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Combining Yeast Display and Bacterial Genomic Library for the Unbiased Isolation of Novel Polysaccharide-Binding Peptides.

Λεπτομέρειες βιβλιογραφικής εγγραφής
Τίτλος: Combining Yeast Display and Bacterial Genomic Library for the Unbiased Isolation of Novel Polysaccharide-Binding Peptides.
Συγγραφείς: Stabile A; Department of Life Sciences, University of Trieste, Via L. Giorgieri 5, 34127 Trieste, Italy., Scaramella G; Department of Life Sciences, University of Trieste, Via L. Giorgieri 5, 34127 Trieste, Italy., Puccio S; Laboratory of Translational Immunology, Istituto di Ricovero e Cura a Carattere Scientifico Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Italy.; Institute of Genetic and Biomedical Research, National Research Council, Via Manzoni 113, 20089 Rozzano, Italy., Brady J; Food Science Department, Cornell University, 101A Stocking Hall, Ithaca, NY 14853, USA., Goltermann L; Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark., Tolker-Nielsen T; Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark., Bellich B; Institute for Maternal and Child Health, Istituto di Ricovero e Cura a Carattere Scientifico 'Burlo Garofolo', Via dell'Istria 65/1, 34137 Trieste, Italy., De Zotti S; Department of Life Sciences, University of Trieste, Via L. Giorgieri 5, 34127 Trieste, Italy., Lagatolla C; Department of Life Sciences, University of Trieste, Via L. Giorgieri 5, 34127 Trieste, Italy., Ferrara F; Specifica Inc., an IQVIA Laboratories Company, Santa Fe, NM 87501, USA., Rizzo R; Department of Life Sciences, University of Trieste, Via L. Giorgieri 5, 34127 Trieste, Italy., Cescutti P; Department of Life Sciences, University of Trieste, Via L. Giorgieri 5, 34127 Trieste, Italy., Sblattero D; Department of Life Sciences, University of Trieste, Via L. Giorgieri 5, 34127 Trieste, Italy.
Πηγή: International journal of molecular sciences [Int J Mol Sci] 2026 Mar 06; Vol. 27 (5). Date of Electronic Publication: 2026 Mar 06.
Τύπος έκδοσης: Journal Article
Γλώσσα: English
Στοιχεία περιοδικού: Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067 (Electronic) Linking ISSN: 14220067 NLM ISO Abbreviation: Int J Mol Sci Subsets: MEDLINE
Imprint Name(s): Original Publication: Basel, Switzerland : MDPI, [2000-
Ιατρικοί όροι (MeSH): Peptides*/metabolism , Peptides*/chemistry , Peptides*/isolation & purification , Peptides*/genetics , Peptides*/pharmacology , Burkholderia*/genetics , Burkholderia*/metabolism , Polysaccharides*/metabolism , Saccharomyces cerevisiae*/genetics , Saccharomyces cerevisiae*/metabolism , Genomic Library* , Genome, Bacterial*, Biofilms/drug effects ; Biofilms/growth & development ; Protein Binding ; Cell Surface Display Techniques ; Peptide Library
Περίληψη: Here, we present a novel yeast surface display-based platform for the discovery of biofilm-associated exopolysaccharide-binding peptides. Unlike conventional synthetic libraries, our approach utilizes the genomic diversity of Burkholderia multivorans strain C1576 through open-reading frame-filtered genomic fragment libraries, thereby enriching for naturally encoded carbohydrate-binding domains. By iterative fluorescence-activated cell sorting, we identified 21 peptides with confirmed binding to two structurally distinct rhamnose-rich polysaccharides: the exopolysaccharide Epol C1576 and the capsular polysaccharide CPS KpB-1. Biophysical characterization revealed that these peptides adopt predominantly α-helical or disordered conformations and undergo structural rearrangements upon polysaccharide binding. Functional assays demonstrated that selected peptides modulate biofilm architecture and bacterial viability in a species-specific manner, although they do not have a direct bactericidal effect against planktonic cells. This proof-of-concept study establishes yeast surface display as a powerful tool for the discovery of biofilm-targeting peptides and provides a basis for development of novel diagnostics and therapeutics to combat biofilm-associated infections.
