40 results on '"Koehorst JJ"'
Search Results
2. Microbial dynamics and bioreactor performance are interlinked with organic matter removal from wastewater treatment plant effluent.
- Author
-
Atasoy M, Scott WT Jr, van Gijn K, Koehorst JJ, Smidt H, and Langenhoff AAM
- Subjects
- Waste Disposal, Fluid, RNA, Ribosomal, 16S genetics, Bioreactors microbiology, Wastewater, Water Purification
- Abstract
Optimizing bioreactor performance for organic matter removal can achieve sustainable and energy-efficient micropollutant removal in subsequent tertiary treatment. Bioreactor performance heavily depends on its resident microbial community; hence, a deeper understanding of community dynamics is essential. The microbial communities of three different bioreactors (biological activated carbon, moving bed biofilm reactor, sand filter), used for organic matter removal from wastewater treatment effluent, were characterized by 16S rRNA gene amplicon sequence analysis. An interdependency between bioreactor performance and microbial community profile was observed. Overall, Proteobacteria was the most predominant phylum, and Comamonadaceae was the most predominant family in all bioreactors. The relative abundance of the genus Roseococcus was positively correlated with organic matter removal. A generalized Lotka-Volterra (gLV) model was established to understand the interactions in the microbial community. By identifying microbial dynamics and their role in bioreactors, a strategy can be developed to improve bioreactor performance., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Author(s). Published by Elsevier Ltd.. All rights reserved.)
- Published
- 2023
- Full Text
- View/download PDF
3. FAIR data station for lightweight metadata management and validation of omics studies.
- Author
-
Nijsse B, Schaap PJ, and Koehorst JJ
- Subjects
- Databases, Factual, Nucleotides, Publishing, Metadata, Biological Science Disciplines
- Abstract
Background: The life sciences are one of the biggest suppliers of scientific data. Reusing and connecting these data can uncover hidden insights and lead to new concepts. Efficient reuse of these datasets is strongly promoted when they are interlinked with a sufficient amount of machine-actionable metadata. While the FAIR (Findable, Accessible, Interoperable, Reusable) guiding principles have been accepted by all stakeholders, in practice, there are only a limited number of easy-to-adopt implementations available that fulfill the needs of data producers., Findings: We developed the FAIR Data Station, a lightweight application written in Java, that aims to support researchers in managing research metadata according to the FAIR principles. It implements the ISA metadata framework and uses minimal information metadata standards to capture experiment metadata. The FAIR Data Station consists of 3 modules. Based on the minimal information model(s) selected by the user, the "form generation module" creates a metadata template Excel workbook with a header row of machine-actionable attribute names. The Excel workbook is subsequently used by the data producer(s) as a familiar environment for sample metadata registration. At any point during this process, the format of the recorded values can be checked using the "validation module." Finally, the "resource module" can be used to convert the set of metadata recorded in the Excel workbook in RDF format, enabling (cross-project) (meta)data searches and, for publishing of sequence data, in an European Nucleotide Archive-compatible XML metadata file., Conclusions: Turning FAIR into reality requires the availability of easy-to-adopt data FAIRification workflows that are also of direct use for data producers. As such, the FAIR Data Station provides, in addition to the means to correctly FAIRify (omics) data, the means to build searchable metadata databases of similar projects and can assist in ENA metadata submission of sequence data. The FAIR Data Station is available at https://fairbydesign.nl., (© The Author(s) 2023. Published by Oxford University Press GigaScience.)
- Published
- 2022
- Full Text
- View/download PDF
4. SALARECON connects the Atlantic salmon genome to growth and feed efficiency.
- Author
-
Zakhartsev M, Rotnes F, Gulla M, Øyås O, van Dam JCJ, Suarez-Diez M, Grammes F, Hafþórsson RA, van Helvoirt W, Koehorst JJ, Schaap PJ, Jin Y, Mydland LT, Gjuvsland AB, Sandve SR, Martins Dos Santos VAP, and Vik JO
- Subjects
- Amino Acids genetics, Animals, Aquaculture, Animal Feed analysis, Salmo salar genetics
- Abstract
Atlantic salmon (Salmo salar) is the most valuable farmed fish globally and there is much interest in optimizing its genetics and rearing conditions for growth and feed efficiency. Marine feed ingredients must be replaced to meet global demand, with challenges for fish health and sustainability. Metabolic models can address this by connecting genomes to metabolism, which converts nutrients in the feed to energy and biomass, but such models are currently not available for major aquaculture species such as salmon. We present SALARECON, a model focusing on energy, amino acid, and nucleotide metabolism that links the Atlantic salmon genome to metabolic fluxes and growth. It performs well in standardized tests and captures expected metabolic (in)capabilities. We show that it can explain observed hypoxic growth in terms of metabolic fluxes and apply it to aquaculture by simulating growth with commercial feed ingredients. Predicted limiting amino acids and feed efficiencies agree with data, and the model suggests that marine feed efficiency can be achieved by supplementing a few amino acids to plant- and insect-based feeds. SALARECON is a high-quality model that makes it possible to simulate Atlantic salmon metabolism and growth. It can be used to explain Atlantic salmon physiology and address key challenges in aquaculture such as development of sustainable feeds., Competing Interests: The authors have declared that no competing interests exist.
- Published
- 2022
- Full Text
- View/download PDF
5. Assembly and Comparison of Ca. Neoehrlichia mikurensis Genomes.
- Author
-
Azagi T, Dirks RP, Yebra-Pimentel ES, Schaap PJ, Koehorst JJ, Esser HJ, and Sprong H
- Abstract
Ca. Neoehrlichia mikurensis is widely prevalent in I. ricinus across Europe and has been associated with human disease. However, diagnostic modalities are limited, and much is still unknown about its biology. Here, we present the first complete Ca. Neoehrlichia mikurensis genomes directly derived from wildlife reservoir host tissues, using both long- and short-read sequencing technologies. This pragmatic approach provides an alternative to obtaining sufficient material from clinical cases, a difficult task for emerging infectious diseases, and to expensive and challenging bacterial isolation and culture methods. Both genomes exhibit a larger chromosome than the currently available Ca. Neoehrlichia mikurensis genomes and expand the ability to find new targets for the development of supportive laboratory diagnostics in the future. Moreover, this method could be utilized for other tick-borne pathogens that are difficult to culture.
- Published
- 2022
- Full Text
- View/download PDF
6. Machine learning approaches to predict the Plant-associated phenotype of Xanthomonas strains.
- Author
-
Te Molder D, Poncheewin W, Schaap PJ, and Koehorst JJ
- Subjects
- Genome, Bacterial, Machine Learning, Phenotype, Plants, Xanthomonas genetics
- Abstract
Background: The genus Xanthomonas has long been considered to consist predominantly of plant pathogens, but over the last decade there has been an increasing number of reports on non-pathogenic and endophytic members. As Xanthomonas species are prevalent pathogens on a wide variety of important crops around the world, there is a need to distinguish between these plant-associated phenotypes. To date a large number of Xanthomonas genomes have been sequenced, which enables the application of machine learning (ML) approaches on the genome content to predict this phenotype. Until now such approaches to the pathogenomics of Xanthomonas strains have been hampered by the fragmentation of information regarding pathogenicity of individual strains over many studies. Unification of this information into a single resource was therefore considered to be an essential step., Results: Mining of 39 papers considering both plant-associated phenotypes, allowed for a phenotypic classification of 578 Xanthomonas strains. For 65 plant-pathogenic and 53 non-pathogenic strains the corresponding genomes were available and de novo annotated for the presence of Pfam protein domains used as features to train and compare three ML classification algorithms; CART, Lasso and Random Forest., Conclusion: The literature resource in combination with recursive feature extraction used in the ML classification algorithms provided further insights into the virulence enabling factors, but also highlighted domains linked to traits not present in pathogenic strains., (© 2021. The Author(s).)
