Table 3.
Three major modules in gene co-expression networka
| Gene | Annotation | Change in expression at: | |||||||||||
| C1' | C5' | C10' | C20' | C40' | C60' | F1' | F5' | F10' | F20' | F40' | F60' | ||
| Iron acquisition | |||||||||||||
| SO0448 | conserved hypothetical inner membrane protein | 3.40 | -- | -- | 5.00 | 3.41 | 4.30 | 0.56 | 0.46 | 0.26 | 0.21 | 0.20 | 0.15 |
| SO0449 | conserved iron-regulated membrane protein | 4.00 | 4.61 | 3.88 | 3.06 | 3.76 | 3.20 | 1.07 | 0.67 | 0.49 | 0.59 | 0.48 | 0.35 |
| SO0744 | iron(III) ABC transporter, periplasmic iron(III)-binding protein | 2.92 | 3.42 | 3.72 | 3.61 | 5.40 | 6.93 | 0.50 | 0.16 | 0.12 | 0.12 | 0.20 | 0.17 |
| SO1111 | bacterioferritin subunit 2 (Bfr2) | 0.53 | 0.45 | 0.41 | 0.36 | 0.41 | 0.56 | 2.56 | 3.41 | 6.00 | -- | 5.75 | 5.61 |
| SO1188 | unknown inner membrane protein | 8.66 | 9.94 | 10.62 | 14.47 | 10.91 | 8.38 | 0.47 | 0.12 | 0.09 | 0.11 | 0.24 | 0.10 |
| SO1190 | ABC-type Co2+ transporter, a periplasmic component | 1.06 | 2.57 | 4.59 | -- | 6.28 | 3.70 | 0.90 | 0.52 | 0.18 | 0.07 | 0.08 | 0.07 |
| SO1482 | TonB-dependent receptor | 3.50 | 3.44 | 6.62 | 7.12 | 8.44 | 8.13 | 0.62 | 0.21 | 0.05 | 0.06 | 0.03 | 0.03 |
| SO1755 | phosphoglucomutase/phosphomannomutase family protein | 1.37 | 1.63 | 2.09 | 2.77 | 3.31 | 4.19 | 0.55 | 0.38 | 0.27 | 0.21 | 0.26 | 0.21 |
| SO1784 | ferrous iron transport protein B (FeoB) | 3.74 | 4.98 | 4.07 | 2.45 | 2.49 | 2.29 | 0.62 | 0.25 | 0.20 | 0.13 | 0.23 | 0.14 |
| SO2039 | signalling protein with EAL domain | 3.09 | 3.89 | 3.39 | 4.86 | 4.81 | -- | -- | -- | -- | -- | -- | -- |
| SO2260 | extragenic suppressor protein (SuhB) | 0.59 | 0.49 | 0.43 | 0.41 | 0.45 | 2.52 | 1.78 | 2.49 | 6.21 | 3.63 | 5.58 | |
| SO2426 | two component transcriptional regulator | 11.65 | 13.67 | 10.06 | 7.88 | 8.90 | 10.00 | 0.57 | 0.11 | 0.07 | 0.06 | 0.05 | 0.06 |
| SO2736 | conserved hypothetical outer membrane protein | 3.88 | 5.33 | 4.47 | 4.37 | 4.78 | 5.23 | 0.56 | 0.33 | 0.40 | 0.27 | 0.28 | 0.25 |
| SO3025 | unknown protein | 1.85 | 2.54 | 3.71 | 5.24 | 6.75 | 6.11 | 0.71 | 0.28 | 0.25 | 0.23 | 0.23 | 0.16 |
| SO3030 | alcaligin biosynthesis enzyme (AlcA) | 6.24 | 8.34 | 14.64 | 12.87 | 23.64 | 12.45 | 1.90 | 0.75 | 0.80 | 0.18 | 0.12 | 0.11 |
