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René T. J. M. van der Heijden

Bio: René T. J. M. van der Heijden is an academic researcher from Radboud University Nijmegen. The author has contributed to research in topics: Gene & Comparative genomics. The author has an hindex of 3, co-authored 3 publications receiving 1340 citations.

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Journal ArticleDOI
Herman Jan Pel1, Johannes H. de Winde1, Johannes H. de Winde2, David B. Archer3, Paul S. Dyer3, Gerald Hofmann4, Peter J. Schaap5, Geoffrey Turner6, Ronald P. de Vries7, Richard Albang8, Kaj Albermann8, Mikael Rørdam Andersen4, Jannick Dyrløv Bendtsen9, Jacques A.E. Benen5, Marco A. van den Berg1, Stefaan Breestraat1, Mark X. Caddick10, Roland Contreras11, Michael Cornell12, Pedro M. Coutinho13, Etienne Danchin13, Alfons J. M. Debets5, Peter J. T. Dekker1, Piet W.M. van Dijck1, Alard Van Dijk1, Lubbert Dijkhuizen14, Arnold J. M. Driessen14, Christophe d'Enfert15, Steven Geysens11, Coenie Goosen14, Gert S.P. Groot1, Piet W. J. de Groot16, Thomas Guillemette17, Bernard Henrissat13, Marga Herweijer1, Johannes Petrus Theodorus Wilhelmus Van Den Hombergh1, Cees A. M. J. J. van den Hondel18, René T. J. M. van der Heijden19, Rachel M. van der Kaaij14, Frans M. Klis16, Harrie J. Kools5, Christian P. Kubicek, Patricia Ann van Kuyk18, Jürgen Lauber, Xin Lu, Marc J. E. C. van der Maarel, Rogier Meulenberg1, Hildegard Henna Menke1, Martin Mortimer10, Jens Nielsen4, Stephen G. Oliver12, Maurien M.A. Olsthoorn1, K. Pal20, K. Pal5, Noël Nicolaas Maria Elisabeth Van Peij1, Arthur F. J. Ram18, Ursula Rinas, Johannes Andries Roubos1, Cornelis Maria Jacobus Sagt1, Monika Schmoll, Jibin Sun, David W. Ussery4, János Varga20, Wouter Vervecken11, Peter J.J. Van De Vondervoort18, Holger Wedler, Han A. B. Wösten7, An-Ping Zeng, Albert J. J. van Ooyen1, Jaap Visser, Hein Stam1 
TL;DR: The filamentous fungus Aspergillus niger is widely exploited by the fermentation industry for the production of enzymes and organic acids, particularly citric acid, and the sequenced genome revealed a large number of major facilitator superfamily transporters and fungal zinc binuclear cluster transcription factors.
Abstract: The filamentous fungus Aspergillus niger is widely exploited by the fermentation industry for the production of enzymes and organic acids, particularly citric acid. We sequenced the 33.9-megabase genome of A. niger CBS 513.88, the ancestor of currently used enzyme production strains. A high level of synteny was observed with other aspergilli sequenced. Strong function predictions were made for 6,506 of the 14,165 open reading frames identified. A detailed description of the components of the protein secretion pathway was made and striking differences in the hydrolytic enzyme spectra of aspergilli were observed. A reconstructed metabolic network comprising 1,069 unique reactions illustrates the versatile metabolism of A. niger. Noteworthy is the large number of major facilitator superfamily transporters and fungal zinc binuclear cluster transcription factors, and the presence of putative gene clusters for fumonisin and ochratoxin A synthesis.

1,161 citations

Journal ArticleDOI
TL;DR: A benchmark for orthology prediction, that takes into account the varying levels of orthology between genes, shows that the phylogeny-based high-resolution orthology assignments made by LOFT are reliable.
Abstract: Orthology is one of the cornerstones of gene function prediction. Dividing the phylogenetic relations between genes into either orthologs or paralogs is however an oversimplification. Already in two-species gene-phylogenies, the complicated, non-transitive nature of phylogenetic relations results in inparalogs and outparalogs. For situations with more than two species we lack semantics to specifically describe the phylogenetic relations, let alone to exploit them. Published procedures to extract orthologous groups from phylogenetic trees do not allow identification of orthology at various levels of resolution, nor do they document the relations between the orthologous groups. We introduce "levels of orthology" to describe the multi-level nature of gene relations. This is implemented in a program LOFT (Levels of Orthology From Trees) that assigns hierarchical orthology numbers to genes based on a phylogenetic tree. To decide upon speciation and gene duplication events in a tree LOFT can be instructed either to perform classical species-tree reconciliation or to use the species overlap between partitions in the tree. The hierarchical orthology numbers assigned by LOFT effectively summarize the phylogenetic relations between genes. The resulting high-resolution orthologous groups are depicted in colour, facilitating visual inspection of (large) trees. A benchmark for orthology prediction, that takes into account the varying levels of orthology between genes, shows that the phylogeny-based high-resolution orthology assignments made by LOFT are reliable. The "levels of orthology" concept offers high resolution, reliable orthology, while preserving the relations between orthologous groups. A Windows as well as a preliminary Java version of LOFT is available from the LOFT website http://www.cmbi.ru.nl/LOFT .

