Table 1 Supplemental Data: Full Score of Genes and Proteins That Were Differentially Expressed

Table 1 supplemental data: Full score of genes and proteins that were differentially expressed in P. putida S12palB1 compared to the control strain.

Transcriptomics data: P. putida S12 pJTTpal on glycerol versus P. putida S12 palB1 on glycerol
Protein description (gene name) / KT2440 locus tag / Fold change
oxidoreductase, GMC family / PP0056 / 4,26
anthranilate synthase, component I (tprE) / PP0417 / 6,53
hypothetical protein / PP0419 / 4,50
anthranilate synthase, component II (trpG) / PP0420 / 4,22
anthranilate phosphoribosyltransferase (trpD) / PP0421 / 4,36
indole-3-glycerol phosphate synthase (trpC) / PP0422 / 2,58
formate dehydrogenase, cytochrome b556 subunit / PP0491 / 2,89
ethanolamine transporter / PP0544 / 0,39
betaine-aldehyde dehydrogenase, putative / PP0708 / 30,47
transporter, NCS1 nucleoside transporter family / PP0709 / 73,06
hypothetical protein / PP0710 / 5,53
methyl-accepting chemotaxis transducer sensory box protein / PP0779 / 0,39
nucleoside diphosphate kinase (ndk) / PP0849 / 0,38
aromatic amino acid transporter (aroP2) / PP0927 / 3,0
porin B (oprB-1) / PP1019 / 0,02
radical activating enzyme / PP1225 / 0,20
exsB protein (exsB) / PP1226 / 0,12
multidrug efflux MFS transporter, putative / PP1271 / 2,61
multidrug efflux MFS membrane fusion protein, putative / PP1272 / 3,51
multidrug efflux MFS membrane fusion protein, putative / PP1272 / 4,02
multidrug efflux MFS outer membrane protein / PP1273 / 4,80
beta-ketoadipyl CoA thiolase (pcaF) / PP1377 / 0,38
hypothetical protein / PP1487 / 3,67
ferredoxin--NADP reductase (fpr) / PP1638 / 3,58
hypothetical protein / PP1833 / 10,86
methyl-accepting chemotaxis transducer / PP2249 / 0,35
sugar ABC transporter, ATP-binding protein / PP2260 / 0,25
sugar ABC transporter, ATP-binding protein / PP2261 / 0,21
sugar ABC transporter, permease protein / PP2262 / 0,31
sugar ABC transporter, permease protein / PP2263 / 0,38
sugar ABC transporter, periplasmic sugar-binding protein, putative / PP2264 / 0,27
phospho-2-dehydro-3-deoxyheptonate aldolase, class I (aroF-1) / PP2324 / 2,5
hypothetical protein / PP2511 / 3,78
quinoprotein ethanol dehydrogenase (qedH) / PP2674 / 0,22
methyl-accepting chemotaxis transducer / PP2861 / 0,35
membrane protein, putative / PP2872 / 0,33
transcriptional regulator, putative / PP2884 / 4,41
Catalase / PP2887 / 52,00
hypothetical protein / PP2894 / 4,16
hypothetical protein / PP2900 / 11,48
glutaredoxin / PP2958 / 3,01
hypothetical protein / PP3007 / 6,76
phospho-2-dehydro-3-deoxyheptonate aldolase, class I (aroF-2) / PP3080 / 3,09
hypothetical protein / PP3112 / 2,72
acyl-CoA dehydrogenase, ferrulic acid biotransformation protein, putative / PP3354 / 2,50
feruloyl-CoA-synthetase (fcs) / PP3356 / 3,60
vanillin dehydrogenase (vdh) / PP3357 / 3,00
enoyl-CoA hydratase aldolase (ech) / PP3358 / 2,50
gamma-glutamyltransferase (ggt-1) / PP3535 / 5,03
4-hydroxybenzoate hydroxylase (pobA) / PP3537 / 22,60
cytosine purine uracil thiamine allantoin permease family protein / PP3641 / 10,03
