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Volume 169, Issue 3

A novel proteinaceous molecule produced by sp. OF-1 depends on the Ami oligopeptide transporter to kill Open Access

Abstract

Infections caused by antibiotic-resistant are of growing concern for healthcare systems, which need new treatment options. Screening microorganisms in terrestrial environments has proved successful for discovering antibiotics, while production of antimicrobials by marine microorganisms remains underexplored. Here we have screened microorganisms sampled from the Oslo Fjord in Norway for production of molecules that prevent the human pathogen from growing. A bacterium belonging to the genus was identified. We show that this bacterium produces a molecule that kills a wide range of streptococcal species. Genome mining in BAGEL4 and AntiSmash suggested that it was a new antimicrobial compound, and we therefore named it lysinicin OF. The compound was resistant to heat (100 °C) and polymyxin acylase but susceptible to proteinase K, showing that it is of proteinaceous nature, but most probably not a lipopeptide. became resistant to lysinicin OF by obtaining suppressor mutations in the locus, which encodes the AmiACDEF oligo peptide transporter. We created Δ and Δ mutants to show that pneumococci expressing a compromised Ami system were resistant to lysinicin OF. Furthermore, by creating mutants expressing an intact but inactive Ami system (AmiED184A and AmiFD175A) we could conclude that the lysinicin OF activity depended on the active form (ATP-hydrolysing) of the Ami system. Microscopic imaging and fluorescent labelling of DNA showed that treated with lysinicin OF had an average reduced cell size with condensed DNA nucleoid, while the integrity of the cell membrane remained intact. The characteristics and possible mode of action of lysinicin OF are discussed.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): antimicrobials , Lysinibacillus , lysinicin OF and Streptococcus pneumoniae
Funding
This study was supported by the:
  • Norges Forskningsråd (Award 287416)
    • Principle Award Recipient: NotApplicable
© 2023 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2023-03-07
2024-04-20
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References

  1. IACG No time to wait: Securing the future from drug-resistant infections; 2019
  2. WHO Global Antimicrobial Resistance Surveillance System (GLASS) Report Early implementation; 2017
  3. O’Brien KL, Wolfson LJ, Watt JP, Henkle E, Deloria-Knoll M et al. Burden of disease caused by Streptococcus pneumoniae in children younger than 5 years: global estimates. Lancet 2009; 374:893–902 [View Article] [PubMed]
     [Google Scholar]
  4. Cherazard R, Epstein M, Doan TL, Salim T, Bharti S et al. Antimicrobial resistant Streptococcus pneumoniae: prevalence, mechanisms, and clinical implications. Am J Ther 2017; 24:e361–e369 [View Article] [PubMed]
     [Google Scholar]
  5. Chewapreecha C, Harris SR, Croucher NJ, Turner C, Marttinen P et al. Dense genomic sampling identifies highways of pneumococcal recombination. Nat Genet 2014; 46:305–309 [View Article] [PubMed]
     [Google Scholar]
  6. Aminov RI. A brief history of the antibiotic era: lessons learned and challenges for the future. Front Microbiol 2010; 1:134 [View Article] [PubMed]
     [Google Scholar]
  7. Newman DJ, Cragg GM. Natural products as sources of new drugs over the last 25 years. J Nat Prod 2007; 70:461–477 [View Article] [PubMed]