| SO3032 | alcaligin biosynthesis protein (AlcC) | 1.65 | 1.80 | 3.94 | 9.20 | 21.09 | 19.42 | 1.23 | -- | 0.72 | 0.14 | 0.42 | -- |
| SO3034 | ferric iron reductase protein (AlcE) | 1.07 | 1.02 | 1.60 | 3.76 | 5.51 | 5.25 | 0.65 | 1.01 | 0.50 | 0.15 | 0.18 | 0.11 |
| SO3063 | sodium:alanine symporter family protein | 1.04 | 1.67 | 2.11 | 4.10 | 4.38 | 4.68 | 0.85 | 0.54 | 0.23 | 0.41 | 0.54 | 0.29 |
| SO3065 | colicin V production protein | -- | -- | 0.33 | 0.35 | 0.37 | 0.42 | 2.16 | -- | 1.29 | 2.73 | 2.93 | 3.30 |
| SO3407 | conserved iron-regulated membrane protein | 11.36 | 17.13 | 18.98 | 18.04 | 13.31 | 10.14 | 0.68 | 0.10 | 0.05 | 0.06 | 0.13 | 0.04 |
| SO3667 | heme iron utilization protein | 1.22 | 2.01 | 6.03 | -- | 17.15 | 13.53 | 0.83 | 0.65 | 0.33 | 0.08 | 0.02 | 0.01 |
| SO3668 | HugX family protein | 1.93 | 3.45 | 9.15 | 12.84 | 20.27 | 18.24 | 0.82 | 0.39 | 0.21 | 0.10 | 0.04 | -- |
| SO3669 | heme transport protein (HugA) | 19.42 | 41.21 | 56.72 | -- | 74.82 | 69.78 | 0.44 | 0.07 | 0.03 | 0.04 | 0.04 | -- |
| SO3670 | TonB1 protein | 22.48 | 45.17 | 62.47 | 34.35 | 41.42 | 64.58 | 0.10 | 0.04 | 0.02 | 0.02 | 0.08 | 0.01 |
| SO3671 | TonB system transport protein (ExbB1) | 16.33 | 37.79 | 50.11 | 56.59 | 51.37 | 56.36 | 0.59 | 0.05 | 0.02 | 0.03 | 0.03 | -- |
| SO3672 | TonB system transport protein (ExbD1) | 2.43 | 7.33 | 11.09 | 13.87 | 10.34 | 9.45 | 0.84 | 0.21 | -- | 0.16 | 0.32 | -- |
| SO3673 | hemin ABC transporter (HmuT) | 2.20 | 7.30 | 13.52 | 26.71 | 17.87 | 19.86 | 0.91 | 0.33 | 0.07 | 0.06 | 0.11 | 0.04 |
| SO3674 | hemin ABC transporter, permease protein (HmuU) | 1.08 | 2.53 | 6.74 | 11.84 | 10.57 | 9.13 | 1.07 | 0.49 | 0.09 | 0.15 | 0.47 | -- |
| SO3675 | hemin ABC transporter, ATP-binding protein (HmuV) | -- | 4.83 | 16.36 | 27.84 | 21.42 | 19.39 | 1.23 | 0.64 | -- | 0.11 | 0.41 | -- |
| SO3914 | TonB-dependent receptor (iron uptake) | 2.89 | 4.45 | 7.32 | -- | 9.38 | 11.30 | 0.74 | 0.24 | 0.14 | 0.05 | 0.15 | 0.03 |
| SO4523 | iron-regulated outer membrane protein (IrgA) | 3.53 | 5.23 | 9.19 | 14.16 | 23.22 | 25.92 | 0.54 | 0.21 | 0.08 | 0.04 | 0.13 | 0.04 |
| SO4690 | dolichyl-phosphate-mannose-protein mannosyltransferase family protein | 1.46 | 1.45 | 1.62 | 2.09 | 2.16 | 2.02 | 1.02 | 0.71 | 0.51 | 0.64 | 0.48 | 0.56 |
