Table 5.
Muropeptide percentage composition of E. coli strains as determined by HPLC and FACE
| Muropeptides | CS109 wild type |
CS12-7 Δ PBP 5 |
CS13-2 Δ PBP la |
CS214-1 Δ PBP la 5 |
CS14-2 Δ ampC |
|||||
|---|---|---|---|---|---|---|---|---|---|---|
| HPLC | FACE | HPLC | FACE | HPLC | FACE | HPLC | FACE | HPLC | FACE | |
| M3 | 9.8±0.1 | 8.2±0.8 | 7.9±0.1 | 7.7±0.6 | 9.6±0.4 | 8.0±0.8 | 8.0±0.5 | 7.5±0.8 | 9.6±1.1 | 7.8±0.8 |
| M4 | 43.9±0.9 | 41.4±3.1 | 42.2±1.7 | 32.1±2.8 | 44.8±1.1 | 41.1±1.6 | 41.6±1.0 | 38.0±5.6 | 46.6±7.5 | 38.4±4.5 |
| M-5 | 0.1±0.0 | 0.5±0.3 | 5.0±1.1 | 6.0±1.3 | 0.1±0.0 | 0.6±0.1 | 4.2±0.2 | 4.9±0.8 | 0.1±0.0 | 1.7±0.1 |
| M3KR | 1.3±0.1 | ND | 1.0±0.4 | ND | 1.7±0.4 | ND | 1.2±0.3 | ND | 1.5±0.3 | ND |
| D44 | 34.3±1.1 | 38.2±2.3 | 31.2±3.1 | 40.9±0.9 | 36.0±0.7 | 36.8±1.6 | 36.9±1.1 | 36.8±8.4 | 33.4±5.5 | 40.0±4.5 |
| D45 | 1.4±0.0 | 7.6±0.1 | ||||||||
| D43 + D43Dap | 2.4±0.3 | 2.5±0.3 | 2.5±0.6 | 1.9±0.3 | 2.4±0.1 | 3.1±1.1 | 2.9±0.6 | 3.2±1.3 | 2.0±0.5 | 1.7±0.4 |
| D43KR | 1.6±0.5 | 1.6±0.6 | 1.4±0.1 | 1.4±0.9 | 1.9±0.3 | 1.9±1.2 | 1.5±0.2 | 1.9 | 1.8±0.7 | 3.1±2.8 |
| Unknown | 2.8±0.9 | 4.7±1.3 | 2.2±0.6 | |||||||
| T444 | 4.3±1.0 | 2.7±0.1 | 2.6±1.2 | 1.9±0.2 | 3.0±1.0 | 3.7±1.6 | 3.1±0.5 | 1.2±0.1 | 3.9±1.3 | 2.4±1.7 |
| T443 + T443Dap | 0.4±0.1 | 0.4±0.1 | 0.4±0.3 | 0.4±0.1 | 0.3±0.2 | 0.5±0.4 | 0.5±0.3 | 0.4±0.0 | 0.6±0.6 | 0.7±0.3 |
| Trimer-KR | 0.2±0.1 | 0.2±0.0 | 0.3±0.0 | 0.2±0.0 | 0.4±0.1 | |||||
| Totals | 99.5±1.1 | 98.1±0.2 | 98.7±0.2 | 96.7±0.6 | 97.9±0.1 | 97.6±0.1 | 98.7±0.2 | 95.7±0.4 | 97.9±0.2 | 94.1±0.5 |
| CS109 wild type |
CS15-3 Δ ampH |
CS362-1 Δ PBP 1a 5 ampC |
CS357-3 Δ PBP 1a 5 ampH |
CS420-2 Δ PBP 1a 5 ampCH |
||||||
|---|---|---|---|---|---|---|---|---|---|---|
| HPLC | FACE | HPLC | FACE | HPLC | FACE | HPLC | FACE | HPLC | FACE | |
| M3 | 9.8±0.1 | 8.2±0.8 | 8.6±0.5 | 7.2±0.3 | 7.5±2.0 | 6.5±0.4 | 7.6±1.3 | 7.1±1.1 | 4.3±0.4 | 3.0±0.9 |
| M4 | 43.9±0.9 | 41.4±3.1 | 42.2±3.1 | 37.8±3.6 | 45.1±1.5 | 38.1±7.1 | 42.3±2.1 | 37.6±4.0 | 38.0±7.8 | 34.5±5.5 |
| M-5 | 0.1±0.0 | 0.5±0.3 | 0.1±0.0 | 1.1±0.7 | 4.8±0.5 | 5.5±1.1 | 4.8±0.2 | 4.9±0.1 | 8.5±2.2 | 6.9±0.4 |
| M3KR | 1.3±0.1 | ND | 1.4±0.1 | ND | 1.4±0.2 | ND | 1.4±0.2 | ND | 2.0±0.6 | ND |
| D44 | 34.3±1.1 | 38.2±2.3 | 37.1±1.0 | 41.4±2.2 | 34.9±4.1 | 40.0±4.6 | 22.8±4.4 | 38.2±4.1 | 30.5±1.2 | 31.0±0.8 |
