The rumen eukaryotome is a source of novel antimicrobial peptides with therapeutic potential
Tóm tắt
The rise of microbial antibiotic resistance is a leading threat to the health of the human population. As such, finding new approaches to tackle these microbes, including development of novel antibiotics is vital. In this study, we mined a rumen eukaryotic metatranscriptomic library for novel Antimicrobial peptides (AMPs) using computational approaches and thereafter characterised the therapeutic potential of the AMPs. We identified a total of 208 potentially novel AMPs from the ruminal eukaryotome, and characterised one of those, namely Lubelisin. Lubelisin (GIVAWFWRLAR) is an α-helical peptide, 11 amino acid long with theoretical molecular weight of 1373.76 D. In the presence of Lubelisin, strains of methicillin-resistant Staphylococcus aureus (MRSA) USA300 and EMRSA-15 were killed within 30 min of exposure with ≥103 and 104 CFU/mL reduction in viable cells respectively. Cytotoxicity of Lubelisin against both human and sheep erythrocytes was low resulting in a therapeutic index of 0.43. Membrane permeabilisation assays using propidium iodide alongside transmission electron microscopy revealed that cytoplasmic membrane damage may contribute to the antimicrobial activities of Lubelisin. We demonstrate that the rumen eukaryotome is a viable source for the discovery of antimicrobial molecules for the treatment of bacterial infections and further development of these may provide part of the potential solution to the ongoing problem of antimicrobial resistance. The role of these AMPs in the ecological warfare within the rumen is also currently unknown.
Tài liệu tham khảo
Woodford N. Glycopeptide-resistant enterococci: a decade of experience. J Med Microbiol. 1998;47(10):849–62. https://doi.org/10.1099/00222615-47-10-849.
Chen LF, Chopra T, Kaye KS. Pathogens resistant to antibacterial agents. Infect Dis Clin N Am. 2009;23(4):817–45. https://doi.org/10.1016/j.idc.2009.06.002.
Siegel RE. Emerging gram-negative antibiotic resistance: daunting challenges, declining sensitivities, and dire consequences. Respir Care. 2008;53(4):471–9.
O'Neill J. The review on Antoimicrobial resistance: Securing new DRUGS for FUTURE GENERATIONS: the pipeline of antibiotics. http://amr-review.org/sites/default/files/SECURING%20NEW%20DRUGS%20FOR%20FUTURE%20GENERATIONS%20FINAL%20WEB_0.pdf (2015). Accessed.
Zasloff M. Antimicrobial peptides of multicellular organisms. Nature. 2002;415(6870):389–95.
Yount NY, Yeaman MR. Multidimensional signatures in antimicrobial peptides. Proc Natl Acad Sci U S A. 2004;101(19):7363–8. https://doi.org/10.1073/pnas.0401567101.
Tavares LS, Santos MO, Viccini LF, Moreira JS, Miller RN, Franco OL. Biotechnological potential of antimicrobial peptides from flowers. Peptides. 2008;29(10):1842–51. https://doi.org/10.1016/j.peptides.2008.06.003.
Hurdle JG, O'neill AJ, Chopra I, Lee RE. Targeting bacterial membrane function: an underexploited mechanism for treating persistent infections. Nat Rev Microbiol. 2011;9(1):62–75. https://doi.org/10.1038/nrmicro2474.
Lehrer RI, Ganz T. Antimicrobial peptides in mammalian and insect host defence. Curr Opin Immunol. 1999;11(1):23–7. https://doi.org/10.1016/S0952-7915(99)80005-3.
Mookherjee N, Hancock R. Cationic host defence peptides: innate immune regulatory peptides as a novel approach for treating infections. Cell Mol Life Sci. 2007;64(7–8):922–33. https://doi.org/10.1007/s00018-007-6475-6.
Lai Y, Gallo RL. AMPed up immunity: how antimicrobial peptides have multiple roles in immune defense. Trends Immunol. 2009;30(3):131–41. https://doi.org/10.1016/j.it.2008.12.003.
