Table 2.
Comparison of predicted Crc regulon of P. putida with transcriptome and proteome data.
| Gene name | putidaa | KT2440b | Function | mRNA | Protein |
|---|---|---|---|---|---|
| NO | PP_0267 | outer membrane ferric siderophore receptor | nd | 1.6 | |
| fruR | NM | PP_0792 | FruR transcriptional regulator | nd | 2.3 |
| fruA | PP_0795 | PP_0795 | PTS fructose IIC component | 2.1 | nd |
| gap-1 | PP_1009 | PP_1009 | glyceraldehyde-3-phosphate dehydrogenase, type I | 2.7 | 3.3 |
| PP_1015 | PP_1015 | probable binding protein component of ABC sugar transporter | 2.3 | 4.9 | |
| oprB-1 | PP_1019 | PP_1019 | Glucose/carbohydrate outer membrane porin OprB precursor | 3.5 | 2.9 |
| PP_1059 | PP_1059 | probable amino acid permease | 6.4 | nd | |
| aatJ | PP_1071 | PP_1071 | probable binding protein component of ABC transporter | 3.3 | 7.7 |
| NM | PP_1400 | dicarboxylate MFS transporter | 2.5 | nd | |
| tctC | PP_1418 | PP_1418 | hypothetical protein | 1.6 | 3.4 |
| cspA-1 | PP_1522 | PP_1522 | cold shock protein CspA | 1.9 | 3.5 |
| ansA | PP_2453 | PP_2453 | L-asparaginase, type II | 2.4 | 3.1 |
| PP_3123 | PP_3123 | 3-oxoacid CoA-transferase subunit B | 9.1 | 4.5 | |
| NO | PP_3434 | hypothetical protein | 6.7 | nd | |
| NM | PP_3530 | conserved hypothetical protein | 2.0 | nd | |
| PP_3593 | PP_3593 | amino acid ABC transporter, periplasmic amino acid-binding protein | nd | 6.3 | |
| bkdA-1 | PP_4401 | PP_4401 | 3-methyl-2-oxobutanoate dehydrogenase | 3.2 | 1.6 |
| phhA | PP_4490 | PP_4490 | phenylalanine-4-hydroxylase | 2.8 | 1.9 |
| PP_4495 | PP_4495 | aromatic amino acid transport protein AroP2 | 2.6 | nd | |
| hmgA | PP_4621 | PP_4621 | homogentisate 1,2-dioxygenase | 5.0 | 7.8 |
| PP_4636 | PP_4636 | acetyl-CoA acetyltransferase | 3.6 | 2.3 | |
| hupA | PP_5313 | PP_5313 | probable DNA-binding protein | 3.8 | nd |
| accC-2 | PP_5347 | PP_5347 | acetyl-CoA carboxylase subunit A | 2.4 | nd |
Genes differentially regulated, based on transcriptome and proteome data, in rich media in a crc mutant of P. putida KT2442 [26] are cross referenced with (a) predicted Crc targets from three P. putida strains (KT2440, F1 and W619) and (b) with predicted Crc targets from P. putida KT2440 alone. Values of mRNA and protein indicate the relative levels of transcripts and protein in transcriptome and proteome analyses respectively [26]. NO (no ortholog) indicates that no orthologous loci were detected in either or both of P. putida F1 and W619. NM (no motif) indicates that no A-rich motif was detected in the upstream region of the orthologous loci in P. putida F1 and W619.