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Table 4 Genes predicted to contain a CcpA- binding motifa in the upstream regions

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

Log2FC, 20 hb

Motif start coordinatec

Motif sequence

Co-transcribed genes

G/R

G/X

X/R

Genes, upregulated on glucose and xylose

 LACOL_0264

Fructokinase gmuE

1.46

−0.4

1.86

−88

ATTAAAACGGTTACAA

 

 LACOL_0353

PTS system mannose-specific EIIAB component manX

2.47

0.49

1.98

−97

ATGAAAGCGTATTCAA

manXYZ

 LACOL_0639

Mannose-6-phosphate isomerase pmi

1.54

−0.52

2.06

−58

TAGGAAGGGCTTACAT

 

 LACOL_0566

Gluconokinase gntK

2.03

0.84

1.19

−112

ATGGAATCGGTTGCTA

LACOL_0567 d

−95

TTGTAACCGATTTCCA

 LACOL_1326

Gluconate permease gntP2

1.81

−0.21

2.02

−155

TTGTTAACGGTTACAA

LACOL_1325 d

 LACOL_0266

Putative xylose-proton symporter xylP2

1.6

0.78

0.82

−130

TTGCAAGCGTTTACAA

LACOL_0265 d

 LACOL_0399

Aldose 1-epimerase xylM

1.09

−0.39

1.47

−144

ATACAAGCGCTTTCAT

xylR d

−46

ATTTAATCGCTTACAT

 LACOL_0400

Transcriptional xylose repressor xylR

1.19

−0.43

1.62

−239

ATGTAAGCGATTAAAT

xylM d

−141

ATGAAAGCGCTTGTAT

 LACOL_0401

Xylose isomerase xylA

2.33

−2.3

4.63

−90

GTGAAAGGGGTTGCAA

xylA-xylB

−68

ATGTAAGCGTTATACT

 LACOL_1587

D-xylose-proton symporter xylT

3.23

−0.9

4.13

−139

TTGGCAGCGGTTTCAT

 

−72

CTGAAAGCGGTTACGC

 LACOL_0614

Phosphocarrier protein Hpr ptsH

1.61

0.26

1.36

−126

AATAAAACGTTTACAT

ptsH-ptsI

 LACOL_1153

Pyruvate dehydrogenase E1 component alpha subunit pdhA

2.54

0.26

2.28

−60

AATAAAGCGCTTACAT

pdhA-pdhB-pdhC-pdhD

 LACOL_0222

1,3-propanediol dehydrogenase dhaT

3.81

2.11

1.7

−41

TTGTAATCGCTTTAAT

LACOL_0223 d

Genes, upregulated on ribose

 LACOL_0444

D-ribose pyranase rbsD1

−2.32

0.55

−2.87

−77

TTGAAAGCGGTTACTA

rbsD1-rbsA-rbsC-rbsB

 LACOL_0616

Putative (deoxy)ribose permease deoP

−4.59

0.04

−4.63

−50

TTGTAAGCGGATTATT

 

 LACOL_0617

D-ribose pyranase rbsD2

−4.57

0.34

−4.9

−108

TTGCAATCGTTTCCAA

 

 LACOL_0618

Ribokinase rbsK2

−5.55

0.59

−6.13

−258

TTGGAAACGATTGCAA

rbsK2-rpiA2

Genes, upregulated on glucose

 LACOL_0233

Glucose-6-phosphate dehydrogenase zwf

1.37

1.19

0.18

−107

GTGTAACCGGTTTATT

 

 LACOL_0255

Aldehyde-alcohol dehydrogenase adhE

5.69

6.37

−0.68

−220

ATGTAAGCGATTACAA

 

 LACOL_0923

Sugar (maltose):cation symporter

7.66

7.46

0.2

−53

CTGTAATCGGTTACAT

LACOL_0923-mdxK-pgmB

Other genes (mostly equally expressed)

 LACOL_0188

CRISPR-associated protein cas9

0.56

−0.52

1.09

−67

ATGAAAGCGTTTAACC

 

 LACOL_0275

L-arabinose isomerase araA

0.81

−0.19

1

−79

TTGTAAGCGATTAACA

 

 LACOL_1004

N-acetylmannosamine-6-phosphate epimerase nanE

0.48

−0.13

0.61

−263

ATGTAAACGTTTTCTT

nanE-nanA-nanR, nanK d

 LACOL_1005

N-acetylmannosamine kinase nanK

0.6

−0.55

1.14

−36

AAGAAAACGTTTACAT

nanE d

 LACOL_0104

PTS system sugar-specific enzyme IIA component

0.4

0.3

0.1

−63

TTGTAAGCCTTTGCAA

LACOL_0104-LACOL_0106

 LACOL_0218

Galactokinase galK

0.21

0.33

−0.12

−133

AATTAACCGTTTTCAT

galK-galT-galR

 LACOL_0521

Beta-galactosidase large subunit lacL

0.39

−0.57

0.97

−63

TTGAAAGCGCTTTAAC

lacL-lacM

 LACOL_1707

Beta-galactosidase lacZ

0.06

0.58

−0.52

−38

AAGAAAGCGCTTTCTA

LacZ-LACOL_1706-LACOL_1705

  1. a CcpA- binding motifs were found by scanning all upstream regions in the genome with the Lactobacillaceae-specific CcpA TFBS profile built using RegPrecise database
  2. b For the designations, such as G/R, see Table 2. Statistically significant changes are marked in bold
  3. c Motif start coordinate is given in relation to the predicted translational start site
  4. d The gene/operon upstream region is overlapped with the upstream region of the adjacent divergently oriented gene
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BMC Genomics

ISSN: 1471-2164

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