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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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