TABLE 3.
Partial list of the most differentially expressed genes for biofilm cells of BW25113 sdiA strains expressing SdiA, no SdiA, and SdiA1E11a
| Functional group and/or gene | b no.b | Change in expression (fold)
|
Description and/or functionc | |
|---|---|---|---|---|
| SdiA vs no SdiA | SdiA1E11 vs SdiA | |||
| Indole-related | ||||
| sdiA | b1916 | 5,043.0 | −2.3 | LuxR/UhpA family, regulation of cell division ftsQAZ genes, sensing AHLs, required for indole signaling |
| tnaC | b3707 | −22.6 | 16.0 | Tryptophanase leader peptide |
| tnaA | b3708 | −7.5 | 6.5 | Tryptophanase |
| tnaB | b3709 | −16.0 | 9.8 | Low-affinity tryptophan permease |
| Fimbria and curli | ||||
| sfmH | b0533 | −2.3 | 4.6 | Fimbrial assembly protein |
| csgG | b1037 | −21.1 | 3.2 | Curli production assembly/transport component |
| csgF | b1038 | −36.8 | 4.3 | Curli production assembly/transport component |
| csgE | b1039 | −24.3 | 3.7 | Curli production assembly/transport component, second curli operon |
| csgD | b1040 | −17.1 | 3.0 | Two-component transcriptional regulator for second curli operon, family of LuxR/UhpA |
| csgB | b1041 | −29.9 | 2.8 | Minor curlin subunit precursor |
| csgA | b1042 | −17.1 | 2.6 | Curlin major subunit, coiled surface structures, cryptic |
| csgC | b1043 | −10.6 | 3.2 | Putative curli production protein |
| yfcV | b2339 | −2.0 | 4.0 | Putative fimbria-like protein |
| AI-2 uptake | ||||
| lsrA | b1513 | −7.0 | 3.0 | AI-2 uptake |
| lsrC | b1514 | −4.9 | 3.0 | AI-2 uptake |
| lsrD | b1515 | −5.3 | 3.5 | AI-2 uptake |
| lsrB | b1516 | −13.9 | 3.2 | AI-2 uptake |
| lsrF | b1517 | −9.8 | 4.0 | Function unknown, involved in AI-2 catabolism |
| lsrG | b1518 | −7.5 | 3.0 | Function unknown, involved in AI-2 catabolism |
| Acid resistance | ||||
| ariR | b1166 | −4.9 | 3.7 | AriR, regulator of acid resistance influenced by indole |
| ymgC | b1167 | −4.0 | 3.7 | Hypothetical protein in AriR operon |
| gadC | b1492 | −14.9 | 3.0 | Glutamic acid decarboxylase |
| gadB | b1493 | −32.0 | 3.5 | Glutamate decarboxylase isozyme |
| gadX | b3516 | −5.7 | 2.5 | Putative AraC-type regulatory protein |
| gadA | b3517 | −21.1 | 3.5 | Glutamate decarboxylase A, isozyme, PLP dependent |
| hdeB | b3509 | −19.7 | 3.2 | Acid resistance protein HdeB |
| hdeA | b3510 | −14.9 | 3.2 | 10K-L protein, periplasmic protein related to acid resistance protein |
| hdeD | b3511 | −11.3 | 2.6 | Acid resistance protein HdeD |
| Cold shock and stress | ||||
| cspH | b0989 | 8.0 | −4.0 | Cold shock protein CspH |
| cspG | b0990 | 4.9 | −3.5 | Cold shock protein CspG |
| cspI | b1552 | 2.8 | −4.0 | Cold shock protein CspI |
| cspB | b1557 | 5.3 | −4.0 | Cold shock protein CspB |
| cspF | b1558 | 10.6 | −4.9 | Cold shock protein CspF |
| rtT | b1228 | 8.0 | −4.6 | rtT RNA, may modulate the stringent response |
| katE | b1732 | −5.7 | 2.1 | Catalase HPII |
