Table 1.
Transcriptomic, proteomic and post-transcriptional changes for selected genes.
| Category | Name | ID | Description | TC | PC | PTV |
|---|---|---|---|---|---|---|
| Catabolism | bauC | PA0130 | 3-Oxopropanoate dehydrogenase | −1,02 | 1,03 | 3,94 |
| Catabolism | bauA | PA0132 | Beta-alanine: pyruvate transaminase | −1,36 | 1,41 | 5,37 |
| Other | siaD | PA0169 | SiaD | 1,27 | 1,05 | 1,72 |
| Other | siaC | PA0170 | Hypothetical protein | 1,39 | 0,96 | 1,33 |
| Other | siaB | PA0171 | Hypothetical protein | 1,5 | 1,44 | 2,6 |
| Catabolism | gabT | PA0266 | Delta-aminovalerate aminotransferase | −1,69 | −0,21 | 1,1 |
| Catabolism | spuA | PA0297 | Probable glutamine amidotransferase | −0,39 | 0,6 | 2,11 |
| Catabolism | spuB | PA0298 | Glutamylpolyamine synthetase | −0,51 | 0,53 | 2,01 |
| Catabolism | spuC | PA0299 | Polyamine:pyruvate transaminase | −0,57 | 0,31 | 1,46 |
| Transport | spuD | PA0300 | Polyamine transport protein | −0,02 | 0,49 | 1,4 |
| Catabolism | gcdG | PA0446 | Conserved hypothetical protein | 1,55 | 1,43 | 2,52 |
| Catabolism | gcdH | PA0447 | Glutaryl-CoA dehydrogenase | 2,64 | 1,09 | 0,48 |
| Iron | fiuA | PA0470 | Ferrichrome receptor FiuA | −0,24 | 1,05 | 3,22 |
| Transport | agtA | PA0603 | AgtA | −6,4 | −0,12 | 6,07 |
| Transport | agtB | PA0604 | AgtB | −5,35 | 0,05 | 5,5 |
| Transport | agtC | PA0605 | AgtC | −5,14 | 0,08 | 5,36 |
| Iron | hemO | PA0672 | Heme oxygenase | 0,51 | 2,55 | 6,75 |
| Catabolism | — | PA0744 | Probable enoyl-CoA hydratase/isomerase | 1,86 | 1,28 | 1,78 |
| Transport | tctC | PA0754 | Hypothetical protein | 0,06 | 2,8 | 7,9 |
| Transport | opdH | PA0755 | Cis-aconitate porin OpdH | −0,5 | 2,54 | 7,72 |
| Catabolism | putA | PA0782 | Proline dehydrogenase PutA | −3,29 | 1,79 | 8,38 |
| Transport | putP | PA0783 | Sodium/proline symporter PutP | −0,79 | 1,58 | 5,3 |
| Transport | — | PA0789 | Probable amino acid permease | 0,38 | 0,86 | 2,08 |
| Iron | pirA | PA0931 | Ferric enterobactin receptor PirA | 0,29 | 0,97 | 2,48 |
| Transport | tolQ | PA0969 | TolQ protein | 0,41 | 1,03 | 2,52 |
| Transport | tolR | PA0970 | TolR protein | 0,33 | 0,62 | 1,43 |
| Transport | gntP | PA1051 | Probable transporter | −2,46 | 0,33 | 3,4 |
| Transport | braG | PA1070 | Branched-chain amino acid transport protein BraG | 0,94 | 0,79 | 1,32 |
| Transport | braF | PA1071 | Branched-chain amino acid transport protein BraF | 1,06 | 1,07 | 2 |
| Transport | braC | PA1074 | Branched-chain amino acid transport protein BraC | 0,96 | 1,47 | 3,21 |
| Transport | fadL | PA1288 | Probable outer membrane protein precursor | −0,13 | 0,57 | 1,74 |
| Catabolism | gbuA | PA1421 | Guanidinobutyrase | −3,52 | −0,37 | 2,45 |
| Transport | kdpB | PA1634 | Potassium-transporting ATPase | 3,46 | 1,19 | −0,06 |
| Catabolism | pauD 2 | PA1742 | Glutamine amidotransferase class I | −0,68 | 0,55 | 2,23 |
| Transport | oppD | PA1808 | NppC | 0,66 | 0,65 | 1,18 |
| Catabolism | ldcA | PA1818 | Lysine decarboxylase | 1,28 | 1,49 | 2,96 |
