Kluyver Centre for Genomics of Industrial Fermentations

Within the Kluyver Centre, four new projects have started in the last few months; three of them in the Lactic Acid Bacteria (LAB) programme and one in the Genomics Tool programme.

The first project deals with the ability of LAB to produce cobalamins. Recently, Lactobacillus reuteri was the first LAB reported to produce vitamin B12 (Fig.). The proposed project will focus on the characterisation of the genes involved B12-biosynthesis, their expression and function. The objectives of the project are to; (i) Elucidate the B12- biosynthetic pathway in lactobacilli and compare with other known production pathways (i.e in Pseudomonas and Propionibacterium); (ii) To improve B12-production through overexpression of B12-genes, through insight in regulatory mechanisms; (iii) to transfer B12-production to other LAB’s. The project will face the scientific challenge of metabolic engineering of a very complicated biosynthetic pathway. The spin-off for industry is the possible development of fermented foods with increased vitamin B12-levels.

The second project focuses on electron transport in LAB. It is related to the first project in the sense that it concentrates on the biosynthesis of cytochromes, which are the major components of electron transfer chains that are thought to be absent in LAB. Lactic acid bacteria like Lactococcus lactis to not have the genes encoding the the enzymes for the biosynthesis of heme, the functional component of cytochromes and is very similar to the major building block of vitamin B12. The project has two main goals; 1. To engineer production of heme in LAB, thus reconstituting aerobic electron transport, and 2. To analyse the overall changes in cellular physiology upon a shift from an anaerobic to an aerobic life-style. Besides these very intriguing scientific questions, the project also offers the possibility of increased biomass production of starter bacteria through introduction of oxidative phosphorylation.

In the third project, metabolomics will be used to compare amino acid metabolism in different lactic acid bacteria. The potential of Lactococcus lactis, Streptococcus thermophilus and Lactobacillus plantarum to synthesise the different amino acids, to accumulate them or to convert them into functional ingredients such as vitamins and flavour components, will be evaluated, in high throughput analysis, by growth in minimal medium, by the activity of biosynthetic enzymes, by the presence of (biosynthetic) precursors and by the formation of the functional ingredients. This metabolome analysis will be performed under different growth conditions and will be compared with the predicted metabolic network based on the genome sequence of the three lactic acid bacteria. It will provide essential information on the potential of these organisms to produce functional food ingredients, but also on regulation of growth in response to differences in medium composition.

The fourth project is part of the Genomics Tools programme and deals with one of the main scientific challenges in Genomics; to obtain an integral ‘systems’ understanding of living cells. A model-based approach that incorporates information on all relevant levels (from genome to cellular performance) is essential to meet this challenge. This project aims to create and compare 'Virtual Cell' databases of industrial microorganisms which are relevant to the Kluyver Center (i.e. lactic acid bacteria, yeast, fungi) by combining data obtained from complete genome sequencing, comparative genomics, transcriptomics, proteomics and metabolomics. Such databases should include information on genes, proteome, reactions, metabolites, metabolic pathways, transport, secretion, signal transduction, regulators and regulons, etc. In this project, a Lactobacillus plantarum database will be set-up and will form the basis for subsequent modelling and dynamic studies of metabolism.

The chemical structure of cyanocobalamin