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Antimicrob Agents Chemother. 2014 Aug;58(8):4399-403. (PMID: 24841267)
Mol Biotechnol. 2025 Jun;67(6):2161-2184. (PMID: 38822912)
Int J Biol Macromol. 2024 Nov;281(Pt 2):136222. (PMID: 39362422)
Cell Rep Phys Sci. 2024 Mar 20;5(3):. (PMID: 38605913)
Nucleic Acids Res. 2016 Jan 4;44(D1):D1087-93. (PMID: 26602694)
Appl Environ Microbiol. 2013 Aug;79(15):4551-63. (PMID: 23686272)
NPJ Biofilms Microbiomes. 2025 Dec 6;12(1):3. (PMID: 41353267)
Biofouling. 2003 Apr;19(2):139-50. (PMID: 14618698)
Biochem Biophys Res Commun. 1998 Mar 6;244(1):253-7. (PMID: 9514864)
Microbiol Spectr. 2015 Jun;3(3):. (PMID: 26185074)
Microbiol Spectr. 2015 Apr;3(2):. (PMID: 26104709)
Anal Biochem. 2006 Jul 1;354(1):54-63. (PMID: 16713984)
Nucleic Acids Res. 2014 Jan;42(Database issue):D490-5. (PMID: 24270786)
Nucleic Acids Res. 2021 Jan 8;49(D1):D288-D297. (PMID: 33151284)
Carbohydr Res. 2015 Jun 26;411:42-8. (PMID: 25974852)
Amino Acids. 2017 Oct;49(10):1755-1771. (PMID: 28756544)
Acta Crystallogr D Biol Crystallogr. 2014 Oct;70(Pt 10):2583-92. (PMID: 25286843)
Genome Res. 2010 Nov;20(11):1605-12. (PMID: 20841432)
J Immunol Methods. 2004 Jul;290(1-2):69-80. (PMID: 15261572)
J Vis Exp. 2018 Oct 3;(140):. (PMID: 30346377)
Expert Opin Drug Discov. 2024 Aug;19(8):887-915. (PMID: 39074492)
Nat Commun. 2019 May 16;10(1):2183. (PMID: 31097723)
Viruses. 2023 Sep 09;15(9):. (PMID: 37766309)
ISME J. 2019 Jan;13(1):104-117. (PMID: 30116044)
Int J Biol Macromol. 2020 Jul 15;155:315-323. (PMID: 32224183)
Nucleic Acids Res. 2020 Jul 2;48(W1):W200-W207. (PMID: 32402076)
Nucleic Acids Res. 2025 Jan 6;53(D1):D403-D410. (PMID: 39526377)
Curr Opin Microbiol. 2016 Oct;33:35-40. (PMID: 27318321)
Chem Rev. 1997 Apr 1;97(2):391-410. (PMID: 11848876)
FEMS Microbiol Rev. 2022 Mar 3;46(2):. (PMID: 34673942)
Antimicrob Agents Chemother. 1988 Apr;32(4):518-23. (PMID: 3132093)
Nature. 2024 Jun;630(8016):493-500. (PMID: 38718835)
Trends Microbiol. 2005 Jan;13(1):20-6. (PMID: 15639628)
Microbiology (Reading). 2001 Jan;147(Pt 1):3-9. (PMID: 11160795)
Front Immunol. 2012 Aug 14;3:249. (PMID: 22912635)
Front Microbiol. 2019 May 03;10:913. (PMID: 31130925)
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Nucleic Acids Res. 2010 May;38(9):e110. (PMID: 20144949)
J Appl Microbiol. 2022 Mar;132(3):1573-1596. (PMID: 34606679)
BMC Genomics. 2011 Jun 15;12 Suppl 1:S5. (PMID: 21810207)
J Pept Sci. 2009 Sep;15(9):595-600. (PMID: 19466693)
Appl Environ Microbiol. 2003 Mar;69(3):1408-16. (PMID: 12620823)
Adv Microb Physiol. 2019;74:97-141. (PMID: 31126537)
J Clin Microbiol. 2000 Feb;38(2):910-3. (PMID: 10655415)
Commun Biol. 2023 Apr 5;6(1):371. (PMID: 37019943)
Nucleic Acids Res. 2025 Jan 6;53(D1):D444-D456. (PMID: 39565202)
Nat Commun. 2025 Jun 25;16(1):5367. (PMID: 40562762)
Nucleic Acids Res. 2024 Jul 5;52(W1):W176-W181. (PMID: 38747347)
Grant Information: R01 GM123283 United States GM NIGMS NIH HHS; GM123283 NIH Common Fund; NNF22OC0080132 Novo Nordisk Foundation
Contributed Indexing: Keywords: antibiofilm peptides; biofilm; polysaccharides; yeast display
Substance Nomenclature: 0 (Peptides)
0 (Polysaccharides)
0 (Peptide Library)
Entry Date(s): Date Created: 20260314 Date Completed: 20260710 Latest Revision: 20260921
Update Code: 20260921
PubMed Central ID: PMC12986056
DOI: 10.3390/ijms27052417
PMID: 41828634
Βάση Δεδομένων: MEDLINE
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  Data: Combining Yeast Display and Bacterial Genomic Library for the Unbiased Isolation of Novel Polysaccharide-Binding Peptides.
