1
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Munk P, Yang D, Röder T, Maier L, Petersen TN, Duarte ASR, Clausen PTLC, Brinch C, Van Gompel L, Luiken R, Wagenaar JA, Schmitt H, Heederik DJJ, Mevius DJ, Smit LAM, Bossers A, Aarestrup FM. The European livestock resistome. mSystems 2024; 9:e0132823. [PMID: 38501800 PMCID: PMC11019871 DOI: 10.1128/msystems.01328-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/21/2024] [Indexed: 03/20/2024] Open
Abstract
Metagenomic sequencing has proven to be a powerful tool in the monitoring of antimicrobial resistance (AMR). Here, we provide a comparative analysis of the resistome from pigs, poultry, veal calves, turkey, and rainbow trout, for a total of 538 herds across nine European countries. We calculated the effects of per-farm management practices and antimicrobial usage (AMU) on the resistome in pigs, broilers, and veal calves. We also provide an in-depth study of the associations between bacterial diversity, resistome diversity, and AMR abundances as well as co-occurrence analysis of bacterial taxa and antimicrobial resistance genes (ARGs) and the universality of the latter. The resistomes of veal calves and pigs clustered together, as did those of avian origin, while the rainbow trout resistome was different. Moreover, we identified clear core resistomes for each specific food-producing animal species. We identified positive associations between bacterial alpha diversity and both resistome alpha diversity and abundance. Network analyses revealed very few taxa-ARG associations in pigs but a large number for the avian species. Using updated reference databases and optimized bioinformatics, previously reported significant associations between AMU, biosecurity, and AMR in pig and poultry farms were validated. AMU is an important driver for AMR; however, our integrated analyses suggest that factors contributing to increased bacterial diversity might also be associated with higher AMR load. We also found that dispersal limitations of ARGs are shaping livestock resistomes, and future efforts to fight AMR should continue to emphasize biosecurity measures.IMPORTANCEUnderstanding the occurrence, diversity, and drivers for antimicrobial resistance (AMR) is important to focus future control efforts. So far, almost all attempts to limit AMR in livestock have addressed antimicrobial consumption. We here performed an integrated analysis of the resistomes of five important farmed animal populations across Europe finding that the resistome and AMR levels are also shaped by factors related to bacterial diversity, as well as dispersal limitations. Thus, future studies and interventions aimed at reducing AMR should not only address antimicrobial usage but also consider other epidemiological and ecological factors.
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Affiliation(s)
- Patrick Munk
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Dongsheng Yang
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, The Netherlands, Utrecht
| | - Timo Röder
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Leonie Maier
- School of Biological Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, United Kingdom
| | | | | | | | - Christian Brinch
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Liese Van Gompel
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, The Netherlands, Utrecht
| | - Roosmarijn Luiken
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, The Netherlands, Utrecht
| | - Jaap A. Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, The Netherlands, Utrecht
| | - Heike Schmitt
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, The Netherlands, Utrecht
| | - Dick J. J. Heederik
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, The Netherlands, Utrecht
| | - Dik J. Mevius
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, The Netherlands, Utrecht
- Wageningen Bioveterinary Research, Wageningen University & Research, Lelystad, The Netherlands
| | - Lidwien A. M. Smit
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, The Netherlands, Utrecht
| | - EFFORT ConsortiumGravelandHaitskeGonzalez-ZornBrunoMoyanoGabrielSandersPascalChauvinClaireBattistiAntonioDewulfJeroenWadepohlKatharinaWasylDariuszSkarzyńskaMagdalenaZajacMagdalenaPękala-SafińskaAgnieszkaDaskalovHristoStärkKatharina D. C.
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, The Netherlands, Utrecht
- School of Biological Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, United Kingdom
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, The Netherlands, Utrecht
- Wageningen Bioveterinary Research, Wageningen University & Research, Lelystad, The Netherlands
| | - Alex Bossers
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, The Netherlands, Utrecht
- Wageningen Bioveterinary Research, Wageningen University & Research, Lelystad, The Netherlands
| | - Frank M. Aarestrup
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
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2
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Nissen JN, Johansen J, Allesøe RL, Sønderby CK, Armenteros JJA, Grønbech CH, Jensen LJ, Nielsen HB, Petersen TN, Winther O, Rasmussen S. Improved metagenome binning and assembly using deep variational autoencoders. Nat Biotechnol 2021; 39:555-560. [PMID: 33398153 DOI: 10.1038/s41587-020-00777-4] [Citation(s) in RCA: 156] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 11/17/2020] [Indexed: 01/28/2023]
Abstract
Despite recent advances in metagenomic binning, reconstruction of microbial species from metagenomics data remains challenging. Here we develop variational autoencoders for metagenomic binning (VAMB), a program that uses deep variational autoencoders to encode sequence coabundance and k-mer distribution information before clustering. We show that a variational autoencoder is able to integrate these two distinct data types without any previous knowledge of the datasets. VAMB outperforms existing state-of-the-art binners, reconstructing 29-98% and 45% more near-complete (NC) genomes on simulated and real data, respectively. Furthermore, VAMB is able to separate closely related strains up to 99.5% average nucleotide identity (ANI), and reconstructed 255 and 91 NC Bacteroides vulgatus and Bacteroides dorei sample-specific genomes as two distinct clusters from a dataset of 1,000 human gut microbiome samples. We use 2,606 NC bins from this dataset to show that species of the human gut microbiome have different geographical distribution patterns. VAMB can be run on standard hardware and is freely available at https://github.com/RasmussenLab/vamb .
