Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry to reveal the substrate specificity of the peptidyl-cysteine decarboxylase EpiD

Enzymatic Formation of an Aminovinyl Cysteine Residue in Ribosomal Peptide Natural Products

The carboxyl-terminal (C-terminal) S-[(Z)-2-aminovinyl]-cysteine (AviCys) analogs have been identified in four families of ribosomally synthesized and post-translationally modified peptides (RiPPs): lanthipeptides, linaridins, thioamitides, and lipolanthines. Within identified biosynthetic pathways, a highly reactive enethiol intermediate, formed through an oxidative decarboxylation catalyzed by a LanD-like flavoprotein, can undergo two types of cyclization: a Michael addition with a dehydroamino acid or a coupling reaction initiated by a radical species. The collaborative actions of LanD-like proteins with diverse enzymes involved in dehydration, dethiolation or cyclization lead to the construction of structurally distinct peptide natural products with analogous C-terminal macrocyclic moieties. This concept summarizes existing knowledge regarding biosynthetic pathways of AviCys analogs to emphasize the diversity of biosynthetic mechanisms that paves the way for future genome mining explorations into diverse peptide natural products.

Two Flavoenzymes Catalyze the Post-Translational Generation of 5-Chlorotryptophan and 2-Aminovinyl-Cysteine during NAI-107 Biosynthesis

Lantibiotics are ribosomally synthesized and post-translationally modified antimicrobial peptides containing thioether rings. In addition to these cross-links, the clinical candidate lantibiotic NAI-107 also possesses a C-terminal S-[(Z)-2-aminovinyl]-d-cysteine (AviCys) and a unique 5-chloro-l-tryptophan (ClTrp) moiety linked to its potent bioactivity. Bioinformatic and genetic analyses on the NAI-107 biosynthetic gene cluster identified mibH and mibD as genes encoding flavoenzymes responsible for the formation of ClTrp and AviCys, respectively. The biochemical basis for the installation of these modifications on NAI-107 and the substrate specificity of either enzyme is currently unknown. Using a combination of mass spectrometry, liquid chromatography, and bioinformatic analyses, we demonstrate that MibD is an FAD-dependent Cys decarboxylase and that MibH is an FADH₂-dependent Trp halogenase. Most FADH₂-dependent Trp halogenases halogenate free Trp, but MibH was only active when Trp was embedded within its cognate peptide substrate deschloro NAI-107. Structural comparison of the 1.88-Å resolution crystal structure of MibH with other flavin-dependent Trp halogenases revealed that subtle amino acid differences within the MibH substrate binding site generates a solvent exposed crevice presumably involved in determining the substrate specificity of this unusual peptide halogenase.

Cyclisation mechanisms in the biosynthesis of ribosomally synthesised and post-translationally modified peptides

Ribosomally synthesised and post-translationally modified peptides (RiPPs) are a large class of natural products that are remarkably chemically diverse given an intrinsic requirement to be assembled from proteinogenic amino acids. The vast chemical space occupied by RiPPs means that they possess a wide variety of biological activities, and the class includes antibiotics, co-factors, signalling molecules, anticancer and anti-HIV compounds, and toxins. A considerable amount of RiPP chemical diversity is generated from cyclisation reactions, and the current mechanistic understanding of these reactions will be discussed here. These cyclisations involve a diverse array of chemical reactions, including 1,4-nucleophilic additions, [4 + 2] cycloadditions, ATP-dependent heterocyclisation to form thiazolines or oxazolines, and radical-mediated reactions between unactivated carbons. Future prospects for RiPP pathway discovery and characterisation will also be highlighted.

Processing methods for signal suppression of FTMS data

Background

Fourier Transform Mass Spectrometry coupled with Liquid Chromatography(LC-FTMS) has been widely used in proteomics. Past investigation has revealed that there exists an intensity dependent random suppression in peptide elution profiles in LC-FTMS data. The suppression is homogenous for the same peptide but non-homogenous for different peptides. The correction of suppressed profiles and an estimation on the range of suppression are necessary for accurate and reliable quantification using FTMS data.

Results

A software package, Gcorr, is presented. The software corrects peptide profiles that satisfy correction conditions, and it can predict fold change null distributions at different intensity levels. Subsequently, the significance P-values of measured fold changes can be estimated based on the predicted null distributions. We have used an 1:1 LC-FTMS label-free dataset pair collected based on the same sample to verify that our predicted null distributions conforms to that of the observed null distribution.

Conclusions

This software is able to provide suppression correction for peptide profiles, suppression distribution analysis and peptide differential expression analysis in terms of its fold change significance. The software is freely available at http://compgenomics.utsa.edu/Suppression_Study.html.

Suppression correction and characteristic study in liquid chromatography/Fourier transform mass spectrometry measurements

Analysis of peptide profiles from liquid chromatography/Fourier transform mass spectrometry (LC/FTMS) reveals a nonlinear distortion in intensity. Investigation of the measured C(13)/C(12) ratios comparing with theoretical ones shows that the nonlinearity can be attributed to signal suppression of low abundance peptide peaks. We find that the suppression is homogenous for different isotopes of identical peptides but non-homogenous for different peptides. We develop an iterative correction algorithm that corrects the intensity distortions for peptides with relatively high abundance. This algorithm can be applied in a wide range of applications using LC/FTMS. We also analyze the distortion characteristics of the instrument for lower abundance peptides, which should be considered when interpreting quantification results of LC/FTMS.

