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. 2018 May 25;62(6):e02656-17. doi: 10.1128/AAC.02656-17

TABLE 1.

Fold changes (relative intensities) in the abundance of amino acid and nucleotide metabolites in the polymyxin-resistant PAKpmrB6 and PAKpmrB12 relative to the wild-type PAK

Pathway Metabolitea Formula Mass (Da) RTb (min) Confidencec Log2 fold changed
PAKpmrB6 PAKpmrB12
Amino acid
    Amino sugar metabolism N-Acetyl-d-glucosamine 6-phosphate C8H16NO9P 301.056 14.26 6 −1.06 −1.77
    Histidine metabolism Hercynine C9H15N3O2 197.116 11.98 6 1.19 0.79
    Lysine biosynthesis l-Lysine C6H14N2O2 146.105 18.73 8 0.53 1.54
l-Carnitine C7H15NO3 161.105 11.73 8 0.58 1.43
l-Pipecolate C6H11NO2 129.079 18.96 8 0.59 1.30
    Methionine metabolism S-Methyl-5-thio-d-ribose C6H12O4S 180.046 7.41 6 10.92 10.71
S-Methyl-5-thio-d-ribose 1-phosphate C6H13O7PS 260.012 11.57 8 6.54 6.11
S-Adenosyl-l-methionine C15H22N6O5S 398.138 15.84 8 −6.63 −5.81
S-Methyl-5′-thioadenosine C11H15N5O3S 297.090 7.42 6 −2.56 0.05
1,2-Dihydroxy-3-keto-5-methyl-thiopentene C6H10O3S 162.035 7.68 6 9.28 7.09
l-Methionine C5H11NO2S 149.051 11.17 8 −0.56 −1.16
S-Adenosyl-l-homocysteine C14H20N6O5S 384.122 13.13 6 −0.93 −1.34
Carbohydrate
    Glycolysis 2-(α-Hydroxyethyl)thiamine diphosphate C14H22N4O8P2S 468.064 13.58 6 −0.53 −1.21
    l-Ara4N biosynthesis UDP-l-Ara4N C14H23N3O15P2 535.060 16.15 8 7.18 6.24
UDP-l-Ara4FN C15H23N3O16P2 563.055 15.32 8 13.78 13.41
UDP-glucuronate C15H22N2O18P2 580.035 18.41 8 5.56 5.91
    Pyruvate metabolism S-Lactoylglutathione C13H21N3O8S 379.105 15.63 8 −0.57 3.71
Nucleotide
    Purine metabolism GDP C10H15N5O11P2 443.025 17.30 8 −0.88 −1.17
Adenosine C10H13N5O4 267.097 8.87 8 −0.51 −1.21
5-Phosphoribosylamine C5H12NO7P 229.035 14.21 8 −2.52 0.19
Adenine C5H5N5 135.054 9.28 8 −1.05 −1.06
AMP C10H14N5O7P 347.063 13.19 8 −0.46 −1.12
    Pyrimidine metabolism CDP C9H15N3O11P2 403.019 16.46 8 −0.99 −1.03
CMP C9H14N3O8P 323.052 15.09 8 −0.67 −1.34
dTMP C10H15N2O8P 322.057 12.44 8 −0.37 −1.61
UDP C9H14N2O12P2 404.002 15.29 6 4.56 4.35
a

Putative metabolite, identified by the exact mass and retention time, with at least 2-fold differences at an FDR of <0.05 and a P value of <0.01 between pmrB mutants and the wild-type PAK. The metabolic data were collected based on five biological replicates.

b

RT, retention time.

c

Confidence, confidence level that gives an indication of the confidence of identification. Confidence level at 8 indicates that the metabolites were putatively identified in the preferred database and related peaks with the variation of standard retention time of <5%, while metabolites with confidence level at 6 were putatively identified based on preferred database and related peaks with calculated retention time within 50%.

d

Fold changes in bold indicate those metabolites with significant change (fold change ≥ 1 log2, P < 0.05) compared to the wild-type PAK.