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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)