| Transport | modA | PA1863 | Molybdate-binding periplasmic protein precursor ModA | 0,21 | 0,76 | 1,94 |
| Catabolism | dhcA | PA1999 | Dehydrocarnitine CoA transferase | 4,29 | 2,37 | 2,46 |
| Catabolism | dhcB | PA2000 | Dehydrocarnitine CoA transferase | 4,07 | 1,99 | 1,61 |
| Catabolism | atoB | PA2001 | Acetyl-CoA acetyltransferase | 3,42 | 2,44 | 3,51 |
| Transport | atoE | PA2002 | Conserved hypothetical protein | 3,7 | 2,84 | 4,37 |
| Catabolism | maiA | PA2007 | Maleylacetoacetate isomerase | 3,66 | 1,86 | 1,62 |
| Catabolism | fahA | PA2008 | Fumarylacetoacetase | 3,24 | 2,58 | 4,09 |
| Catabolism | hmgA | PA2009 | Homogentisate 1-2dioxygenase | 3,36 | 1,68 | 1,43 |
| Catabolism | liuC | PA2013 | Putative 3-methylglutaconyl-CoA hydratase | 2,27 | 1,76 | 2,74 |
| Catabolism | liuB | PA2014 | Methylcrotonyl-CoA carboxylase | 2,37 | 1,32 | 1,39 |
| Catabolism | liuA | PA2015 | Putative isovaleryl-CoA dehydrogenase | 2,16 | 2,06 | 3,69 |
| Catabolism | pauA4 | PA2040 | Glutamylpolyamine synthetase | −1 | 0,16 | 1,47 |
| Catabolism | kynU | PA2080 | Kynureninase KynU | 0,48 | 0,54 | 1,05 |
| Transport | opdO | PA2113 | Pyroglutamate porin OpdO | 7,97 | 3,03 | 0,65 |
| Transport | — | PA2204 | Probable binding protein component of ABC transporter | 2,01 | 1,33 | 1,77 |
| Other | pslA | PA2231 | PslA | 1,56 | 1,16 | 1,74 |
| Other | pslD | PA2234 | PslD | 2,03 | 1,44 | 2,06 |
| Other | pslE | PA2235 | PslE | 1,93 | 1,2 | 1,49 |
| Other | pslF | PA2236 | PslF | 2,03 | 1,08 | 1,05 |
| Other | pslH | PA2238 | PslH | 2,19 | 1,23 | 1,3 |
| Catabolism | bkdA1 | PA2247 | 2-oxoisovalerate dehydrogenase (alpha subunit) | 3,61 | 1,96 | 5,58 |
| Catabolism | bkdA2 | PA2248 | 2-oxoisovalerate dehydrogenase (beta subunit) | 3,98 | 2,79 | 7,95 |
| Catabolism | bkdB | PA2249 | Branched-chain alpha-keto acid dehydrogenase (lipoamide component) | 3,99 | 2,17 | 6,18 |
| Catabolism | lpdV | PA2250 | Lipoamide dehydrogenase-Val | 4,12 | 2,35 | 6,69 |
| Transport | — | PA2252 | Probable AGCS sodium/alanine/glycine symporter | −3,32 | 0,89 | 5,85 |
| Catabolism | ansA | PA2253 | L-asparaginase I | −2,19 | 0,31 | 3,07 |
| CCM/catabolism | gcd | PA2290 | Glucose dehydrogenase | 0,8 | 0,7 | 1,2 |
| Transport | oprB2 | PA2291 | Probable glucose-sensitive porin | 1,37 | 2,56 | 5,91 |
| Iron | pvdA | PA2386 | L-ornithine N5-oxygenase | 1,39 | 3,11 | 7,46 |
| Iron | pvdF | PA2396 | Pyoverdine synthetase F | 0,58 | 2,01 | 5,14 |
| Iron | fpvA | PA2398 | Ferripyoverdine receptor | 1,2 | 1,11 | 1,96 |
| Iron | pvdD | PA2399 | Pyoverdine synthetase D | 1,14 | 0,93 | 1,52 |
| Catabolism | gcvT2 | PA2442 | Glycine cleavage system protein T2 | 2,63 | 1,7 | 2,2 |
| Catabolism | glyA2 | PA2444 | Serine hydroxymethyltransferase | 2,37 | 1,15 | 0,9 |
| Catabolism | gcvP2 | PA2445 | Glycine cleavage system protein P2 | 2,51 | 1,98 | 3,13 |
| Catabolism | gcvH2 | PA2446 | Glycine cleavage system protein H2 | 2,68 | 2,37 | 4,08 |
