Peptide transport in Bacillus subtilis – structure and specificity in the extracellular solute binding proteins OppA and DppE

TY - JOUR

T1 - Peptide transport in Bacillus subtilis – structure and specificity in the extracellular solute binding proteins OppA and DppE

AU - Hughes, Adam M.

AU - Darby, John F.

AU - Dodson, Eleanor J.

AU - Wilson, Samuel J.

AU - Turkenburg, Johan P.

AU - Thomas, Gavin H.

AU - Wilkinson, Anthony J.

N1 - Funding Information: This project was funded by the Biotechnology and Biological Sciences Research Council, UK, through a White Rose DTP Studentship to A.M.H. Acknowledgements We thank the Diamond Light Source for access to beamlines i02, i03 and i04 (proposal numbers mx-9948 and mx-13587) that contributed to the results presented here. Funding Information: This project was funded by the Biotechnology and Biological Sciences Research Council, UK, through a White Rose DTP Studentship to A.M.H. Publisher Copyright: © 2022 The Authors.

PY - 2022/12/1

Y1 - 2022/12/1

N2 - Peptide transporters play important nutritional and cell signalling roles in Bacillus subtilis, which are pronounced during stationary phase adaptations and development. Three high-affinity ATP-binding cassette (ABC) family transporters are involved in peptide uptake – the oligopeptide permease (Opp), another peptide permease (App) and a less well-characterized dipeptide permease (Dpp). Here we report crystal structures of the extracellular substrate binding proteins, OppA and DppE, which serve the Opp and Dpp systems, respectively. The structure of OppA was determined in complex with endogenous peptides, mod-elled as Ser-Asn-Ser-Ser, and with the sporulation-promoting peptide Ser-Arg-Asn-Val-Thr, which bind with Kd values of 0.4 and 2 µM, respectively, as measured by isothermal titration calorimetry. Differential scanning fluorescence experiments with a wider panel of ligands showed that OppA has highest affinity for tetra-and penta-peptides. The structure of DppE revealed the unexpected presence of a murein tripeptide (MTP) ligand, l-Ala-d-Glu-meso-DAP, in the peptide binding groove. The mode of MTP binding in DppE is different to that observed in the murein peptide binding protein, MppA, from Escherichia coli, suggesting independent evolution of these proteins from an OppA-like precursor. The presence of MTP in DppE points to a role for Dpp in the uptake and recycling of cell wall peptides, a conclusion that is supported by analysis of the genomic context of dpp, which revealed adjacent genes encoding enzymes involved in muropeptide catabolism in a gene organization that is widely conserved in Firmicutes.

AB - Peptide transporters play important nutritional and cell signalling roles in Bacillus subtilis, which are pronounced during stationary phase adaptations and development. Three high-affinity ATP-binding cassette (ABC) family transporters are involved in peptide uptake – the oligopeptide permease (Opp), another peptide permease (App) and a less well-characterized dipeptide permease (Dpp). Here we report crystal structures of the extracellular substrate binding proteins, OppA and DppE, which serve the Opp and Dpp systems, respectively. The structure of OppA was determined in complex with endogenous peptides, mod-elled as Ser-Asn-Ser-Ser, and with the sporulation-promoting peptide Ser-Arg-Asn-Val-Thr, which bind with Kd values of 0.4 and 2 µM, respectively, as measured by isothermal titration calorimetry. Differential scanning fluorescence experiments with a wider panel of ligands showed that OppA has highest affinity for tetra-and penta-peptides. The structure of DppE revealed the unexpected presence of a murein tripeptide (MTP) ligand, l-Ala-d-Glu-meso-DAP, in the peptide binding groove. The mode of MTP binding in DppE is different to that observed in the murein peptide binding protein, MppA, from Escherichia coli, suggesting independent evolution of these proteins from an OppA-like precursor. The presence of MTP in DppE points to a role for Dpp in the uptake and recycling of cell wall peptides, a conclusion that is supported by analysis of the genomic context of dpp, which revealed adjacent genes encoding enzymes involved in muropeptide catabolism in a gene organization that is widely conserved in Firmicutes.

KW - Bacillus subtilis

KW - DppE

KW - murein peptide

KW - OppA

KW - peptide transport

KW - sporulation

UR - http://www.scopus.com/inward/record.url?scp=85143275991&partnerID=8YFLogxK

U2 - 10.1099/mic.0.001274

DO - 10.1099/mic.0.001274

M3 - Article

AN - SCOPUS:85143275991

SN - 1350-0872

VL - 168

JO - Microbiology (United Kingdom)

JF - Microbiology (United Kingdom)

IS - 12

M1 - 001274

ER -