246
Views
4
CrossRef citations to date
0
Altmetric
Review

Deciphering bioactive peptides and their action mechanisms through proteomics

, , &
Pages 1007-1016 | Received 17 Jun 2016, Accepted 15 Sep 2016, Published online: 08 Oct 2016

References

  • Trindade M, van Zyl LJ, Navarro-Fernández J, et al. Targeted metagenomics as a tool to tap into marine natural product diversity for the discovery and production of drug candidates. Front Microbiol. 2015;6:890.
  • Vale N, Aguiar L, Gomes P. Antimicrobial peptides: a new class of antimalarial drugs? Front Pharmacol. 2014;5:275.
  • Valdivia-Silva J, Medina-Tamayo J, Garcia-Zepeda EA. Chemokine-derived peptides: novel antimicrobial and antineoplasic agents. Int J Mol Sci. 2015;16:12958–12985.
  • Wang G, Mishra B, Lau K, et al. Antimicrobial peptides in 2014. Pharmaceuticals. 2015;8:123–150.
  • Lewies A, Wentzel JF, Jacobs G, et al. The potential use of natural and structural analogues of antimicrobial peptides in the fight against neglected tropical diseases. Molecules. 2015;20:15392–15433.
  • Guilhelmelli F, Vilela N, Albuquerque P, et al. Antibiotic development challenges: the various mechanisms of action of antimicrobial peptides and of bacterial resistance. Front Microbiol. 2013;4:353.
  • Mandal SM, Roy A, Ghosh AK, et al. Challenges and future prospects of antibiotic therapy: from peptides to phages utilization. Front Pharmacol. 2014;5:105.
  • Wenzel M, Chiriac AI, Otto A, et al. Small cationic antimicrobial peptides delocalize peripheral membrane proteins. Proc Natl Acad Sci U S A. 2014;111:E1409–1418.
  • Wenzel M, Schriek P, Prochnow P, et al. Influence of lipidation on the mode of action of a small RW-rich antimicrobial peptide. Biochim Biophys Acta. 2016;1858:1004–1011.
  • Juba ML, Russo PS, Devine M, et al. Large scale discovery and de novo-assisted sequencing of Cationic Antimicrobial Peptides (CAMPs) by microparticle capture and Electron-Transfer Dissociation (ETD) mass spectrometry. J Proteome Res. 2015;14:4282–4295.
  • Lee MH, Lee J, Nam YD, et al. Characterization of antimicrobial lipopeptides produced by Bacillus sp. LM7 isolated from chungkookjang, a Korean traditional fermented soybean food. Int J Food Microbiol. 2016;221:12–18.
  • Trindade F, Amado F, Pinto da Costa J, et al. Salivary peptidomic as a tool to disclose new potential antimicrobial peptides. J Proteomics. 2015;115:49–57.
  • Mechkarska M, Coquet L, Leprince J, et al. Host-defense peptides from skin secretions of the octoploid frogs Xenopus vestitus and Xenopus wittei (Pipidae): insights into evolutionary relationships. Comp Biochem Physiol Part D Genomics Proteomics. 2014;11:20–28.
  • Bishop BM, Juba ML, Devine MC, et al. Bioprospecting the American alligator (Alligator mississippiensis) host defense peptidome. PLoS One. 2015;10:e0117394.
  • Luchini A, Geho DH, Bishop B, et al. Smart hydrogel particles: biomarker harvesting: one-step affinity purification, size exclusion, and protection against degradation. Nano Lett. 2008;8:350–361.
  • Osaki T, Sasaki K, Minamino N. Peptidomics-based discovery of an antimicrobial peptide derived from insulin-like growth factor binding protein 5. J Proteome Res. 2011;10:1870–1880.
  • Sasaki K, Takahashi N, Satoh M, et al. A peptidomics strategy for discovering endogenous bioactive peptides. J Proteome Res. 2010;9:5047–5052.
  • Yamaguchi H, Sasaki K, Satomi Y, et al. Peptidomic identification and biological validation of neuroendocrine regulatory peptide-1 and −2. J Biol Chem. 2007;282:26354–26360.
  • Kim MS, Pandey A. Electron transfer dissociation mass spectrometry in proteomics. Proteomics. 2012;12:530–542.
  • Shen Y, Tolić N, Purvine SO, et al. Improving collision induced dissociation (CID), high energy collision dissociation (HCD), and electron transfer dissociation (ETD) fourier transform MS/MS degradome-peptidome identifications using high accuracy mass information. J Proteome Res. 2012;11:668–677.
