Cutting the Gordian knot: early and complete amino acid sequence confirmation of class II lasso peptides by HCD fragmentation.
Journal
The Journal of antibiotics
ISSN: 1881-1469
Titre abrégé: J Antibiot (Tokyo)
Pays: England
ID NLM: 0151115
Informations de publication
Date de publication:
11 2020
11 2020
Historique:
received:
17
08
2020
accepted:
17
08
2020
pubmed:
11
9
2020
medline:
20
2
2021
entrez:
10
9
2020
Statut:
ppublish
Résumé
Lasso peptides are a diverse class of ribosomally synthesized and post-translationally modified peptides (RiPPs). Their proteolytic and thermal stability alongside their growing potential as therapeutics has increased attention to these antimicrobial peptides. With the advent of genome mining, the discovery of RiPPs allows for the accurate prediction of putatively encoded structures, however, MS
Identifiants
pubmed: 32908238
doi: 10.1038/s41429-020-00369-z
pii: 10.1038/s41429-020-00369-z
doi:
Substances chimiques
Peptides, Cyclic
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
772-779Références
Hegemann JD, Zimmermann M, Xie X, Marahiel MA. Lasso peptides: an intriguing class of bacterial natural products. Acc Chem Res. 2015;48:1909–19.
doi: 10.1021/acs.accounts.5b00156
Knappe TA, Linne U, Xie X, Marahiel MA. The glucagon receptor antagonist BI-32169 constitutes a new class of lasso peptides. FEBS Lett. 2010;584:785–9.
doi: 10.1016/j.febslet.2009.12.046
Iwatsuki M, Tomoda H, Uchida R, Gouda H, Hirono S, Omura S. Lariatins, antimycobacterial peptides produced by Rhodococcus sp. K01-B0171, have a lasso structure. J Am Chem Soc. 2006;128:7486–91.
doi: 10.1021/ja056780z
Detlefsen DJ, Hill SE, Volk KJ, Klohr SE, Tsunakawa M, Furumai T, et al. Siamycins I and II, new anti-HIV-1 peptides: II. Sequence analysis and structure determination of siamycin I. J Antibiot. 1995;48:1515–7.
doi: 10.7164/antibiotics.48.1515
Gavrish E, Sit CS, Cao S, Kandror O, Spoering A, Peoples A, et al. Lassomycin, a ribosomally synthesized cyclic peptide, kills mycobacterium tuberculosis by targeting the ATP-dependent protease ClpC1P1P2. Chem Biol. 2014;21:509–18.
doi: 10.1016/j.chembiol.2014.01.014
Metelev M, Tietz JI, Melby JO, Blair PM, Zhu L, Livnat I, et al. Structure, bioactivity, and resistance mechanism of streptomonomicin, an unusual lasso Peptide from an understudied halophilic actinomycete. Chem Biol. 2015;22:241–50.
doi: 10.1016/j.chembiol.2014.11.017
Um S, Kim YJ, Kwon H, Wen H, Kim SH, Kwon HC, et al. Sungsanpin, a lasso peptide from a deep-sea streptomycete. J Nat Prod. 2013;76:873–9.
doi: 10.1021/np300902g
Elsayed SS, Trusch F, Deng H, Raab A, Prokes I, Busarakam K, et al. Chaxapeptin, a Lasso Peptide from Extremotolerant Streptomyces leeuwenhoekii Strain C58 from the Hyperarid Atacama Desert. J Org Chem. 2015;80:10252–60.
doi: 10.1021/acs.joc.5b01878
Weber W, Fischli W, Hochuli E, Kupfer E, Weibel EK. Anantin-a peptide antagonist of the atrial natriuretic factor (ANF). I. Producing organism, fermentation, isolation and biological activity. J Antibiot. 1991;44:164–71.
doi: 10.7164/antibiotics.44.164
Potterat O, Wagner K, Gemmecker G, Mack J, Puder C, Vettermann R, et al. BI-32169, a bicyclic 19-peptide with strong glucagon receptor antagonist activity from Streptomyces sp. J Nat Prod. 2004;67:1528–31.
