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Calvete O, Herraiz M, Reyes J, Patiño A, Benitez J. A cumulative effect involving malfunction of the PTH1R and ATP4A genes explains a familial gastric neuroendocrine tumor with hypothyroidism and arthritis. Gastric Cancer 2017; 20:998-1003. [PMID: 28474257 DOI: 10.1007/s10120-017-0723-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 04/23/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND Type I gastric neuroendocrine tumors (gNETs) classically arise because of hypergastrinemia and involve destruction of parietal cells, which are responsible for gastric acid secretion through the ATP4A proton pump and for intrinsic factor production. METHODS By whole exome sequencing, we studied a family with three members with gNETs plus hypothyroidism and rheumatoid arthritis to uncover their genetic origin. RESULTS A heterozygous missense mutation in the ATP4A gene was identified. Carriers of this variant had low ferritin and vitamin B12 levels but did not develop gNETs. A second heterozygous mutation was also uncovered (PTH1R p.E546K). Carriers exhibited hypothyroidism and one of them had rheumatoid arthritis. Gastrin activates parathyroid hormone like hormone/parathyroid hormone 1 receptor (PTH1R) signaling, which is involved in gastric cell homeostasis. Activation of parathyroid hormone/PTH1R, which is upregulated by thyrotropin in the thyroid, is also involved in RANKL expression, which regulates bone homeostasis. Thyrotropin and RANKL expression were deregulated in PTH1R mutation carriers, suggesting a link between the PTH1R gene, hypothyroidism, rheumatoid arthritis, and gastric disease. Only patients with both mutations developed gNETs plus hypothyroidism and rheumatoid arthritis. CONCLUSION Both mutations suggest that a collaborative mechanism is operative in this family, in which mutations in these genes affect the function and viability of parietal cells and lead to the achlorhydria that drives hypergastrinemia and the formation of gNETs.
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Affiliation(s)
- Oriol Calvete
- Human Genetics Group, Spanish National Cancer Research Center (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain.,Biomedical Research Networking Center on Rare Diseases (CIBERER), 28029, Madrid, Spain
| | - Maite Herraiz
- Department of Gastroenterology, University Clinic of Navarra, 31008, Pamplona, Spain
| | - Jose Reyes
- Department of Gastroenterology, Hospital INCA, 07300, Majorca, Spain
| | - Ana Patiño
- Department of Pediatrics and Clinical Genetics Unit, University Clinic of Navarra, 31008, Pamplona, Spain
| | - Javier Benitez
- Human Genetics Group, Spanish National Cancer Research Center (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain. .,Biomedical Research Networking Center on Rare Diseases (CIBERER), 28029, Madrid, Spain.
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302
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Yuan P, D'Lima NG, Slavoff SA. Comparative Membrane Proteomics Reveals a Nonannotated E. coli Heat Shock Protein. Biochemistry 2017; 57:56-60. [PMID: 29039649 PMCID: PMC5761644 DOI: 10.1021/acs.biochem.7b00864] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recent advances in proteomics and genomics have enabled discovery of thousands of previously nonannotated small open reading frames (smORFs) in genomes across evolutionary space. Furthermore, quantitative mass spectrometry has recently been applied to analysis of regulated smORF expression. However, bottom-up proteomics has remained relatively insensitive to membrane proteins, suggesting they may have been underdetected in previous studies. In this report, we add biochemical membrane protein enrichment to our previously developed label-free quantitative proteomics protocol, revealing a never-before-identified heat shock protein in Escherichia coli K12. This putative smORF-encoded heat shock protein, GndA, is likely to be ∼36-55 amino acids in length and contains a predicted transmembrane helix. We validate heat shock-regulated expression of the gndA smORF and demonstrate that a GndA-GFP fusion protein cofractionates with the cell membrane. Quantitative membrane proteomics therefore has the ability to reveal nonannotated small proteins that may play roles in bacterial stress responses.
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Affiliation(s)
- Peijia Yuan
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States.,Chemical Biology Institute, Yale University , West Haven, Connecticut 06516, United States
| | - Nadia G D'Lima
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States.,Chemical Biology Institute, Yale University , West Haven, Connecticut 06516, United States
| | - Sarah A Slavoff
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States.,Chemical Biology Institute, Yale University , West Haven, Connecticut 06516, United States.,Department of Molecular Biophysics and Biochemistry, Yale University , New Haven, Connecticut 06529, United States
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303
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Brandi V, Di Lella V, Marino M, Ascenzi P, Polticelli F. A comprehensive in silico analysis of huntingtin and its interactome. J Biomol Struct Dyn 2017; 36:3155-3171. [PMID: 28920551 DOI: 10.1080/07391102.2017.1381646] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A polyglutamine expansion of the N-terminal region of huntingtin (Htt) causes Huntington's disease, a severe neurodegenerative disorder. Htt huge multidomain structure, the presence of disordered regions, and the lack of sequence homologs of known structure, so far prevented structural studies of Htt, making the study of its structure-function relationships very difficult. In this work, the presence and location of five Htt ordered domains (named from Hunt1 to Hunt5) has been detected and the structure of these domains has been predicted for the first time using a combined threading/ab initio modeling approach. This work has led to the identification of a previously undetected HEAT repeats region in the Hunt3 domain. Furthermore, a putative function has been assigned to four out of the five domains. Hunt1 and Hunt5, displaying structural similarity with the regulatory subunit A of protein phosphatase 2A, are predicted to play a role in regulating the phosphorylation status of cellular proteins. Hunt2 and Hunt3 are predicted to be homologs of two yeast importins and to mediate vescicles transport and protein trafficking. Finally, a comprehensive analysis of the Htt interactome has been carried out and is discussed to provide a global picture of the Htt's structure-function relationships.
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Affiliation(s)
- Valentina Brandi
- a Department of Sciences , Roma Tre University, Viale Guglielmo Marconi 446 , Roma I-00146 , Italy
| | - Valentina Di Lella
- a Department of Sciences , Roma Tre University, Viale Guglielmo Marconi 446 , Roma I-00146 , Italy
| | - Maria Marino
- a Department of Sciences , Roma Tre University, Viale Guglielmo Marconi 446 , Roma I-00146 , Italy
| | - Paolo Ascenzi
- a Department of Sciences , Roma Tre University, Viale Guglielmo Marconi 446 , Roma I-00146 , Italy.,b Interdepartmental Laboratory for Electron Microscopy , Roma Tre University , Roma I-00146 , Italy
| | - Fabio Polticelli
- a Department of Sciences , Roma Tre University, Viale Guglielmo Marconi 446 , Roma I-00146 , Italy.,c National Institute of Nuclear Physics , Roma Tre University, Roma Tre Section , Roma I-00146 , Italy
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304
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Gayarre J, Martín-Gimeno P, Osorio A, Paumard B, Barroso A, Fernández V, de la Hoya M, Rojo A, Caldés T, Palacios J, Urioste M, Benítez J, García MJ. Characterisation of the novel deleterious RAD51C p.Arg312Trp variant and prioritisation criteria for functional analysis of RAD51C missense changes. Br J Cancer 2017; 117:1048-1062. [PMID: 28829762 PMCID: PMC5625680 DOI: 10.1038/bjc.2017.286] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 07/24/2017] [Accepted: 07/27/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Despite a high prevalence of deleterious missense variants, most studies of RAD51C ovarian cancer susceptibility gene only provide in silico pathogenicity predictions of missense changes. We identified a novel deleterious RAD51C missense variant (p.Arg312Trp) in a high-risk family, and propose a criteria to prioritise RAD51C missense changes qualifying for functional analysis. METHODS To evaluate pathogenicity of p.Arg312Trp variant we used sequence homology, loss of heterozygosity (LOH) and segregation analysis, and a comprehensive functional characterisation. To define a functional-analysis prioritisation criteria, we used outputs for the known functionally confirmed deleterious and benign RAD51C missense changes from nine pathogenicity prediction algorithms. RESULTS The p.Arg312Trp variant failed to correct mitomycin and olaparib hypersensitivity and to complement abnormal RAD51C foci formation according to functional assays, which altogether with LOH and segregation data demonstrated deleteriousness. Prioritisation criteria were based on the number of predictors providing a deleterious output, with a minimum of 5 to qualify for testing and a PredictProtein score greater than 33 to assign high-priority indication. CONCLUSIONS Our study points to a non-negligible number of RAD51C missense variants likely to impair protein function, provides a guideline to prioritise and encourage their selection for functional analysis and anticipates that reference laboratories should have available resources to conduct such assays.
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Affiliation(s)
- Javier Gayarre
- Human Genetics Group, Spanish National Cancer Research Center, C/Melchor Fernández Almagro 3, Madrid
28029, Spain
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Madrid 28029, Spain
| | - Paloma Martín-Gimeno
- Human Genetics Group, Spanish National Cancer Research Center, C/Melchor Fernández Almagro 3, Madrid
28029, Spain
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Madrid 28029, Spain
| | - Ana Osorio
- Human Genetics Group, Spanish National Cancer Research Center, C/Melchor Fernández Almagro 3, Madrid
28029, Spain
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Madrid 28029, Spain
| | - Beatriz Paumard
- Human Genetics Group, Spanish National Cancer Research Center, C/Melchor Fernández Almagro 3, Madrid
28029, Spain
| | - Alicia Barroso
- Human Genetics Group, Spanish National Cancer Research Center, C/Melchor Fernández Almagro 3, Madrid
28029, Spain
| | - Victoria Fernández
- Human Genetics Group, Spanish National Cancer Research Center, C/Melchor Fernández Almagro 3, Madrid
28029, Spain
| | - Miguel de la Hoya
- Laboratorio de Oncología Molecular, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital San Carlos (IdISSC), Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid 28040, Spain
| | | | - Trinidad Caldés
- Laboratorio de Oncología Molecular, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital San Carlos (IdISSC), Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid 28040, Spain
| | - José Palacios
- Servicio de Anatomía Patológica. Hospital Universitario Ramón y Cajal (IRYCIS), Departamento de Medicina y Especialidades Médicas, Universidad de Alcalá, Madrid 28034, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid 28029, Spain
| | - Miguel Urioste
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Madrid 28029, Spain
- Familial Cancer Unit, Spanish National Cancer Research Center, C/Melchor Fernández Almagro 3, Madrid
28029, Spain
| | - Javier Benítez
- Human Genetics Group, Spanish National Cancer Research Center, C/Melchor Fernández Almagro 3, Madrid
28029, Spain
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Madrid 28029, Spain
| | - María J García
- Human Genetics Group, Spanish National Cancer Research Center, C/Melchor Fernández Almagro 3, Madrid
28029, Spain
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Madrid 28029, Spain
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305
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The single cyclic nucleotide-specific phosphodiesterase of the intestinal parasite Giardia lamblia represents a potential drug target. PLoS Negl Trop Dis 2017; 11:e0005891. [PMID: 28915270 PMCID: PMC5617230 DOI: 10.1371/journal.pntd.0005891] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 09/27/2017] [Accepted: 08/21/2017] [Indexed: 01/08/2023] Open
Abstract
Background Giardiasis is an intestinal infection correlated with poverty and poor drinking water quality, and treatment options are limited. According to the Center for Disease Control and Prevention, Giardia infections afflict nearly 33% of people in developing countries, and 2% of the adult population in the developed world. This study describes the single cyclic nucleotide-specific phosphodiesterase (PDE) of G. lamblia and assesses PDE inhibitors as a new generation of anti-giardial drugs. Methods An extensive search of the Giardia genome database identified a single gene coding for a class I PDE, GlPDE. The predicted protein sequence was analyzed in-silico to characterize its domain structure and catalytic domain. Enzymatic activity of GlPDE was established by complementation of a PDE-deficient Saccharomyces cerevisiae strain, and enzyme kinetics were characterized in soluble yeast lysates. The potency of known PDE inhibitors was tested against the activity of recombinant GlPDE expressed in yeast and against proliferating Giardia trophozoites. Finally, the localization of epitope-tagged and ectopically expressed GlPDE in Giardia cells was investigated. Results Giardia encodes a class I PDE. Catalytically important residues are fully conserved between GlPDE and human PDEs, but sequence differences between their catalytic domains suggest that designing Giardia-specific inhibitors is feasible. Recombinant GlPDE hydrolyzes cAMP with a Km of 408 μM, and cGMP is not accepted as a substrate. A number of drugs exhibit a high degree of correlation between their potency against the recombinant enzyme and their inhibition of trophozoite proliferation in culture. Epitope-tagged GlPDE localizes as dots in a pattern reminiscent of mitosomes and to the perinuclear region in Giardia. Conclusions Our data strongly suggest that inhibition of G. lamblia PDE activity leads to a profound inhibition of parasite proliferation and that GlPDE is a promising target for developing novel anti-giardial drugs. Cellular signaling by the cyclic nucleotides cAMP and cGMP is ubiquitously found in organisms from human to unicellular parasites. Cyclic nucleotide-specific phosphodiesterases (PDEs) are pivotal regulators of these signaling processes and these enzymes represent important drug targets for a variety of diseases. Eleven PDE families are distinguished in humans and selective inhibition of a single human PDE family without targeting others is feasible. In parasites, interference in the signaling mechanism by PDE inhibition may be fatal. The diarrhea-causing parasite Giardia lamblia contains only one single PDE, named GlPDE. GlPDE activity is highly impaired by a range of PDE inhibitors, which also suppress parasite proliferation in vitro. Thus, there is a good agreement between PDE inhibition and parasite drug susceptibility. We demonstrate molecular differences between human PDEs and GlPDE that can be exploited for the development of GlPDE-selective inhibitors. Finally, our data may suggest localization of GlPDE to mitosome organelles, which are absent in human cells and thus are in the focus as possible targets for the treatment of giardiasis. This may add to the notion that GlPDE represents a potential target for the development of novel anti-giardial drugs.