| Catabolism | — | PA2552 | Probable acyl-CoA dehydrogenase | 3,27 | 1,72 | 1,61 |
| Catabolism | — | PA2553 | Probable acyl-CoA thiolase | 4,09 | 2,36 | 2,63 |
| Transport | oprQ | PA2760 | OprQ | 0,33 | 0,89 | 2,21 |
| Catabolism | pauB3 | PA2776 | FAD-dependent oxidoreductase | −1,55 | 0,2 | 2,13 |
| CCM/catabolism | eda | PA3181 | 2-keto-3-deoxy-6-phosphogluconate aldolase | −0,29 | 1,6 | 4,84 |
| CCM/catabolism | pgl | PA3182 | 6-phosphogluconolactonase | −0,64 | 1,71 | 5,53 |
| CCM/catabolism | zwf | PA3183 | Glucose-6-phosphate 1-dehydrogenase | −1,18 | 1,63 | 5,83 |
| Transport | oprB | PA3186 | Glucose/carbohydrate outer membrane porin OprB precursor | 2,35 | 2,76 | 5,5 |
| Transport | gltK | PA3187 | Probable ATP-binding component of ABC transporter | −0,22 | 2,29 | 6,75 |
| Transport | gltG | PA3188 | Probable permease of ABC sugar transporter | −0,46 | 3,56 | 10,6 |
| Transport | gltB | PA3190 | Probable binding protein component of ABC sugar transporter | 0,2 | 2,92 | 8,1 |
| CCM/catabolism | glk | PA3193 | Glucokinase | 0,02 | 1,11 | 3,15 |
| CCM/catabolism | edd | PA3194 | Phosphogluconate dehydratase | −1,07 | 1,11 | 4,22 |
| CCM | gapA | PA3195 | Glyceraldehyde 3-phosphate dehydrogenase | −0,1 | 2,08 | 6,02 |
| Transport | — | PA3271 | Probable two-component sensor | −2,75 | −0,32 | 1,85 |
| Catabolism | pauA5 | PA3356 | Glutamylpolyamine synthetase | −0,85 | 0,13 | 1,21 |
| Catabolism | amiE | PA3366 | Aliphatic amidase | 1,95 | 1,72 | 2,95 |
| Catabolism | — | PA3579 | Probable carbohydrate kinase | −1,76 | −0,23 | 1,1 |
| Catabolism | glpK | PA3582 | Glycerol kinase | −1,93 | 1,44 | 6,02 |
| Catabolism | glpD | PA3584 | Glycerol-3-phosphate dehydrogenase | −2,87 | 0,16 | 3,31 |
| Transport | — | PA3690 | Probable metal-transporting P-type ATPase | −0,46 | 1,02 | 3,36 |
| Transport | — | PA3760 | N-Acetyl-D-Glucosamine phosphotransferase system transporter | −0,5 | 0,44 | 1,76 |
| Transport | — | PA3779 | Hypothetical protein | 0 | 0,89 | 2,54 |
| Transport | — | PA3838 | Probable ATP-binding component of ABC transporter | −0,44 | 0,49 | 1,84 |
| Iron | fecA | PA3901 | Fe(III) dicitrate transport protein FecA | −0,44 | 1,36 | 4,31 |
| Catabolism | — | PA3925 | Probable acyl-CoA thiolase | 0,33 | 0,85 | 2,1 |
| Catabolism | — | PA4198 | Probable AMP-binding enzyme | −0,83 | 0,88 | 3,32 |
| CCM | fumC1 | PA4470 | Fumarate hydratase | −0,24 | 1,3 | 3,71 |
| Transport | — | PA4496 | Probable binding protein component of ABC transporter | 1,45 | 1,72 | 3,44 |
| Transport | — | PA4500 | Probable binding protein component of ABC transporter | 3,37 | 2,33 | 3,27 |
| Transport | opdP | PA4501 | Glycine-glutamate dipeptide porin OpdP | 4,52 | 2,52 | 2,66 |
| Transport | — | PA4502 | Probable binding protein component of ABC transporter | 4,52 | 2,58 | 2,83 |
| Transport | — | PA4503 | Dipeptide ABC transporter permease DppB | 4,43 | 2,3 | 2,12 |
| Transport | — | PA4504 | Dipeptide ABC transporter permease DppC | 4,85 | 2,37 | 1,88 |