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  Data: <searchLink fieldCode="AU" term="%22Stabile+A%22">Stabile A</searchLink>; Department of Life Sciences, University of Trieste, Via L. Giorgieri 5, 34127 Trieste, Italy.<br /><searchLink fieldCode="AU" term="%22Scaramella+G%22">Scaramella G</searchLink>; Department of Life Sciences, University of Trieste, Via L. Giorgieri 5, 34127 Trieste, Italy.<br /><searchLink fieldCode="AU" term="%22Puccio+S%22">Puccio S</searchLink>; Laboratory of Translational Immunology, Istituto di Ricovero e Cura a Carattere Scientifico Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Italy.; Institute of Genetic and Biomedical Research, National Research Council, Via Manzoni 113, 20089 Rozzano, Italy.<br /><searchLink fieldCode="AU" term="%22Brady+J%22">Brady J</searchLink>; Food Science Department, Cornell University, 101A Stocking Hall, Ithaca, NY 14853, USA.<br /><searchLink fieldCode="AU" term="%22Goltermann+L%22">Goltermann L</searchLink>; Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark.<br /><searchLink fieldCode="AU" term="%22Tolker-Nielsen+T%22">Tolker-Nielsen T</searchLink>; Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark.<br /><searchLink fieldCode="AU" term="%22Bellich+B%22">Bellich B</searchLink>; Institute for Maternal and Child Health, Istituto di Ricovero e Cura a Carattere Scientifico 'Burlo Garofolo', Via dell'Istria 65/1, 34137 Trieste, Italy.<br /><searchLink fieldCode="AU" term="%22De+Zotti+S%22">De Zotti S</searchLink>; Department of Life Sciences, University of Trieste, Via L. Giorgieri 5, 34127 Trieste, Italy.<br /><searchLink fieldCode="AU" term="%22Lagatolla+C%22">Lagatolla C</searchLink>; Department of Life Sciences, University of Trieste, Via L. Giorgieri 5, 34127 Trieste, Italy.<br /><searchLink fieldCode="AU" term="%22Ferrara+F%22">Ferrara F</searchLink>; Specifica Inc., an IQVIA Laboratories Company, Santa Fe, NM 87501, USA.<br /><searchLink fieldCode="AU" term="%22Rizzo+R%22">Rizzo R</searchLink>; Department of Life Sciences, University of Trieste, Via L. Giorgieri 5, 34127 Trieste, Italy.<br /><searchLink fieldCode="AU" term="%22Cescutti+P%22">Cescutti P</searchLink>; Department of Life Sciences, University of Trieste, Via L. Giorgieri 5, 34127 Trieste, Italy.<br /><searchLink fieldCode="AU" term="%22Sblattero+D%22">Sblattero D</searchLink>; Department of Life Sciences, University of Trieste, Via L. Giorgieri 5, 34127 Trieste, Italy.
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  Data: <searchLink fieldCode="JN" term="%22101092791%22">International journal of molecular sciences</searchLink> [Int J Mol Sci] 2026 Mar 06; Vol. 27 (5). <i>Date of Electronic Publication: </i>2026 Mar 06.
