Towards a Neisseria meningitidis B vaccine : introducing systems biology in process development

Towards a Neisseria meningitidis B vaccine Neisseria meningitidis is a bacterium that is only found in humans and can cause the diseases meningitis or septicaemia, especially in young children. At the Netherlands Vaccine Institute a vaccine against serogroup B meningococci, which causes about 50% of the disease cases worldwide, is currently being developed. The pathogen itself is the basis of the vaccine. To obtain more insight in the metabolism of meningococci, a mathematical model of metabolism was constructed, using its genome sequence as a starting point and the validity of this metabolic model was checked under different experimental conditions. The gathered knowledge was used to design a synthetic medium for growth of serogroup B meningococci and for the development of a cultivation process. In addition, the research has led to the realization of equipment in which bulk production of serogroup B meningococci is possible, which brings a publically available vaccine a step closer. <br/

The metabolic blueprint of <i>Phaeodactylum tricornutum</i> reveals a eukaryotic Entner-Doudoroff glycolytic pathway

Diatoms are one of the most successful groups of unicellular eukaryotic algae. Successive endosymbiotic events contributed to their flexible metabolism, making them competitive in variable aquatic habitats. Although the recently sequenced genomes of the model diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana have provided the first insights into their metabolic organization, the current knowledge on diatom biochemistry remains fragmentary. By means of a genome-wide approach, we developed DiatomCyc, a detailed pathway/genome database of P. tricornutum. DiatomCyc contains 286 pathways with 1719 metabolic reactions and 1613 assigned enzymes, spanning both the central and parts of the secondary metabolism of P. tricornutum. Central metabolic pathways, such as those of carbohydrates, amino acids and fatty acids, were covered. Furthermore, our understanding of the carbohydrate model in P. tricornutum was extended. In particular we highlight the discovery of a functional Entner–Doudoroff pathway, an ancient alternative for the glycolytic Embden–Meyerhof–Parnas pathway, and a putative phosphoketolase pathway, both uncommon in eukaryotes. DiatomCyc is accessible online (http://www.diatomcyc.org), and offers a range of software tools for the visualization and analysis of metabolic networks and ‘omics’ data. We anticipate that DiatomCyc will be key to gaining further understanding of diatom metabolism and, ultimately, will feed metabolic engineering strategies for the industrial valorization of diatoms

Bacterial mutants for enhanced succinate production

The present invention relates to a method for obtaining enhanced metabolite production in micro-organisms, and to mutants and/or transformants obtained with said method. More particularly, it relates to bacterial mutants and/or transformants for enhanced succinate production, especially mutants and/or transformants that are affected in the import and export of succinate.BiotechnologyApplied Science

Tracking the sterol biosynthesis pathway of the diatom <i>Phaeodactylum tricornutum</i>

Diatoms are unicellular photosynthetic microalgae that play a major role in global primary production and aquatic biogeochemical cycling. Endosymbiotic events and recurrent gene transfers uniquely shaped the genome of diatoms, which contains features from several domains of life. The biosynthesis pathways of sterols, essential compounds in all eukaryotic cells, and many of the enzymes involved are evolutionarily conserved in eukaryotes. Although well characterized in most eukaryotes, the pathway leading to sterol biosynthesis in diatoms has remained hitherto unidentified.Through the DiatomCyc database we reconstructed the mevalonate and sterol biosynthetic pathways of the model diatom Phaeodactylum tricornutum in silico. We experimentally verified the predicted pathways using enzyme inhibitor, gene silencing and heterologous gene expression approaches.Our analysis revealed a peculiar, chimeric organization of the diatom sterol biosynthesis pathway, which possesses features of both plant and fungal pathways. Strikingly, it lacks a conventional squalene epoxidase and utilizes an extended oxidosqualene cyclase and a multifunctional isopentenyl diphosphate isomerase/squalene synthase enzyme.The reconstruction of the P. tricornutum sterol pathway underscores the metabolic plasticity of diatoms and offers important insights for the engineering of diatoms for sustainable production of biofuels and high-value chemicals.</li