Table 1.
Integration of the transcriptome (RNA-Seq), proteome, metabolome and bioinformatics-based Fnr –binding site analyses for the analysis of C. difficile to low iron conditions.
| Gene | Wild type: low vs. | fur mutant vs. wild type | Fur box | ||||
|---|---|---|---|---|---|---|---|
| Locus_tag | name | high iron (log2 FC) | at high iron (log2 FC) | ||||
| T | P | T | P | ||||
| Metal transport systems | |||||||
| CD630_16470 CDIF630erm_01824 | yclN | Iron family ABC transporter permease | 4.79 | 0.18 | 5.90 | – | + |
| CD630_16480 CDIF630erm_01825 | yclO | Iron family ABC transporter permease | 3.43 | ON | 4.74 | ON | |
| CD630_16490 CDIF630erm_01826 | yclP | Iron family ABC transporter ATP-binding protein | 5.16 | 0.62 | 5.19 | ON | |
| CD630_16500 CDIF630erm_01827 | yclQ | Iron family ABC transporter substrate-binding protein | 4.98 | 7.46 | 4.65 | 8.55 | + |
| CD630_28740 CDIF630erm_03142 | MATE family drug/sodium antiporter | 2.42 | – | 4.12 | – | ||
| CD630_28750 CDIF630erm_03143 | fhuC | Ferrichrome-specific ABC transporter ATP-binding protein | 1.49 | – | 1.86 | ON | |
| CD630_28760 CDIF630erm_03144 | fhuG | Ferrichrome-specific ABC transporter permease | 1.00 | ON | 3.85 | ON | |
| CD630_28770 CDIF630erm_03145 | fhuB | Ferrichrome-specific ABC transporter permease | 1.15 | ON | 3.27 | ON | + |
| CD630_28780 CDIF630erm_03146 | fhuD | Ferrichrome-specific ABC transporter, substrate-binding | 0.78 | 2.43 | 2.73 | 4.47 | + |
| CD630_29890 CDIF630erm_03273 | ssuA2 | Sulfonate family ABC transporter substrate-binding protein | 2.60 | 2.29 | 4.39 | 3.73 | |
| CD630_29900 CDIF630erm_03274 | ssuB2 | Sulfonate family ABC transporter ATP-binding protein | 2.91 | 3.09 | 4.50 | 4.81 | |
| CD630_29910 CDIF630erm_03275 | ssuC2 | Sulfonate family ABC transporter permease | 3.53 | – | 6.10 | – | |
| CD630_29920 CDIF630erm_03276 | Uncharacterized protein, iron hydrogenase-like | 2.93 | 1.07 | 4.38 | 5.83 | ||
| CD630_10870 CDIF630erm_01231 | zupT | Zinc transporter ZupT | 1.85 | ON | 6.19 | ON | + |
| CD630_05910 CDIF630erm_00704 | ATPase | 2.41 | 6.77 | 2.80 | 7.54 | ||
| CD630_05920 CDIF630erm_00705 | Hypothetical protein | 2.04 | 5.21 | 1.93 | 5.64 | + | |
| CD630_29970 CDIF630erm_03281 | Iron family ABC transporter ATP-binding protein | 1.02 | 0.19 | 1.08 | 1.16 | ||
| CD630_29980 CDIF630erm_03282 | Iron family ABC transporter permease | 0.42 | 0.06 | 1.95 | – | ||
| CD630_29990 CDIF630erm_03283 | Iron family ABC transporter substrate-binding protein | 0.17 | -0.83 | 0.65 | 0.48 | ||
| CD630_14770 CDIF630erm_01641 | feoA | Ferrous iron transport protein FeoA | 1.51 | ON | -1.18 | ON | + |
| CD630_14780 CDIF630erm_01642 | feoA | Ferrous iron transport protein FeoA1 | 1.02 | 5.70 | -1.13 | 3.69 | |
| CD630_14790 CDIF630erm_01643 | feoB1 | Ferrous iron transport protein FeoB1 | 0.77 | 7.19 | -0.16 | 4.78 | + |
| CD630_14800 CDIF630erm_01644 | Hypothetical protein | 0.40 | – | -0.01 | – | ||
| CD630_15170 CDIF630erm_01684 | feoB | Ferrous iron transport protein FeoB | -0.63 | – | -0.92 | – | |
| CD630_15180 CDIF630erm_01685 | feoA | Ferrous iron transport protein FeoA | – | - | -0.14 | – | |
| CD630_17451 CDIF630erm_01939 | feoA | Ferrous iron transport protein | -2.34 | 0.36 | -2.08 | 0.98 | + |
| CD630_21680 CDIF630erm_02400 | hcp | Hydroxylamine reductase | -0.81 | 0.29 | -2.21 | OFF | |
| CD630_21690 CDIF630erm_02401 | Iron-sulfur binding protein | -1.86 | – | -3.06 | – | ||
| CD630_03240 CDIF630erm_00452 | cbiM | Cobalamin transport protein CbiM | -2.19 | ON | -2.55 | – | |
| CD630_03250 CDIF630erm_00453 | cbiN | Cobalt ABC transporter substrate-binding protein CbiN | -1.81 | – | -2.81 | – | |
| CD630_03260 CDIF630erm_00454 | cbiQ | Cobalt ABC transporter permease CbiQ | -2.05 | ON | -1.13 | ON | |
| CD630_03270 CDIF630erm_00455 | cbiO | Cobalt ABC transporter ATP-binding protein CbiO | -0.47 | -0.18 | -1.81 | -0.10 | |
| Pili and flagella formation | |||||||
| CD630_35040 CDIF630erm_03817 | Type IV prepilin peptidase | -0.48 | – | -0.33 | – | ||
