Evolution of lanthipeptide synthetases

Zhang, Qi; Yu, Yi; Velásquez, Juan E.; Donk, Wilfred A. van der

doi:10.1073/pnas.1210393109

Cited by 168 publications

(261 citation statements)

References 47 publications

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“…Unlike haloduracin β and microbisporicin, determination of the ring topology of Pcn1.2 is not aided by comparative analysis with other known lanthipeptides (12,26). To further explore the scope, we used HSEE to investigate the topology of cross-links between two residues, which normally poses a great challenge for structural analysis because cross-link formation for lanthipeptides does not involve a change in mass and because cross-link formation generally decreases the fragmentation of the peptide.…”

Section: Resultsmentioning

confidence: 99%

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Structural investigation of ribosomally synthesized natural products by hypothetical structure enumeration and evaluation using tandem MS

Zhang

Ortega

Shi

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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Ribosomally synthesized and posttranslationally modified peptides (RiPPs) are a growing class of natural products that are found in all domains of life. These compounds possess vast structural diversity and have a wide range of biological activities, promising a fertile ground for exploring novel natural products. One challenging aspect of RiPP research is the difficulty of structure determination due to their architectural complexity. We here describe a method for automated structural characterization of RiPPs by tandem mass spectrometry. This method is based on the combined analysis of multiple mass spectra and evaluation of a collection of hypothetical structures predicted based on the biosynthetic gene cluster and molecular weight. We show that this method is effective in structural characterization of complex RiPPs, including lanthipeptides, glycopeptides, and azole-containing peptides. Using this method, we have determined the structure of a previously structurally uncharacterized lanthipeptide, prochlorosin 1.2, and investigated the order of the posttranslational modifications in three biosynthetic systems.dehydration | genome mining | lantibiotics | directionality R ibosomally synthesized and posttranslationally modified peptides (RiPPs) are a major class of natural products as revealed by the genome-sequencing efforts of the past decade (1). RiPPs are biosynthesized from genetically encoded and ribosomally produced precursor peptides, which typically consist of a core peptide that is transformed to the final product and an N-terminal extension called the leader peptide that is usually important for recognition by the posttranslational modification (PTM) enzymes (1). Because of the highly diverse PTMs, these compounds possess vast structural diversity and have a wide range of biological activities, thus representing a fertile ground for exploration. Furthermore, the ribosomal origin of RiPPs makes them particularly well suited for genome mining efforts. By using genome mining to explicitly avoid species harboring biosynthetic gene clusters identical to those that produce known compounds, a combination of strain prioritization and mass spectrometry (MS)-based analysis offers a new route to discovering natural products that can overcome the burden of rediscovery that has increasingly hampered discovery efforts (2, 3). One challenging aspect of high-throughput genome mining for new natural products is the difficulty to determine their molecular structures in high throughput. We present here a method that allows automated RiPP structure elucidation.In contrast to nonribosomal peptides that have an average molecular weight of less than 1,000 Da, as documented in the NORINE database (4), RiPPs in many cases have molecular weights larger than 2,500 Da. Molecules of this size are difficult to rapidly analyze by NMR spectroscopy, rendering MS the most convenient tool for RiPP structural characterization. Even when the precursor peptide sequences are known and the types of PTMs can be predicted based on the sequen...

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Section: Resultsmentioning

confidence: 99%

“…We next applied HSEE to investigate the directionality of catalysis by the nisin dehydratase NisB (33), a prototypical class I lanthipeptide synthetase (19,26). The activity of NisB was recently reconstituted in vitro (33), allowing for a detailed interrogation of its catalytic mechanism.…”

Section: Resultsmentioning

confidence: 99%

Structural investigation of ribosomally synthesized natural products by hypothetical structure enumeration and evaluation using tandem MS

Zhang

Ortega

Shi

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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“…The identification of biosynthetic gene clusters encoding lanthipeptides was facilitated by the fact that several genes involved in lantibiotic biosynthesis, such as LanC, LanM, and LanT, have a relatively conserved nature (45)(46)(47). These characteristics have been incorporated into antiSMASH (version 3) software, which combines analysis for signature motifs for biosynthetic enzymes and analysis for lanthipeptide-specific cleavage site motifs to identify gene clusters encoding lanthipeptides in genomic sequences (48).…”

Section: Discussionmentioning

confidence: 99%

“…Biosynthetic gene clusters encoding class I lanthipeptides typically have two enzymes (LanB and LanC) involved in posttranslational modification, while the gene clusters encoding class II lanthipeptides depend on a multifunctional enzyme (LanM) for the dehydration and cyclization reactions of the precursor peptides (45). The precursor peptides modified by the LanBC enzymes often have a conserved proline at position Ϫ2 relative to the cleavage site and an FNLD motif at about positions Ϫ20 and Ϫ15 in the leader peptide, and these play crucial roles in the posttranslational modification of the antimicrobial peptide (49).…”

Section: Discussionmentioning

confidence: 99%

Distribution and Genetic Diversity of Bacteriocin Gene Clusters in Rumen Microbial Genomes