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306
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Hücker SM, Ardern Z, Goldberg T, Schafferhans A, Bernhofer M, Vestergaard G, Nelson CW, Schloter M, Rost B, Scherer S, Neuhaus K. Discovery of numerous novel small genes in the intergenic regions of the Escherichia coli O157:H7 Sakai genome. PLoS One 2017; 12:e0184119. [PMID: 28902868 PMCID: PMC5597208 DOI: 10.1371/journal.pone.0184119] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 08/20/2017] [Indexed: 12/29/2022] Open
Abstract
In the past, short protein-coding genes were often disregarded by genome annotation pipelines. Transcriptome sequencing (RNAseq) signals outside of annotated genes have usually been interpreted to indicate either ncRNA or pervasive transcription. Therefore, in addition to the transcriptome, the translatome (RIBOseq) of the enteric pathogen Escherichia coli O157:H7 strain Sakai was determined at two optimal growth conditions and a severe stress condition combining low temperature and high osmotic pressure. All intergenic open reading frames potentially encoding a protein of ≥ 30 amino acids were investigated with regard to coverage by transcription and translation signals and their translatability expressed by the ribosomal coverage value. This led to discovery of 465 unique, putative novel genes not yet annotated in this E. coli strain, which are evenly distributed over both DNA strands of the genome. For 255 of the novel genes, annotated homologs in other bacteria were found, and a machine-learning algorithm, trained on small protein-coding E. coli genes, predicted that 89% of these translated open reading frames represent bona fide genes. The remaining 210 putative novel genes without annotated homologs were compared to the 255 novel genes with homologs and to 250 short annotated genes of this E. coli strain. All three groups turned out to be similar with respect to their translatability distribution, fractions of differentially regulated genes, secondary structure composition, and the distribution of evolutionary constraint, suggesting that both novel groups represent legitimate genes. However, the machine-learning algorithm only recognized a small fraction of the 210 genes without annotated homologs. It is possible that these genes represent a novel group of genes, which have unusual features dissimilar to the genes of the machine-learning algorithm training set.
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Affiliation(s)
- Sarah M. Hücker
- Chair for Microbial Ecology, Technische Universität München, Freising, Germany
- ZIEL - Institute for Food & Health, Technische Universität München, Freising, Germany
| | - Zachary Ardern
- Chair for Microbial Ecology, Technische Universität München, Freising, Germany
- ZIEL - Institute for Food & Health, Technische Universität München, Freising, Germany
| | - Tatyana Goldberg
- Department of Informatics—Bioinformatics & TUM-IAS, Technische Universität München, Garching, Germany
| | - Andrea Schafferhans
- Department of Informatics—Bioinformatics & TUM-IAS, Technische Universität München, Garching, Germany
| | - Michael Bernhofer
- Department of Informatics—Bioinformatics & TUM-IAS, Technische Universität München, Garching, Germany
| | - Gisle Vestergaard
- Research Unit Environmental Genomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Chase W. Nelson
- Sackler Institute for Comparative Genomics, American Museum of Natural History New York, New York, United States of America
| | - Michael Schloter
- Research Unit Environmental Genomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Burkhard Rost
- Department of Informatics—Bioinformatics & TUM-IAS, Technische Universität München, Garching, Germany
| | - Siegfried Scherer
- Chair for Microbial Ecology, Technische Universität München, Freising, Germany
- ZIEL - Institute for Food & Health, Technische Universität München, Freising, Germany
| | - Klaus Neuhaus
- Chair for Microbial Ecology, Technische Universität München, Freising, Germany
- Core Facility Microbiome/NGS, ZIEL - Institute for Food & Health, Technische Universität München, Freising, Germany
- * E-mail:
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307
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Liu H, Wei Q, Huang C, Zhang Y, Guo Z. Potential Roles of Intrinsic Disorder in Maternal-Effect Proteins Involved in the Maintenance of DNA Methylation. Int J Mol Sci 2017; 18:E1898. [PMID: 28869544 PMCID: PMC5618547 DOI: 10.3390/ijms18091898] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 08/21/2017] [Accepted: 08/22/2017] [Indexed: 01/14/2023] Open
Abstract
DNA methylation is an important epigenetic modification that needs to be carefully controlled as a prerequisite for normal early embryogenesis. Compelling evidence now suggests that four maternal-effect proteins, primordial germ cell 7 (PGC7), zinc finger protein 57 (ZFP57), tripartite motif-containing 28 (TRIM28) and DNA methyltransferase (cytosine-5) 1 (DNMT1) are involved in the maintenance of DNA methylation. However, it is still not fully understood how these maternal-effect proteins maintain the DNA methylation imprint. We noticed that a feature common to these proteins is the presence of significant levels of intrinsic disorder so in this study we started from an intrinsic disorder perspective to try to understand these maternal-effect proteins. To do this, we firstly analysed the intrinsic disorder predispositions of PGC7, ZFP57, TRIM28 and DNMT1 by using a set of currently available computational tools and secondly conducted an intensive literature search to collect information on their interacting partners and structural characterization. Finally, we discuss the potential effect of intrinsic disorder on the function of these proteins in maintaining DNA methylation.
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Affiliation(s)
- Hongliang Liu
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China.
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling 712100, China.
| | - Qing Wei
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China.
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling 712100, China.
- College of Eco-Environmental Engineering, Qinghai University, Xining 810016, China.
| | - Chenyang Huang
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China.
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling 712100, China.
| | - Yong Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China.
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling 712100, China.
| | - Zekun Guo
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China.
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling 712100, China.
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308
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Meng F, Uversky VN, Kurgan L. Comprehensive review of methods for prediction of intrinsic disorder and its molecular functions. Cell Mol Life Sci 2017; 74:3069-3090. [PMID: 28589442 PMCID: PMC11107660 DOI: 10.1007/s00018-017-2555-4] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 06/01/2017] [Indexed: 12/19/2022]
Abstract
Computational prediction of intrinsic disorder in protein sequences dates back to late 1970 and has flourished in the last two decades. We provide a brief historical overview, and we review over 30 recent predictors of disorder. We are the first to also cover predictors of molecular functions of disorder, including 13 methods that focus on disordered linkers and disordered protein-protein, protein-RNA, and protein-DNA binding regions. We overview their predictive models, usability, and predictive performance. We highlight newest methods and predictors that offer strong predictive performance measured based on recent comparative assessments. We conclude that the modern predictors are relatively accurate, enjoy widespread use, and many of them are fast. Their predictions are conveniently accessible to the end users, via web servers and databases that store pre-computed predictions for millions of proteins. However, research into methods that predict many not yet addressed functions of intrinsic disorder remains an outstanding challenge.
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Affiliation(s)
- Fanchi Meng
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
- Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
| | - Lukasz Kurgan
- Department of Computer Science, Virginia Commonwealth University, Richmond, USA.
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309
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Guevara G, Heras LFDL, Perera J, Llorens JMN. Functional characterization of 3-ketosteroid 9α-hydroxylases in Rhodococcus ruber strain chol-4. J Steroid Biochem Mol Biol 2017. [PMID: 28642093 DOI: 10.1016/j.jsbmb.2017.06.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The 3-Ketosteroid-9α-Hydroxylase, also known as KshAB [androsta-1,4-diene-3,17-dione, NADH:oxygen oxidoreductase (9α-hydroxylating); EC 1.14.13.142)], is a key enzyme in the general scheme of the bacterial steroid catabolism in combination with a 3-ketosteroid-Δ1-dehydrogenase activity (KstD), being both responsible of the steroid nucleus (rings A/B) breakage. KshAB initiates the opening of the steroid ring by the 9α-hydroxylation of the C9 carbon of 4-ene-3-oxosteroids (e.g. AD) or 1,4-diene-3-oxosteroids (e.g. ADD), transforming them into 9α-hydroxy-4-androsten-3,17-dione (9OHAD) or 9α-hydroxy-1,4-androstadiene-3,17-dione (9OHADD), respectively. The redundancy of these enzymes in the actinobacterial genomes results in a serious difficulty for metabolic engineering this catabolic pathway to obtain intermediates of industrial interest. In this work, we have identified three homologous kshA genes and one kshB gen in different genomic regions of R. ruber strain Chol-4. We present a set of data that helps to understand their specific roles in this strain, including: i) description of the KshAB enzymes ii) construction and characterization of ΔkshB and single, double and triple ΔkshA mutants in R. ruber iii) growth studies of the above strains on different substrates and iv) genetic complementation and biotransformation assays with those strains. Our results show that KshA2 isoform is needed for the degradation of steroid substrates with short side chain, while KshA3 works on those molecules with longer side chains. KshA1 is a more versatile enzyme related to the cholic acid catabolism, although it also collaborates with KshA2 or KshA3 activities in the catabolism of steroids. Accordingly to what it is described for other Rhodococcus strains, our results also suggest that the side chain degradation is KshAB-independent.
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Affiliation(s)
- Govinda Guevara
- Department of Biochemistry and Molecular Biology I, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | | | - Julián Perera
- Department of Biochemistry and Molecular Biology I, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Juana María Navarro Llorens
- Department of Biochemistry and Molecular Biology I, Universidad Complutense de Madrid, 28040, Madrid, Spain.
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310
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Chesarino NM, Compton AA, McMichael TM, Kenney AD, Zhang L, Soewarna V, Davis M, Schwartz O, Yount JS. IFITM3 requires an amphipathic helix for antiviral activity. EMBO Rep 2017; 18:1740-1751. [PMID: 28835547 DOI: 10.15252/embr.201744100] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 07/18/2017] [Accepted: 07/25/2017] [Indexed: 12/31/2022] Open
Abstract
Interferon-induced transmembrane protein 3 (IFITM3) is a cellular factor that blocks virus fusion with cell membranes. IFITM3 has been suggested to alter membrane curvature and fluidity, though its exact mechanism of action is unclear. Using a bioinformatic approach, we predict IFITM3 secondary structures and identify a highly conserved, short amphipathic helix within a hydrophobic region of IFITM3 previously thought to be a transmembrane domain. Consistent with the known ability of amphipathic helices to alter membrane properties, we show that this helix and its amphipathicity are required for the IFITM3-dependent inhibition of influenza virus, Zika virus, vesicular stomatitis virus, Ebola virus, and human immunodeficiency virus infections. The homologous amphipathic helix within IFITM1 is also required for the inhibition of infection, indicating that IFITM proteins possess a conserved mechanism of antiviral action. We further demonstrate that the amphipathic helix of IFITM3 is required to block influenza virus hemagglutinin-mediated membrane fusion. Overall, our results provide evidence that IFITM proteins utilize an amphipathic helix for inhibiting virus fusion.
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Affiliation(s)
- Nicholas M Chesarino
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
| | - Alex A Compton
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris, France.,CNRS URA 3015, Paris, France.,HIV Dynamics and Replication Program, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Temet M McMichael
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
| | - Adam D Kenney
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
| | - Lizhi Zhang
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
| | - Victoria Soewarna
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
| | - Matthew Davis
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
| | - Olivier Schwartz
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris, France.,CNRS URA 3015, Paris, France
| | - Jacob S Yount
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
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311
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Kist AM, Lampert A, O'Reilly AO. DIsulfide Mapping PLanner Software Tool. J Comput Biol 2017; 25:430-434. [PMID: 28817312 DOI: 10.1089/cmb.2017.0129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Disulfide bridges are side-chain-mediated covalent bonds between cysteines that stabilize many protein structures. Disulfide mapping experiments to resolve these linkages typically involve proteolytic cleavage of the protein of interest followed by mass spectroscopy to identify fragments corresponding to linked peptides. Here we report the sequence-based "DIMPL" web tool to facilitate the planning and analysis steps of experimental mapping studies. The software tests permutations of user-selected proteases to determine an optimal peptic digest that produces cleavage between cysteine residues, thus separating each to an individual peptide fragment. The webserver returns fragment sequence and mass data that can be dynamically ordered to enable straightforward comparative analysis with mass spectroscopy results, facilitating dipeptide identification.
