TABLE 3.
Genomic variations of the genes encoding c-di-GMP-binding proteins in 61 E. coli strains
| Genea | Mutation(s)b | Consequence for protein expressionc | Strain(s) (pathotype[s]) |
|---|---|---|---|
| ycgR | 1,313-nt insertion of IS element (after nt 594, in codon 199) | YcgR (199 + 35 AAs) is C-terminally truncated | O157:H7 strain EDL933 (EHEC), O157:H7 strain Sakai (EHEC), Xuzhou21 (EHEC) (O157:H7) |
| 5′ deletion including the first 595 nt | YcgR is absent | O157:H7 strain EC4115 (EHEC), O157:H7 strain TW14359 (EHEC) | |
| bcsA | 19-noncontiguous-nt deletion (after nt 83, in codon 28)/frameshift | BcsA (27 + 56 AAs) is C-terminally truncated | IAI39 (ExPEC), CE10 (ExPEC, NMEC) |
| 1-nt (G) deletion (after nt 550, in codon 184)/frameshift | BcsA (184 + 1 AA) is C-terminally truncated | S88 (ExPEC) | |
| 1-nt (A) deletion (after nt 186, in codon 62)/frameshift; 1-nt (G) deletion (after nt 698, in codon 233); 1-nt (A) insertion (after nt 702, in codon 234) | BcsA (62 + 27 AAs) is C-terminally truncated | UMN026 (ExPEC) | |
| Whole gene deletion | BcsA is absent | HS (C) | |
| bcsE | TGT→TGA (stop) (codon 101) | BcsE (100 AAs) is C-terminally truncated | ATCC 8739 (C) |
| 1-nt (C) insertion (after nt 1340, in codon 447) | BcsE (447 + 15 AAs) is C-terminally truncated | O104:H4 strain LB226692 (EAEC), O104:H4 strain 2009EL-2050 (EAEC), O104:H4 strain 2009EL-2071 (EAEC), O104:H4 strain 2011C-3493 (EAEC) | |
| 5′ deletion including the first 779 nt | BcsE is absent | RM13516 (STEC), RM13514 (STEC), RM12761 (STEC), RM12581 (STEC) | |
| Whole gene deletion | BcsE is absent | HS (C) |
a
All of these genes encoded c-di-GMP-binding proteins.
b
nt, nucleotide.
c
AAs, amino acids.