Oren Z, Shai Y. A class of highly potent antibacterial peptides derived from pardaxin, a pore-forming peptide isolated from Moses sole fish Pardachirus marmoratus. Eur J Biochem. 1996;237(1):303–10. https://doi.org/10.1111/j.1432-1033.1996.0303n.x.
Marri L, Dallai R, Marchini D. The novel antibacterial peptide ceratotoxin a alters permeability of the inner and outer membrane of Escherichia coli K-12. Curr Microbiol. 1996;33(1):40–3. https://doi.org/10.1007/s002849900071.
Goulard C, Hlimi S, Rebuffat S, Bodo B. Trichorzins HA and MA, antibiotic peptides from Trichoderma harzianum. J Antibiotics. 1995;48(11):1248–53. https://doi.org/10.7164/antibiotics.48.1248.
Whitford M, McPherson M, Forster R, Teather R. Identification of bacteriocin-like inhibitors from rumen Streptococcus spp. and isolation and characterization of bovicin 255. Appl Environ Microbiol. 2001;67(2):569–74. https://doi.org/10.1128/AEM.67.2.569-574.2001.
Morovský M, Pristaš P, Czikková S, Javorský P. A bacteriocin-mediated antagonism by Enterococcus faecium BC25 against ruminal Streptococcus bovis. Microbiol Res. 1998;153(3):277–281; doi: https://doi.org/10.1016/S0944-5013(98)80012-8.
Oyama LB, Crochet J-A, Edwards JE, Girdwood SE, Cookson AR, Fernandez-Fuentes N, et al. Buwchitin: A Ruminal Peptide with Antimicrobial Potential against Enterococcus faecalis. Front Chemistry. 2017;5(51). https://doi.org/10.3389/fchem.2017.00051.
Oyama LB, Girdwood SE, Cookson AR, Fernandez-Fuentes N, Prive F, Vallin HE, et al. The rumen microbiome: an underexplored resource for novel antimicrobial discovery. NPJ Biofilms Microbiomes. 2017;3(1):33. https://doi.org/10.1038/s41522-017-0042-1.
Oyama LB, Olleik H, Teixeira ACN, Guidini MM, Pickup JA, Cookson AR, et al. In silico identification of novel peptides with antibacterial activity against multidrug resistant Staphylococcus aureus: Cold Spring Harbor Laboratory; 2019.
Wang G, Li X, Wang Z. APD3: the antimicrobial peptide database as a tool for research and education. Nucleic Acids Res. 2016;44(D1):D1087–D93. https://doi.org/10.1093/nar/gkv1278.
Sievers F, Higgins DG. Clustal omega for making accurate alignments of many protein sequences. Protein Sci. 2018;27(1):135–45. https://doi.org/10.1002/pro.3290.
Kautsar SA, Blin K, Shaw S, Navarro-Muñoz JC, Terlouw BR, van der Hooft JJJ, et al. MIBiG 2.0: a repository for biosynthetic gene clusters of known function. Nucleic Acids Res. 2019;48(D1):D454–D8. https://doi.org/10.1093/nar/gkz882.
Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics. 2004;5(1):113. https://doi.org/10.1186/1471-2105-5-113.
Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012;28(23):3150–2. https://doi.org/10.1093/bioinformatics/bts565.
Blin K, Shaw S, Steinke K, Villebro R, Ziemert N, Lee SY, et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res. 2019;47(W1):W81–W7. https://doi.org/10.1093/nar/gkz310.
Alder J, Eisenstein B. The advantage of bactericidal drugs in the treatment of infection. Curr Infect Dis Rep. 2004;6(4):251–3. https://doi.org/10.1007/s11908-004-0042-1.
Dathe M, Wieprecht T, Nikolenko H, Handel L, Maloy WL, MacDonald DL, et al. Hydrophobicity, hydrophobic moment and angle subtended by charged residues modulate antibacterial and haemolytic activity of amphipathic helical peptides. FEBS Lett. 1997;403(2):208–12. https://doi.org/10.1016/S0014-5793(97)00055-0.
