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Structural Characterization of Thioether-Bridged Bacteriocins

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Structural Characterization of Thioether-Bridged Bacteriocins The Journal of Antibiotics (2014) 67, 23–30 & 2014 Japan Antibiotics Research Association All rights reserved 0021-8820/14 www.nature.com/ja REVIEW ARTICLE Structural characterization of thioether-bridged bacteriocins Christopher T Lohans and John C Vederas Bacteriocins are a group of ribosomally synthesized antimicrobial peptides produced by bacteria, some of which are extensively post-translationally modified. Some bacteriocins, namely the lantibiotics and sactibiotics, contain one or more thioether bridges. However, these modifications complicate the structural elucidation of these bacteriocins using conventional techniques. This review will discuss the techniques and strategies that have been applied to determine the primary structures of lantibiotics and sactibiotics. A major challenge is to identify the topology of thioether bridges in these peptides (i.e., which amino-acid residues are involved in which bridges). Edman degradation, NMR spectroscopy and tandem MS have all been commonly applied to characterize these bacteriocins, but can be incompatible with the post-translational modifications present. Chemical modifications to the modified residues, such as desulfurization and reduction, make the treated bacteriocins more compatible to analysis by these standard peptide analytical techniques. Despite their differences in structure, similar strategies have proved useful to study the structures of both lantibiotics and sactibiotics. The Journal of Antibiotics (2014) 67, 23–30; doi:10.1038/ja.2013.81; published online 11 September 2013 Keywords: bacteriocin structure; desulfurization; Edman degradation; lantibiotics; NMR spectroscopy; sactibiotics; thioether bridge INTRODUCTION not involved in Lan/MeLan formation are sometimes found in the Bacteriocins are a diverse group of antimicrobial peptides and mature peptide. proteins that are ribosomally synthesized by bacteria. A multitude The sactibiotics are another group of sulfur-bridged bacteriocins.1 of bacteriocins have been reported, exhibiting a range of sizes and Sactibiotics are characterized by the presence of a linkage between a post-translational modifications.1 Many of the more extensively post- cysteine thiol and the a-carbon of another residue (Figure 1c). This translationally modified bacteriocins feature cyclic structures. Some of too serves to form a thioether bridge, thereby conformationally thesecyclizedstructuresarisefromamidebondformation,suchas constraining the peptide. Some aspects of sactibiotic biosynthesis were the circular bacteriocins that feature an amide bond linking the N and recently elucidated, wherein a radical SAM (S-adenosylmethionine) Ctermini.2 Others are cyclized through the formation of a covalent enzyme was shown to be responsible for thioether bridge formation.4 bond between a cysteine thiol and a carbon atom of another residue, Thioether formation in sactibiotics is believed to be a radical process, thereby forming a thioether bridge. These thioether linkages are requiring the abstraction of a hydrogen atom from the a-position of primarily found in two groups of bacteriocins: the lantibiotics and the an amino acid. sactibiotics, which are the focus of this review.1 Although some Despite the large number of bacteriocins reported in the literature, bacteriocins contain other sulfur-containing bridges, such as relatively few of them have been fully structurally characterized. disulfides, they will not be further discussed. However, knowledge regarding their structures is an important The lantibiotics are characterized by the presence of lanthionine prerequisite for understanding how they exert their antimicrobial (Lan) and methyllanthionine (MeLan), amino acids containing effects. Comparison of their structures to previously characterized thioether bridges (Figure 1a and b).1,3 Biosynthetically, these bacteriocins may indicate their probable mode of action. Knowledge residues originate from cysteine, serine and threonine residues. of the structure also allows for structure–activity relationship studies First, selected serine and threonine residues are enzymatically to be performed, which may permit the rational development of dehydrated to form dehydroalanine (Dha) and dehydrobutyrine novel bacteriocins with increased activity. Furthermore, knowledge (Dhb) residues, respectively. Then, the nucleophilic addition of a regarding the structures of bacteriocins provides information about cysteine thiol onto a Dha or Dhb residue in Michael manner forms a their biosynthetic machinery, which may prove useful for future Lan or MeLan residue, respectively. These modifications establish a bioengineering efforts.5 covalent linkage between a cysteine