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Volume 168, Issue 12

Peptide transport in structure and specificity in the extracellular solute binding proteins OppA and DppE Open Access

Abstract

Peptide transporters play important nutritional and cell signalling roles in 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, modelled as Ser-Asn-Ser-Ser, and with the sporulation-promoting peptide Ser-Arg-Asn-Val-Thr, which bind with 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, -Ala--Glu--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 , 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 , which revealed adjacent genes encoding enzymes involved in muropeptide catabolism in a gene organization that is widely conserved in .

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  • Accepted:
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Keyword(s): Bacillus subtilis , DppE , murein peptide , OppA , peptide transport and sporulation
Funding
This study was supported by the:
  • Biotechnology and Biological Sciences Research Council (Award White Rose DTP Studentship)
    • Principle Award Recipient: AdamM Hughes
© 2022 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2022-12-01
2024-04-19
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References

  1. Hoch JA. Regulation of the phosphorelay and the initiation of sporulation in Bacillus subtilis. Annu Rev Microbiol 1993; 47:441–465 [View Article] [PubMed]
     [Google Scholar]
  2. Muchová K, Lewis RJ, Perecko D, Brannigan JA, Ladds JC et al. Dimer-induced signal propagation in Spo0A. Mol Microbiol 2004; 53:829–842 [View Article] [PubMed]
     [Google Scholar]
  3. Molle V, Fujita M, Jensen ST, Eichenberger P, González-Pastor JE et al. The Spo0A regulon of Bacillus subtilis. Mol Microbiol 2003; 50:1683–1701 [View Article] [PubMed]
     [Google Scholar]
  4. Burbulys D, Trach KA, Hoch JA. Initiation of sporulation in B. subtilis is controlled by a multicomponent phosphorelay. Cell 1991; 64:545–552 [View Article] [PubMed]
     [Google Scholar]
  5. Jiang M, Shao W, Perego M, Hoch JA. Multiple histidine kinases regulate entry into stationary phase and sporulation in Bacillus subtilis. Mol Microbiol 2000; 38:535–542 [View Article] [PubMed]
     [Google Scholar]
  6. Perego M, Hanstein C, Welsh KM, Djavakhishvili T, Glaser P et al. Multiple protein-aspartate phosphatases provide a mechanism for the integration of diverse signals in the control of development in B. subtilis. Cell 1994; 79:1047–1055 [View Article] [PubMed]
     [Google Scholar]
  7. Ohlsen KL, Grimsley JK, Hoch JA. Deactivation of the sporulation transcription factor Spo0A by the Spo0E protein phosphatase. Proc Natl Acad Sci U S A 1994; 91:1756–1760 [View Article] [PubMed]
     [Google Scholar]
  8. Wu R, Gu M, Wilton R, Babnigg G, Kim Y et al. Insight into the sporulation phosphorelay: crystal structure of the sensor domain of Bacillus subtilis histidine kinase, KinD. Protein Sci 2013; 22:564–576 [View Article] [PubMed]
     [Google Scholar]
  9. Piggot PJ, Coote JG. Genetic aspects of bacterial endospore formation. Bacteriol Rev 1976; 40:908–962 [View Article] [PubMed]
     [Google Scholar]
  10. Rudner DZ, LeDeaux JR, Ireton K, Grossman AD. The spo0K locus of Bacillus subtilis is homologous to the oligopeptide permease locus and is required for sporulation and competence. J Bacteriol 1991; 173:1388–1398 [View Article] [PubMed]
     [Google Scholar]
  11. Perego M, Higgins CF, Pearce SR, Gallagher MP, Hoch JA. The oligopeptide transport system of Bacillus subtilis plays a role in the initiation of sporulation. Mol Microbiol 1991; 5:173–185 [View Article] [PubMed]
     [Google Scholar]