| Transport | — | PA4505 | Dipeptide ABC transporter ATP-binding protein DppD | 4,61 | 2,35 | 2,08 |
| Transport | — | PA4506 | Dipeptide ABC transporter ATP-binding protein DppF | 4,55 | 2,16 | 1,59 |
| Iron | piuB | PA4513 | Probable oxidoreductase | 0,66 | 0,84 | 1,73 |
| Iron | piuA | PA4514 | Probable outer membrane receptor for iron transport | 0,87 | 1,99 | 4,8 |
| Iron | piuC | PA4515 | Conserved hypothetical protein | 0,73 | 0,93 | 1,91 |
| Iron | chtA | PA4675 | ChtA | −0,11 | 1,03 | 3,03 |
| Iron/transport | phuT | PA4708 | Heme-transport protein | 0,22 | 1,91 | 5,22 |
| Iron/transport | phuS | PA4709 | PhuS | 0,29 | 1,98 | 5,33 |
| Iron/transport | phuR | PA4710 | Heme/Hemoglobin uptake outer membrane receptor PhuR precursor | −0,46 | 2,31 | 7,03 |
| CCM | aceE | PA5015 | Pyruvate dehydrogenase | 0,5 | 0,56 | 1,09 |
| Transport | — | PA5152 | Probable ATP-binding component of ABC transporter | −0,09 | 1,2 | 3,51 |
| Transport | — | PA5153 | Amino acid (lysine/arginine/ornithine/histidine/octopine) ABC transporter periplasmic binding protein | 0,8 | 1,32 | 2,95 |
| Transport | dctP | PA5167 | DctP | 2,07 | 2,44 | 4,87 |
| Transport | dctQ | PA5168 | DctQ | 1,98 | 2 | 3,72 |
| Transport | — | PA5217 | Probable binding protein component of ABC iron transporter | −0,01 | 0,83 | 2,37 |
| Catabolism | dadX | PA5302 | Catabolic alanine racemase | 1,34 | 1,41 | 2,67 |
| Catabolism | dadA | PA5304 | D-amino acid dehydrogenase | 0,99 | 1,32 | 2,76 |
| Catabolism | pauB4 | PA5309 | FAD-dependent oxidoreductase | −0,73 | 0,14 | 1,14 |
| Catabolism | pauC | PA5312 | Aldehyde dehydrogenase | −1,49 | 0,2 | 2,07 |
| Transport | pstB | PA5366 | ATP-binding component of ABC phosphate transporter | −0,44 | 0,24 | 1,13 |
| Transport | pstA | PA5367 | Membrane protein component of ABC phosphate transporter | 0 | 0,5 | 1,42 |
| Transport | pstS | PA5369 | Phosphate ABC transporter | −0,22 | 0,28 | 1,02 |
| Catabolism | aspA | PA5429 | Aspartate ammonia-lyase | −0,05 | 0,6 | 1,76 |
| CCM | pycB | PA5435 | Probable transcarboxylase subunit | 1,69 | 1,05 | 1,29 |
| CCM | pycA | PA5436 | Probable biotin carboxylase subunit of a transcarboxylase | 1,09 | 0,88 | 1,4 |
| Transport | — | PA5504 | D-methionine ABC transporter membrane protein | −0,19 | 0,29 | 1,01 |
| Catabolism | pauA7 | PA5508 | Glutamylpolyamine synthetase homologue | −4,03 | 0,8 | 6,32 |
| Transport | — | PA5510 | Probable transporter | −2,56 | 0,44 | 3,82 |
| Catabolism | — | PA5523 | Probable aminotransferase | −0,55 | 0,33 | 1,49 |
| Iron | tonB1 | PA5531 | TonB1 | 0,28 | 1,18 | 3,08 |
| Transport | — | PA5545 | Conserved hypothetical protein | −0,19 | 0,86 | 2,64 |
ID: Gene code as annotated in http://pseudomonas.com, TC: transcript change; PC: protein change; PTV: post-transcriptional variation parameter. CCM: Central carbon metabolism. Underlined, genes that have been described as potential Crc targets in10. Highlighted in bold contiguous genes, transcribed in the same strand, which can form operons.