- Published
- 2021
- Full Text
- View/download PDF
7. Genomic convergence between Akkermansia muciniphila in different mammalian hosts.
- Author
-
Geerlings SY, Ouwerkerk JP, Koehorst JJ, Ritari J, Aalvink S, Stecher B, Schaap PJ, Paulin L, de Vos WM, and Belzer C
- Subjects
- Akkermansia classification, Akkermansia genetics, Akkermansia isolation & purification, Akkermansia metabolism, Animals, Feces microbiology, Gastrointestinal Tract microbiology, Genetic Variation, Genomics, Humans, Mammals classification, Mice, Mucins metabolism, Phylogeny, RNA, Ribosomal, 16S genetics, Verrucomicrobia classification, Verrucomicrobia genetics, Verrucomicrobia isolation & purification, Genome, Bacterial genetics, Mammals microbiology
- Abstract
Background: Akkermansia muciniphila is a member of the human gut microbiota where it resides in the mucus layer and uses mucin as the sole carbon, nitrogen and energy source. A. muciniphila is the only representative of the Verrucomicrobia phylum in the human gut. However, A. muciniphila 16S rRNA gene sequences have also been found in the intestines of many vertebrates., Results: We detected A. muciniphila-like bacteria in the intestines of animals belonging to 15 out of 16 mammalian orders. In addition, other species belonging to the Verrucomicrobia phylum were detected in fecal samples. We isolated 10 new A. muciniphila strains from the feces of chimpanzee, siamang, mouse, pig, reindeer, horse and elephant. The physiology and genome of these strains were highly similar in comparison to the type strain A. muciniphila Muc
T . Overall, the genomes of the new strains showed high average nucleotide identity (93.9 to 99.7%). In these genomes, we detected considerable conservation of at least 75 of the 78 mucin degradation genes that were previously detected in the genome of the type strain MucT ., Conclusions: The low genomic divergence observed in the new strains may indicate that A. muciniphila favors mucosal colonization independent of the differences in hosts. In addition, the conserved mucus degradation capability points towards a similar beneficial role of the new strains in regulating host metabolic health., (© 2021. The Author(s).)- Published
- 2021
- Full Text
- View/download PDF
8. A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of growth-associated genes.
- Author
-
Uengwetwanit T, Pootakham W, Nookaew I, Sonthirod C, Angthong P, Sittikankaew K, Rungrassamee W, Arayamethakorn S, Wongsurawat T, Jenjaroenpun P, Sangsrakru D, Leelatanawit R, Khudet J, Koehorst JJ, Schaap PJ, Martins Dos Santos V, Tangy F, and Karoonuthaisiri N
- Subjects
- Animals, Aquaculture, Chromosomes, Transcriptome, Genome, Penaeidae genetics, Penaeidae growth & development
- Abstract
To salvage marine ecosystems from fishery overexploitation, sustainable and efficient aquaculture must be emphasized. The knowledge obtained from available genome sequence of marine organisms has accelerated marine aquaculture in many cases. The black tiger shrimp (Penaeus monodon) is one of the most prominent cultured penaeid shrimps (Crustacean) with an average annual global production of half a million tons in the last decade. However, its currently available genome assemblies lack the contiguity and completeness required for accurate genome annotation due to the highly repetitive nature of the genome and technical difficulty in extracting high-quality, high-molecular weight DNA. Here, we report the first chromosome-level whole-genome assembly of P. monodon. The combination of long-read Pacific Biosciences (PacBio) and long-range Chicago and Hi-C technologies enabled a successful assembly of this first high-quality genome sequence. The final assembly covered 2.39 Gb (92.3% of the estimated genome size) and contained 44 pseudomolecules, corresponding to the haploid chromosome number. Repetitive elements occupied a substantial portion of the assembly (62.5%), the highest of the figures reported among crustacean species. The availability of this high-quality genome assembly enabled the identification of genes associated with rapid growth in the black tiger shrimp through the comparison of hepatopancreas transcriptome of slow-growing and fast-growing shrimps. The results highlighted several growth-associated genes. Our high-quality genome assembly provides an invaluable resource for genetic improvement and breeding penaeid shrimp in aquaculture. The availability of P. monodon genome enables analyses of ecological impact, environment adaptation and evolution, as well as the role of the genome to protect the ecological resources by promoting sustainable shrimp farming., (© 2021 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.)
- Published
- 2021
- Full Text
- View/download PDF
9. Galactocerebroside biosynthesis pathways of Mycoplasma species: an antigen triggering Guillain-Barré-Stohl syndrome.
- Author
-
Gaspari E, Koehorst JJ, Frey J, Martins Dos Santos VAP, and Suarez-Diez M
- Subjects
- Galactosylceramides, Glycolipids, Humans, Mycoplasma pneumoniae genetics, Guillain-Barre Syndrome, Pneumonia, Mycoplasma
- Abstract
Infection by Mycoplasma pneumoniae has been identified as a preceding factor of Guillain-Barré-Stohl syndrome. The Guillain-Barré-Stohl syndrome is triggered by an immune reaction against the major glycolipids and it has been postulated that M. pneumoniae infection triggers this syndrome due to bacterial production of galactocerebroside. Here, we present an extensive comparison of 224 genome sequences from 104 Mycoplasma species to characterize the genetic determinants of galactocerebroside biosynthesis. Hidden Markov models were used to analyse glycosil transferases, leading to identification of a functional protein domain, termed M2000535 that appears in about a third of the studied genomes. This domain appears to be associated with a potential UDP-glucose epimerase, which converts UDP-glucose into UDP-galactose, a main substrate for the biosynthesis of galactocerebroside. These findings clarify the pathogenic mechanisms underlining the triggering of Guillain-Barré-Stohl syndrome by M. pneumoniae infections., (© 2021 The Authors. Microbial Biotechnology published by Society for Applied Microbiology and John Wiley & Sons Ltd.)
- Published
- 2021
- Full Text
- View/download PDF
10. A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses.
- Author
-
Waagmeester A, Willighagen EL, Su AI, Kutmon M, Gayo JEL, Fernández-Álvarez D, Groom Q, Schaap PJ, Verhagen LM, and Koehorst JJ
- Subjects
- COVID-19 metabolism, COVID-19 virology, Coronavirus genetics, Coronavirus physiology, Coronavirus Infections metabolism, Coronavirus Infections pathology, Coronavirus Infections virology, Genome, Viral, Humans, Internet, Pandemics, SARS-CoV-2 genetics, Viral Proteins genetics, Viral Proteins metabolism, Workflow, COVID-19 pathology, Genomics methods, Knowledge Bases, Proteomics methods, SARS-CoV-2 physiology
- Abstract
Background: Pandemics, even more than other medical problems, require swift integration of knowledge. When caused by a new virus, understanding the underlying biology may help finding solutions. In a setting where there are a large number of loosely related projects and initiatives, we need common ground, also known as a "commons." Wikidata, a public knowledge graph aligned with Wikipedia, is such a commons and uses unique identifiers to link knowledge in other knowledge bases. However, Wikidata may not always have the right schema for the urgent questions. In this paper, we address this problem by showing how a data schema required for the integration can be modeled with entity schemas represented by Shape Expressions., Results: As a telling example, we describe the process of aligning resources on the genomes and proteomes of the SARS-CoV-2 virus and related viruses as well as how Shape Expressions can be defined for Wikidata to model the knowledge, helping others studying the SARS-CoV-2 pandemic. How this model can be used to make data between various resources interoperable is demonstrated by integrating data from NCBI (National Center for Biotechnology Information) Taxonomy, NCBI Genes, UniProt, and WikiPathways. Based on that model, a set of automated applications or bots were written for regular updates of these sources in Wikidata and added to a platform for automatically running these updates., Conclusions: Although this workflow is developed and applied in the context of the COVID-19 pandemic, to demonstrate its broader applicability it was also applied to other human coronaviruses (MERS, SARS, human coronavirus NL63, human coronavirus 229E, human coronavirus HKU1, human coronavirus OC4).
- Published
- 2021
- Full Text
- View/download PDF
11. A metabolic and physiological design study of Pseudomonas putida KT2440 capable of anaerobic respiration.
- Author
-
Kampers LFC, Koehorst JJ, van Heck RJA, Suarez-Diez M, Stams AJM, and Schaap PJ
- Subjects
- Anaerobiosis, Computer Simulation, Databases, Genetic, Fermentation, Gene Expression Profiling, Microbial Viability, Pseudomonas putida genetics, Pseudomonas putida metabolism, Pyrimidines metabolism, Bacterial Proteins genetics, Bacterial Proteins metabolism, Metabolic Engineering methods, Pseudomonas putida growth & development
- Abstract
Background: Pseudomonas putida KT2440 is a metabolically versatile, HV1-certified, genetically accessible, and thus interesting microbial chassis for biotechnological applications. However, its obligate aerobic nature hampers production of oxygen sensitive products and drives up costs in large scale fermentation. The inability to perform anaerobic fermentation has been attributed to insufficient ATP production and an inability to produce pyrimidines under these conditions. Addressing these bottlenecks enabled growth under micro-oxic conditions but does not lead to growth or survival under anoxic conditions., Results: Here, a data-driven approach was used to develop a rational design for a P. putida KT2440 derivative strain capable of anaerobic respiration. To come to the design, data derived from a genome comparison of 1628 Pseudomonas strains was combined with genome-scale metabolic modelling simulations and a transcriptome dataset of 47 samples representing 14 environmental conditions from the facultative anaerobe Pseudomonas aeruginosa., Conclusions: The results indicate that the implementation of anaerobic respiration in P. putida KT2440 would require at least 49 additional genes of known function, at least 8 genes encoding proteins of unknown function, and 3 externally added vitamins.
