TABLE 2.
Genes or proteins induced (class III) or repressed (class IV) independently of the stringent response, which was provoked by norvaline addition, as revealed by DNA macroarray and proteome analysisa
| Class and cellular function affected | Gene (synonym)/ protein | Identity/similarity/ function | (Putative) transcriptional unit | Transcriptional repression factors
|
Translational repression factors
|
||||
|---|---|---|---|---|---|---|---|---|---|
| Wild type | relA mutant | Wild type
|
relA mutant
|
||||||
| 10 min | 10 min | 10 min | 20 min | 10 min | 20 min | ||||
| Class III: RelA-independent induction | |||||||||
| Metabolism of nucleotides and nucleic acids | guaB/GuaB* (two spots) | Inosine-monophosphate dehydrogenase | guaB | 3.1 | 1.4 | 1.7 | 2.2 | 1.0 | 2.4 |
| Metabolism of amino acids and related proteins | yjcI/YjcI* (two spots) | Similar to cystathione γ-synthase/probable part of the S-box regulon/unknown | yjcI-yjcJ | 3.7 | 3.6 | 4.3 | 4.5 | >2.0 | >6.0 |
| Metabolism of amino acids and related proteins | yjcJ/YjcJ* (two spots) | Similar to cystathione β-lyase/probable part of the S-box regulon/unknown | yjcI-yjcJ | 3.0 | 4.3 | 6.0 | 4.5 | 2.7 | 3.9 |
| Specific pathways | yoaD | Similar to unknown proteins/probable part of the S-box regulon/unknown | yoaD-yoaC-yoaB? | 3.2 | 2.6 | ||||
| Specific pathways | yoaC | Similar to unknown proteins/probable part of the S-box regulon/unknown | yoaD-yoaC-yoaB? | 3.8 | 3.0 | ||||
| Transport | yheI | Similar to ABC transporter (ATP-binding protein)/unknown | yheJ-yheI-yheH | 4.0 | 3.3 | ||||
| Transport | yheH | Similar to ABC transporter (ATP-binding protein)/unknown | yheJ-yheI-yheH | 4.0 | 4.9 | ||||
| Unknown | ykrT/YkrT* | Similar to unknown proteins/probable part of the S-box regulon/unknown | ykrT-ykrS | 3.7 | 3.4 | 4.2 | 3.2 | 1.5 | 3.0 |
| Unknown | ykrS/YkrS* | Similar to eukaryotic initiation factor eIF-2B (alpha subunit)/probable part of the S-box regulon/unknown | ykrT-ykrS | 3.9 | 5.0 | >5.0 | >6.0 | >2.0 | >6.0 |
| Unknown | yitJ/YitJ* (two spots) | Similar to unknown proteins/probable part of the S-box regulon/unknown | yitJ | 5.7 | 3.3 | >5.0 | >6.0 | >2.0 | 1.8 |
| Unknown | ykrX | Similar to unknown proteins/probable part of the S-box regulon/unknown | ykrX-ykrY-ykrZ | 3.4 | 3.1 | ||||
| Unknown | ykrZ/YkrZ | Similar to unknown proteins/probable part of the S-box regulon/unknown | ykrX-ykrY-ykrZ | 4.1 | 2.8 | ND | ND | ND | ND |
| Arginine biosynthesis | argG/ArgG* (two spots) | Argininosuccinate synthase | argG-argH-ytzD | 7.0 | 4.4 | 5.0 | >6.0 | 1.5 | 4.1 |
