Table 1.
Gene expression changes between early Agg and early FL and between late Agg and early Agg
| Category and Genes | Log2FC | ||||
|---|---|---|---|---|---|
| Label | Product | COG | earlyAgg /earlyFL |
lateAgg /earlyAgg |
|
| Ammonia oxidation-related genes | |||||
| 0350049 | amoE1, conserved exported protein of unknown function | 0.99 | –1.26 | ||
| 0880004 | amoE2, conserved exported protein of unknown function | 1.01 | –1.25 | ||
| Energy production and conversion | |||||
| 0140010 | atpH, ATP synthase subunit delta | C | –1.15 | 0.81 | |
| 0140012 | atpG, F1 sector of membrane-bound ATP synthase, gamma subunit | C | –1.02 | 0.73 | |
| 0140014 | atpC, F1 sector of membrane-bound ATP synthase, epsilon subunit | C | –1.03 | 0.49 | |
| Translation, ribosomal structure, and biogenesis | |||||
| 0110006 | rplI, 50S ribosomal subunit protein L9 | J | –1.31 | 0.89 | |
| 0110007 | rpsR, 30S ribosomal protein S18 | J | –1.68 | 1.31 | |
| 0110009 | rpsF, 30S ribosomal protein S6 | J | –1.43 | 1.17 | |
| 0360010 | rplP, 50S ribosomal protein L16 | J | –1.09 | 1.10 | |
| C fixation | |||||
| 0380014 | cbbS, Ribulose bisphosphate carboxylase small chain | –0.51 | 1.36 | ||
| 0500025 | cbbX, Protein CbbX | O | 0.57 | 1.80 | |
| 0500026 | cbxSP, Ribulose bisphosphate carboxylase small chain, plasmid | 0.41 | 2.67 | ||
| 0500027 | cbbL, Ribulose bisphosphate carboxylase large chain | G | 0.47 | 2.55 | |
| Cell motility | |||||
| 0150046 | fliG, flagellar motor switching and energizing component | N | 2.08 | –0.13 | |
| 0150048 | fleS, putative two-component sensor | T | 2.30 | –0.18 | |
| 0150060 | fliC, Flagellin | N | 2.41 | –0.15 | |
| 0150140 | fliL, putative flagellar fliL transmembrane protein | N | 2.29 | 0.05 | |
| 0310032 | pilT, Twitching motility protein | N | 1.89 | 0.08 | |
| 0380017 | cheY, chemotaxis regulator transmitting signals to the flagellar motor component | T | 1.30 | 0.08 | |
| 0380032 | pilM, putative type 4 fimbrial biogenesis protein PilM | N | 2.42 | –0.27 | |
| 0380033 | pilN, putative type 4 fimbrial biogenesis protein PilN | N | 2.22 | –0.33 | |
| 0480032 | cheA, fused chemotactic sensory histidine kinase in the two-component regulatory system | N | 2.52 | –0.18 | |
| 0480033 | cheW, purine-binding chemotaxis protein | N | 1.88 | 0.53 | |
| 0800052 | yrbD, toluene transporter subunit: membrane component of the ABC superfamily | Q | 1.12 | –1.04 | |
| Exopolysaccharide | |||||
| 0150022 | Exopolysaccharide synthesis, ExoD | 1.44 | –0.93 | ||
| Posttranslational modification, protein turnover, chaperones | |||||
| 0150067 | dnaJ, chaperone Hsp40, co-chaperone with DnaK | O | 1.89 | 0.04 | |
| 0150019 | clpB, protein disaggregation chaperone | O | 2.20 | –3.58 | |
| 0150066 | dnaK, chaperone Hsp70 in DNA biosynthesis/cell division | O | 1.72 | –2.61 | |
| 0250024 | lon, DNA-binding ATP-dependent protease La | O | 1.94 | –2.92 | |
| 0340021 | Serine proteases, subtilase family | O | 2.29 | –0.86 | |
| 0380114 | clpA, ATPase and specificity subunit of ClpA-ClpP ATP-dependent serine protease, chaperone activity | O | 1.13 | –1.16 | |
| CRISPR and restriction-modification system | |||||
| 160022 | Type I restriction-modification system, M subunit | V | 1.59 | –2.00 | |
| 260103 | CRISPR-associated helicase Cas3 | R | 2.37 | –0.50 | |
| 260105 | CRISPR-associated protein, Csd1 family | 1.67 | –0.35 | ||
| 0260111 | cas, CRISPR-associated endoribonuclease Cas2 3 | L | 1.12 | –0.92 | |
| 480070 | Type III restriction enzyme, res subunit | V | 1.08 | –1.03 | |
| 0480084 | hsdR, Type-1 restriction enzyme R protein | V | 1.01 | –0.81 | |
| Gene transfer | |||||
| 70001 | transposase | L | 1.32 | –1.71 | |
| 330006 | Type-F conjugative transfer system protein TraW | 1.78 | –1.08 | ||
| 330008 | Type-F conjugative transfer system pilin assembly protein TrbC | 1.21 | –0.86 | ||
| 330050 | TraB pilus assembly | E | 1.86 | –1.30 | |
| 0380006 | int, Integrase/recombinase | L | 1.32 | –1.00 | |
| 0540044 | insH, IS5 transposase and trans-activator; CP4-44 prophage | L | 1.13 | –0.95 | |