Article Figures & Data
Figures
- Fig. 1.
The mutS-rpoS genomic region located at 61 min on E. coli K-12 chromosome. Primers designed fromfhlA (FP1) and rpoS (RP1) of the K-12 genomic sequences (1) produce a long PCR amplicon of 10.9 kb. Previous studies have shown that Salmonella strains have a 40-kb pathogenicity island (SPI-1) between fhlA andmutS (27) and that the genomic region betweenmutS and rpoS in E. coli O157:H7 andShigella strains is variable in length (19, 20).
- Fig. 2.
(A) Neighbor-joining tree of 27 E. colistrains based on genetic distances estimated from MLEE data. The clonal groups based on electrophoretic type (ET) and strain names are, from left to right: K-12, ECOR group A (ECOR 1, ECOR 10, ECOR 7, ECOR 2, and ECOR 3), EPEC 2 (DEC 12e, 125-55, DEC 12c, DEC 12d, and DEC 11a), 921-B4, EHEC 2 (DEC 9e, DEC 8c, DEC 8b, 928/91, and CL 37), EPEC 1 (DEC 2a, D55, DEC 1a, E2348/69, and E851/71), and EHEC 1 (DEC 5d, OK-1, 86-24, EDL-933, and 93-111). (B) Resolution of long PCR amplicons corresponding to the genomic region extending from mutS torpoS. The molecular weight marker (MW) is the lambda DNA/HindIII ladder. (C) Restriction fragments (>200 bp in length) of the mutS-rpoS long PCR products digested withAluI. The molecular weight marker is a 100-bp DNA ladder.
- Fig. 3.
Restriction maps of the mutS-rpoS chromosomal region. Approximate locations of restriction sites for five restriction enzymes: EcoRV (E), NdeI (N), AccI (A), Csp45 (C), and NspI (Ns). The pattern of restriction sites is conserved among strains of each pathogenic group with the exception of the second NspI site inmutS [(Ns)*], which is present in EPEC 2 strains but absent in EHEC 2 strains. A distinct NspI map was obtained for 921-B4 (not shown). The novel DNA segment found in EPEC and EHEC strains is located at the 3′ end of rpoS and is highlighted with the gray bar.
- Fig. 4.
Polymorphic codons (pc) of four protein-coding genes in the mutS-rpoS region. Boxes highlight amino acid replacements. (A) Three out of 22 pc predict replacements (I191V, K202T, and A206T) in o454 (1,362 bp); (B) 5 out of 86 pc predict replacements (A36D, T58I, A63T, T83A, and D119E) inyclC (1,425 bp); (C) 6 out of 22 pc predict replacements (C12C, K37T, R52H, T70I, M124T, and H179Y) in pad1 (591 bp); (D) 6 out of 21 pc predict replacements (A2T, A81P, I98V, A119G, M126V, and T135A) in slyA (405 bp).
- Fig. 5.
Phylogenetic trees of the genomic region betweenmutS and rpoS. The trees were constructed by the neighbor-joining algorithm, with genetic distance measured by the number of synonymous substitutions per 100 synonymous sites. (A) Gene phylogeny for the combined coding sequences o258 ando454 found in K-12, EPEC, and EHEC strains; (B) gene phylogeny for the combined sequences of yclC,pad1, and slyA found in E. coliO157:H7, EPEC, and EHEC strains.
- Fig. 6.
Evolutionary model of the mutS-rpoS genomic region. (A) The left side is a cladogram of the phylogeny of the groups; the right side shows a diagram of the genes in themutS-rpoS region. The EPEC 1, EPEC 2, and EHEC 2 strains have a conserved ancestral sequence in both the f265-o454and yclC-slyA gene segments. The model predicts two independent deletions of gene segments: the loss ofyclC-slyA in the branch leading to K-12 and the ECOR group A strains and the loss of the f265-o454 segment in the branch leading to O55:H7, O157:H7, and other EHEC 1 strains. It is not clear if the additional DNA upstream of mutS in the EPEC 1 strains is acquired (as marked here) or is ancestral and has been lost early in divergence. (B) Orientation of the genes for ancestral E. coli and Salmonella. The location of a short sequence with high homology to the Salmonella rpoS gene is marked as the rpoS remnant.
Tables
- Table 1.
Serotypes and sources of 26 E. coli strains
ET groupa Strain Serotypeb Location Reference or source EPEC 1 1 DEC 1a O55:H6 Pennsylvania 3;Centers for6 2 DEC 2a O55:H6 Congo 36 3 E2348/69 O127:H6 United Kingdom 21 4 D55 O127:ND Thailand 9 5 E851/71 O142:H6 Scotland 21 EPEC 2 6 DEC 11a O128:H2 Montana 26 7 DEC 12c O111:NM Panama 36 8 DEC 12d O111:H2 Peru 36 9 DEC 12e O111:H− Kenya 36 10 124-55 O111:H− Florida 28 EHEC 1 11 EDL-933 O157:H7 Oregon 37 12 86-24 O157:H7 Washington 10 13 93-111 O157:H7 Washington P. Tarr 14 OK-1 O157:H7 Japan T. Takeda 15 DEC 5d O55:H7 Sri Lanka 26 EHEC 2 16 DEC 8b O111:H8 Idaho 2 17 DEC 8c O111:NM South Dakota 5 18 CL 37 O111:H8 Canada 15 19 DEC 9f O26:NM South Dakota CDCc 20 928/91 O111:H− Germany H. Karch Others 22 ECOR 1 ON:H− Iowa 33 23 ECOR 2 ON:H32 New York 33 24 ECOR 3 O1:NM Massachusetts 33 25 ECOR 7 O85:H− Washington 33 26 ECOR 10 O6:H10 Sweden 33 27 921-B4 O111:H9 Finland 42 - Table 2.
