The requirement for the LysR-type regulator PtrA for Pseudomonas chlororaphis PA23 biocontrol revealed through proteomic and phenotypic analysis

Natasha Klaponski; Carrie Selin; Kelly Duke; Vic Spicer; Dilantha WG Fernando; Mark F Belmonte; Teresa R de Kievit

doi:10.1186/1471-2180-14-94

Table 1 Differentially expressed proteins in mutant PA23-443 compared to the PA23 wild type

From: The requirement for the LysR-type regulator PtrA for Pseudomonas chlororaphis PA23 biocontrol revealed through proteomic and phenotypic analysis

COG Category	Locus Tag	Predicted Function	Fold Change^a	V_diffScore
Amino acid transport and metabolism	MOK_00491	4-aminobutyrate aminotransferase and related aminotransferases	1.59	2.24
	MOK_03651	Monoamine oxidase	−2.39	−2.7
	MOK_04019	ornithine carbamoyltransferase	−1.48	−1.67
Nucleotide transport and metabolism	MOK_04929	hypothetical protein	−3.13	−2.54
Carbohydrate transport and metabolism	MOK_03378	Chitinase	−3.30	−3.76
	MOK_05029	Glucose/sorbosone dehydrogenases	−1.68	−2.04
	MOK_05478	Chitinase	−2.61	−1.66
Lipid transport and metabolism	MOK_04573	Acyl dehydratase	−2.16	−2.42
Translation, ribosomal structure and biogenesis	MOK_00565	Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF-5A)	1.61	1.94
	MOK_01324	ribosomal protein L32	2.33	2.77
	MOK_02337	aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C subunit	2.09	1.7
	MOK_04471	ribosomal protein S19, bacterial/organelle	1.49	1.7
Transcription	MOK_02056	cold shock domain protein CspD	−2.31	−1.81
	MOK_02888	Cold shock proteins	2.30	2.44
	MOK_03359	Cold shock proteins	1.26	1.65
Replication, recombination and repair	MOK_00606	competence protein ComEA helix-hairpin-helix repeat region	−2.78	−3.04
Cell wall, membrane and envelope biogenesis	MOK_05137	Outer membrane protein and related peptidoglycan-associated (lipo)proteins	−1.65	−1.79
Cell motility	MOK_01499	Flagellin and related hook-associated proteins	2.71	3.26
Post-translational modification, protein turnover and chaperones	MOK_00750	monothiol glutaredoxin, Grx4 family	1.20	1.81
	MOK_01830	peroxiredoxin, OsmC subfamily	−2.61	−2.69
	MOK_05742	Peroxiredoxin	−1.84	−1.78
	MOK_05953	Peptidyl-prolyl cis-trans isomerase (rotamase) - cyclophilin family	2.00	1.73
Inorganic ion transport and metabolism	MOK_05447	Predicted periplasmic lipoprotein involved in iron transport	1.42	1.73
Secondary metabolites biosynthesis, transport and catabolism	MOK_01048	Phenazine biosynthesis protein A/B.	−4.22	−4.58
	MOK_01049	Phenazine biosynthesis protein A/B.	−3.25	−4.26
	MOK_01053	phenazine biosynthesis protein PhzF family	−1.19	−2.1
	MOK_01054	Pyridoxamine-phosphate oxidase	−1.25	−2.18
	MOK_01055	Aromatic ring hydroxylase	−2.45	−2.43
General function prediction only	MOK_01152	Predicted periplasmic or secreted lipoprotein	−2.29	−2.42
	MOK_02985	intracellular protease, PfpI family	1.67	1.93
	MOK_03813	Predicted O-methyltransferase	−2.12	−1.73
	MOK_05714	Serine protease inhibitor ecotin	−1.33	−1.65
Function unknown	MOK_00258	Protein of unknown function (DUF3313).	−1.81	−2.03
	MOK_00808	hypothetical protein	−8.28	−7.73
	MOK_01097	hypothetical protein	−2.10	−2.22
	MOK_01302	hypothetical protein	−1.32	−2.08
	MOK_01398	hypothetical protein	−2.04	−2.19
	MOK_01832	Protein of unknown function (DUF1161).	−1.14	−1.94
	MOK_02425	Sigma 54 modulation protein/S30EA ribosomal protein.	1.36	2.22
	MOK_02468	poly(hydroxyalkanoate) granule-associated protein	−2.70	−3.66
	MOK_02469	poly(hydroxyalkanoate) granule-associated protein	−1.75	−2.32
	MOK_03057	Uncharacterized protein conserved in bacteria	−1.86	−2.29
	MOK_03064	type VI secretion protein, VC_A0107 family	−2.87	−3.14
	MOK_03065	type VI secretion protein, EvpB/VC_A0108 family	−2.72	−3.02
	MOK_03231	outer membrane porin, OprD family.	1.49	1.8
	MOK_03379	Uncharacterized protein conserved in bacteria	−4.52	−5.06
	MOK_03717	hypothetical protein	−5.36	−6.81
	MOK_03859	hypothetical protein	−2.60	−2.27
	MOK_04005	Protein of unknown function (DUF3613).	−2.39	−2.06
	MOK_04318	Predicted integral membrane protein	−1.80	−2.21
	MOK_04378	Putative phospholipid-binding domain./LysM domain.	−2.22	−3.47
	MOK_04746	hypothetical protein	−2.29	−2.71
	MOK_04755	hypothetical protein	−3.36	−3.84
	MOK_05477	Uncharacterized protein conserved in bacteria	−2.09	−1.41
	MOK_05648	hypothetical protein	−4.51	−4.7
	MOK_05758	hypothetical protein	−4.00	−4.19
	MOK_06084	Iron-sulfur cluster assembly accessory protein	1.72	1.73
	MOK_06136	hypothetical protein	−5.20	−5.37
Signal transduction mechanisms	MOK_04087	Putative Ser protein kinase	−1.38	−2.06

Proteins with V_diff ≥ +1.65 or V_diff ≤ −1.65, corresponding to proteins expressed in the upper or lower 5% of the population distribution are shown.
^alog₂(tag₁₁₅/tag₁₁₇).

Back to article page