Articulation of three core metabolic processes in Arabidopsis: fatty acid biosynthesis, leucine catabolism and starch metabolism.
BACKGROUND
Elucidating metabolic network structures and functions in multicellular organisms is an emerging goal of functional genomics. We describe the co-expression network of three core metabolic processes in the genetic model plant Arabidopsis thaliana: fatty acid biosynthesis, starch metabolism and amino acid (leucine) catabolism.


RESULTS
These co-expression networks form modules populated by genes coding for enzymes that represent the reactions generally considered to define each pathway. However, the modules also incorporate a wider set of genes that encode transporters, cofactor biosynthetic enzymes, precursor-producing enzymes, and regulatory molecules. We tested experimentally the hypothesis that one of the genes tightly co-expressed with starch metabolism module, a putative kinase AtPERK10, will have a role in this process. Indeed, knockout lines of AtPERK10 have an altered starch accumulation. In addition, the co-expression data define a novel hierarchical transcript-level structure associated with catabolism, in which genes performing smaller, more specific tasks appear to be recruited into higher-order modules with a broader catabolic function.


CONCLUSIONS
Each of these core metabolic pathways is structured as a module of co-expressed transcripts that co-accumulate over a wide range of environmental and genetic perturbations and developmental stages, and represent an expanded set of macromolecules associated with the common task of supporting the functionality of each metabolic pathway. As experimentally demonstrated, co-expression analysis can provide a rich approach towards understanding gene function.
Mentzen
Wieslawa I
WI
1CRS4 Bioinformatics Laboratory, Loc. Piscinamanna, 09010 Pula, CA, Italy. wiesia@crs4.it
Peng
Jianling
J
Ransom
Nick
N
Nikolau
Basil J
BJ
Wurtele
Eve Syrkin
ES
D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism; D050260:Carbohydrate Metabolism; D016208:Databases, Factual; D005227:Fatty Acids / Q000378:metabolism*; D018506:Gene Expression Regulation, Plant; D007930:Leucine / Q000378:metabolism*; D050155:Lipogenesis; D008928:Mitochondria / Q000378:metabolism; D008954:Models, Biological; D009154:Mutation; D030821:Plants, Genetically Modified / Q000235:genetics / Q000378:metabolism; D015398:Signal Transduction / Q000235:genetics; D012984:Software; D013213:Starch / Q000378:metabolism*
D029681:Arabidopsis Proteins; D005227:Fatty Acids; D013213:Starch; D007930:Leucine