Wieprecht T, Dathe M, Beyermann M, Krause E, Maloy WL, MacDonald DL, et al. Peptide hydrophobicity controls the activity and selectivity of magainin 2 amide in interaction with membranes. Biochemistry. 1997;36(20):6124–32. https://doi.org/10.1021/bi9619987.
Tossi A, Sandri L, Giangaspero A. Amphipathic, α-helical antimicrobial peptides. Pept Sci. 2000;55(1):4–30. https://doi.org/10.1002/1097-0282(2000)55:1<4::AID-BIP30>3.0.CO;2-M.
Chan DI, Prenner EJ, Vogel HJ. Tryptophan-and arginine-rich antimicrobial peptides: structures and mechanisms of action. Biochimica et Biophysica Acta (BBA)-Biomembranes. 2006;1758(9):1184–202.
Wimley WC, White SH. Experimentally determined hydrophobicity scale for proteins at membrane interfaces. Nat Struct Mol Biol. 1996;3(10):842–8. https://doi.org/10.1038/nsb1096-842.
Liu Y, Shi J, Tong Z, Jia Y, Yang B, Wang Z. The revitalization of antimicrobial peptides in the resistance era. Pharm Res. 2021;163:105276. https://doi.org/10.1016/j.phrs.2020.105276.
Huang Y, Huang J, Chen Y. Alpha-helical cationic antimicrobial peptides: relationships of structure and function. Protein Cell. 2010;1(2):143–52. https://doi.org/10.1007/s13238-010-0004-3.
Landon C, Meudal H, Boulanger N, Bulet P, Vovelle F. Solution structures of stomoxyn and spinigerin, two insect antimicrobial peptides with an α-helical conformation. Biopolymers. 2006;81(2):92–103. https://doi.org/10.1002/bip.20370.
Zasloff M. Magainins, a class of antimicrobial peptides from Xenopus skin: isolation, characterization of two active forms, and partial cDNA sequence of a precursor. Proc Natl Acad Sci. 1987;84(15):5449–53. https://doi.org/10.1073/pnas.84.15.5449.
Hemmi H, Ishibashi J, Hara S, Yamakawa M. Solution structure of moricin, an antibacterial peptide, isolated from the silkworm Bombyx mori. FEBS Lett. 2002;518(1–3):33–8. https://doi.org/10.1016/s0014-5793(02)02637-6.
Knappe D, Ruden S, Langanke S, Tikkoo T, Ritzer J, Mikut R, et al. Optimization of oncocin for antibacterial activity using a SPOT synthesis approach: extending the pathogen spectrum to Staphylococcus aureus. Amino Acids. 2016;48(1):269–80. https://doi.org/10.1007/s00726-015-2082-2.
Evans BA, Hamouda A, Amyes SG. The rise of carbapenem-resistant Acinetobacter baumannii. Curr Pharm Des. 2013;19(2):223–38. https://doi.org/10.2174/138161213804070285.
Moffatt JH, Harper M, Harrison P, Hale JDF, Vinogradov E, Seemann T, et al. Colistin Resistance in <em>Acinetobacter baumannii</em> Is Mediated by Complete Loss of Lipopolysaccharide Production. Antimicrob Agents Chemother. 2010;54(12):4971–7. https://doi.org/10.1128/AAC.00834-10, Colistin Resistance in Acinetobacter baumannii Is Mediated by Complete Loss of Lipopolysaccharide Production.
Thet KT, Lunha K, Srisrattakarn A, Lulitanond A, Tavichakorntrakool R, Kuwatjanakul W, et al. Colistin heteroresistance in carbapenem-resistant Acinetobacter baumannii clinical isolates from a Thai university hospital. World J Microbiol Biotechnol. 2020;36(7):102. https://doi.org/10.1007/s11274-020-02873-8.