oxidoreductase, putative / PP3643 / 6,86
monooxygenase subunit, putative / PP3644 / 53,85
hydrolase / PP3645 / 9,00
aldehyde dehydrogenase family protein / PP3646 / 10,95
oxidoreductase, putative / PP3647 / 6,01
carboxymuconolactone decarboxylase family protein / PP3648 / 10,47
amino acid transporter, AAT family / PP3727 / 2,50
hypothetical protein / PP3795 / 0,33
hypothetical protein / PP3798 / 39,49
hypothetical protein / PP3799 / 11,36
hypothetical protein / PP3800 / 4,38
cation ABC transporter, permease protein, putative / PP3803 / 8,60
hypothetical protein / PP3804 / 9,87
hypothetical protein / PP3808 / 4,49
polyamine ABC transporter, periplasmic polyamine-binding protein / PP3814 / 22,13
polyamine ABC transporter, permease protein / PP3815 / 20,20
polyamine ABC transporter, permease protein / PP3816 / 63,78
polyamine ABC transporter, ATP-binding protein / PP3817 / 16,56
carbon storage regulator / PP3832 / 3,65
glutathione S-transferase domain protein / PP3998 / 4,63
non-ribosomal siderophore peptide synthetase (ppsD) / PP4219 / 2,65
cytochrome c oxidase, cbb3-type, subunit I (ccoN-1) / PP4250 / 2,62
oxygen-independent coproporphyrinogen III oxidase (HemN) / PP4264 / 5,37
phenylalanine-4-hydroxylase (phhA) / PP4490 / 3,39
pterin-4-alpha-carbinolamine dehydratase (phhB) / PP4491 / 3,50
aromatic amino acid transporter (aroP1) / PP4495 / 4,0
aerotaxis receptor, putative / PP4521 / 0,35
agmatinase, putative / PP4523 / 9,39
sodium-solute symporter, putative / PP4524 / 26,13
transcriptional regulator, AraC family / PP4605 / 3,67
protocatechuate 3,4-dioxygenase, beta subunit (pcaH) / PP4656 / 2,57
gamma-glutamyltransferase (ggt-2) / PP4659 / 0,35
hypothetical protein / PP4685 / 0,29
osmY-related protein / PP4707 / 7,42
methyl-accepting chemotaxis transducer / PP5020 / 0,40
amino acid ABC transporter, periplasmic amino acid-binding protein / PP5024 / 0,40
acetylpolyamine aminohydrolase / PP5340 / 3,97
Transcriptomics data: P. putida S12 pJNNmcs (t) on glucose versus P. putida S12 palB1 on glucose
Protein description (gene name) / KT2440 locus tag / Fold change
Ralstonia sp. U2 plasmid pWWU2 putative chemotaxis protein gene, partial cds; LysR-like regular protein (nagR) complete cds / 0,05
inner membrane protein, 60 kDa (yidC) / PP0006 / 0,24
conserved hypothetical protein TIGR00278 / PP0007 / 0,21
ribonuclease P protein component (rnpA) / PP0008 / 0,30
hypothetical protein / PP0022 / 0,29
hypothetical protein / PP0023 / 0,25
porin, putative / PP0046 / 0,20
oxidoreductase, GMC family / PP0056 / 5,7
major facilitator family transporter / PP0057 / 5,9
hypothetical protein / PP0150 / 0,26
pyridine nucleotide transhydrogenase, beta subunit (pntB) / PP0155 / 0,27
hypothetical protein / PP0174 / 0,36
hypothetical protein / PP0193 / 0,12
sensory box protein / PP0216 / 0,37
oxalate formate antiporter, putative / PP0288 / 0,29
coenzyme PQQ synthesis protein A (pqqA) / PP0380 / 0,30
O-sialoglycoprotein endopeptidase (gcp) / PP0390 / 0,33
polyamine ABC transporter, periplasmic polyamine-binding protein / PP0412 / 4,3