| CD630_35050 CDIF630erm_03818 | Twitching motility protein PilT | -0.91 | -0.52 | -1.71 | 0.12 | ||
| CD630_35060 CDIF630erm_03819 | Hypothetical protein | -0.64 | – | -2.01 | – | ||
| CD630_35070 CDIF630erm_03820 | Type IV pilin | -0.29 | – | -2.62 | – | ||
| CD630_35080 CDIF630erm_03821 | Type IV pilin | -1.40 | – | -1.74 | – | ||
| CD630_35090 CDIF630erm_03822 | Type IV pilus assembly protein | -1.01 | – | -2.43 | – | ||
| CD630_35100 CDIF630erm_03823 | Membrane protein | -1.30 | 0.08 | -1.91 | -0.21 | ||
| CD630_35110 CDIF630erm_03824 | Type IV pilus secretion protein | 0.79 | -1.43 | -2.74 | OFF | ||
| CD630_35120 CDIF630erm_03825 | Type IV pilus transporter system | -0.93 | 0.40 | -2.50 | -0.02 | ||
| CD630_35130 CDIF630erm_03826 | Pilin protein | -1.61 | 0.21 | -3.13 | -0.52 | 03828 | |
| CD630_02520 CDIF630erm_00375 | fliJ | Flagellar protein FliJ | 2.37 | ON | 2.25 | ON | |
| CD630_02530 CDIF630erm_00376 | fliK | Flagellar hook-length control protein FliK | 2.60 | 1.15 | 2.96 | 1.36 | |
| CD630_02540 CDIF630erm_00377 | flgD | Basal-body rod modification protein FlgD | 2.68 | – | 2.41 | – | |
| CD630_02550 CDIF630erm_00378 | flgE | Flagellar hook protein FlgE | 1.42 | 0.43 | 2.27 | -0.18 | |
| CD630_02551 CDIF630erm_00379 | FlbD | Flagellar protein FlbD | 3.26 | 1.56 | 1.28 | 0.91 | |
| CD630_02560 CDIF630erm_00380 | motA | Flagellar motor rotation protein MotA | 2.38 | -0.73 | 2.19 | -0.39 | |
| CD630_02570 CDIF630erm_00381 | motB | Flagellar motor rotation protein MotB | 1.97 | -0.16 | 2.04 | -0.79 | |
| CD630_02580 CDIF630erm_00382 | fliL | Flagellar basal body-associated protein FliL | 1.84 | 0.53 | 2.60 | 0.24 | |
| CD630_02590 CDIF630erm_00383 | fliZ | Flagellar protein FliZ | 1.05 | ON | 2.28 | ON | |
| CD630_02600 CDIF630erm_00384 | fliP | Flagellar biosynthesis protein FliP | 1.80 | OFF | 3.06 | -0.14 | |
| CD630_02610 CDIF630erm_00385 | fliQ | Flagellar biosynthetic protein FliQ | 1.07 | – | 2.50 | – | |
| CD630_02620 CDIF630erm_00386 | flhB | Bifunctional flagellar biosynthesis protein FliR/FlhB | 2.38 | – | 3.59 | – | |
| CD630_02630 CDIF630erm_00387 | flhA | Flagellar biosynthesis protein FlhA | 3.84 | 0.18 | 4.44 | 0.10 | |
| CD630_02640 CDIF630erm_00388 | flhF | Flagellar biosynthesis regulator FlhF | 3.61 | 1.04 | 3.84 | 1.30 | |
| CD630_02650 CDIF630erm_00389 | flhG | Flagellar biosynthesis protein FlhG | 1.99 | 0.28 | 3.57 | 0.21 | |
| CD630_02660 CDIF630erm_00390 | fliA | Flagellar operon RNA polymerase sigma-28 factor | 3.54 | -0.01 | 4.15 | OFF | |
| CD630_02670 CDIF630erm_00391 | Flagellar protein | 2.80 | 0.65 | 3.76 | OFF | ||
| CD630_02671 | Flagellar protein | 3.57 | – | 4.06 | ON | ||
| CD630_02680 CDIF630erm_00392 | flgG1 | Flagellar basal body rod protein FlgG | 3.44 | 0.74 | 2.92 | 2.00 | |
| CD630_02690 CDIF630erm_00393 | flgG | Flagellar basal body rod protein FlgG | 3.25 | 0.78 | 3.47 | OFF | |
| CD630_02700 CDIF630erm_00394 | fliM | Flagellar motor switch protein FliM | 2.98 | 0.18 | 3.41 | -0.12 | |
| CD630_02710 CDIF630erm_00395 | fliN | Flagellar motor switch phosphatase FliN | 3.33 | 0.43 | 2.97 | 0.04 | |
| CD630_02260 CDIF630erm_00348 | Lytic transglycosylase | -3.23 | 0.78 | -3.18 | 1.96 | + | |
| CD630_02270 CDIF630erm_00349 | Hypothetical protein | -1.99 | 0.13 | -3.99 | -0.01 | ||
| CD630_02280 CDIF630erm_00350 | fliN | Flagellar motor switch protein FliN | -2.25 | 0.25 | -2.84 | 0.16 | |
| CD630_02290 CDIF630erm_00351 | flgM | Negative regulator of flagellin synthesis | -2.08 | 1.19 | -3.40 | OFF | |
| CD630_02300 CDIF630erm_00352 | Flagellar biosynthesis protein | -2.41 | 0.92 | -3.12 | 0.59 | ||
| CD630_02310 CDIF630erm_00353 | flgK | Flagellar hook-associated protein FlgK | -2.08 | 1.58 | -3.51 | 0.08 | |
| CD630_02320 CDIF630erm_00354 | flgL | Flagellar hook-associated protein FlgL | -2.21 | 0.22 | -3.88 | -0.46 | |
| CD630_02330 CDIF630erm_00355 | fliW | Flagellar assembly factor FliW | -2.66 | -0.81 | -3.16 | 0.15 | |