     [Google Scholar]
  8. Lacks S, Hotchkiss RD. A study of the genetic material determining an enzyme in pneumococcus. Biochim Biophys Acta 1960; 39:508–518 [View Article] [PubMed]
     [Google Scholar]
  9. Higuchi R, Krummel B, Saiki RK. A general method of in vitro preparation and specific mutagenesis of DNA fragments: study of protein and DNA interactions. Nucleic Acids Res 1988; 16:7351–7367 [View Article] [PubMed]
     [Google Scholar]
  10. Sung CK, Li H, Claverys JP, Morrison DA. An rpsL cassette, janus, for gene replacement through negative selection in Streptococcus pneumoniae. Appl Environ Microbiol 2001; 67:5190–5196 [View Article] [PubMed]
     [Google Scholar]
  11. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
     [Google Scholar]
  12. Ducret A, Quardokus EM, Brun YV. MicrobeJ, a tool for high throughput bacterial cell detection and quantitative analysis. Nat Microbiol 2016; 1:16077 [View Article]
     [Google Scholar]
  13. Laemmli UK. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 1970; 227:680–685 [View Article] [PubMed]
     [Google Scholar]
  14. Stamsås GA, Straume D, Salehian Z, Håvarstein LS. Evidence that pneumococcal WalK is regulated by StkP through protein-protein interaction. Microbiology 2017; 163:383–399 [View Article]
     [Google Scholar]
  15. Avram O, Rapoport D, Portugez S, Pupko T. M1CR0B1AL1Z3R-a user-friendly web server for the analysis of large-scale microbial genomics data. Nucleic Acids Res 2019; 47:W88–W92 [View Article] [PubMed]
     [Google Scholar]
  16. van Heel AJ, de Jong A, Song C, Viel JH, Kok J et al. BAGEL4: a user-friendly web server to thoroughly mine ripps and bacteriocins. Nucleic Acids Res 2018; 46:W278–W281
     [Google Scholar]
  17. Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, van Wezel GP et al. AntiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res 2021; 49:W29–W35
     [Google Scholar]
  18. Steller S, Vollenbroich D, Leenders F, Stein T, Conrad B et al. Structural and functional organization of the fengycin synthetase multienzyme system from Bacillus subtilis b213 and A1/3. Chem Biol 1999; 6:31–41 [View Article] [PubMed]
     [Google Scholar]
  19. Abriouel H, Franz CMAP, Ben Omar N, Gálvez A. Diversity and applications of Bacillus bacteriocins. FEMS Microbiol Rev 2011; 35:201–232 [View Article] [PubMed]
     [Google Scholar]
  20. Caulier S, Nannan C, Gillis A, Licciardi F, Bragard C et al. Overview of the antimicrobial compounds produced by members of the Bacillus subtilis group. Front Microbiol 2019; 10:302 [View Article] [PubMed]
     [Google Scholar]
  21. Yim G, Thaker MN, Koteva K, Wright G. Glycopeptide antibiotic biosynthesis. J Antibiot 2014; 67:31–41 [View Article]
     [Google Scholar]
  22. Diep DB, Skaugen M, Salehian Z, Holo H, Nes IF. Common mechanisms of target cell recognition and immunity for class II bacteriocins. Proc Natl Acad Sci 2007; 104:2384–2389 [View Article] [PubMed]
     [Google Scholar]
  23. Kjos M, Oppegård C, Diep DB, Nes IF, Veening J-W et al. Sensitivity to the two-peptide bacteriocin lactococcin G is dependent on UppP, an enzyme involved in cell-wall synthesis. Mol Microbiol 2014; 92:1177–1187 [View Article] [PubMed]
     [Google Scholar]
  24. Oftedal TF, Ovchinnikov KV, Hestad KA, Goldbeck O, Porcellato D et al. Ubericin K, a new pore-forming bacteriocin targeting mannose-PTS. Microbiol Spectr 2021; 9:e0029921 [View Article]
     [Google Scholar]
