Supplemental Material Carbohydrate utilization
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- Haemophilus -specific uptake sequences
ExopolysaccharideH. somnus produces an exopolysaccharide that contains mannose and galactose, whose production is upregulated when the bacteria are grown anaerobically and in high salt (T.J. Inzana, A. Cox, and G. Glindemann, Abstr. 102nd General Meeting of the American Society for Microbiology, abstr. Z-26, 2002) (40). We found in H. somnus 129Pt all but one of the genes involved in the pathways leading to GDP-D-mannose and GDP-D-galactose (Table S16), which are incorporated into the exopolysaccharide of Burkholderia cepacia (39). The genes necessary for GDP-D-galactose synthesis included phosphoglucomutase (HS_0730), UDP-glucose pyrophosphorylase (galU; HS_1117) and UDP-glucose epimerase (galE; HS_0789). For GDP-D-mannose synthesis, the genes that were present in H. somnus 129Pt included phosphoglucose isomerase (pgi; HS_0938), phosphomannose isomerase/mannose-6-phosphate isomerase (manA; HS_0605) and phosphomannomutase (manB; HS_1118 and HS_1670). Missing from H. somnus 129Pt was the manC gene encoding GDP-D-mannose-pyrophosphorylase, which catalyzes the last step in the formation of GDP-D-mannose, the conversion of mannose-1-phosphate to GDP-D-mannose. Haemophilus-specific uptake sequencesThe H. influenzae DNA uptake signal sequence is overrepresented in H. ducreyi and H. somnus (2). Bakkali et al. (2) report 41 Haemophilus-specific uptake sequences (hUSs) in H. ducreyi, most of which cluster in 2 islands of bacteriophage genes. We found the H. influenzae consensus of “AAGTGCGGT” (and its reverse complement “ACCGCACTT”) in 37 locations throughout the H. ducreyi 35000HP genome, and in agreement with the previous report, most of these were in areas containing bacteriophage genes. In addition, 32 (87%) of the consensus sequence locations in H. ducreyi 35000HP were in CDSs. Bakkali et al. (2) also reported that the unfinished sequence of H. somnus 129Pt has 1205 hUSs. We found that the finished genome sequence of H. somnus 129Pt had approximately 1244 potential hUSs. 62% (776) of these sites were within coding sequences and the rest were in intergenic regions. H. somnus 129Pt, H. ducreyi 35000HP and H. influenzae Rd all had genes involved in DNA uptake and transformation (11, 12, 45)(Table S13). Restriction modification systems As shown in Table S15, H. somnus 129Pt had genes encoding components of type I and the BcgI restriction-modification systems. H. ducreyi 35000HP had one gene encoding a possible type I methytransferase protein(HD0914), as well as genes encoding a type III system and possibly the BcgI system. H. influenzae Rd had genes encoding components of type I, II and III systems, but not BcgI. In terms of type I systems, H. somnus 129Pt had hsdS (HS_0556) and an hsdR gene (HS_0559) that was also present in H. influenzae Rd (HI1285). H. somnus 129Pt had a second hsdS (HS_0560), but not hsdM. H. influenzae Rd had one complete type I system composed of the genes HI1285 – HI1287 (hsdR, hsdS and hsdM). Another type I system in H. influenzae Rd consisted of HI0215 (hsdM, which contained a frameshift), HI0216 (hsdS) and hsdR (HI0218). Neither H. somnus 129Pt nor H. ducreyi 35000HP had any type II system genes. H. influenzae Rd had three complete type II systems, encoded by HI0512 and HI0513, HI1040 and HI1041, HI1393 and HI1392. H. somnus 129Pt did not have any type III restriction-modification system genes. H. influenzae Rd had a type III methylase gene (HI1056), while H. ducreyi 35000HP had a complete type III system (HD1690 to HD1693). There is evidence supporting the hypothesis that restriction modification systems may move between and within genomes and may cause evolutionary changes in genomes (25). This evidence includes observations of the proximity of mobile genetic elements to restriction modification gene complexes. Our results indicated that all of the restriction modification system gene complexes in H. somnus 129Pt were in the vicinity of mobile elements, including putative prophage regions and transposases (Table 15). Also, as the H. influenzae DNA uptake signal sequence is overrepresented in H. somnus (2), mobile elements may not be necessary for the movement of restriction modification gene complexes. Several of the restriction-modification genes either contain the H. influenzae DNA uptake signal sequence or are close to H. influenzae DNA uptake signal sequences, so they may have been acquired by DNA uptake.
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