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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0171

PubMed

27353652, J Bacteriol. 2016 Aug 25;198(18):2410-8. doi: 10.1128/JB.00381-16. Print 2016 Sep 15.

Characterization method

qRT-PCR,RNA-Seq

Genomic accession number

FQ312004.1

Nucelotide position range

4060271-4070266

Substrate

N-glycan

Loci

BF638R_3437-BF638R_3443

Species

Bacteroides fragilis/817

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BF638R_3437 CBW23899.1 0 - 540 (+) FQ312004.1:4060271-4060811 -
- BF638R_3438 CBW23900.1 586 - 1576 (+) FQ312004.1:4060857-4061847 -
omp117 BF638R_3439 CBW23901.1 1756 - 5026 (+) FQ312004.1:4062027-4065297 -
- BF638R_3440 CBW23902.1 5046 - 6675 (+) FQ312004.1:4065317-4066946 -
- BF638R_3441 CBW23903.1 6706 - 7747 (+) FQ312004.1:4066977-4068018 -
- BF638R_3442 CBW23904.1 7770 - 8952 (+) FQ312004.1:4068041-4069223 -
- BF638R_3443 CBW23905.1 8964 - 9996 (+) FQ312004.1:4069235-4070267 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 540 (+) TF: DBD-Pfam|GerE No
- 587 - 1576 (+) STP: STP|FecR No
omp117 1757 - 5026 (+) TC: gnl|TC-DB|Q8A8X1|1.B.14.6.13 Yes
- 5047 - 6675 (+) TC: gnl|TC-DB|Q8A0N7|8.A.46.2.2 Yes
- 6707 - 7747 (+) CAZyme: GH18 Yes
- 7771 - 8952 (+) CDS No
- 8965 - 9996 (+) CDS No

PUL ID

PUL0171

PubMed

27353652, J Bacteriol. 2016 Aug 25;198(18):2410-8. doi: 10.1128/JB.00381-16. Print 2016 Sep 15.

Title

cis-Encoded Small RNAs, a Conserved Mechanism for Repression of Polysaccharide Utilization in Bacteroides.

Author

Cao Y, Forstner KU, Vogel J, Smith CJ

Abstract

Bacteroides is a major component of the human gut microbiota which has a broad impact on the development and physiology of its host and a potential role in a wide range of disease syndromes. The predominance of this genus is due in large part to expansion of paralogous gene clusters, termed polysaccharide utilization loci (PULs), dedicated to the uptake and catabolism of host-derived and dietary polysaccharides. The nutritive value and availability of polysaccharides in the gut vary greatly; thus, their utilization is hierarchical and strictly controlled. A typical PUL includes regulatory genes that induce PUL expression in response to the presence of specific glycan substrates. However, the existence of additional regulatory mechanisms has been predicted to explain phenomena such as hierarchical control and catabolite repression. In this report, a previously unknown layer of regulatory control was discovered in Bacteroides fragilis Exploratory transcriptome sequencing (RNA-seq) analysis revealed the presence of cis-encoded antisense small RNAs (sRNAs) associated with 15 (30%) of the B. fragilis PULs. A model system using the Don (degradation of N-glycans) PUL showed that the donS sRNA negatively regulated Don expression at the transcriptional level, resulting in a decrease in N-glycan utilization. Additional studies performed with other Bacteroides species indicated that this regulatory mechanism is highly conserved and, interestingly, that the regulated PULs appear to be closely linked to the utilization of host-derived glycans rather than dietary plant polysaccharides. The findings described here demonstrate a global control mechanism underlying known PUL regulatory circuits and provide insight into regulation of Bacteroides physiology. IMPORTANCE: The human gut is colonized by a dense microbiota which is essential to the health and normal development of the host. A key to gut homeostasis is the preservation of a stable, diverse microbiota. Bacteroides is a dominant genus in the gut, and the ability of Bacteroides species to efficiently compete for a wide range of glycan energy sources is a crucial advantage for colonization. Glycan utilization is mediated by a large number of polysaccharide utilization loci (PULs) which are regulated by substrate induction. In this report, a novel family of antisense sRNAs is described whose members repress gene expression in a distinct subset of PULs. This repression downregulates PUL expression in the presence of energy sources that are more readily utilized such as glucose, thereby allowing efficient glycan utilization.