TABLE 1

Target candidates for DicF sRNAa

CategoryAnnotationGene(s)Fold changeb (pDicF/vec)q valueComp. predicted
Transport of sugarsMaltose transport, metabolism malM, malF, malG, malP, malEc0.003–0.010
Ribose transport, metabolism rbsD 0.020
rbsA 0.030
rbsC 0.040x
rbsB 0.050
rbsK 0.10
rbsR 0.152.9E−186
Mannose and glucose transport manX 0.311.0E−134x
manY 0.234.4E−122
manZ 0.242.1E−153
Galactitol transport and metabolism gatB 0.030
gatC, gatDc0.040
gatZ 0.050
gatY, gatAc0.060
Xylose transport operon activator xylRd 0.671x
Central/carbon metabolismPyruvate kinase pykA 0.10x
Glycerol kinase glpK 0.060x
Succinate dehydrogenase sdhA, sdhB, sdhCc0.08–0.10
NADH:ubiquinone oxidoreductase nuoF 0.20
nuoE 0.23.46E−163
nuoC 0.247.82E−123
nuoG 0.259.1E−201
nuoB 0.257.6E−123
nuoL 0.296.17E−98x
nuoA 0.276.72E−98
Cytochrome oxidase subunit II cyoAe 0.51.63E−22
l-Glutamine:d-fructose-6-phosphate aminotransferase glmSf 0.76.6E−4
PTS enzyme ptsPd 1.020.11x
Phosphofructokinase pfkAf 1.65.57E−11
MiscellaneousTubulin-like cell division protein ftsZg 0.64.3E−12x
Polyphosphate kinase ppKd 0.90.44x
Methyltransferase for rRNA rlmNg 1.61.2E−8x
Tryptophan transporter mtrd 1.51x
Carbamyl phosphatase synthase carBd 2.131x
Polysaccharide production pgaAd 2.51x
Phosphate starvation psiEd 81x
  • 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.