Azevedo

Bento

Ruiz

et al. 2015

Appl Environ Microbiol

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b Some species of ruminal bacteria are known to produce antimicrobial peptides, but the screening procedures have mostly been based on in vitro assays using standardized methods. Recent sequencing efforts have made available the genome sequences of hundreds of ruminal microorganisms. In this work, we performed genome mining of the complete and partial genome sequences of 224 ruminal bacteria and 5 ruminal archaea to determine the distribution and diversity of bacteriocin gene clusters. A total of 46 bacteriocin gene clusters were identified in 33 strains of ruminal bacteria. Twenty gene clusters were related to lanthipeptide biosynthesis, while 11 gene clusters were associated with sactipeptide production, 7 gene clusters were associated with class II bacteriocin production, and 8 gene clusters were associated with class III bacteriocin production. The frequency of strains whose genomes encode putative antimicrobial peptide precursors was 14.4%. Clusters related to the production of sactipeptides were identified for the first time among ruminal bacteria. BLAST analysis indicated that the majority of the gene clusters (88%) encoding putative lanthipeptides contained all the essential genes required for lanthipeptide biosynthesis. Most strains of Streptococcus (66.6%) harbored complete lanthipeptide gene clusters, in addition to an open reading frame encoding a putative class II bacteriocin. Albusin B-like proteins were found in 100% of the Ruminococcus albus strains screened in this study. The in silico analysis provided evidence of novel biosynthetic gene clusters in bacterial species not previously related to bacteriocin production, suggesting that the rumen microbiota represents an underexplored source of antimicrobial peptides.T he production of low-molecular-weight antimicrobial peptides is a trait widely distributed among species of bacteria and archaea (1). Although a variety of functions has been assigned to these compounds (e.g., toxins, virulence factors, bacterial hormones), the bacteriocins have mainly been investigated due to their potential as alternatives to antibiotics and food preservatives (2-4). With the rise in antibiotic resistance among commensal and pathogenic strains of bacteria, there is an urgent need to identify and develop novel therapeutic strategies for clinical applications in human and animal health (5).Bacteriocins are often defined as ribosomally synthesized antimicrobial peptides produced by bacteria or archaea (6). Bacteriocins show great diversity in their chemical structures and mechanisms of action, and at least four main groups have been proposed to classify these antimicrobial agents (7). Class I contains posttranslationally modified antimicrobial peptides, such as lanthipeptides, sactipeptides, and lasso peptides, which differ in their molecular structures, their mechanisms of action, and the enzymatic apparatuses involved in modifying the precursor peptides (7,8). Class II bacteriocins consist of antimicrobial peptides without posttranslationally modified residues and ca...

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“…1B). The four distinct classes of biosynthetic machinery reflect the functional importance of lanthionine scaffolds and a convergent evolution process to produce them (12). Notably, products generated by these four classes of lanthionine synthetases are not limited to lanthipeptides.…”

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confidence: 99%

Expanded Natural Product Diversity Revealed by Analysis of Lanthipeptide-Like Gene Clusters in Actinobacteria

Zhang

Doroghazi

Zhao

et al. 2015

Appl Environ Microbiol

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Lanthionine-containing peptides (lanthipeptides) are a rapidly growing family of polycyclic peptide natural products belonging to the large class of ribosomally synthesized and posttranslationally modified peptides (RiPPs). Lanthipeptides are widely distributed in taxonomically distant species, and their currently known biosynthetic systems and biological activities are diverse. Building on the recent natural product gene cluster family (GCF) project, we report here large-scale analysis of lanthipeptidelike biosynthetic gene clusters from Actinobacteria. Our analysis suggests that lanthipeptide biosynthetic pathways, and by extrapolation the natural products themselves, are much more diverse than currently appreciated and contain many different posttranslational modifications. Furthermore, lanthionine synthetases are much more diverse in sequence and domain topology than currently characterized systems, and they are used by the biosynthetic machineries for natural products other than lanthipeptides. The gene cluster families described here significantly expand the chemical diversity and biosynthetic repertoire of lanthionine-related natural products. Biosynthesis of these novel natural products likely involves unusual and unprecedented biochemistries, as illustrated by several examples discussed in this study. In addition, class IV lanthipeptide gene clusters are shown not to be silent, setting the stage to investigate their biological activities. Lanthipeptides are a rapidly growing family of polycyclic peptides characterized by the presence of the thioether crosslinked amino acids lanthionine and methyllanthionine (1-5). These compounds are widely distributed in taxonomically distant species and display very diverse biological activities, ranging from antimicrobial to antiallodynic (5-7). Antibacterial lanthipeptides, such as the commercially used food preservative nisin, are termed lantibiotics (8). Lanthipeptides are generated from a ribosomally synthesized linear precursor peptide (generically termed LanA) and therefore belong to the large class of natural products that are ribosomally synthesized and posttranslationally modified peptides (RiPPs) (9). The precursor peptide LanA consists of a C-terminal core peptide where all posttranslational modifications take place and an N-terminal leader peptide that is important for posttranslational modifications and that is subsequently removed by proteolysis (10, 11). The installation of the (methyl)lanthionine thioether bridges is achieved by the initial dehydration of Ser and Thr residues in the precursor peptides, followed by stereoselective intramolecular Michael-type addition of Cys thiols to the newly formed dehydroamino acids (Fig. 1A).Four classes of biosynthetic enzymes are known to catalyze lanthionine formation (2, 12) (Fig. 1B). Class I lanthionine synthetases consist of a dehydratase and a cyclase that are generically termed LanB and LanC, respectively (8). Class II enzymes are generically named LanMs, which are single polypeptides containing an N-termi...

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Evolution of lanthipeptide synthetases

Cited by 168 publications

References 47 publications

Structural investigation of ribosomally synthesized natural products by hypothetical structure enumeration and evaluation using tandem MS

Structural investigation of ribosomally synthesized natural products by hypothetical structure enumeration and evaluation using tandem MS

Distribution and Genetic Diversity of Bacteriocin Gene Clusters in Rumen Microbial Genomes

Expanded Natural Product Diversity Revealed by Analysis of Lanthipeptide-Like Gene Clusters in Actinobacteria

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