| csiE | b2535 | −7.0 | 4.0 | Stationary-phase inducible protein |
| csiD | b2659 | −14.9 | 3.7 | Carbon starvation-induced (csi) gene |
| uspB | b3494 | −6.5 | 2.3 | Universal stress protein B |
| ibpB | b3686 | 4.0 | 1.1 | 16-kDa heat shock protein B |
| ibpA | b3687 | 5.3 | −1.6 | 16-kDa heat shock protein A |
| oxyS | b4458 | 4.9 | −4.0 | Global regulatory RNA OxyS |
| Metabolism and transport | ||||
| psiF | b0384 | −7.5 | 2.5 | Phosphate starvation-inducible protein psiF precursor |
| queA | b0405 | 4.3 | −2.6 | S-Adenosylmethionine:tRNA ribosyltransferase-isomerase |
| poxB | b0871 | −6.1 | 1.6 | Pyruvate dehydrogenase/oxidase, FAD and thiamine PPi binding |
| agp | b1002 | −6.1 | 4.9 | Acid glucose-1-phosphatase |
| potB | b1125 | 4.0 | −2.5 | Spermidine/putrescine transport system permease protein |
| potA | b1126 | 4.6 | −2.5 | Spermidine/putrescine transport ATP-binding protein |
| narY | b1467 | −6.1 | 3.2 | Cryptic nitrate reductase 2 β subunit |
| narZ | b1468 | −8.0 | 4.3 | Cryptic nitrate reductase 2 α subunit |
| narU | b1469 | −5.3 | 3.2 | Nitrite extrusion protein 2 |
| osmC | b1482 | −6.1 | 1.9 | Osmotically inducible protein C |
| osmE | b1739 | −8.0 | 2.1 | Osmotically inducible lipoprotein E precursor |
| rnfB | b1628 | 4.0 | −2.5 | Electron transport complex protein |
| astE | b1744 | −8.6 | 4.6 | Succinylglutamate desuccinylase |
| astB | b1745 | −12.1 | 4.3 | Succinylarginine dihydrolase |
| astD | b1746 | −8.0 | 4.0 | Succinylglutamic semialdehyde dehydrogenase |
| astA | b1747 | −13.9 | 4.6 | Arginine succinyltransferase |
| cstC | b1748 | −12.1 | 4.9 | Succinylornithine transaminase |
| flu | b2000 | −1.4 | 7.0 | Antigen 43 (Ag43) phase-variable biofilm formation autotransporter |
| fbaB | b2097 | −8.6 | 2.8 | Fructose-bisphosphate aldolase class I |
| yojH | b2210 | 5.7 | −2.6 | Malate:quinone oxidoreductase |
| tktB | b2465 | −6.5 | 1.7 | Transketolase 2 |
| gabD | b2661 | −13.0 | 2.6 | Succinate-semialdehyde dehydrogenase [NADP+] |
| gabT | b2662 | −13.0 | 3.5 | 4-Aminobutyrate aminotransferase |
| gabP | b2663 | −8.6 | 3.5 | GABA permease |
| hycB | b2724 | −3.5 | 4.6 | Formate hydrogenlyase subunit 2 |
| hyuA | b2873 | −2.6 | 4.0 | Phenylhydantoinase |
| ravA | b3012 | −5.3 | 2.3 | 2,5-Diketo-d-gluconic acid reductase A |
| glgS | b3049 | −7.0 | 2.5 | Glycogen synthesis protein |
| secG | b3175 | 4.0 | −2.6 | Protein export membrane protein |
| rpsI | b3230 | 4.6 | −2.6 | 30S ribosomal protein S9 |
| rpsQ | b3311 | 4.6 | −2.6 | 30S ribosomal protein S17 |
| glpD | b3426 | 5.7 | −4.9 | sn-Glycerol-3-phosphate dehydrogenase (aerobic) |
| ggt | b3447 | −6.5 | 2.6 | γ-Glutamyltranspeptidase |
| ugpB | b3453 | −5.7 | 2.1 | Glycerol-3-phosphate-binding periplasmic protein precursor |
| ddpX | b1488 | −7.5 | 3.0 | d-Ala-d-Ala dipeptidase, Zn dependent |
| dppF | b3540 | −8.0 | 3.5 | Dipeptide transport ATP-binding protein |