- Published
- 2021
- Full Text
- View/download PDF
12. Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing.
- Author
-
Lieven C, Beber ME, Olivier BG, Bergmann FT, Ataman M, Babaei P, Bartell JA, Blank LM, Chauhan S, Correia K, Diener C, Dräger A, Ebert BE, Edirisinghe JN, Faria JP, Feist AM, Fengos G, Fleming RMT, García-Jiménez B, Hatzimanikatis V, van Helvoirt W, Henry CS, Hermjakob H, Herrgård MJ, Kaafarani A, Kim HU, King Z, Klamt S, Klipp E, Koehorst JJ, König M, Lakshmanan M, Lee DY, Lee SY, Lee S, Lewis NE, Liu F, Ma H, Machado D, Mahadevan R, Maia P, Mardinoglu A, Medlock GL, Monk JM, Nielsen J, Nielsen LK, Nogales J, Nookaew I, Palsson BO, Papin JA, Patil KR, Poolman M, Price ND, Resendis-Antonio O, Richelle A, Rocha I, Sánchez BJ, Schaap PJ, Sheriff RSM, Shoaie S, Sonnenschein N, Teusink B, Vilaça P, Vik JO, Wodke JAH, Xavier JC, Yuan Q, Zakhartsev M, and Zhang C
- Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
- Published
- 2020
- Full Text
- View/download PDF
13. Organohalide-respiring Desulfoluna species isolated from marine environments.
- Author
-
Peng P, Goris T, Lu Y, Nijsse B, Burrichter A, Schleheck D, Koehorst JJ, Liu J, Sipkema D, Sinninghe Damste JS, Stams AJM, Häggblom MM, Smidt H, and Atashgahi S
- Subjects
- Bacterial Proteins genetics, Bacterial Proteins metabolism, Corrinoids biosynthesis, Deltaproteobacteria classification, Deltaproteobacteria genetics, Halogenation, Multigene Family, Oxidation-Reduction, Proteomics, Deltaproteobacteria isolation & purification, Deltaproteobacteria metabolism, Seawater microbiology, Sulfates metabolism
- Abstract
The genus Desulfoluna comprises two anaerobic sulfate-reducing strains, D. spongiiphila AA1
T and D. butyratoxydans MSL71T , of which only the former was shown to perform organohalide respiration (OHR). Here we isolated a third strain, designated D. spongiiphila strain DBB, from marine intertidal sediment using 1,4-dibromobenzene and sulfate as the electron acceptors and lactate as the electron donor. Each strain harbors three reductive dehalogenase gene clusters (rdhABC) and corrinoid biosynthesis genes in their genomes, and dehalogenated brominated but not chlorinated organohalogens. The Desulfoluna strains maintained OHR in the presence of 20 mM sulfate or 20 mM sulfide, which often negatively affect other organohalide-respiring bacteria. Strain DBB sustained OHR with 2% oxygen in the gas phase, in line with its genetic potential for reactive oxygen species detoxification. Reverse transcription-quantitative PCR revealed differential induction of rdhA genes in strain DBB in response to 1,4-dibromobenzene or 2,6-dibromophenol. Proteomic analysis confirmed expression of rdhA1 with 1,4-dibromobenzene, and revealed a partially shared electron transport chain from lactate to 1,4-dibromobenzene and sulfate, which may explain accelerated OHR during concurrent sulfate reduction. Versatility in using electron donors, de novo corrinoid biosynthesis, resistance to sulfate, sulfide and oxygen, and concurrent sulfate reduction and OHR may confer an advantage to marine Desulfoluna strains.- Published
- 2020
- Full Text
- View/download PDF
14. MEMOTE for standardized genome-scale metabolic model testing.
- Author
-
Lieven C, Beber ME, Olivier BG, Bergmann FT, Ataman M, Babaei P, Bartell JA, Blank LM, Chauhan S, Correia K, Diener C, Dräger A, Ebert BE, Edirisinghe JN, Faria JP, Feist AM, Fengos G, Fleming RMT, García-Jiménez B, Hatzimanikatis V, van Helvoirt W, Henry CS, Hermjakob H, Herrgård MJ, Kaafarani A, Kim HU, King Z, Klamt S, Klipp E, Koehorst JJ, König M, Lakshmanan M, Lee DY, Lee SY, Lee S, Lewis NE, Liu F, Ma H, Machado D, Mahadevan R, Maia P, Mardinoglu A, Medlock GL, Monk JM, Nielsen J, Nielsen LK, Nogales J, Nookaew I, Palsson BO, Papin JA, Patil KR, Poolman M, Price ND, Resendis-Antonio O, Richelle A, Rocha I, Sánchez BJ, Schaap PJ, Malik Sheriff RS, Shoaie S, Sonnenschein N, Teusink B, Vilaça P, Vik JO, Wodke JAH, Xavier JC, Yuan Q, Zakhartsev M, and Zhang C
- Subjects
- Genome, Models, Biological, Molecular Sequence Annotation, Workflow, Computational Biology methods, Metabolic Networks and Pathways
- Published
- 2020
- Full Text
- View/download PDF
15. NG-Tax 2.0: A Semantic Framework for High-Throughput Amplicon Analysis.
- Author
-
Poncheewin W, Hermes GDA, van Dam JCJ, Koehorst JJ, Smidt H, and Schaap PJ
- Abstract
NG-Tax 2.0 is a semantic framework for FAIR high-throughput analysis and classification of marker gene amplicon sequences including bacterial and archaeal 16S ribosomal RNA (rRNA), eukaryotic 18S rRNA and ribosomal intergenic transcribed spacer sequences. It can directly use single or merged reads, paired-end reads and unmerged paired-end reads from long range fragments as input to generate de novo amplicon sequence variants (ASV). Using the RDF data model, ASV's can be automatically stored in a graph database as objects that link ASV sequences with the full data-wise and element-wise provenance, thereby achieving the level of interoperability required to utilize such data to its full potential. The graph database can be directly queried, allowing for comparative analyses of over thousands of samples and is connected with an interactive Rshiny toolbox for analysis and visualization of (meta) data. Additionally, NG-Tax 2.0 exports an extended BIOM 1.0 (JSON) file as starting point for further analyses by other means. The extended BIOM file contains new attribute types to include information about the command arguments used, the sequences of the ASVs formed, classification confidence scores and is backwards compatible. The performance of NG-Tax 2.0 was compared with DADA2, using the plugin in the QIIME 2 analysis pipeline. Fourteen 16S rRNA gene amplicon mock community samples were obtained from the literature and evaluated. Precision of NG-Tax 2.0 was significantly higher with an average of 0.95 vs 0.58 for QIIME2-DADA2 while recall was comparable with an average of 0.85 and 0.77, respectively. NG-Tax 2.0 is written in Java. The code, the ontology, a Galaxy platform implementation, the analysis toolbox, tutorials and example SPARQL queries are freely available at http://wurssb.gitlab.io/ngtax under the MIT License., (Copyright © 2020 Poncheewin, Hermes, van Dam, Koehorst, Smidt and Schaap.)
- Published
- 2020
- Full Text
- View/download PDF
16. Metabolic shift induced by synthetic co-cultivation promotes high yield of chain elongated acids from syngas.
- Author
-
Diender M, Parera Olm I, Gelderloos M, Koehorst JJ, Schaap PJ, Stams AJM, and Sousa DZ
- Abstract
Bio-catalytic processes for sustainable production of chemicals and fuels receive increased attention within the concept of circular economy. Strategies to improve these production processes include genetic engineering of bio-catalysts or process technological optimization. Alternatively, synthetic microbial co-cultures can be used to enhance production of chemicals of interest. It remains often unclear however how microbe to microbe interactions affect the overall production process and how this can be further exploited for application. In the present study we explored the microbial interaction in a synthetic co-culture of Clostridium autoethanogenum and Clostridium kluyveri, producing chain elongated products from carbon monoxide. Monocultures of C. autoethanogenum converted CO to acetate and traces of ethanol, while during co-cultivation with C. kluyveri, it shifted its metabolism significantly towards solventogenesis. In C. autoethanogenum, expression of the genes involved in the central carbon- and energy-metabolism remained unchanged during co-cultivation compared to monoculture condition. Therefore the shift in the metabolic flux of C. autoethanogenum appears to be regulated by thermodynamics, and results from the continuous removal of ethanol by C. kluyveri. This trait could be further exploited, driving the metabolism of C. autoethanogenum to solely ethanol formation during co-cultivation, resulting in a high yield of chain elongated products from CO-derived electrons. This research highlights the important role of thermodynamic interactions in (synthetic) mixed microbial communities and shows that this can be exploited to promote desired conversions.