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  Data: <i>Publisher: </i><searchLink fieldCode="PB" term="%22MDPI%22">MDPI </searchLink><i>Country of Publication: </i>Switzerland <i>NLM ID: </i>101092791 <i>Publication Model: </i>Electronic <i>Cited Medium: </i>Internet <i>ISSN: </i>1422-0067 (Electronic) <i>Linking ISSN: </i><searchLink fieldCode="IS" term="%2214220067%22">14220067 </searchLink><i>NLM ISO Abbreviation: </i>Int J Mol Sci <i>Subsets: </i>MEDLINE
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  Data: <i>Original Publication</i>: Basel, Switzerland : MDPI, [2000-
– Name: SubjectMESH
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  Data: <searchLink fieldCode="MM" term="%22Peptides%22">Peptides*</searchLink>/<searchLink fieldCode="MM" term="%22Peptides+metabolism%22">metabolism</searchLink> <br /><searchLink fieldCode="MM" term="%22Peptides%22">Peptides*</searchLink>/<searchLink fieldCode="MM" term="%22Peptides+chemistry%22">chemistry</searchLink> <br /><searchLink fieldCode="MM" term="%22Peptides%22">Peptides*</searchLink>/<searchLink fieldCode="MM" term="%22Peptides+isolation+%26+purification%22">isolation & purification</searchLink> <br /><searchLink fieldCode="MM" term="%22Peptides%22">Peptides*</searchLink>/<searchLink fieldCode="MM" term="%22Peptides+genetics%22">genetics</searchLink> <br /><searchLink fieldCode="MM" term="%22Peptides%22">Peptides*</searchLink>/<searchLink fieldCode="MM" term="%22Peptides+pharmacology%22">pharmacology</searchLink> <br /><searchLink fieldCode="MM" term="%22Burkholderia%22">Burkholderia*</searchLink>/<searchLink fieldCode="MM" term="%22Burkholderia+genetics%22">genetics</searchLink> <br /><searchLink fieldCode="MM" term="%22Burkholderia%22">Burkholderia*</searchLink>/<searchLink fieldCode="MM" term="%22Burkholderia+metabolism%22">metabolism</searchLink> <br /><searchLink fieldCode="MM" term="%22Polysaccharides%22">Polysaccharides*</searchLink>/<searchLink fieldCode="MM" term="%22Polysaccharides+metabolism%22">metabolism</searchLink> <br /><searchLink fieldCode="MM" term="%22Saccharomyces+cerevisiae%22">Saccharomyces cerevisiae*</searchLink>/<searchLink fieldCode="MM" term="%22Saccharomyces+cerevisiae+genetics%22">genetics</searchLink> <br /><searchLink fieldCode="MM" term="%22Saccharomyces+cerevisiae%22">Saccharomyces cerevisiae*</searchLink>/<searchLink fieldCode="MM" term="%22Saccharomyces+cerevisiae+metabolism%22">metabolism</searchLink> <br /><searchLink fieldCode="MM" term="%22Genomic+Library%22">Genomic Library*</searchLink> <br /><searchLink fieldCode="MM" term="%22Genome%2C+Bacterial%22">Genome, Bacterial*</searchLink><br /><searchLink fieldCode="MH" term="%22Biofilms%22">Biofilms</searchLink>/<searchLink fieldCode="MH" term="%22Biofilms+drug+effects%22">drug effects</searchLink> ; <searchLink fieldCode="MH" term="%22Biofilms%22">Biofilms</searchLink>/<searchLink fieldCode="MH" term="%22Biofilms+growth+%26+development%22">growth & development</searchLink> ; <searchLink fieldCode="MH" term="%22Protein+Binding%22">Protein Binding</searchLink> ; <searchLink fieldCode="MH" term="%22Cell+Surface+Display+Techniques%22">Cell Surface Display Techniques</searchLink> ; <searchLink fieldCode="MH" term="%22Peptide+Library%22">Peptide Library</searchLink>
– Name: Abstract
  Label: Abstract
  Group: Ab
  Data: Here, we present a novel yeast surface display-based platform for the discovery of biofilm-associated exopolysaccharide-binding peptides. Unlike conventional synthetic libraries, our approach utilizes the genomic diversity of Burkholderia multivorans strain C1576 through open-reading frame-filtered genomic fragment libraries, thereby enriching for naturally encoded carbohydrate-binding domains. By iterative fluorescence-activated cell sorting, we identified 21 peptides with confirmed binding to two structurally distinct rhamnose-rich polysaccharides: the exopolysaccharide Epol C1576 and the capsular polysaccharide CPS KpB-1. Biophysical characterization revealed that these peptides adopt predominantly α-helical or disordered conformations and undergo structural rearrangements upon polysaccharide binding. Functional assays demonstrated that selected peptides modulate biofilm architecture and bacterial viability in a species-specific manner, although they do not have a direct bactericidal effect against planktonic cells. This proof-of-concept study establishes yeast surface display as a powerful tool for the discovery of biofilm-targeting peptides and provides a basis for development of novel diagnostics and therapeutics to combat biofilm-associated infections.