polyamine ABC transporter, permease protein / PP0414 / 2,5
anthranilate synthase, component I (trpE) / PP0417 / 9,2
hypothetical protein / PP0419 / 8,7
anthranilate synthase, component II (trpG) / PP0420 / 10,3
anthranilate phosphoribosyltransferase (trpD) / PP0421 / 7,8
indole-3-glycerol phosphate synthase (trpC) / PP0422 / 5,6
hypothetical protein / PP0423 / 3,7
birA bifunctional protein (birA) / PP0437 / 0,29
transcriptional activator, putative / PP0438 / 0,37
hypothetical protein / PP0439 / 0,39
acetyl-CoA carboxylase, biotin carboxyl carrier protein (accB) / PP0559 / 0,37
extracellular protein, putative / PP0570 / 0,27
conserved hypothetical protein TIGR00645 / PP0682 / 0,35
hypothetical protein / PP0693 / 0,38
betaine-aldehyde dehydrogenase, putative / PP0708 / 105,0
transporter, NCS1 nucleoside transporter family / PP0709 / 230,0
hypothetical protein / PP0710 / 99,0
peptidyl-tRNA hydrolase (pth) / PP0720 / 0,29
ribose-phosphate pyrophosphokinase (prsA) / PP0722 / 0,25
hypothetical protein / PP0728 / 0,29
methyl-accepting chemotaxis transducer sensory box protein / PP0779 / 0,24
protein secretion ABC efflux system, membrane fusion protein / PP0803 / 0,31
protein secretion ABC efflux system, permease and ATP-binding protein / PP0804 / 0,34
hypothetical protein / PP0831 / 6,3
protein-export membrane protein (SecF) / PP0836 / 0,35
ornithine decarboxylase, putative / PP0864 / 0,30
fumarate hydratase, class I / PP0897 / 0,33
hypothetical protein / PP0898 / 0,37
aromatic amino acid transporter (aroP2) / PP0927 / 9,0
pmbA protein (pmbA) / PP0942 / 0,39
hypothetical protein / PP0974 / 0,38
DNA-binding protein HU, form N (hupN) / PP0975 / 0,34
glycine cleavage system P protein (gcvP-1) / PP0988 / 0,37
glycine cleavage system H protein (gcvH-1) / PP0989 / 0,25
sugar ABC transporter, permease protein / PP1016 / 0,34
porin B (oprB-1) / PP1019 / 0,01
hypothetical protein / PP1020 / 0,10
transcriptional regulator (HexR) / PP1021 / 0,16
acetolactate synthase, catabolic, putative / PP1157 / 0,35
conserved hypothetical protein TIGR00051 / PP1218 / 0,38
tolB protein (tolB) / PP1222 / 0,31
radical activating enzyme / PP1225 / 0,34
exsB protein (exsB) / PP1226 / 0,39
hypothetical protein / PP1245 / 0,21
hypothetical protein / PP1246 / 0,06
lipoprotein, putative / PP1249 / 0,13
universal stress protein family / PP1269 / 2,9
multidrug efflux MFS transporter, putative / PP1271 / 7,7
multidrug efflux MFS membrane fusion protein, putative / PP1272 / 17,4
multidrug efflux MFS outer membrane protein, putative / PP1273 / 10,1
general amino acid ABC transporter, periplasmic binding protein (aapJ) / PP1297 / 3,4
general amino acid ABC transporter, permease protein (aapQ) / PP1298 / 4,6
general amino acid ABC transporter, permease protein (aapM) / PP1299 / 2,9
general amino acid ABC transporter, ATP-binding protein (aapP) / PP1300 / 3,0
methyl-accepting chemotaxis transducer / PP1371 / 0,26
low-affinity inorganic phosphate transporter / PP1373 / 0,39
tricarboxylate transport protein TctA, putative / PP1416 / 0,39
tricarboxylate transport protein TctB, putative / PP1417 / 0,34