156 citations

Journal ArticleDOI
TL;DR: Comparative genomics and transcriptional analysis of the sequences acquired during this study suggests a functional link between coenzyme B(12) biosynthesis and reuterin production, which might be implicated in Lb.
Abstract: The coenzyme B12 production pathway in Lactobacillus reuteri has been deduced using a combination of genetic, biochemical and bioinformatics approaches. The coenzyme B12 gene cluster of Lb. reuteri CRL1098 has the unique feature of clustering together the cbi, cob and hem genes. It consists of 29 ORFs encoding the complete enzymic machinery necessary for de novo biosynthesis. Transcriptional analysis showed it to be expressed as two tandem transcripts of approximately 22 and 4 kb, carrying cobD, cbiABCDETFGHJ, cobA/hemD, cbiKLMNQOP, sirA, hemACBL, and cobUSC, hemD, cobT, respectively. Both transcripts appear to be similarly regulated, and under the conditions assayed are induced in the late-exponential growth phase. Evidence for a regulatory mechanism of negative feedback inhibition by vitamin B12 itself was observed. Comparative genomics analysis of the coding sequences showed them to be most similar to those coding for the anaerobic coenzyme B12 pathways previously characterized in a few representatives of the genera Listeria and Salmonella. This contrasts with the trusted species phylogeny and suggests horizontal gene transfer of the B12 biosynthesis genes. G+C content and codon adaptation index analysis is suggestive that the postulated transfer of these genes was not a recent event. Additional comparative genomics and transcriptional analysis of the sequences acquired during this study suggests a functional link between coenzyme B12 biosynthesis and reuterin production, which might be implicated in Lb. reuteri's success in colonizing the gastrointestinal tract. This information on gene organization, gene transcription and gene acquisition is relevant for the development of (fermented) foods and probiotics enriched in B12.

99 citations


Cited by
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TL;DR: This work assembled 89 scaffolds to generate 34 Mbp of nearly contiguous T. reesei genome sequence comprising 9,129 predicted gene models, providing a roadmap for constructing enhanced T.Reesei strains for industrial applications such as biofuel production.
Abstract: Trichoderma reesei is the main industrial source of cellulases and hemicellulases used to depolymerize biomass to simple sugars that are converted to chemical intermediates and biofuels, such as ethanol. We assembled 89 scaffolds (sets of ordered and oriented contigs) to generate 34 Mbp of nearly contiguous T. reesei genome sequence comprising 9,129 predicted gene models. Unexpectedly, considering the industrial utility and effectiveness of the carbohydrate-active enzymes of T. reesei, its genome encodes fewer cellulases and hemicellulases than any other sequenced fungus able to hydrolyze plant cell wall polysaccharides. Many T. reesei genes encoding carbohydrate-active enzymes are distributed nonrandomly in clusters that lie between regions of synteny with other Sordariomycetes. Numerous genes encoding biosynthetic pathways for secondary metabolites may promote survival of T. reesei in its competitive soil habitat, but genome analysis provided little mechanistic insight into its extraordinary capacity for protein secretion. Our analysis, coupled with the genome sequence data, provides a roadmap for constructing enhanced T. reesei strains for industrial applications such as biofuel production.

1,085 citations

Journal ArticleDOI
TL;DR: In this review, fermented foods with elevated levels of B-group vitamins produced by LAB used as starter cultures will be covered and genetic abilities for vitamin biosynthesis by selected human gut commensals will be discussed.

1,020 citations

Journal ArticleDOI
TL;DR: This review addresses the advances in the understanding of the probiotic-host interaction with a focus on the molecular microbiology of lactobacilli, facing the challenge of molecular characterization of probiotic traits.
Abstract: Summary: Lactobacilli have been crucial for the production of fermented products for centuries. They are also members of the mutualistic microbiota present in the human gastrointestinal and urogenital tract. Recently, increasing attention has been given to their probiotic, health-promoting capacities. Many human intervention studies demonstrating health effects have been published. However, as not all studies resulted in positive outcomes, scientific interest arose regarding the precise mechanisms of action of probiotics. Many reported mechanistic studies have addressed mainly the host responses, with less attention being focused on the specificities of the bacterial partners, notwithstanding the completion of Lactobacillus genome sequencing projects, and increasing possibilities of genomics-based and dedicated mutant analyses. In this emerging and highly interdisciplinary field, microbiologists are facing the challenge of molecular characterization of probiotic traits. This review addresses the advances in the understanding of the probiotic-host interaction with a focus on the molecular microbiology of lactobacilli. Insight into the molecules and genes involved should contribute to a more judicious application of probiotic lactobacilli and to improved screening of novel potential probiotics.

836 citations

Journal ArticleDOI
TL;DR: Through analysis of the current advances in production of citric, lactic and succinic acid production, guidelines for future developments in this fast-moving field are presented.

750 citations

Journal ArticleDOI
TL;DR: This review summarizes the current strategies that have been successfully applied during the last years to activate silent gene clusters in filamentous fungi, especially in the genus Aspergillus, and attempts to simulate the natural habitat by co-cultivation of microorganisms from the same ecosystem.

622 citations