| Arginine biosynthesis | argH/ArgH* (two spots) | Argininosuccinate lyase | argG-argH-ytzD | 7.0 | 4.4 | ND | ND | ND | ND |
| Unknown | ytzD | Unknown | argG-argH-ytzD | 14.2 | 5.2 | ||||
| Transport | yqiX/YqiX* | Similar to amino acid ABC transporter/unknown | yqiX | 3.3 | 1.6 | 2.4 | 2.1 | 1.3 | 2.9 |
| Arginine biosynthesis | argC/ArgC* | N-Acetylglutamate γ-semialdehyde dehydrogenase | argC-argJ-argB-argD-carA-carB-argF | 10.8 | 3.0 | 6.2 | 6.0 | 2.0 | 7.1 |
| Arginine biosynthesis | argJ | Omithine acetyltransferase/amino acid acetyltransferase | argC-argJ-argB-argD-carA-carB-argF | 10.1 | 2.8 | ||||
| Arginine biosynthesis | argB/ArgB* | N-Acetylglutamate 5-phosphotransferase | argC-argJ-argB-argD-carA-carB-argF | 10.3 | 4.5 | 5.7 | 4.7 | 1.5 | 6.0 |
| Arginine biosynthesis | argD/argD* | N-Acetylomithine aminotransferase | argC-argJ-argB-argD-carA-carB-argF | 10.9 | 4.3 | 4.0 | 5.5 | ND | 6.7 |
| Arginine biosynthesis | carA/CarA* | Carbamoyl-phosphate transferase-arginine (subunit A) | argC-argJ-argB-argD-carA-carB-argF | 5.6 | 3.4 | >5.0 | 2.4 | ND | 2.0 |
| Arginine biosynthesis | carB/carB* | Carbamoyl-phosphate transferase-arginine (subunit B) | argC-argJ-argB-argD-carA-carB-argF | 3.5 | 3.1 | 1.9 | 9.0 | 1.2 | 7.1 |
| Arginine biosynthesis | argF/ArgF* | Ornithine carbamoyltransferase | argC-argJ-argB-argD-carA-carB-argF | 11.6 | 3.9 | ND | ND | ND | ND |
| Class IV: RelA-independent repression | |||||||||
| Main glycolytic pathways | pgk/Pgk* | Phosphoglycerate kinase | cggR-gapA-pgk-tpi-pgm-eno | 3.0 | 2.5 | 1.3 | 1.5 | 2.8 | ND |
| Main glycolytic pathways | tpi/Tpi* | Triose phosphate isomerase | cggR-gapA-pgk-tpi-pgm-eno | 3.8 | 3.6 | 1.3 | 1.9 | ND | 1.5 |
| Main glycolytic pathways | pgm/Pgm* | Phosphoglycerate mutase | cggR-gapA-pgk-tpi-pgm-eno | 3.3 | 6.0 | 2.4 | 3.2 | 1.5 | ND |
| Main glycolytic pathways | eno/Eno* | Enolase | cggR-gapA-pgk-tpi-pgm-eno | 5.3 | 3.9 | 1.5 | 1.8 | 1.5 | 1.8 |
| Main glycolytic pathways | pfk/Pfk* | 6-Phosphofructokinase | pfk | 2.3 | 2.4 | >5.0 | >6.0 | >3.0 | 2.1 |
| Main glycolytic pathways | pdhA/PdhA | Pyruvate dehydrogenase (E1 alpha subunit) | pdhA-pdhB-pdhC-pdhD | 5.5 | 3.8 | >5.0 | >6.0 | 3.0 | 2.4 |
| Main glycolytic pathways | pdhB/PdhB | Pyruvate dehydrogenase (E1 beta subunit) | pdhA-pdhB-pdhC-pdhD | 18.2 | 8.1 | 11.2 | 10.3 | 3.3 | 4.6 |
| Main glycolytic pathways | pdhC/PdhC | Pyruvate dehydrogenase (dihydrolipoamide acetyltransferase E2 subunit) | pdhA-pdhB-pdhC-pdhD | 23.7 | 6.4 | 2.7 | 3.1 | 5.2 | 3.2 |
| Main glycolytic pathways | pdhD/PdhD* | Pyruvate dehydrogenase/2-oxoglutarate DH | pdhA-pdhB-pdhC-pdhD | 6.6 | 3.3 | >5.0 | 5.3 | 2.7 | 2.2 |