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Affiliation(s)
- Jakob Nybo Nissen
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Joachim Johansen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rosa Lundbye Allesøe
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Casper Kaae Sønderby
- Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Christopher Heje Grønbech
- Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Department of Applied Mathematics and Computer Science, Technical University of Denmark, Lyngby, Denmark
| | - Lars Juhl Jensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Ole Winther
- Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Department of Applied Mathematics and Computer Science, Technical University of Denmark, Lyngby, Denmark.,Center for Genomic Medicine, Copenhagen University Hospital, Copenhagen, Denmark
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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3
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Duarte ASR, Röder T, Van Gompel L, Petersen TN, Hansen RB, Hansen IM, Bossers A, Aarestrup FM, Wagenaar JA, Hald T. Metagenomics-Based Approach to Source-Attribution of Antimicrobial Resistance Determinants - Identification of Reservoir Resistome Signatures. Front Microbiol 2021; 11:601407. [PMID: 33519742 PMCID: PMC7843941 DOI: 10.3389/fmicb.2020.601407] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 12/14/2020] [Indexed: 12/11/2022] Open
Abstract
Metagenomics can unveil the genetic content of the total microbiota in different environments, such as food products and the guts of humans and livestock. It is therefore considered of great potential to investigate the transmission of foodborne hazards as part of source-attribution studies. Source-attribution of antimicrobial resistance (AMR) has traditionally relied on pathogen isolation, while metagenomics allows investigating the full span of AMR determinants. In this study, we hypothesized that the relative abundance of fecal resistome components can be associated with specific reservoirs, and that resistomes can be used for AMR source-attribution. We used shotgun-sequences from fecal samples of pigs, broilers, turkeys- and veal calves collected across Europe, and fecal samples from humans occupationally exposed to livestock in one country (pig slaughterhouse workers, pig and broiler farmers). We applied both hierarchical and flat forms of the supervised classification ensemble algorithm Random Forests to classify resistomes into corresponding reservoir classes. We identified country-specific and -independent AMR determinants, and assessed the impact of country-specific determinants when attributing AMR resistance in humans. Additionally, we performed a similarity percentage analysis with the full spectrum of AMR determinants to identify resistome signatures for the different reservoirs. We showed that the number of AMR determinants necessary to attribute a resistome into the correct reservoir increases with a larger reservoir heterogeneity, and that the impact of country-specific resistome signatures on prediction varies between countries. We predicted a higher occupational exposure to AMR determinants among workers exposed to pigs than among those exposed to broilers. Additionally, results suggested that AMR exposure on pig farms was higher than in pig slaughterhouses. Human resistomes were more similar to pig and veal calves’ resistomes than to those of broilers and turkeys, and the majority of these resistome dissimilarities can be explained by a small set of AMR determinants. We identified resistome signatures for each individual reservoir, which include AMR determinants significantly associated with on-farm antimicrobial use. We attributed human resistomes to different livestock reservoirs using Random Forests, which allowed identifying pigs as a potential source of AMR in humans. This study thus demonstrates that it is possible to apply metagenomics in AMR source-attribution.
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Affiliation(s)
- Ana Sofia Ribeiro Duarte
- Division of Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Timo Röder
- Division of Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Liese Van Gompel
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Thomas Nordahl Petersen
- Division of Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
| | | | - Inge Marianne Hansen
- Division of Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Alex Bossers
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands.,Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Frank M Aarestrup
- Division of Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Jaap A Wagenaar
- Wageningen Bioveterinary Research, Lelystad, Netherlands.,Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Tine Hald
- Division of Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
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4
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Nielsen RL, Helenius M, Garcia SL, Roager HM, Aytan-Aktug D, Hansen LBS, Lind MV, Vogt JK, Dalgaard MD, Bahl MI, Jensen CB, Muktupavela R, Warinner C, Aaskov V, Gøbel R, Kristensen M, Frøkiær H, Sparholt MH, Christensen AF, Vestergaard H, Hansen T, Kristiansen K, Brix S, Petersen TN, Lauritzen L, Licht TR, Pedersen O, Gupta R. Data integration for prediction of weight loss in randomized controlled dietary trials. Sci Rep 2020; 10:20103. [PMID: 33208769 PMCID: PMC7674420 DOI: 10.1038/s41598-020-76097-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 10/22/2020] [Indexed: 12/11/2022] Open
Abstract
Diet is an important component in weight management strategies, but heterogeneous responses to the same diet make it difficult to foresee individual weight-loss outcomes. Omics-based technologies now allow for analysis of multiple factors for weight loss prediction at the individual level. Here, we classify weight loss responders (N = 106) and non-responders (N = 97) of overweight non-diabetic middle-aged Danes to two earlier reported dietary trials over 8 weeks. Random forest models integrated gut microbiome, host genetics, urine metabolome, measures of physiology and anthropometrics measured prior to any dietary intervention to identify individual predisposing features of weight loss in combination with diet. The most predictive models for weight loss included features of diet, gut bacterial species and urine metabolites (ROC-AUC: 0.84-0.88) compared to a diet-only model (ROC-AUC: 0.62). A model ensemble integrating multi-omics identified 64% of the non-responders with 80% confidence. Such models will be useful to assist in selecting appropriate weight management strategies, as individual predisposition to diet response varies.
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Affiliation(s)
- Rikke Linnemann Nielsen
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
- Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences, Beijing, China
| | - Marianne Helenius
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Sara L Garcia
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Henrik M Roager
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Copenhagen, Denmark
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Derya Aytan-Aktug
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Mads Vendelbo Lind
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Copenhagen, Denmark
| | - Josef K Vogt
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Marlene Danner Dalgaard
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Martin I Bahl
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Cecilia Bang Jensen
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Rasa Muktupavela
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | | | - Vincent Aaskov
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Rikke Gøbel
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Mette Kristensen
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Copenhagen, Denmark
| | - Hanne Frøkiær
- Institute for Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | | | - Henrik Vestergaard
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
- Department of Medicine, Bornholms Hospital, Rønne, Denmark
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Susanne Brix
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Lotte Lauritzen
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Copenhagen, Denmark.
| | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark.
| | - Oluf Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark.
| | - Ramneek Gupta
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark.
- Novo Nordisk Research Centre Oxford, Oxford, OX3 7FZ, UK.
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5
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Höper D, Grützke J, Brinkmann A, Mossong J, Matamoros S, Ellis RJ, Deneke C, Tausch SH, Cuesta I, Monzón S, Juliá M, Petersen TN, Hendriksen RS, Pamp SJ, Leijon M, Hakhverdyan M, Walsh AM, Cotter PD, Chandrasekaran L, Tay MYF, Schlundt J, Sala C, De Cesare A, Nitsche A, Beer M, Wylezich C. Proficiency Testing of Metagenomics-Based Detection of Food-Borne Pathogens Using a Complex Artificial Sequencing Dataset. Front Microbiol 2020; 11:575377. [PMID: 33250869 PMCID: PMC7672002 DOI: 10.3389/fmicb.2020.575377] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 10/13/2020] [Indexed: 01/16/2023] Open
Abstract
Metagenomics-based high-throughput sequencing (HTS) enables comprehensive detection of all species comprised in a sample with a single assay and is becoming a standard method for outbreak investigation. However, unlike real-time PCR or serological assays, HTS datasets generated for pathogen detection do not easily provide yes/no answers. Rather, results of the taxonomic read assignment need to be assessed by trained personnel to gain information thereof. Proficiency tests are important instruments of validation, harmonization, and standardization. Within the European Union funded project COMPARE [COllaborative Management Platform for detection and Analyses of (Re-) emerging and foodborne outbreaks in Europe], we conducted a proficiency test to scrutinize the ability to assess diagnostic metagenomics data. An artificial dataset resembling shotgun sequencing of RNA from a sample of contaminated trout was provided to 12 participants with the request to provide a table with per-read taxonomic assignments at species level and a report with a summary and assessment of their findings, considering different categories like pathogen, background, or contaminations. Analysis of the read assignment tables showed that the software used reliably classified the reads taxonomically overall. However, usage of incomplete reference databases or inappropriate data pre-processing caused difficulties. From the combination of the participants' reports with their read assignments, we conclude that, although most species were detected, a number of important taxa were not or not correctly categorized. This implies that knowledge of and awareness for potentially dangerous species and contaminations need to be improved, hence, capacity building for the interpretation of diagnostic metagenomics datasets is necessary.
