Table 1. Significant genes identified by microarray transcriptomic analysis in the biofilm bacteria exposed to 170/mL ampicillin.
| UPREGULATED GENES | ||||||
| Gene Name | Ordered Locus | Uniprot | Fold Change | p-Value | Biological Process/function | |
| Carbohydrate Metabolism | ||||||
| ADP-glucose synthase | glgC | NTHI1807 | Q4QK69 | 1.66 | 0.0008 | glycogen biosynthesis |
| 4-alpha-glucanotransferase | malQ | NTHI1810 | Q4QK66 | 1.58 | 0.0003 | glycosyltransferase |
| 1,4-alpha-glucan branching enzyme | glgB | NTHI1809 | Q4QK67 | 1.62 | 0.0007 | glycogen biosynthesis |
| Glycogen operon protein GlgX | glgX | NTHI1808 | Q4QK68 | 1.55 | 0.0009 | glycogen catabolism |
| Glycogen synthase | glgA | NTHI1806 | Q4QK70 | 1.86 | 0.0003 | glycogen biosynthesis |
| Transporter | ||||||
| Predicted cobalt transport protein | NTHI1421 | Q4QL56 | 1.57 | 0.001 | ABC transporter | |
| Pyrimidine Metabolism | ||||||
| Cytidine deaminase | cdd | NTHI1816 | Q4QK60 | 1.65 | 0.0006 | UMP synthesis |
| Hypothetical Protein | ||||||
| Uncharacterized protein:pH regulation | NTHI0443 | Q4QNL4 | 1.58 | 0.001 | Na:H antiporter activity | |
| DOWNREGULATED GENES | ||||||
| Amino-acid biosynthesis | ||||||
| Bifunctional protein FolD | folD | NTHI0864 | Q4QMI7 | −2.36 | 0.001 | Amino-acid biosynthesis |
| Phosphoglycerol transferase-like protein | NTHI1918 | Q4QJX3 | −2.09 | 1E-05 | Transferase | |
| Amino Acid Metabolism | ||||||
| Anthranilate synthase component I | trpE | NTHI1768 | Q4QK98 | −1.52 | 0.001 | Lyase |
| Peptide methionine sulfoxide reductase | msaB | NTHI1677 | Q4QKI0 | −1.56 | 0.001 | Oxidoreductase |
| Glutamate racemase | murI | NTHI205 | Q4QJK7 | −1.77 | 0.001 | Cell wall biogenesis |
| Folate Biosynthesis | ||||||
| dihydroneopterin aldolase | folB | NTHI0372 | Q4QNS3 | −1.71 | 0.001 | Lyase |
| Purine Metabolism | ||||||
| Bifunctional purine biosynthesis protein | purH | NTHI1051 | Q4QM21 | −1.98 | 0.001 | Hydrolase |
| Phosphoribosylaminoimidazole carboxylase ATPase subunit | purK | NTHI1424 | Q4QL53 | −1.96 | 0.001 | Lyase |
| N5-carboxyaminoimidazole ribonucleotide mutase | purE | NTHI1425 | Q4QL52 | −3.70 | 5E-05 | Lyase |
| Phosphoribosylformylglycinamidine cyclo-ligase | purM | NTHI1704 | Q4QKF3 | −3.45 | 9E-05 | Ligase |
| Phosphoribosylaminoimidazole-succinocarboxamide synthase | purC | NTHI2033 | Q4QJM1 | −2.50 | 0.0003 | Ligase |
| Phosphoribosylglycinamide formyltransferase | purN | NTHI1706 | Q4QKF2 | −2.66 | 1E-04 | Transferase |
| adenylosuccinase | purB | NTHI0758 | Q4QMS8 | −1.52 | 0.001 | Lyase |
| Regulation of transcription | ||||||
| BirA bifunctional protein | birA | NTHI0323 | Q4QNW6 | −2.63 | 0.0004 | Ligase |
| Ribose operon repressor | rbsR | NTHI0634 | Q4QN40 | −1.62 | 0.001 | DNA binding |
| Xylose operon regulatory protein | xylR | NTHI1273 | Q4QLI5 | −2.15 | 9E-05 | DNA binding |
| Toxin biosynthetic process | ||||||
| Colicin V production protein | cvpA | NTHI1377 | Q4QL93 | −1.92 | 0.001 | Membrane protein |
| Carbohydrate metabolism | ||||||
| D,D-heptose 1,7-bisphosphate phosphatase | NTHI0880 | Q4QMH3 | −3.21 | 0.0003 | Hydrolase | |
