the largest known chemical and thermal ranges (from 5 to 105°C). This tube-dwelling worm forms dense colonies on the surface of hydrothermal chimneys and can withstand long periods of hypo/anoxia and long phases of exposure to hydrogen sulphides. A. pompejana specifically inhabits chimney walls of hydrothermal vents on the East Pacific Rise. To survive, Alvinella has developed numerous adaptations at the physiological and molecular levels, such as an increase in the thermostability of proteins and protein complexes. It represents an outstanding model organism for studying adaptation to harsh physicochemical conditions and for isolating stable macromolecules resistant to high temperatures. Results We have constructed four full length enriched cDNA libraries to investigate the biology and evolution of this intriguing animal. Analysis of more than 75,000 high quality reads led to the identification of 15,858 transcripts and 9,221 putative protein sequences. Our annotation reveals a good coverage of most animal pathways and networks with a prevalence of transcripts involved in oxidative stress resistance, detoxification, anti-bacterial defence, and heat shock protection. Alvinella proteins seem to show a slow evolutionary rate and a higher similarity with proteins from Vertebrates compared to proteins from Arthropods or Nematodes. Their composition shows enrichment in positively charged amino acids that might contribute to their thermostability. The gene content of Alvinella reveals that an important pool of genes previously considered to be specific to Deuterostomes were in fact already present in the last common ancestor of the Bilaterian animals, but have been secondarily lost in model invertebrates. This pool is enriched in glycoproteins that play a key role in intercellular communication, hormonal regulation and immunity. Conclusions Our study starts to unravel the gene content and sequence evolution of a deep-sea annelid, revealing key features in eukaryote adaptation to extreme environmental conditions and highlighting the proximity of Annelids and Vertebrates.
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Affiliation(s)
- Nicolas Gagnière
- Department of Structural Biology and Genomics, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CERBM F-67400 Illkirch, France
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Xu Q, Abdubek P, Astakhova T, Axelrod HL, Bakolitsa C, Cai X, Carlton D, Chen C, Chiu HJ, Chiu M, Clayton T, Das D, Deller MC, Duan L, Ellrott K, Farr CL, Feuerhelm J, Grant JC, Grzechnik A, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Lam WW, Marciano D, Miller MD, Morse AT, Nigoghossian E, Nopakun A, Okach L, Puckett C, Reyes R, Tien HJ, Trame CB, van den Bedem H, Weekes D, Wooten T, Yeh A, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. Structure of the γ-D-glutamyl-L-diamino acid endopeptidase YkfC from Bacillus cereus in complex with L-Ala-γ-D-Glu: insights into substrate recognition by NlpC/P60 cysteine peptidases. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:1354-64. [PMID: 20944232 PMCID: PMC2954226 DOI: 10.1107/s1744309110021214] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Accepted: 06/03/2010] [Indexed: 08/10/2023]
Abstract
Dipeptidyl-peptidase VI from Bacillus sphaericus and YkfC from Bacillus subtilis have both previously been characterized as highly specific γ-D-glutamyl-L-diamino acid endopeptidases. The crystal structure of a YkfC ortholog from Bacillus cereus (BcYkfC) at 1.8 Å resolution revealed that it contains two N-terminal bacterial SH3 (SH3b) domains in addition to the C-terminal catalytic NlpC/P60 domain that is ubiquitous in the very large family of cell-wall-related cysteine peptidases. A bound reaction product (L-Ala-γ-D-Glu) enabled the identification of conserved sequence and structural signatures for recognition of L-Ala and γ-D-Glu and, therefore, provides a clear framework for understanding the substrate specificity observed in dipeptidyl-peptidase VI, YkfC and other NlpC/P60 domains in general. The first SH3b domain plays an important role in defining substrate specificity by contributing to the formation of the active site, such that only murein peptides with a free N-terminal alanine are allowed. A conserved tyrosine in the SH3b domain of the YkfC subfamily is correlated with the presence of a conserved acidic residue in the NlpC/P60 domain and both residues interact with the free amine group of the alanine. This structural feature allows the definition of a subfamily of NlpC/P60 enzymes with the same N-terminal substrate requirements, including a previously characterized cyanobacterial L-alanine-γ-D-glutamate endopeptidase that contains the two key components (an NlpC/P60 domain attached to an SH3b domain) for assembly of a YkfC-like active site.
