Appendix 1—table 3. List of genes encoding outer membrane proteins (i.e. porins) and efflux pumps compiled using EcoCyc as previously reported (Kortright et al., 2020), alongside their transcript reads after a 2 hr growth period in lysogeny broth (LB) (i.e. the time point at which antibiotic treatment starts in our microfluidic experiments) measured via RNA-sequencing as previously reported (Smith et al., 2018). Note that it has been reported that permeability of solutes through OmpA (with the most highly expressed transcripts) is a 100-fold lower compared to that through OmpC (Sugawara and Nikaido, 1992) (with the second most highly expressed transcripts), hence we decided to investigate the role played by OmpC in the heterogeneity in the intracellular accumulation of roxithromycin (Figure 4E).
| Membrane genes | Transcript reads | Membrane genes | Transcript reads | Membrane genes | Transcript reads | Membrane genes | Transcript reads |
|---|---|---|---|---|---|---|---|
| ompA | 60,955 | mltA | 398 | acrZ | 47 | yaiO | 6 |
| ompC | 57,458 | yncD | 388 | yfiB | 39 | cusB | 6 |
| ompX | 19,210 | lolB | 345 | cusA | 39 | yehB | 5 |
| lptD | 10,977 | nlpD | 326 | macb | 36 | bglH | 5 |
| tolC | 4722 | mdtK | 312 | yhcD | 33 | wza | 5 |
| fhuA | 4360 | yiaD | 292 | fimD | 31 | blc | 5 |
| bamA | 4237 | nplE | 291 | acrF | 30 | acrE | 5 |
| acrB | 4044 | fepA | 289 | pgaA | 29 | yfgH | 4 |
| bamB | 3796 | yraP | 256 | mdtL | 28 | nanC | 4 |
| ompF | 3650 | emtA | 252 | mdtG | 28 | yqhH | 4 |
| slyB | 3516 | ydiY | 241 | mdtF | 27 | phoE | 4 |
| nlpI | 3367 | tamA | 236 | yfaL | 25 | mdtQ | 3 |
| fadL | 2612 | yjgL | 222 | gfcD | 24 | yliI | 3 |
| ompT | 2601 | mdfA | 220 | gspD | 23 | ompN | 3 |
| mipA | 2289 | ynfB | 220 | yraJ | 22 | mdtO | 3 |
| mltD | 2045 | ypjA | 220 | gfcE | 22 | cusC | 2 |
| fecA | 2009 | pgpB | 193 | flgG | 22 | cusF | 2 |
| tsx | 1971 | mltC | 187 | mdtJ | 21 | mdtP | 2 |
| pal | 1945 | mdtC | 166 | mdtD | 19 | yfeN | 2 |
| skp | 1553 | lpoB | 155 | ydeT | 17 | mdtN | 2 |
| bamD | 1544 | macA | 153 | slp | 16 | csgF | 2 |
| acrA | 1505 | loiP | 137 | yceK | 16 | yjbF | 1 |
| mepS | 1303 | mltF | 134 | mdtI | 13 | csgB | 1 |
| lpp | 1168 | yaiW | 131 | chiP | 12 | envY | 1 |
| borD | 1167 | bhsA | 119 | pagP | 11 | ybgQ | 1 |
| nmpC | 1146 | pqiC | 114 | yedS | 11 | acrS | 1 |
| cirA | 1127 | rsxG | 107 | yjbH | 10 | uidC | 1 |
| bamC | 1123 | rcsF | 105 | rhsD | 9 | csgE | 0 |
| ygiB | 1115 | yfaZ | 101 | elfC | 9 | ompL | 0 |
| flu | 1064 | cusR | 99 | rhsB | 9 | ompG | 0 |
| lptA | 1052 | nfrA | 98 | yfcU | 8 | rzoD | 0 |
| mlaA | 1042 | cusS | 92 | lamB | 8 | rzoR | 0 |
| ybhC | 1021 | acrR | 85 | pgaB | 8 | yddL | 0 |
| lptE | 924 | yghG | 83 | sfmD | 8 | appX | ND |
| bamE | 732 | fhuE | 81 | htrE | 8 | bcsC | ND |
| rlpA | 637 | amiD | 80 | mdtH | 7 | epcC | ND |
| lpoA | 620 | yddB | 76 | yiaT | 7 | qseG | ND |
| fiu | 607 | acrD | 72 | mliC | 7 | ychO | ND |
| btuB | 489 | ecnB | 69 | mdtE | 7 | ypjB | ND |
| tamB | 408 | mdtB | 64 | flgH | 7 | yzcX | ND |
| mltB | 406 | mdtA | 54 | csgG | 6 | ||
| pldA | 404 | ecnA | 51 | hofQ | 6 | ||
| ppk | 404 | mdtM | 49 | ompW | 6 |