Camargo CH, Cunha MPV, de Barcellos TAF, Bueno MS, AMdJ B, dos Santos CA, et al. Genomic and phenotypic characterisation of antimicrobial resistance in carbapenem-resistant Acinetobacter baumannii hyperendemic clones CC1, CC15, CC79 and CC25. Int J Antimicrob Agents. 2020;56(6):106195. https://doi.org/10.1016/j.ijantimicag.2020.106195.
Ko KS, Choi Y, Lee J-Y. Old drug, new findings: colistin resistance and dependence of Acinetobacter baumannii. Precis Future Med. 2017;1(4):159–67. https://doi.org/10.23838/pfm.2017.00184.
Lesho E, Yoon EJ, McGann P, Snesrud E, Kwak Y, Milillo M, et al. Emergence of colistin-resistance in extremely drug-resistant Acinetobacter baumannii containing a novel pmrCAB operon during colistin therapy of wound infections. J Infect Dis. 2013;208(7):1142–51. https://doi.org/10.1093/infdis/jit293.
Pelletier MR, Casella LG, Jones JW, Adams MD, Zurawski DV, Hazlett KR, et al. Unique structural modifications are present in the lipopolysaccharide from colistin-resistant strains of Acinetobacter baumannii. Antimicrob Agents Chemother. 2013;57(10):4831–40. https://doi.org/10.1128/aac.00865-13.
Qureshi ZA, Hittle LE, O'Hara JA, Rivera JI, Syed A, Shields RK, et al. Colistin-resistant Acinetobacter baumannii: beyond Carbapenem resistance. Clin Infect Dis. 2015;60(9):1295–303. https://doi.org/10.1093/cid/civ048.
Yang M, Zhang C, Zhang MZ, Zhang S. Beta-defensin derived cationic antimicrobial peptides with potent killing activity against gram negative and gram positive bacteria. BMC Microbiol. 2018;18(1):54. https://doi.org/10.1186/s12866-018-1190-z.
Ling LL, Schneider T, Peoples AJ, Spoering AL, Engels I, Conlon BP, et al. A new antibiotic kills pathogens without detectable resistance. Nature. 2015;517(7535):455–9. https://doi.org/10.1038/nature14098.
Huws SA, Edwards JE, Creevey CJ, Rees Stevens P, Lin W, Girdwood SE, et al. Temporal dynamics of the metabolically active rumen bacteria colonizing fresh perennial ryegrass. FEMS Microbiol Ecol. 2016;92(1). https://doi.org/10.1093/femsec/fiv137.
Ougham HJ, Davies TGE. Leaf development in Lolium temulentum: Gradients of RNA complement and plastid and non-plastid transcripts. Physiol Plant. 1990;79(2):331–8. https://doi.org/10.1111/j.1399-3054.1990.tb06750.x.
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–20. https://doi.org/10.1093/bioinformatics/btu170.
Wingett SW, Andrews S. FastQ Screen: A tool for multi-genome mapping and quality control. F1000Res. 2018;7:1338. https://doi.org/10.12688/f1000research.15931.2.
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011;29(7):644–52. https://doi.org/10.1038/nbt.1883.
Torrent M, Di Tommaso P, Pulido D, Nogués MV, Notredame C, Boix E, et al. AMPA: an automated web server for prediction of protein antimicrobial regions. Bioinformatics. 2012;28(1):130–1. https://doi.org/10.1093/bioinformatics/btr604.
Hammami R, Zouhir A, Le Lay C, Hamida JB, Fliss I. BACTIBASE second release: a database and tool platform for bacteriocin characterization. BMC Microbiol. 2010;10(1):22. https://doi.org/10.1186/1471-2180-10-22.
Waghu FH, Barai RS, Gurung P, Idicula-Thomas S. CAMPR3: a database on sequences, structures and signatures of antimicrobial peptides. Nucleic Acids Res. 2015;44(D1):D1094–D7.