| SO4743 | TonB-dependent receptor | 8.12 | 9.18 | 7.07 | 4.48 | 4.29 | 3.23 | 0.66 | 0.18 | 0.09 | 0.08 | 0.19 | 0.13 |
| Anaerobic energy metabolism | |||||||||||||
| SO0261 | heme exporter protein (CcmC) | 0.85 | -- | -- | 0.26 | 0.23 | 0.21 | 1.24 | 2.05 | 1.53 | 2.81 | 2.49 | 2.57 |
| SO0262 | heme exporter protein (CcmB) | 1.76 | 1.38 | 0.79 | 0.21 | 0.23 | -- | -- | -- | -- | -- | -- | -- |
| SO0263 | heme exporter protein (CcmA) | 1.01 | 0.73 | 0.59 | 0.12 | 0.14 | 0.15 | 1.45 | 2.15 | 2.17 | 2.63 | 2.49 | 3.13 |
| SO0325 | dsrE-related protein | 0.66 | 0.56 | 0.67 | 0.12 | 0.08 | 0.09 | 1.56 | 3.36 | 2.41 | 2.59 | 2.64 | 2.23 |
| SO0398 | FAD-binding subunit of inner membrane respiratory complex (FrdA) | 1.72 | 1.74 | 1.04 | 0.24 | 0.23 | 0.20 | 0.96 | 2.14 | 1.99 | 2.55 | 2.03 | 2.61 |
| SO0403 | expressed protein | -- | -- | -- | 0.11 | 0.09 | 0.12 | 1.35 | 2.16 | 2.46 | 0.91 | 1.63 | 1.27 |
| SO0435 | uroporphyrinogen decarboxylase (HemE) | 1.27 | 1.46 | 0.95 | 0.32 | 0.19 | 0.15 | 1.50 | 2.33 | 2.72 | 3.64 | 5.01 | 5.42 |
| SO0490 | transcriptional regulator | -- | 0.89 | 0.78 | 0.08 | 0.10 | -- | -- | -- | -- | -- | -- | -- |
| SO0595 | expressed protein | 1.04 | 0.97 | 0.92 | -- | 0.09 | -- | -- | -- | -- | -- | -- | -- |
| SO0975 | conserved hypothetical inner membrane protein | 1.07 | 1.15 | 0.58 | 0.06 | 0.06 | 0.05 | 1.09 | 2.02 | 1.80 | 4.74 | 3.06 | 3.56 |
| SO1250 | conserved hypothetical protein | 1.02 | 1.01 | 0.53 | 0.15 | 0.14 | 0.15 | 1.20 | 2.54 | 3.09 | 2.14 | 1.61 | 1.32 |
| SO1415 | transcriptional regulator, TetR family | 1.05 | 0.88 | 0.57 | 0.04 | 0.05 | -- | -- | -- | -- | -- | -- | -- |
| SO1522 | L-lactate permease, integral IM protein | 1.08 | 0.95 | 0.70 | 0.18 | 0.24 | 0.15 | 2.13 | 3.43 | 3.33 | 5.55 | 4.03 | 4.27 |
| SO1777 | periplasmic decaheme cytochrome c, Fe(III) and Mn(IV) reduction (MtrA) | 0.97 | -- | -- | 0.11 | 0.08 | 0.11 | 1.64 | 3.47 | 4.26 | 3.19 | 3.99 | 5.14 |
| SO1778 | decaheme cytochrome c (MtrC) | 0.97 | 1.26 | 0.69 | 0.07 | 0.08 | 0.06 | 2.44 | 6.04 | 3.47 | 4.27 | 3.93 | 7.85 |
| SO1779 | Outer membrane decaheme cytochrome c (OmcA) | 1.65 | 1.93 | 0.94 | 0.09 | 0.07 | 0.06 | 2.10 | 7.04 | 6.76 | 8.51 | 6.91 | 10.11 |
