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Volume 12, Issue 4

Systematic characterization of PBP2 as the primary siderophore recognizer in and other Gram-positive bacteria Open Access

This article is part of the Advances in the biology of Actinomycetes collection.

Abstract

Iron is a scarce yet essential nutrient for bacteria. Microbes often acquire iron by secreting siderophores, a diverse group of small molecules that form high-affinity complexes with iron for microbial uptake. Understanding microbial iron interaction networks requires detailed characterization of siderophore recognition specificity. In Gram-positive bacteria, substrate-binding proteins (SBPs) bind iron-siderophore complexes and deliver them to ABC transporters for import. However, the SBPs responsible for selective recognition remain poorly characterized, hindering large-scale data mining and network reconstruction. Here, we addressed this knowledge gap by systematically analysing siderophore uptake systems, first in five representative genera and then across a comprehensive dataset of 16,232 Gram-positive bacterial genomes. Through a pipeline integrating genome mining, coevolutionary analysis and structural modelling, we established PBP2 (Peripla_BP_2) subtype SBPs as the primary siderophore recognizer family. We revealed that, unlike the physically clustered systems in Gram-negative bacteria, synthetase and recognizer genes in Gram-positive bacteria are sometimes genomically decoupled, yet display coordinated transcriptional regulation by iron-responsive transcription factors. Our findings underscore key differences between Gram-positive and Gram-negative iron acquisition systems, providing foundational knowledge for large-scale inference of siderophore-mediated microbial interactions.

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Keyword(s): Actinomycetes , Gram-positive bacteria , iron acquisition , siderophore and substrate-binding protein
Funding
This study was supported by the:
  • Key Technologies Research and Development Program (Award 2024YFA0919500)
    • Principal Award Recipient: ZhiyuanLi
  • National Natural Science Foundation of China (Award T2321001)
    • Principal Award Recipient: ZhiyuanLi
  • Fundamental and Interdisciplinary Disciplines Breakthrough Plan of the Ministry of Education of China (Award JYB2025XDXM502)
    • Principal Award Recipient: ZhiyuanLi
© 2026 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2026-04-02
2026-04-22

