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Structure paper

TitleOuter membrane utilisomes mediate glycan uptake in gut Bacteroidetes.
Journal, issue, pagesNature, Vol. 618, Issue 7965, Page 583-589, Year 2023
Publish dateJun 7, 2023
AuthorsJoshua B R White / Augustinas Silale / Matthew Feasey / Tiaan Heunis / Yiling Zhu / Hong Zheng / Akshada Gajbhiye / Susan Firbank / Arnaud Baslé / Matthias Trost / David N Bolam / Bert van den Berg / Neil A Ranson /
PubMed AbstractBacteroidetes are abundant members of the human microbiota, utilizing a myriad of diet- and host-derived glycans in the distal gut. Glycan uptake across the bacterial outer membrane of these bacteria ...Bacteroidetes are abundant members of the human microbiota, utilizing a myriad of diet- and host-derived glycans in the distal gut. Glycan uptake across the bacterial outer membrane of these bacteria is mediated by SusCD protein complexes, comprising a membrane-embedded barrel and a lipoprotein lid, which is thought to open and close to facilitate substrate binding and transport. However, surface-exposed glycan-binding proteins and glycoside hydrolases also play critical roles in the capture, processing and transport of large glycan chains. The interactions between these components in the outer membrane are poorly understood, despite being crucial for nutrient acquisition by our colonic microbiota. Here we show that for both the levan and dextran utilization systems of Bacteroides thetaiotaomicron, the additional outer membrane components assemble on the core SusCD transporter, forming stable glycan-utilizing machines that we term utilisomes. Single-particle cryogenic electron microscopy structures in the absence and presence of substrate reveal concerted conformational changes that demonstrate the mechanism of substrate capture, and rationalize the role of each component in the utilisome.
External linksNature / PubMed:37286596
MethodsEM (single particle) / X-ray diffraction
Resolution2.3 - 3.5 Å
Structure data

15288

8a9y

EMDB-15288, PDB-8a9y:
Substrate-free levan utilisation machinery (utilisome)
Method: EM (single particle) / Resolution: 3.5 Å

15289

8aa0

EMDB-15289, PDB-8aa0:
Levan utilisation machinery (utilisome) with levan fructo-oligosaccharides DP 8-12
Method: EM (single particle) / Resolution: 3.2 Å

15290

8aa1

EMDB-15290, PDB-8aa1:
Core SusCD transporter units from the levan utilisome with levan fructo-oligosaccharides DP 8-12
Method: EM (single particle) / Resolution: 2.9 Å

15291

8aa2

EMDB-15291, PDB-8aa2:
Inactive levan utilisation machinery (utilisome) in the presence of levan fructo-oligosaccharides DP 15-25
Method: EM (single particle) / Resolution: 3.1 Å

15292

8aa3

EMDB-15292, PDB-8aa3:
Core SusCD transporter units from the inactive levan utilisome in the presence of levan fructo-oligosaccharides DP 15-25
Method: EM (single particle) / Resolution: 2.7 Å

15293

8aa4

EMDB-15293: Consensus reconstruction of the dextran utilisation system
PDB-8aa4: SusC components of the dextran utilisation system (utilisome)
Method: EM (single particle) / Resolution: 3.1 Å

PDB-7znr:
Inactive D62N mutant of BT1760 Endo-acting levanase from Bacteroides thetaiotaomicron VPI-5482
Method: X-RAY DIFFRACTION / Resolution: 2.65 Å

PDB-7zns:
Inactive D62N mutant of BT1760 Endo-acting levanase from Bacteroides thetaiotaomicron VPI-5482
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

Chemicals

ChemComp-SO4:
SULFATE ION / Sulfate

ChemComp-HOH:
WATER / Water

ChemComp-MG:
Unknown entry

Source
  • bacteroides thetaiotaomicron (bacteria)
  • bacteroides thetaiotaomicron vpi-5482 (bacteria)
  • bacteroides thetaiotaomicron (strain atcc 29148 / dsm 2079 / jcm 5827 / ccug 10774 / nctc 10582 / vpi-5482 / e50) (bacteria)
KeywordsHYDROLASE / Levan / fructan / endo levanase / gut microbiota / TRANSPORT PROTEIN / Membrane protein transporter / glycan transporter / SusCD / utilisome / TonB dependent transporter / TBDT / MEMBRANE PROTEIN

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