| SO1910 | 1,4-dihydroxy-2-naphthoate octaprenyltransferase (MenA) | 1.24 | 1.04 | 0.71 | 0.29 | 0.28 | 0.22 | 1.41 | 2.21 | 2.22 | 3.21 | 2.87 | 3.29 |
| SO1911 | oxidoreductase, short chain dehydrogenase/reductase family | 0.71 | 0.66 | 0.47 | 0.03 | 0.06 | 0.04 | 1.90 | 3.72 | 2.60 | 5.44 | 3.71 | 3.01 |
| SO2005 | dksA-type zinc finger protein | 0.46 | 0.47 | 0.19 | 0.05 | 0.07 | -- | -- | -- | -- | -- | -- | -- |
| SO2019 | ferrochelatase (HemH 1) | 1.33 | 0.94 | 0.82 | 0.18 | 0.18 | 0.16 | 1.29 | 2.53 | 2.14 | 4.77 | 3.84 | 5.56 |
| SO2136 | aldehyde-alcohol dehydrogenase (AdhE) | 0.62 | 0.41 | 0.43 | 0.09 | 0.11 | 0.08 | 2.29 | 3.05 | 3.05 | 7.13 | 3.75 | 5.88 |
| SO2834 | anaerobic ribonucleoside-triphosphate reductase (NrdD) | 1.16 | 1.83 | 0.47 | 0.12 | 0.09 | 0.12 | 0.80 | 2.27 | 2.19 | 2.12 | 1.55 | 1.24 |
| SO2865 | L-lysine exporter, putative | 1.66 | 1.31 | 0.70 | 0.16 | 0.30 | -- | -- | -- | -- | -- | -- | -- |
| SO3119 | conserved hypothetical protein | -- | -- | -- | 0.19 | 0.20 | 0.26 | 2.18 | 5.48 | 2.87 | 2.11 | 1.70 | 2.00 |
| SO3297 | transcriptional regulator, LysR family | 1.24 | 0.98 | 0.72 | 0.16 | 0.21 | 0.29 | 1.09 | 0.92 | 1.08 | 1.50 | 1.57 | -- |
| SO3416 | hypothetical protein | 1.13 | 1.27 | 0.95 | 0.24 | 0.25 | 0.38 | 1.77 | 1.89 | 2.25 | 1.05 | 1.98 | 1.37 |
| SO3507 | conserved hypothetical protein | 2.08 | 1.70 | 1.45 | 0.19 | 0.17 | 0.10 | 1.73 | -- | 8.41 | 3.10 | 3.00 | 2.60 |
| SO3553 | sulfate permease family protein | 0.68 | 0.74 | 0.67 | 0.19 | 0.17 | 0.11 | 2.24 | 3.94 | 3.60 | 7.45 | 5.47 | 6.92 |
| SO3627 | transcriptional regulator, TetR family | 1.17 | 1.07 | 0.72 | 0.03 | 0.06 | 0.06 | 0.92 | 6.40 | 3.07 | 3.19 | 2.99 | 1.74 |
| SO3874 | transcriptional regulator, LysR family | 0.60 | 0.48 | 0.30 | 0.07 | 0.05 | 0.05 | 1.72 | 4.56 | 3.75 | 3.81 | 2.79 | 2.96 |
| SO3901 | lacZ expression regulator (icc) | 1.15 | 0.75 | 0.60 | 0.21 | 0.20 | 0.15 | 1.71 | 3.61 | 2.74 | 3.24 | 2.23 | 2.74 |
| SO4138 | expressed periplasmic protein | 0.95 | 0.96 | 0.68 | 0.13 | 0.09 | 0.11 | 1.42 | 4.10 | 2.55 | 3.76 | 3.46 | 3.63 |
| SO4155 | sensor histidine kinase for thiosulfate/tetrathionate response (TtrS) | 0.72 | 0.65 | 0.72 | 0.10 | -- | -- | -- | -- | -- | -- | -- | -- |
| SO4157 | two component transciptional regulator for thiosulfate/tetrathionate response (TtrR) | 0.39 | 0.66 | -- | 0.12 | -- | 0.09 | 1.66 | 2.78 | -- | 1.98 | 2.02 | 2.60 |
