Functional genomics and SNP analysis of human genes encoding proline metabolic enzymes

Abstract

Proline metabolism in mammals involves two other amino acids, glutamate and ornithine, and five enzymatic activities, Delta(1)-pyrroline-5-carboxylate (P5C) reductase (P5CR), proline oxidase, P5C dehydrogenase, P5C synthase and ornithine-delta-aminotransferase (OAT). With the exception of OAT, which catalyzes a reversible reaction, the other four enzymes are unidirectional, suggesting that proline metabolism is purpose-driven, tightly regulated, and compartmentalized. In addition, this tri-amino-acid system also links with three other pivotal metabolic systems, namely the TCA cycle, urea cycle, and pentose phosphate pathway. Abnormalities in proline metabolism are relevant in several diseases: six monogenic inborn errors involving metabolism and/or transport of proline and its immediate metabolites have been described. Recent advances in the Human Genome Project, in silico database mining techniques, and research in dissecting the molecular basis of proline metabolism prompted us to utilize functional genomic approaches to analyze human genes which encode proline metabolic enzymes in the context of gene structure, regulation of gene expression, mRNA variants, protein isoforms, and single nucleotide polymorphisms.

Fig 1

Metabolic pathways concerning proline in mammalian cells (see text for details).

Fig 2

Regulation of expression of human genes encoding P5CS, OAT, POX and P5CDH by p53 (see text for details). P21 was used as a positive control p53 inducible gene. β-actin was used as a loading control.

Fig 3

Northern blot analysis of human P5CR2 expression in various human tissues and Reh cells. a Expression of P5CR2 investigated in 16 different tissues (see text for details). b P5CR2 is highly expressed in Reh cells. In contrast, expression of P5CR1 is lost in Reh cells. CCL-114 is a control B lymphoblast cell line. β-actin was used as a loading control.