| Protein synthesis | pheS | Phenylalanyl-tRNA synthetase (alpha subunit) | pheS-pheT | 4.0 | 3.2 | ||||
| Protein synthesis | pheT/PheT* | Phenylalanyl-tRNA synthetase (beta subunit) | pheS-pheT | 2.6 | 1.8 | 4.8 | 4.0 | 2.0 | 2.5 |
| Thiamin biosynthesis | thiA (thiC)/ThiA | Biosynthesis of the pyrimidine moiety of thiamine | thiA | 4.9 | 2.7 | >5.0 | >6.0 | 2.0 | ND |
| Transport | fhuD | Ferrichrome ABC transporter (ferrichrome-binding protein) | fhuD | 4.0 | 4.2 | ||||
| Transport | cysP (ylnA) | Sulfate permease | cysP-prkC | 5.1 | 3.3 | ||||
| Transport | prkC (yloP) | Probable membrane-linked protein kinase | cysP-prkC | 4.0 | 3.1 | ||||
| Long chain fatty acid biosynthesis | accB (fabE, yqhW) | Acetyl-CoA carboxylase (biotin carboxyl carrier subunit) | accB-accC | 4.0 | 3.1 | ||||
| Long chain fatty acid biosynthesis | accC | Acetyl-CoA carboxylase (biotin carboxylase subunit) | accB-accC | 4.5 | 3.1 | ||||
| Histidine biosynthesis | hisD | Histidinol dehydrogenase | hisZ-hisG-hisD-hisB-hisH-hisA-hisF-hisI | 3.1 | 7.3 | ||||
| Histidine biosynthesis | hisB | Imidazoleglycerol-phosphate dehydratase | hisZ-hisG-hisD-hisB-hisH-hisA-hisF-hisI | 3.3 | 6.8 | ||||
| Histidine biosynthesis | hisH | Amidotransferase | hisZ-hisG-hisD-hisB-hisH-hisA-hisF-hisI | 2.7 | 4.4 | ||||
| Histidine biosynthesis | hisA | Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase | hisZ-hisG-hisD-hisB-hisH-hisA-hisF-hisI | 2.0 | 4.3 | ||||
| Histidine biosynthesis | hisF | HisF cyclase-like protein | hisZ-hisG-hisD-hisB-hisH-hisA-hisF-hisI | 4.0 | 8.0 | ||||
| Histidine biosynthesis | hisI | Phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophospho-hydrolase | hisZ-hisG-hisD-hisB-hisH-hisA-hisF-hisI | 5.7 | 5.7 | ||||
| Purine biosynthesis | purE | Phosphoribosylaminoimidazole carboxylase I | purE-K-B-C-L-Q-F-purM-purN-H-D | 3.8 | 5.1 | ||||
| Purine biosynthesis | purK | Phosphoribosylaminoimidazole carboxylase II | purE-K-B-C-L-Q-F-purM-purN-H-D | 3.6 | 4.3 | ||||
| Purine biosynthesis | purB/PurB | Adenylosuccinate lyase | purE-K-B-C-L-Q-F-purM-purN-H-D | 7.9 | 4.6 | >5.0 | >6.0 | 3.1 | >3.0 |
| Purine biosynthesis | purC/PurC | Phosphoribosylaminoimidazole succinocarboxamide synthetase | purE-K-B-C-L-Q-F-purM-purN-H-D | 9.0 | 4.6 | 3.4 | 3.0 | 1.7 | ND |
| Purine biosynthesis | purL/PurL* | Phosphoribosylformylglycinamidine synthetase II | purE-K-B-C-L-Q-F-purM-purN-H-D | 6.8 | 4.2 | >5.0 | >6.0 | >3.0 | >3.0 |
| Purine biosynthesis | purQ | Phosphoribosylformylglycinamidine synthetase I | purE-K-B-C-L-Q-F-purM-purN-H-D | 3.6 | 3.0 | ||||