| CD630_02340 CDIF630erm_00356 | crsA | Carbon storage regulator CsrA | -1.87 | 0.09 | -2.57 | -0.46 | |
| CD630_02350 CDIF630erm_00357 | fliS1 | Flagellar protein FliS1 | -1.33 | 1.91 | -3.04 | 1.89 | |
| CD630_02360 CDIF630erm_00358 | fliS2 | Flagellar protein FliS2 | -1.03 | 0.15 | -2.30 | 0.20 | |
| CD630_02370 CDIF630erm_00359 | fliD | Flagellar hook-associated protein FliD | -0.94 | 1.65 | -2.45 | 0.30 | |
| CD630_02380 CDIF630erm_00360 | Hypothetical protein | -0.69 | 1.30 | -3.06 | -0.56 | ||
| CD630_02390 CDIF630erm_00361 | fliC | Flagellin C | -0.09 | 0.14 | -1.57 | -0.93 | |
| CD630_22140 CDIF630erm_02447 | sinR | HTH-type transcriptional regulator | 1.85 | OFF | 2.46 | 0.72 | |
| CD630_22150 CDIF630erm_02448 | HTH-type transcriptional regulator | 2.17 | – | 2.68 | – | 02449 | |
| CD630_19970 CDIF630erm_02215 | Proline iminopeptidae | 2.04 | 0.26 | 4.07 | 1.63 | ||
| CD630_19980 CDIF630erm_02216 | TetR family transcriptional regulator | 1.85 | ON | 3.73 | ON | ||
| Polyamine biosynthesis and transport | |||||||
| CD630_08880 CDIF630erm_01008 | speA | Arginine decarboxylase | 3.92 | ON | 4.48 | ON | + |
| CD630_08890 CDIF630erm_01009 | speH | S-adenosylmethionine decarboxylase | 2.57 | ON | 2.95 | ON | |
| CD630_08900 CDIF630erm_01010 | speE | Polyamine aminopropyl transferase | 4.53 | 0.38 | 3.78 | 0.59 | |
| CD630_08910 CDIF630erm_01011 | speB | Agmatinase | 5.41 | -0.31 | 4.95 | 0.53 | |
| CD630_10230 CDIF630erm_01159 | Transcriptional regulator | 3.64 | -0.32 | 2.21 | 0.66 | ||
| CD630_10240 CDIF630erm_01160 | potA | Spermidine/putrescine ABC transporter ATP-binding protein | 3.43 | -0.06 | 3.05 | 0.43 | |
| CD630_10250 CDIF630erm_01161 | potB | Spermidine/putrescine ABC transporter permease | 3.24 | -0.66 | 3.22 | -0.66 | |
| CD630_10260 CDIF630erm_01162 | potC | Spermidine/putrescine ABC transporter permease | 2.98 | – | 3.23 | – | |
| CD630_10270 CDIF630erm_01163 | potD | Spermidine/putrescine ABC transporter substrate-binding protein | 2.57 | -0.58 | 2.94 | 1.78 | |
| Antibiotic/CAMP resistance and cell wall restructuring | |||||||
| CD630_28510 CDIF630erm_03118 | dltC | D-alanine–poly(phosphoribitol) ligase subunit 2 | 1.51 | – | 2.10 | – | |
| CD630_28520 CDIF630erm_03119 | dltB | D-alanyl transferase DltB | 2.84 | OFF | 2.79 | OFF | |
| CD630_28530 CDIF630erm_03120 | dltA | D-alanine–poly(phosphoribitol) ligase subunit 1 | 1.37 | -0.80 | 1.68 | -1.19 | |
| CD630_28540 CDIF630erm_03122 | dltD | D-alanine transferase DltD | 1.49 | 0.13 | 1.37 | 0.01 | |
| CD630_16260 CDIF630erm_01803 | vanG | D-alanyl-alanine synthetase A | -1.00 | – | 2.91 | – | |
| CD630_16270 CDIF630erm_01804 | vanY | D-alanyl-D-alanine carboxypeptidase | -0.89 | – | 3.13 | – | |
| CD630_16280 CDIF630erm_01805 | vanTG | Alanine racemase 1 | 0.64 | – | 3.47 | – | |
| CD630_03160 CDIF630erm_00443 | ABC transporter permease | 1.10 | – | 2.42 | – | ||
| CD630_03170 CDIF630erm_00444 | ABC transporter permease | 0.67 | – | 2.61 | – | ||
| CD630_03180 CDIF630erm_00445 | Bacitracin/multidrug family ABC transporter ATP-binding protein | 1.51 | -0.19 | 2.85 | 0.45 | ||
| CD630_08200 CDIF630erm_00938 | Two-component response regulator | 0.72 | ON | 1.58 | ON | ||
| CD630_08210 CDIF630erm_00939 | Two-component sensor histidine kinase | 1.39 | ON | 2.76 | ON | ||
| CD630_08220 CDIF630erm_00940 | Multidrug family ABC transporter ATP-binding protein | 1.04 | – | 2.35 | – | ||
| CD630_08230 CDIF630erm_00941 | Multidrug family ABC transporter permease | -0.38 | – | 1.62 | – | ||
| CD630_08240 CDIF630erm_00943 | Multidrug family ABC transporter permease | 0.78 | – | 3.41 | – | ||
| CD630_20030 CDIF630erm_02221 | effD | MATE family drug/sodium antiporter | -3.56 | – | -1.20 | – | |
| CD630_20040 CDIF630erm_02222 | effR | MarR family transcriptional regulator | -5.25 | -0.75 | -2.98 | 3.12 | |
| CD630_15570 CDIF630erm_01726 | Peptidyl-prolyl isomerase | 1.07 | -0.58 | 3.69 | 0.16 | + | |
| CD630_15580 CDIF630erm_01727 | csfV | ECF RNA polymerase sigma factor CsfV | 2.29 | 3.42 | – | ||