- Published
- 2019
- Full Text
- View/download PDF
17. The Empusa code generator and its application to GBOL, an extendable ontology for genome annotation.
- Author
-
van Dam JCJ, Koehorst JJ, Vik JO, Martins Dos Santos VAP, Schaap PJ, and Suarez-Diez M
- Subjects
- Animals, Humans, Molecular Sequence Annotation, Gene Ontology, Genome, Software
- Abstract
The RDF data model facilitates integration of diverse data available in structured and semi-structured formats. To obtain a coherent RDF graph the chosen ontology must be consistently applied. However, addition of new diverse data causes the ontology to evolve, which could lead to accumulation of unintended erroneous composites. Thus, there is a need for a gate keeping system that compares the intended content described in the ontology with the actual content of the resource. The Empusa code generator facilitates creation of composite RDF resources from disparate sources. Empusa can convert a schema into an associated application programming interface (API), that can be used to perform data consistency checks and generates Markdown documentation to make persistent URLs resolvable. Using Empusa consistency is ensured within and between the ontology and the content of the resource. As an illustration of the potential of Empusa, we present the Genome Biology Ontology Language (GBOL). GBOL uses and extends current ontologies to provide a formal representation of genomic entities, along with their properties, relations and provenance.
- Published
- 2019
- Full Text
- View/download PDF
18. Diversity of tryptophan halogenases in sponges of the genus Aplysina.
- Author
-
Gutleben J, Koehorst JJ, McPherson K, Pomponi S, Wijffels RH, Smidt H, and Sipkema D
- Subjects
- Actinobacteria isolation & purification, Animals, Caribbean Region, Chloroflexi isolation & purification, Cyanobacteria isolation & purification, Hydrolases chemistry, Phylogeny, Porifera enzymology, Proteobacteria isolation & purification, Symbiosis, Actinobacteria enzymology, Chloroflexi enzymology, Cyanobacteria enzymology, Oxidoreductases chemistry, Porifera microbiology, Proteobacteria enzymology
- Abstract
Marine sponges are a prolific source of novel enzymes with promising biotechnological potential. Especially halogenases, which are key enzymes in the biosynthesis of brominated and chlorinated secondary metabolites, possess interesting properties towards the production of pharmaceuticals that are often halogenated. In this study we used a polymerase chain reaction (PCR)-based screening to simultaneously examine and compare the richness and diversity of putative tryptophan halogenase protein sequences and bacterial community structures of six Aplysina species from the Mediterranean and Caribbean seas. At the phylum level, bacterial community composition was similar amongst all investigated species and predominated by Actinobacteria, Chloroflexi, Cyanobacteria, Gemmatimonadetes, and Proteobacteria. We detected four phylogenetically diverse clades of putative tryptophan halogenase protein sequences, which were only distantly related to previously reported halogenases. The Mediterranean species Aplysina aerophoba harbored unique halogenase sequences, of which the most predominant was related to a sponge-associated Psychrobacter-derived sequence. In contrast, the Caribbean species shared numerous novel halogenase sequence variants and exhibited a highly similar bacterial community composition at the operational taxonomic unit (OTU) level. Correlations of relative abundances of halogenases with those of bacterial taxa suggest that prominent sponge symbiotic bacteria, including Chloroflexi and Actinobacteria, are putative producers of the detected enzymes and may thus contribute to the chemical defense of their host., (© FEMS 2019.)
- Published
- 2019
- Full Text
- View/download PDF
19. SAPP: functional genome annotation and analysis through a semantic framework using FAIR principles.
- Author
-
Koehorst JJ, van Dam JCJ, Saccenti E, Martins Dos Santos VAP, Suarez-Diez M, and Schaap PJ
- Subjects
- Semantics, Genomics methods, Molecular Sequence Annotation, Software
- Abstract
Summary: To unlock the full potential of genome data and to enhance data interoperability and reusability of genome annotations we have developed SAPP, a Semantic Annotation Platform with Provenance. SAPP is designed as an infrastructure supporting FAIR de novo computational genomics but can also be used to process and analyze existing genome annotations. SAPP automatically predicts, tracks and stores structural and functional annotations and associated dataset- and element-wise provenance in a Linked Data format, thereby enabling information mining and retrieval with Semantic Web technologies. This greatly reduces the administrative burden of handling multiple analysis tools and versions thereof and facilitates multi-level large scale comparative analysis., Availability and Implementation: SAPP is written in JAVA and freely available at https://gitlab.com/sapp and runs on Unix-like operating systems. The documentation, examples and a tutorial are available at https://sapp.gitlab.io., Contact: jasperkoehorst@gmail.com or peter.schaap@wur.nl.
- Published
- 2018
- Full Text
- View/download PDF
20. Comparative Genomics Highlights Symbiotic Capacities and High Metabolic Flexibility of the Marine Genus Pseudovibrio.
- Author
-
Versluis D, Nijsse B, Naim MA, Koehorst JJ, Wiese J, Imhoff JF, Schaap PJ, van Passel MWJ, Smidt H, and Sipkema D
- Subjects
- Animals, Drug Resistance, Bacterial, Genome, Bacterial, Genomics, Multigene Family, Porifera physiology, Quorum Sensing, Rhodobacteraceae physiology, Secondary Metabolism, Porifera microbiology, Rhodobacteraceae genetics, Symbiosis
- Abstract
Pseudovibrio is a marine bacterial genus members of which are predominantly isolated from sessile marine animals, and particularly sponges. It has been hypothesized that Pseudovibrio spp. form mutualistic relationships with their hosts. Here, we studied Pseudovibrio phylogeny and genetic adaptations that may play a role in host colonization by comparative genomics of 31 Pseudovibrio strains, including 25 sponge isolates. All genomes were highly similar in terms of encoded core metabolic pathways, albeit with substantial differences in overall gene content. Based on gene composition, Pseudovibrio spp. clustered by geographic region, indicating geographic speciation. Furthermore, the fact that isolates from the Mediterranean Sea clustered by sponge species suggested host-specific adaptation or colonization. Genome analyses suggest that Pseudovibrio hongkongensis UST20140214-015BT is only distantly related to other Pseudovibrio spp., thereby challenging its status as typical Pseudovibrio member. All Pseudovibrio genomes were found to encode numerous proteins with SEL1 and tetratricopeptide repeats, which have been suggested to play a role in host colonization. For evasion of the host immune system, Pseudovibrio spp. may depend on type III, IV, and VI secretion systems that can inject effector molecules into eukaryotic cells. Furthermore, Pseudovibrio genomes carry on average seven secondary metabolite biosynthesis clusters, reinforcing the role of Pseudovibrio spp. as potential producers of novel bioactive compounds. Tropodithietic acid, bacteriocin, and terpene biosynthesis clusters were highly conserved within the genus, suggesting an essential role in survival, for example through growth inhibition of bacterial competitors. Taken together, these results support the hypothesis that Pseudovibrio spp. have mutualistic relations with sponges., (© The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)
