Supplemental text

Sulfate assimilation and cysteine metabolism

As in H. influenzae Rd (43), both H. somnus 129Pt and H. ducreyi 35000HP had genes encoding the enzymes that convert L-serine to cysteine (cysE; cysK), as well as a sulfate transporter (cysZ). Also like H. influenzae Rd, both H. somnus 129Pt and H. ducreyi 35000HP lacked the cysA,C,D,G,H,I,J,M genes for sulfate assimilation. H. somnus 129Pt had both tnaA (HS_0801) and metC (HS_0475) genes involved in cysteine degradation, H. influenzae Rd had metC (HI0122), and H. ducreyi 35000HP did not have these genes.
Lysine, threonine and methionine

The pathway from L-aspartate to L-lysine was complete in all three organisms, H. influenzae Rd and H. somnus 129Pt had all of the components to make L-threonine from L-aspartate, and none of the three organisms had all of the components to make S-adenosyl-L-methionine from L-aspartate (Table S6). In E. coli, thrA, metL, and lysC encode similar aspartokinase isozymes that show feedback inhibition by threonine, methionine, and lysine, respectively (23). metL was missing in H. influenzae Rd, H. somnus 129Pt and H. ducreyi 35000HP. H. ducreyi 35000HP had a lysC homolog (HD1375), which encodes lysine-sensitive aspartokinase III, but H. influenzae Rd and H. somnus 129Pt had genes that were similar to E. coli thrA (HS_1214 63% amino acid identity; HI0089 62% amino acid identity), which encodes a bifunctional protein containing aspartokinase I (N-terminal) and homoserine dehydrogenase I (C-terminal). Only H. somnus 129Pt had cadB and cadA, involved in lysine degradation. In E. coli, CadB exhibits cadaverine uptake activity and cadaverine excretion activity, acting as a cadaverine-lysine antiporter. cadA encodes lysine decarboxylase (41). H. somnus 129Pt and H. influenzae Rd had ilvA (HS_0183; HI0738a), encoding threonine deaminase. Both H. somnus 129Pt and H. influenzae Rd had metB (HS_1345; HI0086), encoding cystathionine gamma-synthase. H. influenzae Rd, H. somnus 129Pt and H. ducreyi 35000HP all had genes encoding formate acetyltransferase (HS_1136; HD0990; HI0180) and propionate kinase (HS_0803; HD1456; HI1204), which comprise the branch of threonine metabolism leading to propionate. H. influenzae Rd, H. somnus 129Pt and H. ducreyi 35000HP all had metK, which would allow them to convert L-methionine to S-adenosyl-L-methionine (8). H. somnus 129Pt also had a gene encoding DNA-cytosine methyltransferase, which forms S-adenosyl-homocysteine from S-adenosyl-L-methionine (8).