  • Sasaki K, Osaki T, Ninamino N. Large-scale identification of endogenous secretory peptides using electron transfer dissociation mass spectrometry. Mol Cell Proteomics. 2013;12:700–709.
  • Azkargorta M, Soria J, Ojeda C, et al. Human basal tear peptidome characterization by CID, HCD, and ETD followed by in silico and in vitro analyses for antimicrobial peptide identification. J Proteome Res. 2015;14:2649–2658.
  • Burman R, Yeshak MY, Larsson S, et al. Distribution of circular proteins in plants: large-scale mapping of cyclotides in the violaceae. Front Plant Sci. 2015;6:855.
  • Zhang J, Li J, Huang Z, et al. Transcriptomic screening for cyclotides and other cysteine-rich proteins in the metallophyte Viola baoshanensis. J Plant Physiol. 2015;178:17−26.
  • Weidmann J, Craik DJ. Discovery, structure, function, and applications of cyclotides: circular proteins from plants. J Exp Bot. 2016;67:4801–4812.
  • Burman R, Gunasekera S, Strömstedt AA, et al. Chemistry and biology of cyclotides: circular plant peptides outside the box. J Nat Prod. 2014;77:724–736.
  • Hellinger R, Koehbach J, Soltis DE, et al. Peptidomics of circular cysteine-rich plant peptides: analysis of the diversity of cyclotides from Viola tricolor by transcriptome and proteome mining. J Proteome Res. 2015;14:4851–4862.
  • Boddy CN. Bioinformatics tools for genome mining of polyketide and non-ribosomal peptides. J Ind Microbiol Biotechnol. 2014;41:443–450.
  • Abdo A, Caboche S, Leclère V, et al. A new fingerprint to predict nonribosomal peptides activity. J Comput Aided Mol Des. 2012;26:1187–1194.
  • Morton JT, Freed SD, Lee SW, et al. A large scale prediction of bacteriocin gene blocks suggests a wide functional spectrum for bacteriocins. BMC Bioinformatics. 2015;16:381.
  • Esmaeel Q, Pupin M, Kieu NP, et al. Burkholderia genome mining for nonribosomal peptide synthetases reveals a great potential for novel siderophores and lipopeptides synthesis. Microbiologyopen. 2016;5:512–526.
  • Azevedo AC, Bento CB, Ruiz JC, et al. Distribution and genetic diversity of bacteriocin gene clusters in rumen microbial genomes. Appl Environ Microbiol. 2015;81:7290–7304.
  • Goering AW, McClure RA, Doroghazi JR, et al. Metabologenomics: correlation of microbial gene clusters with metabolites drives discovery of a nonribosomal peptide with an unusual amino acid monomer. ACS Cent Sci. 2016;2:99–108.
  • Weber T, Blin K, Duddela S, et al. antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res. 2015;43:W237–W243.
  • Ziemert N, Alanjary M, Weber T. The evolution of genome mining in microbes–a review. Nat Prod Rep. 2016;33:988–1005.
  • Skinnider MA, Dejong CA, Rees PN, et al. Genomes to natural products prediction informatics for secondary metabolomes (PRISM). Nucleic Acids Res. 2015;43:9645–9662.
  • Chen Y, Unger M, Ntai I, et al. Gobichelin A and B: mixed-ligand siderophores discovered using proteomics. Medchemcomm. 2013;4:233–238.
  • Chen Y, McClure RA, Zheng Y, et al. Proteomics guided discovery of flavopeptins: anti-proliferative aldehydes synthesized by a reductase domain-containing nonribosomal peptide synthetase. J Am Chem Soc. 2013;135:10449–10456.
  • Albrighta JC, Goeringa AW, Doroghazib JR, et al. Strain-specific proteogenomics accelerates discovery of natural products via their biosynthetic pathways. J Ind Microbiol Biotechnol. 2014;41:451–459.
  • Mohimani H, Liu WT, Liang Y, et al. Multiplex de novo sequencing of peptide antibiotics. J Comput Biol. 2011;18:1371−1381.
  • Mohimani H, Liu WT, Kersten RD, et al. NRPquest: coupling mass spectrometry and genome mining for nonribosomal peptide discovery. J Nat Prod. 2014;77:1902−1909.
