Table 6. Conditional rates of indels accumulated in the MA experiments.
| Conditional indel rates ×108 | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| MA experiments on LB medium | MA experiments on minimal medium | ||||||||
| Type of indel | Wild-type ×103a | mutLb | mutD5 | mutD5mutL | mutD5dinB | mutD5dinBumuDC | mutD5lexA3 | mutD5 | mutD5mutL |
| Total | 2.06 ± 0.05 | 0.48 ± 0.01 | 6.3 ± 0.9 | 9.8 ± 0.5 | 4.9 ± 0.6 | 6.5 ± 0.8 | 7.0 ± 0.8 | 0.67 ± 0.14 | 4.9 ± 1.0 |
| +1 bp | 0.53 ± 0.02 | 0.26 ± 0.01 | 2.8 ± 0.4 | 5.0 ± 0.3 | 2.7 ± 0.2 | 3.5 ± 0.5 | 3.5 ± 0.4 | 0.41 ± 0.10 | 2.6 ± 0.5 |
| −1 bp | 1.40 ± 0.05 | 0.20 ± 0001 | 3.4 ± 0.6 | 5.0 ± 0.4 | 2.2 ± 0.4 | 3.0 ± 0.4 | 3.5 ± 0.4 | 0.25 ± 0.07 | 2.3 ± 0.5 |
| +>1 bp | 0.02 ± 0.004 | 0.01 ± 0.001 | 0.01 ± 0.02 | 0.04 ± 0.02 | 0.006 ± 0.0003 | 0.02 ± 0.02 | 0.02 ± 0.02 | < 0.003 | 0.04 ± 0.06 |
| −>1 bp | 0.11 ± 0.01 | 0.01 ± 0.0004 | 0.006 ± 0.02 | 0.003 ± 0.007 | < 0.006 | 0.01 ± 0.01 | 0.01 ± 0.02 | 0.003 ± 0.007 | 0.02 ± 0.04 |
| +1 A:T | 0.74 ± 0.04 | 0.10 ± 0.002 | 3.0 ± 0.5 | 6.9 ± 0.5 | 3.1 ± 0.2 | 4.1 ± 0.7 | 4.4 ± 0.6 | 0.70 ± 0.18 | 3.5 ± 0.7 |
| +1 G:C | 0.34 ± 0.01 | 0.41 ± 0.01 | 2.6 ± 0.5 | 3.1 ± 0.3 | 2.3 ± 0.3 | 2.8 ± 0.5 | 2.6 ± 0.5 | 0.13 ± 0.06 | 1.8 ± 0.5 |
| −1 A:T | 1.91 ± 0.08 | 0.24 ± 0.004 | 4.0 ± 0.7 | 4.0 ± 0.4 | 2.6 ± 0.2 | 3.5 ± 0.6 | 3.5 ± 0.5 | 0.33 ± 0.12 | 2.5 ± 0.6 |
| −1 G:C | 0.91 ± 0.09 | 0.16 ± 0.002 | 2.9 ± 0.6 | 5.5 ± 0.5 | 1.9 ± 0.6 | 2.6 ± 0.5 | 3.5 ± 0.5 | 0.18 ± 0.07 | 2.1 ± 0.5 |
| In run | 10 ± 0.3 | 2.9 ± 0.04 | 33 ± 4 | 55 ± 3 | 24 ± 3 | 34 ± 4 | 37 ± 4 | 3.7 ± 0.8 | 29 ± 5 |
| Not in run | 0.47 ± 0.03 | 0.01 ± 0.001 | 1.0 ± 0.2 | 0.9 ± 0.2 | 1.1 ± 0.1 | 1.1 ± 0.3 | 1.0 ± 0.2 | 0.07 ± 0.03 | 0.27 ± 0.15 |
| Noncoding | 7.0 ± 0.2 | 1.3 ± 0.02 | 11 ± 2 | 19 ± 1 | 9.7 ± 0.6 | 11 ± 2 | 13 ± 2 | 1.7 ± 0.5 | 11 ± 2 |
| Coding | 1.22 ± 0.04 | 0.34 ± 0.004 | 5.4 ± 0.7 | 8.3 ± 0.5 | 4.1 ± 0.6 | 5.7 ± 0.7 | 6.0 ± 0.7 | 0.48 ± 0.12 | 3.9 ± 0.9 |
A run is three or more of the same base pairs in sequence. Data are the conditional mutation rates, which is the number of mutations/number of generations/relevant number of nucleotides. When few indels were recovered, the 95% CL can include 0. MA, mutation accumulation experiments.
a
Data from Foster et al. (2015) for strains PFM2, PFM35, PFM40, PFM88, PFM91, PFM101, and PFM122.
b
Combined results from the mutL mutant strains PFM5, PFM144, and PFM288.