Gesellschaft für Biotechnologische Forschung mbH,
Biochemical Engineering Division,
Mascheroder Weg 1,
D-38124 Braunschweig, Germany
Klebsiella pneumoniae is a microorganism of interest in many areas. First, it is one of the most important opportunistic pathogens in hospital patients and can cause infections of intestinal, urinary and respiratory tract. It is also the most frequent cause of Gram-negative community-acquired pneumoniae. Second, K. pneumoniae can fix atmospheric nitrogen into ammonium. It is naturally found as a free-living soil bacterium that does not participate in symbiotic interactions with leguminous plants. Therefore, it is a good experimental organism for studying the biochemistry and genetics of nitrogen fixation. Last but not least, species of K. pneumoniae have important biotechnological applications such as for the production of human vaccines, enzymes and metabolites. The reconstruction and analysis of metabolic and regulatory networks of K. pneumoniae is thus desirable for both biomedical and biotechnological researches.
K. pneumoniae strain MGH78578 was recently sequenced by the Genome Sequencing Center of Washington University in Saint Louis using the whole genome shotgun approach. The genome data of 920 contigs were published. However, the genome map of this strain was not reconstructed because of the absence of overlapping fragments between different contigs. From these genome data, WIT (Integrated Genomics) predicted most of the open reading frames (ORFs) and their functions. Because of possible sequencing errors such as gaps and mismatches, some ORFs were not correctly predicted and functions of some of the ORFs were uncertain. As a result, only part of the pathways were predicted and confirmed.
In this work, the graphical pathway maps (metabolic and regulatory pathways) from KEGG (http://www.genome.ad.jp/kegg/) were used as the blue prints for our study. The metabolic pathways and functions of ORFs of K. pneumoniae MGH78578 were either manually searched in a local database of Klebsiela contigs based on the sequence similarity to the sequence of KEGG database or searched in the WIT database based on the enzyme number. Some pathways reported in the literature for other organisms but not included in the KEGG and WIT databases were also checked.
In particular, metabolic pathways related to catabolic and anabolic functions (metabolism of carbohydrate, energy, lipids, amino acids, nucleotides, vitamins etc.) and regulatory pathways related to genetic and environmental information processing (transcription, translation, signal transduction, membrane transport, sensing of environmental conditions etc.) are examined. The metabolic and regulatory networks of K. pneumoniae were compared to those of E. coli. Generally speaking, E.coli and K.pneumoniae have very similar genetic functions and metabolic network. These organisms exhibit however also several differences in their metabolic potential. For example, K. pneumoniae has the ability to use glycerol as the sore carbon source and electron acceptor under anaerobic conditions and produces 1,3-propanediol as a metabolite. E.coli can use glycerol only under aerobic conditions and does not produce this useful metabolite. The information from genomic data gives useful hints for this difference. In E.coli, all the genes related to glycerol utilization are organized separately in five operators. Under anaerobic conditions, E. coli needs fumarate or Fe3+ as an electron acceptor for glycerol metabolism. In K. pneumoniae, beside these five operators, there is another regulon (dha regulon) that codes genes for an anaerobic utilization of glycerol. Differently from E. coli, K. pneumoniae does not have pathways for the flagella system and thus not the ability to transport protein through the type II secretion system.
The reconstructed metabolic network of K. pneumoniae is being used for structural and functional analysis of metabolism related to pathogenicity on the one hand and to metabolic engineering of this organism for the production of 1,3-propanedil on the other hand.