  25. Ovchinnikov KV, Kristiansen PE, Straume D, Jensen MS, Aleksandrzak-Piekarczyk T et al. The leaderless bacteriocin enterocin K1 is highly potent against Enterococcus faecium: a study on structure, target spectrum and receptor. Front Microbiol 2017; 8:774 [View Article]
     [Google Scholar]
  26. Zhu L, Zeng J, Wang C, Wang J. Structural basis of pore formation in the mannose phosphotransferase system by pediocin PA-1. Appl Environ Microbiol 2022; 88:e0199221 [View Article]
     [Google Scholar]
  27. Pérez-Ramos A, Madi-Moussa D, Coucheney F, Drider D. Current knowledge of the mode of action and immunity mechanisms of LAB-bacteriocins. Microorganisms 2021; 9:10 [View Article] [PubMed]
     [Google Scholar]
  28. Abee T, Klaenhammer TR, Letellier L. Kinetic studies of the action of lactacin F, a bacteriocin produced by Lactobacillus johnsonii that forms poration complexes in the cytoplasmic membrane. Appl Environ Microbiol 1994; 60:1006–1013 [View Article]
     [Google Scholar]
  29. Héchard Y, Sahl HG. Mode of action of modified and unmodified bacteriocins from Gram-positive bacteria. Biochimie 2002; 84:545–557 [View Article] [PubMed]
     [Google Scholar]
  30. Alloing G, Trombe MC, Claverys JP. The ami locus of the gram-positive bacterium Streptococcus pneumoniae is similar to binding protein-dependent transport operons of gram-negative bacteria. Mol Microbiol 1990; 4:633–644 [View Article] [PubMed]
     [Google Scholar]
  31. Rees DC, Johnson E, Lewinson O. ABC transporters: the power to change. Nat Rev Mol Cell Biol 2009; 10:218–227 [View Article] [PubMed]
     [Google Scholar]
  32. Alloing G, de Philip P, Claverys JP. Three highly homologous membrane-bound lipoproteins participate in oligopeptide transport by the Ami system of the gram-positive Streptococcus pneumoniae. J Mol Biol 1994; 241:44–58 [View Article] [PubMed]
     [Google Scholar]
  33. Garault P, Le Bars D, Besset C, Monnet V. Three oligopeptide-binding proteins are involved in the oligopeptide transport of Streptococcus thermophilus. J Biol Chem 2002; 277:32–39 [View Article] [PubMed]
     [Google Scholar]
  34. Davidson AL. Mechanism of coupling of transport to hydrolysis in bacterial ATP-binding cassette transporters. J Bacteriol 2002; 184:1225–1233 [View Article] [PubMed]
     [Google Scholar]
  35. Khan YA, White KI, Brunger AT. The AAA+ superfamily: a review of the structural and mechanistic principles of these molecular machines. Crit Rev Biochem Mol Biol 2022; 57:156–187 [View Article]
     [Google Scholar]
  36. Walker JE, Saraste M, Runswick MJ, Gay NJ. Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J 1982; 1:945–951 [View Article] [PubMed]
     [Google Scholar]
  37. Story RM, Steitz TA. Structure of the recA protein-ADP complex. Nature 1992; 355:374–376 [View Article] [PubMed]
     [Google Scholar]
  38. Sham LT, Jensen KR, Bruce KE, Winkler ME. Involvement of FtsE ATPase and FtsX extracellular loops 1 and 2 in FtsEX-PcsB complex function in cell division of Streptococcus pneumoniae D39. mBio 2013; 4:e00431-13 [View Article]
     [Google Scholar]
  39. Arends SJR, Kustusch RJ, Weiss DS. ATP-binding site lesions in FtsE impair cell division. J Bacteriol 2009; 191:3772–3784 [View Article] [PubMed]
     [Google Scholar]
  40. Breukink E, Wiedemann I, van Kraaij C, Kuipers OP, Sahl HG et al. Use of the cell wall precursor lipid II by a pore-forming peptide antibiotic. Science 1999; 286:2361–2364 [View Article] [PubMed]
     [Google Scholar]