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Affiliation(s)
- Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Josephine Grützke
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Annika Brinkmann
- Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Joël Mossong
- Département de Microbiologie, Laboratoire National de Santé, Dudelange, Luxembourg
| | - Sébastien Matamoros
- Department of Medical Microbiology, Amsterdam UMC University of Amsterdam, Amsterdam, Netherlands
| | | | - Carlus Deneke
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Simon H. Tausch
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Isabel Cuesta
- Bioinformatics Unit, Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Sara Monzón
- Bioinformatics Unit, Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Miguel Juliá
- Bioinformatics Unit, Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Thomas Nordahl Petersen
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Rene S. Hendriksen
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Sünje J. Pamp
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Mikael Leijon
- Department of Microbiology, National Veterinary Institute (SVA), Uppsala, Sweden
| | - Mikhayil Hakhverdyan
- Department of Microbiology, National Veterinary Institute (SVA), Uppsala, Sweden
| | - Aaron M. Walsh
- Teagasc Food Research Centre, APC Microbiome Ireland and Vistamilk, Moorepark, Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, APC Microbiome Ireland and Vistamilk, Moorepark, Ireland
| | - Lakshmi Chandrasekaran
- Nanyang Technological University Food Technology Centre (NAFTEC), Nanyang Technological University (NTU), Singapore, Singapore
| | - Moon Y. F. Tay
- Nanyang Technological University Food Technology Centre (NAFTEC), Nanyang Technological University (NTU), Singapore, Singapore
| | - Joergen Schlundt
- Nanyang Technological University Food Technology Centre (NAFTEC), Nanyang Technological University (NTU), Singapore, Singapore
| | - Claudia Sala
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
| | - Alessandra De Cesare
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Andreas Nitsche
- Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Claudia Wylezich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
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6
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Brinkmann A, Andrusch A, Belka A, Wylezich C, Höper D, Pohlmann A, Nordahl Petersen T, Lucas P, Blanchard Y, Papa A, Melidou A, Oude Munnink BB, Matthijnssens J, Deboutte W, Ellis RJ, Hansmann F, Baumgärtner W, van der Vries E, Osterhaus A, Camma C, Mangone I, Lorusso A, Marcacci M, Nunes A, Pinto M, Borges V, Kroneman A, Schmitz D, Corman VM, Drosten C, Jones TC, Hendriksen RS, Aarestrup FM, Koopmans M, Beer M, Nitsche A. Proficiency Testing of Virus Diagnostics Based on Bioinformatics Analysis of Simulated In Silico High-Throughput Sequencing Data Sets. J Clin Microbiol 2019; 57:e00466-19. [PMID: 31167846 PMCID: PMC6663916 DOI: 10.1128/jcm.00466-19] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 05/28/2019] [Indexed: 12/22/2022] Open
Abstract
Quality management and independent assessment of high-throughput sequencing-based virus diagnostics have not yet been established as a mandatory approach for ensuring comparable results. The sensitivity and specificity of viral high-throughput sequence data analysis are highly affected by bioinformatics processing using publicly available and custom tools and databases and thus differ widely between individuals and institutions. Here we present the results of the COMPARE [Collaborative Management Platform for Detection and Analyses of (Re-)emerging and Foodborne Outbreaks in Europe] in silico virus proficiency test. An artificial, simulated in silico data set of Illumina HiSeq sequences was provided to 13 different European institutes for bioinformatics analysis to identify viral pathogens in high-throughput sequence data. Comparison of the participants' analyses shows that the use of different tools, programs, and databases for bioinformatics analyses can impact the correct identification of viral sequences from a simple data set. The identification of slightly mutated and highly divergent virus genomes has been shown to be most challenging. Furthermore, the interpretation of the results, together with a fictitious case report, by the participants showed that in addition to the bioinformatics analysis, the virological evaluation of the results can be important in clinical settings. External quality assessment and proficiency testing should become an important part of validating high-throughput sequencing-based virus diagnostics and could improve the harmonization, comparability, and reproducibility of results. There is a need for the establishment of international proficiency testing, like that established for conventional laboratory tests such as PCR, for bioinformatics pipelines and the interpretation of such results.