- Published
- 2018
- Full Text
- View/download PDF
21. Concurrent Haloalkanoate Degradation and Chlorate Reduction by Pseudomonas chloritidismutans AW-1 T .
- Author
-
Peng P, Zheng Y, Koehorst JJ, Schaap PJ, Stams AJM, Smidt H, and Atashgahi S
- Subjects
- Amino Acid Sequence, Bacterial Proteins chemistry, Bacterial Proteins genetics, Bacterial Proteins metabolism, Biodegradation, Environmental, Hydrolases chemistry, Hydrolases genetics, Hydrolases metabolism, Molecular Sequence Data, Oxidation-Reduction, Oxygen metabolism, Pseudomonas chemistry, Pseudomonas enzymology, Pseudomonas genetics, Sequence Alignment, Chlorates metabolism, Halogens metabolism, Pseudomonas metabolism
- Abstract
Haloalkanoates are environmental pollutants that can be degraded aerobically by microorganisms producing hydrolytic dehalogenases. However, there is a lack of information about the anaerobic degradation of haloalkanoates. Genome analysis of Pseudomonas chloritidismutans AW-1
T , a facultative anaerobic chlorate-reducing bacterium, showed the presence of two putative haloacid dehalogenase genes, the l-DEX gene and dehI , encoding an l-2-haloacid dehalogenase (l-DEX) and a halocarboxylic acid dehydrogenase (DehI), respectively. Hence, we studied the concurrent degradation of haloalkanoates and chlorate as a yet-unexplored trait of strain AW-1T The deduced amino acid sequences of l-DEX and DehI revealed 33 to 37% and 26 to 86% identities with biochemically/structurally characterized l-DEX and the d- and dl-2-haloacid dehalogenase enzymes, respectively. Physiological experiments confirmed that strain AW-1T can grow on chloroacetate, bromoacetate, and both l- and d-α-halogenated propionates with chlorate as an electron acceptor. Interestingly, growth and haloalkanoate degradation were generally faster with chlorate as an electron acceptor than with oxygen as an electron acceptor. In line with this, analyses of l-DEX and DehI dehalogenase activities using cell-free extract (CFE) of strain AW-1T grown on dl-2-chloropropionate under chlorate-reducing conditions showed up to 3.5-fold higher dehalogenase activity than the CFE obtained from AW-1T cells grown on dl-2-chloropropionate under aerobic conditions. Reverse transcription-quantitative PCR showed that the l-DEX gene was expressed constitutively independently of the electron donor (haloalkanoates or acetate) or acceptor (chlorate or oxygen), whereas the expression of dehI was induced by haloalkanoates. Concurrent degradation of organic and inorganic halogenated compounds by strain AW-1T represents a unique metabolic capacity in a single bacterium, providing a new piece of the puzzle of the microbial halogen cycle. IMPORTANCE Halogenated organic and inorganic compounds are important environmental pollutants that have carcinogenic and genotoxic effects on both animals and humans. Previous research studied the degradation of organic and inorganic halogenated compounds separately but not concurrently. This study shows concurrent degradation of halogenated alkanoates and chlorate as an electron donor and acceptor, respectively, coupled to growth in a single bacterium, Pseudomonas chloritidismutans AW-1T Hence, besides biogenesis of molecular oxygen from chlorate reduction enabling a distinctive placement of strain AW-1T between aerobic and anaerobic microorganisms, we can now add another unique metabolic potential of this bacterium to the roster. The degradation of different halogenated compounds under anoxic conditions by a single bacterium is also of interest for the natural halogen cycle in different aquatic and terrestrial ecosystems where ample natural production of halogenated compounds has been documented., (Copyright © 2017 American Society for Microbiology.)- Published
- 2017
- Full Text
- View/download PDF
22. Persistence of Functional Protein Domains in Mycoplasma Species and their Role in Host Specificity and Synthetic Minimal Life.
- Author
-
Kamminga T, Koehorst JJ, Vermeij P, Slagman SJ, Martins Dos Santos VA, Bijlsma JJ, and Schaap PJ
- Subjects
- Animals, Bacterial Proteins genetics, Genes, Bacterial, Genome Size, Humans, Mycoplasma classification, Mycoplasma pathogenicity, Mycoplasma Infections, Phylogeny, Proteome, RNA, Ribosomal, 16S genetics, Species Specificity, Spiroplasma genetics, Spiroplasma physiology, Swine, Genome, Bacterial genetics, Host Specificity, Host-Pathogen Interactions genetics, Host-Pathogen Interactions physiology, Mycoplasma genetics, Mycoplasma metabolism, Protein Domains genetics, Protein Domains physiology
- Abstract
Mycoplasmas are the smallest self-replicating organisms and obligate parasites of a specific vertebrate host. An in-depth analysis of the functional capabilities of mycoplasma species is fundamental to understand how some of simplest forms of life on Earth succeeded in subverting complex hosts with highly sophisticated immune systems. In this study we present a genome-scale comparison, focused on identification of functional protein domains, of 80 publically available mycoplasma genomes which were consistently re-annotated using a standardized annotation pipeline embedded in a semantic framework to keep track of the data provenance. We examined the pan- and core-domainome and studied predicted functional capability in relation to host specificity and phylogenetic distance. We show that the pan- and core-domainome of mycoplasma species is closed. A comparison with the proteome of the "minimal" synthetic bacterium JCVI-Syn3.0 allowed us to classify domains and proteins essential for minimal life. Many of those essential protein domains, essential Domains of Unknown Function (DUFs) and essential hypothetical proteins are not persistent across mycoplasma genomes suggesting that mycoplasma species support alternative domain configurations that bypass their essentiality. Based on the protein domain composition, we could separate mycoplasma species infecting blood and tissue. For selected genomes of tissue infecting mycoplasmas, we could also predict whether the host is ruminant, pig or human. Functionally closely related mycoplasma species, which have a highly similar protein domain repertoire, but different hosts could not be separated. This study provides a concise overview of the functional capabilities of mycoplasma species, which can be used as a basis to further understand host-pathogen interaction or to design synthetic minimal life.
- Published
- 2017
- Full Text
- View/download PDF
23. Complete Genome Sequence of Akkermansia glycaniphila Strain PytT, a Mucin-Degrading Specialist of the Reticulated Python Gut.
- Author
-
Ouwerkerk JP, Koehorst JJ, Schaap PJ, Ritari J, Paulin L, Belzer C, and de Vos WM
- Abstract
Akkermansia glycaniphila is a novel Akkermansia species that was isolated from the intestine of the reticulated python and shares the capacity to degrade mucin with the human strain Akkermansia muciniphila Muc
T Here, we report the complete genome sequence of strain PytT of 3,074,121 bp. The genomic analysis reveals genes for mucin degradation and aerobic respiration., (Copyright © 2017 Ouwerkerk et al.)- Published
- 2017
- Full Text
- View/download PDF
24. Reverse Methanogenesis and Respiration in Methanotrophic Archaea.
- Author
-
Timmers PH, Welte CU, Koehorst JJ, Plugge CM, Jetten MS, and Stams AJ
- Subjects
- Anaerobiosis, Oxidation-Reduction, Archaea metabolism, Methane metabolism
- Abstract
Anaerobic oxidation of methane (AOM) is catalyzed by anaerobic methane-oxidizing archaea (ANME) via a reverse and modified methanogenesis pathway. Methanogens can also reverse the methanogenesis pathway to oxidize methane, but only during net methane production (i.e., "trace methane oxidation"). In turn, ANME can produce methane, but only during net methane oxidation (i.e., enzymatic back flux). Net AOM is exergonic when coupled to an external electron acceptor such as sulfate (ANME-1, ANME-2abc, and ANME-3), nitrate (ANME-2d), or metal (oxides). In this review, the reversibility of the methanogenesis pathway and essential differences between ANME and methanogens are described by combining published information with domain based (meta)genome comparison of archaeal methanotrophs and selected archaea. These differences include abundances and special structure of methyl coenzyme M reductase and of multiheme cytochromes and the presence of menaquinones or methanophenazines. ANME-2a and ANME-2d can use electron acceptors other than sulfate or nitrate for AOM, respectively. Environmental studies suggest that ANME-2d are also involved in sulfate-dependent AOM. ANME-1 seem to use a different mechanism for disposal of electrons and possibly are less versatile in electron acceptors use than ANME-2. Future research will shed light on the molecular basis of reversal of the methanogenic pathway and electron transfer in different ANME types., Competing Interests: The authors declare that there is no conflict of interests regarding the publication of this paper.
- Published
- 2017
- Full Text
- View/download PDF
25. Comparison of 432 Pseudomonas strains through integration of genomic, functional, metabolic and expression data.
- Author
-
Koehorst JJ, van Dam JC, van Heck RG, Saccenti E, Dos Santos VA, Suarez-Diez M, and Schaap PJ
- Subjects
- Humans, Molecular Sequence Annotation, Phylogeny, Pseudomonas classification, Workflow, Computational Biology methods, Energy Metabolism, Gene Expression Regulation, Bacterial, Genome, Bacterial, Genomics methods, Pseudomonas genetics, Pseudomonas metabolism
- Abstract
Pseudomonas is a highly versatile genus containing species that can be harmful to humans and plants while others are widely used for bioengineering and bioremediation. We analysed 432 sequenced Pseudomonas strains by integrating results from a large scale functional comparison using protein domains with data from six metabolic models, nearly a thousand transcriptome measurements and four large scale transposon mutagenesis experiments. Through heterogeneous data integration we linked gene essentiality, persistence and expression variability. The pan-genome of Pseudomonas is closed indicating a limited role of horizontal gene transfer in the evolutionary history of this genus. A large fraction of essential genes are highly persistent, still non essential genes represent a considerable fraction of the core-genome. Our results emphasize the power of integrating large scale comparative functional genomics with heterogeneous data for exploring bacterial diversity and versatility.