Lantibiotics: diverse activities and unique modes of action

Lantibiotics are one of the most promising alternative candidates for future antibiotics that maintain their antibacterial efficacy through many mechanisms. Of these mechanisms, some modes of activity have recently been reported, providing opportunities to show these peptides as potential candidates for forthcoming applications. Many findings providing new insight into the detailed molecular activities of numerous lantibiotics are constantly being uncovered. The combination of antibiotic mechanisms in one lantibiotic molecule shows its diverse antimicrobial usefulness as a future generation of antibiotic. Since lantibiotics do not have any known candidate resistance mechanisms, the discovered distinct modes of activity may revolutionize the design of anti-infective drugs through the knowledge provided by these super molecules. In this review, we discuss the rising assortment of lantibiotics, with special emphasis on their structure-function relationships, addressing the unique activities involved in their individual modes of action.

Ribosomal peptide natural products: bridging the ribosomal and nonribosomal worlds

Ribosomally synthesized bacterial natural products rival the nonribosomal peptides in their structural and functional diversity. The last decade has seen substantial progress in the identification and characterization of biosynthetic pathways leading to ribosomal peptide natural products with new and unusual structural motifs. In some of these cases, the motifs are similar to those found in nonribosomal peptides, and many are constructed by convergent or even paralogous enzymes. Here, we summarize the major structural and biosynthetic categories of ribosomally synthesized bacterial natural products and, where applicable, compare them to their homologs from nonribosomal biosynthesis.

Characterization of orphan monooxygenases by rapid substrate screening using FT-ICR mass spectrometry

Characterization of orphan enzymes, for which the catalytic functions and actual substrates are still not elucidated, is a significant challenge in the postgenomic era. Here, we describe a general strategy for exploring the catalytic potentials of orphan monooxygenases based on direct infusion analysis by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR/MS). Eight cytochromes P450 from Bacillus subtilis were recombinantly expressed in Escherichia coli and subjected to a reconstitution system containing appropriate electron transfer components and many potential substrates. The reaction mixtures were directly analyzed using FT-ICR/MS, and substrates of the putative enzymes were readily identified from the mass spectral data. This allowed identification of previously unreported CYP109B1 substrates and the functional assignment of two putative cytochromes P450, CYP107J1 and CYP134A1. The FT-ICR/MS-based approach can be easily applied to large-scale screening with the aid of the extremely high mass resolution and accuracy.

Lantibiotics: peptides of diverse structure and function

The current need for antibiotics with novel target molecules has coincided with advances in technical approaches for the structural and functional analysis of the lantibiotics, which are ribosomally synthesized peptides produced by gram-positive bacteria. These peptides have antibiotic or morphogenetic activity and are structurally defined by the presence of unusual amino acids introduced by posttranslational modification. Lantibiotics are complex polycyclic molecules formed by the dehydration of select Ser and Thr residues and the intramolecular addition of Cys thiols to the resulting unsaturated amino acids to form lanthionine and methyllanthionine bridges, respectively. Importantly, the structural and functional diversity of the lantibiotics is much broader than previously imagined. Here we discuss this growing collection of molecules and introduce some recently discovered peptides, review advances in enzymology and protein engineering, and discuss the regulatory networks that govern the synthesis of the lantibiotics by the producing organisms.

Lantibiotics: insight and foresight for new paradigm

Lantibiotics are a unique type of antimicrobial peptide produced by a large number of gram-positive bacteria that contain unusual amino acids, such as lanthionine and dehydrated amino acids. Ribosomally synthesized lantibiotic prepeptide consists of an N-terminal leader peptide followed by a C-terminal propeptide moiety that undergoes several post-translational modification events to yield a biologically active lantibiotic. Research on lantibiotics has drawn much attention in recent years and has undergone extensive progress as a step forward to the next paradigm. Unusual amino acids in lantibiotics solely contribute to their biological activity and also enhance their structural stability. Thus, enzymes involved in lantibiotic biosynthesis would have a high potential for peptide engineering by introducing unusual amino acids into desired peptides, which may establish a universal approach to advance the structural design of novel peptides, termed lantibiotic engineering. In this review, we focus on recent development with contemporary innovations and perspective of lantibiotic research.

New developments in lantibiotic biosynthesis and mode of action

Lantibiotics are a unique class of peptide antibiotics. Recent studies of the proteins involved in the elaborate post-translational modifications of lantibiotics have revealed that these enzymes have relaxed substrate specificity. These modifications include the dehydration of serine and threonine residues followed by the intramolecular addition of cysteine thiols to the unsaturated amino acids to create an intricate polycyclic peptide. The use of peptide engineering in vivo and in vitro has allowed investigation of their biosynthetic machinery. Several members utilize a unique mode of biological action that involves the sequestration of lipid II, a crucial intermediate in peptidoglycan biosynthesis, to form pores in bacterial membranes.

A method for connecting solution-phase enzyme activity assays with immobilized format analysis by mass spectrometry

This paper reports an enzyme activity assay that combines the assets of both homogeneous and solid-phase formats. In this method, enzyme reactions are carried out in solution using substrates that are tagged with an immobilization reagent that allows the substrates to be selectively immobilized to self-assembled monolayers (SAMs), for direct analysis by matrix assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). As a model enzyme reaction, this work examined the transfer of a methyl group from S-adenosyl-l-methionine (AdoMet) to an arginine side chain of a peptide substrate by the enzyme protein arginine methyltransferase 1 (RMT1). A cysteine-terminated peptide substrate was methylated by RMT1 in solution and then applied to a maleimide-presenting SAM to give selective immobilization of the peptide. Time-dependent analysis of methylation using MALDI-TOFMS clearly showed that both the presence and relative amount of the two reaction products-the mono- and dimethylated peptides-can be conveniently evaluated. This assay strategy is rapid, takes advantage of solution-phase assay conditions, avoids the use of labels and complicated purification steps, and is applicable to multianalyte analyses.