  41. Ruhr E, Sahl HG. Mode of action of the peptide antibiotic nisin and influence on the membrane potential of whole cells and on cytoplasmic and artificial membrane vesicles. Antimicrob Agents Chemother 1985; 27:841–845 [View Article] [PubMed]
     [Google Scholar]
  42. Wiedemann I, Breukink E, van Kraaij C, Kuipers OP, Bierbaum G et al. Specific binding of nisin to the peptidoglycan precursor lipid II combines pore formation and inhibition of cell wall biosynthesis for potent antibiotic activity. J Biol Chem 2001; 276:1772–1779 [View Article] [PubMed]
     [Google Scholar]
  43. Schmitt MA, Weisblum B, Gellman SH. Interplay among folding, sequence, and lipophilicity in the antibacterial and hemolytic activities of alpha/beta-peptides. J Am Chem Soc 2007; 129:417–428 [View Article] [PubMed]
     [Google Scholar]
  44. Wang G, Li X, Wang Z. APD3: the antimicrobial peptide database as a tool for research and education. Nucleic Acids Res 2016; 44:D1087–93 [View Article] [PubMed]
     [Google Scholar]
  45. Lorian V, Atkinson B. Abnormal forms of bacteria produced by antibiotics. Am J Clin Pathol 1975; 64:678–688 [View Article] [PubMed]
     [Google Scholar]
  46. Georgopapadakou NH, Bertasso A. Effects of quinolones on nucleoid segregation in Escherichia coli. Antimicrob Agents Chemother 1991; 35:2645–2648 [View Article] [PubMed]
     [Google Scholar]
  47. Rajendram M, Hurley KA, Foss MH, Thornton KM, Moore JT et al. Gyramides prevent bacterial growth by inhibiting DNA gyrase and altering chromosome topology. ACS Chem Biol 2014; 9:1312–1319 [View Article] [PubMed]
     [Google Scholar]
  48. Hawkey PM. Mechanisms of quinolone action and microbial response. J Antimicrob Chemother 2003; 51 Suppl 1:29–35 [View Article]
     [Google Scholar]
  49. Hartmann G, Honikel KO, Knüsel F, Nüesch J. The specific inhibition of the DNA-directed RNA synthesis by rifamycin. Biochim Biophys Acta 1967; 145:843–844 [View Article] [PubMed]
     [Google Scholar]
  50. Wehrli W, Knüsel F, Schmid K, Staehelin M. Interaction of rifamycin with bacterial RNA polymerase. Proc Natl Acad Sci 1968; 61:667–673 [View Article] [PubMed]
     [Google Scholar]
  51. Connamacher RH, Mandel HG. Binding of tetracycline to the 30S ribosomes and to polyuridylic acid. Biochem Biophys Res Commun 1965; 20:98–103 [View Article] [PubMed]
     [Google Scholar]
  52. Gale EF, Folkes JP. The assimilation of amino-acids by bacteria. XV. Actions of antibiotics on nucleic acid and protein synthesis in Staphylococcus aureus. Biochem J 1953; 53:493–498 [View Article] [PubMed]
     [Google Scholar]
  53. Izaki K, Matsuhashi M, Strominger JL. Glycopeptide transpeptidase and D-alanine carboxypeptidase: penicillin-sensitive enzymatic reactions. Proc Natl Acad Sci 1966; 55:656–663 [View Article] [PubMed]
     [Google Scholar]
  54. Lawrence PJ, Strominger JL. Biosynthesis of the peptidoglycan of bacterial cell walls. XV. The binding of radioactive penicillin to the particulate enzyme preparation of Bacillus subtilis and its reversal with hydroxylamine or thiols. J Biol Chem 1970; 245:3653–3659
     [Google Scholar]
  55. Sugino A, Peebles CL, Kreuzer KN, Cozzarelli NR. Mechanism of action of nalidixic acid: purification of Escherichia coli nalA gene product and its relationship to DNA gyrase and a novel nicking-closing enzyme. Proc Natl Acad Sci 1977; 74:4767–4771 [View Article] [PubMed]
     [Google Scholar]
  56. Emmerson AM, Jones AM. The quinolones: decades of development and use. J Antimicrob Chemother 2003; 51 Suppl 1:13–20 [View Article]
     [Google Scholar]