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Affiliation(s)
- Andreas M Kist
- 1 Institute of Physiology and Pathophysiology, Friedrich-Alexander-University , Erlangen-Nuremberg, Erlangen, Germany .,2 Max-Planck-Institute of Neurobiology , Martinsried, Germany
| | - Angelika Lampert
- 1 Institute of Physiology and Pathophysiology, Friedrich-Alexander-University , Erlangen-Nuremberg, Erlangen, Germany .,3 Institute of Physiology , Uniklinik RWTH Aachen, 52074 Aachen, Germany
| | - Andrias O O'Reilly
- 1 Institute of Physiology and Pathophysiology, Friedrich-Alexander-University , Erlangen-Nuremberg, Erlangen, Germany .,4 School of Natural Sciences and Psychology, Liverpool John Moores University , Liverpool, United Kingdom
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312
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Compensatory mutations improve general permissiveness to antibiotic resistance plasmids. Nat Ecol Evol 2017; 1:1354-1363. [PMID: 29046540 PMCID: PMC5649373 DOI: 10.1038/s41559-017-0243-2] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 06/16/2017] [Indexed: 11/08/2022]
Abstract
Horizontal gene transfer mediated by broad-host-range plasmids is an important mechanism of antibiotic resistance spread. While not all bacteria maintain plasmids equally well, plasmid persistence can improve over time, yet no general evolutionary mechanisms have emerged. Our goal was to identify these mechanisms and to assess if adaptation to one plasmid affects the permissiveness to others. We experimentally evolved Pseudomonas sp. H2 containing multidrug resistance plasmid RP4, determined plasmid persistence and cost using a joint experimental-modelling approach, resequenced evolved clones, and reconstructed key mutations. Plasmid persistence improved in fewer than 600 generations because the fitness cost turned into a benefit. Improved retention of naive plasmids indicated that the host evolved towards increased plasmid permissiveness. Key chromosomal mutations affected two accessory helicases and the RNA polymerase β-subunit. Our and other findings suggest that poor plasmid persistence can be caused by a high cost involving helicase-plasmid interactions that can be rapidly ameliorated.
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313
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Reinstein E, Drasinover V, Lotan R, Gal-Tanamy M, Bolocan Nachman I, Eyal E, Jaber L, Magal N, Shohat M. Mutations in ERGIC1 cause Arthrogryposis multiplex congenita, neuropathic type. Clin Genet 2017; 93:160-163. [PMID: 28317099 DOI: 10.1111/cge.13018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 03/13/2017] [Accepted: 03/15/2017] [Indexed: 11/29/2022]
Abstract
Arthrogryposis multiplex congenita (AMC) is heterogeneous group of disorders characterized by non-progressive joint contractures from birth that involve more than 1 part of the body. There are various etiologies for AMC including genetic and environmental depends on the specific type, however, for most types, the cause is not fully understood. We previously reported large Israeli Arab kindred consisting of 16 patients affected with AMC neuropathic type, and mapped the locus to a 5.5 cM interval on chromosome 5qter. Using whole exome sequencing, we have now identified homozygous pathogenic variant in the ERGIC1 gene within the previously defined linked region. ERGIC1 encodes a cycling membrane protein which has a possible role in transport between endoplasmic reticulum and Golgi. We further show that this mutation was absent in more than 200 samples of healthy unrelated individuals of the Israeli Arab population. Thus, our findings expand the spectrum of hereditary AMC and suggest that abnormalities in protein trafficking may underlie AMC-related disorders.
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Affiliation(s)
- E Reinstein
- Medical Genetics Institute, Meir Medical Center, Kfar-Saba, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - V Drasinover
- Medical Genetics Institute, Rabin Medical Center, Petah Tikva, Israel
| | - R Lotan
- Medical Genetics Institute, Rabin Medical Center, Petah Tikva, Israel
| | - M Gal-Tanamy
- Medical Genetics Institute, Rabin Medical Center, Petah Tikva, Israel
| | - I Bolocan Nachman
- Medical Genetics Institute, Rabin Medical Center, Petah Tikva, Israel
| | - E Eyal
- Cancer Research Center, Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - L Jaber
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Medical Genetics Institute, Rabin Medical Center, Petah Tikva, Israel
| | - N Magal
- Medical Genetics Institute, Rabin Medical Center, Petah Tikva, Israel
| | - M Shohat
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Cancer Research Center, Chaim Sheba Medical Center, Tel Hashomer, Israel.,Medical Genetics institute, Maccabi HMO, Rechovot, Israel
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314
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A putative ATP/GTP binding protein affects Leishmania mexicana growth in insect vectors and vertebrate hosts. PLoS Negl Trop Dis 2017; 11:e0005782. [PMID: 28742133 PMCID: PMC5542692 DOI: 10.1371/journal.pntd.0005782] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 08/03/2017] [Accepted: 07/06/2017] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Leishmania virulence factors responsible for the complicated epidemiology of the various leishmaniases remain mainly unidentified. This study is a characterization of a gene previously identified as upregulated in two of three overlapping datasets containing putative factors important for Leishmania's ability to establish mammalian intracellular infection and to colonize the gut of an insect vector. METHODOLOGY/PRINCIPAL FINDINGS The investigated gene encodes ATP/GTP binding motif-containing protein related to Leishmania development 1 (ALD1), a cytosolic protein that contains a cryptic ATP/GTP binding P-loop. We compared differentiation, growth rates, and infective abilities of wild-type and ALD1 null mutant cell lines of L. mexicana. Loss of ALD1 results in retarded growth kinetics but not defects in differentiation in axenic culture. Similarly, when mice and the sand fly vector were infected with the ALD1 null mutant, the primary difference in infection and colonization phenotype relative to wild type was an inability to achieve maximal host pathogenicity. While ability of the ALD1 null mutant cells to infect macrophages in vitro was not affected, replication within macrophages was clearly curtailed. CONCLUSIONS/SIGNIFICANCE L. mexicana ALD1, encoding a protein with no assigned functional domains or motifs, was identified utilizing multiple comparative analyses with the related and often experimentally overlooked monoxenous flagellates. We found that it plays a role in Leishmania infection and colonization in vitro and in vivo. Results suggest that ALD1 functions in L. mexicana's general metabolic network, rather than function in specific aspect of virulence as anticipated from the compared datasets. This result validates our comparative genomics approach for finding relevant factors, yet highlights the importance of quality laboratory-based analysis of genes tagged by these methods.
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315
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Abstract
Background Recently we surveyed the dark-proteome, i.e., regions of proteins never observed by experimental structure determination and inaccessible to homology modelling. Surprisingly, we found that most of the dark proteome could not be accounted for by conventional explanations (e.g., intrinsic disorder, transmembrane domains, and compositional bias), and that nearly half of the dark proteome comprised dark proteins, in which the entire sequence lacked similarity to any known structure. In this paper we will present the Dark Proteome Database (DPD) and associated web services that provide access to updated information about the dark proteome. Results We assembled DPD from several external web resources (primarily Aquaria and Swiss-Prot) and stored it in a relational database currently containing ~10 million entries and occupying ~2 GBytes of disk space. This database comprises two key tables: one giving information on the ‘darkness’ of each protein, and a second table that breaks each protein into dark and non-dark regions. In addition, a second version of the database is created using also information from the Protein Model Portal (PMP) to determine darkness. To provide access to DPD, a web server has been implemented giving access to all underlying data, as well as providing access to functional analyses derived from these data. Conclusions Availability of this database and its web service will help focus future structural and computational biology efforts to study the dark proteome, thus providing a basis for understanding a wide variety of biological functions that currently remain unknown. Availability and implementation DPD is available at http://darkproteome.ws . The complete database is also available upon request. Data use is permitted via the Creative Commons Attribution-NonCommercial International license (http://creativecommons.org/licenses/by-nc/4.0/ ). Electronic supplementary material The online version of this article (doi:10.1186/s13040-017-0144-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nelson Perdigão
- Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
- Instituto de Sistemas e Robótica, 1049-001 Lisbon, Portugal
| | - Agostinho C. Rosa
- Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
- Instituto de Sistemas e Robótica, 1049-001 Lisbon, Portugal
| | - Seán I. O’Donoghue
- Garvan Institute of Medical Research, Sydney, NSW 2010 Australia
- The University of Sydney, Sydney, NSW 2006 Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Sydney, NSW 1670 Australia
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316
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Loftus KM, Cui H, Coutavas E, King DS, Ceravolo A, Pereiras D, Solmaz SR. Mechanism for G2 phase-specific nuclear export of the kinetochore protein CENP-F. Cell Cycle 2017; 16:1414-1429. [PMID: 28723232 DOI: 10.1080/15384101.2017.1338218] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Centromere protein F (CENP-F) is a component of the kinetochore and a regulator of cell cycle progression. CENP-F recruits the dynein transport machinery and orchestrates several cell cycle-specific transport events, including transport of the nucleus, mitochondria and chromosomes. A key regulatory step for several of these functions is likely the G2 phase-specific export of CENP-F from the nucleus to the cytosol, where the cytoplasmic dynein transport machinery resides; however, the molecular mechanism of this process is elusive. Here, we have identified 3 phosphorylation sites within the bipartite classical nuclear localization signal (cNLS) of CENP-F. These sites are specific for cyclin-dependent kinase 1 (Cdk1), which is active in G2 phase. Phosphomimetic mutations of these residues strongly diminish the interaction of the CENP-F cNLS with its nuclear transport receptor karyopherin α. These mutations also diminish nuclear localization of the CENP-F cNLS in cells. Notably, the cNLS is phosphorylated in the -1 position, which is important to orient the adjacent major motif for binding into its pocket on karyopherin α. We propose that localization of CENP-F is regulated by a cNLS, and a nuclear export pathway, resulting in nuclear localization during most of interphase. In G2 phase, the cNLS is weakened by phosphorylation through Cdk1, likely resulting in nuclear export of CENP-F via the still active nuclear export pathway. Once CENP-F resides in the cytosol, it can engage in pathways that are important for cell cycle progression, kinetochore assembly and the faithful segregation of chromosomes into daughter cells.
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Affiliation(s)
- Kyle M Loftus
- a Department of Chemistry , State University of New York at Binghamton , New York , NY , USA
| | - Heying Cui
- a Department of Chemistry , State University of New York at Binghamton , New York , NY , USA
| | - Elias Coutavas
- b Laboratory of Cell Biology , The Rockefeller University , New York , NY , USA
| | - David S King
- c Howard Hughes Medical Institute, Mass Spectrometry Laboratory , University of California at Berkeley , Berkeley , CA , USA
| | - Amanda Ceravolo
- a Department of Chemistry , State University of New York at Binghamton , New York , NY , USA
| | - Dylan Pereiras
- a Department of Chemistry , State University of New York at Binghamton , New York , NY , USA
| | - Sozanne R Solmaz
- a Department of Chemistry , State University of New York at Binghamton , New York , NY , USA
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317
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Jiang J, Wang N, Chen P, Zheng C, Wang B. Prediction of Protein Hotspots from Whole Protein Sequences by a Random Projection Ensemble System. Int J Mol Sci 2017; 18:ijms18071543. [PMID: 28718782 PMCID: PMC5536031 DOI: 10.3390/ijms18071543] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Revised: 07/03/2017] [Accepted: 07/05/2017] [Indexed: 11/30/2022] Open
Abstract
Hotspot residues are important in the determination of protein-protein interactions, and they always perform specific functions in biological processes. The determination of hotspot residues is by the commonly-used method of alanine scanning mutagenesis experiments, which is always costly and time consuming. To address this issue, computational methods have been developed. Most of them are structure based, i.e., using the information of solved protein structures. However, the number of solved protein structures is extremely less than that of sequences. Moreover, almost all of the predictors identified hotspots from the interfaces of protein complexes, seldom from the whole protein sequences. Therefore, determining hotspots from whole protein sequences by sequence information alone is urgent. To address the issue of hotspot predictions from the whole sequences of proteins, we proposed an ensemble system with random projections using statistical physicochemical properties of amino acids. First, an encoding scheme involving sequence profiles of residues and physicochemical properties from the AAindex1 dataset is developed. Then, the random projection technique was adopted to project the encoding instances into a reduced space. Then, several better random projections were obtained by training an IBk classifier based on the training dataset, which were thus applied to the test dataset. The ensemble of random projection classifiers is therefore obtained. Experimental results showed that although the performance of our method is not good enough for real applications of hotspots, it is very promising in the determination of hotspot residues from whole sequences.
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Affiliation(s)
- Jinjian Jiang
- School of Electronics and Information Engineering, Anhui University, Hefei 230601, China.
- School of Computer and Information, Anqing Normal University, Anqing 246133, China.
| | - Nian Wang
- School of Electronics and Information Engineering, Anhui University, Hefei 230601, China.
| | - Peng Chen
- Institute of Health Sciences, Anhui University, Hefei 230601, China.
| | - Chunhou Zheng
- School of Electronic Engineering & Automation, Anhui University, Hefei 230601, China.
| | - Bing Wang
- School of Electrical and Information Engineering, Anhui University of Technology, Ma'anshan 243032, China.