  • Schimana J, Gebhardt K, Höltzel A, et al. Arylomycins A and B, new biaryl-bridged lipopeptide antibiotics produced by Streptomyces sp. Tü 6075. I. Taxonomy, fermentation, isolation and biological activities. J Antibiot (Tokyo). 2002;55:565–570.
  • Rao M, Wei W, Ge M, et al. A new antibacterial lipopeptide found by UPLC-MS from an actinomycete Streptomyces sp. HCCB10043. Nat Prod Res. 2013;27:2190–2195.
  • Johnston CW, Skinnider MA, Wyatt MA, et al. An automated Genomes-to-Natural Products platform (GNP) for the discovery of modular natural products. Nat Commun. 2015;6:842.
  • Arnison PG, Bibb MJ, Bierbaum G, et al. Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature. Nat Prod Rep. 2013;30(1):108–160.
  • Mohr KI, Volz C, Jansen R, et al. Pinensins: the first antifungal lantibiotics. Angew Chem Int. 2015;54:11254–11258.
  • Zheng Q, Wang Q, Wang S, et al. Thiopeptide antibiotics exhibit a dual mode of action against intracellular pathogens by affecting both host and microbe. Chem Biol. 2015;22:1002–1007.
  • Ortega MA, van der Donk WA. New insights into the biosynthetic logic of ribosomally synthesized and post-translationally modified peptide natural products. Cell Chem Biol. 2016;23:31–44.
  • Cotter PD, Ross RP, Hill C. Bacteriocins - a viable alternative to antibiotics? Nat Rev Microbiol. 2013;11:95–105.
  • Cox CL, Doroghazi JR, Mitchell DA. The genomic landscape of ribosomal peptides containing thiazole and oxazole heterocycles. BMC Genomics. 2015;16:778.
  • Yang X, van der Donk WA. Ribosomally synthesized and post‐translationally modified peptide natural products: new insights into the role of leader and core peptides during biosynthesis. Chemistry. 2013;19:7662–7677.
  • Zhang Q, Ortega M, Shi Y, et al. Structural investigation of ribosomally synthesized natural products by hypothetical structure enumeration and evaluation using tandem MS. Proc Natl Acad Sci USA. 2014;111:12031–12036.
  • van Heel AJ, de Jong A, Montalbán-López M, et al. BAGEL3: automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides. Nucleic Acids Res. 2013;41:W448–53.
  • Letzel AC, Pidot SJ, Hertweck C. Genome mining for ribosomally synthesized and post-translationally modified peptides (RiPPs) in anaerobic bacteria. BMC Genomics. 2014;15:983.
  • Mohimani H, Kersten RD, Liu WT, et al. Automated genome mining of ribosomal peptide natural products. ACS Chem Biol. 2014;9:1545–1551.
  • van der Lee TAJ, Medema MH. Computational strategies for genome-based natural product discovery and engineering in fungi. Fungal Genet Biol. 2016;89:29–36.
  • Gupta VK, Sreenivasaprasad S, Mach RL, editor Fungal bio-molecules: sources, applications and recent developments. London (UK): John Wiley & Sons; 2015.
  • Susca A, Proctor RH, Butchko RAE, et al. Variation in the fumonisin biosynthetic gene cluster in fumonisin-producing and nonproducing black aspergilli. Fungal Genet Biol. 2014;73:39–52.
  • Umemura M, Koike H, Machida M. Motif-independent de novo detection of secondary metabolite gene clusters—toward identification from filamentous fungi. Front Microbiol. 2015;6:371.
  • Umemura M, Nagano N, Koike H, et al. Characterization of the biosynthetic gene cluster for the ribosomally synthesized cyclic peptide ustiloxin B in Aspergillus flavus. Fungal Genet Biol. 2014;68:23–30.
  • Li YF, Tsai KJS, Harvey CJB, et al. Complete curation of fungal gene clusters encoding experimentally verified natural products. Fungal Genet Biol. 2016;89:18–28.
  • Jiménez JJ, Diep DB, Borrero J, et al. Cloning strategies for heterologous expression of the bacteriocin enterocin A by Lactobacillus sakei Lb790, Lb. plantarum NC8 and Lb. casei CECT475. Microb Cell Fact. 2015;14:166.
  • Dobson A, Cotter PD, Ross RP, et al. Bacteriocin production: a probiotic trait? Appl Environ Microbiol. 2012;78:1–6.
