TABLE 1

Target candidates for DicF sRNAa

CategoryAnnotationGene(s)Fold changeb (pDicF/vec)q valueComp. predicted
Transport of sugarsMaltose transport, metabolismmalM, malF, malG, malP, malEc0.003–0.010
Ribose transport, metabolismrbsD0.020
rbsA0.030
rbsC0.040x
rbsB0.050
rbsK0.10
rbsR0.152.9E−186
Mannose and glucose transportmanX0.311.0E−134x
manY0.234.4E−122
manZ0.242.1E−153
Galactitol transport and metabolismgatB0.030
gatC, gatDc0.040
gatZ0.050
gatY, gatAc0.060
Xylose transport operon activatorxylRd0.671x
Central/carbon metabolismPyruvate kinasepykA0.10x
Glycerol kinaseglpK0.060x
Succinate dehydrogenasesdhA, sdhB, sdhCc0.08–0.10
NADH:ubiquinone oxidoreductasenuoF0.20
nuoE0.23.46E−163
nuoC0.247.82E−123
nuoG0.259.1E−201
nuoB0.257.6E−123
nuoL0.296.17E−98x
nuoA0.276.72E−98
Cytochrome oxidase subunit IIcyoAe0.51.63E−22
l-Glutamine:d-fructose-6-phosphate aminotransferaseglmSf0.76.6E−4
PTS enzymeptsPd1.020.11x
PhosphofructokinasepfkAf1.65.57E−11
MiscellaneousTubulin-like cell division proteinftsZg0.64.3E−12x
Polyphosphate kinaseppKd0.90.44x
Methyltransferase for rRNArlmNg1.61.2E−8x
Tryptophan transportermtrd1.51x
Carbamyl phosphatase synthasecarBd2.131x
Polysaccharide productionpgaAd2.51x
Phosphate starvationpsiEd81x
  • a RNA-Seq experiments and biocomputational analyses were used to generate a list of potential DicF targets. Each “x” in the “Comp. predicted” column indicates that the results were predicted by a computational program. PTS, phosphotransferase system.

  • b Data represent normalized read counts from cells carrying Plac-dicF plasmid divided by counts from vector control (vec) cells. Values of <1 indicate repression by DicF; values of >1 indicate activation by DicF.

  • c The fold change and q values for the gene were the same.

  • d The gene did not meet the normalized read count cutoff (it had <100 reads) but was chosen because it were predicted by computational programs, as described in the text.

  • e The gene did not meet the cutoff fold change for RNA-Seq analyses but was chosen because it was 2-fold downregulated and because several genes encoding other components of the enzyme were also downregulated ~2-fold.

  • f The gene did not meet the cutoff fold change and q values for RNA-Seq data analyses (although it fulfilled the copy number criteria) but was chosen because it was predicted by computational programs, as described in the text.

  • g The gene neither fulfilled the RNA-Seq cutoff fold change criteria nor was predicted by computational programs but was chosen based on other experimental evidence.