  12. Perego M, Hoch JA. Cell-cell communication regulates the effects of protein aspartate phosphatases on the phosphorelay controlling development in Bacillus subtilis. Proc Natl Acad Sci U S A 1996; 93:1549–1553 [View Article] [PubMed]
     [Google Scholar]
  13. Perego M. A peptide export-import control circuit modulating bacterial development regulates protein phosphatases of the phosphorelay. Proc Natl Acad Sci U S A 1997; 94:8612–8617 [View Article] [PubMed]
     [Google Scholar]
  14. Perego M, Brannigan JA. Pentapeptide regulation of aspartyl-phosphate phosphatases. Peptides 2001; 22:1541–1547 [View Article] [PubMed]
     [Google Scholar]
  15. Maqbool A, Horler RSP, Muller A, Wilkinson AJ, Wilson KS et al. The substrate-binding protein in bacterial ABC transporters: dissecting roles in the evolution of substrate specificity. Biochem Soc Trans 2015; 43:1011–1017 [View Article] [PubMed]
     [Google Scholar]
  16. Berntsson RP-A, Smits SHJ, Schmitt L, Slotboom D-J, Poolman B. A structural classification of substrate-binding proteins. FEBS Lett 2010; 584:2606–2617 [View Article] [PubMed]
     [Google Scholar]
  17. Koide A, Hoch JA. Identification of a second oligopeptide transport system in Bacillus subtilis and determination of its role in sporulation. Mol Microbiol 1994; 13:417–426 [View Article] [PubMed]
     [Google Scholar]
  18. Picon A, van Wely KHM. Peptide binding to the Bacillus subtilis oligopeptide-binding proteins OppA and AppA. Molecular Biology Today 2001; 2:21–25
     [Google Scholar]
  19. Levdikov VM, Blagova EV, Brannigan JA, Wright L, Vagin AA et al. The structure of the oligopeptide-binding protein, AppA, from Bacillus subtilis in complex with a nonapeptide. J Mol Biol 2005; 345:879–892 [View Article] [PubMed]
     [Google Scholar]
  20. Mathiopoulos C, Mueller JP, Slack FJ, Murphy CG, Patankar S et al. A Bacillus subtilis dipeptide transport system expressed early during sporulation. Mol Microbiol 1991; 5:1903–1913 [View Article] [PubMed]
     [Google Scholar]
  21. Levdikov VM, Blagova E, Young VL, Belitsky BR, Lebedev A et al. Structure of the branched-chain amino acid and GTP-sensing global regulator, CodY, from Bacillus subtilis. J Biol Chem 2017; 292:2714–2728 [View Article] [PubMed]
     [Google Scholar]
  22. Molle V, Nakaura Y, Shivers RP, Yamaguchi H, Losick R et al. Additional targets of the Bacillus subtilis global regulator CodY identified by chromatin immunoprecipitation and genome-wide transcript analysis. J Bacteriol 2003; 185:1911–1922 [View Article] [PubMed]
     [Google Scholar]
  23. Brinsmade SR, Alexander EL, Livny J, Stettner AI, Segrè D et al. Hierarchical expression of genes controlled by the Bacillus subtilis global regulatory protein CodY. Proc Natl Acad Sci U S A 2014; 111:8227–8232 [View Article] [PubMed]
     [Google Scholar]
  24. Slack FJ, Serror P, Joyce E, Sonenshein AL. A gene required for nutritional repression of the Bacillus subtilis dipeptide permease operon. Mol Microbiol 1995; 15:689–702 [View Article] [PubMed]
     [Google Scholar]
  25. Tame JR, Murshudov GN, Dodson EJ, Neil TK, Dodson GG et al. The structural basis of sequence-independent peptide binding by OppA protein. Science 1994; 264:1578–1581 [View Article] [PubMed]
     [Google Scholar]
  26. Fogg MJ, Wilkinson AJ. Higher-throughput approaches to crystallization and crystal structure determination. Biochem Soc Trans 2008; 36:771–775 [View Article] [PubMed]
     [Google Scholar]
  27. Hughes A, Wilson S, Dodson EJ, Turkenburg JP, Wilkinson AJ. Crystal structure of the putative peptide-binding protein AppA from Clostridium difficile. Acta Crystallogr F Struct Biol Commun 2019; 75:246–253 [View Article] [PubMed]
     [Google Scholar]
  28. Emsley P, Lohkamp B, Scott WG, Cowtan K. Features and development of Coot. Acta Crystallogr D Biol Crystallogr 2010; 66:486–501 [View Article] [PubMed]
     [Google Scholar]