- Published
- 2016
- Full Text
- View/download PDF
26. Genome and proteome analysis of Pseudomonas chloritidismutans AW-1 T that grows on n-decane with chlorate or oxygen as electron acceptor.
- Author
-
Mehboob F, Oosterkamp MJ, Koehorst JJ, Farrakh S, Veuskens T, Plugge CM, Boeren S, de Vos WM, Schraa G, Stams AJ, and Schaap PJ
- Subjects
- Cytochrome P-450 CYP4A genetics, Cytochrome P-450 CYP4A metabolism, Gene Expression Profiling, Genome, Bacterial genetics, Oxidants, Oxidation-Reduction, Oxidoreductases genetics, Oxidoreductases metabolism, Phylogeny, Proteome metabolism, Proteomics, Pseudomonas stutzeri genetics, Alkanes metabolism, Chlorates metabolism, Oxygen metabolism, Pseudomonas stutzeri growth & development, Pseudomonas stutzeri metabolism
- Abstract
Growth of Pseudomonas chloritidismutans AW-1
T on C7 to C12 n-alkanes with oxygen or chlorate as electron acceptor was studied by genome and proteome analysis. Whole genome shotgun sequencing resulted in a 5 Mbp assembled sequence with a G + C content of 62.5%. The automatic annotation identified 4767 protein-encoding genes and a putative function could be assigned to almost 80% of the predicted proteins. The distinct phylogenetic position of P. chloritidismutans AW-1T within the Pseudomonas stutzeri cluster became clear by comparison of average nucleotide identity values of sequenced genomes. Analysis of the proteome of P. chloritidismutans AW-1T showed the versatility of this bacterium to adapt to aerobic and anaerobic growth conditions with acetate or n-decane as substrates. All enzymes involved in the alkane oxidation pathway were identified. An alkane monooxygenase was detected in n-decane-grown cells, but not in acetate-grown cells. The enzyme was found when grown in the presence of oxygen or chlorate, indicating that under both conditions an oxygenase-mediated pathway is employed for alkane degradation. Proteomic and biochemical data also showed that both chlorate reductase and chlorite dismutase are constitutively present, but most abundant under chlorate-reducing conditions., (© 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.)- Published
- 2016
- Full Text
- View/download PDF
27. Complete genome sequence of thermophilic Bacillus smithii type strain DSM 4216(T).
- Author
-
Bosma EF, Koehorst JJ, van Hijum SA, Renckens B, Vriesendorp B, van de Weijer AH, Schaap PJ, de Vos WM, van der Oost J, and van Kranenburg R
- Abstract
Bacillus smithii is a facultatively anaerobic, thermophilic bacterium able to use a variety of sugars that can be derived from lignocellulosic feedstocks. Being genetically accessible, it is a potential new host for biotechnological production of green chemicals from renewable resources. We determined the complete genomic sequence of the B. smithii type strain DSM 4216(T), which consists of a 3,368,778 bp chromosome (GenBank accession number CP012024.1) and a 12,514 bp plasmid (GenBank accession number CP012025.1), together encoding 3880 genes. Genome annotation via RAST was complemented by a protein domain analysis. Some unique features of B. smithii central metabolism in comparison to related organisms included the lack of a standard acetate production pathway with no apparent pyruvate formate lyase, phosphotransacetylase, and acetate kinase genes, while acetate was the second fermentation product.
- Published
- 2016
- Full Text
- View/download PDF
28. Protein domain architectures provide a fast, efficient and scalable alternative to sequence-based methods for comparative functional genomics.
- Author
-
Koehorst JJ, Saccenti E, Schaap PJ, Martins Dos Santos VA, and Suarez-Diez M
- Abstract
A functional comparative genome analysis is essential to understand the mechanisms underlying bacterial evolution and adaptation. Detection of functional orthologs using standard global sequence similarity methods faces several problems; the need for defining arbitrary acceptance thresholds for similarity and alignment length, lateral gene acquisition and the high computational cost for finding bi-directional best matches at a large scale. We investigated the use of protein domain architectures for large scale functional comparative analysis as an alternative method. The performance of both approaches was assessed through functional comparison of 446 bacterial genomes sampled at different taxonomic levels. We show that protein domain architectures provide a fast and efficient alternative to methods based on sequence similarity to identify groups of functionally equivalent proteins within and across taxonomic boundaries. As the computational cost scales linearly, and not quadratically with the number of genomes, it is suitable for large scale comparative analysis. Running both methods in parallel pinpoints potential functional adaptations that may add to bacterial fitness.
- Published
- 2016
- Full Text
- View/download PDF
29. Protein domain architectures provide a fast, efficient and scalable alternative to sequence-based methods for comparative functional genomics.
- Author
-
Koehorst JJ, Saccenti E, Schaap PJ, Martins Dos Santos VA, and Suarez-Diez M
- Abstract
A functional comparative genome analysis is essential to understand the mechanisms underlying bacterial evolution and adaptation. Detection of functional orthologs using standard global sequence similarity methods faces several problems; the need for defining arbitrary acceptance thresholds for similarity and alignment length, lateral gene acquisition and the high computational cost for finding bi-directional best matches at a large scale. We investigated the use of protein domain architectures for large scale functional comparative analysis as an alternative method. The performance of both approaches was assessed through functional comparison of 446 bacterial genomes sampled at different taxonomic levels. We show that protein domain architectures provide a fast and efficient alternative to methods based on sequence similarity to identify groups of functionally equivalent proteins within and across taxonomic bounderies. As the computational cost scales linearly, and not quadratically with the number of genomes, it is suitable for large scale comparative analysis. Running both methods in parallel pinpoints potential functional adaptations that may add to bacterial fitness., Competing Interests: No competing interests were disclosed.
- Published
- 2016
- Full Text
- View/download PDF
30. Protein domain architectures provide a fast, efficient and scalable alternative to sequence-based methods for comparative functional genomics.
- Author
-
Koehorst JJ, Saccenti E, Schaap PJ, Martins Dos Santos VAP, and Suarez-Diez M
- Abstract
A functional comparative genome analysis is essential to understand the mechanisms underlying bacterial evolution and adaptation. Detection of functional orthologs using standard global sequence similarity methods faces several problems; the need for defining arbitrary acceptance thresholds for similarity and alignment length, lateral gene acquisition and the high computational cost for finding bi-directional best matches at a large scale. We investigated the use of protein domain architectures for large scale functional comparative analysis as an alternative method. The performance of both approaches was assessed through functional comparison of 446 bacterial genomes sampled at different taxonomic levels. We show that protein domain architectures provide a fast and efficient alternative to methods based on sequence similarity to identify groups of functionally equivalent proteins within and across taxonomic boundaries, and it is suitable for large scale comparative analysis. Running both methods in parallel pinpoints potential functional adaptations that may add to bacterial fitness., Competing Interests: Competing interests: No competing interests were disclosed.
- Published
- 2016
- Full Text
- View/download PDF
31. RDF2Graph a tool to recover, understand and validate the ontology of an RDF resource.
- Author
-
van Dam JC, Koehorst JJ, Schaap PJ, Martins Dos Santos VA, and Suarez-Diez M
- Abstract
Background: Semantic web technologies have a tremendous potential for the integration of heterogeneous data sets. Therefore, an increasing number of widely used biological resources are becoming available in the RDF data model. There are however, no tools available that provide structural overviews of these resources. Such structural overviews are essential to efficiently query these resources and to assess their structural integrity and design, thereby strengthening their use and potential., Results: Here we present RDF2Graph, a tool that automatically recovers the structure of an RDF resource. The generated overview allows to create complex queries on these resources and to structurally validate newly created resources., Conclusion: RDF2Graph facilitates the creation of complex queries thereby enabling access to knowledge stored across multiple RDF resources. RDF2Graph facilitates creation of high quality resources and resource descriptions, which in turn increases usability of the semantic web technologies.