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Affiliation(s)
- Annika Brinkmann
- Robert Koch Institute, Centre for Biological Threats and Special Pathogens 1, Berlin, Germany
| | - Andreas Andrusch
- Robert Koch Institute, Centre for Biological Threats and Special Pathogens 1, Berlin, Germany
| | - Ariane Belka
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - Claudia Wylezich
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - Dirk Höper
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - Anne Pohlmann
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - Thomas Nordahl Petersen
- Technical University of Denmark, National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Foodborne Pathogens and Genomics and European Union Reference Laboratory for Antimicrobial Resistance, Kongens Lyngby, Denmark
| | - Pierrick Lucas
- French Agency for Food, Environmental and Occupational Health and Safety, Laboratory of Ploufragan, Unit of Viral Genetics and Biosafety, Ploufragan, France
| | - Yannick Blanchard
- French Agency for Food, Environmental and Occupational Health and Safety, Laboratory of Ploufragan, Unit of Viral Genetics and Biosafety, Ploufragan, France
| | - Anna Papa
- Microbiology Department, Aristotle University of Thessaloniki, School of Medicine, Thessaloniki, Greece
| | - Angeliki Melidou
- Microbiology Department, Aristotle University of Thessaloniki, School of Medicine, Thessaloniki, Greece
| | - Bas B Oude Munnink
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands
| | | | | | | | - Florian Hansmann
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Erhard van der Vries
- Department of Infectious Diseases and Immunology, University of Utrecht, Utrecht, The Netherlands
| | | | - Cesare Camma
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise G. Caporale, National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Teramo, Italy
| | - Iolanda Mangone
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise G. Caporale, National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Teramo, Italy
| | - Alessio Lorusso
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise G. Caporale, National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Teramo, Italy
| | - Maurilia Marcacci
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise G. Caporale, National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Teramo, Italy
| | - Alexandra Nunes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), Lisbon, Portugal
| | - Miguel Pinto
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), Lisbon, Portugal
| | - Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), Lisbon, Portugal
| | - Annelies Kroneman
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Dennis Schmitz
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Victor Max Corman
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Terry C Jones
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Rene S Hendriksen
- Technical University of Denmark, National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Foodborne Pathogens and Genomics and European Union Reference Laboratory for Antimicrobial Resistance, Kongens Lyngby, Denmark
| | - Frank M Aarestrup
- Technical University of Denmark, National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Foodborne Pathogens and Genomics and European Union Reference Laboratory for Antimicrobial Resistance, Kongens Lyngby, Denmark
| | - Marion Koopmans
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Martin Beer
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - Andreas Nitsche
- Robert Koch Institute, Centre for Biological Threats and Special Pathogens 1, Berlin, Germany
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7
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Hendriksen RS, Munk P, Njage P, van Bunnik B, McNally L, Lukjancenko O, Röder T, Nieuwenhuijse D, Pedersen SK, Kjeldgaard J, Kaas RS, Clausen PTLC, Vogt JK, Leekitcharoenphon P, van de Schans MGM, Zuidema T, de Roda Husman AM, Rasmussen S, Petersen B, Amid C, Cochrane G, Sicheritz-Ponten T, Schmitt H, Alvarez JRM, Aidara-Kane A, Pamp SJ, Lund O, Hald T, Woolhouse M, Koopmans MP, Vigre H, Petersen TN, Aarestrup FM. Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage. Nat Commun 2019; 10:1124. [PMID: 30850636 PMCID: PMC6408512 DOI: 10.1038/s41467-019-08853-3] [Citation(s) in RCA: 455] [Impact Index Per Article: 91.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 01/31/2019] [Indexed: 12/11/2022] Open
Abstract
Antimicrobial resistance (AMR) is a serious threat to global public health, but obtaining representative data on AMR for healthy human populations is difficult. Here, we use metagenomic analysis of untreated sewage to characterize the bacterial resistome from 79 sites in 60 countries. We find systematic differences in abundance and diversity of AMR genes between Europe/North-America/Oceania and Africa/Asia/South-America. Antimicrobial use data and bacterial taxonomy only explains a minor part of the AMR variation that we observe. We find no evidence for cross-selection between antimicrobial classes, or for effect of air travel between sites. However, AMR gene abundance strongly correlates with socio-economic, health and environmental factors, which we use to predict AMR gene abundances in all countries in the world. Our findings suggest that global AMR gene diversity and abundance vary by region, and that improving sanitation and health could potentially limit the global burden of AMR. We propose metagenomic analysis of sewage as an ethically acceptable and economically feasible approach for continuous global surveillance and prediction of AMR.
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Affiliation(s)
- Rene S Hendriksen
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Patrick Munk
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Patrick Njage
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Bram van Bunnik
- Usher Institute, University of Edinburgh, Edinburgh, EH8 9AG, UK
| | - Luke McNally
- Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JD, UK
| | - Oksana Lukjancenko
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Timo Röder
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | | | | | - Jette Kjeldgaard
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Rolf S Kaas
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | | | - Josef Korbinian Vogt
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | | | | | - Tina Zuidema
- RIKILT Wageningen University and Research, Wageningen, 6708, The Netherlands
| | - Ana Maria de Roda Husman
- National Institute for Public Health and the Environment (RIVM), Bilthoven, 3721, The Netherlands
| | - Simon Rasmussen
- Department of Bio and Health Informatics, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Bent Petersen
- Department of Bio and Health Informatics, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | | | - Clara Amid
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD, UK
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD, UK
| | - Thomas Sicheritz-Ponten
- Centre of Excellence for Omics-Driven Computational Biodiscovery, AIMST University, Kedah, 08100, Malaysia
| | - Heike Schmitt
- National Institute for Public Health and the Environment (RIVM), Bilthoven, 3721, The Netherlands
| | | | | | - Sünje J Pamp
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Ole Lund
- Department of Bio and Health Informatics, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Tine Hald
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Mark Woolhouse
- Usher Institute, University of Edinburgh, Edinburgh, EH8 9AG, UK
| | - Marion P Koopmans
- Viroscience, Erasmus Medical Center, Rotterdam, 3015, The Netherlands
| | - Håkan Vigre
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | | | - Frank M Aarestrup
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark.
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8
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Al-Nakeeb K, Petersen TN, Sicheritz-Pontén T. Norgal: extraction and de novo assembly of mitochondrial DNA from whole-genome sequencing data. BMC Bioinformatics 2017; 18:510. [PMID: 29162031 PMCID: PMC5699183 DOI: 10.1186/s12859-017-1927-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 11/06/2017] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Whole-genome sequencing (WGS) projects provide short read nucleotide sequences from nuclear and possibly organelle DNA depending on the source of origin. Mitochondrial DNA is present in animals and fungi, while plants contain DNA from both mitochondria and chloroplasts. Current techniques for separating organelle reads from nuclear reads in WGS data require full reference or partial seed sequences for assembling. RESULTS Norgal (de Novo ORGAneLle extractor) avoids this requirement by identifying a high frequency subset of k-mers that are predominantly of mitochondrial origin and performing a de novo assembly on a subset of reads that contains these k-mers. The method was applied to WGS data from a panda, brown algae seaweed, butterfly and filamentous fungus. We were able to extract full circular mitochondrial genomes and obtained sequence identities to the reference sequences in the range from 98.5 to 99.5%. We also assembled the chloroplasts of grape vines and cucumbers using Norgal together with seed-based de novo assemblers. CONCLUSION Norgal is a pipeline that can extract and assemble full or partial mitochondrial and chloroplast genomes from WGS short reads without prior knowledge. The program is available at: https://bitbucket.org/kosaidtu/norgal .