  • Hong SY, Roze LV, Linz JE. Oxidative stress-related transcription factors in the regulation of secondary metabolism. Toxins (Basel). 2013;5:683–702.
  • Reen FJ, Romano S, Dobson AD, et al. The sound of silence: activating silent biosynthetic gene clusters in marine microorganisms. Mar Drugs. 2015;13:4754–4783.
  • Bok JW, Ye R, Clevenger KD, et al. Fungal artificial chromosomes for mining of the fungal secondary metabolome. BMC Genomics. 2015;16:343.
  • Guo CJ, Wang CC. Recent advances in genome mining of secondary metabolites in Aspergillus terreus. Front Microbiol. 2014;23;5:717.
  • Yin WB, Baccile JA, Bok JW, et al. A nonribosomal peptide synthetase-derived iron(III) complex from the pathogenic fungus Aspergillus fumigatus. J Am Chem Soc. 2013;135:2064–2067.
  • Rutledge PJ, Challis GL. Discovery of microbial natural products by activation of silent biosynthetic gene clusters. Nat Rev Microbiol. 2015;13:509–523.
  • Mattern DJ, Valiante V, Unkles SE, et al. Synthetic biology of fungal natural products. Front Microbiol. 2015;6:775.
  • Doudna JA, Charpentier E. The new frontier of genome engineering with CRISPR-Cas9. Science. 2014;346:1258096.
  • Hsu PD, Lander ES, Zhang F. Development and applications of CRISPR-Cas9 for genome engineering. Cell. 2014;157:1262–1278.
  • Kim HU, Charusanti P, Lee SY, et al. Metabolic engineering with systems biology tools to optimize production of prokaryotic secondary metabolites. Nat Prod Rep. 2016;33:933–941. published online April 2016. doi:10.1039/c6np00019c
  • Wenzel M, Senges CH, Zhang J, et al. Antimicrobial peptides from the aurein family form ion-selective pores in bacillus subtilis. Chembiochem. 2015;16:1101–1108.
  • Miao J, Chen F, Duan S, et al. iTRAQ-based quantitative proteomic analysis of the antimicrobial mechanism of peptide F1 against escherichia coli. J Agric Food Chem. 2015;63:7190–7197.
  • Chung MC, Dean SN, van Hoek ML. Acyl carrier protein is a bacterial cytoplasmic target of cationic antimicrobial peptide LL-37. Biochem J. 2015;470:243–253.
  • Ho YH, Shah P, Chen YW, et al. Systematic analysis of intracellular-targeting antimicrobial peptides, bactenecin 7, hybrid of pleurocidin and dermaseptin, proline-arginine-rich peptide, and lactoferricin B, by using Escherichia coli proteome microarrays. Mol Cell Proteomics. 2016;15:1837–1847. pii: mcp.M115.054999.
  • Maria-Neto S, de Almeida KC, Macedo AL, et al. Understanding bacterial resistance to antimicrobial peptides: from the surface to deep inside. Biochim Biophys Acta. 2015;1848:3078–3088.
  • Ramos S, Chafsey I, Silva N, et al. Effect of vancomycin on the proteome of the multiresistant Enterococcus faecium SU18 strain. J Proteomics. 2015;113:378–387.
  • Hessling B, Bonn F, Otto A, et al. Global proteome analysis of vancomycin stress in Staphylococcus aureus. Int J Med Microbiol. 2013;303:624–634.
  • Chen H, Liu Y, Zhao C, et al. Comparative proteomics-based identification of genes associated with glycopeptide resistance in clinically derived heterogeneous vancomycin-intermediate Staphylococcus aureus strains. PLoS One. 2013;8:e66880.
  • Maria-Neto S, Cândido Ede S, Rodrigues DR, et al. Deciphering the magainin resistance process of Escherichia coli strains in light of the cytosolic proteome. Antimicrob Agents Chemother. 2012;56:1714–1724.
  • Fischer A, Yang SJ, Bayer AS, et al. Daptomycin resistance mechanisms in clinically derived Staphylococcus aureus strains assessed by a combined transcriptomics and proteomics approach. J Antimicrob Chemother. 2011;66:1696–1711.
  • Miyamoto KN, Monteiro KM, da Silva Caumo K, et al. Comparative proteomic analysis of Listeria monocytogenes ATCC 7644 exposed to a sublethal concentration of nisin. J Proteomics. 2015;119:230–237.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.