| CD630_15590 CDIF630erm_01728 | rsiV | Anti ECF RNA polymerase sigma factor RsiV | 1.55 | – | 2.73 | – | |
| CD630_26510 CDIF630erm_02905 | murG | UDP-N-acetylglucosamine-N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N- acetylglucosamine transferase | 1.30 | 0.63 | 1.54 | 1.34 | |
| CD630_26520 CDIF630erm_02906 | spoVE | Cell division/stage V sporulation protein | 0.91 | – | 2.04 | – | |
| CD630_26530 CDIF630erm_02907 | murD | UDP-N-acetylmuramoylalanine–D-glutamate ligase | 0.77 | 0.11 | 1.45 | 0.42 | |
| CD630_26540 CDIF630erm_02908 | mraY | Phospho-N-acetylmuramoyl-pentapeptide-transferase | 0.82 | – | 2.37 | – | |
| CD630_26550 CDIF630erm_02909 | murF | UDP-N-acetylmuramoyl-tripeptide–D-alanyl-D-alanine ligase | 2.59 | -0.26 | 2.74 | 0.21 | |
| CD630_27780 CDIF630erm_03041 | Glycosyl transferase family protein | 0.98 | -0.10 | 1.26 | 0.10 | ||
| CD630_27790 CDIF630erm_03042 | manC | Mannose-1-phosphate guanylyltransferase | 1.33 | 0.81 | 2.47 | 0.33 | |
| CD630_27800 CDIF630erm_03043 | pgm | Phosphoglucomutase | 2.75 | 0.22 | 3.20 | 0.06 | |
| CD630_27810 CDIF630erm_03044 | mviN | Transmembrane virulence factor | 3.67 | -0.93 | 4.13 | 0.78 | |
| CD630_02840 CDIF630erm_00408 | PTS system mannose/fructose/sorbose transporter subunit IIA | – | -0.04 | – | 0.88 | ||
| CD630_02850 CDIF630erm_00409 | PTS system mannose/fructose/sorbose transporter subunit IIB | 1.86 | 0.14 | 2.61 | 0.62 | ||
| CD630_02860 CDIF630erm_00410 | PTS system mannose/fructose/sorbose transporter subunit IIA | 2.27 | -0.52 | 2.43 | 0.64 | ||
| CD630_02870 CDIF630erm_00411 | PTS system mannose/fructose/sorbose transporter subunit IIB | 1.90 | 0.20 | 2.70 | 1.00 | ||
| CD630_02880 CDIF630erm_00412 | PTS system mannose/fructose/sorbose transporter subunit IIC | 1.51 | -0.14 | 2.68 | 0.06 | ||
| CD630_02890 CDIF630erm_00413 | PTS system mannose/fructose/sorbose transporter subunit IID | 1.90 | -0.08 | 1.68 | 0.46 | ||
| CD630_32070 CDIF630erm_03501 | Multi antimicrobial extrusion protein | 1.30 | – | 2.93 | – | ||
| CD630_32080 CDIF630erm_03502 | MarR family transcriptional regulator | 0.99 | ON | 2.77 | ON | ||
| CD630_35140 CDIF630erm_03828 | prs | Ribose-phosphate pyrophosphokinase | 1.89 | -0.10 | 2.31 | 0.30 | |
| CD630_35150 CDIF630erm_03829 | glmU | Bifunctional N-acetylglucosamine-1- phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase | 1.51 | -0.27 | 2.04 | 0.40 | + |
| CD630_10090 CDIF630erm_01145 | GntR family transcriptional regulator | -3.62 | – | -2.36 | – | ||
| CD630_10100 CDIF630erm_01146 | nagA | N-acetylglucosamine-6-phosphate deacetylase | -2.69 | -2.60 | -2.02 | -0.22 | |
| CD630_10110 CDIF630erm_01147 | nagB | Glucosamine-6-phosphate deaminase | -2.74 | 1.69 | -1.74 | 0.19 | |
| Energy metabolism | |||||||
| CD630_32370 CDIF630erm_03533 | prdF | Proline racemase | 3.03 | -1.48 | 4.04 | -1.14 | |
| CD630_32380 CDIF630erm_03534 | Proline reductase PrdE-like protein | 4.31 | – | 4.34 | – | ||
| CD630_32390 CDIF630erm_03535 | prdE | Proline reductase PrdE | 4.14 | -2.05 | 4.48 | -2.14 | |
| CD630_32400 CDIF630erm_03536 | prdD | Proline reductase PrdD | 4.18 | -1.83 | 4.88 | -1.00 | |
| CD630_32410 CDIF630erm_03537 | prdB | Proline reductase | 1.74 | -0.53 | 2.69 | -0.80 | |
| CD630_32430 CDIF630erm_03539 | Hypothetical protein | 2.90 | -0.79 | 2.07 | -0.39 | ||
| CD630_32440 CDIF630erm_03540 | prdA | D-proline reductase PrdA | 2.98 | -0.67 | 3.05 | -0.83 | |
| CD630_32450 CDIF630erm_03541 | prdR | Sigma-54 dependent transcriptional regulator | 0.61 | 0.02 | -1.02 | -0.80 | |
| CD630_32460 CDIF630erm_03542 | Surface protein | -1.35 | – | -2.85 | – | ||
| CD630_32470 CDIF630erm_03544 | prdC | Electron transfer protein | 4.62 | -0.96 | 4.78 | -0.90 | |
| CD630_11370 CDIF630erm_01284 | rnfC | Electron transport complex protein RnfC | 2.64 | -0.73 | 2.91 | -0.49 | |
| CD630_11380 CDIF630erm_01285 | rnfD | Electron transport complex protein RnfD | 2.01 | -1.19 | 3.58 | -0.62 | |