| SO4204 | Sec-independent periplasmic protein translocation protein (TatC) | 0.87 | 0.64 | 0.61 | -- | 0.27 | 0.25 | 1.64 | -- | 1.72 | 2.53 | 2.95 | 3.58 |
| SO4355 | cAMP-binding protein | 2.73 | 2.02 | 1.62 | 0.19 | 0.26 | 0.22 | 2.01 | 2.24 | 1.33 | 2.44 | 1.86 | 2.69 |
| SO4448 | molybdenum ABC transporter, periplasmic molybdenum-binding protein (ModA-2) | 1.65 | 1.84 | 1.00 | 0.33 | 0.33 | 0.43 | 1.17 | 1.39 | 1.28 | 1.35 | 1.18 | 1.06 |
| SO4591 | tetraheme cytochrome c (CymA) | -- | -- | -- | 0.17 | 0.15 | 0.11 | 2.83 | 7.01 | 3.75 | 3.76 | 5.27 | 7.71 |
| SO4623 | two component transcriptional regulator | 0.68 | 0.51 | 0.44 | 0.11 | 0.12 | 0.14 | 1.21 | 1.69 | 1.30 | 1.31 | 1.46 | 1.39 |
| SO4718 | two component Sigma54 specific transcriptional regulator for tungstate (molybdate) transport | 1.79 | 1.69 | 1.42 | 0.42 | 0.40 | 0.47 | 1.30 | 1.86 | 1.83 | 2.25 | 2.38 | 2.82 |
| Protein degradation | |||||||||||||
| SO0052 | protein export chaperone (SecB) | 0.93 | 1.00 | 0.68 | 0.66 | 2.44 | -- | -- | -- | -- | -- | -- | -- |
| SO1126 | chaperone protein (DnaK) | 0.80 | 1.14 | 0.84 | 0.68 | 1.79 | 1.60 | 0.76 | 0.95 | 0.41 | 0.05 | 0.06 | 0.04 |
| SO1127 | chaperone protein (DnaJ) | 1.19 | 1.07 | 0.73 | 1.00 | 1.67 | 1.11 | 1.22 | 1.29 | 0.76 | 0.23 | 0.17 | 0.24 |
| SO2016 | heat shock protein (HtpG) | 0.88 | 0.82 | 0.58 | 1.15 | 2.53 | 1.74 | 0.93 | 1.05 | 0.71 | 0.10 | 0.22 | 0.06 |
| SO2017 | Unknown Protein | 0.83 | 0.81 | 0.56 | 1.07 | 2.78 | 1.64 | 1.19 | 0.91 | 0.61 | 0.16 | 0.20 | 0.14 |
| SO2265 | scaffold protein for Fe-S cluster assembly (IscU) | -- | 1.48 | 1.33 | 1.45 | 4.66 | 3.74 | 0.82 | 0.59 | 0.36 | 0.09 | 0.25 | 0.19 |
| SO2266 | iron recruitment protein (IscA) | 1.18 | 1.28 | 1.05 | 1.45 | 4.46 | 4.68 | 1.04 | 0.81 | 0.23 | 0.12 | 0.25 | 0.23 |
| SO3588 | gpr1/fun34/yaaH family protein | 1.09 | 1.08 | 1.02 | 1.39 | 1.98 | 2.88 | 1.20 | 0.61 | 0.38 | 0.44 | 0.57 | 0.76 |
| SO4699 | oligopeptidase A (PrlC) | 0.98 | 0.92 | 0.75 | 1.49 | 2.36 | 1.61 | 1.05 | 1.08 | 0.44 | 0.13 | 0.28 | 0.12 |
Expression ratio values greater than 1 denote increases in gene expression and values between 0 and 1 indicate decreases in gene expression. --: not detected.