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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Distant Non-Obvious Mutations Influence the Activity of a Hyperthermophilic Pyrococcusfuriosus Phosphoglucose Isomerase
Subramanian, Kalyanasundaram ; Mitusińska, Karolina ; Raedts, John ; Almourfi, Feras ; Joosten, Henk Jan ; Hendriks, Sjon ; Sedelnikova, Svetlana E. ; Kengen, Servé W.M. ; Hagen, Wilfred R. ; Góra, Artur ; Martins Dos Santos, Vitor A.P. ; Baker, Patrick J. ; Oost, John van der; Schaap, Peter J. - \ 2019
Biomolecules 9 (2019)6. - ISSN 2218-273X
Comulator - cupin phosphoglucose isomerase - Protein engineering - Pyrococcus furiosus - solvent access

The cupin-type phosphoglucose isomerase (PfPGI) from the hyperthermophilic archaeon Pyrococcus furiosus catalyzes the reversible isomerization of glucose-6-phosphate to fructose-6-phosphate. We investigated PfPGI using protein-engineering bioinformatics tools to select functionally-important residues based on correlated mutation analyses. A pair of amino acids in the periphery of PfPGI was found to be the dominant co-evolving mutation. The position of these selected residues was found to be non-obvious to conventional protein engineering methods. We designed a small smart library of variants by substituting the co-evolved pair and screened their biochemical activity, which revealed their functional relevance. Four mutants were further selected from the library for purification, measurement of their specific activity, crystal structure determination, and metal cofactor coordination analysis. Though the mutant structures and metal cofactor coordination were strikingly similar, variations in their activity correlated with their fine-tuned dynamics and solvent access regulation. Alternative, small smart libraries for enzyme optimization are suggested by our approach, which is able to identify non-obvious yet beneficial mutations.

Modulating D-amino acid oxidase (DAAO) substrate specificity through facilitated solvent access
Subramanian, Kalyanasundaram ; Góra, Artur ; Spruijt, Ruud ; Mitusińska, Karolina ; Suarez-Diez, Maria ; Martins Dos Santos, Vitor ; Schaap, Peter J. - \ 2018
PLoS ONE 13 (2018)6. - ISSN 1932-6203

D-amino acid oxidase (DAAO) degrades D-amino acids to produce α-ketoacids, hydrogen peroxide and ammonia. DAAO has often been investigated and engineered for industrial and clinical applications. We combined information from literature with a detailed analysis of the structure to engineer mammalian DAAOs. The structural analysis was complemented with molecular dynamics simulations to characterize solvent accessibility and product release mechanisms. We identified non-obvious residues located on the loops on the border between the active site and the secondary binding pocket essential for pig and human DAAO substrate specificity and activity. We engineered DAAOs by mutating such critical residues and characterised the biochemical activity of the resulting variants. The results highlight the importance of the selected residues in modulating substrate specificity, product egress and enzyme activity, suggesting further steps of DAAO re-engineering towards desired clinical and industrial applications.

Divergent growth of Norway spruce on Babia Góra Mountain in the western Carpathians
Buras, Allan ; Spyt, Barbara ; Janecka, Karolina ; Kaczka, Ryszard - \ 2018
Dendrochronologia 50 (2018). - ISSN 1125-7865 - p. 33 - 43.
Air pollution - Blue intensity - Climate growth relationships - Individualistic tree growth - Principal Component Gradient Analysis
Growth divergence – i.e. the expression of divergent growth trends of neighboring trees – has certain implications for dendrochronological research, for instance in the context of climate reconstructions but also in terms of estimating net ecosystem productivity. Thus, understanding the underlying mechanisms is essential to extend our fundamental dendroecological knowledge. In this context, the Picea genus plays an important role since several of its species were reported to exhibit growth divergence. Here, we investigate a well sampled Norway spruce (Picea abies (L.) Karst) data set for growth divergence comprising ring-width and Blue Intensity measurements from seven sites on Babia Góra Mountain, at the border between Poland and Slovakia. By means of Principal Component Gradient Analysis, inter-series correlations, and climate growth relationships, we are able to show that I) Norway spruce on Babia Góra expressed growth divergence since the 1970s, II) the definition of groups increased the strength of population signals and the stability of climate-growth relationships, and III) Blue Intensity appeared as a more robust proxy for environmental conditions. We discuss soil heterogeneity, genetics, and air pollution as possible underlying mechanisms, thereby indicating further research avenues to obtain a better understanding of growth divergence.
Plastic Growth response of European beech provenances to dry site conditions
Stojnic, S. ; Sass, U.G.W. ; Orlovic, S. ; Matovic, B. ; Eilmann, B. - \ 2013
Iawa Journal 34 (2013)4. - ISSN 0928-1541 - p. 475 - 484.
fagus-sylvatica l. - phenotypic plasticity - drought tolerance - climate-change - life-history - tree-growth - xylem - cavitation - variability - embolism
Due to projected global warming, there is a great concern about the ability of European beech to adapt to future climate conditions. Provenance trials provide an excellent basis to assess the potential of various provenances to adjust to given climate conditions. In this study we compared the performance of four European beech (Fagus sylvatica L.) provenances growing in a provenance trial at the Fruška Gora Mountain, Serbia. Three of the investigated provenances (Höllerbach and Hasbruch from Germany and Vrani Kamen from Croatia) originate from moist sites, with annual precipitation sums being twice as high as at the provenance trial in Serbia. The performance of these provenances are compared to the growth of the local provenance Fruška Gora which is well adapted to dry site conditions. We analysed tree-ring width, mean vessel area, vessel density and water-conductive area for the period from 2006 to 2012. In spite of differences in climate conditions at their place of origin all beech provenances showed a similar pattern in radial increment. Also the wood- anatomical variables showed similar inter-annual patterns for all provenances and no significant differences between the provenances. This indicates that beech provenances from moist environments can adjust to the relatively dry temperate climate in Serbia.
Effect of feed lysine supplementation on shift in amino acid profile after a meal: no indication for a 'time lag' effect on 1L:2D.
Doeschate, R.A.H.M. ten; Scheele, C.W. ; Schreurs, V.V.A.M. - \ 1993
In: Abstract 9th Eur. Symp. Poultry nutrition, Jelenia Góra, Poland / Jamroz, D., - p. 322 - 322.
Two new Hygromiidae from Crna Gora and Kosovo (Gastropoda Pulmonata), with a checklist of the hygromiid species described from the western Balkan.
Winter, A.J. de; Maassen, W.J.M. - \ 1992
Basteria 56 (1992). - ISSN 0005-6219 - p. 173 - 192.
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