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Affiliation(s)
- Qingping Xu
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Polat Abdubek
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Tamara Astakhova
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Herbert L. Axelrod
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Constantina Bakolitsa
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Xiaohui Cai
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Dennis Carlton
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Connie Chen
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Hsiu-Ju Chiu
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Michelle Chiu
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Thomas Clayton
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Debanu Das
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Marc C. Deller
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Lian Duan
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Kyle Ellrott
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Carol L. Farr
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Julie Feuerhelm
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Joanna C. Grant
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Anna Grzechnik
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Gye Won Han
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Lukasz Jaroszewski
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Kevin K. Jin
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Heath E. Klock
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Mark W. Knuth
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Piotr Kozbial
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - S. Sri Krishna
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Abhinav Kumar
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Winnie W. Lam
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - David Marciano
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Mitchell D. Miller
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Andrew T. Morse
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Edward Nigoghossian
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Amanda Nopakun
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Linda Okach
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Christina Puckett
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Ron Reyes
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Henry J. Tien
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Christine B. Trame
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Henry van den Bedem
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Dana Weekes
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Tiffany Wooten
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Andrew Yeh
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Keith O. Hodgson
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Photon Science, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - John Wooley
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Marc-André Elsliger
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ashley M. Deacon
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Adam Godzik
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Scott A. Lesley
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ian A. Wilson
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
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44
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Niazi UH, Bibby J, Sutcliffe MJ. In-silico characterization of the effects of phosphorylated tyrosines 86 and 106 on structure and binding of MAL: insight into hyperinflammatory response to infection by the human malaria parasites. J Recept Signal Transduct Res 2010; 31:53-65. [DOI: 10.3109/10799893.2010.512014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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45
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Wilke S, Krausze J, Gossen M, Groebe L, Jäger V, Gherardi E, van den Heuvel J, Büssow K. Glycoprotein production for structure analysis with stable, glycosylation mutant CHO cell lines established by fluorescence-activated cell sorting. Protein Sci 2010; 19:1264-71. [PMID: 20512979 DOI: 10.1002/pro.390] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Stable mammalian cell lines are excellent tools for the expression of secreted and membrane glycoproteins. However, structural analysis of these molecules is generally hampered by the complexity of N-linked carbohydrate side chains. Cell lines with mutations are available that result in shorter and more homogenous carbohydrate chains. Here, we use preparative fluorescence-activated cell sorting (FACS) and site-specific gene excision to establish high-yield glycoprotein expression for structural studies with stable clones derived from the well-established Lec3.2.8.1 glycosylation mutant of the Chinese hamster ovary (CHO) cell line. We exemplify the strategy by describing novel clones expressing single-chain hepatocyte growth factor/scatter factor (HGF/SF, a secreted glycoprotein) and a domain of lysosome-associated membrane protein 3 (LAMP3d). In both cases, stable GFP-expressing cell lines were established by transfection with a genetic construct including a GFP marker and two rounds of cell sorting after 1 and 2 weeks. The GFP marker was subsequently removed by heterologous expression of Flp recombinase. Production of HGF/SF and LAMP3d was stable over several months. 1.2 mg HGF/SF and 0.9 mg LAMP3d were purified per litre of culture, respectively. Homogenous glycoprotein preparations were amenable to enzymatic deglycosylation under native conditions. Purified and deglycosylated LAMP3d protein was readily crystallized. The combination of FACS and gene excision described here constitutes a robust and fast procedure for maximizing the yield of glycoproteins for structural analysis from glycosylation mutant cell lines.
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Affiliation(s)
- Sonja Wilke
- Division of Structural Biology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
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46
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Abstract
M-ORBIS is a Molecular Cartography approach that performs integrative high-throughput analysis of structural data to localize all types of binding sites and associated partners by homology and to characterize their properties and behaviors in a systemic way. The robustness of our binding site inferences was compared to four curated datasets corresponding to protein heterodimers and homodimers and protein–DNA/RNA assemblies. The Molecular Cartographies of structurally well-detailed proteins shows that 44% of their surfaces interact with non-solvent partners. Residue contact frequencies with water suggest that ∼86% of their surfaces are transiently solvated, whereas only 15% are specifically solvated. Our analysis also reveals the existence of two major binding site families: specific binding sites which can only bind one type of molecule (protein, DNA, RNA, etc.) and polyvalent binding sites that can bind several distinct types of molecule. Specific homodimer binding sites are for instance nearly twice as hydrophobic than previously described and more closely resemble the protein core, while polyvalent binding sites able to form homo and heterodimers more closely resemble the surfaces involved in crystal packing. Similarly, the regions able to bind DNA and to alternatively form homodimers, are more hydrophobic and less polar than previously described DNA binding sites.