– Name: Ref
  Label: References
  Group: RefInfo
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  Data: R01 GM123283 United States GM NIGMS NIH HHS; GM123283 NIH Common Fund; NNF22OC0080132 Novo Nordisk Foundation
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  Data: <i>Keywords: </i>antibiofilm peptides; biofilm; polysaccharides; yeast display
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  Label: PubMed Central ID
  Group: ID
  Data: PMC12986056
– Name: DOI
  Label: DOI
  Group: ID
  Data: 10.3390/ijms27052417
– Name: AN
  Label: PMID
  Group: ID
  Data: 41828634
PLink https://search.ebscohost.com/login.aspx?direct=true&site=eds-live&db=cmedm&AN=41828634
RecordInfo BibRecord:
  BibEntity:
    Identifiers:
      – Type: doi
        Value: 10.3390/ijms27052417
    Languages:
      – Code: eng
        Text: English
    Subjects:
      – SubjectFull: Biofilms drug effects
        Type: general
      – SubjectFull: Biofilms growth & development
        Type: general
      – SubjectFull: Protein Binding
        Type: general
      – SubjectFull: Cell Surface Display Techniques
        Type: general
      – SubjectFull: Peptide Library
        Type: general
      – SubjectFull: Peptides metabolism
        Type: general
      – SubjectFull: Peptides chemistry
        Type: general
      – SubjectFull: Peptides isolation & purification
        Type: general
      – SubjectFull: Peptides genetics
        Type: general
      – SubjectFull: Peptides pharmacology
        Type: general
      – SubjectFull: Burkholderia genetics
        Type: general
      – SubjectFull: Burkholderia metabolism
        Type: general
      – SubjectFull: Polysaccharides metabolism
        Type: general
      – SubjectFull: Saccharomyces cerevisiae genetics
        Type: general
      – SubjectFull: Saccharomyces cerevisiae metabolism
        Type: general
      – SubjectFull: Genomic Library
        Type: general
      – SubjectFull: Genome, Bacterial
        Type: general
    Titles:
      – TitleFull: Combining Yeast Display and Bacterial Genomic Library for the Unbiased Isolation of Novel Polysaccharide-Binding Peptides.
        Type: main
  BibRelationships:
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      – PersonEntity:
          Name:
            NameFull: Stabile A
      – PersonEntity:
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            NameFull: Scaramella G
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            NameFull: Puccio S
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            NameFull: Brady J
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            NameFull: Goltermann L
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            NameFull: Tolker-Nielsen T
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            NameFull: Bellich B
      – PersonEntity:
          Name:
            NameFull: De Zotti S
      – PersonEntity:
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            NameFull: Lagatolla C
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            NameFull: Ferrara F
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            NameFull: Rizzo R
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            NameFull: Cescutti P
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          Name:
            NameFull: Sblattero D
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      – BibEntity:
          Dates:
            – D: 06
              M: 03
              Text: 2026 Mar 06
              Type: published
              Y: 2026
          Identifiers:
            – Type: issn-electronic
              Value: 1422-0067
          Numbering:
            – Type: volume
              Value: 27
            – Type: issue
              Value: 5
          Titles:
            – TitleFull: International journal of molecular sciences
              Type: main
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