ATP-dependent protease La (lon-1) / PP1443 / 0,36
long-chain acyl-CoA thioester hydrolase family protein / PP1466 / 0,21
OmpA family protein / PP1502 / 0,28
hypothetical protein / PP1503 / 0,31
hypothetical protein / PP1512 / 0,38
RND membrane fusion protein / PP1516 / 0,19
RND efflux transporter / PP1517 / 0,05
2-dehydro-3-deoxyphosphooctonate aldolase (kdsA-1) / PP1611 / 0,36
ferrodoxin, 4Fe-4S / PP1625 / 0,26
DNA mismatch repair protein (MutS) / PP1626 / 0,22
glycine betaine-binding protein, putative / PP1741 / 3,2
hypothetical protein / PP1810 / 0,21
benzoate transport protein / PP1820 / 0,32
hypothetical protein / PP1838 / 0,26
cytochrome c family protein / PP1841 / 2,8
ATP-dependent RNA helicase, DEAD box family / PP1868 / 0,27
ABC transporter, ATP-binding protein / PP1895 / 0,39
lipoprotein, putative / PP1970 / 0,39
3-isopropylmalate dehydratase, large subunit (LeuC) / PP1985 / 0,32
3-isopropylmalate dehydratase, small subunit (LeuD) / PP1986 / 0,28
methlytransferase, UbiE COQ5 family / PP1987 / 0,39
hypothetical protein / PP1991 / 2,6
semialdehyde dehydrogenase family protein / PP1992 / 0,31
aerotaxis receptor(Aer-2) / PP2111 / 0,26
sensor histidine kinase / PP2127 / 0,38
hypothetical protein / PP2172 / 0,21
transcriptional regulator, AraC family / PP2173 / 0,39
methyl-accepting chemotaxis transducer / PP2249 / 0,21
aerotaxis receptor (Aer-1) / PP2257 / 0,16
sensory box protein / PP2258 / 0,17
phospho-2-dehydro-3-deoxyheptonate aldolase, class I (aroF-1) / PP2324 / 2,6
hypothetical protein / PP2352 / 2,6
hypothetical protein / PP2464 / 0,30
4-oxalocrotonate tautomerase (dmpI) / PP2504 / 0,33
hypothetical protein / PP2511 / 3,1
tyrosine decarboxylase, putative / PP2552 / 48,0
hypothetical protein / PP2564 / 3,2
aldehyde dehydrogenase family protein / PP2585 / 26,4
dihydrodipicolinate synthase, putative / PP2639 / 8,6
DNA-binding response regulator (AgmR) / PP2665 / 2,7
hydrolase, UxaA family / PP2834 / 78,4
oxidoreductase, Ldh family / PP2835 / 32,8
fumarylacetoacetate hydrolase family protein / PP2836 / 7,3
major facilitator family transporter / PP2837 / 99,3
hypothetical protein / PP2850 / 2,7
oxidoreductase, FMN-binding / PP2869 / 3,1
hypothetical protein / PP2875 / 0,30
Catalase / PP2887 / 11,0
hypothetical protein / PP2928 / 0,29
hypothetical protein / PP3007 / 42,1
phospho-2-dehydro-3-deoxyheptonate aldolase, class I (aroF-2) / PP3080 / 9,3
hypothetical protein / PP3112 / 2,6
oxidoreductase, putative / PP3249 / 3,8
universal stress protein family / PP3288 / 3,4
metallo-beta-lactamase family protein / PP3291 / 2,6
major facilitator family transporter / PP3349 / 13,3
hypothetical protein / PP3350 / 62,9
acyl-CoA dehydrogenase, ferrulic acid biotransformation protein, putative / PP3354 / 28,2
beta-ketothiolase / PP3355 / 11,9
feruloyl-CoA-synthetase (fcs) / PP3356 / 72,8
vanillin dehydrogenase (vdh) / PP3357 / 37,7
enoyl-CoA hydratase aldolase (ech) / PP3358 / 12,2
hydroxycinnamic acid degradation regulator, putative / PP3359 / 2,9
hypothetical protein / PP3418 / 2,6
sigma-54 dependent transcriptional regulator response regulator / PP3419 / 3,8