  57. Kjos M, Veening JW. Tracking of chromosome dynamics in live Streptococcus pneumoniae reveals that transcription promotes chromosome segregation. Mol Microbiol 2014; 91:1088–1105 [View Article] [PubMed]
     [Google Scholar]
  58. von Meyenburg K, Hansen FG, Riise E, Bergmans HE, Meijer M et al. Origin of replication, oriC, of the Escherichia coli K12 chromosome: genetic mapping and minichromosome replication. Cold Spring Harb Symp Quant Biol 1979; 43 Pt 1:121–128 [View Article]
     [Google Scholar]
  59. Ahmad V, Iqbal A, Haseeb M, Khan MS. Antimicrobial potential of bacteriocin producing Lysinibacillus jx416856 against foodborne bacterial and fungal pathogens, isolated from fruits and vegetable waste. Anaerobe 2014; 27:87–95 [View Article] [PubMed]
     [Google Scholar]
  60. Akintayo SO, Treinen C, Vahidinasab M, Pfannstiel J, Bertsche U et al. Exploration of surfactin production by newly isolated Bacillus and Lysinibacillus strains from food-related sources. Lett Appl Microbiol 2022; 75:378–387 [View Article] [PubMed]
     [Google Scholar]
  61. Satapute P, Jogaiah S. A biogenic microbial biosurfactin that degrades difenoconazole fungicide with potential antimicrobial and oil displacement properties. Chemosphere 2022; 286:131694 [View Article]
     [Google Scholar]
  62. Trombe MC. Alteration of Streptococcus pneumoniae membrane properties by the folate analog methotrexate. J Bacteriol 1984; 160:849–853 [View Article] [PubMed]
     [Google Scholar]
  63. Nasher F, Aguilar F, Aebi S, Hermans PWM, Heller M et al. Peptide ligands of AmiA, AliA, and AliB proteins determine pneumococcal phenotype. Front Microbiol 2018; 9:3013 [View Article] [PubMed]
     [Google Scholar]
  64. Monnet V. Bacterial oligopeptide-binding proteins. Cell Mol Life Sci 2003; 60:2100–2114 [View Article] [PubMed]
     [Google Scholar]
  65. Sicard AM. A new synthetic medium for Diplococcus pneumoniae, and its use for the study of reciprocal transformations at the Amia Locus. Genetics 1964; 50:31–44 [View Article] [PubMed]
     [Google Scholar]
  66. Martinac B, Saimi Y, Kung C. Ion channels in microbes. Physiol Rev 2008; 88:1449–1490 [View Article] [PubMed]
     [Google Scholar]
  67. Duquesne S, Destoumieux-Garzón D, Peduzzi J, Rebuffat S. Microcins, gene-encoded antibacterial peptides from enterobacteria. Nat Prod Rep 2007; 24:708–734 [View Article] [PubMed]
     [Google Scholar]
  68. Oda Y, Hayashi F, Okada M. Longitudinal study of dental caries incidence associated with Streptococcus mutans and Streptococcus sobrinus in patients with intellectual disabilities. BMC Oral Health 2015; 15:102 [View Article]
     [Google Scholar]
  69. Kerr AR, Adrian PV, Estevão S, de Groot R, Alloing G et al. The Ami-AliA/AliB permease of Streptococcus pneumoniae is involved in nasopharyngeal colonization but not in invasive disease. Infect Immun 2004; 72:3902–3906 [View Article] [PubMed]
     [Google Scholar]
  70. Slager J, Aprianto R, Veening JW. Deep genome annotation of the opportunistic human pathogen Streptococcus pneumoniae D39. Nucleic Acids Res 2018; 46:9971–9989 [View Article] [PubMed]
     [Google Scholar]
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A novel proteinaceous molecule produced by Lysinibacillus sp. OF-1 depends on the Ami oligopeptide transporter to kill Streptococcus pneumoniae
Microbiology 169, 001313 (2023); https://doi.org/10.1099/mic.0.001313
/content/journal/micro/10.1099/mic.0.001313
/content/journal/micro/10.1099/mic.0.001313
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