| CD630_11390 CDIF630erm_01286 | rnfG | Electron transport complex protein RnfG | 2.67 | 0.47 | 3.31 | 0.41 | |
| CD630_11400 CDIF630erm_01287 | rnfE | Electron transport complex protein RnfE | 1.17 | OFF | 3.47 | OFF | |
| CD630_11410 CDIF630erm_01288 | rnfA | Electron transport complex protein RnfA | 1.88 | – | 3.55 | – | |
| CD630_11420 CDIF630erm_01289 | rnfB | Electron transport complex protein RnfB | 1.61 | -1.38 | 2.47 | -0.91 | |
| CD630_11700 CDIF630erm_01318 | larA | Lactate racemase | 1.41 | – | 2.86 | – | |
| CD630_11710 CDIF630erm_01319 | etfB | Lactate dehydrogenase, electron transfer flavoprotein beta subunit | 0.67 | OFF | 2.43 | OFF | |
| CD630_11720 CDIF630erm_01320 | etfA | Lactate dehydrogenase, electron transfer flavoprotein alpha subunit | -0.66 | – | 0.63 | – | |
| CD630_11730 CDIF630erm_01321 | lactate dehydrogenase (electron bifurcating), catalytic subunit | -0.30 | -0.57 | 0.73 | OFF | ||
| CD630_03940 CDIF630erm_00522 | ldhA | (R)-2-hydroxyisocaproate dehydrogenase | -8.37 | OFF | -8.66 | OFF | |
| CD630_03950 CDIF630erm_00523 | hadA | Isocaprenoyl-CoA:2-hydroxyisocaproate CoA-transferase | -8.33 | OFF | -11.10 | OFF | 00519 |
| CD630_03960 CDIF630erm_00524 | hadI | 2-hydroxyisocaproyl-CoA dehydratase activator | -0.79 | OFF | -11 | OFF | |
| CD630_03970 CDIF630erm_00525 | hadB | Oxygen-sensitive 2-hydroxyisocaproyl-CoA dehydratase subunit B | -7.47 | OFF | -10.52 | OFF | |
| CD630_03980 CDIF630erm_00526 | hadC | Oxygen-sensitive 2-hydroxyisocaproyl-CoA dehydratase subunit C | -7.81 | -4.86 | -10.94 | OFF | |
| CD630_03990 CDIF630erm_00527 | acdB | Acyl-CoA dehydrogenase | -7.43 | -4.27 | -10.17 | -4.76 | |
| CD630_04000 CDIF630erm_00528 | etfB1 | Electron transfer flavoprotein subunit beta | -7.28 | -3.90 | -10.48 | -4.50 | |
| CD630_04010 CDIF630erm_00529 | etfA1 | Electron transfer flavoprotein subunit alpha | -7.50 | -3.90 | -10.39 | -4.98 | |
| CD630_10540 CDIF630erm_01194 | bcd2 | Butyryl-CoA dehydrogenase | -5.89 | OFF | -8.00 | OFF | |
| CD630_10550 CDIF630erm_01195 | etfB | Electron transfer flavoprotein subunit beta | -7.47 | OFF | -7.70 | OFF | |
| CD630_10560 CDIF630erm_01196 | etfA | Electron transfer flavoprotein subunit alpha | -6.75 | OFF | -7.75 | OFF | |
| CD630_10570 CDIF630erm_01197 | crt2 | 3-hydroxybutyryl-CoA dehydratase | -6.37 | – | -7.48 | OFF | |
| CD630_10580 CDIF630erm_01198 | hbd | 3-hydroxybutyryl-CoA dehydrogenase | -5.21 | OFF | -5.97 | OFF | |
| CD630_10590 CDIF630erm_01199 | thlA1 | Acetyl-CoA acetyltransferase | -6.22 | OFF | -6.43 | OFF | |
| CD630_29660 CDIF630erm_03250 | adhE | Bifunctional acetaldehyde-CoA/alcohol dehydrogenase | -8.19 | -4.52 | -9.86 | -5.91 | |
| CD630_23380 CDIF630erm_02577 | 4hbD | 4-hydroxybutyrate dehydrogenase | -1.00 | -0.87 | -1.23 | -1.06 | 02575 |
| CD630_23390 CDIF630erm_02578 | cat2 | 4-hydroxybutyrate CoA-transferase | -0.87 | OFF | -0.50 | OFF | |
| CD630_23400 CDIF630erm_02579 | Hypothetical protein | -2.16 | – | -1.55 | – | ||
| CD630_23410 CDIF630erm_02580 | abfD | Gamma-aminobutyrate metabolism dehydratase/isomerase | -1.41 | -1.74 | -1.23 | -1.16 | |
| CD630_23420 CDIF630erm_02581 | sucD | Succinate-semialdehyde dehydrogenase | -2.47 | – | -3.77 | – | |
| CD630_23430 CDIF630erm_02582 | cat1 | Succinyl-CoA:coenzyme A transferase | -3.35 | – | -3.58 | – | |
| CD630_23440 CDIF630erm_02583 | Membrane protein | -4.79 | – | -5.28 | – | ||
| CD630_23480 CDIF630erm_02587 | grdD | Glycine reductase complex component D | – | OFF | – | OFF | |
| CD630_23490 CDIF630erm_02588 | grdC | Glycine reductase complex component C | -3.70 | – | -3.70 | – | |
| CD630_23510 CDIF630erm_02589 | grdB | Glycine reductase complex component B | – | OFF | – | OFF | |
| CD630_23520 CDIF630erm_02592 | grdA | Glycine reductase complex component A | – | - | – | - | |
| CD630_23540 CDIF630erm_02594 | grdE | Glycine reductase complex component E | -5.02 | -2.84 | -5.22 | OFF | |
| CD630_23550 CDIF630erm_02595 | trxA2 | Thioredoxin 2 | -3.66 | – | -3.66 | – | + |
