Supplemental text

Energy Metabolism

Based on the TCA cycle genes that they do have, H. somnus 129Pt and H. influenzae Rd should be able to generate alpha-ketoglutarate by the reductive branch, from oxaloacetate through malate, fumarate, succinate and succinyl-CoA to alpha-ketoglutarate. Because H. ducreyi 35000HP was also missing the gene encoding succinyl-CoA synthetase (converts succinate to succinyl-CoA), it apparently can only generate alpha-ketoglutarate (within the context of the TCA cycle) by the action of aspartate aminotransferase, encoded by aspC. Aspartate aminotransferase also appeared to be a key enzyme for H. ducreyi production of glutamate, as it did not have the complete glutamine synthetase/glutamate synthetase pathway, or glutamate dehydrogenase (Table S8). However, it is likely that H. ducreyi can generate alpha-ketoglutarate by some other reactions that are not tied to the TCA cycle. For example, alpha-ketoglutarate is a by-product of the action of dTDP-4-oxo-6-deoxy-D-glucose transaminase, encoded by wecE(rffA) (30), which H. ducreyi did have. H. somnus 129Pt was unlike H. influenzae Rd and H. ducreyi 35000HP, in that it was only missing isocitrate dehydrogenase. Since H. somnus 129Pt had gltA and acnB, it should be able to make isocitrate from oxaloacetate, but it did not have icd, so it probably cannot convert isocitrate to alpha-ketoglutarate.

Like H. influenzae Rd (43), both H. somnus 129Pt and H. ducreyi 35000HP were missing the aerobic respiratory nitrate reductases 1 (narGHJI) and 2 (narZYWV), formate hydrogen lyase (hyc), hydrogenase 1 (hya), and hydrogenase 2 (hyb, hyp).