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References

  1. Yu L, Xiong G, Li Z. Systematic characterization of PBP2 as the primary siderophore recognizer in Actinomycetes and other Gram-positive bacteria Figshare 2026 [View Article]
     [Google Scholar]
  2. Schalk IJ. Bacterial siderophores: diversity, uptake pathways and applications. Nat Rev Microbiol 2025; 23:24–40 [View Article]
     [Google Scholar]
  3. Coughlan MP. The role of iron in microbial metabolism. Sci Prog 1971; 59:1–23 [PubMed]
     [Google Scholar]
  4. Carter A, Racey S, Veuger S. The role of iron in DNA and genomic instability in cancer, a target for iron chelators that can induce ROS. Appl Sci 2022; 12:10161 [View Article]
     [Google Scholar]
  5. Gu S, Shao J, He R, Xiong G, Qu Z et al. Forging the iron‐net: towards a quantitative understanding of microbial communities via siderophore‐mediated interactions. Quant Biol 2025; 13:e84 [View Article]
     [Google Scholar]
  6. Jiang H, Hutchins DA, Ma W, Zhang R, Wells M et al. Natural ocean iron fertilization and climate variability over geological periods. Global Change Biology 2023; 29:6856–6866 [View Article]
     [Google Scholar]
  7. Ilbert M, Bonnefoy V. Insight into the evolution of the iron oxidation pathways. Biochim Biophys Acta 2013; 1827:161–175 [View Article]
     [Google Scholar]
  8. Guerinot ML. Microbial iron transport. Annu Rev Microbiol 1994; 48:743–772 [View Article] [PubMed]
     [Google Scholar]
  9. He R, Gu S, Xu J, Li X, Chen H et al. SIDERITE: unveiling hidden siderophore diversity in the chemical space through digital exploration. Imeta 2024; 3: [View Article]
     [Google Scholar]
  10. Hider RC, Kong X. Chemistry and biology of siderophores. Nat Prod Rep 2010; 27:637–657 [View Article] [PubMed]
     [Google Scholar]
  11. Barry SM, Challis GL. Recent advances in siderophore biosynthesis. Curr Opin Chem Biol 2009; 13:205–215 [View Article]
     [Google Scholar]
  12. Krewulak KD, Vogel HJ. Structural biology of bacterial iron uptake. Biochim Biophys Acta 2008; 1778:1781–1804 [View Article] [PubMed]
     [Google Scholar]
  13. Grigg JC, Cheung J, Heinrichs DE, Murphy MEP. Specificity of Staphyloferrin B recognition by the SirA receptor from Staphylococcus aureus. J Biol Chem 2010; 285:34579–34588 [View Article] [PubMed]
     [Google Scholar]
  14. Meyer J-M, Stintzi A, De Vos D, Cornelis P, Tappe R et al. Use of siderophores to type pseudomonads: the three Pseudomonas aeruginosa pyoverdine systems. Microbiology 1997; 143 (Pt 1):35–43 [View Article] [PubMed]
     [Google Scholar]
  15. de Chial M, Ghysels B, Beatson SA, Geoffroy V, Meyer JM et al. Identification of type II and type III pyoverdine receptors from Pseudomonas aeruginosa. Microbiology 2003; 149:821–831 [View Article] [PubMed]
     [Google Scholar]
  16. Gu S, Shao Z, Qu Z, Zhu S, Shao Y et al. Siderophore synthetase-receptor gene coevolution reveals habitat- and pathogen-specific bacterial iron interaction networks. Sci Adv 2025; 11:eadq5038 [View Article]
     [Google Scholar]
  17. Grandchamp GM, Caro L, Shank EA. Pirated siderophores promote sporulation in Bacillus subtilis. Appl Environ Microbiol 2017; 83:e03293–16 [View Article]
     [Google Scholar]
  18. Peuckert F, Miethke M, Albrecht AG, Essen L, Marahiel MA. Structural basis and stereochemistry of triscatecholate siderophore binding by FeuA. Angew Chem Int Ed 2009; 48:7924–7927 [View Article]
     [Google Scholar]
  19. Hotta K, Kim C-Y, Fox DT, Koppisch AT. Siderophore-mediated iron acquisition in Bacillus anthracis and related strains. Microbiology 2010; 156:1918–1925 [View Article] [PubMed]
     [Google Scholar]
  20. Figueiredo ART, Özkaya Ö, Kümmerli R, Kramer J. Siderophores drive invasion dynamics in bacterial communities through their dual role as public good versus public bad. Ecol Lett 2022; 25:138–150 [View Article]
     [Google Scholar]
  21. Timofeeva AM, Galyamova MR, Sedykh SE. Bacterial siderophores: classification, biosynthesis, perspectives of use in agriculture. Plants 2022; 11:3065 [View Article]
     [Google Scholar]
  22. Schalk IJ, Mislin GLA, Brillet K. Structure, function and binding selectivity and stereoselectivity of siderophore-iron outer membrane transporters. Curr Top Membr 2012; 69:37–66 [View Article]
     [Google Scholar]
