TABLE 3 .
Genes with significantly increased expression and their putative relation to reductive stress
| Gene tag | Gene name |
Growth phase |
Functional categoryb |
Function | Putative influence on reductive stressc |
RPKM ratiod |
P valuee |
|---|---|---|---|---|---|---|---|
| Rv0243a | fadA2 | FS | 1 | Lipid degradation | 1.60 | 9.87 E-05 | |
| Rv0570a | nrdZ | FS | 2 | Ribonucleoside-diphosphate reductase | NADH/NADPH
|
2.67 | 0.004 |
| Rv0694 | lldD1 | FE | 7 | l-Lactate dehydrogenase | 1.09 | 0.029 | |
| Rv0697 | FE | 7 | Unknown; probable dehydrogenase | 4.33 | 0.001 | ||
| Rv1180 | pks-3 | FE | 1 | Probable polyketide synthase | Polymer deposition
|
3.20 | 5.9 E-04 |
| Rv1436a | gap | FE | 7 | Probable GADPHf | NADH
|
1.15 | 0.028 |
| Rv1652a | argC | FS | 7 | Arginine biosynthesis | NADH/NADPH
|
3.00 | 8.33 E-05 |
| Rv1908c | katG | FE | 0 | Catalase/peroxidase | 1.57 | 0.004 | |
| Rv2382c | mbtC | FE | 1 | Polyketide synthase | Polymer deposition
|
4.00 | 0.032 |
| Rv2590 | fadD9 | FE | 1 | Lipid degradation | NADH/NADPH
|
3.71 | 5.68 E-07 |
| Rv2781 | FE | 7 | Oxidoreductase | 3.80 | 1.94 E-10 | ||
| Rv2794c | pptT | FE | 1 | 4′-Phosphopantetheinyl transferase | Polymer deposition
|
1.18 | 0.041 |
| FS | 3.00 | 8.33 E-05 | |||||
| Rv2931 | ppsA | FS | 1 | PDIM biosynthesis | Polymer deposition
|
2.00 | 0.041 |
| Rv2995c | leuB | FS | 7 | Leucine synthesis | NADH/NADPH
|
2.60 | 6.54 E-05 |
| Rv2996c | serA1 | FS | 7 | l-Serine synthesis | NADH/NADPH
|
3.00 | 0.019 |
| Rv3130ca | tgs-1 | FS | 1 | TAG synthase | Polymer deposition
|
2.31 | 2.07 E-13 |
| Rv3131a | FE | 10 | Unknown | Reductant collector
|
2.89 | 1.09 E-12 | |
| FS | Putative NAD(P)H nitroreductase | 4.00 | 9.04 E-13 | ||||
| Rv3145 | nuoA | FE | 7 | Probable NADH-dehydrogenase | Reductant collector
|
1.03 | 0.008 |
| Rv3229c | desA3 | FE | 1 | Lipid desaturase | Polymer deposition
|
3.80 | 1.09 E-12 |
| Rv3230 | FE | 7 | Oxidoreductase | 1.32 | 0.006 | ||
| Rv3371 | FS | 1 | TAG synthesis | Polymer deposition
|
2.00 | 0.041 | |
| Rv3825c | pks-2 | FE | 1 | Probable polyketide synthase | Polymer deposition
|
1.27 | 1.34 E-04 |
Member of the DosR regulon.
Functional categories based on http://www.tuberculist.epfl.ch: 0, virulence, detoxification, and adaptation; 1, lipid metabolism; 2, information pathways; 7, intermediary metabolism and respiration; 10, conserved hypothetical proteins.
RPKM ratio according to phase of growth: exponential (FE/DE) or stationary (FS/DS). The gene is overexpressed in FE or FS if the ratio is >1. See Table S1A and B in the supplemental material for the complete set of data.
Arrows indicate the putative contributions of genes to the increase (up arrow) or decrease (down arrow) in reductive equivalents. Absence of an arrow indicates a gene that could contribute to both an increase and a decrease in reductive equivalents, for example, an oxidoreductase-encoding gene.
Determined by Fisher exact test, in which statistically significant differential expression between two conditions was determined by looking at genes with FDRs of <0.05 (see Materials and Methods for details).
GAPDH, glyceraldehyde 3-phosphate dehydrogenase.