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318
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Random mutagenesis analysis and identification of a novel C 2H 2-type transcription factor from the nematode-trapping fungus Arthrobotrys oligospora. Sci Rep 2017; 7:5640. [PMID: 28717216 PMCID: PMC5514059 DOI: 10.1038/s41598-017-06075-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 06/12/2017] [Indexed: 01/04/2023] Open
Abstract
Arthrobotrys oligospora is a typical nematode-trapping fungus. In this study, 37 transformants of A. oligospora were obtained by REMI (restriction enzyme mediated integration) method and phenotypic properties of nine transformants were analyzed. The nine transformants showed differences in growth, conidiation, trap formation, stress tolerance, and/or pathogenicity among each other and with those of the parental wild-type strain (WT). The insertional sites of the hph cassette were identified in transformants X5 and X13. In X5, the cassette was inserted in the non-coding region between AOL_s00076g273 (76g273) and AOL_s00076g274 (76g274) and the transcription of 76g274, but not 76g273, was enhanced in X5. 76g274p had two conserved domains and was predicted as a nucleoprotein, which we confirmed by its nuclear localization in Saccharomyces cerevisiae using the green fluorescent protein-fused 76g274p. The transcription of 76g274 was stimulated or inhibited by several environmental factors. The sporulation yields of 76g274-deficient mutants were decreased by 70%, and transcription of several sporulation-related genes was severely diminished compared to the WT during the conidiation. In summary, a method for screening mutants was established in A. oligospora and using the method, we identified a novel C2H2-type transcription factor that positively regulates the conidiation of A. oligospora.
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319
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De Franco E, Flanagan SE, Yagi T, Abreu D, Mahadevan J, Johnson MB, Jones G, Acosta F, Mulaudzi M, Lek N, Oh V, Petz O, Caswell R, Ellard S, Urano F, Hattersley AT. Dominant ER Stress-Inducing WFS1 Mutations Underlie a Genetic Syndrome of Neonatal/Infancy-Onset Diabetes, Congenital Sensorineural Deafness, and Congenital Cataracts. Diabetes 2017; 66:2044-2053. [PMID: 28468959 PMCID: PMC5482085 DOI: 10.2337/db16-1296] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 04/23/2017] [Indexed: 12/31/2022]
Abstract
Neonatal diabetes is frequently part of a complex syndrome with extrapancreatic features: 18 genes causing syndromic neonatal diabetes have been identified to date. There are still patients with neonatal diabetes who have novel genetic syndromes. We performed exome sequencing in a patient and his unrelated, unaffected parents to identify the genetic etiology of a syndrome characterized by neonatal diabetes, sensorineural deafness, and congenital cataracts. Further testing was performed in 311 patients with diabetes diagnosed before 1 year of age in whom all known genetic causes had been excluded. We identified 5 patients, including the initial case, with three heterozygous missense mutations in WFS1 (4/5 confirmed de novo). They had diabetes diagnosed before 12 months (2 before 6 months) (5/5), sensorineural deafness diagnosed soon after birth (5/5), congenital cataracts (4/5), and hypotonia (4/5). In vitro studies showed that these WFS1 mutations are functionally different from the known recessive Wolfram syndrome-causing mutations, as they tend to aggregate and induce robust endoplasmic reticulum stress. Our results establish specific dominant WFS1 mutations as a cause of a novel syndrome including neonatal/infancy-onset diabetes, congenital cataracts, and sensorineural deafness. This syndrome has a discrete pathophysiology and differs genetically and clinically from recessive Wolfram syndrome.
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Affiliation(s)
- Elisa De Franco
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, U.K
| | - Sarah E Flanagan
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, U.K
| | - Takuya Yagi
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO
| | - Damien Abreu
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO
| | - Jana Mahadevan
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO
| | - Matthew B Johnson
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, U.K
| | - Garan Jones
- Department of Molecular Genetics, Royal Devon & Exeter NHS Foundation Trust, Exeter, U.K
| | - Fernanda Acosta
- Department of Pediatrics, Centro Médico Nacional 20 de Noviembre ISSSTE, Mexico City, Mexico
| | - Mphele Mulaudzi
- Department of Paediatrics and Child Health, University of Pretoria Medical School, Pretoria, South Africa
| | - Ngee Lek
- KK Women's and Children's Hospital, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore
| | - Vera Oh
- KK Women's and Children's Hospital, Singapore
| | - Oliver Petz
- Praxis für Kinder-und Jugendmedizin, Diabetologische Schwerpunktpraxis, Coesfeld, Germany
| | - Richard Caswell
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, U.K
| | - Sian Ellard
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, U.K
- Department of Molecular Genetics, Royal Devon & Exeter NHS Foundation Trust, Exeter, U.K
| | - Fumihiko Urano
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO
| | - Andrew T Hattersley
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, U.K.
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320
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Hastie KM, Zandonatti MA, Kleinfelter LM, Heinrich ML, Rowland MM, Chandran K, Branco LM, Robinson JE, Garry RF, Saphire EO. Structural basis for antibody-mediated neutralization of Lassa virus. Science 2017; 356:923-928. [PMID: 28572385 PMCID: PMC6007842 DOI: 10.1126/science.aam7260] [Citation(s) in RCA: 155] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 04/28/2017] [Indexed: 12/25/2022]
Abstract
The arenavirus Lassa causes severe hemorrhagic fever and a significant disease burden in West Africa every year. The glycoprotein, GPC, is the sole antigen expressed on the viral surface and the critical target for antibody-mediated neutralization. Here we present the crystal structure of the trimeric, prefusion ectodomain of Lassa GP bound to a neutralizing antibody from a human survivor at 3.2-angstrom resolution. The antibody extensively anchors two monomers together at the base of the trimer, and biochemical analysis suggests that it neutralizes by inhibiting conformational changes required for entry. This work illuminates pH-driven conformational changes in both receptor-binding and fusion subunits of Lassa virus, illustrates the unique assembly of the arenavirus glycoprotein spike, and provides a much-needed template for vaccine design against these threats to global health.
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Affiliation(s)
- Kathryn M Hastie
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michelle A Zandonatti
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Lara M Kleinfelter
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | | | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | - James E Robinson
- Department of Pediatrics, School of Medicine, Tulane University, New Orleans, LA, USA
| | - Robert F Garry
- Zalgen Labs, Germantown, MD, USA
- Department of Microbiology and Immunology, Tulane University, New Orleans, LA, USA
| | - Erica Ollmann Saphire
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA.
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
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321
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Elouej S, Beleza-Meireles A, Caswell R, Colclough K, Ellard S, Desvignes JP, Béroud C, Lévy N, Mohammed S, De Sandre-Giovannoli A. Exome sequencing reveals a de novo POLD1 mutation causing phenotypic variability in mandibular hypoplasia, deafness, progeroid features, and lipodystrophy syndrome (MDPL). Metabolism 2017; 71:213-225. [PMID: 28521875 DOI: 10.1016/j.metabol.2017.03.011] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 03/17/2017] [Accepted: 03/21/2017] [Indexed: 01/19/2023]
Abstract
BACKGROUND Mandibular hypoplasia, deafness, progeroid features, and lipodystrophy syndrome (MDPL) is an autosomal dominant systemic disorder characterized by prominent loss of subcutaneous fat, a characteristic facial appearance and metabolic abnormalities. This syndrome is caused by heterozygous de novo mutations in the POLD1 gene. To date, 19 patients with MDPL have been reported in the literature and among them 14 patients have been characterized at the molecular level. Twelve unrelated patients carried a recurrent in-frame deletion of a single codon (p.Ser605del) and two other patients carried a novel heterozygous mutation in exon 13 (p.Arg507Cys). Additionally and interestingly, germline mutations of the same gene have been involved in familial polyposis and colorectal cancer (CRC) predisposition. PATIENTS AND METHODS We describe a male and a female patient with MDPL respectively affected with mild and severe phenotypes. Both of them showed mandibular hypoplasia, a beaked nose with bird-like facies, prominent eyes, a small mouth, growth retardation, muscle and skin atrophy, but the female patient showed such a severe and early phenotype that a first working diagnosis of Hutchinson-Gilford Progeria was made. The exploration was performed by direct sequencing of POLD1 gene exon 15 in the male patient with a classical MDPL phenotype and by whole exome sequencing in the female patient and her unaffected parents. RESULTS Exome sequencing identified in the latter patient a de novo heterozygous undescribed mutation in the POLD1 gene (NM_002691.3: c.3209T>A), predicted to cause the missense change p.Ile1070Asn in the ZnF2 (Zinc Finger 2) domain of the protein. This mutation was not reported in the 1000 Genome Project, dbSNP and Exome sequencing databases. Furthermore, the Isoleucine1070 residue of POLD1 is highly conserved among various species, suggesting that this substitution may cause a major impairment of POLD1 activity. For the second patient, affected with a typical MDPL phenotype, direct sequencing of POLD1 exon 15 revealed the recurrent in-frame deletion (c.1812_1814del, p.S605del). CONCLUSION Our work highlights that mutations in different POLD1 domains can lead to phenotypic variability, ranging from dominantly inherited cancer predisposition syndromes, to mild MDPL phenotypes without lifespan reduction, to very severe MDPL syndromes with major premature aging features. These results also suggest that POLD1 gene testing should be considered in patients presenting with severe progeroid features.
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Affiliation(s)
- Sahar Elouej
- Aix Marseille Univ, INSERM, GMGF, Marseille, France
| | - Ana Beleza-Meireles
- Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Richard Caswell
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Kevin Colclough
- Department of Molecular Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Sian Ellard
- Department of Molecular Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | | | - Christophe Béroud
- Aix Marseille Univ, INSERM, GMGF, Marseille, France; Department of Medical Genetics, Molecular genetics Laboratory, La Timone Children's Hospital, 264 Rue Saint Pierre, 13005, Marseille, France
| | - Nicolas Lévy
- Aix Marseille Univ, INSERM, GMGF, Marseille, France; Department of Medical Genetics, Molecular genetics Laboratory, La Timone Children's Hospital, 264 Rue Saint Pierre, 13005, Marseille, France
| | - Shehla Mohammed
- Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Annachiara De Sandre-Giovannoli
- Aix Marseille Univ, INSERM, GMGF, Marseille, France; Department of Medical Genetics, Molecular genetics Laboratory, La Timone Children's Hospital, 264 Rue Saint Pierre, 13005, Marseille, France.
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322
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Reoxidation of the Thiol-Disulfide Oxidoreductase MdbA by a Bacterial Vitamin K Epoxide Reductase in the Biofilm-Forming Actinobacterium Actinomyces oris. J Bacteriol 2017; 199:JB.00817-16. [PMID: 28289087 DOI: 10.1128/jb.00817-16] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 02/23/2017] [Indexed: 12/18/2022] Open
Abstract
Posttranslocational protein folding in the Gram-positive biofilm-forming actinobacterium Actinomyces oris is mediated by a membrane-bound thiol-disulfide oxidoreductase named MdbA, which catalyzes oxidative folding of nascent polypeptides transported by the Sec translocon. Reoxidation of MdbA involves a bacterial vitamin K epoxide reductase (VKOR)-like protein that contains four cysteine residues, C93/C101 and C175/C178, with the latter forming a canonical CXXC thioredoxin-like motif; however, the mechanism of VKOR-mediated reoxidation of MdbA is not known. We present here a topological view of the A. oris membrane-spanning protein VKOR with these four exoplasmic cysteine residues that participate in MdbA reoxidation. Like deletion of the VKOR gene, alanine replacement of individual cysteine residues abrogated polymicrobial interactions and biofilm formation, concomitant with the failure to form adhesive pili on the bacterial surface. Intriguingly, the mutation of the cysteine at position 101 to alanine (C101A mutation) resulted in a high-molecular-weight complex that was positive for MdbA and VKOR by immunoblotting and was absent in other alanine substitution mutants and the C93A C101A double mutation and after treatment with the reducing agent β-mercaptoethanol. Consistent with this observation, affinity purification followed by immunoblotting confirmed this MdbA-VKOR complex in the C101A mutant. Furthermore, ectopic expression of the Mycobacterium tuberculosis VKOR analog in the A. oris VKOR deletion (ΔVKOR) mutant rescued its defects, in contrast to the expression of M. tuberculosis VKOR variants known to be nonfunctional in the disulfide relay that mediates reoxidation of the disulfide bond-forming catalyst DsbA in Escherichia coli Altogether, the results support a model of a disulfide relay, from its start with the pair C93/C101 to the C175-X-X-C178 motif, that is required for MdbA reoxidation and appears to be conserved in members of the class ActinobacteriaIMPORTANCE It has recently been shown in the high-GC Gram-positive bacteria (or Actinobacteria) Actinomyces oris and Corynebacterium diphtheriae that oxidative folding of nascent polypeptides transported by the Sec machinery is catalyzed by a membrane-anchored oxidoreductase named MdbA. In A. oris, reoxidation of MdbA requires a bacterial VKOR-like protein, and yet, how VKOR mediates MdbA reoxidation is unknown. We show here that the A. oris membrane-spanning protein VKOR employs two pairs of exoplasmic cysteine residues, including the canonical CXXC thioredoxinlike motif, to oxidize MdbA via a disulfide relay mechanism. This mechanism of disulfide relay is essential for pilus assembly, polymicrobial interactions, and biofilm formation and appears to be conserved in members of the class Actinobacteria, including Mycobacterium tuberculosis.
