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Table 2 Comparison of predicted Crc regulon of P. putida with transcriptome and proteome data.

From: Computational prediction of the Crc regulon identifies genus-wide and species-specific targets of catabolite repression control in Pseudomonas bacteria

Gene name

putida a

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

  1. 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.