| D45 | 1.4±0.0 | 11.4±0.2 | 7.0±0.1 | |||||||
| D43 + D43Dap | 2.4±0.3 | 2.5±0.3 | 2.7±0.4 | 3.2±1.2 | 2.2±0.2 | 3.6±1.6 | 2.2±0.4 | 3.2±1.1 | 2.9±1.4 | 1.9±0.6 |
| D43KR | 1.6±0.5 | 1.6±0.6 | 2.1±0.6 | 0.8±0.5 | 1.9±0.8 | ND | 1.4±0.0 | ND | 1.7±0.7 | ND |
| Unknown | 2.8±0.9 | |||||||||
| T444 | 4.3±1.0 | 2.7±0.1 | 4.5±1.2 | 5.2±1.3 | 3.0±0.3 | 3.8 | 3.3±0.1 | 1.6±1.5 | 4.4±1.4 | 4.5±0.1 |
| T443 + T443Dap | 0.4±0.1 | 0.4±0.1 | 0.7±0.8 | 0.5±0.2 | 0.3±0.0 | 0.6 | 0.7±0.6 | 0.5±0.2 | 0.9±0.3 | 1.3±0.8 |
| Trimer-KR | 0.2±0.1 | 0.3±0.1 | 0.6±0.6 | 0.2±0.0 | 0.3±0.2 | |||||
| Totals | 99.5±1.1 | 98.1±0.2 | 97.9±0.3 | 96.0±2.9 | 94.8±1.5 | 90.3±6.8 | 94.2±0.3 | 88.9±2.5 | 89.7±2.1 | 82.9±6.4 |
PBP genes deleted from each strain are listed below the strain name. Muropeptide designations: monomers (M), dimers (D), and trimers (T) are classified as those having tripeptide (three), tetrapeptide (four), or pentapeptide (five) side chains attached to the muramic acid residue. The muropeptides are designated according to the abbreviations described in Table 6. Muropeptides with lipoprotein attached to the side chain had this moiety removed by proteolysis during peptidoglycan preparation but retained the Lys-Arg (KR) residues. The peptide linkages between dimers and trimers were either alanine-to-diaminopimelic acid (no suffix) or DAP-to-DAP (“Dap” suffix). HPLC data are the mean±standard deviation (SD) of measurements from two different gels. For comparison purposes, the amount of anhydromuramic acid muropeptides (<5% of the total) was omitted from the HPLC data because it could not be detected by the FACE technique. The FACE data for CS109, CS14-2, and CS15-3 are the mean±SD of measurements from three different gels. FACE data for all other strains are the mean±SD of measurements from two different gels. Percentages enclosed in solid boxes denote those that are significantly higher than those in the wild type. Percentages enclosed in the dotted boxes denote those that are significantly lower than those in the wild type. Underlined percentages denote results given by the FACE procedure that are significantly different from those given by HPLC analysis. Unknown, a band appearing in some FACE gels but whose chemical identity is not known; ND, not detected.