sensor histidine kinase / PP3420 / 2,6
4-hydroxyphenylpyruvate dioxygenase (hpd) / PP3433 / 2,8
hypothetical protein / PP3434 / 3,9
transcriptional regulator, AraC family / PP3516 / 3,0
gamma-glutamyltransferase (ggt-1) / PP3535 / 9,7
4-hydroxybenzoate hydroxylase (pobA) / PP3537 / 227,0
transcriptional regulator (PobR) / PP3538 / 3,9
methyl-accepting chemotaxis transducer / PP3557 / 0,28
quinate dehydrogenase (pyrroloquinoline-quinone), putative / PP3569 / 2,8
D-glucarate permease / PP3600 / 3,2
sulfonate ABC transporter, permease protein, putative / PP3635 / 0,34
cytosine purine uracil thiamine allantoin permease family protein / PP3641 / 14,0
oxidoreductase, putative / PP3643 / 15,0
monooxygenase subunit, putative / PP3644 / 47,9
hydrolase, alpha beta fold family / PP3645 / 16,5
aldehyde dehydrogenase family protein / PP3646 / 13,1
oxidoreductase, putative / PP3647 / 4,1
carboxymuconolactone decarboxylase family protein / PP3648 / 6,2
amino acid transporter, AAT family / PP3727 / 4,2
hypothetical protein / PP3795 / 0,38
polyamine ABC transporter, periplasmic polyamine-binding protein / PP3814 / 40,7
polyamine ABC transporter, permease protein / PP3815 / 16,5
polyamine ABC transporter, permease protein / PP3816 / 40,8
polyamine ABC transporter, ATP-binding protein / PP3817 / 19,2
hypothetical protein / PP3826 / 0,39
hypothetical protein / PP3963 / 4,1
glutathione S-transferase domain protein / PP3998 / 11,2
translation initiation factor IF-1 (infA) / PP4007 / 0,38
hypothetical protein / PP4054 / 0,38
NADH dehydrogenase I, I subunit (nuoI) / PP4126 / 0,31
phenazine biosynthesis protein, PhzF family / PP4315 / 0,28
flagellar hook-associated protein (FlgK) / PP4381 / 0,32
phenylalanine-4-hydroxylase (phhA) / PP4490 / 107,0
pterin-4-alpha-carbinolamine dehydratase (phhB) / PP4491 / 76,3
aromatic amino acid transporter (aroP1) / PP4495 / 14,1
aromatic amino acid transporter / PP4495 / 16,7
agglutination protein (tolC) / PP4519 / 0,39
agmatinase, putative / PP4523 / 30,0
sodium-solute symporter, putative / PP4524 / 125,0
acyl carrier protein phosphodiesterase, putative / PP4538 / 5,6
glutamine synthetase, putative / PP4547 / 2,9
hypothetical protein / PP4554 / 3,1
hypothetical protein / PP4555 / 2,6
membrane protein, putative / PP4592 / 0,19
membrane protein, putative / PP4652 / 0,32
protocatechuate 3,4-dioxygenase, alpha subunit (pcaG) / PP4655 / 2,8
methyl-accepting chemotaxis transducer / PP4658 / 0,30
OmpA family protein / PP4669 / 0,32
3-methyl-2-oxobutanoate hydroxymethyltransferase (panB) / PP4699 / 0,35
dnaJ protein (dnaJ) / PP4726 / 0,38
heat shock protein (GrpE) / PP4728 / 0,34
metal ion transporter, putative / PP4789 / 0,39
SPFH domain Band 7 family protein / PP4834 / 0,25
transporter, NCS1 nucleoside transporter family / PP4921 / 0,38
outer membrane efflux protein / PP4923 / 0,23
methyl-accepting chemotaxis transducer / PP5020 / 0,32
hypothetical protein / PP5038 / 0,33
GTP-binding protein TypA BipA / PP5044 / 0,38
glutamine synthetase, type I (glnA) / PP5046 / 0,30
thermonuclease family protein / PP5086 / 0,38