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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    Role of phosphate in the central metabolism of two lactic acid bacteria-a comparative systems biology approach
    Levering, J. ; Musters, M.W.J.M. ; Bekker, M. ; Bellomo, D. ; Fiedler, T. ; Vos, W.M. de; Hugenholtz, F. ; Kreikemeyer, B. ; Kummer, U. ; Teusink, B. - \ 2012
    FEBS Journal 279 (2012)7. - ISSN 1742-464X - p. 1274 - 1290.
    pyruvate formate-lyase - group-a streptococci - lactococcus-lactis - phosphotransferase system - lactate-dehydrogenase - comparative genomics - in-vivo - glyceraldehyde-3-phosphate dehydrogenase - enterococcus-faecalis - inducer expulsion
    Lactic acid-producing bacteria survive in distinct environments, but show common metabolic characteristics. Here we studied the dynamic interactions of the central metabolism in Lactococcus lactis, extensively used as a starter culture in the dairy industry, and Streptococcus pyogenes, a human pathogen. Glucose-pulse experiments and enzymatic measurements were performed to parameterize kinetic models of glycolysis. Significant improvements were made to existing kinetic models for L. lactis, which subsequently accelerated the development of the first kinetic model of S. pyogenes glycolysis. The models revealed an important role for extracellular phosphate in the regulation of central metabolism and the efficient use of glucose. Thus, phosphate, which is rarely taken into account as an independent species in models of central metabolism, should be considered more thoroughly in the analysis of metabolic systems in the future. Insufficient phosphate supply can lead to a strong inhibition of glycolysis at high glucose concentrations in both species, but this was more severe in S. pyogenes. S. pyogenes is more efficient at converting glucose to ATP, showing a higher tendency towards heterofermentative energy metabolism than L. lactis. Our comparative systems biology approach revealed that the glycolysis of L. lactis and S. pyogenes have similar characteristics, but are adapted to their individual natural habitats with respect to phosphate regulation
    Systems solutions by lactic acid bacteria: from paradigms to practice
    Vos, W.M. de - \ 2011
    Microbial Cell Factories 10 (2011)Suppl 1. - ISSN 1475-2859
    complete genome sequence - lactobacillus-plantarum wcfs1 - lactococcus-lactis - serine proteinase - gene-expression - transcriptome analysis - streptococcus-thermophilus - molecular characterization - phosphotransferase system - gastrointestinal-tract
    Lactic acid bacteria are among the powerhouses of the food industry, colonize the surfaces of plants and animals, and contribute to our health and well-being. The genomic characterization of LAB has rocketed and presently over 100 complete or nearly complete genomes are available, many of which serve as scientific paradigms. Moreover, functional and comparative metagenomic studies are taking off and provide a wealth of insight in the activity of lactic acid bacteria used in a variety of applications, ranging from starters in complex fermentations to their marketing as probiotics. In this new era of high throughput analysis, biology has become big science. Hence, there is a need to systematically store the generated information, apply this in an intelligent way, and provide modalities for constructing self-learning systems that can be used for future improvements. This review addresses these systems solutions with a state of the art overview of the present paradigms that relate to the use of lactic acid bacteria in industrial applications. Moreover, an outlook is presented of the future developments that include the transition into practice as well as the use of lactic acid bacteria in synthetic biology and other next generation applications
    Expression of phosphofructokinase in Neisseria meningitidis
    Baart, G.J.E. ; Langenhof, M. ; Waterbeemd, B. van de; Hamstra, H.J. ; Zomer, B. ; Pol, L.A. van der; Beuvery, E.C. ; Tramper, J. ; Martens, D.E. - \ 2010
    Microbiology 156 (2010)2. - ISSN 1350-0872 - p. 530 - 542.
