Table 1

Genes with enhanced expression in C. glutamicum ΔrshA compared with C. glutamicum RES167 (reference) sorted by function
Coding sequencea Gene Predicted function Fold changeb
Disulphide stress related genes
NADPH:quinone reductase 13.27
Alkanal monooxygenase (FMN-linked) 12.3
Putative dithiol-disulfide isomerase 11.71
msrA Protein-methionine-S-oxide reductase 6.59
mtr Putative NADPH-dependent mycothiol reductase 4.92
cg1709▫- mshC Putative 1-D-myo-inosityl-2-amino-2-deoxy-alpha- D-glucopyranoside—L-cysteine ligase 4.47
trxB1 Thioredoxin (TRX) 3.73
msrB Peptide methionine sulfoxide reductase 3.61
trxB Thioredoxin reductase 3.53
trxC Thioredoxin 2.97
Putative dithiol-disulfide isomerase 2.68
Putative nitroreductase 2.66
cg1127▪ mca Putative mycothiol S-conjugate amidase 2.46
Putative Fe-S-cluster redox enzyme 2.27
mca Glutamyl-tRNA reductase 2.07
sufR Transcriptional repressor of suf operon 1.75
cg1553 qor2 quinone oxidoreductase involved in disulfide stress response 1.60
Putative thioredoxin 1.58
Heat stress-related genes
dnaJ2 Chaperone, contains C-terminal Zn-finger domain 1.85
clpP2 Endopeptidase Clp, proteolytic subunit 1.68
clpB Putative ATP-dependent protease (heat-shock protein) 1.57
clpP1 Endopeptidase Clp, proteolytic subunit 1.57
SOS and DNA repair genes
cg1555 uvrD3 DNA/RNA helicase, superfamily I 3.78
cg1560 uvrA Excinuclease ABC, ATPase subunit A 2.23
cg0184^* Putative RNA-binding protein 1.95
cg0185^ Putative glyoxalase 1.91
cg0186^ Putative methylated-DNA--protein-cysteine methyltransferase 1.91
cg1795 uvrC Excinuclease subunit C 1.53
Proteasome components
pafA2 Putative proteasome component 2.71
cg1689°::* pup prokaryotic ubiquitin-like protein 2.48
cg0998 Trypsin-like serine protease 1.54
Genes with other function
cg3407◊ Putative membrane protein 6.41
Conserved hypothetical protein 6.19
Hypothetical protein 4.20
cg1288 Putative multidrug efflux permease, MFS-type 3.94
cg1432 ilvD Dihydroxy-acid dehydratase 3.84
cg1398‡ Conserved hypothetical protein 3.78
cg0614† Hypothetical protein 3.71
cg0616† fdhD Putative formate dehydrogenase, FdhD-family 3.71
trmU tRNA (5-methylaminomethyl-2-thiouridylate) -methyltransferase 3.71
cg2423 lipA Lipoyl synthetase 3.34
cg0378 Putative phage-associated protein 2.93
cg2411 Conserved hypothetical protein, HesB/YadR/YfhF family 2.81
cg1799·* ribC Riboflavin synthase, alpha chain 2.73
cg2247 Hypothetical protein 2.41
cg1282 Conserved hypothetical protein 2.35
cg2127 Hypothetical protein 2.35
cg3424○ cwlM N-Acetylmuramoyl-L-alanine amidase 2.33
cg1798· ribA Putative GTP cyclohydrolase II/3,4-dihydroxy-2-butanone-4-phosphatesynthase 2.22
cg2835 Putative acetyltransferase 2.17
cg1281 ABC-type putative multidrug transporter, ATPase and permease subunit 2.16
cg1687°:: Putative transcriptional regulatory protein 2.13
cg1797· ribH Riboflavin synthase, beta chain 2.10
cg1779 opcA Glucose-6-phosphate 1-dehydrogenase subunit 2.06
murI Glutamate racemase 2.03
cg3078● Hypothetical protein 1.97
cg1411° rbsA ABC-type ribose transporter, ATPase subunit (TC 3.A.1.2.1) 1.92
cg2636 catA Catechol 1,2-dioxygenase 1.88
cg1780 pgl 6-Phosphogluconolactonase 1.87
cg1413° rbsB ABC-type ribose transporter, substrate-binding lipoprotein (TC 3.A.1.2.1) 1.85
cg0498□ hemC Porphobilinogen deaminase 1.84
cg2665 Hypothetical protein 1.82
cg2181†* ABC-type putative dipeptide/oligopeptide transporter, substrate-binding lipoprotein 1.80
cg1128▪ Hypothetical protein, similar to ribosomal protein S2 1.79
cg1139 Allophanate hydrolase subunit 2 1.75
cg1708- Conserved hypothetical protein 1.75
cg2560 aceA Isocitrate lyase 1.72
cg2183† ABC-type putative dipeptide/oligopeptide transporter, permease subunit 1.71
cg2434 Putative monooxygenase, luciferase 1.68
cg0380 Hypothetical protein 1.67
cg0043 ABC-type putative manganese/zinc transporter, ATPase subunit 1.65
cg0228 Two-component system, sensory histidine kinase, putative pseudogene 1.65
cg1412° rbsC ABC-type ribose transporter, permease subunit (TC 3.A.1.2.1) 1.65
cg1778 zwf Glucose-6-phosphate 1-dehydrogenase 1.65
cg1686° Putative transcriptional regulatory protein 1.61
cg1482 Putative Zn-dependent hydrolase 1.61
cg2514 Conserved hypothetical protein 1.59
cg2206 ispG 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase 1.58
cg2546 Putative secondary C4-dicarboxylate transporter, tripartite ATP-independent transporter (TRAP-T) family 1.58
cg0699 guaB2 IMP dehydrogenase 1.56
cg2184 ABC-type putative dipeptide/oligopeptide transporter, ATPase subunit 1.56
cg3077● Putative membrane protein 1.56
cg1410°* rbsR Transcriptional repressor of ribose importer RbsACBD, LacI-family 1.54
cg1464 Putative transcriptional regulator, HTH_3-family 1.52

aGenes constituting a putative operon are indicated with the same symbol. The first gene in the operon is indicated with an asterisk. Underlined genes were previously described as SigH-dependent [14,16].

bfold change, signal intensity ratio as defined by 2(m-value).

Busche et al.

Busche et al. BMC Genomics 2012 13:445   doi:10.1186/1471-2164-13-445

Open Data