TABLE 2.
List of identified proteins that were found to be produced in a progressive manner over the course of biofilm developmenta
| Pattern or protein identified | Gene |
|---|---|
| Trend I: onset of protein production at maturation-1 stage | |
| Pattern A | None identified |
| Pattern B | |
| Conserved hypothetical protein | PA0344 |
| Conserved hypothetical protein | PA0423 |
| Conserved hypothetical protein | PA1122 |
| Hypothetical protein | PA4788 |
| 3-Demethylubiquinone-9 3-methyltransferase UbiG | PA3171 |
| Thioredoxin reductase, TrxB1 | PA2616 |
| PvdS, sigma factor | PA2426 |
| PvdQ, probable acylase | PA2385 |
| PvdA, l-ornithine N5-oxygenase | PA2386 |
| Superoxide dismutase | PA4468 |
| Probable glutathione peroxidase | PA2826 |
| Probable c-type cytochrome NirN, part of nirSMCFDLGHJEN gene cluster | PA0509 |
| Mismatch repair system component of mutS | PA3620 |
| Non-hemolytic phospholipase C precursor | PA3319 |
| Probable pilus assembly chaperone CupA2 | PA2129 |
| Probable transcriptional regulator | PA4878 |
| Probable chemotaxis transducer | PA4844 |
| Probable two-component sensor | PA1336 |
| Probable acid phosphatase | PA0190 |
| Probable outer membrane component of multidrug efflux pump (OprN homologue) | PA1238 |
| RND multidrug efflux transporter MexF | PA2494 |
| Probable ribosomal protein L25 | PA4671 |
| Pattern C | None identified |
| Pattern D | |
| Heat shock protein HtpG (chaperone hsp90) | PA1596 |
| Probable serine/threonine protein kinase | PA1782 |
| Secreted hemolysin-coregulated protein Hcp | PA0263 |
| Trend II: onset of protein production at maturation-2 stage | |
| Pattern E | |
| Hypothetical protein | PA3068 |
| Hypothetical protein | PA1893 |
| Probable two-component response regulator | PA4101 |
| Probable transcriptional regulator | PA3420 |
| Probable chemotaxis transducer | PA0180 |
| Probable chemotaxis transducer | PA5072 |
| LasR (fragment) | PA1430 |
| Probable cytochrome c oxidase subunit | PA1553 |
| Probable electron transfer flavoprotein alpha subunit energy | PA5400 |
| Phosphopantetheine adenylyltransferase; CoaD | PA0363 |
| Probable outer membrane efflux protein precursor OpmD, part of mexGHI-opmD operon | PA4208 |
| RND multidrug efflux membrane fusion protein MexC precursor, part of mexCD-oprJ operon | PA4599 |
| Probable bacteriophage protein | PA0641 |
| PvdD, pyoverdine synthase D | PA2399 |
| PvdJ | PA2400 |
| PvdL | PA2424 |
| Pattern F | |
| Conserved hypothetical protein | PA4939 |
| Hypothetical protein | PA0588 |
| Hypothetical protein | PA2363 |
| Probable chemotaxis transducer | PA1608 |
| Probable transcriptional regulator | PA4145 |
| Exopolyphosphatase (fragment) | PA5241 |
| Trend III: onset of protein production at dispersion stage | |
| Pattern G | None identified |
| Pattern or protein identified | Gene |
| Trend IV: Proteins present at all stages | |
| Pattern H | |
| Probable molybdopterin-guanine dinucleotide biosynthesis protein MobA | PA3030 |
| Glyceraldehyde-3-phosphate dehydrogenase | PA3001 |
| Succinate semialdehyde dehydrogenase | PA0265 |
| Aconitate hydratase 2; AcnB | PA1787 |
| Arginine deiminase; ArcA | PA5171 |
| Ornithine carbamoyltransferase; ArcB | PA5172 |
| Carbamate kinase; ArcC | PA5173 |
| Dihydrolipoamide dehydrogenase 3 | PA4829 |
| NADH dehydrogenase I chain B; NuoB | PA2638 |
| Probable electron transfer flavoprotein alpha subunit | PA5400 |
| Alkyl hydroxyperoxide reductase subunit C | PA0139 |
| β-hydroxydecanoyl-acyl carrier protein dehydrase, FabA | PA1610 |
| Biotin carboxylase, AccC | PA4848 |
| Probable ClpA/ClpB-type chaperone | PA0090 |
| Probable heme utilization protein precursor HxuC | PA1302 |
| Sulfate-binding protein precursor | PA0283 |
| Nucleotide sugar epimerase/dehydratase WbpM | PA3141 |
| Probable chemotaxis sensor/effector fusion protein | PA3704 |
| Conserved hypothetical protein | PA2627 |
| Sigma factor RpoD (C-terminal portion) | PA0576 |
| DNA polymerase alpha chain | PA0669 |
| DNA polymerase II | PA1886 |
| Probable type II secretion protein | PA2677 |
| Alternate pattern (see reference 52) | |
| Probable helix-destabilizing protein of bacteriophage Pf1 | PA0720 |
a
The protein production patterns correlated with the patterns shown in Fig. 1. Proteins were identified by tryptic in-gel digest, followed by peptide mass fingerprinting using the ProFound and Mascot databases. All proteins listed here were identified with significant certainty (Est-Z score of >1 or probability score of <0.02). Proteins were identified with 3 to 15 matched peptides and a minimum of 5% sequence coverage. The correlation between apparent and theoretical molecular masses of the proteins identified was found to be very similar (y = 0.9553x − 0.2294) with R2 = 0.9736.