| dppD | b3541 | −8.0 | 3.5 | Dipeptide transport ATP-binding protein |
| dppC | b3542 | −8.6 | 4.0 | Dipeptide transport system permease protein |
| aldB | b3588 | −12.1 | 4.0 | Aldehyde dehydrogenase B (lactaldehyde dehydrogenase) |
| rnpA | b3704 | 4.3 | −3.0 | RNase P protein component |
| bglF | b3722 | 4.3 | 2.6 | Glucoside PTS transporter |
| qor | b4051 | −6.5 | 1.9 | Quinone oxidoreductase |
| actP | b4067 | −17.1 | 5.3 | Acetate permease |
| acs | b4069 | −10.6 | 4.6 | Acetyl-coenzyme A synthetase |
| melA | b4119 | −6.1 | 2.6 | α-Galactosidase |
| blc | b4149 | −6.1 | 2.1 | Outer-membrane lipoprotein blc precursor |
| aidB | b4187 | −6.1 | 2.0 | AidB protein |
| ytfQ | b4227 | −6.1 | 2.1 | Putative d-ribose transport protein (ABC superfamily) |
| treA | b1197 | −7.5 | 2.8 | Periplasmic trehalase precursor |
| treC | b4239 | 4.3 | −3.0 | Trehalose-6-phosphate hydrolase |
| treB | b4240 | 4.3 | −3.0 | PTS system, trehalose-specific IIBC component |
| Other | ||||
| rhlE | b0797 | 6.5 | −3.7 | Putative ATP-dependent RNA helicase |
| rmf | b0953 | 9.8 | 2.6 | Hypothetical protein |
| sfa | b0991 | 4.9 | −3.5 | Sfa protein |
| wrbA | b1004 | −16.0 | 3.2 | Flavoprotein WrbA |
| ftsT | b1569 | −2.3 | 4.0 | Transcriptional repressor of cell division inhibition protein |
| hisL | b2018 | 2.3 | −9.8 | His operon leader peptide |
| fis | b3261 | 4.3 | −2.3 | DNA-binding protein Fis gene |
| slp | b3506 | −14.9 | 1.9 | Outer-membrane protein slp precursor |
| spf | b3864 | 4.9 | −3.7 | Spot 42 RNA |
| phnB | b4107 | −9.8 | 2.8 | PhnB protein |
| mutL | b4170 | −1.3 | −4.3 | MutHLS complex, enzyme in methyl-directed mismatch repair |
| isrB | b4434 | 6.1 | −6.1 | Intergenic sequence sRNA |
| isrC | b4435 | −1.3 | 4.0 | Intergenic sequence sRNA |
| micF | b4439 | −7.0 | 2.1 | Regulatory antisense RNA affecting ompF expression |
| Hypothetical | ||||
| yahK | b0325 | −5.7 | 2.6 | Hypothetical zinc-type alcohol dehydrogenase-like protein |
| yahO | b0329 | −7.0 | 2.8 | Hypothetical protein |
| ybaS | b0485 | −7.5 | 2.3 | Probable glutaminase YbaS |
| ybaT | b0486 | −6.5 | 2.5 | Hypothetical transport protein |
| ybcL | b0545 | −5.3 | 2.6 | DLP12 prophage |
| ybgA | b0707 | −5.3 | 2.3 | Hypothetical protein |
| ybgS | b0753 | −9.2 | 2.8 | Hypothetical protein |
| ybhB | b0773 | −5.3 | 2.1 | Hypothetical protein |
| ybiY | b0824 | −2.5 | 4.3 | Putative pyruvate formate-lyase 3 activating enzyme gene |
| ybjP | b0865 | −7.0 | 1.7 | Putative lipoprotein |
| ycaC | b0897 | −9.8 | 4.9 | Hypothetical protein |
| ycgB | b1188 | −9.8 | 2.8 | Hypothetical protein |
| ychH | b1205 | −6.5 | 2.5 | Hypothetical protein |
| yciD | b1256 | −9.8 | 2.5 | Hypothetical protein |
| yciL | b1269 | 4.0 | −2.8 | Hypothetical protein |
| ydfK | b1375 | 6.1 | −4.0 | Hypothetical protein |
| ynaF | b1376 | −5.7 | 1.7 | Hypothetical protein |
