Table 3. Genotype markers in ER2796 and underlying sequence features.
| Allele | Old Allele Name (if changed) | Alteration | Genes Affected | ER2796 Sequence | MG1655 Sequence | Amino Acid Changes |
|---|---|---|---|---|---|---|
| fhuA2::IS2 | fhuA2 | IS2 disruption | fhuA (b0150) | 167920–169255 (169251–169255 is target site duplication) | between 167919–167920 | ER2796_149 (aa 1–145 + 13 aa), and ER2796_151 (aa 158–747) |
| ΔlacZ4826 | Δ(lacZ)r1 | deletion | lacZ (b0344) | between 365092–365093 | 362419–364862 | Δ223–1024; adds 40 aa extension overlapping lacY |
| glnX44 a | glnV44 | tRNA transition | glnX (b0664) | 693302 (T) | 695693 (C) | (DNA nt) G34A |
| e14 – (McrA–) | mcr-62 | excision | ymfDE, lit, intE, xisE, ymfIJ, cohE, croE, ymfLM, oweE, aaaE, ymfR, bee, jayE, ymfQ, stfP, tfaPE, stfE, pinE, mcrA (b1137-b1141, b1143-b1148, b4692-b4693, b1150-b1159, respectively) | between 1193386–1193387 | 1195598–1210801 | null; associated changes in icd sequence |
| trpE31 | trp-31 | missense | trpE (b1264) | 1302017 (T) | 1319610 (C) | G454D (ER2796_1284) |
| dcm-6 | silent | dcm (b1961) | 2012149 (T) | 2029184 (C) | E386 | |
| nonsense (TGA) b | dcm (b1961) | 2013172 (T) | 2030207 (C) | W45stop (ER2796_2013; also ER2796_2012 from internal start at aa 111) | ||
| yedZ501::Tn10(TetR) | zed-501::Tn10 | Tn10 insertion | yedZ (b1972) | 2021730–2030885 (2030877–2030885 is target site duplication) | between 2038764–2038765 | Δ87–211; ER2796_2025 (aa 1–86 + 15 aa), and ER2796_2035 (from internal start at aa 102) |
| Δ(hisG)1 | hisG1(Fs) | deletion, in-frame | hisG (b2019) | between 2080789–2080790 | 2088669–2088704 | Δ152–163 (ER2796_2082) |
| luxS11 c | –1 frameshift | luxS (b2687) | between 2798558–2798559 | 2812480 (A) | Δ92–171; ER2796_2763 (aa 1–90 + 20 aa), and ER2796_2762 (from internal start at aa 108) | |
| silent | luxS (b2687) | 2798561 (C) | 2812483 (T) | L91 (ER2796_2762) | ||
| rpoS396(Am) d | nonsense (TAG) | rpoS (b2741) | 2851555 (A) | 2865477 (G) | E33stop ER2796_2821 (from internal start at aa 40) | |
| argG6(Fs) | argG6 | –1 frameshift | argG (b3172) | between 3304561–3304562 | 3317286 (C) | Δ210–447 ER2796_3265 (aa 1–209 + 13 aa), and ER2796_3266 (from internal start at aa 221) |
| rpsL104 | missense | rpsL (b3342) | 3443238 (G) | 3472313 (T) | K88Q | |
| missense | rpsL (b3342) | 3443372 (G) | 3472447 (T) | K43T (ER2796_3428) | ||
| Δdam-16::Kan R | deletion + 1266 bp KanR insertion | dam (b3387) | 3484166–3485431 | 3513241–3513773 | Δ55–242 ER2796_3474 (from internal start at aa 242) | |
| xyl-7 | missense | xylB (b3564) | 3699368 (A) | 3726511 (G) | A295V (ER2796_3669) | |
| missense | xylA (b3565) | 3700835 (A) | 3727978 (G) | H271Y (ER2796_3670) | ||
| silent | xylA (b3565) | 3700836 (G) | 3727979 (A) | N270 | ||
| insertion (IS1) | xylF (b3566) | 3702309–3703085 | between 3729451–3729452 | Δ100–330; adds 1 aa extension (ER2796_3671) | ||
| mtlA2(Fs) | mtlA2 | –2 frameshift | mtlA (b3599) | between 3744696–3744697 | 3771063–3771064 (GG) | Δ254–637 ER2796_3708 (aa 1–253 + 60 aa), and ER2796_3709 (from internal start at aa 306) |
| rph WT e | +1 frameshift | rph (b3643) | 3787535 (C) | between 3813902–3813903 | ER2796_3754 | |
| metB1(Fs) | metB1 | –2 frameshift | metB (b3939) | between 4100468–4100469 | 4126836–4126837 (CG) | Δ48–386; ER2796_4061 (8 aa + aa 48–386) |
| Δ(fimB-opgB)114::IS10(RM–) f | Δ(mcr-hsd-mrr)114::IS10 | deletion of 60,679 bp + insertion of 2 IS10 elements in direct repeat | fimBEAICDFGH, gntP, uxuABR, yjiC, iraD, yjiE, iadA, yjiGH, kptA, yjiJKLMN, mdtM, yjiPRSTV, mcrCB, symER, hsdSMR, mrr, yjiAXY, tsr, yjjLMN, opgB (b4312-b4337, b4339-b4342, b4486, b4345-b4347, b4625 [ncRNA], b4348-b4359, respectively) | 4511776–4514442 (4511776–4513104 and 4513114–4514442 are IS10, 4513105–4513113 is target site duplication [inverted]) | 4537567–4595455 | null, except opgB (b4359) Δ671–763; ER2796_4466 (aa 1–670) |
a The reassignment of glnV44 (supE44) was noted previously [43].
b The double mutation (one silent) is in agreement with a previous study [35].
c The sequence of luxS reported here is identical to a previous study [70], although our alignment differs slightly, moving the frameshift 3 nt and inferring a transition instead of a transversion. The steps that resulted in the shared luxS11 allele clearly include a base deletion and a base change, but exactly which deletion and which base change depend on the local alignment. Spontaneous unselected transitions are somewhat more frequent than transversions [71], so our alignment may be preferable. The mutation is present in DH1 [72] (see Table 1), an ancestor of the strain used in [70] and may have been present in sibling strains JC1552 (ancestral to ER2796; RecA+) and JC1553 (source of the recA1 allele of the DH1 and its descendants [73, 74]). The luxS and recA genes are very close, about 8 kb apart, and introduction of recA1 was the last step in construction of DH1.
d This nonsense mutation, which is common in laboratory E. coli strains [75], was most likely ancestral, not introduced by transduction. It may be partially suppressed in this strain. The rpoS mutation and the accompanying supE44 mutation (identified here as glnX44) can be traced to strain Y10, very early in the K-12 pedigree [28].
e This frameshift mutation presumably restores the wild type state, reverting the frameshift present in early K-12 derivative strains MG1655 and W3110 [76].
f The position of the parental zjj202::Tn10 is inferred to be 4597466–4597474 of MG1655 (NC_000913.2), the nine base target sequence that is duplicated upon insertion.