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Zhang QL, Zhang L, Zhao TX, Wang J, Zhu QH, Chen JY, Yuan ML. Gene sequence variations and expression patterns of mitochondrial genes are associated with the adaptive evolution of two Gynaephora species (Lepidoptera: Lymantriinae) living in different high-elevation environments. Gene 2017; 610:148-155. [DOI: 10.1016/j.gene.2017.02.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 01/05/2017] [Accepted: 02/06/2017] [Indexed: 01/06/2023]
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324
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Guevara G, Fernández de Las Heras L, Perera J, Navarro Llorens JM. Functional differentiation of 3-ketosteroid Δ 1-dehydrogenase isozymes in Rhodococcus ruber strain Chol-4. Microb Cell Fact 2017; 16:42. [PMID: 28288625 PMCID: PMC5348764 DOI: 10.1186/s12934-017-0657-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 03/07/2017] [Indexed: 12/17/2022] Open
Abstract
Background The Rhodococcus ruber strain Chol-4 genome contains at least three putative 3-ketosteroid Δ1-dehydrogenase ORFs (kstD1, kstD2 and kstD3) that code for flavoenzymes involved in the steroid ring degradation. The aim of this work is the functional characterization of these enzymes prior to the developing of different biotechnological applications. Results The three R. ruber KstD enzymes have different substrate profiles. KstD1 shows preference for 9OHAD and testosterone, followed by progesterone, deoxy corticosterone AD and, finally, 4-BNC, corticosterone and 19OHAD. KstD2 shows maximum preference for progesterone followed by 5α-Tes, DOC, AD testosterone, 4-BNC and lastly 19OHAD, corticosterone and 9OHAD. KstD3 preference is for saturated steroid substrates (5α-Tes) followed by progesterone and DOC. A preliminary attempt to model the catalytic pocket of the KstD proteins revealed some structural differences probably related to their catalytic differences. The expression of kstD genes has been studied by RT-PCR and RT-qPCR. All the kstD genes are transcribed under all the conditions assayed, although an additional induction in cholesterol and AD could be observed for kstD1 and in cholesterol for kstD3. Co-transcription of some correlative genes could be stated. The transcription initiation signals have been searched, both in silico and in vivo. Putative promoters in the intergenic regions upstream the kstD1, kstD2 and kstD3 genes were identified and probed in an apramycin-promoter-test vector, leading to the functional evidence of those R. ruber kstD promoters. Conclusions At least three putative 3-ketosteroid Δ1-dehydrogenase ORFs (kstD1, kstD2 and kstD3) have been identified and functionally confirmed in R. ruber strain Chol-4. KstD1 and KstD2 display a wide range of substrate preferences regarding to well-known intermediaries of the cholesterol degradation pathway (9OHAD and AD) and other steroid compounds. KstD3 shows a narrower substrate range with a preference for saturated substrates. KstDs differences in their catalytic properties was somehow related to structural differences revealed by a preliminary structural modelling. Transcription of R. ruber kstD genes is driven from specific promoters. The three genes are constitutively transcribed, although an additional induction is observed in kstD1 and kstD3. These enzymes have a wide versatility and allow a fine tuning-up of the KstD cellular activity. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0657-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Govinda Guevara
- Department of Biochemistry and Molecular Biology I, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Laura Fernández de Las Heras
- Faculty of Science and Engineering, Microbial Physiology-Gron Inst Biomolecular Sciences & Biotechnology, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Julián Perera
- Department of Biochemistry and Molecular Biology I, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Juana María Navarro Llorens
- Department of Biochemistry and Molecular Biology I, Universidad Complutense de Madrid, 28040, Madrid, Spain.
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325
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In silico analysis for predicting pathogenicity of five unclassified mitochondrial DNA mutations associated with mitochondrial cytopathies' phenotypes. Eur J Med Genet 2017; 60:172-177. [DOI: 10.1016/j.ejmg.2016.12.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 12/13/2016] [Accepted: 12/21/2016] [Indexed: 11/17/2022]
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326
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Bridges HR, Mohammed K, Harbour ME, Hirst J. Subunit NDUFV3 is present in two distinct isoforms in mammalian complex I. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2017; 1858:197-207. [PMID: 27940020 PMCID: PMC5293009 DOI: 10.1016/j.bbabio.2016.12.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 11/29/2016] [Accepted: 12/07/2016] [Indexed: 01/10/2023]
Abstract
Complex I (NADH:ubiquinone oxidoreductase) is the first enzyme of the electron transport chain in mammalian mitochondria. Extensive proteomic and structural analyses of complex I from Bos taurus heart mitochondria have shown it comprises 45 subunits encoded on both the nuclear and mitochondrial genomes; 44 of them are different and one is present in two copies. The bovine heart enzyme has provided a model for studying the composition of complex I in other mammalian species, including humans, but the possibility of additional subunits or isoforms in other species or tissues has not been explored. Here, we describe characterization of the complexes I purified from five rat tissues and from a rat hepatoma cell line. We identify a~50kDa isoform of subunit NDUFV3, for which the canonical isoform is only ~10kDa in size. We combine LC-MS and MALDI-TOF mass spectrometry data from two different purification methods (chromatography and immuno-purification) with information from blue native PAGE analyses to show the long isoform is present in the mature complex, but at substoichiometric levels. It is also present in complex I in cultured human cells. We describe evidence that the long isoform is more abundant in both the mitochondria and purified complexes from brain (relative to in heart, liver, kidney and skeletal muscle) and more abundant still in complex I in cultured cells. We propose that the long 50kDa isoform competes with its canonical 10kDa counterpart for a common binding site on the flavoprotein domain of complex I.
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Affiliation(s)
- Hannah R Bridges
- The Medical Research Council Mitochondrial Biology Unit, Wellcome Trust / MRC Building, Hills Road, Cambridge, CB2 0XY, U. K
| | - Khairunnisa Mohammed
- The Medical Research Council Mitochondrial Biology Unit, Wellcome Trust / MRC Building, Hills Road, Cambridge, CB2 0XY, U. K
| | - Michael E Harbour
- The Medical Research Council Mitochondrial Biology Unit, Wellcome Trust / MRC Building, Hills Road, Cambridge, CB2 0XY, U. K
| | - Judy Hirst
- The Medical Research Council Mitochondrial Biology Unit, Wellcome Trust / MRC Building, Hills Road, Cambridge, CB2 0XY, U. K..
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327
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Vazquez-Albacete D, Montefiori M, Kol S, Motawia MS, Møller BL, Olsen L, Nørholm MHH. The CYP79A1 catalyzed conversion of tyrosine to (E)-p-hydroxyphenylacetaldoxime unravelled using an improved method for homology modeling. PHYTOCHEMISTRY 2017; 135:8-17. [PMID: 28088302 DOI: 10.1016/j.phytochem.2016.11.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 11/01/2016] [Accepted: 11/27/2016] [Indexed: 06/06/2023]
Abstract
The vast diversity and membrane-bound nature of plant P450s makes it challenging to study the structural characteristics of this class of enzymes especially with respect to accurate intermolecular enzyme-substrate interactions. To address this problem we here apply a modified hybrid structure strategy for homology modeling of plant P450s. This allows for structural elucidation based on conserved motifs in the protein sequence and secondary structure predictions. We modeled the well-studied Sorghum bicolor cytochrome P450 CYP79A1 catalyzing the first step in the biosynthesis of the cyanogenic glucoside dhurrin. Docking experiments identified key regions of the active site involved in binding of the substrate and facilitating catalysis. Arginine 152 and threonine 534 were identified as key residues interacting with the substrate. The model was validated experimentally using site-directed mutagenesis. The new CYP79A1 model provides detailed insights into the mechanism of the initial steps in cyanogenic glycoside biosynthesis. The approach could guide functional characterization of other membrane-bound P450s and provide structural guidelines for elucidation of key structure-function relationships of other plant P450s.
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Affiliation(s)
- Dario Vazquez-Albacete
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark
| | - Marco Montefiori
- Faculty of Health and Medical Sciences, Department of Drug Design and Pharmacology, University of Copenhagen, Denmark
| | - Stefan Kol
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark
| | - Mohammed Saddik Motawia
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Copenhagen, Denmark; Center for Synthetic Biology bioSYNergy, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Copenhagen, Denmark
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Copenhagen, Denmark; Center for Synthetic Biology bioSYNergy, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Copenhagen, Denmark
| | - Lars Olsen
- Faculty of Health and Medical Sciences, Department of Drug Design and Pharmacology, University of Copenhagen, Denmark
| | - Morten H H Nørholm
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark; Center for Synthetic Biology bioSYNergy, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Copenhagen, Denmark.
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328
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Kuttiyatveetil JRA, Sanders DAR. Analysis of plant UDP-arabinopyranose mutase (UAM): Role of divalent metals and structure prediction. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:510-519. [PMID: 28192204 DOI: 10.1016/j.bbapap.2017.02.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Revised: 01/16/2017] [Accepted: 02/03/2017] [Indexed: 11/16/2022]
Abstract
UDP-arabinopyranose mutase (UAM) is a plant enzyme which interconverts UDP-arabinopyranose (UDP-Arap; a six-membered sugar) to UDP-arabinofuranose (UDP-Araf; a five-membered sugar). Plant mutases belong to a small gene family called Reversibly Glycosylated Proteins (RGPs). So far, UAM has been identified in Oryza sativa (Rice), Arabidopsis thaliana and Hordeum vulgare (Barley). The enzyme requires divalent metal ions for catalytic activity. Here, the divalent metal ion dependency of UAMs from O. sativa (rice) and A. thaliana have been studied using HPLC-based kinetic assays. It was determined that UAM from these species had the highest relative activity in a range of 40-80μM Mn2+. Excess Mn2+ ion concentration decreased the enzyme activity. This trend was observed when other divalent metal ions were used to test activity. To gain a perspective of the role played by the metal ion in activity, an ab initio structural model was generated based on the UAM amino acid sequence and a potential metal binding region was identified. Based on our results, we propose that the probable role of the metal in UAM is stabilizing the diphosphate of the substrate, UDP-Arap.
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Affiliation(s)
- Jijin R A Kuttiyatveetil
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, Saskatchewan, S7N 5C9, Canada
| | - David A R Sanders
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, Saskatchewan, S7N 5C9, Canada.
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329
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Zerbs S, Korajczyk PJ, Noirot PH, Collart FR. Transport capabilities of environmental Pseudomonads for sulfur compounds. Protein Sci 2017; 26:784-795. [PMID: 28127814 DOI: 10.1002/pro.3124] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 01/16/2017] [Accepted: 01/17/2017] [Indexed: 11/11/2022]
Abstract
Sulfur is an essential element in plant rhizospheres and microbial activity plays a key role in increasing the biological availability of sulfur in soil environments. To better understand the mechanisms facilitating the exchange of sulfur-containing molecules in soil, we profiled the binding specificities of eight previously uncharacterized ABC transporter solute-binding proteins from plant-associated Pseudomonads. A high-throughput screening procedure indicated eighteen significant organosulfur binding ligands, with at least one high-quality screening hit for each protein target. Calorimetric and spectroscopic methods were used to validate the best ligand assignments and catalog the thermodynamic properties of the protein-ligand interactions. Two novel high-affinity ligand-binding activities were identified and quantified in this set of solute-binding proteins. Bacteria were cultured in minimal media with screening library components supplied as the sole sulfur sources, demonstrating that these organosulfur compounds can be metabolized and confirming the relevance of ligand assignments. These results expand the set of experimentally validated ligands amenable to transport by this ABC transporter family and demonstrate the complex range of protein-ligand interactions that can be accomplished by solute-binding proteins. Characterizing new nutrient import pathways provides insight into Pseudomonad metabolic capabilities which can be used to further interrogate bacterial survival and participation in soil and rhizosphere communities.
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Affiliation(s)
- Sarah Zerbs
- Biosciences Division, Argonne National Laboratory, 9700 S Cass Ave, Lemont, Illinois, 60439
| | - Peter J Korajczyk
- Biosciences Division, Argonne National Laboratory, 9700 S Cass Ave, Lemont, Illinois, 60439
| | - Philippe H Noirot
- Biosciences Division, Argonne National Laboratory, 9700 S Cass Ave, Lemont, Illinois, 60439
| | - Frank R Collart
- Biosciences Division, Argonne National Laboratory, 9700 S Cass Ave, Lemont, Illinois, 60439
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330
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Banach M, Wiśniowski Z, Kalinowska B, Konieczny L, Roterman I. The variability of protein structure with respect to the hydrophobic core. BIO-ALGORITHMS AND MED-SYSTEMS 2017. [DOI: 10.1515/bams-2017-0004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractThe application of the fuzzy oil drop model to the analysis of protein structure is shown using two proteins. The selection of these two examples is due to their opposite character. Two proteins were selected representing very high order and very high disorder with respect to the organized uni-central hydrophobic core in proteins (one centrally localized concentration of high hydrophobicity). These two cases are to show examples of the large spectrum of variability of local organization of the hydrophobic core in proteins. The importance of the observation presented in this paper is significant with respect to large sets of proteins discussed in separate publications.