  23. Greenwald J, Nader M, Celia H, Gruffaz C, Geoffroy V et al. FpvA bound to non-cognate pyoverdines: molecular basis of siderophore recognition by an iron transporter. Mol Microbiol 2009; 72:1246–1259 [View Article] [PubMed]
     [Google Scholar]
  24. Bouvier B, Cézard C, Sonnet P. Selectivity of pyoverdine recognition by the FpvA receptor of Pseudomonas aeruginosa from molecular dynamics simulations. Phys Chem Chem Phys 2015; 17:18022–18034 [View Article] [PubMed]
     [Google Scholar]
  25. Gu S, Shao Y, Rehm K, Bigler L, Zhang D et al. Feature sequence-based genome mining uncovers the hidden diversity of bacterial siderophore pathways. Elife 2024; 13:RP96719 [View Article] [PubMed]
     [Google Scholar]
  26. Gu S, Shao Z, Qu Z, Zhu S, Shao Y et al. Siderophore synthetase-receptor gene coevolution reveals habitat- and pathogen-specific bacterial iron interaction networks. Microbiology 20232023 [View Article]
     [Google Scholar]
  27. Fukushima T, Allred BE, Sia AK, Nichiporuk R, Andersen UN et al. Gram-positive siderophore-shuttle with iron-exchange from Fe-siderophore to apo-siderophore by Bacillus cereus YxeB. Proc Natl Acad Sci USA 2013; 110:13821–13826 [View Article] [PubMed]
     [Google Scholar]
  28. Nguyen M-T, Matsuo M, Niemann S, Herrmann M, Götz F. Lipoproteins in Gram-positive bacteria: abundance, function, fitness. Front Microbiol 2020; 11:582582 [View Article]
     [Google Scholar]
  29. Akhtar AA, Turner DP. The role of bacterial ATP-binding cassette (ABC) transporters in pathogenesis and virulence: therapeutic and vaccine potential. Microb Pathog 2022; 171:105734 [View Article] [PubMed]
     [Google Scholar]
  30. Fukushima T, Allred BE, Raymond KN. Direct evidence of iron uptake by the gram-positive siderophore-shuttle mechanism without iron reduction. ACS Chem Biol 2014; 9:2092–2100 [View Article]
     [Google Scholar]
  31. Cerna-Vargas JP, Sánchez-Romera B, Matilla MA, Ortega Á, Krell T. Sensing preferences for prokaryotic solute binding protein families. Microb Biotechnol 2023; 16:1823–1833 [View Article] [PubMed]
     [Google Scholar]
  32. Chandravanshi M, Tripathi SK, Kanaujia SP. An updated classification and mechanistic insights into ligand binding of the substrate-binding proteins. FEBS Lett 2021; 595:2395–2409 [View Article] [PubMed]
     [Google Scholar]
  33. Heinrichs DE et al. Staphylococcus, Streptococcus, and Bacillus. In Iron Transport in Bacteria 2014 pp 387–401 [View Article]
     [Google Scholar]
  34. Segond D, Abi Khalil E, Buisson C, Daou N, Kallassy M et al. Iron acquisition in Bacillus cereus: the roles of IlsA and bacillibactin in exogenous ferritin iron mobilization. PLoS Pathog 2014; 10:e1003935 [View Article] [PubMed]
     [Google Scholar]
  35. Beasley FC, Marolda CL, Cheung J, Buac S, Heinrichs DE. Staphylococcus aureus transporters Hts, Sir, and Sst capture iron liberated from human transferrin by Staphyloferrin A, Staphyloferrin B, and catecholamine stress hormones, respectively, and contribute to virulence. Infect Immun 2011; 79:2345–2355 [View Article] [PubMed]
     [Google Scholar]
  36. Alam K, Mazumder A, Sikdar S, Zhao Y-M, Hao J et al. Streptomyces: the biofactory of secondary metabolites. Front Microbiol 2022; 13:2022 [View Article]
     [Google Scholar]
  37. Blin K, Shaw S, Augustijn HE, Reitz ZL, Biermann F et al. antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation. Nucleic Acids Res 2023; 51:W46–W50 [View Article]
     [Google Scholar]
  38. Mohite OS, Jørgensen TS, Booth TJ, Charusanti P, Phaneuf PV et al. Pangenome mining of the Streptomyces genus redefines species’ biosynthetic potential. Genome Biol 2025; 26:9 [View Article] [PubMed]
     [Google Scholar]
  39. Zdouc MM, Blin K, Louwen NLL, Navarro J, Loureiro C et al. MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration. Nucleic Acids Res 2025; 53:D678–D690 [View Article] [PubMed]
     [Google Scholar]
  40. Draisma A, Loureiro C, Louwen NLL, Kautsar SA, Navarro-Muñoz JC et al. BiG-SCAPE 2.0 and BiG-SLiCE 2.0: scalable, accurate and interactive sequence clustering of metabolic gene clusters. Nat Commun 2026; 17: [View Article]
     [Google Scholar]
  41. Matilla MA, Velando F, Martín-Mora D, Monteagudo-Cascales E, Krell T. A catalogue of signal molecules that interact with sensor kinases, chemoreceptors and transcriptional regulators. FEMS Microbiol Rev 2022; 46: [View Article]
     [Google Scholar]