  29. Murshudov GN, Skubák P, Lebedev AA, Pannu NS, Steiner RA et al. REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr 2011; 67:355–367 [View Article] [PubMed]
     [Google Scholar]
  30. Winter G, Lobley CMC, Prince SM. Decision making in xia2. Acta Crystallogr D Biol Crystallogr 2013; 69:1260–1273 [View Article] [PubMed]
     [Google Scholar]
  31. McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC et al. Phaser crystallographic software. J Appl Crystallogr 2007; 40:658–674 [View Article] [PubMed]
     [Google Scholar]
  32. Cowtan K. The Buccaneer software for automated model building. 1. Tracing protein chains. Acta Crystallogr D Biol Crystallogr 2006; 62:1002–1011 [View Article] [PubMed]
     [Google Scholar]
  33. Berntsson RP-A, Schuurman-Wolters GK, Dunny G, Slotboom D-J, Poolman B. Structure and mode of peptide binding of pheromone receptor PrgZ. J Biol Chem 2012; 287:37165–37170 [View Article] [PubMed]
     [Google Scholar]
  34. Emsley P, Lohkamp B, Scott WG, Cowtan K. Features and development of Coot. Acta Crystallogr D Biol Crystallogr 2010; 66:486–501 [View Article] [PubMed]
     [Google Scholar]
  35. Evans P. Scaling and assessment of data quality. Acta Crystallogr D Biol Crystallogr 2006; 62:72–82 [View Article] [PubMed]
     [Google Scholar]
  36. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res 2014; 42:D206–14 [View Article] [PubMed]
     [Google Scholar]
  37. Niesen FH, Berglund H, Vedadi M. The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability. Nat Protoc 2007; 2:2212–2221 [View Article] [PubMed]
     [Google Scholar]
  38. Sleigh SH, Seavers PR, Wilkinson AJ, Ladbury JE, Tame JR. Crystallographic and calorimetric analysis of peptide binding to OppA protein. J Mol Biol 1999; 291:393–415 [View Article] [PubMed]
     [Google Scholar]
  39. Müller A, Thomas GH, Horler R, Brannigan JA, Blagova E et al. An ATP-binding cassette-type cysteine transporter in Campylobacter jejuni inferred from the structure of an extracytoplasmic solute receptor protein. Mol Microbiol 2005; 57:143–155 [View Article] [PubMed]
     [Google Scholar]
  40. Maqbool A, Levdikov VM, Blagova EV, Hervé M, Horler RSP et al. Compensating stereochemical changes allow murein tripeptide to be accommodated in a conventional peptide-binding protein. J Biol Chem 2011; 286:31512–31521 [View Article] [PubMed]
     [Google Scholar]
  41. Mao B, Pear MR, McCammon JA, Quiocho FA. Hinge-bending in L-arabinose-binding protein. The “Venus’s-flytrap” model. J Biol Chem 1982; 257:1131–1133
     [Google Scholar]
  42. Maqbool A, Hervé M, Mengin-Lecreulx D, Wilkinson AJ, Thomas GH. MpaA is a murein-tripeptide-specific zinc carboxypeptidase that functions as part of a catabolic pathway for peptidoglycan-derived peptides in γ-proteobacteria. Biochem J 2012; 448:329–341 [View Article] [PubMed]
     [Google Scholar]
  43. Schmidt DM, Hubbard BK, Gerlt JA. Evolution of enzymatic activities in the enolase superfamily: functional assignment of unknown proteins in Bacillus subtilis and Escherichia coli as L-Ala-D/L-Glu epimerases. Biochemistry 2001; 40:15707–15715 [View Article] [PubMed]
     [Google Scholar]
  44. Cheggour A, Fanuel L, Duez C, Joris B, Bouillenne F et al. The dppA gene of Bacillus subtilis encodes a new D-aminopeptidase. Mol Microbiol 2000; 38:504–513 [View Article] [PubMed]
     [Google Scholar]
  45. Remaut H, Bompard-Gilles C, Goffin C, Frère JM, Van Beeumen J. Structure of the Bacillus subtilis D-aminopeptidase DppA reveals a novel self-compartmentalizing protease. Nat Struct Biol 2001; 8:674–678 [View Article] [PubMed]
     [Google Scholar]
  46. Slamti L, Lereclus D. The oligopeptide ABC-importers are essential communication channels in Gram-positive bacteria. Res Microbiol 2019; 170:338–344 [View Article] [PubMed]
     [Google Scholar]