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331
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Mathot L, Kundu S, Ljungström V, Svedlund J, Moens L, Adlerteg T, Falk-Sörqvist E, Rendo V, Bellomo C, Mayrhofer M, Cortina C, Sundström M, Micke P, Botling J, Isaksson A, Moustakas A, Batlle E, Birgisson H, Glimelius B, Nilsson M, Sjöblom T. Somatic Ephrin Receptor Mutations Are Associated with Metastasis in Primary Colorectal Cancer. Cancer Res 2017; 77:1730-1740. [PMID: 28108514 DOI: 10.1158/0008-5472.can-16-1921] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 12/12/2016] [Accepted: 12/29/2016] [Indexed: 11/16/2022]
Abstract
The contribution of somatic mutations to metastasis of colorectal cancers is currently unknown. To find mutations involved in the colorectal cancer metastatic process, we performed deep mutational analysis of 676 genes in 107 stages II to IV primary colorectal cancer, of which half had metastasized. The mutation prevalence in the ephrin (EPH) family of tyrosine kinase receptors was 10-fold higher in primary tumors of metastatic colorectal than in nonmetastatic cases and preferentially occurred in stage III and IV tumors. Mutational analyses in situ confirmed expression of mutant EPH receptors. To enable functional studies of EPHB1 mutations, we demonstrated that DLD-1 colorectal cancer cells expressing EPHB1 form aggregates upon coculture with ephrin B1 expressing cells. When mutations in the fibronectin type III and kinase domains of EPHB1 were compared with wild-type EPHB1 in DLD-1 colorectal cancer cells, they decreased ephrin B1-induced compartmentalization. These observations provide a mechanistic link between EPHB receptor mutations and metastasis in colorectal cancer. Cancer Res; 77(7); 1730-40. ©2017 AACR.
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Affiliation(s)
- Lucy Mathot
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Sweden
| | - Snehangshu Kundu
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Sweden
| | - Viktor Ljungström
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Sweden
| | - Jessica Svedlund
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Lotte Moens
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Sweden
| | - Tom Adlerteg
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Sweden
| | - Elin Falk-Sörqvist
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Sweden
| | - Verónica Rendo
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Sweden
| | - Claudia Bellomo
- Department of Medical Biochemistry and Microbiology, Ludwig Cancer Research, Science for Life Laboratory, Uppsala University, Sweden
| | - Markus Mayrhofer
- Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Sweden
| | - Carme Cortina
- Oncology Programme, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Magnus Sundström
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Sweden
| | - Patrick Micke
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Sweden
| | - Johan Botling
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Sweden
| | - Anders Isaksson
- Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Sweden
| | - Aristidis Moustakas
- Department of Medical Biochemistry and Microbiology, Ludwig Cancer Research, Science for Life Laboratory, Uppsala University, Sweden
| | - Eduard Batlle
- Oncology Programme, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Helgi Birgisson
- Department of Surgical Sciences, Colorectal Surgery, Uppsala University, Sweden
| | - Bengt Glimelius
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Sweden
| | - Mats Nilsson
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Sweden.,Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Tobias Sjöblom
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Sweden.
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332
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Galea CA, Roberts KD, Zhu Y, Thompson PE, Li J, Velkov T. Functional Characterization of the Unique Terminal Thioesterase Domain from Polymyxin Synthetase. Biochemistry 2017; 56:657-668. [PMID: 28071053 DOI: 10.1021/acs.biochem.6b01139] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Polymyxins remain one of the few antibiotics available for treating antibiotic resistant bacteria. Here we describe polymyxin B thioesterase which performs the final step in polymyxin B biosynthesis. Isolated thioesterase catalyzed cyclization of an N-acetylcystamine polymyxin B analogue to form polymyxin B. The thioesterase contained a catalytic cysteine unlike most thioesterases which possess a serine. Supporting this, incubation of polymyxin B thioesterase with reducing agents abolished enzymatic activity, while mutation of the catalytic cysteine to serine significantly decreased activity. NMR spectroscopy demonstrated that uncyclized polymyxin B was disordered in solution, unlike other thioesterase substrates which adopt a transient structure similar to their product. Modeling showed the thioesterase substrate-binding cleft was highly negatively charged, suggesting a mechanism for the cyclization of the substrate. These studies provide new insights into the role of polymyxin thioesterase in polymyxin biosynthesis and highlight its potential use for the chemoenzymatic synthesis of polymyxin lipopeptides.
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Affiliation(s)
| | | | - Yan Zhu
- Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University , Parkville, Victoria 3800, Australia
| | | | - Jian Li
- Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University , Parkville, Victoria 3800, Australia
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333
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Ren H, Zhang Y, Su J, Lin P, Wang B, Fang B, Wang S. Encapsulation of amine dehydrogenase in hybrid titania nanoparticles by polyethylenimine coating and templated biomineralization. J Biotechnol 2017; 241:33-41. [DOI: 10.1016/j.jbiotec.2016.11.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 11/04/2016] [Accepted: 11/07/2016] [Indexed: 10/20/2022]
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334
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Wang S, Qu M, Peng J. PROSNET: INTEGRATING HOMOLOGY WITH MOLECULAR NETWORKS FOR PROTEIN FUNCTION PREDICTION. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2017; 22:27-38. [PMID: 27896959 PMCID: PMC5319591 DOI: 10.1142/9789813207813_0004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Automated annotation of protein function has become a critical task in the post-genomic era. Network-based approaches and homology-based approaches have been widely used and recently tested in large-scale community-wide assessment experiments. It is natural to integrate network data with homology information to further improve the predictive performance. However, integrating these two heterogeneous, high-dimensional and noisy datasets is non-trivial. In this work, we introduce a novel protein function prediction algorithm ProSNet. An integrated heterogeneous network is first built to include molecular networks of multiple species and link together homologous proteins across multiple species. Based on this integrated network, a dimensionality reduction algorithm is introduced to obtain compact low-dimensional vectors to encode proteins in the network. Finally, we develop machine learning classification algorithms that take the vectors as input and make predictions by transferring annotations both within each species and across different species. Extensive experiments on five major species demonstrate that our integration of homology with molecular networks substantially improves the predictive performance over existing approaches.
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Affiliation(s)
- Sheng Wang
- Department of Computer Science, University of Illinois at Urbana-Champaign, Champaign, IL, USA
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335
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Michalko J, Renner T, Mészáros P, Socha P, Moravčíková J, Blehová A, Libantová J, Polóniová Z, Matušíková I. Molecular characterization and evolution of carnivorous sundew (Drosera rotundifolia L.) class V β-1,3-glucanase. PLANTA 2017; 245:77-91. [PMID: 27580619 DOI: 10.1007/s00425-016-2592-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 08/25/2016] [Indexed: 06/06/2023]
Abstract
MAIN CONCLUSION A gene for β-1,3-glucanase was isolated from carnivorous sundew. It is active in leaves and roots, but not in digestive glands. Analyses in transgenic tobacco suggest its function in germination. Ancestral plant β-1,3-glucanases (EC 3.2.1.39) played a role in cell division and cell wall remodelling, but divergent evolution has extended their roles in plant defense against stresses to decomposition of prey in carnivorous plants. As available gene sequences from carnivorous plants are rare, we isolated a glucanase gene from roundleaf sundew (Drosera rotundifolia L.) by a genome walking approach. Computational predictions recognized typical gene features and protein motifs described for other plant β-1,3-glucanases. Phylogenetic reconstructions suggest strong support for evolutionary relatedness to class V β-1,3-glucanases, including homologs that are active in the traps of related carnivorous species. The gene is expressed in sundew vegetative tissues but not in flowers and digestive glands, and encodes for a functional enzyme when expressed in transgenic tobacco. Detailed analyses of the supposed promoter both in silico and in transgenic tobacco suggest that this glucanase plays a role in development. Specific spatiotemporal activity was observed during transgenic seed germination. Later during growth, the sundew promoter was active in marginal and sub-marginal areas of apical true leaf meristems of young tobacco plants. These results suggest that the isolated glucanase gene is regulated endogenously, possibly by auxin. This is the first report on a nuclear gene study from sundew.
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Affiliation(s)
- Jaroslav Michalko
- Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences, Akademická 2, P.O. Box 39A, 950 07, Nitra, Slovak Republic
| | - Tanya Renner
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182-4614, USA
| | - Patrik Mészáros
- Department of Botany and Genetics, Faculty of Natural Sciences, Constantine the Philosopher University, Nábrežie mládeže 91, 949 74, Nitra, Slovak Republic
| | - Peter Socha
- Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences, Akademická 2, P.O. Box 39A, 950 07, Nitra, Slovak Republic
| | - Jana Moravčíková
- Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences, Akademická 2, P.O. Box 39A, 950 07, Nitra, Slovak Republic
| | - Alžbeta Blehová
- Department of Plant Physiology, Faculty of Natural Sciences, Comenius University, Mlynská dolina B2, 842 15, Bratislava, Slovak Republic
| | - Jana Libantová
- Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences, Akademická 2, P.O. Box 39A, 950 07, Nitra, Slovak Republic
| | - Zuzana Polóniová
- Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences, Akademická 2, P.O. Box 39A, 950 07, Nitra, Slovak Republic
| | - Ildikó Matušíková
- Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences, Akademická 2, P.O. Box 39A, 950 07, Nitra, Slovak Republic.
- Department of Ecochemistry and Radioecology, University of SS. Cyril and Methodius, J. Herdu 2, 917 01, Trnava, Slovak Republic.
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336
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Sheff JG, Hepburn M, Yu Y, Lees-Miller SP, Schriemer DC. Nanospray HX-MS configuration for structural interrogation of large protein systems. Analyst 2017; 142:904-910. [DOI: 10.1039/c6an02707e] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An in-source column chiller supports nanoHX-MS workflows for analyzing proteins from cellular extracts.
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Affiliation(s)
- Joey G. Sheff
- Department of Chemistry
- University of Calgary
- Calgary
- Canada
| | - Morgan Hepburn
- Department of Biochemistry and Molecular Biology
- University of Calgary
- Calgary
- Canada
| | - Yaping Yu
- Department of Biochemistry and Molecular Biology
- University of Calgary
- Calgary
- Canada
| | - Susan P. Lees-Miller
- Department of Biochemistry and Molecular Biology
- University of Calgary
- Calgary
- Canada
| | - David C. Schriemer
- Department of Chemistry
- University of Calgary
- Calgary
- Canada
- Department of Biochemistry and Molecular Biology
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337
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Gupta A, Mohanty P, Bhatnagar S. Protein Structure Prediction Using Homology Modeling. PHARMACEUTICAL SCIENCES 2017. [DOI: 10.4018/978-1-5225-1762-7.ch034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Sequence-structure deficit marks one of the critical problems in today's scenario where high-throughput sequencing has resulted in large datasets of protein sequences but their corresponding 3D structures still needs to be determined. Homology modeling, also termed as Comparative modeling refers to modeling of 3D structure of a protein by exploiting structural information from other known protein structures with good sequence similarity. Homology models contain sufficient information about the spatial arrangement of important residues in the protein and are often used in drug design for screening of large libraries by molecular docking techniques. This chapter provides a brief description about protein tertiary structure prediction and Homology modeling. The authors provide a description of the steps involved in homology modeling protocols and provide information on the various resources available for the same.
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338
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Akiba T, Okumura S. Parasporins 1 and 2: Their structure and activity. J Invertebr Pathol 2017; 142:44-49. [DOI: 10.1016/j.jip.2016.10.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 09/14/2016] [Accepted: 10/17/2016] [Indexed: 11/25/2022]
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339
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Structured States of Disordered Proteins from Genomic Sequences. Cell 2016; 167:158-170.e12. [PMID: 27662088 DOI: 10.1016/j.cell.2016.09.010] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 07/08/2016] [Accepted: 09/06/2016] [Indexed: 12/22/2022]
Abstract
Protein flexibility ranges from simple hinge movements to functional disorder. Around half of all human proteins contain apparently disordered regions with little 3D or functional information, and many of these proteins are associated with disease. Building on the evolutionary couplings approach previously successful in predicting 3D states of ordered proteins and RNA, we developed a method to predict the potential for ordered states for all apparently disordered proteins with sufficiently rich evolutionary information. The approach is highly accurate (79%) for residue interactions as tested in more than 60 known disordered regions captured in a bound or specific condition. Assessing the potential for structure of more than 1,000 apparently disordered regions of human proteins reveals a continuum of structural order with at least 50% with clear propensity for three- or two-dimensional states. Co-evolutionary constraints reveal hitherto unseen structures of functional importance in apparently disordered proteins.
