Table 2. QS and QS-controlled genes differentially expressed in PA14 grown in whole blood from severely burned patients.
| Gene | Product name | Pt 1 | Pt 2 | Pt 3 |
|---|---|---|---|---|
| Functional classification(s) // Gene ontology (GO) terms | ||||
| Pathways // Functional prediction(s)a | ||||
| lasR | Transcriptional Regulator LasR | -2b | -2 | -2 |
| Transcriptional regulators // Regulation of transcription, DNA-templated; Sequence-specific DNA-binding transcription factor activity | ||||
| // Transcription factor LuxR-like, autoinducer-binding domain | ||||
| lasB | Elastase LasB | -4 | -4 | -4 |
| Secreted factors; translation, post-translational modification, degradation; amino acid biosynthesis and metabolism // Proteolysis; metalloendopeptidase activity | ||||
| // Thermolysin metalloprotease (M4) family signature | ||||
| lasA | LasA protease | -83 | -71 | -76 |
| Secreted factors; translation, post-translational modification, degradation // proteolysis; endopeptidase activity; metalloendopeptidase activity | ||||
| // Peptidase M23A, B-lytic metalloendopeptidase | ||||
| rhlR | Transcriptional regulator RhlR | -4 | -4 | -4 |
| Transcriptional regulators // Regulation of transcription, DNA-templated; sequence-specific DNA-binding transcription factor activity | ||||
| // Transcription factor LuxR-like, autoinducer-binding domain | ||||
| rhlA | Rhamnosyltransferase chain A | -12 | -11 | -12 |
| Secreted factors // | ||||
| // Alpha/beta hydrolase family | ||||
| rhlB | Rhamnosyltransferase chain B | -11 | -11 | -11 |
| Secreted factors // Metabolic process; carbohydrate metabolic process; lipid glycosylation; transferase activity (hexosyl groups) | ||||
| Peptidoglycan biosynthesis // UDP-glucoronosyl and UDP-glucosyl transferase | ||||
| plcB | Phospholipase C, PlcB | -3 | -3 | -2 |
| Hypothetical, unclassified, unknown // Chemotaxis; phospholipase C activity; hydrolase activity (ester bonds) | ||||
| // Phospholipase C/P1 nuclease domain | ||||
| pqsH | FAD-dependent monooxygenase | 5 | 5 | 4 |
| Biosynthesis of cofactors, prosthetic groups, and carriers // Metabolic process; secondary metabolite biosynthetic process | ||||
| // Aromatic-ring hydroxylase (flavoprotein monooxygenase) signature; FAD binding domain | ||||
| pqsCc | PqsC | -2 | -2 | -2 |
| Hypothetical, unclassified, unknown; biosynthesis of cofactors, prosthetic groups, and carriers // Metabolic process; secondary metabolite biosynthetic process; lipid biosynthetic process; fatty acid biosynthetic process; catalytic activity; 3-oxoacyl-[acyl-carrier-protein] synthase activity | ||||
| Fatty acid biosynthesis // 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III | ||||
| pqsB | PqsB | -2 | -2 | -2 |
| Hypothetical, unclassified, unknown; biosynthesis of cofactors, prosthetic groups, and carriers // Metabolic process; secondary metabolite biosynthetic process; catalytic activity | ||||
| // Thiolase-like | ||||
| pqsA | PqsA | -2 | -2 | -2 |
| Hypothetical, unclassified, unknown; biosynthesis of cofactors, prosthetic groups, and carriers // Metabolic process; secondary metabolite biosynthetic process; catalytic activity | ||||
| // AMP-dependent synthetase/ligase | ||||
| phzH | Potential phenazine-modifying enzyme | 2 | 2 | 2 |
| Putative enzymes // Metabolic process; asparagine biosynthetic process; asparagine synthase activity (glutamine-hydrolyzing) | ||||
| Phenazine biosynthesis // Glutamine amidotransferase type 2 domain | ||||
| phzS | Hypothetical protein | 2 | 2 | 2 |
| Putative enzymes // Metabolic process; oxidoreductase activity | ||||
| Phenazine biosynthesis // aromatic-ring hydroxylase (flavoprotein monooxygenase signature; FAD binding domain | ||||
| phzG1c | Pyrodoxamine 5'-phosphate oxidase | 2 | 2 | 2 |