| Fructose-1,6-bisphosphatase | glpX | NTHI0789 | Q4QMP9 | −1.85 | 0.002 | Hydrolase |
| Acetoacetate CoA transferase alpha subunit | atoD | NTHI0935 | Q4QMC5 | −1.75 | 0.0006 | Transferase |
| DNA replication | ||||||
| DNA polymerase III subunit epsilon | dnaQ | NTHI0223 | Q4QP50 | −2.29 | 7E-05 | Transferase |
| Ribonuclease H | rnhA | NTHI0224 | Q4QP49 | −3.09 | 0.0001 | Endonuclease |
| Protein transporter | ||||||
| Competence protein E | comE | NTHI0560 | Q4QNB0 | −1.87 | 0.001 | Protein secretion |
| Type IV pilin secretion protein | pilB | NTHI0408 | Q4QNP5 | −1.64 | 0.0006 | |
| Type IV pilin secretion protein | pilC | NTHI0407 | Q4QNP6 | −1.74 | 0.001 | |
| Cellular cell wall organization | ||||||
| Membrane-bound lytic murein transglycosylase F | mltF | NTHI0338 | Q4QNV4 | −2.21 | 2E-04 | |
| Aminoacyl-tRNA biosynthesis | ||||||
| Lysine–tRNA ligase | genX | NTHI1003 | Q4QM64 | −1.60 | 0.001 | |
| ABC transporter | ||||||
| periplasmic oligopeptide-binding protein | oppA | NTHI1292 | Q4QLH0 | −1.74 | 0.0003 | |
| ABC-type chelated iron transport system | hfeD | NTHI0477 | Q4QNI3 | −1.5 | 0.001 | |
| DNA packaging | ||||||
| Phage terminase large subunit | NTHI1741 | Q4QKB9 | −2.02 | 0.001 | ||
| Protein deacetylation | ||||||
| NAD-dependent deacetylase sirtuin 5 | NTHI1634 | Q4QKL5 | −2.80 | 2E-04 | Hydrolase | |
| RNA repair | ||||||
| Multifunctional CCA protein | cca | NTHI1436 | Q4QL41 | −1.97 | 0.002 | |
| Amino acid transporter | ||||||
| Tryptophan-specific transport protein | mtr | NTHI0396 | Q4QNQ4 | −1.84 | 0.0002 | |
| Hypothetical Proteins | ||||||
| NTHI0215 | Q4QP56 | −3.28 | 0.001 | transmembrane transport | ||
| NTHI0680 | Q4QMZ6 | −1.73 | 0.0004 | |||
| NTHI0735 | Q4QMU6 | −1.64 | 0.0005 | Predicated membrane protein | ||
| NTHI1330 | Q4QLD5 | −1.64 | 0.001 | |||
| Conserved FAD/FMN-containing dehydrogenase | NTHI1331 | Q4QLD4 | −1.77 | 0.001 | ||
| NTHI1505 | Q4QKY1 | −2.25 | 0.001 | |||
| NTHI1511 | Q4QKX6 | −2.54 | 0.0007 | DNA replication | ||
| NTHI1528 | Q4QKW1 | −2.17 | 0.0005 | |||
| NTHI1534 | Q4QKV5 | −1.84 | 0.002 | |||
| NTHI1635 | Q4QKL4 | −4.08 | 0.001 | Catalytic activity | ||
| NTHI1721 | Q4QKD8 | −3.11 | 0.001 | DNA binding | ||
| NTHI1726 | Q4QKD3 | −1.92 | 0.0006 | |||
| NTHI1735 | Q4QKC5 | −2.31 | 0.001 | |||
| NTHI1736 | Q4QKC4 | −2.10 | 0.0008 | Cell wall catabolism | ||
| NTHI1738 | Q4QKC2 | −2.04 | 0.0003 | |||
| NTHI1739 | Q4QKC1 | −2.12 | 0.0005 | DNA binding | ||
| Putative recombination protein NinB | ninB | NTHI1727 | Q4QKD2 | −2.54 | 0.0006 | |
| Putative recombination protein NinG | ninG | NTHI1728 | Q4QKD1 | −2.49 | 0.0007 | |
Genes that were either up or down regulated (≥1.5-fold plus P≤0.05, T-test and FDR≤0.05) when biofilms were formed in the presence of 170 ng/mL ampicillin are listed. Eight genes were up-regulated and 51 were down-regulated. Of the eight up-regulated genes, 5 were involved in carbohydrate metabolism and were enzymes involved in glycogen processing. The down-regulated genes were involved in a wide range of metabolic processes and 18 genes were unannotated (hypothetical).