TABLE 4.
Continuous culture transcriptional response of selected ORFs before and after exposure to CAM in the T. maritima MSB8 WT and RM strains
| Function and GeneID no. | Change (fold) of ORF before/after exposure to CAM
|
Annotation | ||||
|---|---|---|---|---|---|---|
| Before exposure (RM vs WT) | After exposure for:
|
|||||
| WT
|
TM
|
|||||
| 5 min | 30 min | 5 min | 30 min | |||
| Ribosomal proteins | ||||||
| TM0150 | NCb | 1.8 | 1.6 | NC | NC | Ribosomal protein L32 |
| TM0451 | NC | 1.7 | NC | NC | NC | Ribosomal protein L33 |
| TM0452 | NC | 1.6 | 1.7 | NC | NC | Pre-protein translocase SecE |
| TM1451 | NC | 3.7 | 2.8 | NC | NC | RNA polymerase sigma A factor |
| TM1453-1458a | NC | 3.9 | 2.7 | NC | NC | Ribosomal proteins |
| TM1480 | NC | 1.8 | NC | NC | NC | Pre-protein translocase SecY |
| TM1471-1487a | NC | 1.8 | NC | NC | NC | Ribosomal proteins |
| TM1489-1505a | NC | NC | 2.1 | NC | NC | Ribosomal proteins |
| TM1565 | NC | 4.3 | 4.4 | NC | NC | Signal recognition particle protein |
| TM1568 | NC | 3.2 | 2.3 | NC | NC | 16S rRNA processing protein |
| TM1569 | NC | 2.3 | 2.0 | NC | NC | tRNA guanine-N1 methyltransferase |
| TM1590-1593a | NC | 3.8 | 3.0 | NC | NC | Ribosomal proteins/translation factor |
| TM1627 | NC | 3.5 | 3.2 | NC | NC | General stress protein Ctc |
| Translation factors | ||||||
| TM1502 | 1.7 | NC | 2.2 | 1.7 | 2.1 | Translation elongation factor Tu |
| TM1503 | NC | NC | 2.4 | NC | NC | Translation elongation factor G |
| TM1590 | NC | 4.1 | 2.6 | NC | NC | Translation initiation factor IF-3 |
| Polyamines/oxidative response | ||||||
| TM0654-0659a | NC | 3.7 | 5.1 | NC | NC | Polyamine biosynthesis, rubrerythrin, neelaredoxin, rubredoxin |
| Defense mechanism | ||||||
| TM0119 | NC | NC | 1.6 | NC | 1.6 | Acetamidase, putative |
| TM0120 | NC | NC | NC | NC | NC | Oxidoreductase, putative |
| ATP synthase | ||||||
| TM1609-1616a | NC | 2.1↓c | NC | NC | NC | F1 ATP synthase subunits |
| Purine biosynthesis | ||||||
| TM1245-1251a | NC | 1.6↓ | NC | NC | NC | Purine biosynthetic pathway |
| Amino acid biosynthesis | ||||||
| TM0545-0555a | NC | 2.3↓ | NC | NC | NC | Thr, Val, Leu, Ile biosynthesis |
| Sugar utilization | ||||||
| TM1068 | NC | 1.6 | NC | NC | NC | α-Glucosidase |
| TM1195 | NC | 1.7↓ | NC | NC | NC | β-Galactosidase |
| TM1219-1223a | NC | 3.7↓ | 3.6↓ | NC | NC | β-Linked sugar utilization operon |
| TM1835 | NC | 4.2↓ | 3.9↓ | NC | NC | Cyclomaltodextrinase, putative |
| TM1840 | NC | NC | 2.2↓ | 1.6 | 1.7 | α-Amylase |
| TM1845 | NC | NC | NC | NC | NC | Pullulanase |
| DNA repair | ||||||
| TM0266 | NC | 3.1 | 1.6 | NC | NC | DNA-binding protein, HU |
| TM0480 | NC | NC | NC | NC | NC | Exonuclease ABC, subunit A |
| TM0604 | NC | 5.8 | 3.4 | NC | NC | DNA-binding protein |
| Cold shock proteins/chaperones | ||||||
| TM0198 | NC | 2.6 | 1.8 | NC | NC | Clp protease, ATPase subunit |
| TM0505 | NC | 3.4 | 1.6 | 1.8 | 2.8 | GroES |
| TM0506 | NC | 4.5 | NC | 2.1 | 3.3 | GroEL |
| TM0571 | 1.8 | 2.9 | 1.6 | NC | NC | Heat shock serine protease |
| TM1683 | NC | 2.7 | NC | 1.6↓ | 3.0↓ | Cold shock protein |
| TM1874 | NC | 3.1 | 2.8 | NC | NC | Cold shock protein |
| tmRNA | ||||||
| TM0504 | NC | NC | NC | NC | NC | tmRNA/signaling peptide |
a
For operons, change (fold) is reported as the arithmetic average for all ORFs in the locus.
b
NC, change was ≤1.5-fold.
c
↓, down-regulation.