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340
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Bresso E, Togawa R, Hammond-Kosack K, Urban M, Maigret B, Martins NF. GPCRs from fusarium graminearum detection, modeling and virtual screening - the search for new routes to control head blight disease. BMC Bioinformatics 2016; 17:463. [PMID: 28105916 PMCID: PMC5249037 DOI: 10.1186/s12859-016-1342-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGOUND Fusarium graminearum (FG) is one of the major cereal infecting pathogens causing high economic losses worldwide and resulting in adverse effects on human and animal health. Therefore, the development of new fungicides against FG is an important issue to reduce cereal infection and economic impact. In the strategy for developing new fungicides, a critical step is the identification of new targets against which innovative chemicals weapons can be designed. As several G-protein coupled receptors (GPCRs) are implicated in signaling pathways critical for the fungi development and survival, such proteins could be valuable efficient targets to reduce Fusarium growth and therefore to prevent food contamination. RESULTS In this study, GPCRs were predicted in the FG proteome using a manually curated pipeline dedicated to the identification of GPCRs. Based on several successive filters, the most appropriate GPCR candidate target for developing new fungicides was selected. Searching for new compounds blocking this particular target requires the knowledge of its 3D-structure. As no experimental X-Ray structure of the selected protein was available, a 3D model was built by homology modeling. The model quality and stability was checked by 100 ns of molecular dynamics simulations. Two stable conformations representative of the conformational families of the protein were extracted from the 100 ns simulation and were used for an ensemble docking campaign. The model quality and stability was checked by 100 ns of molecular dynamics simulations previously to the virtual screening step. The virtual screening step comprised the exploration of a chemical library with 11,000 compounds that were docked to the GPCR model. Among these compounds, we selected the ten top-ranked nontoxic molecules proposed to be experimentally tested to validate the in silico simulation. CONCLUSIONS This study provides an integrated process merging genomics, structural bioinformatics and drug design for proposing innovative solutions to a world wide threat to grain producers and consumers.
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Affiliation(s)
- Emmanuel Bresso
- EMBRAPA Genetic Resources and Biotechnology, Brasília, DF 70770-917 Brazil
| | - Roberto Togawa
- EMBRAPA Genetic Resources and Biotechnology, Brasília, DF 70770-917 Brazil
| | - Kim Hammond-Kosack
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ UK
| | - Martin Urban
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ UK
| | - Bernard Maigret
- EMBRAPA Genetic Resources and Biotechnology, Brasília, DF 70770-917 Brazil
- CAPSID Team, LORIA, UMR 7503, CNRS, Lorraine University, Vandœuvre-lès-Nancy, 54506 France
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341
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Martínez-Montes AM, Muiños-Bühl A, Fernández A, Folch JM, Ibáñez-Escriche N, Fernández AI. Deciphering the regulation of porcine genes influencing growth, fatness and yield-related traits through genetical genomics. Mamm Genome 2016; 28:130-142. [PMID: 27942838 DOI: 10.1007/s00335-016-9674-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 11/25/2016] [Indexed: 10/20/2022]
Abstract
Genetical genomics approaches aim at identifying quantitative trait loci for molecular traits, also known as intermediate phenotypes, such as gene expression, that could link variation in genetic information to physiological traits. In the current study, an expression GWAS has been carried out on an experimental Iberian × Landrace backcross in order to identify the genomic regions regulating the gene expression of those genes whose expression is correlated with growth, fat deposition, and premium cut yield measures in pig. The analyses were conducted exploiting Porcine 60K SNP BeadChip genotypes and Porcine Expression Microarray data hybridized on mRNA from Longissimus dorsi muscle. In order to focus the analysis on productive traits and reduce the number of analyses, only those probesets whose expression showed significant correlation with at least one of the seven phenotypes of interest were selected for the eGWAS. A total of 63 eQTL regions were identified with effects on 36 different transcripts. Those eQTLs overlapping with phenotypic QTLs on SSC4, SSC9, SSC13, and SSC17 chromosomes previously detected in the same animal material were further analyzed. Moreover, candidate genes and SNPs were analyzed. Among the most promising results, a long non-coding RNA, ALDBSSCG0000001928, was identified, whose expression is correlated with premium cut yield. Association analysis and in silico sequence domain annotation support TXNRD3 polymorphisms as candidate to regulate ALDBSSCG0000001928 expression, which can be involved in the transcriptional regulation of surrounding genes, affecting productive and meat quality traits.
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Affiliation(s)
- Angel M Martínez-Montes
- Departamento de Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040, Madrid, Spain.
| | - Anixa Muiños-Bühl
- Departamento de Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040, Madrid, Spain
| | - Almudena Fernández
- Departamento de Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040, Madrid, Spain
| | - Josep M Folch
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain.,Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (CRAG), Consorci CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Spain
| | - Noelia Ibáñez-Escriche
- Departament de Genètica i Millora Animal, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), 25198, Lleida, Spain
| | - Ana I Fernández
- Departamento de Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040, Madrid, Spain
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342
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Piano V, Nenci S, Magnani F, Aliverti A, Mattevi A. Recombinant human dihydroxyacetonephosphate acyl-transferase characterization as an integral monotopic membrane protein. Biochem Biophys Res Commun 2016; 481:51-58. [PMID: 27836547 PMCID: PMC5146282 DOI: 10.1016/j.bbrc.2016.11.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 11/05/2016] [Indexed: 11/26/2022]
Abstract
Although the precise functions of ether phospholipids are still poorly understood, significant alterations in their physiological levels are associated either to inherited disorders or to aggressive metastatic cancer. The essential precursor, alkyl-dihydroxyacetone phosphate (DHAP), for all ether phospholipids species is synthetized in two consecutive reactions performed by two enzymes sitting on the inner side of the peroxisomal membrane. Here, we report the characterization of the recombinant human DHAP acyl-transferase, which performs the first step in alkyl-DHAP synthesis. By exploring several expression systems and designing a number of constructs, we were able to purify the enzyme in its active form and we found that it is tightly bound to the membrane through the N-terminal residues. Human DHAPAT is associated to peroxisomal membrane through the N-terminal region. Recombinant human DHAPAT expressed and purified from P. pastoris cells is active. Evidence of the in vitro reconstitution of DHAPAT/ADPS enzymatic complex.
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Affiliation(s)
- Valentina Piano
- Department of Biology and Biotechnology, University of Pavia, V. Ferrata 9, 27100, Pavia, Italy
| | - Simone Nenci
- Department of Biology and Biotechnology, University of Pavia, V. Ferrata 9, 27100, Pavia, Italy
| | - Francesca Magnani
- Department of Biology and Biotechnology, University of Pavia, V. Ferrata 9, 27100, Pavia, Italy
| | - Alessandro Aliverti
- Department of Biosciences, University of Milan, V. Celoria 26, 20133, Milan, Italy
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of Pavia, V. Ferrata 9, 27100, Pavia, Italy.
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343
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Two crystal structures reveal design for repurposing the C-Ala domain of human AlaRS. Proc Natl Acad Sci U S A 2016; 113:14300-14305. [PMID: 27911835 DOI: 10.1073/pnas.1617316113] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The 20 aminoacyl tRNA synthetases (aaRSs) couple each amino acid to their cognate tRNAs. During evolution, 19 aaRSs expanded by acquiring novel noncatalytic appended domains, which are absent from bacteria and many lower eukaryotes but confer extracellular and nuclear functions in higher organisms. AlaRS is the single exception, with an appended C-terminal domain (C-Ala) that is conserved from prokaryotes to humans but with a wide sequence divergence. In human cells, C-Ala is also a splice variant of AlaRS. Crystal structures of two forms of human C-Ala, and small-angle X-ray scattering of AlaRS, showed that the large sequence divergence of human C-Ala reshaped C-Ala in a way that changed the global architecture of AlaRS. This reshaping removes the role of C-Ala in prokaryotes for docking tRNA and instead repurposes it to form a dimer interface presenting a DNA-binding groove. This groove cannot form with the bacterial ortholog. Direct DNA binding by human C-Ala, but not by bacterial C-Ala, was demonstrated. Thus, instead of acquiring a novel appended domain like other human aaRSs, which engendered novel functions, a new AlaRS architecture was created by diversifying a preexisting appended domain.
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344
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Meng F, Kurgan L. Computational Prediction of Protein Secondary Structure from Sequence. ACTA ACUST UNITED AC 2016; 86:2.3.1-2.3.10. [DOI: 10.1002/cpps.19] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Fanchi Meng
- Department of Electrical and Computer Engineering, University of Alberta Edmonton Canada
| | - Lukasz Kurgan
- Department of Computer Science, Virginia Commonwealth University Richmond Virginia
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345
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Richter AS, Hochheuser C, Fufezan C, Heinze L, Kuhnert F, Grimm B. Phosphorylation of GENOMES UNCOUPLED 4 Alters Stimulation of Mg Chelatase Activity in Angiosperms. PLANT PHYSIOLOGY 2016; 172:1578-1595. [PMID: 27688621 PMCID: PMC5100749 DOI: 10.1104/pp.16.01036] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 09/27/2016] [Indexed: 05/07/2023]
Abstract
GENOMES UNCOUPLED 4 (GUN4) is a positive regulator of light-dependent chlorophyll biosynthesis. GUN4 activates Mg chelatase (MgCh) that catalyzes the insertion of an Mg2+ ion into protoporphyrin IX. We show that Arabidopsis (Arabidopsis thaliana) GUN4 is phosphorylated at Ser 264 (S264), the penultimate amino acid residue at the C terminus. While GUN4 is preferentially phosphorylated in darkness, phosphorylation is reduced upon accumulation of Mg porphyrins. Expression of a phosphomimicking GUN4(S264D) results in an incomplete complementation of the white gun4-2 null mutant and a chlorotic phenotype comparable to gun4 knockdown mutants. Phosphorylated GUN4 has a reduced stimulatory effect on MgCh in vitro and in vivo but retains its protein stability and tetrapyrrole binding capacity. Analysis of GUN4 found in oxygenic photosynthetic organisms reveals the evolution of a C-terminal extension, which harbors the phosphorylation site of GUN4 expressed in angiosperms. Homologs of GUN4 from Synechocystis and Chlamydomonas lack the conserved phosphorylation site found in a C-terminal extension of angiosperm GUN4. Biochemical studies proved the importance of the C-terminal extension for MgCh stimulation and inactivation of GUN4 by phosphorylation in angiosperms. An additional mechanism regulating MgCh activity is proposed. In conjunction with the dark repression of 5-aminolevulinic acid synthesis, GUN4 phosphorylation minimizes the flow of intermediates into the Mg branch of the tetrapyrrole metabolic pathway for chlorophyll biosynthesis.
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Affiliation(s)
- Andreas Sven Richter
- Plant Physiology, Institute of Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany (A.S.R., C.H., L.H., F.K., B.G.); and
- Computational Biology, Institute for Biology and Biotechnology of Plants, University of Münster, 48143 Münster, Germany (C.F.)
| | - Caroline Hochheuser
- Plant Physiology, Institute of Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany (A.S.R., C.H., L.H., F.K., B.G.); and
- Computational Biology, Institute for Biology and Biotechnology of Plants, University of Münster, 48143 Münster, Germany (C.F.)
| | - Christian Fufezan
- Plant Physiology, Institute of Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany (A.S.R., C.H., L.H., F.K., B.G.); and
- Computational Biology, Institute for Biology and Biotechnology of Plants, University of Münster, 48143 Münster, Germany (C.F.)
| | - Laura Heinze
- Plant Physiology, Institute of Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany (A.S.R., C.H., L.H., F.K., B.G.); and
- Computational Biology, Institute for Biology and Biotechnology of Plants, University of Münster, 48143 Münster, Germany (C.F.)
| | - Franziska Kuhnert
- Plant Physiology, Institute of Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany (A.S.R., C.H., L.H., F.K., B.G.); and
- Computational Biology, Institute for Biology and Biotechnology of Plants, University of Münster, 48143 Münster, Germany (C.F.)
| | - Bernhard Grimm
- Plant Physiology, Institute of Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany (A.S.R., C.H., L.H., F.K., B.G.); and
- Computational Biology, Institute for Biology and Biotechnology of Plants, University of Münster, 48143 Münster, Germany (C.F.)