- Published
- 2015
- Full Text
- View/download PDF
32. Assessing the Metabolic Diversity of Streptococcus from a Protein Domain Point of View.
- Author
-
Saccenti E, Nieuwenhuijse D, Koehorst JJ, Martins dos Santos VA, and Schaap PJ
- Subjects
- Bacterial Proteins genetics, Protein Structure, Tertiary, Species Specificity, Streptococcus suis genetics, Adaptation, Physiological, Bacterial Proteins metabolism, Streptococcus suis metabolism
- Abstract
Understanding the diversity and robustness of the metabolism of bacteria is fundamental for understanding how bacteria evolve and adapt to different environments. In this study, we characterised 121 Streptococcus strains and studied metabolic diversity from a protein domain perspective. Metabolic pathways were described in terms of the promiscuity of domains participating in metabolic pathways that were inferred to be functional. Promiscuity was defined by adapting existing measures based on domain abundance and versatility. The approach proved to be successful in capturing bacterial metabolic flexibility and species diversity, indicating that it can be described in terms of reuse and sharing functional domains in different proteins involved in metabolic activity. Additionally, we showed striking differences among metabolic organisation of the pathogenic serotype 2 Streptococcus suis and other strains.
- Published
- 2015
- Full Text
- View/download PDF
33. Comparative genomics of Streptococcus pyogenes M1 isolates differing in virulence and propensity to cause systemic infection in mice.
- Author
-
Fiebig A, Loof TG, Babbar A, Itzek A, Koehorst JJ, Schaap PJ, and Nitsche-Schmitz DP
- Subjects
- Animals, Bacterial Proteins genetics, Bacterial Proteins metabolism, Bacteriophages genetics, Exotoxins genetics, Exotoxins metabolism, Male, Mice, Mice, Inbred C57BL, Mutation, Streptococcal Infections microbiology, Streptococcal Infections pathology, Streptococcus pyogenes isolation & purification, Comparative Genomic Hybridization methods, Gene Expression Regulation, Bacterial, Streptococcus pyogenes genetics
- Abstract
Streptococcus pyogenes serotype M1 is a frequent cause of severe infections in humans. Some M1 isolates are pathogenic in mice and used in studies on infection pathogenesis. We observed marked differences in murine infections caused by M1 strain SF370, 5448, 5448AP or AP1 which prompted us to sequence the whole genome of isolates 5448 and AP1 for comparative analysis. Strain 5448 is known to acquire inactivating mutations in the CovRS two-component system during mouse infection, producing hypervirulent progeny such as 5448AP. Isolates AP1 and 5448AP, more than 5448, caused disseminating infections that became systemic and lethal. SF370 was not pathogenic. Phages caused gross genetic differences and increased the gene content of AP1 by 8% as compared to 5448 and SF370. Each of six examined M1 genomes contained two CRISPR-Cas systems. Phage insertion destroyed a type II CRISPR-Cas system in AP1 and other strains of serotypes M1, M3, M6 and M24, but not in M1 strains 5448, SF370, MGAS5005, A20 or M1 476. A resulting impaired defence against invading genetic elements could have led to the wealth of phages in AP1. AP1 lacks genetic features of the MGAS5005-like clonal complex including the streptodornase that drives selection for hypervirulent clones with inactivated CovRS system. Still, inactivating mutations in covS were a common genetic feature of AP1 and the MGAS5005-like isolate 5448AP. Abolished expression of the cysteine proteinase SpeB, due to CovRS inactivation could be a common cause for hypervirulence of the two isolates. Moreover, an additional protein H-coding gene and a mutation in the regulator gene rofA distinguished AP1 form other M1 isolates. In conclusion, hypervirulence of S. pyogenes M1 in mice is not limited to the MGAS5005-like genotype., (Copyright © 2015 Elsevier GmbH. All rights reserved.)
- Published
- 2015
- Full Text
- View/download PDF
34. Effects of Argonaute on Gene Expression in Thermus thermophilus.
- Author
-
Swarts DC, Koehorst JJ, Westra ER, Schaap PJ, and van der Oost J
- Subjects
- Base Sequence, CRISPR-Cas Systems genetics, DNA metabolism, Genes, Bacterial, Genetic Loci, Molecular Sequence Data, Mutation genetics, Plasmids metabolism, RNA, Bacterial metabolism, Stochastic Processes, Up-Regulation genetics, Argonaute Proteins metabolism, Bacterial Proteins metabolism, Gene Expression Regulation, Bacterial, Thermus thermophilus genetics
- Abstract
Background: Eukaryotic Argonaute proteins mediate RNA-guided RNA interference, allowing both regulation of host gene expression and defense against invading mobile genetic elements. Recently, it has become evident that prokaryotic Argonaute homologs mediate DNA-guided DNA interference, and play a role in host defense. Argonaute of the bacterium Thermus thermophilus (TtAgo) targets invading plasmid DNA during and after transformation. Using small interfering DNA guides, TtAgo can cleave single and double stranded DNAs. Although TtAgo additionally has been demonstrated to cleave RNA targets complementary to its DNA guide in vitro, RNA targeting by TtAgo has not been demonstrated in vivo., Methods: To investigate if TtAgo also has the potential to control RNA levels, we analyzed RNA-seq data derived from cultures of four T. thermophilus strain HB27 variants: wild type, TtAgo knockout (Δago), and either strain transformed with a plasmid. Additionally we determined the effect of TtAgo on expression of plasmid-encoded RNA and plasmid DNA levels., Results: In the absence of exogenous DNA (plasmid), TtAgo presence or absence had no effect on gene expression levels. When plasmid DNA is present, TtAgo reduces plasmid DNA levels 4-fold, and a corresponding reduction of plasmid gene transcript levels was observed. We therefore conclude that TtAgo interferes with plasmid DNA, but not with plasmid-encoded RNA. Interestingly, TtAgo presence stimulates expression of specific endogenous genes, but only when exogenous plasmid DNA was present. Specifically, the presence of TtAgo directly or indirectly stimulates expression of CRISPR loci and associated genes, some of which are involved in CRISPR adaptation. This suggests that TtAgo-mediated interference with plasmid DNA stimulates CRISPR adaptation.
- Published
- 2015
- Full Text
- View/download PDF
35. A genomic view on syntrophic versus non-syntrophic lifestyle in anaerobic fatty acid degrading communities.
- Author
-
Worm P, Koehorst JJ, Visser M, Sedano-Núñez VT, Schaap PJ, Plugge CM, Sousa DZ, and Stams AJM
- Subjects
- Anaerobiosis, Bacteria, Anaerobic classification, Bacteria, Anaerobic metabolism, Butyrates metabolism, Ecosystem, Hydrogen metabolism, Methane metabolism, Phylogeny, Bacteria, Anaerobic genetics, Fatty Acids metabolism, Genome, Bacterial genetics, Genomics methods
- Abstract
In sulfate-reducing and methanogenic environments complex biopolymers are hydrolyzed and degraded by fermentative micro-organisms that produce hydrogen, carbon dioxide and short chain fatty acids. Degradation of short chain fatty acids can be coupled to methanogenesis or to sulfate-reduction. Here we study from a genome perspective why some of these micro-organisms are able to grow in syntrophy with methanogens and others are not. Bacterial strains were selected based on genome availability and upon their ability to grow on short chain fatty acids alone or in syntrophic association with methanogens. Systematic functional domain profiling allowed us to shed light on this fundamental and ecologically important question. Extra-cytoplasmic formate dehydrogenases (InterPro domain number; IPR006443), including their maturation protein FdhE (IPR024064 and IPR006452) is a typical difference between syntrophic and non-syntrophic butyrate and propionate degraders. Furthermore, two domains with a currently unknown function seem to be associated with the ability of syntrophic growth. One is putatively involved in capsule or biofilm production (IPR019079) and a second in cell division, shape-determination or sporulation (IPR018365). The sulfate-reducing bacteria Desulfobacterium autotrophicum HRM2, Desulfomonile tiedjei and Desulfosporosinus meridiei were never tested for syntrophic growth, but all crucial domains were found in their genomes, which suggests their possible ability to grow in syntrophic association with methanogens. In addition, profiling domains involved in electron transfer mechanisms revealed the important role of the Rnf-complex and the formate transporter in syntrophy, and indicate that DUF224 may have a role in electron transfer in bacteria other than Syntrophomonas wolfei as well. This article is a part of a Special Issue entitled: 18th European Bioenergetics Conference (Biochim. Biophys. Acta, Volume 1837, Issue 7, July 2014)., (Copyright © 2014. Published by Elsevier B.V.)