| ydbC | b1406 | −5.7 | 3.0 | Hypothetical protein |
| ydcJ | b1423 | −8.6 | 4.0 | Hypothetical protein |
| ydcS | b1440 | −13.9 | 4.6 | Putative ABC transporter periplasmic-binding protein gene |
| ydcT | b1441 | −11.3 | 5.7 | Putative ABC transporter ATP-binding protein |
| ydcU | b1442 | −7.5 | 3.2 | Hypothetical ABC transporter permease protein |
| ydcV | b1443 | −8.0 | 3.7 | Hypothetical ABC transporter |
| ydcW | b1444 | −12.1 | 5.7 | Putative betaine aldehyde dehydrogenase |
| yddJ | b1470 | −2.6 | 4.6 | Hypothetical protein |
| yddS | b1487 | −6.1 | 3.0 | Putative ABC transport system periplasmic binding protein |
| ydeI | b1536 | −5.7 | 3.5 | Hypothetical protein |
| ydgN | b1629 | 4.6 | −2.6 | Electron transport complex protein |
| ydiM | b1690 | −3.2 | 4.3 | Putative transport protein (MFS family) |
| ydjN | b1729 | 4.6 | −2.1 | Hypothetical symporter |
| yeaH | b1784 | −8.6 | 2.8 | Hypothetical protein |
| yedP | b1955 | −5.3 | 2.3 | Hypothetical protein |
| yedU | b1967 | −8.6 | 2.5 | Hypothetical protein |
| yeeF | b2014 | 5.7 | −2.1 | Hypothetical protein |
| yegP | b2080 | −6.5 | 2.3 | Hypothetical protein |
| yehE | b2112 | −6.1 | 1.6 | Hypothetical protein |
| yohC | b2135 | −5.7 | 2.8 | Hypothetical protein |
| yeiN | b2165 | −3.0 | 4.3 | Hypothetical protein |
| ygaF | b2660 | −9.8 | 2.6 | Hypothetical protein |
| ygaQ | b2654 | −2.6 | 4.0 | Hypothetical protein |
| ygaR | b2655 | −2.3 | 4.0 | Hypothetical protein |
| yqaD | b2658 | −2.3 | 4.0 | Hypothetical protein |
| ygaM | b2672 | −7.5 | 2.1 | Hypothetical protein |
| ygdI | b2809 | −6.1 | 1.7 | Hypothetical protein |
| ygeL | b2856 | −1.4 | 4.0 | Predicted DNA-binding transcriptional regulator |
| ygeN | b2857 | −2.1 | 4.0 | Hypothetical protein |
| yqjE | b3099 | −5.7 | −1.5 | Hypothetical protein |
| yhbC | b3170 | 3.5 | −4.0 | Hypothetical protein |
| yhbE | b3184 | 4.6 | −3.5 | Hypothetical protein |
| yhdG | b3260 | 4.3 | −2.5 | Hypothetical protein |
| yhiE | b3512 | −12.1 | 2.8 | Hypothetical protein |
| yjcH | b4068 | −24.3 | 5.7 | Hypothetical protein |
| yjdI | b4126 | −6.5 | 1.5 | Hypothetical protein |
| yjdJ | b4127 | −5.3 | 2.0 | Hypothetical protein |
a
Strains BW25113 sdiA/pCA24N-sdiA (expressing SdiA), BW25113 sdiA/pCA24N (expressing no SdiA), and BW25113 sdiA/pCA24N-sdiA1E11 (expressing SdiA1E11) were grown in LB medium with 30 μg/ml chloramphenicol and 1 mM IPTG for 12 h at 30°C. Raw data for the two DNA microarrays are available using GEO series accession number GSE11779. Primarily, genes differentially expressed above fourfold are shown, although some related genes are shown for completeness.
b
Blattner number.
c
PLP, pyridoxal phosphate; FAD, flavin adenine dinucleotide; GABA, gamma-aminobutyric acid; PTS, phosphotransferase system; IIBC, PTS permease II domains B and C; sRNA, noncoding small RNA; MFS, major facilitator superfamily.