Probable DNA-binding protein acetyl-CoA carboxylase subunit A mRNA nd nd 2.1 2.7 2.3 3.5 6.4 3.3 2.5 1.6 1.9 2.4 9.1 6.7 2.0 nd 3.2 2.8 2.6 5.0 3.6 3.8 2.4 Protein 1.6 2.3 nd 3.3 4.9 2.9 nd 7.7 nd 3.4 3.5 3.1 4.5 nd nd 6.3 1.6 1.9 nd 7.8 2.3 nd ndGenes 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.conditions used favoured some classes of genes. Of course, some hits may represent false positives, and our analysis predicted that there are rates of 18 and 26 false positive hits for P. aeruginosa and P. putidarespectively. These are also possible explanations for differences between our data set and the PAO1 proteome data despite the higher level of overlap between our data with PAO1 (13/46) than between our data withTable 3 Comparison of predicted Crc regulon of P. aeruginosa with proteome dataGene name hpd oprD PAO1 PA0534 PA0865 PA0958 PA1069 PA2553a PA2555 PA2776 PA3187b edd PA3194 PA4500 PA4502c PA4506c dadA PA5304 Function conserved hypothetical protein 4-hydroxyphenylpyruvate dioxygenase Basic amino acid, basic peptide and imipenem outer membrane porin OprD precursor hypothetical protein probable acyl-CoA thiolase probable AMP-binding enzyme conserved hypothetical protein probable ATP-binding component of ABC transporter phosphogluconate dehydratase probable binding protein component of ABC transporter probable binding protein component of ABC transporter probable ATP-binding component of ABC dipeptide transporter D-amino acid dehydrogenase, small subunit protein 2.03 4.71 1.75 4.28 1.59 1.54 1.71 10.28 2.17 3.48 3.35 8.43 2.Genes differentially regulated, based on proteome data, in rich media in a crc mutant of P. aeruginosa PAO1 [27] are cross referenced with predicted targets from all P. aeruginosa strains considered in this study. Values of protein indicate relative levels of protein in the crc mutant relative to levels in the wild type strain. Some genes are proximal to, and possibly in CI-1011 web operons with, bioinformatically predicted Crc targets: (a) PA2553 is proximal to PA2555, (b) PA3187 is proximal to PA3186 and (c) PA4502 and PA4506 are proximal to PA4501.Browne et al. BMC Microbiology 2010, 10:300 http://www.biomedcentral.com/1471-2180/10/Page 7 ofKT2440. It is interesting that all three studies identify amino acid metabolism as an important component of the Crc-regulon. This reflects Crc metabolic adaptations in a nutrient rich environment (which was the experimental condition) where various amino acids are the major carbon sources. Performing the PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28212752 transcriptome/ proteome experiments under different growth conditions, would be likely to yield a different set of genes. Conversely, there were also targets identified in the experimental studies that did not feature in the bioinformatic analysis. The most likely explanation for this is that these are indirect rather than direct targets of Crc as they lack the predicte.