| CD630_23560 CDIF630erm_02596 | trxB3 | Thioredoxin reductase | – | - | – | OFF | |
| CD630_23570 CDIF630erm_02597 | grdDX | – | OFF | – | |||
| CD630_08530 CDIF630erm_00972 | oppB | Oligopeptide family ABC transporter permease | -2.81 | OFF | -2.26 | OFF | |
| CD630_08540 CDIF630erm_00973 | oppC | Oligopeptide family ABC transporter permease | -2.67 | – | -2.28 | – | |
| CD630_08550 CDIF630erm_00974 | oppA | Oligopeptide family ABC transporter substrate-binding protein | -2.48 | -0.37 | -3.22 | -1.02 | |
| CD630_08560 CDIF630erm_00975 | oppD | ABC transporter ATP-binding protein | -2.38 | – | -3.65 | – | |
| CD630_15360 CDIF630erm_01704 | nfnA | NADH-dependent reduced ferredoxin:NADP oxidoreductase | -2.56 | -1.18 | -2.43 | -0.71 | |
| CD630_15370 CDIF630erm_01705 | nfnB | NADH-dependent reduced ferredoxin:NADP oxidoreductase | -2.69 | -1.77 | -3.01 | -1.53 | |
| CD630_08820 CDIF630erm_01002 | glgC | Glucose-1-phosphate adenylyltransferase | -1.89 | – | -3.38 | – | |
| CD630_08830 CDIF630erm_01003 | glgD | Glycogen biosynthesis protein | -1.70 | -2.42 | -4.22 | OFF | |
| CD630_08840 CDIF630erm_01004 | glgA | Glycogen synthase | -2.45 | 1.98 | -3.24 | -0.37 | |
| CD630_08850 CDIF630erm_01005 | glgP | Glycogen phosphorylase | -1.62 | 0.49 | -3.38 | 0.14 | |
| CD630_08860 CDIF630erm_01006 | amyB | Amylopullulanase | -0.12 | -0.29 | -2.68 | 0.05 | |
| CD630_23180 CDIF630erm_02556 | Phosphohexomutase | 2.01 | 0.58 | 1.56 | 0.21 | ||
| CD630_23190 CDIF630erm_02557 | rpe | Ribulose-phosphate 3-epimerase | 1.24 | ON | 1.19 | ON | |
| CD630_23200 CDIF630erm_02558 | rpiB1 | Ribose-5-phosphate isomerase B | 3.19 | 0.00 | 2.23 | -0.02 | |
| CD630_23210 CDIF630erm_02559 | Transketolase | 1.75 | 0.44 | 2.01 | 0.22 | ||
| CD630_23220 CDIF630erm_02560 | tkt | Transketolase | 1.48 | 0.23 | 2.63 | 0.29 | |
| CD630_11200 CDIF630erm_01264 | pflD | Formate acetyltransferase | -0.51 | -0.12 | 2.03 | 1.70 | |
| CD630_11210 CDIF630erm_01265 | pflC | Pyruvate formate-lyase activating enzyme | -0.32 | – | 2.21 | – | |
| CD630_11220 CDIF630erm_01266 | Transcriptional regulator | -1.51 | -0.63 | 1.48 | 0.05 | ||
| CD630_32820 CDIF630erm_03582 | pflD | Pyruvate formate-lyase | -1.38 | -2.38 | -2.88 | -2.94 | |
| CD630_32830 CDIF630erm_03583 | pflE | Pyruvate formate-lyase | -2.11 | – | -3.53 | – | |
| CD630_33130 CDIF630erm_03614 | hydN1 | Oxidoreductase Fe-S subunit | -2.44 | – | -3.60 | – | |
| CD630_33140 CDIF630erm_03615 | hydA | Iron hydrogenase | -2.59 | OFF | -3.08 | -1.30 | |
| CD630_33150 CDIF630erm_03616 | hydN2 | Oxidoreductase Fe-S subunit | -3.54 | -1.13 | -3.00 | -0.86 | + |
| CD630_33151 CDIF630erm_03617 | Hypothetical protein | -1.53 | – | -3.00 | – | ||
| CD630_33160 CDIF630erm_03618 | fdhD | Formate dehydrogenase accessory protein FdhD | -2.22 | – | -3.03 | – | |
| CD630_33170 CDIF630erm_03619 | fdhF | Formate dehydrogenase-H | -2.88 | -1.63 | -3.37 | -1.72 | |
| CD630_01740 CDIF630erm_00296 | cooS | Carbon monoxide dehydrogenase | -3.57 | -1.46 | -4.70 | -2.05 | |
| CD630_01750 CDIF630erm_00297 | cooF | Oxidoreductase Fe-S subunit | -2.43 | – | -4.33 | – | |
| CD630_01760 CDIF630erm_00298 | Oxidoreductase NAD/FAD binding subunit | -2.12 | OFF | -3.96 | OFF | ||
| CD630_12780 CDIF630erm_01431 | iscR | Rrf2 family transcriptional regulator | 4.43 | 3.30 | -0.27 | 1.44 | |
| CD630_12790 CDIF630erm_01432 | iscS2 | Cysteine desulfurase | 0.55 | 2.69 | -3.25 | 0.03 | |
| CD630_12800 CDIF630erm_01433 | NifU family iron-sulfur cluster assembly protein | 0.83 | 3.83 | -2.97 | 0.31 | ||
| CD630_34670 CDIF630erm_03778 | atpC | ATP synthase subunit epsilon | 3.83 | 0.56 | 1.37 | 1.04 | |
| CD630_34680 CDIF630erm_03779 | atpD | ATP synthase subunit beta | 2.25 | 0.60 | 2.04 | 0.94 | |
| CD630_34690 CDIF630erm_03780 | atpG | ATP synthase subunit gamma | 3.91 | 0.51 | 2.83 | 0.55 | |
| CD630_34700 CDIF630erm_03781 | atpA | ATPase subunit alpha | 3.72 | 0.61 | 2.44 | 1.00 | |
| CD630_34710 CDIF630erm_03782 | atpH | ATP synthase subunit delta | 3.65 | 0.49 | 2.67 | 0.72 | |