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346
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Baculovirus FP25K Localization: Role of the Coiled-Coil Domain. J Virol 2016; 90:9582-9597. [PMID: 27512078 DOI: 10.1128/jvi.01241-16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 08/03/2016] [Indexed: 11/20/2022] Open
Abstract
Two types of viruses are produced during the baculovirus life cycle: budded virus (BV) and occlusion-derived virus (ODV). A particular baculovirus protein, FP25K, is involved in the switch from BV to ODV production. Previously, FP25K from the model alphabaculovirus Autographa californica multiple nucleopolyhedrovirus (AcMNPV) was shown to traffic ODV envelope proteins. However, FP25K localization and the domains involved are inconclusive. Here we used a quantitative approach to study FP25K subcellular localization during infection using an AcMNPV bacmid virus that produces a functional AcMNPV FP25K-green fluorescent protein (GFP) fusion protein. During cell infection, FP25K-GFP localized primarily to the cytoplasm, particularly amorphous structures, with a small fraction being localized in the nucleus. To investigate the sequences involved in FP25K localization, an alignment of baculovirus FP25K sequences revealed that the N-terminal putative coiled-coil domain is present in all alphabaculoviruses but absent in betabaculoviruses. Structural prediction indicated a strong relatedness of AcMNPV FP25K to long interspersed element 1 (LINE-1) open reading frame 1 protein (ORF1p), which contains an N-terminal coiled-coil domain responsible for cytoplasmic retention. Point mutations and deletions of this domain lead to a change in AcMNPV FP25K localization from cytoplasmic to nuclear. The coiled-coil and C-terminal deletion viruses increased BV production. Furthermore, a betabaculovirus FP25K protein lacking this N-terminal coiled-coil domain localized predominantly to the nucleus and exhibited increased BV production. These data suggest that the acquisition of this N-terminal coiled-coil domain in FP25K is important for the evolution of alphabaculoviruses. Moreover, with the divergence of preocclusion nuclear membrane breakdown in betabaculoviruses and membrane integrity in alphabaculoviruses, this domain represents an alphabaculovirus adaptation for nuclear trafficking of occlusion-associated proteins. IMPORTANCE Baculovirus infection produces two forms of viruses: BV and ODV. Manufacturing of ODV involves trafficking of envelope proteins to the inner nuclear membrane, mediated partly through the FP25K protein. Since FP25K is present in alpha-, beta-, and gammabaculoviruses, it is uncertain if this trafficking function is conserved. In this study, we looked at alpha- and betabaculovirus FP25K trafficking by its localization. Alphabaculovirus FP25K localized primarily to the cytoplasm, whereas betabaculovirus FP25K localized to the nucleus. We found that an N-terminal coiled-coil domain present in all alphabaculovirus FP25K proteins, but absent in betabaculovirus FP25K, was critical for alphabaculovirus FP25K cytoplasmic localization. We believe that this represents an evolutionary process that partly led to the gain of function of this N-terminal coiled-coil domain in alphabaculovirus FP25K to aid in nuclear trafficking of occlusion-associated proteins. Due to betabaculovirus breakdown of the nuclear membrane before occlusion, this function is not needed, and the domain was lost or never acquired.
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347
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Dimitrova YN, Jenni S, Valverde R, Khin Y, Harrison SC. Structure of the MIND Complex Defines a Regulatory Focus for Yeast Kinetochore Assembly. Cell 2016; 167:1014-1027.e12. [PMID: 27881300 PMCID: PMC5856483 DOI: 10.1016/j.cell.2016.10.011] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 09/02/2016] [Accepted: 10/03/2016] [Indexed: 11/25/2022]
Abstract
Kinetochores connect centromeric nucleosomes with mitotic-spindle microtubules through conserved, cross-interacting protein subassemblies. In budding yeast, the heterotetrameric MIND complex (Mtw1, Nnf1, Nsl1, Dsn1), ortholog of the metazoan Mis12 complex, joins the centromere-proximal components, Mif2 and COMA, with the principal microtubule-binding component, the Ndc80 complex (Ndc80C). We report the crystal structure of Kluyveromyces lactis MIND and examine its partner interactions, to understand the connection from a centromeric nucleosome to a much larger microtubule. MIND resembles an elongated, asymmetric Y; two globular heads project from a coiled-coil shaft. An N-terminal extension of Dsn1 from one head regulates interactions of the other head, blocking binding of Mif2 and COMA. Dsn1 phosphorylation by Ipl1/Aurora B relieves this autoinhibition, enabling MIND to join an assembling kinetochore. A C-terminal extension of Dsn1 recruits Ndc80C to the opposite end of the shaft. The structure and properties of MIND show how it integrates phospho-regulatory inputs for kinetochore assembly and disassembly.
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Affiliation(s)
- Yoana N Dimitrova
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
| | - Simon Jenni
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
| | - Roberto Valverde
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
| | - Yadana Khin
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
| | - Stephen C Harrison
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA; Howard Hughes Medical Institute, 250 Longwood Avenue, Boston, MA 02115, USA.
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348
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The Cytoplasmic C-Tail of the Mouse Cytomegalovirus 7 Transmembrane Receptor Homologue, M78, Regulates Endocytosis of the Receptor and Modulates Virus Replication in Different Cell Types. PLoS One 2016; 11:e0165066. [PMID: 27760189 PMCID: PMC5070858 DOI: 10.1371/journal.pone.0165066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 10/05/2016] [Indexed: 12/03/2022] Open
Abstract
Virus homologues of seven-transmembrane receptors (7TMR) are encoded by all beta- and gammaherpesviruses, suggesting important functional roles. M78 of mouse cytomegalovirus (MCMV) is representative of a family of 7TMR conserved in all betaherpesviruses. M78 family members have been found to exhibit cell-type specific effects upon virus replication in tissue culture and to affect virus pathogenesis in vivo. We reported previously that M78, for which no ligands are known, undergoes rapid, constitutive endocytosis. In this study, we have investigated the role of the M78 cytoplasmic C-tail in mediating endocytosis and consequences of C-tail deletion upon replication and pathogenesis. Mutations of M78 (C-tail truncations or point mutations) and CCR5-M78 chimeras identified two distinct regions affecting endocytosis. The first was a classical acidic di-leucine motif (DDxxxLL), located close to the C-terminus. The second region, the activity of which was suppressed by downstream sequences, included the putative 8th helix, located close to the 7th transmembrane domain. A recombinant MCMV expressing an endocytosis-deficient M78, lacking most of the C-tail (M78_CΔ155), had a cell-type specific replication phenotype. M78_CΔ155 had restricted replication in bone marrow macrophages, indistinguishable from an M78-null recombinant. In contrast, M78_CΔ155 replicated normally or with enhanced titres to wild type virus in other tested cell-types, whereas M78-null was attenuated. Distinct phenotypes for M78_CΔ155 and M78-null suggest that the C-tail deletion resulted in M78 dysfunction, rather than complete loss of function; furthermore, they highlight a cell-type specific role of M78 during replication. Infection of mice (intranasal) demonstrated that M78_CΔ155, similar to M78-null, was cleared more rapidly from the lungs than wild type virus and was severely attenuated for replication in salivary glands. It may be speculated that attenuation of both M78_CΔ155 and M78-null for replication in macrophages may have contributed to their similar pathogenic phenotypes.
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349
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Kienle N, Kloepper TH, Fasshauer D. Shedding light on the expansion and diversification of the Cdc48 protein family during the rise of the eukaryotic cell. BMC Evol Biol 2016; 16:215. [PMID: 27756227 PMCID: PMC5070193 DOI: 10.1186/s12862-016-0790-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 10/04/2016] [Indexed: 11/22/2022] Open
Abstract
Background A defining feature of eukaryotic cells is the presence of various distinct membrane-bound compartments with different metabolic roles. Material exchange between most compartments occurs via a sophisticated vesicle trafficking system. This intricate cellular architecture of eukaryotes appears to have emerged suddenly, about 2 billion years ago, from much less complex ancestors. How the eukaryotic cell acquired its internal complexity is poorly understood, partly because no prokaryotic precursors have been found for many key factors involved in compartmentalization. One exception is the Cdc48 protein family, which consists of several distinct classical ATPases associated with various cellular activities (AAA+) proteins with two consecutive AAA domains. Results Here, we have classified the Cdc48 family through iterative use of hidden Markov models and tree building. We found only one type, Cdc48, in prokaryotes, although a set of eight diverged members that function at distinct subcellular compartments were retrieved from eukaryotes and were probably present in the last eukaryotic common ancestor (LECA). Pronounced changes in sequence and domain structure during the radiation into the LECA set are delineated. Moreover, our analysis brings to light lineage-specific losses and duplications that often reflect important biological changes. Remarkably, we also found evidence for internal duplications within the LECA set that probably occurred during the rise of the eukaryotic cell. Conclusions Our analysis corroborates the idea that the diversification of the Cdc48 family is closely intertwined with the development of the compartments of the eukaryotic cell. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0790-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nickias Kienle
- Département des neurosciences fondamentales, Université de Lausanne, Rue du Bugnon 9, CH-1005, Lausanne, Switzerland
| | - Tobias H Kloepper
- Sir William Dunn School of Pathology, Research Group Cell Biology of Intercellular Signaling, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Dirk Fasshauer
- Département des neurosciences fondamentales, Université de Lausanne, Rue du Bugnon 9, CH-1005, Lausanne, Switzerland.
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Moen MN, Fjær R, Hamdani EH, Laerdahl JK, Menchini RJ, Vigeland MD, Sheng Y, Undlien DE, Hassel B, Salih MA, El Khashab HY, Selmer KK, Chaudhry FA. Pathogenic variants in KCTD7 perturb neuronal K+ fluxes and glutamine transport. Brain 2016; 139:3109-3120. [PMID: 27742667 DOI: 10.1093/brain/aww244] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 06/11/2016] [Accepted: 08/17/2016] [Indexed: 12/11/2022] Open
Abstract
Progressive myoclonus epilepsy is a heterogeneous group of disorders characterized by myoclonic and tonic-clonic seizures, ataxia and cognitive decline. We here present two affected brothers. At 9 months of age the elder brother developed ataxia and myoclonic jerks. In his second year he lost the ability to walk and talk, and he developed drug-resistant progressive myoclonus epilepsy. The cerebrospinal fluid level of glutamate was decreased while glutamine was increased. His younger brother manifested similar symptoms from 6 months of age. By exome sequencing of the proband we identified a novel homozygous frameshift variant in the potassium channel tetramerization domain 7 (KCTD7) gene (NM_153033.1:c.696delT: p.F232fs), which results in a truncated protein. The identified F232fs variant is inherited in an autosomal recessive manner, and the healthy consanguineous parents carry the variant in a heterozygous state. Bioinformatic analyses and structure modelling showed that KCTD7 is a highly conserved protein, structurally similar to KCTD5 and several voltage-gated potassium channels, and that it may form homo- or heteromultimers. By heterologous expression in Xenopus laevis oocytes, we demonstrate that wild-type KCTD7 hyperpolarizes cells in a K+ dependent manner and regulates activity of the neuronal glutamine transporter SAT2 (Slc38a2), while the F232fs variant impairs K+ fluxes and obliterates SAT2-dependent glutamine transport. Characterization of four additional disease-causing variants (R94W, R184C, N273I, Y276C) bolster these results and reveal the molecular mechanisms involved in the pathophysiology of KCTD7-related progressive myoclonus epilepsy. Thus, our data demonstrate that KCTD7 has an impact on K+ fluxes, neurotransmitter synthesis and neuronal function, and that malfunction of the encoded protein may lead to progressive myoclonus epilepsy.
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Affiliation(s)
- Marivi Nabong Moen
- 1 The Institute of Basic Medical Sciences, Department of Molecular Medicine, University of Oslo, Oslo, Norway
| | - Roar Fjær
- 2 Department of Medical Genetics, Oslo University Hospital and University of Oslo, Norway
| | - El Hassan Hamdani
- 1 The Institute of Basic Medical Sciences, Department of Molecular Medicine, University of Oslo, Oslo, Norway.,3 Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
| | - Jon K Laerdahl
- 4 Department of Microbiology, Oslo University Hospital, Oslo, Norway.,5 Bioinformatics Core Facility, Department of Informatics, University of Oslo, Oslo, Norway
| | - Robin Johansen Menchini
- 1 The Institute of Basic Medical Sciences, Department of Molecular Medicine, University of Oslo, Oslo, Norway
| | - Magnus Dehli Vigeland
- 2 Department of Medical Genetics, Oslo University Hospital and University of Oslo, Norway
| | - Ying Sheng
- 2 Department of Medical Genetics, Oslo University Hospital and University of Oslo, Norway
| | - Dag Erik Undlien
- 2 Department of Medical Genetics, Oslo University Hospital and University of Oslo, Norway
| | - Bjørnar Hassel
- 6 Department of Complex Neurology and Neurohabilitation, Oslo University Hospital, Oslo, Norway
| | - Mustafa A Salih
- 7 Division of Paediatric Neurology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Heba Y El Khashab
- 7 Division of Paediatric Neurology, College of Medicine, King Saud University, Riyadh, Saudi Arabia.,8 Department of Paediatrics, Ain Shams University, Cairo, Egypt
| | - Kaja Kristine Selmer
- 2 Department of Medical Genetics, Oslo University Hospital and University of Oslo, Norway.,9 National Centre for Rare Epilepsy-related Disorders, Oslo University Hospital, Oslo, Norway
| | - Farrukh Abbas Chaudhry
- 1 The Institute of Basic Medical Sciences, Department of Molecular Medicine, University of Oslo, Oslo, Norway .,3 Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
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