| Purine biosynthesis | purF | Phosphoribosylpyrophosphate amidotransferase | purE-K-B-C-L-Q-F-purM-purN-H-D | 3.6 | 2.6 | ||||
| Purine biosynthesis | purM/PurM | Phosphoribosylaminoimidazole synthetase | purE-K-B-C-L-Q-F-purM-purN-H-D | 1.9 | 2.6 | >5.0 | >6.0 | 2.1 | >3.0 |
| Purine biosynthesis | purN | Phosphoribosylglycinamide formyltransferase | purE-K-B-C-L-Q-F-purM-purN-H-D | 18.5 | 5.5 | ||||
| Purine biosynthesis | purH/PurH* | Phosphoribosylaminoimidazole carboxy formyl formyltransferase | purE-K-B-C-L-Q-F-purM-purN-H-D | 10.8 | 2.7 | 1.5 | 1.7 | ND | 1.5 |
| Purine biosynthesis | purD/PurD* | Phosphoribosylglycinamide synthetase | purE-K-B-C-L-Q-F-purM-purN-H-D | 3.5 | 1.3 | >5.0 | >6.0 | ND | >3.0 |
| Purine biosynthesis | purS (yexA) | Required for phosphoribosylformylglycinamidine synthetase activity | purS | 3.5 | 4.2 | ||||
| Purine biosynthesis | purA | Adenylosuccinate synthetase | purA | 2.1 | 5.4 | ||||
| Pyrimidine biosynthesis | pyrR | Transcriptional attenuation of the pyrimidine operon/uracil phosphoribosyltransferase activity | pyrR-pyrP-pyrB-C-pyrAA-pyrAB-DII-D-pyrF-E | 4.3 | 10.2 | ||||
| Pyrimidine biosynthesis | pyrB | Aspartate carbamoyltransferase | pyrR-pyrP-pyrB-C-pyrAA-pyrAB-DII-D-pyrF-E | 6.6 | 8.0 | ||||
| Pyrimidine biosynthesis | pyrC | Dihydrooratase | pyrR-pyrP-pyrB-C-pyrAA-pyrAB-DII-D-pyrF-E | 8.6 | 8.5 | ||||
| Pyrimidine biosynthesis | pyrAA/PyrAA* | Carbamoyl-phosphate synthetase | pyrR-pyrP-pyrB-C-pyrAA-pyrAB-DII-D-pyrF-E | 5.3 | 11.5 | >5.0 | >6.0 | >3.0 | >3.0 |
| Pyrimidine biosynthesis | pyrAB/PyrAB | Carbamoyl-phosphate synthetase (catalytic subunit) | pyrR-pyrP-pyrB-C-pyrAA-pyrAB-DII-D-pyrF-E | 2.1 | 2.0 | >5.0 | >6.0 | >3.0 | >3.0 |
| Pyrimidine biosynthesis | pyrF | Orotidine 5′-phosphate decarboxylase | pyrR-pyrP-pyrB-C-pyrAA-pyrAB-DII-D-pyrF-E | 3.2 | 2.7 | ||||
| Pyrimidine biosynthesis | pyrE | Orotate phosphoribosyltransferase | pyrR-pyrP-pyrB-C-pyrAA-pyrAB-DII-D-pyrF-E | 11.6 | 4.8 | ||||
| Unknown | yclP | Similar to ferrichrome ABC transporter (ATP-binding protein)/unknown | yclP | 4.3 | 5.1 | ||||
| Unknown | yclQ | Similar to ferrichrome ABC transporter (binding protein)/unknown | yclQ | 3.0 | 4.8 | ||||
| Unknown | yukC | Similar to unknown proteins/unknown | yukC | 4.2 | 4.6 | ||||
| Unknown | yumC/YumC* | Similar to thioredoxin reductase/unknown | yumC | 1.8 | 2.1 | >5.0 | >6.0 | >3.0 | >3.0 |
| Unknown | yaaD/YaaD* | Similar to superoxide-inducible protein/unknown | yaaD | 1.0 | 1.4 | 2.4 | 3.0 | 1.7 | 1.9 |
a
For the complete legend, see Table 1. Note that the repression of YumC and YaaD synthesis was not reflected at the mRNA level. CoA, coenzyme A.