| CD630_34720 CDIF630erm_03783 | atpF | ATP synthase subunit B | 3.33 | 0.16 | 2.31 | 0.47 | |
| CD630_34730 CDIF630erm_03784 | atpE | ATP synthase subunit C | 2.81 | ON | 1.58 | ON | |
| CD630_34740 CDIF630erm_03785 | atpB | ATP synthase subunit A | 1.59 | – | 1.77 | 0.94 | |
| CD630_29540 CDIF630erm_03237 | atpD | V-type ATP synthase subunit D | -1.47 | – | -2.46 | – | |
| CD630_29550 CDIF630erm_03238 | atpB | V-type ATP synthase subunit B | -3.00 | -0.98 | -2.58 | -1.34 | |
| CD630_29560 CDIF630erm_03239 | atpA | V-type ATP synthase subunit A | -2.35 | -0.73 | -2.54 | -0.95 | + |
| CD630_29561 CDIF630erm_03240 | atpF | V-type ATP synthase subunit F | -2.40 | – | -1.52 | – | |
| CD630_29570 CDIF630erm_03241 | atpC | V-type ATP synthase subunit C | -2.32 | – | -2.56 | – | |
| CD630_29580 CDIF630erm_03242 | atpE | V-type ATP synthase subunit E | -1.47 | OFF | -2.92 | OFF | |
| CD630_29590 CDIF630erm_03243 | atpK | V-type ATP synthase subunit K | -1.47 | -2.10 | -2.48 | -1.20 | |
| CD630_29600 CDIF630erm_03244 | atpI | V-type ATP synthase subunit I | -2.73 | OFF | -3.24 | OFF | |
| CD630_29610 CDIF630erm_03245 | Hypothetical protein | -1.78 | 0.00 | -2.92 | -0.80 | ||
| Flavodoxin formation | |||||||
| CD630_19990 CDIF630erm_02217 | fldx | Flavodoxin | 4.54 | ON | 4.54 | ON | |
| CD630_16970 CDIF630erm_01882 | ribH | 6.7-dimethyl-8-ribityllumazine synthase | 2.82 | 0.31 | 3.86 | 0.68 | + |
| CD630_16980 CDIF630erm_01883 | ribBA | Riboflavin biosynthesis bifunctional 3.4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase | 2.10 | 0.40 | 2.62 | 0.99 | |
| CD630_16990 CDIF630erm_01884 | ribE | Riboflavin synthase subunit alpha | 1.82 | 0.26 | 1.55 | -0.07 | |
| CD630_17000 CDIF630erm_01885 | ribD | Riboflavin biosynthesis bifunctional diaminohydroxyphosphoribosylamino pyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase | 1.39 | 0.35 | 1.81 | 1.02 | |
| CD630_23310 CDIF630erm_02570 | mtlD | Mannitol-1-phosphate 5-dehydrogenase | -6.28 | -2.60 | -5.79 | -1.91 | |
| CD630_23320 CDIF630erm_02571 | mtlF | PTS system mannitol-specific transporter subunit IIA | -5.98 | OFF | -5.53 | -1.54 | |
| CD630_23330 CDIF630erm_02572 | mtlR | PTS operon transcription antiterminator | -5.78 | OFF | -6.17 | OFF | |
| CD630_23340 CDIF630erm_02573 | mtlA | PTS system mannitol-specific transporter subunit IICB | -6.29 | OFF | -5.92 | -3.14 | |
| Fatty acid metabolism | |||||||
| CD630_11770 CDIF630erm_01326 | fapR | Fatty acid biosynthesis transcriptional regulator | 2.53 | 0.17 | 3.16 | 0.11 | |
| CD630_11780 CDIF630erm_01327 | plsX | Phosphate acyltransferase | 1.93 | -1.29 | 3.25 | -0.22 | |
| CD630_11790 CDIF630erm_01328 | fabH | 3-oxoacyl-ACP synthase | 2.12 | 0.09 | 4.00 | 0.92 | |
| CD630_11800 CDIF630erm_01329 | fabK | Enoyl-(acyl-carrier-protein) reductase II | 2.86 | -0.16 | 3.61 | 0.50 | |
| CD630_11810 CDIF630erm_01330 | fabD | Malonyl CoA-acyl carrier protein transacylase | 3.03 | -0.18 | 3.87 | 0.41 | |
| CD630_11820 CDIF630erm_01331 | fabG | 3-oxoacyl-ACP reductase | 3.65 | -0.06 | 3.94 | 0.23 | |
| CD630_11830 CDIF630erm_01332 | acpP | Acyl carrier protein | 2.95 | – | 4.28 | – | |
| CD630_11840 CDIF630erm_01333 | fabF | 3-oxoacyl-ACP synthase | 2.98 | 0.07 | 4.71 | 0.69 | 01334 |
| CRISPR/Cas and prophages | |||||||
| CD630_29750 CDIF630erm_03259 | CRISPR-associated endoribonuclease Cas2 | -0.74 | – | -2.13 | – | ||
| CD630_29760 CDIF630erm_03260 | CRISPR-associated endonuclease Cas1 | -0.87 | – | -1.67 | – | ||
| CD630_29770 CDIF630erm_03261 | CRISPR-associated Cas4 family protein | -0.41 | – | -2.72 | – | ||
| CD630_29780 CDIF630erm_03262 | CRISPR-associated Cas3 family helicase | -0.26 | – | -2.20 | – | ||
| CD630_29790 CDIF630erm_03263 | CRISPR-associated Cas5 family protein | -1.30 | – | -1.66 | – | ||
| CD630_29800 CDIF630erm_03264 | CRISPR-associated autoregulatorDevR family protein | 0.20 | -0.55 | -1.97 | -1.28 | ||
| CD630_29810 CDIF630erm_03265 | CRISPR-associated protein | -1.27 | -1.20 | -1.78 | OFF | ||
