Extended Data Figure 3. Summary of biochemical pathways for AAA metabolism by C. sporogenes.

Phenylalanine, tyrosine and tryptophan are all metabolized through the reductive pathway by the same enzymes. The first step is an aminotransferase reaction, probably catalysed by aromatic amino acid aminotransferase (Aat). This enzyme activity has been demonstrated in C. sporogenes cells, however, the gene encoding this enzyme has not been identified. The arylpyruvates are then converted to their corresponding aryllactates by phenyllactate dehydrogenase (FldH, CLOSPO_00316). The aryllactates are then dehydrated by phenyllactate dehydratase (FldBC, CLOSPO_00310-311) along with its activator (FldI, CLOSPO_00309). Previous studies indicate that the dehydration reaction requires the substrate to first be activated to a CoA thioester, probably catalysed by acyl-CoA ligase (FldL, CLOSPO_00307), and that the CoA is recycled by the action of acyl-CoA transferase (FldA, CLOSPO_00308). Finally, the arylacrylates are reduced by acyl-CoA dehydrogenase (AcdA, CLOSPO_00312) involving its two electron transport factors (EtfA-EtfB, CLOSPO_00313-314). For the oxidative pathway, phenylpyruvate and 4-OH-phenylpyruvate are first oxidatively decarboxylated by pyruvate:ferredoxin oxidoreductase A (PorA, CLOSPO_00147-149), followed by phosphate acyltransferase and acyl kinase reactions that remain to be studied. The enzyme involved in indoleacetic acid production remains unknown, however, candidate genes in the genome include pyruvate:ferredoxin oxidoreductases B and C (PorB, CLOSPO_02262; PorC, CLOSPO_03792). Transformations for which the specific genes involved are not known are indicated in red.