doi: 10.1021/np040093o
Cheung-Lee WL, Parry ME, Jaramillo Cartagena A, Darst SA, Link AJ. Discovery and structure of the antimicrobial lasso peptide citrocin. J Biol Chem. 2019;294:6822–30.
doi: 10.1074/jbc.RA118.006494
Kaweewan I, Hemmi H, Komaki H, Harada S, Kodani S. Isolation and structure determination of a new lasso peptide specialicin based on genome mining. Bioorg Medicinal Chem. 2018;26:6050–5.
doi: 10.1016/j.bmc.2018.11.007
Santos-Aberturas J, Chandra G, Frattaruolo L, Lacret R, Pham TH, Vior NM, et al. Uncovering the unexplored diversity of thioamidated ribosomal peptides in Actinobacteria using the RiPPER genome mining tool. Nucleic Acids Res. 2019;47:4624–37.
doi: 10.1093/nar/gkz192
Hudson G, Burkhart B, DiCaprio A, Schwalen C, Kille B, Pogorelov T, et al. Bioinformatic mapping of radical S-adenosylmethionine-dependent ribosomally synthesized and post-translationally modified peptides identifies new Cα, Cβ, and Cγ-linked thioether-containing peptides. J Am Chem Soc. 2019;141:8228–38.
pubmed: 31059252
pmcid: 6622460
Tietz JI, Schwalen CJ, Patel PS, Maxson T, Blair PM, Tai HC, et al. A new genome-mining tool redefines the lasso peptide biosynthetic landscape. Nat Chem Biol. 2017;13:470–8.
doi: 10.1038/nchembio.2319
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:W81–7.
doi: 10.1093/nar/gkz310
Paizs B, Suhai S. Fragmentation pathways of protonated peptides. Mass Spectrom Rev. 2005;24:508–48.
doi: 10.1002/mas.20024
Ngoka LC, Gross ML. Multistep tandem mass spectrometry for sequencing cyclic peptides in an ion-trap mass spectrometer. J Am Soc Mass Spectrom. 1999;10:732–46.
doi: 10.1016/S1044-0305(99)00049-5
Medzihradszky KF, Chalkley RJ. Lessons in de novo peptide sequencing by tandem mass spectrometry. Mass Spec Rev. 2013;34:43–63.
doi: 10.1002/mas.21406
Mohimani H, Gurevich A, Mikheenko A, Garg N, Nothias L, Ninomiya A, et al. Dereplication of peptidic natural products through database search of mass spectra. Nat Chem Biol. 2017;13:30–7.
doi: 10.1038/nchembio.2219
Mohimani H, Kersten RD, Liu WT, Wang M, Purvine SO, Wu S, et al. Automated genome mining of ribosomal peptide natural products. ACS Chem Biol. 2014;9:1545–51.
doi: 10.1021/cb500199h
Mohimani H, Yang YL, Liu WT, Hsieh PW, Dorrestein PC, Pevzner PA. Sequencing cyclic peptides by multistage mass spectrometry. Proteomics. 2011;11:3642–50.
doi: 10.1002/pmic.201000697
Niedermeyer, Timo H J, Strohalm M. mMass as a software tool for the annotation of cyclic peptide tandem mass spectra. PLoS ONE. 2012;7:e44913.
Xie X, Marahiel MA. NMR as an effective tool for the structure determination of lasso peptides. Chem Biochem. 2012;13:621–5.
Rosengren KJ, Clark RJ, Daly NL, Göransson U, Jones A, Craik DJ. Microcin J25 Has a threaded sidechain-to-backbone ring structure and not a head-to-tail cyclized backbone. J Am Chem Soc. 2003;125:12464–74.
doi: 10.1021/ja0367703
Wilson K, Kalkum M, Ottesen J, Yuzenkova J, Chait BT, Landick R, et al. Structure of microcin J25, a peptide inhibitor of bacterial RNA polymerase, is a lassoed tail. J Am Chem Soc. 2003;125:12475–83.