| CD630_29820 CDIF630erm_03266 | CRISPR-associated Cas6 family protein | -0.60 | – | -2.92 | – | ||
| CD630_13650 CDIF630erm_01522 | XkdN-like protein | – | - | -2.30 | – | + | |
| CD630_13660 CDIF630erm_01524 | Tail protein | -1.33 | ON | -3.28 | – | ||
| CD630_13680 CDIF630erm_01526 | Cell wall XkdQ-like hydrolase | 0.02 | – | -3.93 | – | ||
| CD630_13700 CDIF630erm_01528 | XkdS-like protein | – | - | -1.07 | – | ||
| CD630_13710 CDIF630erm_01529 | Baseplate assembly protein | -1.33 | – | -2.06 | – | ||
| CD630_13720 CDIF630erm_01530 | XkdT-like protein | -1.27 | – | -2.90 | – | ||
| CD630_13740 CDIF630erm_01532 | Beta-lactamase-inhibitor protein II | 0.64 | ON | -1.58 | – | ||
| DNA/RNA nucleotide metabolism | |||||||
| CD630_02180 CDIF630erm_00340 | purE | 5-carboxyaminoimidazole ribonucleotide mutase | 0.09 | -0.24 | 2.12 | 0.80 | |
| CD630_02190 CDIF630erm_00341 | purC | Phosphoribosylaminoimidazolesuccino carboxamide synthase | -0.22 | -0.21 | 2.59 | 0.41 | |
| CD630_02200 CDIF630erm_00342 | purF | Amidophosphoribosyltransferase | 1.65 | -0.69 | 2.96 | 0.09 | |
| CD630_02210 CDIF630erm_00343 | purG | Phosphoribosylformylglycinamidinecyclo-ligase | 0.60 | -0.76 | 2.94 | -0.69 | |
| CD630_02220 CDIF630erm_00344 | purN | Phosphoribosylglycinamideformyl transferase | 2.66 | -0.41 | 3.49 | -0.04 | |
| CD630_02230 CDIF630erm_00345 | purH | Bifunctional phosphoribosylaminoimidazole carboxamideformyltransferase/IMP cyclohydrolase | 2.49 | -0.08 | 3.37 | 0.24 | |
| CD630_02240 CDIF630erm_00346 | purD | Phosphoribosylamine–glycine ligase | 2.19 | -0.28 | 3.07 | 0.32 | |
| CD630_02250 CDIF630erm_00347 | purL | Phosphoribosylformylglycinamidine synthase | 1.24 | -0.06 | 2.23 | 0.19 | 00348 |
| CD630_01840 CDIF630erm_00305 | pyrB | Aspartate carbamoyltransferase | 0.19 | 0.47 | 1.01 | 0.60 | |
| CD630_01850 CDIF630erm_00306 | pyrK | Dihydroorotate dehydrogenase electron transfer subunit | 2.94 | 0.82 | 2.82 | 0.74 | |
| CD630_01860 CDIF630erm_00307 | pyrD | Dihydroorotate dehydrogenase 1B | 1.96 | 0.21 | 2.72 | 0.16 | |
| CD630_01870 CDIF630erm_00308 | pyrE | Orotatephosphoribosyltransferase | 3.92 | 0.19 | 3.38 | 0.54 | |
| CD630_25940 CDIF630erm_02848 | uraA | Uracil-specific ABC transporter permease | 0.96 | 0.17 | 3.83 | -0.46 | |
| CD630_25950 CDIF630erm_02849 | pyrR | Bifunctional pyrimidine operon regulatory protein/uracil phosphoribosyltransferase | – | 0.05 | 2.17 | 0.62 | + |
| CD630_25960 CDIF630erm_02850 | Pseudouridylate synthase | 1.85 | – | 2.05 | – | ||
| CD630_25970 CDIF630erm_02851 | lspA | Lipoprotein signal peptidase | 2.47 | – | 3.02 | – | |
| CD630_27690 CDIF630erm_03032 | Polysaccharide biosynthesis protein | 1.95 | 0.29 | 2.73 | -0.39 | ||
| CD630_27700 CDIF630erm_03033 | Group 1 glycosyl transferase | 1.22 | -0.32 | 2.55 | 0.20 | ||
| CD630_27710 CDIF630erm_03034 | rkpK | UDP-glucose 6-dehydrogenase | 2.13 | -0.05 | 2.59 | 0.41 | |
| CD630_27720 CDIF630erm_03035 | tuaG | Family 2 glycosyl transferase | 2.23 | -0.23 | 3.25 | 0.35 | |
| CD630_27730 CDIF630erm_03036 | Family 2 glycosyl transferase | 2.45 | -0.53 | 2.59 | 0.06 | ||
| CD630_27740 CDIF630erm_03037 | Family 2 glycosyl transferase | 1.24 | -0.52 | 2.30 | 0.64 | ||
| CD630_27750 CDIF630erm_03038 | Glycerophosphotransferase | 2.64 | -0.61 | 2.73 | -0.07 | ||
| CD630_27760 CDIF630erm_03039 | Family 2 glycosyl transferase | 0.78 | -0.06 | 1.99 | 0.17 | ||
T, transcriptome, P, proteome, FC, fold change, shown are corresponding locus tags of C. difficile 630 [according to (Monot et al., 2011)] and 630Δerm [according to (Dannheim et al., 2017a)]. The gene number in the Fur column identifies a gene close to the regulated genes shown in the table possessing a potential Fur box in its upstream region. ON and OFF describe proteomics result, where under one of the two compared conditions/strains no protein was detected. If the first protein is detectable under conditions of interest, it is ON, if it is absent, it is OFF.