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Table 5 Genes containing Rex TFBS-like motifa in the upstream regions and upregulated on glucose

From: Lactobacillus oligofermentans glucose, ribose and xylose transcriptomes show higher similarity between glucose and xylose catabolism-induced responses in the early exponential growth phase

Gene locus_tag Gene function/name Motif start coordinateb Motif sequence Log2FCc
20 h 24 h 30 h
G/R G/X G/R G/X G/R G/X
LACOL_0123 Glycerol dehydrogenase gldA −38 TCGTTAACTATTTCACAA 1.5 2.7 1.4 2.0 0.7 2.1
LACOL_0137 CoA-substrate-specific enzyme activase −186 TTGTTCATTGAAACACAA 0.2 0.9 0.7 1.7 0.7 1.3
LACOL_0222d 1,3-propanediol dehydrogenase dhaT −64 TTGTGAAATGCGTTACAA 3.8 2.1 2.5 1.4 2.3 1.3
LACOL_0230 Phosphogluconate dehydrogenase gnd −103 TTGTGAATTTTTTAACTT 0.9 1.4 0.4 0.9 0.5 0.9
−283 TTGAAAAACAATTCACTA
LACOL_0239e RpiR family transcriptional regulator −56 ATGCAAATGTTTTCACAA 2.6 2.2 1.0 1.2 0.8 1.4
LACOL_0253d R-specific alcohol dehydrogenase radh −192 TTGTAAACTAGTTAACCT 2.9 2.4 2.9 2.1 2.3 2.1
−67 TTGTGCTATAGTTCACAT
LACOL_0255d Aldehyde-alcohol dehydrogenase adhE −48 TTGTGAATTAAGTAACAA 5.7 6.4 4.9 5.8 3.5 4.3
−203 TTGTACACTAAATCACAA
LACOL_0628 Peptidoglycan-binding protein −171 ATGTGCACTTTTTAACAA 0.1 0.4 1.6 1.1 2.2 3.1
LACOL_0760d Alcohol dehydrogenase adhA −56 TTGTTAAGTATTTAACTT 5.4 4.1 5.0 4.4 3.8 4.2
−105 TTGTTAATAATTTCACTT
LACOL_1011d Diacetyl reductase butA2 −34 TTGTGAATTAAATAACTT 3.6 2.4 4.7 4.0 3.3 3.5
LACOL_1481 Short-chain-enoyl-CoA hydratase −65 TTGTGAAAATGATATCAT 1.9 2.1 2.0 2.4 1.7 2.1
LACOL_1537d NADH oxidase nox −44 TTGTAAAAGTTTTCACAA 1.3 1.6 0.7 2.5 1.6 1.2
  1. aRex TFBS-like motifs were found by scanning all upstream regions in the genome with the motif profile discovered in the group of genes overexpressed on glucose in comparison with xylose at 20 h (Table 3)
  2. bMotif start coordinate is given in relation to the predicted translational start site
  3. cFor the designations, such as G/R, see Table 2. Statistically significant changes are marked in bold
  4. dGenes, (putatively) involved in NAD(P)H re-oxidation
  5. eLACOL_0239 shares its upstream region with LACOL_0240 (phosphogluconate dehydrogenase yqeC)