- Published
- 2014
- Full Text
- View/download PDF
36. RNA targeting by the type III-A CRISPR-Cas Csm complex of Thermus thermophilus.
- Author
-
Staals RH, Zhu Y, Taylor DW, Kornfeld JE, Sharma K, Barendregt A, Koehorst JJ, Vlot M, Neupane N, Varossieau K, Sakamoto K, Suzuki T, Dohmae N, Yokoyama S, Schaap PJ, Urlaub H, Heck AJ, Nogales E, Doudna JA, Shinkai A, and van der Oost J
- Subjects
- Amino Acid Sequence, Bacterial Proteins chemistry, Bacterial Proteins ultrastructure, Base Sequence, CRISPR-Associated Proteins chemistry, CRISPR-Associated Proteins ultrastructure, Endoribonucleases chemistry, Endoribonucleases metabolism, Endoribonucleases ultrastructure, Microscopy, Electron, Models, Molecular, Molecular Sequence Data, Protein Binding, Protein Structure, Quaternary, RNA, Bacterial genetics, RNA, Bacterial metabolism, Thermus thermophilus enzymology, Bacterial Proteins metabolism, CRISPR-Associated Proteins metabolism, Clustered Regularly Interspaced Short Palindromic Repeats, RNA Cleavage, Thermus thermophilus genetics
- Abstract
CRISPR-Cas is a prokaryotic adaptive immune system that provides sequence-specific defense against foreign nucleic acids. Here we report the structure and function of the effector complex of the Type III-A CRISPR-Cas system of Thermus thermophilus: the Csm complex (TtCsm). TtCsm is composed of five different protein subunits (Csm1-Csm5) with an uneven stoichiometry and a single crRNA of variable size (35-53 nt). The TtCsm crRNA content is similar to the Type III-B Cmr complex, indicating that crRNAs are shared among different subtypes. A negative stain EM structure of the TtCsm complex exhibits the characteristic architecture of Type I and Type III CRISPR-associated ribonucleoprotein complexes. crRNA-protein crosslinking studies show extensive contacts between the Csm3 backbone and the bound crRNA. We show that, like TtCmr, TtCsm cleaves complementary target RNAs at multiple sites. Unlike Type I complexes, interference by TtCsm does not proceed via initial base pairing by a seed sequence., (Copyright © 2014 Elsevier Inc. All rights reserved.)
- Published
- 2014
- Full Text
- View/download PDF
37. Genome analyses of the carboxydotrophic sulfate-reducers Desulfotomaculum nigrificans and Desulfotomaculum carboxydivorans and reclassification of Desulfotomaculum caboxydivorans as a later synonym of Desulfotomaculum nigrificans.
- Author
-
Visser M, Parshina SN, Alves JI, Sousa DZ, Pereira IA, Muyzer G, Kuever J, Lebedinsky AV, Koehorst JJ, Worm P, Plugge CM, Schaap PJ, Goodwin LA, Lapidus A, Kyrpides NC, Detter JC, Woyke T, Chain P, Davenport KW, Spring S, Rohde M, Klenk HP, and Stams AJ
- Abstract
Desulfotomaculum nigrificans and D. carboxydivorans are moderately thermophilic members of the polyphyletic spore-forming genus Desulfotomaculum in the family Peptococcaceae. They are phylogenetically very closely related and belong to 'subgroup a' of the Desulfotomaculum cluster 1. D. nigrificans and D. carboxydivorans have a similar growth substrate spectrum; they can grow with glucose and fructose as electron donors in the presence of sulfate. Additionally, both species are able to ferment fructose, although fermentation of glucose is only reported for D. carboxydivorans. D. nigrificans is able to grow with 20% carbon monoxide (CO) coupled to sulfate reduction, while D. carboxydivorans can grow at 100% CO with and without sulfate. Hydrogen is produced during growth with CO by D. carboxydivorans. Here we present a summary of the features of D. nigrificans and D. carboxydivorans together with the description of the complete genome sequencing and annotation of both strains. Moreover, we compared the genomes of both strains to reveal their differences. This comparison led us to propose a reclassification of D. carboxydivorans as a later heterotypic synonym of D. nigrificans.
- Published
- 2014
- Full Text
- View/download PDF
38. Structure and activity of the RNA-targeting Type III-B CRISPR-Cas complex of Thermus thermophilus.
- Author
-
Staals RHJ, Agari Y, Maki-Yonekura S, Zhu Y, Taylor DW, van Duijn E, Barendregt A, Vlot M, Koehorst JJ, Sakamoto K, Masuda A, Dohmae N, Schaap PJ, Doudna JA, Heck AJR, Yonekura K, van der Oost J, and Shinkai A
- Subjects
- Bacterial Proteins chemistry, Bacterial Proteins genetics, CRISPR-Associated Proteins chemistry, CRISPR-Associated Proteins genetics, Clustered Regularly Interspaced Short Palindromic Repeats, High-Throughput Nucleotide Sequencing, Microscopy, Electron, Models, Molecular, Protein Conformation, Protein Subunits, RNA, Bacterial chemistry, RNA, Bacterial genetics, Ribonucleases chemistry, Ribonucleases genetics, Sequence Analysis, RNA, Spectrometry, Mass, Electrospray Ionization, Structure-Activity Relationship, Thermus thermophilus genetics, Bacterial Proteins metabolism, CRISPR-Associated Proteins metabolism, RNA, Bacterial metabolism, Ribonucleases metabolism, Thermus thermophilus metabolism
- Abstract
The CRISPR-Cas system is a prokaryotic host defense system against genetic elements. The Type III-B CRISPR-Cas system of the bacterium Thermus thermophilus, the TtCmr complex, is composed of six different protein subunits (Cmr1-6) and one crRNA with a stoichiometry of Cmr112131445361:crRNA1. The TtCmr complex copurifies with crRNA species of 40 and 46 nt, originating from a distinct subset of CRISPR loci and spacers. The TtCmr complex cleaves the target RNA at multiple sites with 6 nt intervals via a 5' ruler mechanism. Electron microscopy revealed that the structure of TtCmr resembles a "sea worm" and is composed of a Cmr2-3 heterodimer "tail," a helical backbone of Cmr4 subunits capped by Cmr5 subunits, and a curled "head" containing Cmr1 and Cmr6. Despite having a backbone of only four Cmr4 subunits and being both longer and narrower, the overall architecture of TtCmr resembles that of Type I Cascade complexes., (Copyright © 2013 Elsevier Inc. All rights reserved.)
- Published
- 2013
- Full Text
- View/download PDF
39. Differential translation tunes uneven production of operon-encoded proteins.
- Author
-
Quax TE, Wolf YI, Koehorst JJ, Wurtzel O, van der Oost R, Ran W, Blombach F, Makarova KS, Brouns SJ, Forster AC, Wagner EG, Sorek R, Koonin EV, and van der Oost J
- Subjects
- Base Sequence, Codon, Gene Expression, Molecular Sequence Data, Peptide Chain Elongation, Translational genetics, Peptide Chain Initiation, Translational genetics, RNA, Messenger genetics, Ribosomes genetics, Transcription, Genetic, Operon, Protein Biosynthesis genetics, Proteins genetics
- Abstract
Clustering of functionally related genes in operons allows for coregulated gene expression in prokaryotes. This is advantageous when equal amounts of gene products are required. Production of protein complexes with an uneven stoichiometry, however, requires tuning mechanisms to generate subunits in appropriate relative quantities. Using comparative genomic analysis, we show that differential translation is a key determinant of modulated expression of genes clustered in operons and that codon bias generally is the best in silico indicator of unequal protein production. Variable ribosome density profiles of polycistronic transcripts correlate strongly with differential translation patterns. In addition, we provide experimental evidence that de novo initiation of translation can occur at intercistronic sites, allowing for differential translation of any gene irrespective of its position on a polycistronic messenger. Thus, modulation of translation efficiency appears to be a universal mode of control in bacteria and archaea that allows for differential production of operon-encoded proteins., (Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.)
- Published
- 2013
- Full Text
- View/download PDF
40. The Constructor: a web application optimizing cloning strategies based on modules from the registry of standard biological parts.
- Author
-
Hesselman MC, Koehorst JJ, Slijkhuis T, Odoni DI, Hugenholtz F, and van Passel MWJ
- Abstract
Synthetic biology is an emerging field that combines molecular biology with engineering principles, which requires abstraction levels applied to a modular biological componentry. The Registry of Standard Biological Parts harbours such a repository of standardized parts, and thereby facilitates the combination of complex molecular modules to novel genetic circuits and devices. However, since finding the best parts for a pre-determined genetic design can be time consuming, we devised the Constructor, a web tool that recommends the smallest number of cloning steps for pre-designed circuits, and implements user-defined quality checks.We present the Constructor ( http://www.systemsbiology.nl/the_constructor) as a constructive web tool that simplifies the in silico assembly of pre-designed gene circuitries from standard parts, reducing both planning and subsequent cloning time.
- Published
- 2012
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.