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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0353

PubMed

16968696, J Biol Chem. 2006 Nov 24;281(47):36269-79. doi: 10.1074/jbc.M606509200. Epub 2006 Sep 12.
32060313, Nat Commun. 2020 Feb 14;11(1):899. doi: 10.1038/s41467-020-14754-7.

Characterization method

microarray,enzyme activity assay,strcutural analysis,clone and expression

Genomic accession number

AE015928.1

Nucelotide position range

5185604-5202908

Substrate

arabinan,xylan,levan,pectin,rhamnogalacturonan

Loci

BT_3983-BT_3993

Species

Bacteroides thetaiotaomicron/818

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BT_3983 AAO79088.1 0 - 3408 (+) AE015928.1:5185604-5189012 -
- BT_3984 AAO79089.1 3424 - 5038 (+) AE015928.1:5189028-5190642 -
- BT_3985 AAO79090.1 5062 - 6139 (+) AE015928.1:5190666-5191743 -
- BT_3986 AAO79091.1 6147 - 7302 (+) AE015928.1:5191751-5192906 -
- BT_3987 AAO79092.1 7335 - 8766 (+) AE015928.1:5192939-5194370 -
- BT_3988 AAO79093.1 8796 - 10131 (+) AE015928.1:5194400-5195735 -
- BT_3989 AAO79094.1 10400 - 10835 (-) AE015928.1:5196004-5196439 -
- BT_3990 AAO79095.1 11029 - 13297 (-) AE015928.1:5196633-5198901 -
- BT_3991 AAO79096.1 13394 - 15671 (-) AE015928.1:5198998-5201275 -
- BT_3992 AAO79097.1 15702 - 16632 (-) AE015928.1:5201306-5202236 -
- BT_3993 AAO79098.1 16750 - 17305 (-) AE015928.1:5202354-5202909 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 3408 (+) TC: gnl|TC-DB|Q8A8X1|1.B.14.6.13 Yes
- 3425 - 5038 (+) TC: gnl|TC-DB|Q8A0N7|8.A.46.2.2 Yes
- 5063 - 6139 (+) CAZyme: GH0 Yes
- 6148 - 7302 (+) other Yes
- 7336 - 8766 (+) other Yes
- 8797 - 10131 (+) other Yes
- 10401 - 10835 (-) other Yes
- 11030 - 13297 (-) CAZyme: GH92 Yes
- 13395 - 15671 (-) CAZyme: GH92 Yes
- 15703 - 16632 (-) STP: STP|FecR No
- 16751 - 17305 (-) TF: DBD-Pfam|GerE No

PUL ID

PUL0353

PubMed

16968696, J Biol Chem. 2006 Nov 24;281(47):36269-79. doi: 10.1074/jbc.M606509200. Epub 2006 Sep 12.

Title

Functional genomic and metabolic studies of the adaptations of a prominent adult human gut symbiont, Bacteroides thetaiotaomicron, to the suckling period.

Author

Bjursell MK, Martens EC, Gordon JI

Abstract

The adult human gut microbiota is dominated by two divisions of Bacteria, the Bacteroidetes and the Firmicutes. Assembly of this community begins at birth through processes that remain largely undefined. In this report, we examine the adaptations of Bacteroides thetaiotaomicron, a prominent member of the adult distal intestinal microbiota, during the suckling and weaning periods. Germ-free NMRI mice were colonized at birth from their gnotobiotic mothers, who harbored this anaerobic Gram-negative saccharolytic bacterium. B. thetaiotaomicron was then harvested from the ceca of these hosts during the suckling period (postnatal day 17) and after weaning (postnatal day 30). Whole genome transcriptional profiles were obtained at these two time points using custom B. thetaiotaomicron GeneChips. Transcriptome-based in silico reconstructions of bacterial metabolism and gas chromatography-mass spectrometry and biochemical assays of carbohydrate utilization in vivo indicated that in the suckling gut B. thetaiotaomicron prefers host-derived polysaccharides, as well as mono- and oligosaccharides present in mother's milk. After weaning, B. thetaiotaomicron expands its metabolism to exploit abundant, plant-derived dietary polysaccharides. The bacterium's responses to postnatal alterations in its nutrient landscape involve expression of gene clusters encoding environmental sensors, outer membrane proteins involved in binding and import of glycans, and glycoside hydrolases. These expression changes are interpreted in light of a phylogenetic analysis that revealed unique expansions of related polysaccharide utilization loci in three human alimentary tract-associated Bacteroidetes, expansions that likely reflect the evolutionary adaptations of these species to different nutrient niches.

PubMed

32060313, Nat Commun. 2020 Feb 14;11(1):899. doi: 10.1038/s41467-020-14754-7.

Title

Structural basis of mammalian high-mannose N-glycan processing by human gut Bacteroides.

Author

Trastoy B, Du JJ, Klontz EH, Li C, Cifuente JO, Wang LX, Sundberg EJ, Guerin ME

Abstract

The human gut microbiota plays a central role not only in regulating the metabolism of nutrients but also promoting immune homeostasis, immune responses and protection against pathogen colonization. The genome of the Gram-negative symbiont Bacteroides thetaiotaomicron, a dominant member of the human intestinal microbiota, encodes polysaccharide utilization loci PULs, the apparatus required to orchestrate the degradation of a specific glycan. EndoBT-3987 is a key endo-beta-N-acetylglucosaminidase (ENGase) that initiates the degradation/processing of mammalian high-mannose-type (HM-type) N-glycans in the intestine. Here, we provide structural snapshots of EndoBT-3987, including the unliganded form, the EndoBT-3987-Man(9)GlcNAc(2)Asn substrate complex, and two EndoBT-3987-Man(9)GlcNAc and EndoBT-3987-Man(5)GlcNAc product complexes. In combination with alanine scanning mutagenesis and activity measurements we unveil the molecular mechanism of HM-type recognition and specificity for EndoBT-3987 and an important group of the GH18 ENGases, including EndoH, an enzyme extensively used in biotechnology, and for which the mechanism of substrate recognition was largely unknown.