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Affiliation(s)
- Kosai Al-Nakeeb
- Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, Building 208, Kgs Lyngby, 2800 Denmark
| | - Thomas Nordahl Petersen
- Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, Building 208, Kgs Lyngby, 2800 Denmark
| | - Thomas Sicheritz-Pontén
- Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, Building 208, Kgs Lyngby, 2800 Denmark
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9
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Geertz-Hansen HM, Kiemer L, Nielsen M, Stanchev K, Blom N, Brunak S, Petersen TN. Protein features as determinants of wild-type glycoside hydrolase thermostability. Proteins 2017; 85:2036-2044. [DOI: 10.1002/prot.25357] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 06/26/2017] [Accepted: 07/21/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Henrik Marcus Geertz-Hansen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark; DK-2800 Lyngby Denmark
- Department of Bio and Health Informatics; Technical University of Denmark, Kemitorvet; DK-2800 Lyngby Denmark
- Novozymes A/S; DK-2880 Bagsvaerd Denmark
| | | | - Morten Nielsen
- Department of Bio and Health Informatics; Technical University of Denmark, Kemitorvet; DK-2800 Lyngby Denmark
- Instituto de Investigaciones Biotecnologicas, Universidad Nacional de San Martin, San Martin, B 1650 HMP; Buenos Aires Argentina
| | - Kiril Stanchev
- Department of Bio and Health Informatics; Technical University of Denmark, Kemitorvet; DK-2800 Lyngby Denmark
| | - Nikolaj Blom
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark; DK-2800 Lyngby Denmark
- Department of Bio and Health Informatics; Technical University of Denmark, Kemitorvet; DK-2800 Lyngby Denmark
| | - Søren Brunak
- Department of Bio and Health Informatics; Technical University of Denmark, Kemitorvet; DK-2800 Lyngby Denmark
- Faculty of Health and Medical Sciences; Novo Nordisk Foundation Center for Protein Research, University of Copenhagen; DK-2200 Copenhagen N Denmark
| | - Thomas Nordahl Petersen
- Department of Bio and Health Informatics; Technical University of Denmark, Kemitorvet; DK-2800 Lyngby Denmark
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10
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Petersen TN, Lukjancenko O, Thomsen MCF, Maddalena Sperotto M, Lund O, Møller Aarestrup F, Sicheritz-Pontén T. Correction: MGmapper: Reference based mapping and taxonomy annotation of metagenomics sequence reads. PLoS One 2017; 12:e0179778. [PMID: 28604817 PMCID: PMC5467888 DOI: 10.1371/journal.pone.0179778] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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11
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Nordahl Petersen T, Rasmussen S, Hasman H, Carøe C, Bælum J, Schultz AC, Bergmark L, Svendsen CA, Lund O, Sicheritz-Pontén T, Aarestrup FM. Meta-genomic analysis of toilet waste from long distance flights; a step towards global surveillance of infectious diseases and antimicrobial resistance. Sci Rep 2015; 5:11444. [PMID: 26161690 PMCID: PMC4498435 DOI: 10.1038/srep11444] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 04/17/2015] [Indexed: 11/09/2022] Open
Abstract
Human populations worldwide are increasingly confronted with infectious diseases and antimicrobial resistance spreading faster and appearing more frequently. Knowledge regarding their occurrence and worldwide transmission is important to control outbreaks and prevent epidemics. Here, we performed shotgun sequencing of toilet waste from 18 international airplanes arriving in Copenhagen, Denmark, from nine cities in three world regions. An average of 18.6 Gb (14.8 to 25.7 Gb) of raw Illumina paired end sequence data was generated, cleaned, trimmed and mapped against reference sequence databases for bacteria and antimicrobial resistance genes. An average of 106,839 (0.06%) reads were assigned to resistance genes with genes encoding resistance to tetracycline, macrolide and beta-lactam resistance genes as the most abundant in all samples. We found significantly higher abundance and diversity of genes encoding antimicrobial resistance, including critical important resistance (e.g. blaCTX-M) carried on airplanes from South Asia compared to North America. Presence of Salmonella enterica and norovirus were also detected in higher amounts from South Asia, whereas Clostridium difficile was most abundant in samples from North America. Our study provides a first step towards a potential novel strategy for global surveillance enabling simultaneous detection of multiple human health threatening genetic elements, infectious agents and resistance genes.
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Affiliation(s)
| | - Simon Rasmussen
- Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Henrik Hasman
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Christian Carøe
- Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jacob Bælum
- Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Lasse Bergmark
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Ole Lund
- Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Frank M Aarestrup
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
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12
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Geertz-Hansen HM, Blom N, Feist AM, Brunak S, Petersen TN. Cofactory: sequence-based prediction of cofactor specificity of Rossmann folds. Proteins 2014; 82:1819-28. [PMID: 24523134 DOI: 10.1002/prot.24536] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 02/04/2014] [Accepted: 02/05/2014] [Indexed: 11/11/2022]
Abstract
Obtaining optimal cofactor balance to drive production is a challenge in metabolically engineered microbial production strains. To facilitate identification of heterologous enzymes with desirable altered cofactor requirements from native content, we have developed Cofactory, a method for prediction of enzyme cofactor specificity using only primary amino acid sequence information. The algorithm identifies potential cofactor binding Rossmann folds and predicts the specificity for the cofactors FAD(H2), NAD(H), and NADP(H). The Rossmann fold sequence search is carried out using hidden Markov models whereas artificial neural networks are used for specificity prediction. Training was carried out using experimental data from protein-cofactor structure complexes. The overall performance was benchmarked against an independent evaluation set obtaining Matthews correlation coefficients of 0.94, 0.79, and 0.65 for FAD(H2), NAD(H), and NADP(H), respectively. The Cofactory method is made publicly available at http://www.cbs.dtu.dk/services/Cofactory.
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Affiliation(s)
- Henrik Marcus Geertz-Hansen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2970, Hørsholm, Denmark; Center for Biological Sequence Analysis Department of Systems Biology, Technical University of Denmark, DK-2800, Lyngby, Denmark; Novozymes A/S, DK-2880, Bagsvaerd, Denmark
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13
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Johansen MB, Izarzugaza JMG, Brunak S, Petersen TN, Gupta R. Prediction of disease causing non-synonymous SNPs by the Artificial Neural Network Predictor NetDiseaseSNP. PLoS One 2013; 8:e68370. [PMID: 23935863 PMCID: PMC3723835 DOI: 10.1371/journal.pone.0068370] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 05/29/2013] [Indexed: 01/10/2023] Open
Abstract
We have developed a sequence conservation-based artificial neural network predictor called NetDiseaseSNP which classifies nsSNPs as disease-causing or neutral. Our method uses the excellent alignment generation algorithm of SIFT to identify related sequences and a combination of 31 features assessing sequence conservation and the predicted surface accessibility to produce a single score which can be used to rank nsSNPs based on their potential to cause disease. NetDiseaseSNP classifies successfully disease-causing and neutral mutations. In addition, we show that NetDiseaseSNP discriminates cancer driver and passenger mutations satisfactorily. Our method outperforms other state-of-the-art methods on several disease/neutral datasets as well as on cancer driver/passenger mutation datasets and can thus be used to pinpoint and prioritize plausible disease candidates among nsSNPs for further investigation. NetDiseaseSNP is publicly available as an online tool as well as a web service: http://www.cbs.dtu.dk/services/NetDiseaseSNP.
