Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Discovering novel hydrolases from hot environments
Wohlgemuth, Roland ; Littlechild, Jennifer ; Monti, Daniela ; Schnorr, Kirk ; Rossum, Teunke van; Siebers, Bettina ; Menzel, Peter ; Kublanov, Ilya V. ; Rike, Anne Gunn ; Skretas, Georgios ; Szabo, Zalan ; Peng, Xu ; Young, Mark J. - \ 2018
Biotechnology Advances 36 (2018)8. - ISSN 0734-9750 - p. 2077 - 2100.
Biocatalysis - Enrichment - Enzyme characterization - Enzyme screening - Gene expression - Genomics - Hydrolases - Metagenomics - Sequencing - Thermophiles

Novel hydrolases from hot and other extreme environments showing appropriate performance and/or novel functionalities and new approaches for their systematic screening are of great interest for developing new processes, for improving safety, health and environment issues. Existing processes could benefit as well from their properties. The workflow, based on the HotZyme project, describes a multitude of technologies and their integration from discovery to application, providing new tools for discovering, identifying and characterizing more novel thermostable hydrolases with desired functions from hot terrestrial and marine environments. To this end, hot springs worldwide were mined, resulting in hundreds of environmental samples and thousands of enrichment cultures growing on polymeric substrates of industrial interest. Using high-throughput sequencing and bioinformatics, 15 hot spring metagenomes, as well as several sequenced isolate genomes and transcriptomes were obtained. To facilitate the discovery of novel hydrolases, the annotation platform Anastasia and a whole-cell bioreporter-based functional screening method were developed. Sequence-based screening and functional screening together resulted in about 100 potentially new hydrolases of which more than a dozen have been characterized comprehensively from a biochemical and structural perspective. The characterized hydrolases include thermostable carboxylesterases, enol lactonases, quorum sensing lactonases, gluconolactonases, epoxide hydrolases, and cellulases. Apart from these novel thermostable hydrolases, the project generated an enormous amount of samples and data, thereby allowing the future discovery of even more novel enzymes.

Discovery of anaerobic lithoheterotrophic haloarchaea, ubiquitous in hypersaline habitats
Sorokin, Dimitry Y. ; Messina, Enzo ; Smedile, Francesco ; Roman, Pawel ; Sinninghe Damsté, J.S. ; Ciordia, Sergio ; Mena, Maria Carmen ; Ferrer, Manuel ; Golyshin, Peter N. ; Kublanov, Ilya V. - \ 2017
ISME Journal 11 (2017)5. - ISSN 1751-7362 - p. 1245 - 1260.

Hypersaline anoxic habitats harbour numerous novel uncultured archaea whose metabolic and ecological roles remain to be elucidated. Until recently, it was believed that energy generation via dissimilatory reduction of sulfur compounds is not functional at salt saturation conditions. Recent discovery of the strictly anaerobic acetotrophic Halanaeroarchaeum compels to change both this assumption and the traditional view on haloarchaea as aerobic heterotrophs. Here we report on isolation and characterization of a novel group of strictly anaerobic lithoheterotrophic haloarchaea, which we propose to classify as a new genus Halodesulfurarchaeum. Members of this previously unknown physiological group are capable of utilising formate or hydrogen as electron donors and elemental sulfur, thiosulfate or dimethylsulfoxide as electron acceptors. Using genome-wide proteomic analysis we have detected the full set of enzymes required for anaerobic respiration and analysed their substrate-specific expression. Such advanced metabolic plasticity and type of respiration, never seen before in haloarchaea, empower the wide distribution of Halodesulfurarchaeum in hypersaline inland lakes, solar salterns, lagoons and deep submarine anoxic brines. The discovery of this novel functional group of sulfur-respiring haloarchaea strengthens the evidence of their possible role in biogeochemical sulfur cycling linked to the terminal anaerobic carbon mineralisation in so far overlooked hypersaline anoxic habitats.

Elemental sulfur and acetate can support life of a novel strictly anaerobic haloarchaeon
Sorokin, Dimitry Y. ; Kublanov, Ilya V. ; Gavrilov, Sergei N. ; Rojo, David ; Roman, Pawel ; Golyshin, Peter N. ; Slepak, Vladlen Z. ; Smedile, Francesco ; Ferrer, Manuel ; Messina, Enzo ; Cono, Violetta La; Yakimov, Michail M. - \ 2015
ISME Journal 10 (2015)1. - ISSN 1751-7362 - p. 240 - 252.

Archaea domain is comprised of many versatile taxa that often colonize extreme habitats. Here, we report the discovery of strictly anaerobic extremely halophilic euryarchaeon, capable of obtaining energy by dissimilatory reduction of elemental sulfur using acetate as the only electron donor and forming sulfide and CO2 as the only products. This type of respiration has never been observed in hypersaline anoxic habitats and is the first example of such metabolic capability in the entire Archaea domain. We isolated and cultivated these unusual organisms, selecting one representative strain, HSR2, for detailed characterization. Our studies including physiological tests, genome sequencing, gene expression, metabolomics and [14C]-bicarbonate assimilation assays revealed that HSR2 oxidized acetate completely via the tricarboxylic acid cycle. Anabolic assimilation of acetate occurred via activated glyoxylate bypass and anaplerotic carboxylation. HSR2 possessed sulfurtransferase and an array of membrane-bound polysulfide reductase genes, all of which were expressed during the growth. Our findings suggest the biogeochemical contribution of haloarchaea in hypersaline anoxic environments must be reconsidered.

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