Table 4. Biomarker candidate panel for capturing the biofilm molecular process.
| protein name | UniProt ID | prot | Trans | control | # species | function context |
|---|---|---|---|---|---|---|
|
chaperonin GroEL (O: Post-translational modification, protein turnover, chaperone functions) |
I0IPK2 | +0.6 | +2.6 | -0.19 | 24 | regulation of protein fate and transport, thermal stability, protection from oxidative damage caused by copper |
|
chaperone DnaK (O: Post-translational modification, protein turnover, chaperone functions) |
I0IPF3 | +1.0 | +3.0* | -0.08 | 23 | DNA stability, defense against reactive oxygen species |
|
GrpE protein, putative (O: Post-translational modification, protein turnover, chaperone functions) |
I0IPF4 | +2.8 | +3.0* | -0.35 | 23 | mediation of acid tolerance |
|
dimethyladenosine transferase (J: Translation) |
I0IQ48 | +2.7 | 24 | quorum sensing: environmental adaptation through cross-species synchronization | ||
|
UDP-glucose 4-epimerase, putative (M: Cell wall/membrane/envelop biogenesis) |
I0IN00 | -0.01 | 17 | EPS biosynthesis: adhesion, production of EPS precursors | ||
|
diguanylate cyclase, putative (T: Signal transduction) |
I0IKF7 | +2.0 | -0.4 | 8 | regulation of bacterial biofilm formation and motility | |
|
diguanylate cyclase/phosphodiesterase (M: Cell wall/membrane/envelop biogenesis) |
A5FTD7 | +0.43 | 16 | EPS biosynthesis: signal transduction | ||
|
peptidoglycan glycosyltransferase, putative (D: Cell cycle control and mitosis; M: Cell wall/membrane/envelop biogenesis) |
I0IRD8 | +2.0 | 21 | EPS biosynthesis: cell wall modification | ||
|
signal transduction histidine kinase (N: Cell motility; T: Signal transduction) |
I0IL64 | +6.2 | +2.8 | -0.33 | 16 | two-component system: chemotaxis regulation |
|
chaperone clpB (O: Post-translational modification, protein turnover, chaperone functions) |
I0IRT5 | +7.0 | -0.05 | 20 | regulation of stress-response, temperature adaptation: membrane fluidity, pH tolerance | |
|
signal recognition particle subunit FFH/SRP54 (U: Intracellular trafficking and secretion) |
I0IPL2 | +2.8 | +0.13 | 25 | chemotaxis, acid tolerance, secretion of EPS material | |
|
sensor protein PilS, putative (T: Signal transduction) |
B7J3T0 | -0.28 | 13 | motility: regulation of tight adherence, auto-aggregation, and pili formation |
Given are protein name and respective COG term assignment, UniProt database identifier, fold change (optimized vs. standard laboratory culture) in the proteomics data set (prot), fold change (biofilm vs. planktonic fraction) in the transcriptomics data set (trans), fold change (continuous vs. bioleaching culture) in the control data set (control), number of species coding the protein (in the set of 25 species), and protein molecular function context. EPS: extracellular polymeric substance.