  47. Perego M, Higgins CF, Pearce SR, Gallagher MP, Hoch JA. The oligopeptide transport system of Bacillus subtilis plays a role in the initiation of sporulation. Mol Microbiol 1991; 5:173–185 [View Article] [PubMed]
     [Google Scholar]
  48. Auchtung JM, Lee CA, Monson RE, Lehman AP, Grossman AD. Regulation of a Bacillus subtilis mobile genetic element by intercellular signaling and the global DNA damage response. Proc Natl Acad Sci U S A 2005; 102:12554–12559 [View Article] [PubMed]
     [Google Scholar]
  49. Erez Z, Steinberger-Levy I, Shamir M, Doron S, Stokar-Avihail A et al. Communication between viruses guides lysis-lysogeny decisions. Nature 2017; 541:488–493 [View Article] [PubMed]
     [Google Scholar]
  50. Leonard BA, Podbielski A, Hedberg PJ, Dunny GM. Enterococcus faecalis pheromone binding protein, PrgZ, recruits a chromosomal oligopeptide permease system to import sex pheromone cCF10 for induction of conjugation. Proc Natl Acad Sci U S A 1996; 93:260–264 [View Article] [PubMed]
     [Google Scholar]
  51. Gominet M, Slamti L, Gilois N, Rose M, Lereclus D. Oligopeptide permease is required for expression of the Bacillus thuringiensis plcR regulon and for virulence. Mol Microbiol 2001; 40:963–975 [View Article] [PubMed]
     [Google Scholar]
  52. Krypotou E, Scortti M, Grundström C, Oelker M, Luisi BF. Control of bacterial virulence through the peptide signature of the habitat. Cell Rep 2019; 26:1815–1827 [View Article]
     [Google Scholar]
  53. Berntsson RP-A, Thunnissen A-MWH, Poolman B, Slotboom D-J. Importance of a hydrophobic pocket for peptide binding in lactococcal OppA. J Bacteriol 2011; 193:4254–4256 [View Article] [PubMed]
     [Google Scholar]
  54. Dunten P, Mowbray SL. Crystal structure of the dipeptide binding protein from Escherichia coli involved in active transport and chemotaxis. Protein Sci 1995; 4:2327–2334 [View Article] [PubMed]
     [Google Scholar]
  55. Nicolas P, Mäder U, Dervyn E, Rochat T, Leduc A et al. Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis. Science 2012; 335:1103–1106 [View Article] [PubMed]
     [Google Scholar]
  56. Chan H, Taib N, Gilmore MC, Mohamed AMT, Hanna K et al. Genetic screens identify additional genes implicated in envelope remodeling during the engulfment stage of Bacillus subtilis sporulation. mBio 2022; 13:e0173222 [View Article] [PubMed]
     [Google Scholar]
  57. Park JT. Why does Escherichia coli recycle its cell wall peptides?. Mol Microbiol 1995; 17:421–426 [View Article] [PubMed]
     [Google Scholar]
  58. Mauck J, Chan L, Glaser L. Turnover of the cell wall of Gram-positive bacteria. J Biol Chem 1971; 246:1820–1827 [View Article] [PubMed]
     [Google Scholar]
  59. Litzinger S, Duckworth A, Nitzsche K, Risinger C, Wittmann V et al. Muropeptide rescue in Bacillus subtilis involves sequential hydrolysis by beta-N-acetylglucosaminidase and N-acetylmuramyl-L-alanine amidase. J Bacteriol 2010; 192:3132–3143 [View Article] [PubMed]
     [Google Scholar]
  60. Borisova M, Gaupp R, Duckworth A, Schneider A, Dalügge D et al. Peptidoglycan recycling in Gram-positive bacteria is crucial for survival in stationary phase. mBio 2016; 7:e00923-16 [View Article] [PubMed]
     [Google Scholar]
  61. McNicholas S, Potterton E, Wilson KS, Noble MEM. Presenting your structures: the CCP4mg molecular-graphics software. Acta Crystallogr D Biol Crystallogr 2011; 67:386–394 [View Article] [PubMed]
     [Google Scholar]
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Peptide transport in Bacillus subtilis – structure and specificity in the extracellular solute binding proteins OppA and DppE
Microbiology 168, 001274 (2022); https://doi.org/10.1099/mic.0.001274
/content/journal/micro/10.1099/mic.0.001274
/content/journal/micro/10.1099/mic.0.001274
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