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Affiliation(s)
- Morten Bo Johansen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Jose M. G. Izarzugaza
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Søren Brunak
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Nordahl Petersen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Ramneek Gupta
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
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14
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Petersen TN, Brunak S, von Heijne G, Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 2011; 8:785-6. [PMID: 21959131 DOI: 10.1038/nmeth.1701] [Citation(s) in RCA: 6785] [Impact Index Per Article: 521.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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15
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Petersen TN, Brunak S, von Heijne G, Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 2011. [PMID: 21959131 DOI: 10.1038/nmeth1701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
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16
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Schjoldager KTBG, Vester-Christensen MB, Goth CK, Petersen TN, Brunak S, Bennett EP, Levery SB, Clausen H. A systematic study of site-specific GalNAc-type O-glycosylation modulating proprotein convertase processing. J Biol Chem 2011; 286:40122-32. [PMID: 21937429 DOI: 10.1074/jbc.m111.287912] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Site-specific GalNAc-type O-glycosylation is emerging as an important co-regulator of proprotein convertase (PC) processing of proteins. PC processing is crucial in regulating many fundamental biological pathways and O-glycans in or immediately adjacent to processing sites may affect recognition and function of PCs. Thus, we previously demonstrated that deficiency in site-specific O-glycosylation in a PC site of the fibroblast growth factor, FGF23, resulted in marked reduction in secretion of active unprocessed FGF23, which cause familial tumoral calcinosis and hyperostosis hyperphosphatemia. GalNAc-type O-glycosylation is found on serine and threonine amino acids and up to 20 distinct polypeptide GalNAc transferases catalyze the first addition of GalNAc to proteins making this step the most complex and differentially regulated steps in protein glycosylation. There is no reliable prediction model for O-glycosylation especially of isolated sites, but serine and to a lesser extent threonine residues are frequently found adjacent to PC processing sites. In the present study we used in vitro enzyme assays and ex vivo cell models to systematically address the boundaries of the region within site-specific O-glycosylation affect PC processing. The results demonstrate that O-glycans within at least ±3 residues of the RXXR furin cleavage site may affect PC processing suggesting that site-specific O-glycosylation is a major co-regulator of PC processing.
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Affiliation(s)
- Katrine Ter-Borch Gram Schjoldager
- Center for Glycomics, Department of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
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17
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Petersen B, Lundegaard C, Petersen TN. NetTurnP--neural network prediction of beta-turns by use of evolutionary information and predicted protein sequence features. PLoS One 2010; 5:e15079. [PMID: 21152409 PMCID: PMC2994801 DOI: 10.1371/journal.pone.0015079] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Accepted: 10/19/2010] [Indexed: 11/30/2022] Open
Abstract
β-turns are the most common type of non-repetitive structures, and constitute on average 25% of the amino acids in proteins. The formation of β-turns plays an important role in protein folding, protein stability and molecular recognition processes. In this work we present the neural network method NetTurnP, for prediction of two-class β-turns and prediction of the individual β-turn types, by use of evolutionary information and predicted protein sequence features. It has been evaluated against a commonly used dataset BT426, and achieves a Matthews correlation coefficient of 0.50, which is the highest reported performance on a two-class prediction of β-turn and not-β-turn. Furthermore NetTurnP shows improved performance on some of the specific β-turn types. In the present work, neural network methods have been trained to predict β-turn or not and individual β-turn types from the primary amino acid sequence. The individual β-turn types I, I', II, II', VIII, VIa1, VIa2, VIba and IV have been predicted based on classifications by PROMOTIF, and the two-class prediction of β-turn or not is a superset comprised of all β-turn types. The performance is evaluated using a golden set of non-homologous sequences known as BT426. Our two-class prediction method achieves a performance of: MCC = 0.50, Qtotal = 82.1%, sensitivity = 75.6%, PPV = 68.8% and AUC = 0.864. We have compared our performance to eleven other prediction methods that obtain Matthews correlation coefficients in the range of 0.17 – 0.47. For the type specific β-turn predictions, only type I and II can be predicted with reasonable Matthews correlation coefficients, where we obtain performance values of 0.36 and 0.31, respectively. Conclusion The NetTurnP method has been implemented as a webserver, which is freely available at http://www.cbs.dtu.dk/services/NetTurnP/. NetTurnP is the only available webserver that allows submission of multiple sequences.
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Affiliation(s)
- Bent Petersen
- Department of Systems Biology, Center for Biological Sequence Analysis (CBS), Technical University of Denmark, Lyngby, Denmark
| | - Claus Lundegaard
- Department of Systems Biology, Center for Biological Sequence Analysis (CBS), Technical University of Denmark, Lyngby, Denmark
| | - Thomas Nordahl Petersen
- Department of Systems Biology, Center for Biological Sequence Analysis (CBS), Technical University of Denmark, Lyngby, Denmark
- * E-mail:
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18
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Nielsen M, Lundegaard C, Lund O, Petersen TN. CPHmodels-3.0--remote homology modeling using structure-guided sequence profiles. Nucleic Acids Res 2010; 38:W576-81. [PMID: 20542909 PMCID: PMC2896139 DOI: 10.1093/nar/gkq535] [Citation(s) in RCA: 251] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
CPHmodels-3.0 is a web server predicting protein 3D structure by use of single template homology modeling. The server employs a hybrid of the scoring functions of CPHmodels-2.0 and a novel remote homology-modeling algorithm. A query sequence is first attempted modeled using the fast CPHmodels-2.0 profile–profile scoring function suitable for close homology modeling. The new computational costly remote homology-modeling algorithm is only engaged provided that no suitable PDB template is identified in the initial search. CPHmodels-3.0 was benchmarked in the CASP8 competition and produced models for 94% of the targets (117 out of 128), 74% were predicted as high reliability models (87 out of 117). These achieved an average RMSD of 4.6 Å when superimposed to the 3D structure. The remaining 26% low reliably models (30 out of 117) could superimpose to the true 3D structure with an average RMSD of 9.3 Å. These performance values place the CPHmodels-3.0 method in the group of high performing 3D prediction tools. Beside its accuracy, one of the important features of the method is its speed. For most queries, the response time of the server is <20 min. The web server is available at http://www.cbs.dtu.dk/services/CPHmodels/.