| Secreted factors // Phenazine biosynthetic process; oxidation-reduction process; pyridoxine biosynthetic process; FMN binding; pyridoxamine-phosphate oxidase activity; oxidation-reduction activity, acting on CH-NH2 group | ||||
| Phenazine biosynthesis; vitamin B6 metabolism // Pyridoxamine 5’-phosphate oxidae | ||||
| phzF1 | PhzF | 3 | 3 | 4 |
| Secreted factors // Biosynthetic process; catalytic activity | ||||
| Phenazine biosynthesis // Phenazine biosynthesis PhzF protein | ||||
| phzE1 | Phenazine biosynthesis protein PhzE | 4 | 4 | 4 |
| Secreted factors // Biosynthetic process | ||||
| Phenazine biosynthesis // Chorismate binding enzyme; anthranilate synthase component II signature; glutamine amidotransferase | ||||
| phzD1 | Phenazine biosynthesis protein PhzD | 6 | 6 | 6 |
| Secreted factors // Metabolic process; isochorismatase activity; catalytic activity | ||||
| Phenazine biosynthesis // Isochorismatase signature | ||||
| phzC1 | Phenazine biosynthesis protein PhzC | 4 | 4 | 4 |
| Secreted factors // Aromatic amino acid family biosynthetic process; 3-deoxy-7-phosphoheptulonate synthase activity | ||||
| Phenylalanine, tyrosine and tryptophan biosynthesis // DAHP synthetase, class II | ||||
| phzG2c | Pyridoxamine 5'-phosphate oxidase | 3 | 3 | 3 |
| Secreted factors // Oxidation-reduction process; pyridoxine biosynthetic process; oxidoreductase activity, acting on the CH-NH2 group; FMN binding; pyridoxamine-phosphate oxidase activity | ||||
| Phenazine biosynthetic process; vitamin B6 metabolism / Pyridoxamine 5'-phosphate oxidase | ||||
| phzF2 | Phenazine biosynthesis proteinprotein | 3 | 3 | 3 |
| Secreted factors // Biosynthetic process; catalytic activity | ||||
| Phenazine biosynthesis // Phenazine biosynthesis PhzF | ||||
| rsaL | Regulatory protein RsaL | -9 | -8 | -7 |
| Transcriptional regulators; adaptation, protection // Regulation of transcription, DNA-templated; positive-regulation single-species biofilm formation; negative-regulation of cytolysis in other organism; negative-regulation of elastin catabolism; negative-regulation of cell motility; negative-regulation of secondary metabolism and biosynthesis; quorum sensing; DNA binding | ||||
| // Lambda repressor-like, DNA-binding domain | ||||
| mvaT | Transcriptional regulator MvaT, P16 subunit | -4 | -3 | -3 |
| Transcriptional regulators // No GO terms listed | ||||
| // | ||||
| rsmA | Carbon storage regulator | -2 | -2 | -2 |
| Transcriptional regulators; translation, post-translational modification, degradation; adaptation, protection // Regulation of carbohydrate metabolic process; mRNA catabolic process; RNA binding | ||||
| Two-component system // Carbon storage regulator [VsrA] | ||||
| PA14_30580 | LuxR family transcriptional regulator | -3 | -3 | -4 |
| Transcriptional regulators // Regulation of transcription, DNA-templated; sequence-specific DNA binding transcription factor activity | ||||
| // Signal transduction response regulator, C-terminal effector; LuxR bacterial regulatory protein HTH signature |
aProduct names, functional classification(s), gene ontology terms, pathways, and functional predictions for PA14 genes were obtained from the MGH-ParaBioSys:NHLBI Program for Genomic Applications, Massachusetts General Hospital and Harvard Medical School, Boston, MA (http://pga.mgh.harvard.edu; accessed 10Nov2015) [45] made available by the Pseudomonas Genome Database (http://www.pseudomonas.com/; accessed 10Nov2015) [44].
bGene expression within PA14 grown in whole blood from the three severely burned patients (Pt) was compared with expression when PA14 was grown in whole blood from a healthy volunteer.
cGenes found in operons: pqsA/pqsB/pqsC; phzG1/phzF1/phzE1/phzD1/phzC1; phzG2/phzF2.