thiol and the b-carbon of another Edman degradation and tandem MS/MS are techniques that are residue, thereby forming a thioether bridge. Dha and Dhb residues commonly applied to the study of bacteriocins. The post-translational Department of Chemistry, University of Alberta, Edmonton, AB, Canada Correspondence: Professor JC Vederas, Department of Chemistry, University of Alberta, Chemistry Centre, 30 University Campus, Edmonton, Canada AB T6G 2G2. E-mail: [email protected] Received 4 June 2013; revised 23 July 2013; accepted 27 July 2013; published online 11 September 2013 Lantibiotic and sactibiotic structural elucidation CT Lohans and JC Vederas 24 modifications that typify the lantibiotics and sactibiotics complicate Treatment of nisin with cyanogen bromide, cleaving the peptide bond their characterization by these techniques. This review will describe C terminal to methionine residues, generated an N-terminal fragment the structural information that these analytical techniques, in addition of 21 amino acids and a C-terminal fragment of 13 amino acids to NMR spectroscopy, can obtain for the lantibiotics and sactibiotics. (Figure 2).8 The N-terminal fragment was further cleaved with Chemical and enzymatic transformations that have been used to trypsin, generating peptides of 12 and 9 amino acids. Similarly, the modify bacteriocins to make them more amenable to analysis will also C-terminal nisin fragment was digested with chymotrypsin, the be discussed. products of which were further digested with aminopeptidase and carboxypeptidases. Structural information was gathered through the analyses of these fragments, using techniques such as Edman LANTIBIOTICS degradation, analysis of peptide hydrolysates, desulfurization and Background and challenges other chemical modifications. Finally, the structural information Some early studies of nisin, the most well-studied lantibiotic, were obtained for these fragments was pieced together, providing the published in the mid-1940s.6,7 It was not until more than 25 years structure of nisin. This kind of approach was used for other early later that the structure of nisin was fully elucidated.8 Over the structural characterization efforts, for such lantibiotics as subtilin9 following decades, the primary structures of several other lantibiotics and epidermin.11 were solved, such as subtilin,9 gallidermin10 and epidermin.11 More The drawback of such an approach is the requirements it places on recently, the number of solved lantibiotic structures has quickly the lantibiotic amino-acid sequence. Protease and chemical cleavage increased, partly coincident with improved capabilities in NMR sites must be distributed at convenient positions throughout the spectroscopy and MS.12 lantibiotic. For this reason, such an approach is not easily generalized Earlier structural elucidations of lantibiotics were highly reliant toward novel lantibiotics with unknown amino-acid sequences. More upon protease- and chemical-mediated cleavages. These were used to recent approaches, based largely on NMR spectroscopy and MS, are cut a lantibiotic into smaller, more easily characterized fragments. less sequence dependent and are more versatile for this purpose. The post-translational modifications typical of the lantibiotics pose H O challenges for typical peptide analysis techniques. Lan and MeLan N residues are generally not observed by Edman degradation analysis, H O H O H O H O N N N N resulting in a gap in the observed peptide sequence. Dehydrated S R residues Dha and Dhb are more detrimental to Edman-based analysis, S S N as no sequence information following these residues can be obtained. H O Once a dehydro residue becomes the N-terminal amino acid, it DL-Lanthionine (Lan) DL-Methyllanthionine Sactibiotic tautomerizes to the corresponding imine, which reacts with water to (MeLan) α-thio linkage form an a-ketoamide. Without an amino group, the peptide can no Figure 1 Structures of (a) lanthionine, (b) methyllanthionine and (c)a longer undergo Edman degradation. Furthermore, some lantibiotics sactibiotic linkage. are produced with an N-terminal blockage (e.g., Pep513 and lacticin Leu Pro Gly His H2N Ile Ile Val Ala Met S Abu Ala Dhb Abu Ala His Ser Dha S S Gly Gly Ala Ala Lys Lys Ala Abu Ala Abu Ala Lys CO H Asn Met S 2 Ile Leu Dha S CNBr His Ile Val Leu Hse CO2H S H N Ile Pro Gly Abu His 2 Ala Ala Ser Dha H N Dhb Abu Ala H2N 2 Lys Ala Abu Ala Lys CO H S S Gly Gly S 2 Ala Ala Lys Abu Ala Asn Hse CO H Ile Leu S 2 Dha Chymotrypsin Trypsin His CO H Ile 2 Leu Hse CO2H S H N Pro Gly Abu Ala His Ser 2 H2N Ile Ala H2N H N Lys Ala Abu Ala Val Dhb Abu Ala 2 Gly Gly S S S Dha Ala Ala Lys H N Abu Ala 2 Asn Hse CO H 2 Lys CO H Ile Leu CO H S 2 Dha 2 Figure 2 Degradation analysis of nisin, using cyanogen bromide, trypsin and chymotrypsin. The Journal of Antibiotics Lantibiotic and sactibiotic structural
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