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Affiliation(s)
- Morten Nielsen
- Center for Biological Sequence Analysis, Department of systems Biology, The Technical University of Denmark, Denmark
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19
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Petersen B, Petersen TN, Andersen P, Nielsen M, Lundegaard C. A generic method for assignment of reliability scores applied to solvent accessibility predictions. BMC Struct Biol 2009; 9:51. [PMID: 19646261 PMCID: PMC2725087 DOI: 10.1186/1472-6807-9-51] [Citation(s) in RCA: 474] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2009] [Accepted: 07/31/2009] [Indexed: 11/25/2022]
Abstract
BACKGROUND Estimation of the reliability of specific real value predictions is nontrivial and the efficacy of this is often questionable. It is important to know if you can trust a given prediction and therefore the best methods associate a prediction with a reliability score or index. For discrete qualitative predictions, the reliability is conventionally estimated as the difference between output scores of selected classes. Such an approach is not feasible for methods that predict a biological feature as a single real value rather than a classification. As a solution to this challenge, we have implemented a method that predicts the relative surface accessibility of an amino acid and simultaneously predicts the reliability for each prediction, in the form of a Z-score. RESULTS An ensemble of artificial neural networks has been trained on a set of experimentally solved protein structures to predict the relative exposure of the amino acids. The method assigns a reliability score to each surface accessibility prediction as an inherent part of the training process. This is in contrast to the most commonly used procedures where reliabilities are obtained by post-processing the output. CONCLUSION The performance of the neural networks was evaluated on a commonly used set of sequences known as the CB513 set. An overall Pearson's correlation coefficient of 0.72 was obtained, which is comparable to the performance of the currently best public available method, Real-SPINE. Both methods associate a reliability score with the individual predictions. However, our implementation of reliability scores in the form of a Z-score is shown to be the more informative measure for discriminating good predictions from bad ones in the entire range from completely buried to fully exposed amino acids. This is evident when comparing the Pearson's correlation coefficient for the upper 20% of predictions sorted according to reliability. For this subset, values of 0.79 and 0.74 are obtained using our and the compared method, respectively. This tendency is true for any selected subset.
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Affiliation(s)
- Bent Petersen
- Center for Biological Sequence Analysis – CBS, Department of Systems Biology, Kemitorvet 208, Technical University of Denmark – DTU, DK-2800 Lyngby, Denmark
| | - Thomas Nordahl Petersen
- Center for Biological Sequence Analysis – CBS, Department of Systems Biology, Kemitorvet 208, Technical University of Denmark – DTU, DK-2800 Lyngby, Denmark
| | - Pernille Andersen
- Center for Biological Sequence Analysis – CBS, Department of Systems Biology, Kemitorvet 208, Technical University of Denmark – DTU, DK-2800 Lyngby, Denmark
- Centre for Medical Parasitology – CMP, CSS Building 22, University of Copenhagen, DK-1014 Copenhagen, Denmark
| | - Morten Nielsen
- Center for Biological Sequence Analysis – CBS, Department of Systems Biology, Kemitorvet 208, Technical University of Denmark – DTU, DK-2800 Lyngby, Denmark
| | - Claus Lundegaard
- Center for Biological Sequence Analysis – CBS, Department of Systems Biology, Kemitorvet 208, Technical University of Denmark – DTU, DK-2800 Lyngby, Denmark
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Jørgensen JR, Juliusson B, Henriksen KF, Hansen C, Knudsen S, Petersen TN, Blom N, Seiger A, Wahlberg LU. Identification of novel genes regulated in the developing human ventral mesencephalon. Exp Neurol 2006; 198:427-37. [PMID: 16473350 DOI: 10.1016/j.expneurol.2005.12.023] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2005] [Revised: 10/18/2005] [Accepted: 12/13/2005] [Indexed: 10/25/2022]
Abstract
In the human embryo, from approximately 6 weeks gestational age (GA), dopaminergic (DA) neurons can be found in the ventral mesencephalon (VM). More specifically, the post-mitotic neurons are located in the ventral part of the tegmentum (VT), whereas no mature DA neurons are found in the neighboring dorsal part. We used Affymetrix HG-U133 GeneChip technology to compare genome-wide expression profiles of ventral and dorsal tegmentum from 8 weeks GA human embryos, in order to identify genes involved in specification, differentiation, and survival of mesencephalic DA (mDA) neurons. Known mDA marker genes including ALDH1A1, DAT1, VMAT2, TH, CALB1, NURR1, FOXA1, GIRK2, PITX3, RET, and DRD2 topped the list of 96 genes from HG-U133A with higher expression in VT, validating the experimental set-up. In addition, 28 probes from HG-U133B were identified whereof most are annotated to UniGene clusters with no gene associated or to genes of unknown function. Of these, the fifteen most regulated transcripts, representing changes down to 56% could be verified by quantitative real-time PCR (Q-PCR) on a developmental series of subdissected human embryonic and fetal brain material, resulting in not only a regional but also a temporal expression profile. This revealed a distinct DA-associated profile for in particular a putative transcription factor (FLJ45455) and the uncharacterized transmembrane proteins KIAA1145 and SLC10A4. The data presented here may help to device cell replacement and regenerative therapies for Parkinson's disease (PD).
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Petersen TN, Henriksen A, Gajhede M. Structure of porcine pancreatic spasmolytic polypeptide at 1.95 A resolution. Acta Crystallogr D Biol Crystallogr 2005; 52:730-7. [PMID: 15299636 DOI: 10.1107/s0907444996001345] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The structure of a trigonal crystal form of porcine pancreatic spasmolytic polypeptide (PSP) has been solved by molecular replacement and refined to 1.95 A resolution. Three heavy-atom derivatives were prepared, giving unbiased phase information, which was used in the model building of the protein molecules. The final conventional R value is 19.8% with the inclusion of 183 water molecules. PSP crystallizes as a dimer in space group P3(1)21 with a non-crystallographic twofold axis relating the monomers. The monomer consists of two very similar domains each composed of three loop regions. Two clefts are found in the monomer, one in each domain, that are proposed as possible substrate-binding sites. Important interactions have been identified in the proposed substrate-binding sites, where conserved water molecules probably mimic the hydrophilic positions of the substrate. The estimated cleft size is 9 x 9 x 12 A. Analysis of the charge distribution within the clefts, by an electrostatic potential calculation, shows the clefts to be essentially non-charged.
