The Rut metabolic pathway in Escherichia coli is composed of seven proteins, all required by E. coli K-12 to grow on uracil as the sole nitrogen source. This pathway degrades pyrimidine rings to release both nitrogens as ammonia. David E. Wemmer and colleagues of the University of California, Berkeley, defined the function of the proteins along this pathway. The first of these catalyzes a novel reaction, using activated molecular oxygen to cleave the pyrimidine ring between carbon 4 and nitrogen 3. Both atoms of oxygen insert at C4 to form a peroxyacid, which is thought to be toxic to cells. Another pathway enzyme reduces flavin used in this reaction, and a third is required to release both atoms of nitrogen from the ring. Three other pathway enzymes appear to accelerate spontaneous steps to prevent buildup of toxic intermediates and possibly of byproducts. The last pathway member is amembrane transporter for pyrimidines. "No one expected to find another central metabolic pathway, particularly in E. coli," says coauthor Sydney Kustu. The work should further the understanding of how cells replicate themselves. "Despite the fact that E. coli is probably the best-studied cell on the planet, some 30% of its ~4,500 proteins have not been studied experimentally."

(K.-S. Kim, J. G. Pelton, W. B. Inwood, U. Andersen, S. Kustu, and D. E. Wemmer. 2010. The rut pathway for pyrimidine degradation: novel chemistry and toxicity problems. J. Bacteriol. 192:4089-4102.)