    c14 labelled glucose - horizontal gene-transfer - escherichia-coli - meningococcal disease - microbial-growth - phosphotransferase system - saccharomyces-cerevisiae - chromosomal genes - mass-spectrometry - metabolism
    Neisseria meningitidis serogroup B is a pathogen that can infect diverse sites within the human host. According to the N. meningitidis genomic information and experimental observations, glucose can be completely catabolized through the Entner–Doudoroff pathway and the pentose phosphate pathway. The Embden–Meyerhof–Parnas pathway is not functional, because the gene for phosphofructokinase (PFK) is not present. The phylogenetic distribution of PFK indicates that in most obligate aerobic organisms, PFK is lacking. We conclude that this is because of the limited contribution of PFK to the energy supply in aerobically grown organisms in comparison with the energy generated through oxidative phosphorylation. Under anaerobic or microaerobic conditions, the available energy is limiting, and PFK provides an advantage, which explains the presence of PFK in many (facultatively) anaerobic organisms. In accordance with this, in silico flux balance analysis predicted an increase of biomass yield as a result of PFK expression. However, analysis of a genetically engineered N. meningitidis strain that expressed a heterologous PFK showed that the yield of biomass on substrate decreased in comparison with a pfkA-deficient control strain, which was associated mainly with an increase in CO2 production, whereas production of by-products was similar in the two strains. This might explain why the pfkA gene has not been obtained by horizontal gene transfer, since it is initially unfavourable for biomass yield. No large effects related to heterologous expression of pfkA were observed in the transcriptome. Although our results suggest that introduction of PFK does not contribute to a more efficient strain in terms of biomass yield, achievement of a robust, optimal metabolic network that enables a higher growth rate or a higher biomass yield might be possible after adaptive evolution of the strain, which remains to be investigated
    Unity in organisation and regulation of catabolic operons in Lactobacillus plantarum, Lactococcus lactis and Listeria monocytogenes
    Andersson, U. ; Molenaar, D. ; Radstrom, P. ; Vos, W.M. de - \ 2005
    Systematic and Applied Microbiology 28 (2005)3. - ISSN 0723-2020 - p. 187 - 195.
    gram-positive bacteria - complete genome sequence - phosphotransferase system - bacillus-subtilis - streptococcus-lactis - lactate-dehydrogenase - acid bacteria - gene - repression - metabolism
    Global regulatory circuits together with more specific local regulators play a notable role when cells are adapting to environmental changes. Lactococcus lactis is a lactic acid bacterium abundant in nature fermenting most mono- and disaccharides. Comparative genomics analysis of the operons encoding the proteins and enzymes crucial for catabolism of lactose, maltose and threhalose revealed an obvious unity in operon organisation. The local regulator of each operon was located in a divergent transcriptional direction to the rest of the operon including the transport protein-encoding genes. Furthermore, in all three operons a catabolite responsive element (CRE) site was detected inbetween the gene encoding the local regulator and one of the genes encoding ! sugar transport protein. It is evident that regardless of type of transport system and catabolic enzymes acting upon lactose, maltose and trehalose, respectively, Lc. lactis shows unity in both operon organisation and regulation of these catabolic operons. This knowledge was further extended to other catabolic operons in Lc. lactis and the two related bacteria Lactobacillus plantarum and Listeria monocytogenes. Thirty-nine catabolic operons responsible for degradation of sugars and sugar alcohols in Lc. lactis, Lb. plantarum and L. monocytogenes were investigated and the majority of those possessed the same organisation as the lactose, maltose and trehalose operons of Lc. lactis. Though, the frequency of CRE sites and their location varied among the bacteria. Both Lc. lactis and Lb. plantarum showed CRE sites in direct proximity to genes coding for proteins responsible for sugar uptake. However, in, L. monocytogenes CRE sites were not frequently found and not in the vicinity of genes encoding transport proteins, suggesting a more local mode of regulation of the catabolic operons found and/or the use of inducer control in this bacterium. © 2004 Elsevier GrnbH. All rights reserved.
    Metabolic Engineering of Mannitol Production in Lactococcus lactis: Influence of Overexpression of Mannitol 1-Phosphate Dehydrogenase in Different Genetic Backgrounds
    Wisselink, H.W. ; Mars, A.E. ; Meer, P. van der; Eggink, G. ; Hugenholtz, J. - \ 2004
    Applied and Environmental Microbiology 70 (2004)7. - ISSN 0099-2240 - p. 4286 - 4292.
    complete genome sequence - lactate-dehydrogenase - lactobacillus-plantarum - acid bacteria - phosphotransferase system - expression systems - protects - nisin - phosphorylation - activation
    To obtain a mannitol-producing Lactococcus lactis strain, the mannitol 1-phosphate dehydrogenase gene (mtlD) from Lactobacillus plantarum was overexpressed in a wild-type strain, a lactate dehydrogenase(LDH)-deficient strain, and a strain with reduced phosphofructokinase activity. High-performance liquid chromatography and 13C nuclear magnetic resonance analysis revealed that small amounts (
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