title: Use of pathway analysis and genome context methods for functional genomics of Mycoplasma pneumoniae nucleotide metabolism.
abstract: Elementary modes analysis allows one to reveal whether a set of known enzymes is sufficient to sustain functionality of the cell. Moreover, it is helpful in detecting missing reactions and predicting which enzymes could fill these gaps. Here, we perform a comprehensive elementary modes analysis and a genomic context analysis of Mycoplasma pneumoniae nucleotide metabolism, and search for new enzyme activities. The purine and pyrimidine networks are reconstructed by assembling enzymes annotated in the genome or found experimentally. We show that these reaction sets are sufficient for enabling synthesis of DNA and RNA in M. pneumoniae. Special focus is on the key modes for growth. Moreover, we make an educated guess on the nutritional requirements of this micro-organism. For the case that M. pneumoniae does not require adenine as a substrate, we suggest adenylosuccinate synthetase (EC 6.3.4.4), adenylosuccinate lyase (EC 4.3.2.2) and GMP reductase (EC 1.7.1.7) to be operative. GMP reductase activity is putatively assigned to the NRDI_MYCPN gene on the basis of the genomic context analysis. For the pyrimidine network, we suggest CTP synthase (EC 6.3.4.2) to be active. Further experiments on the nutritional requirements are needed to make a decision. Pyrimidine metabolism appears to be more appropriate as a drug target than purine metabolism since it shows lower plasticity.
authors.affiliation: Department of Bioinformatics, Faculty of Biology and Pharmaceutics, Friedrich-Schiller University Jena, Ernst-Abbe-Platz 2, D-07743 Jena, Germany. mikhail.pachkov@unibas.ch
authors.forename: Mikhail
authors.initials: M
authors.lastname: Pachkov
authors.forename: Thomas
authors.initials: T
authors.lastname: Dandekar
authors.forename: Jan
authors.initials: J
authors.lastname: Korbel
authors.forename: Peer
authors.initials: P
authors.lastname: Bork
authors.forename: Stefan
authors.initials: S
authors.lastname: Schuster
mesh_terms: D000225:Adenine / Q000737:chemistry; D001482:Base Composition; D001671:Biochemistry / Q000379:methods; D004247:DNA / Q000737:chemistry; D016680:Genome, Bacterial; D023281:Genomics; D008954:Models, Biological; D008957:Models, Genetic; D008962:Models, Theoretical; D009177:Mycoplasma pneumoniae / Q000235:genetics*; D009711:Nucleotides / Q000737:chemistry; D011687:Purines / Q000737:chemistry; D011743:Pyrimidines / Q000737:chemistry; D012313:RNA / Q000737:chemistry; D013379:Substrate Specificity
chemical_list: D009711:Nucleotides; D011687:Purines; D011743:Pyrimidines; D012313:RNA; D004247:DNA; D000225:Adenine