Table 2.
Genes with the most deletions, duplications, insertions, and intergenic point mutations
| Genes
|
Mutations
|
Number
|
IS
|
MAE
|
Annotation
|
|---|---|---|---|---|---|
| rbsD | mostly large deletions | 41 | yes | no | D-ribose utilization; most deletions affect entire rbs operon |
| nupC | various intergenic | 19 | yes | yes | nucleoside transporter |
| iap | mostly large indels | 19 | yes | no | alkaline-phosphatase isozyme conversion; most indels affect tens of adjacent genes including rpoS, which encodes stationary-phase σ factor |
| mokB | various indels | 17 | yes | yes | enables hokB toxin expression |
| yhgI/gntT | intergenic point mutations | 16 | no | no | gluconate transport |
| mokC | various indels | 15 | yes | yes | enables hokC toxin expression |
| ybcU (borD) | large indels | 14 | yes | no | indels affect this and adjacent remnants of DLP12 prophage |
| ECB_02013 | various indels | 14 | no | yes | indels affect this and adjacent remnants of P2-like prophage |
| ECB_02816 (kpsD) | various indels | 14 | yes | no | polysialic-acid transport protein precursor |
| acs/nrfA | various intergenic | 14 | no | no | acetyl-CoA synthase; nitrite reductase |
| hokE | large indels | 12 | yes | no | toxin in plasmid-derived toxin-antitoxin system; most indels affect several adjacent genes involved in iron acquisition |
| ybeB/phpB | various intergenic | 11 | yes | no | unknown functions, but adjacent to genes involved in cell-wall synthesis |
| ydiJ/ydiK | various intergenic | 11 | no | no | predicted FAD-linked oxidoreductase; putative inner membrane protein |
| ldrC | various indels | 10 | yes | yes | small toxic polypeptide |
| menC | IS insertions | 10 | yes | yes | menaquinone biosynthesis |
| fimA | mostly IS insertions | 10 | yes | no | component of fimbrial complex |
Genes are ranked by total mutations excluding nonsynonymous and synonymous point mutations. When two genes are separated by a slash, the affected sequence includes the intergenic region between them. Parenthetical gene names are synonyms. IS column indicates whether the majority of mutations involve IS elements. MAE column indicates whether the same or nearly identical mutations occurred in one or more MAE lines. Data are from populations with the ancestral point-mutation rate throughout and others before they evolved hypermutability.