Table 3.
Relative expression of quinone biosynthesis and oxidoreductase genes belonging to the K. pneumoniae Kp13 respiratory chain
| Enzyme name | Gene name | Locus ID | log2FC |
|---|---|---|---|
| Primary dehydrogenases (DH): | |||
| Formate dehydrogenase-N subunit alpha (FDH-N subunit alpha) | fdnG | KP13_32232 | 0.1 |
| Formate dehydrogenase-N subunit beta (FDH-N subunit beta) | fdnH | KP13_04527 | −0.3 |
| Formate dehydrogenase-N subunit (FDH-N subunit gamma) | fdnI | KP13_04529 | 0.1 |
| Formate hydrogenlyase H | fdhF | KP13_05320 | 1.1 |
| Formate hydrogenlyase regulatory protein hycA | hycA | KP13_02572 | 0.6 |
| Formate hydrogenlyase subunit 2 to 7 | hycB-G | KP13_02573-8 | 0.9, 1.6, 0.9, 0.8, 0.9, 1.2 |
| Formate hydrogenlyase maturation protein HycH | hycH | KP13_02579 | 1.3 |
| NADH-quinone oxidoreductase (NDH-1) | nuoA-nuoN | KP13_00993-81 | 0.1, 0, 0.2, 0, 0, −0.2, 0, −0.3, −0.1, −0.2, −0.1, −0.1, −0.1 |
| NADH-quinone oxidoreductase (NDH-2) | ndh | KP13_04904 | −0.5 |
| Glycerol-3-P DHO | glpD | KP13_00670 | −1.5 |
| Glycerol-3-P DH N (subunit A) | glpA | KP13_00962 | −3.6 |
| Glycerol-3-P DH N (subunit B) | glpB | KP13_00963 | −2.1 |
| Glycerol-3-P DH N (subunit C) | glpC | KP13_00964 | −1.4 |
| Pyruvate oxidase | poxB | KP13_04234 | 0.1 |
| D -Lactate DH | dld | KP13_03193 | −0.1 |
| L -Lactate DH | lctD or lldD | KP13_00216 | 0.2 |
| D -Amino acid DH | dad (dad2) | KP13_04669 | 0.9 |
| Glucose dehydrogenase | gcD | KP13_32152 | 0.1 b |
| Succinate DH | sdhCDAB | KP13_03281-77 | 0.3, 0.1, 0.1, 0, −0.1 |
| Quinone biosynthesis: | |||
| Ubiquinone (UQ) | ubiA-ubiH ubiX | KP13_00377 KP13_01733 KP13_00376 KP13_01739 KP13_01731 KP13_03318 KP13_00956 KP13_02174 KP13_01019 |
−0.3
−0.1 −0.1 0.3 0.1 0 0.2 0.4 0 |
| Naphthoquinone menaquinone (MK) | menB-menF menH | KP13_00975 KP13_00974 KP13_00977 KP13_00973 KP13_00978 KP13_00976 |
−0.1 0.2 −0.5 −0.1 0.1 −0.4 |
| Terminal reductases: | |||
| Quinol oxidase bo 3 | cyoABCE | KP13_03683 KP13_03684 KP13_20485 KP13_03687 |
0.1
−0.1 −0.2 −0.1 |
| Quinol oxidase bd | cydAB | KP13_03271-2 | −0.3 |
| Quinol oxidase III (Cyx) | appBC | KP13_04076-5 | 0.3 |
| Nitrate reductase A | narGHJI | KP13_04712-09 | 0.2, 0.5, 0.6, 0.3 |
| Nitrate reductase Z | narZYWV | KP13_04512-09 | 0.6, 0.3, 0.7, 0.5 |
| Nitrate reductase, periplasmic | nasAB | KP13_04717-8 | 0.8, −1.1 |
| DMSO reductase | dmsBAD | KP13_01159-61 | 0.8, 0.5, −0.2 |
| Fumarate reductase | frdABCD | KP13_31481 KP13_00513 KP13_00512 KP13_00511 |
−0.2
−0.1 0.5 −0.3 |
Relative expression (log2(fold-change) [log2FC]) of genes encoding for quinone biosynthesis and oxido-reductases of the respiratory chains of Kp13 for bacterial growth in polymyxin (PB) versus control condition (non-induced). Criteria for significance: FDR≤0.01. log2FC values in bold, positive denotes up-regulation in PB and log2FC in bold, negative denotes down-regulation in polymyxin. log2FC in italic font are not significant based on FDR. bThese comparisons gave significant differentially expressed genes at a FDR of ≤0.05