Hilpert K, Winkler DFH, Hancock REW. Peptide arrays on cellulose support: SPOT synthesis, a time and cost efficient method for synthesis of large numbers of peptides in a parallel and addressable fashion. Nat Protoc. 2007;2(6):1333–49. https://doi.org/10.1038/nprot.2007.160.
Maupetit J, Derreumaux P, Tuffery P. PEP-FOLD: an online resource for de novo peptide structure prediction. Nucleic Acids Res. 2009;37(Web Server issue):W498–503. https://doi.org/10.1093/nar/gkp323.
Maupetit J, Tuffery P, Derreumaux P. A coarse-grained protein force field for folding and structure prediction. Proteins. 2007;69(2):394–408. https://doi.org/10.1002/prot.21505.
Schrödinger LLC. The PyMOL Molecular Graphics System, Version 1.7.6; 2010.
Gautier R, Douguet D, Antonny B, Drin G. HELIQUEST: a web server to screen sequences with specific alpha-helical properties. Bioinformatics. 2008;24(18):2101–2. https://doi.org/10.1093/bioinformatics/btn392.
Friedrich CL, Moyles D, Beveridge TJ, Hancock RE. Antibacterial action of structurally diverse cationic peptides on gram-positive bacteria. Antimicrob Agents Chemother. 2000;44(8):2086–92. https://doi.org/10.1128/AAC.44.8.2086-2092.2000.
Mikut R. Computer-based analysis, visualization, and interpretation of antimicrobial peptide activities. In: Giuliani A, Rinaldi AC, editors. Antimicrobial peptides: methods and protocols. Totowa, NJ: Humana Press; 2010. p. 287–99. https://doi.org/10.1007/978-1-60761-594-1_18.
Mikut R, Bartschat A, Doneit W, González-Ordiano JA, Schott B, Stegmaier J, et al. The MATLAB Toolbox SciXMiner: user’s manual and programmer’s guide. arXiv. 2017;170403298:1–189.
Jorgensen JH. Development of global standards for antimicrobial susceptibility testing: The ISO initiative. Clin Microbiol Newsl. 2006;28(20):153–7. https://doi.org/10.1016/j.clinmicnews.2006.10.001.
Kim T, Bak G, Lee J, Kim KS. Systematic analysis of the role of bacterial Hfq-interacting sRNAs in the response to antibiotics. J Antimicrob Chemother. 2015. https://doi.org/10.1093/jac/dkv042.
Oliva B, Miller K, Caggiano N, O'Neill AJ, Cuny GD, Hoemann MZ, et al. Biological properties of novel antistaphylococcal quinoline-indole agents. Antimicrob Agents Chemother. 2003;47(2):458–66. https://doi.org/10.1128/AAC.47.2.458-466.2003.
Friedman L, Alder JD, Silverman JA. Genetic changes that correlate with reduced susceptibility to daptomycin in Staphylococcus aureus. Antimicrob Agents Chemother. 2006;50(6):2137–45. https://doi.org/10.1128/AAC.00039-06.
Di Pasquale E, Salmi-Smail C, Brunel J-M, Sanchez P, Fantini J, Maresca M. Biophysical studies of the interaction of squalamine and other cationic amphiphilic molecules with bacterial and eukaryotic membranes: importance of the distribution coefficient in membrane selectivity. Chem Phys Lipids. 2010;163(2):131–40. https://doi.org/10.1016/j.chemphyslip.2009.10.006.
Baindara P, Gautam A, Raghava GPS, Korpole S. Anticancer properties of a defensin like class IId bacteriocin Laterosporulin10. Sci Rep. 2017;7:46541. https://doi.org/10.1038/srep46541.
Huws SA, Mayorga OL, Theodorou MK, Onime LA, Kim EJ, Cookson AH, et al. Successional colonization of perennial ryegrass by rumen bacteria. Lett Appl Microbiol. 2013;56(3):186–96. https://doi.org/10.1111/lam.12033.