Comprehensive analysis of the mouse metabolome based on the transcriptome

Abstract

The complete set of cDNAs encoding the enzymes of known metabolic pathways has not previously been available for any mammal. Here, transcripts encoding the metabolic pathways of the mouse (mouse metabolome) were reconstructed by making use of the KEGG metabolic pathway database and gene ontology (GO) assignment to the mouse representative transcript and protein set (RTPS), which contains all available mouse transcript sequences including the FANTOM set of RIKEN mouse cDNA clones. By assigning EC numbers extracted from the molecular function ontology in GO, the known mouse transcriptome was predicted to encode enzymes with 726 unique EC numbers. Of these, 648 EC numbers were newly assigned based on the FANTOM set. The mouse metabolome confirmed by cDNA analysis includes almost all of the enzymes of well known pathways such as the tricarboxylic acid cycle and urea cycle. On the other hand, analysis of enzymes required for the tryptophan metabolism pathway revealed a lack of connectivity, indicating that cDNAs/genes encoding several key enzymes remain to be identified. The information derived from coexpression from the cDNA microarray analysis of enzymes of known function may lead to identification of the missing components of the metabolome, and will add new insights into the connectivity of the mammalian metabolic pathways.

Figure 1

Comparison of EC numbers in human and mouse. Enzymatic genes coded in human and transcribed in mouse are compared in EC number. The difference comes mainly from the variation in ligand specificity in enzymes that are difficult to predict only from computational sequence analyses.

Figure 2

Reconstruction of mouse tryptophan metabolism pathway in silico. (A) An example of an automatically reconstructed pathway using the KEGG Web interface by specifying multiple EC numbers in the query. The EC number in the green box was found in the human metabolome set, and the EC number drawn in red was covered by the RTPS. There were missing enzymes on the pathway that were assigned computationally. These enzymes are described in Table 2. Four of six missing clones were finally identified after intensive human curation. (B) Gene expression of mRNAs coding enzymes in the tryptophan metabolism pathway by microarray. Genes are sorted by order of the cascade of tryptophan degradation to Acetyl-CoA, not by clustering by similar expression profiles. It is apparent that the genes in the upper stream of this cascade are highly expressed in liver and kidney, and those downstream of the cascade are highly expressed in heart. 09, spleen; 58, thymus; 06, kidney; 10, heart; 12, lung; 13, liver; 07, brain; 15, cerebellum; 65, cerebellum neonate 10 day; 16, placenta; 17, testis; 83, uterus; 18, pancreas; 20, small intestine; 22, stomach; 90, colon; 47, skin neonate 10 day; 98, bone; xm, muscle; ak, adipose dorsal kidney; ae, adipose epididymal; am, adipose mesenteric.