Fragment sizes from six-base cutter restriction enzyme digests of the mutS-rpoS genomic region
Strain or group (n) mutS-rpoS PCR fragment size (kb) Fragment sizes (kb) EcoRV NdeI Csp45 AccI NspI K-12 10.9 1.4, 2.2, 2.5, 4.8 0.4, 0.8, 1.9, 2.3, 5.6 0.7, 2.1, 3.9, 4.2 0.2, 1.3, 1.5, 1.7, 6.2 0.3, 0.6, 1.0, 1.3, 1.7, 2.7, 3.3 ECOR A (5) 10.9 1.4, 2.2, 2.5, 4.8 0.4, 0.8, 1.9, 2.3, 5.6 0.7, 2.1, 3.9, 4.2 0.2, 1.3, 1.5, 1.7, 6.2 0.3, 0.6, 1.0, 1.3, 1.7, 2.7, 3.3 EPEC 2 (5) 13.8 1.4, 2.2, 2.5, 2.8, 4.8 0.4, 0.8, 1.9, 2.3, 8.4 0.7, 2.9, 4.2, 6.0 0.2, 1.0, 1.3, 1.5, 3.6, 6.2 0.3, 0.6, 1.3, 1.7, 2.7, 7.2 921-B4 13.8 1.4, 2.2, 2.5, 2.8, 4.8 0.4, 0.8, 1.9, 2.3, 8.4 0.7, 2.9, 4.2, 6.0 0.2, 1.0, 1.3, 1.5, 3.6, 6.2 0.5, 0.6, 1.6, 1.7, 2.7, 2.7, 3.9 EHEC 2 (5) 13.8 1.4, 2.2, 2.5, 2.8, 4.8 0.4, 0.8, 1.9, 2.3, 8.4 0.7, 2.9, 4.2, 6.0 0.2, 1.0, 1.3, 1.5, 3.6, 6.2 0.6, 1.6, 1.7, 2.7, 7.2 EPEC 1 (5) 14.2 1.8, 2.4, 2.5, 2.7, 4.8 0.4, 0.8, 2.3, 2.3, 8.4 0.7, 2.1, 2.9, 4.2, 4.5 0.2, 0.5, 1.0, 1.3, 1.4, 1.5, 2.1, 6.2 0.3, 1.0, 1.2, 1.2, 1.7, 2.7, 2.7, 3.3 EHEC 1 (5) 7.8 1.4, 2.2, 4.2 1.9, 2.3, 3.6 2.9, 5.0 0.2, 1.0, 6.6 1.0, 2.8, 4.0 - Table 3.
Sequence divergencea between genes in the mutS-rpoS region
Comparison %p Mean ± SD dN − dSb dS dN DEC 1a vs DEC 9f mutS 5.5 25.02 ± 2.49 0.19 ± 0.11 −24.8 o258 2.7 6.65 ± 1.55 1.55 ± 0.52 −5.1 o454 1.2 4.22 ± 1.10 0.10 ± 0.10 −4.1 yclC 3.8 17.10 ± 2.43 0.19 ± 0.13 −16.9 pad1 2.4 7.12 ± 2.28 0.91 ± 0.45 −6.2 slyA 3.7 13.18 ± 4.07 1.28 ± 0.64 −11.9 rpoS 1.3 5.21 ± 1.75 0.00 ± 0.00 −5.2 DEC 1a vs K-12 mutS 5.9 27.17 ± 2.63 0.26 ± 0.13 −26.9 o258 2.5 5.50 ± 1.76 1.55 ± 0.52 −4.0 o454 1.3 4.52 ± 1.14 0.10 ± 0.14 −4.4 rpoS 1.3 5.21 ± 1.75 0.00 ± 0.00 −5.2 DEC 1a vs O157:H7 mutS 5.6 25.53 ± 2.52 0.19 ± 0.11 −25.3 yclC 3.9 16.38 ± 2.37 0.19 ± 0.13 −16.2 pad1 2.4 7.10 ± 2.27 0.91 ± 0.45 −6.2 slyA 3.2 11.80 ± 3.81 0.96 ± 0.56 −10.8 rpoS 0.4 5.81 ± 1.86 0.00 ± 0.00 −5.8 ↵a Measured by the percentage of polymorphic nucleotide sites (% p), the number of synonymous substitutions per 100 synonymous sites (dS), and the number of nonsynonymous substitutions per 100 nonsynonymous sites (dN).
↵b A measure of the level of selective constraint and conservation of amino acid sequence.