  42. Crits-Christoph A, Bhattacharya N, Olm MR, Song YS, Banfield JF. Transporter genes in biosynthetic gene clusters predict metabolite characteristics and siderophore activity. Genome Res 2021; 31:239–250 [View Article]
     [Google Scholar]
  43. Zawadzka AM, Kim Y, Maltseva N, Nichiporuk R, Fan Y et al. Characterization of a Bacillus subtilis transporter for petrobactin, an anthrax stealth siderophore. Proc Natl Acad Sci USA 2009; 106:21854–21859 [View Article] [PubMed]
     [Google Scholar]
  44. Wang Z, Hou X, Guo Z, Lei X, Peng M. Biodegradation of sodium selenite by a highly tolerant strain Rhodococcus qingshengii PM1: biochemical characterization and comparative genome analysis. Curr Res Microbial Sci 2025; 9:100426 [View Article]
     [Google Scholar]
  45. Khilyas IV, Sorokina AV, Markelova MI, Belenikin M, Shafigullina L et al. Genomic and phenotypic analysis of siderophore-producing Rhodococcus qingshengii strain S10 isolated from an arid weathered serpentine rock environment. Arch Microbiol 2021; 203:855–860 [View Article] [PubMed]
     [Google Scholar]
  46. Wang X, Wang H, Jin H, Liao H, Qian X et al. Complete genome sequence of Rhodococcus qingshengii strain R isolated from Antarctic soil. Microbiol Resour Announc 2025; 14:e0131624 [View Article] [PubMed]
     [Google Scholar]
  47. Patel P, Song L, Challis GL. Distinct extracytoplasmic siderophore binding proteins recognize ferrioxamines and ferricoelichelin in Streptomyces coelicolor A3(2). Biochemistry 2010; 49:8033–8042 [View Article] [PubMed]
     [Google Scholar]
  48. Baichoo N, Helmann JD. Recognition of DNA by Fur: a reinterpretation of the Fur box consensus sequence. J Bacteriol 2002; 184:5826–5832 [View Article]
     [Google Scholar]
  49. Flores FJ, Barreiro C, Coque JJR, Martín JF. Functional analysis of two divalent metal-dependent regulatory genes dmdR1 and dmdR2 in Streptomyces coelicolor and proteome changes in deletion mutants. FEBS J 2005; 272:725–735 [View Article] [PubMed]
     [Google Scholar]
  50. Ollinger J, Song K-B, Antelmann H, Hecker M, Helmann JD. Role of the Fur regulon in iron transport in Bacillus subtilis. J Bacteriol 2006; 188:3664–3673 [View Article] [PubMed]
     [Google Scholar]
  51. Sutcliffe IC. A phylum level perspective on bacterial cell envelope architecture. Trends Microbiol 2010; 18:464–470 [View Article] [PubMed]
     [Google Scholar]
  52. Tomasek D, Kahne D. The assembly of β-barrel outer membrane proteins. Curr Opin Microbiol 2021; 60:16–23 [View Article] [PubMed]
     [Google Scholar]
  53. Peuckert F, Ramos-Vega AL, Miethke M, Schwörer CJ, Albrecht AG et al. The siderophore binding protein FeuA shows limited promiscuity toward exogenous triscatecholates. Chem Biol 2011; 18:907–919 [View Article]
     [Google Scholar]
  54. Sheinman M, Arkhipova K, Arndt PF, Dutilh BE, Hermsen R et al. Identical sequences found in distant genomes reveal frequent horizontal transfer across the bacterial domain. Elife 2021; 10:e62719 [View Article] [PubMed]
     [Google Scholar]
  55. Michaelis C, Grohmann E. Horizontal gene transfer of antibiotic resistance genes in biofilms. Antibiotics 2023; 12:328 [View Article] [PubMed]
     [Google Scholar]
  56. Groussin M, Poyet M, Sistiaga A, Kearney SM, Moniz K et al. Elevated rates of horizontal gene transfer in the industrialized human microbiome. Cell 2021; 184:2053–2067 [View Article] [PubMed]
     [Google Scholar]
  57. Martinez-Gutierrez CA, Uyeda JC, Aylward FO. A timeline of bacterial and archaeal diversification in the ocean. Elife 2023; 12:RP88268 [View Article] [PubMed]
     [Google Scholar]
  58. Davín AA, Woodcroft BJ, Soo RM, Morel B, Murali R et al. A geological timescale for bacterial evolution and oxygen adaptation. Science 2025; 388:eadp1853 [View Article] [PubMed]
     [Google Scholar]
  59. Wade J, Byrne DJ, Ballentine CJ, Drakesmith H. Temporal variation of planetary iron as a driver of evolution. Proc Natl Acad Sci USA 2021; 118:e2109865118 [View Article]
     [Google Scholar]
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Systematic characterization of PBP2 as the primary siderophore recognizer in Actinomycetes and other Gram-positive bacteria
M Gen 12, 001671 (2026); https://doi.org/10.1099/mgen.0.001671
/content/journal/mgen/10.1099/mgen.0.001671
/content/journal/mgen/10.1099/mgen.0.001671
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