Targeted metabolic reconstruction: a novel approach for the characterization of plant-pathogen interactions
Genome-scale metabolic reconstruction (GEMR), along with flux balance analysis, has been widely used to study complex metabolic networks in several microbial organisms. This approach is of particular applicability in biological systems where the lack of kinetics data is typical. This is the case of...
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| Veröffentlicht in: | Briefings in bioinformatics 2011-03, Vol.12 (2), p.151-162 |
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| creator | PINZON, Andrés RODRIGUEZ-R, Luis M GONZALEZ, Andrés BERNAL, Adriana RESTREPO, Silvia |
| description | Genome-scale metabolic reconstruction (GEMR), along with flux balance analysis, has been widely used to study complex metabolic networks in several microbial organisms. This approach is of particular applicability in biological systems where the lack of kinetics data is typical. This is the case of plant-pathogen interactions, where these methods open the possibility of studying host metabolic network phenotype during the interaction with pathogens. Since GEMRs are based on sequenced genomes, its applicability to organisms where genomic information is lacking is limited. Here we describe an alternative approach to GEMR: targeted metabolic reconstruction, where network reconstruction is guided by transcriptomic data instead of genomic information. This approach is being applied successfully in our laboratory for the Phytophthora infestans--Solanum tuberosum pathosystem. |
| doi_str_mv | 10.1093/bib/bbq009 |
| format | Article |
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This approach is of particular applicability in biological systems where the lack of kinetics data is typical. This is the case of plant-pathogen interactions, where these methods open the possibility of studying host metabolic network phenotype during the interaction with pathogens. Since GEMRs are based on sequenced genomes, its applicability to organisms where genomic information is lacking is limited. Here we describe an alternative approach to GEMR: targeted metabolic reconstruction, where network reconstruction is guided by transcriptomic data instead of genomic information. 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This approach is of particular applicability in biological systems where the lack of kinetics data is typical. This is the case of plant-pathogen interactions, where these methods open the possibility of studying host metabolic network phenotype during the interaction with pathogens. Since GEMRs are based on sequenced genomes, its applicability to organisms where genomic information is lacking is limited. Here we describe an alternative approach to GEMR: targeted metabolic reconstruction, where network reconstruction is guided by transcriptomic data instead of genomic information. This approach is being applied successfully in our laboratory for the Phytophthora infestans--Solanum tuberosum pathosystem.</description><subject>Bioinformatics</subject><subject>Biological and medical sciences</subject><subject>Computational Biology - methods</subject><subject>Flowers & plants</subject><subject>Fundamental and applied biological sciences. 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| source | MEDLINE; EBSCOhost Business Source Complete; Oxford Journals Open Access Collection; EZB-FREE-00999 freely available EZB journals; PubMed Central |
| subjects | Bioinformatics Biological and medical sciences Computational Biology - methods Flowers & plants Fundamental and applied biological sciences. Psychology General aspects Genetically altered foods Genome Genomes Genomics Host-Parasite Interactions Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) Metabolic Networks and Pathways Metabolism Pathogens Phytophthora Phytophthora infestans - pathogenicity Plant Diseases - parasitology Solanum tuberosum - parasitology |
| title | Targeted metabolic reconstruction: a novel approach for the characterization of plant-pathogen interactions |
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