Multiplex de novo sequencing of peptide antibiotics.
Proliferation of drug-resistant diseases raises the challenge of searching for new, more efficient antibiotics. Currently, some of the most effective antibiotics (i.e., Vancomycin and Daptomycin) are cyclic peptides produced by non-ribosomal biosynthetic pathways. The isolation and sequencing of cyclic peptide antibiotics, unlike the same activity with linear peptides, is time-consuming and error-prone. The dominant technique for sequencing cyclic peptides is nuclear magnetic resonance (NMR)-based and requires large amounts (milligrams) of purified materials that, for most compounds, are not possible to obtain. Given these facts, there is a need for new tools to sequence cyclic non-ribosomal peptides (NRPs) using picograms of material. Since nearly all cyclic NRPs are produced along with related analogs, we develop a mass spectrometry approach for sequencing all related peptides at once (in contrast to the existing approach that analyzes individual peptides). Our results suggest that instead of attempting to isolate and NMR-sequence the most abundant compound, one should acquire spectra of many related compounds and sequence all of them simultaneously using tandem mass spectrometry. We illustrate applications of this approach by sequencing new variants of cyclic peptide antibiotics from Bacillus brevis, as well as sequencing a previously unknown family of cyclic NRPs produced by marine bacteria. Supplementary Material is available online at www.liebertonline.com/cmb.
Department of Electrical and Computer Engineering, University of California San Diego, San Diego, California 92092, USA.
Hosein
H
Mohimani
Wei-Ting
WT
Liu
Yu-Liang
YL
Yang
Susana P
SP
Gaudêncio
William
W
Fenical
Pieter C
PC
Dorrestein
Pavel A
PA
Pevzner
D000465:Algorithms; D000595:Amino Acid Sequence; D000900:Anti-Bacterial Agents / Q000737:chemistry*; D009842:Oligopeptides / Q000737:chemistry; D010456:Peptides, Cyclic / Q000737:chemistry*; D020539:Sequence Analysis, Protein / Q000379:methods*; D053719:Tandem Mass Spectrometry; D014440:Tyrocidine / Q000737:chemistry
D000900:Anti-Bacterial Agents; D009842:Oligopeptides; D010456:Peptides, Cyclic; D014440:Tyrocidine; C459019:cyclomarin A