doi: 10.1021/ja036756q
Jeanne Dit Fouque K, Lavanant H, Zirah S, Hegemann JD, Fage CD, Marahiel MA, et al. General rules of fragmentation evidencing lasso structures in CID and ETD. Analyst. 2018;143:1157–70.
doi: 10.1039/C7AN02052J
Dit Fouque KJ, Moreno J, Hegemann JD, Zirah S, Rebuffat S, Fernandez-Lima F. Identification of lasso peptide topologies using native nanoelectrospray ionization-trapped ion mobility spectrometry—mass spectrometry. Anal Chem. 2018;90:5139–46.
doi: 10.1021/acs.analchem.7b05230
Cortés-Albayay C, Jarmusch S, Trusch F, Ebel R, Andrews B, Jaspars M, et al. Downsizing class II lasso peptides: genome mining-guided isolation of huascopeptin containing the first Gly1-Asp7 macrocycle. J Org Chem. 2020;85:1661–7.
doi: 10.1021/acs.joc.9b02231
Gomez-Escribano JP, Castro JF, Razmilic V, Jarmusch SA, Saalbach G, Ebel R, et al. Heterologous expression of a cryptic gene cluster from Streptomyces leeuwenhoekii C34T yields a novel lasso peptide, leepeptin. Appl Environ Microbiol. 2019;85:e01752–19.
doi: 10.1128/AEM.01752-19
Elashal HE, Cohen RD, Elashal HE, Zong C, Link AJ, Raj M. Cyclic and lasso peptides: sequence determination, topology analysis, and rotaxane formation. Angew Chem Int Ed Engl. 2018;57:6150–4.
doi: 10.1002/anie.201801299
Brodbelt JS. Ion activation methods for peptides and proteins. Anal Chem. 2016;88:30–51.
doi: 10.1021/acs.analchem.5b04563
Chekan JR, Koos JD, Zong C, Maksimov MO, Link AJ, Nair SK. Structure of the lasso peptide isopeptidase identifies a topology for processing threaded substrates. J Am Chem Soc. 2016;138:16452–8.
doi: 10.1021/jacs.6b10389
Okoro CK, Brown R, Jones AL, Andrews BA, Asenjo JA, Goodfellow M, et al. Diversity of culturable actinomycetes in hyper-arid soils of the Atacama Desert, Chile. Antonie Van Leeuwenhoek. 2009;95:121–33.
doi: 10.1007/s10482-008-9295-2
Cortés-Albayay C, Dorador C, Schumann P, Andrews B, Asenjo J, Nouioui I. Streptomyces huasconensis sp. nov., an haloalkalitolerant actinobacterium isolated from a high altitude saline wetland at the Chilean Altiplano. Int J Syst Evolut Microbiol. 2019;69:2315–22.
doi: 10.1099/ijsem.0.003468
Rateb ME, Houssen WE, Harrison WT, Deng H, Okoro CK, Asenjo JA, et al. Diverse metabolic profiles of a Streptomyces strain isolated from a hyper-arid environment. J Nat Prod. 2011;74:1965–71.
doi: 10.1021/np200470u
Goodfellow M, Nouioui I, Sanderson R, Xie F, Bull AT. Rare taxa and dark microbial matter: novel bioactive actinobacteria abound in Atacama Desert soils. Antonie Van Leeuwenhoek. 2018;111:1315–32.
doi: 10.1007/s10482-018-1088-7
Manfio GP, Atalan E, Zakrzewska-Czerwinska J, Mordarski M, Rodriguez C, Collins MD, et al. Classification of novel soil streptomycetes as Streptomyces aureus sp. nov., Streptomyces laceyi sp. nov. and Streptomyces sanglieri sp. nov. Antonie Van Leeuwenhoek. 2003;83:245–55.
doi: 10.1023/A:1023332427794
Rateb ME, Houssen WE, Arnold M, Abdelrahman MH, Deng H, Harrison WT, et al. Chaxamycins A-D, bioactive ansamycins from a hyper-arid desert Streptomyces sp. J Nat Prod. 2011;74:1491–9.
doi: 10.1021/np200320u