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 identifiedGene
Trend I: onset of protein production at maturation-1 stage
    Pattern ANone identified
    Pattern B
        Conserved hypothetical proteinPA0344
        Conserved hypothetical proteinPA0423
        Conserved hypothetical proteinPA1122
        Hypothetical proteinPA4788
        3-Demethylubiquinone-9 3-methyltransferase UbiGPA3171
  Thioredoxin reductase, TrxB1PA2616
        PvdS, sigma factorPA2426
        PvdQ, probable acylasePA2385
        PvdA, l-ornithine N5-oxygenasePA2386
        Superoxide dismutasePA4468
        Probable glutathione peroxidasePA2826
        Probable c-type cytochrome NirN, part of nirSMCFDLGHJEN gene clusterPA0509
        Mismatch repair system component of mutSPA3620
        Non-hemolytic phospholipase C precursorPA3319
        Probable pilus assembly chaperone CupA2PA2129
        Probable transcriptional regulatorPA4878
        Probable chemotaxis transducerPA4844
        Probable two-component sensorPA1336
        Probable acid phosphatasePA0190
        Probable outer membrane component of multidrug efflux pump (OprN homologue)PA1238
        RND multidrug efflux transporter MexFPA2494
        Probable ribosomal protein L25PA4671
    Pattern CNone identified
    Pattern D
        Heat shock protein HtpG (chaperone hsp90)PA1596
        Probable serine/threonine protein kinasePA1782
        Secreted hemolysin-coregulated protein HcpPA0263
Trend II: onset of protein production at maturation-2 stage
    Pattern E
        Hypothetical proteinPA3068
        Hypothetical proteinPA1893
        Probable two-component response regulatorPA4101
        Probable transcriptional regulatorPA3420
        Probable chemotaxis transducerPA0180
        Probable chemotaxis transducerPA5072
        LasR (fragment)PA1430
        Probable cytochrome c oxidase subunitPA1553
        Probable electron transfer flavoprotein alpha subunit energyPA5400
        Phosphopantetheine adenylyltransferase; CoaDPA0363
        Probable outer membrane efflux protein precursor OpmD, part of mexGHI-opmD operonPA4208
        RND multidrug efflux membrane fusion protein MexC precursor, part of mexCD-oprJ operonPA4599
        Probable bacteriophage proteinPA0641
        PvdD, pyoverdine synthase DPA2399
        PvdJPA2400
        PvdLPA2424
    Pattern F
        Conserved hypothetical proteinPA4939
        Hypothetical proteinPA0588
        Hypothetical proteinPA2363
        Probable chemotaxis transducerPA1608
        Probable transcriptional regulatorPA4145
        Exopolyphosphatase (fragment)PA5241
Trend III: onset of protein production at dispersion stage
    Pattern GNone identified
Pattern or protein identifiedGene
Trend IV: Proteins present at all stages
    Pattern H
        Probable molybdopterin-guanine dinucleotide biosynthesis protein MobAPA3030
        Glyceraldehyde-3-phosphate dehydrogenasePA3001
        Succinate semialdehyde dehydrogenasePA0265
        Aconitate hydratase 2; AcnBPA1787
        Arginine deiminase; ArcAPA5171
        Ornithine carbamoyltransferase; ArcBPA5172
        Carbamate kinase; ArcCPA5173
        Dihydrolipoamide dehydrogenase 3PA4829
        NADH dehydrogenase I chain B; NuoBPA2638
        Probable electron transfer flavoprotein alpha subunitPA5400
        Alkyl hydroxyperoxide reductase subunit CPA0139
        β-hydroxydecanoyl-acyl carrier protein dehydrase, FabAPA1610
        Biotin carboxylase, AccCPA4848
        Probable ClpA/ClpB-type chaperonePA0090
        Probable heme utilization protein precursor HxuCPA1302
        Sulfate-binding protein precursorPA0283
        Nucleotide sugar epimerase/dehydratase WbpMPA3141
        Probable chemotaxis sensor/effector fusion proteinPA3704
        Conserved hypothetical proteinPA2627
        Sigma factor RpoD (C-terminal portion)PA0576
        DNA polymerase alpha chainPA0669
        DNA polymerase IIPA1886
        Probable type II secretion proteinPA2677
    Alternate pattern (see reference 52)
        Probable helix-destabilizing protein of bacteriophage Pf1PA0720
  • 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.