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47
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Aniba MR, Poch O, Marchler-Bauer A, Thompson JD. AlexSys: a knowledge-based expert system for multiple sequence alignment construction and analysis. Nucleic Acids Res 2010; 38:6338-49. [PMID: 20530533 PMCID: PMC2965243 DOI: 10.1093/nar/gkq526] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Multiple sequence alignment (MSA) is a cornerstone of modern molecular biology and represents a unique means of investigating the patterns of conservation and diversity in complex biological systems. Many different algorithms have been developed to construct MSAs, but previous studies have shown that no single aligner consistently outperforms the rest. This has led to the development of a number of ‘meta-methods’ that systematically run several aligners and merge the output into one single solution. Although these methods generally produce more accurate alignments, they are inefficient because all the aligners need to be run first and the choice of the best solution is made a posteriori. Here, we describe the development of a new expert system, AlexSys, for the multiple alignment of protein sequences. AlexSys incorporates an intelligent inference engine to automatically select an appropriate aligner a priori, depending only on the nature of the input sequences. The inference engine was trained on a large set of reference multiple alignments, using a novel machine learning approach. Applying AlexSys to a test set of 178 alignments, we show that the expert system represents a good compromise between alignment quality and running time, making it suitable for high throughput projects. AlexSys is freely available from http://alnitak.u-strasbg.fr/∼aniba/alexsys.
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Affiliation(s)
- Mohamed Radhouene Aniba
- Department of Structural Biology and Genomics, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Institut National de la Santé et de la Recherche Médicale, The Centre National de la Recherche Scientifique, UMR7104, F-67400 Illkirch, Université Louis Pasteur, F-67000 Strasbourg, France
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48
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Friedrich A, Garnier N, Gagnière N, Nguyen H, Albou LP, Biancalana V, Bettler E, Deléage G, Lecompte O, Muller J, Moras D, Mandel JL, Toursel T, Moulinier L, Poch O. SM2PH-db: an interactive system for the integrated analysis of phenotypic consequences of missense mutations in proteins involved in human genetic diseases. Hum Mutat 2010; 31:127-35. [PMID: 19921752 DOI: 10.1002/humu.21155] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Understanding how genetic alterations affect gene products at the molecular level represents a first step in the elucidation of the complex relationships between genotypic and phenotypic variations, and is thus a major challenge in the postgenomic era. Here, we present SM2PH-db (http://decrypthon.igbmc.fr/sm2ph), a new database designed to investigate structural and functional impacts of missense mutations and their phenotypic effects in the context of human genetic diseases. A wealth of up-to-date interconnected information is provided for each of the 2,249 disease-related entry proteins (August 2009), including data retrieved from biological databases and data generated from a Sequence-Structure-Evolution Inference in Systems-based approach, such as multiple alignments, three-dimensional structural models, and multidimensional (physicochemical, functional, structural, and evolutionary) characterizations of mutations. SM2PH-db provides a robust infrastructure associated with interactive analysis tools supporting in-depth study and interpretation of the molecular consequences of mutations, with the more long-term goal of elucidating the chain of events leading from a molecular defect to its pathology. The entire content of SM2PH-db is regularly and automatically updated thanks to a computational grid data federation facilities provided in the context of the Decrypthon program.
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Affiliation(s)
- Anne Friedrich
- Département de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire (UMR7104), Centre National de la Recherche Scientifique/Institut National de la Santé et de la Recherche Médicale/Université de Strasbourg, Illkirch, France
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49
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Albou LP, Schwarz B, Poch O, Wurtz JM, Moras D. Defining and characterizing protein surface using alpha shapes. Proteins 2009; 76:1-12. [DOI: 10.1002/prot.22301] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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50
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Meesters C, Brack A, Hellmann N, Decker H. Structural characterization of the alpha-hemolysin monomer from Staphylococcus aureus. Proteins 2009; 75:118-26. [PMID: 18798569 DOI: 10.1002/prot.22227] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Alpha-hemolysin from Staphylococcus aureus is secreted as a water-soluble monomer and assembles on membranes to oligomerize into a homo-heptameric, water-filled pore. These pores lead to lysis and cell death. Although the structure of the heptameric pore is solved by means of X-ray crystallography, structures of intermediate states-from the soluble monomer to all potential "pre-pore" structures-are yet unknown. Here, we propose a model of the monomeric alpha-hemolysin in solution based on molecular modeling, verified by small angle X-ray scattering data. This structure reveals details of the monomeric conformation of the alpha-hemolysin, for example inherent flexibility, along with definite differences in comparison to the structures used as templates.
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