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Affiliation(s)
- T N Petersen
- Centre for Crystallographic Studies, Universitetsparken, Department of Chemsistry, University of Copenhagen, Denmark
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Petersen TN, Lundegaard C, Nielsen M, Bohr H, Bohr J, Brunak S, Gippert GP, Lund O. Prediction of protein secondary structure at 80% accuracy. Proteins 2000; 41:17-20. [PMID: 10944389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Secondary structure prediction involving up to 800 neural network predictions has been developed, by use of novel methods such as output expansion and a unique balloting procedure. An overall performance of 77.2%-80.2% (77.9%-80.6% mean per-chain) for three-state (helix, strand, coil) prediction was obtained when evaluated on a commonly used set of 126 protein chains. The method uses profiles made by position-specific scoring matrices as input, while at the output level it predicts on three consecutive residues simultaneously. The predictions arise from tenfold, cross validated training and testing of 1032 protein sequences, using a scheme with primary structure neural networks followed by structure filtering neural networks. With respect to blind prediction, this work is preliminary and awaits evaluation by CASP4.
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Affiliation(s)
- T N Petersen
- Structural Bioinformatics Advanced Technologies A/S, Horsholm, Denmark.
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Nordahl Petersen T, Lundegaard C, Nielsen M, Bohr H, Bohr J, Brunak S, Gippert GP, Lund O. Prediction of protein secondary structure at 80% accuracy using a combination of many neural networks. J Mol Graph Model 2000. [DOI: 10.1016/s1093-3263(00)80118-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Abstract
BACKGROUND Pectic substances are the major polysaccharide components of the middle lamella and primary cell wall of dicotyledonous plants. They consist of homogalacturonan 'smooth' regions and highly rhamnified 'hairy' regions of rhamnogalacturonan. The backbone in rhamnogalacturonan-l (RG-l), which is composed of alternating galacturonic acid and rhamnose residues, is the substrate for a new class of enzymes known as rhamnogalacturnoases (RGases). RGase A is a novel enzyme implicated in the enzymatic degradation of RG-l. RESULTS The structure of RGase A from Aspergillus aculeatus has been solved by the single isomorphous replacement method including anomalous scattering (SIRAS method) to 2.0 A resolution. The enzyme folds into a large right-handed parallel beta helix, with a core composed of 13 turns of beta strands. Four parallel beta sheets (PB1, PB1a, PB2 and PB3), formed by the consecutive turns, are typically separated by a residue in the conformation of a left-handed alpha helix. As a consequence of the consecutive turns, 32% of all residues have their sidechains aligned at the surface or in the interior of the parallel beta helix. The aligned residues at the surface are dominated by threonine, aspartic acid and asparagine, whereas valine, leucine and isoleucine are most frequently found in the interior. A very large hydrophobic cavity is found in the interior of the parallel beta helix. The potential active site is a groove, oriented almost perpendicular to the helical axis, containing a cluster of three aspartic acid residues and one glutamic acid residue. The enzyme is highly glycosylated; two N-linked and eighteen O-linked glycosylation sites have been found in the structure. CONCLUSIONS Rhamnogalacturonase A from A. aculeatus is the first three-dimensional structure of an enzyme hydrolyzing glycoside bonds within the backbone of RG-l. The large groove, which is the potential active site of RGase A, is also seen in the structures of pectate lyases. Two catalytic aspartic acid residues, which have been proposed to have a catalytic role, reside in this area of RGase A. The distance between the aspartic acid residues is consistent with the inverting mechanism of catalysis. The glycan groups bound to RGase A are important to the stability of the crystal, as the carbohydrate moiety is involved in most of the intermolecular hydrogen bonds.
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Affiliation(s)
- T N Petersen
- Centre for Crystallographic Studies, Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark
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Petersen TN, Christgau S, Kofod LV, Kauppinen S, Johnson AH, Larsen S. Crystallization and preliminary X-ray studies of rhamnogalacturonase A from Aspergillus aculeatus. Acta Crystallogr D Biol Crystallogr 1997; 53:105-7. [PMID: 15299976 DOI: 10.1107/s0907444996010785] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Recombinant rhamnogalacturonase A from Aspergillus aculeatus has been crystallized and X-ray diffraction data has been collected. Crystals were grown by the hanging-drop vapour-diffusion technique, under the conditions 10% PEG 8000, 0.05 M KH(2)PO(4) and 0.1 M sodium acetate buffered at pH 3.5. The crystals diffract beyond 2.0 A resolution and belong to one of the orthorhombic space groups I2(1)2(1)2(1) or I222, with the unit-cell parameters a = 62.9, b = 125.4 and c = 137.0 A. There is one molecule in the asymmetric unit and a solvent content of approximately 54%. The enzyme is highly glycosylated corresponding to 5.9 kDa.
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Affiliation(s)
- T N Petersen
- Centre for Crystallographic Studies, H. C. Ørsted Institute, University of Copenhagen, Denmark
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Ólafsson SN, Petersen TN, Andersen P, Yagasaki A, Andersson L, Holmström K, Undheim K, Rosendahl CN, Haugg M, Trabesinger-Rüf N, Weinhold EG. Crystal Structure of Diphenylbis(diphenyldithiophosphinato)lead(IV), PbPh2(S2PPh2)2. ACTA ACUST UNITED AC 1996. [DOI: 10.3891/acta.chem.scand.50-0745] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Gajhede M, Petersen TN, Henriksen A, Petersen JF, Dauter Z, Wilson KS, Thim L. Pancreatic spasmolytic polypeptide: first three-dimensional structure of a member of the mammalian trefoil family of peptides. Structure 1993; 1:253-62. [PMID: 8081739 DOI: 10.1016/0969-2126(93)90014-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
BACKGROUND The trefoil peptides are a rapidly growing family of peptides, mainly found in the gastrointestinal tract. There is circumstantial evidence that they stabilize the mucus layer, and may affect the rate of healing of the mucosal epithelium. RESULTS We have determined the structure of porcine pancreatic spasmolytic polypeptide (PSP) to 2.5 A resolution. The polypeptide contains two trefoil domains. The domain structure is compact, and is composed of a central short antiparallel beta-sheet with one short helix above and one below it. This is a novel motif. The two domains are related by two-fold symmetry, and each domain contains a cleft. CONCLUSIONS The cleft within each domain could accommodate a polysaccharide chain, and may therefore be responsible for binding mucin glycoproteins. We suggest that PSP may cross-link glycoproteins, explaining its ability to stabilize the mucus layer.
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Affiliation(s)
- M Gajhede
- Department of Chemistry, H.C. Orsted Institute, University of Copenhagen, Denmark
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