PUL ID

PUL0232

PubMed

24705323, Appl Environ Microbiol. 2014 Jun;80(12):3604-14. doi: 10.1128/AEM.00130-14.

Characterization method

microarray, electrophoretic mobility shift assay

Genomic accession number

CP000303.1

Nucelotide position range

2337397-2344915

Substrate

raffinose

Loci

bbr_1865-bbr_1870

Species

Bifidobacterium breve/1685

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- Bbr_1865 ABE96527.1 0 - 867 (-) CP000303.1:2337397-2338264 -
- Bbr_1866 ABE96528.1 885 - 1833 (-) CP000303.1:2338282-2339230 -
- Bbr_1867 ABE96529.1 1854 - 3144 (-) CP000303.1:2339251-2340541 -
- Bbr_1868 ABE96530.1 3316 - 4525 (+) CP000303.1:2340713-2341922 -
aga Bbr_1869 ABE96531.1 4637 - 6953 (-) CP000303.1:2342034-2344350 3.2.1.22
mesJ Bbr_1870 ABE96532.1 7069 - 7519 (-) CP000303.1:2344466-2344916 3.5.4.-

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 867 (-) TC: gnl|TC-DB|Q00751|3.A.1.1.28 Yes
- 886 - 1833 (-) TC: gnl|TC-DB|Q00750|3.A.1.1.28 Yes
- 1855 - 3144 (-) TC: gnl|TC-DB|Q00749|3.A.1.1.28 Yes
- 3317 - 4525 (+) other Yes
aga 4638 - 6953 (-) CAZyme: GH36 Yes
mesJ 7070 - 7519 (-) CDS No

PUL ID

PUL0232

PubMed

24705323, Appl Environ Microbiol. 2014 Jun;80(12):3604-14. doi: 10.1128/AEM.00130-14.

Title

Transcription of two adjacent carbohydrate utilization gene clusters in Bifidobacterium breve UCC2003 is controlled by LacI- and repressor open reading frame kinase (ROK)-type regulators.

Author

O'Connell KJ, Motherway MO, Liedtke A, Fitzgerald GF, Paul Ross R, Stanton C, Zomer A, van Sinderen D

Abstract

Members of the genus Bifidobacterium are commonly found in the gastrointestinal tracts of mammals, including humans, where their growth is presumed to be dependent on various diet- and/or host-derived carbohydrates. To understand transcriptional control of bifidobacterial carbohydrate metabolism, we investigated two genetic carbohydrate utilization clusters dedicated to the metabolism of raffinose-type sugars and melezitose. Transcriptomic and gene inactivation approaches revealed that the raffinose utilization system is positively regulated by an activator protein, designated RafR. The gene cluster associated with melezitose metabolism was shown to be subject to direct negative control by a LacI-type transcriptional regulator, designated MelR1, in addition to apparent indirect negative control by means of a second LacI-type regulator, MelR2. In silico analysis, DNA-protein interaction, and primer extension studies revealed the MelR1 and MelR2 operator sequences, each of which is positioned just upstream of or overlapping the correspondingly regulated promoter sequences. Similar analyses identified the RafR binding operator sequence located upstream of the rafB promoter. This study indicates that transcriptional control of gene clusters involved in carbohydrate metabolism in bifidobacteria is subject to conserved regulatory systems, representing either positive or negative control.