Determining the structure and mode of action of microbisporicin, a potent lantibiotic active against multiresistant pathogens

In vivo pharmacokinetics and pharmacodynamics of the lantibiotic NAI-107 in a neutropenic murine thigh infection model

NAI-107 is a novel lantibiotic compound with potent in vitro activity against Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus (MRSA). The purpose of this study was to examine the activity of NAI-107 against S. aureus strains, including MRSA, in the neutropenic murine thigh infection model. Serum pharmacokinetics were determined and time-kill studies were performed following administration of single subcutaneous doses of 5, 20, and 80 mg/kg body weight. The dose fractionation included total doses ranging from 1.56 to 400 mg/kg/72 h, divided into 1, 2, 3, or 6 doses. Studies of treatment effects against 9 S. aureus strains (4 methicillin-susceptible Staphylococcus aureus [MSSA] and 5 MRSA) using a 12-h dosing interval and total dose range of 1.56 to 400 mg/kg/72 h were also performed. A maximum effect (Emax) model was used to determine the pharmacokinetic/pharmacodynamic (PK/PD) index that best described the dose-response data and to estimate the doses required to achieve a net bacteriostatic dose (SD) and a 1-log reduction in CFU/thigh. The pharmacokinetic studies demonstrated an area under the concentration-time curve (AUC) range of 26.8 to 276 mg·h/liter and half-lives of 4.2 to 8.2 h. MICs ranged from 0.125 to 0.5 μg/ml. The 2 highest single doses produced more than a 2-log kill and prolonged postantibiotic effects (PAEs) ranging from 36 to >72 h. The dose fractionation-response curves were similar, and the AUC/MIC ratio was the most predictive PD index (AUC/MIC, coefficient of determination [R2]=0.89; maximum concentration of drug in serum [Cmax]/MIC, R2=0.79; time [T]>MIC, R2=0.63). A ≥2-log kill was observed against all 9 S. aureus strains. The total drug 24-h AUC/MIC values associated with stasis and a 1-log kill for the 9 S. aureus strains were 371±130 and 510±227, respectively. NAI-107 demonstrated concentration-dependent killing and prolonged PAEs. The AUC/MIC ratio was the predictive PD index. Extensive killing was observed for S. aureus organisms, independent of the MRSA status. The AUC/MIC target should be useful for the design of clinical dosing regimens.

Inorganic phosphate is a trigger factor for Microbispora sp. ATCC-PTA-5024 growth and NAI-107 production

BACKGROUND

NAI-107, produced by the actinomycete Microbispora sp. ATCC-PTA-5024, is a promising lantibiotic active against Gram-positive bacteria and currently in late preclinical-phase. Lantibiotics (lanthionine-containing antibiotics) are ribosomally synthesized and post-translationally modified peptides (RiPPs), encoded by structural genes as precursor peptides. The biosynthesis of biologically active compounds is developmentally controlled and it depends upon a variety of environmental stimuli and conditions. Inorganic phosphate (Pi) usually negatively regulates biologically-active molecule production in Actinomycetes, while it has been reported to have a positive control on lantibiotic production in Firmicutes strains. So far, no information is available concerning the Pi effect on lantibiotic biosynthesis in Actinomycetes.

RESULTS

After having developed a suitable defined medium, Pi-limiting conditions were established and confirmed by quantitative analysis of polyphosphate accumulation and of expression of selected Pho regulon genes, involved in the Pi-limitation stress response. Then, the effect of Pi on Microbispora growth and NAI-107 biosynthesis was investigated in a defined medium containing increasing Pi amounts. Altogether, our analyses revealed that phosphate is necessary for growth and positively influences both growth and NAI-107 production up to a concentration of 5 mM. Higher Pi concentrations were not found to further stimulate Microbispora growth and NAI-107 production.

CONCLUSION

These results, on one hand, enlarge the knowledge on Microbispora physiology, and, on the other one, could be helpful to develop a robust and economically feasible production process of NAI-107 as a drug for human use.

Growing the seeds sown by Piero Sensi

Piero Sensi is probably known primarily for his role in the discovery of rifamycin and for developing it to be a drug of fundamental importance in the treatment of tuberculosis. He has also contributed to promote screening programs of microbial products and research approaches for antibacterial agents that have been further developed up to the present day. This paper reports a sequence of discovery approaches, failures and successes that spans for about 50 years and is still in progress.

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

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.

The expression of antibiotic resistance genes in antibiotic-producing bacteria

Antibiotic-producing bacteria encode antibiotic resistance genes that protect them from the biologically active molecules that they produce. The expression of these genes needs to occur in a timely manner: either in advance of or concomitantly with biosynthesis. It appears that there have been at least two general solutions to this problem. In many cases, the expression of resistance genes is tightly linked to that of antibiotic biosynthetic genes. In others, the resistance genes can be induced by their cognate antibiotics or by intermediate molecules from their biosynthetic pathways. The regulatory mechanisms that couple resistance to antibiotic biosynthesis are mechanistically diverse and potentially relevant to the origins of clinical antibiotic resistance.

Discovering new bioactive molecules from microbial sources

There is an increased need for new drug leads to treat diseases in humans, animals and plants. A dramatic example is represented by the need for novel and more effective antibiotics to combat multidrug-resistant microbial pathogens. Natural products represent a major source of approved drugs and still play an important role in supplying chemical diversity, despite a decreased interest by large pharmaceutical companies. Novel approaches must be implemented to decrease the chances of rediscovering the tens of thousands of known natural products. In this review, we present an overview of natural product screening, focusing particularly on microbial products. Different approaches can be implemented to increase the probability of finding new bioactive molecules. We thus present the rationale and selected examples of the use of hypersensitive assays; of accessing unexplored microorganisms, including the metagenome; and of genome mining. We then focus our attention on the technology platform that we are currently using, consisting of approximately 70,000 microbial strains, mostly actinomycetes and filamentous fungi, and discuss about high-quality screening in the search for bioactive molecules. Finally, two case studies are discussed, including the spark that arose interest in the compound: in the case of orthoformimycin, the novel mechanism of action predicted a novel structural class; in the case of NAI-112, structural similarity pointed out to a possible in vivo activity. Both predictions were then experimentally confirmed.

The lantibiotic NAI-107 binds to bactoprenol-bound cell wall precursors and impairs membrane functions

The lantibiotic NAI-107 is active against Gram-positive bacteria including vancomycin-resistant enterococci and methicillin-resistant Staphylococcus aureus. To identify the molecular basis of its potency, we studied the mode of action in a series of whole cell and in vitro assays and analyzed structural features by nuclear magnetic resonance (NMR). The lantibiotic efficiently interfered with late stages of cell wall biosynthesis and induced accumulation of the soluble peptidoglycan precursor UDP-N-acetylmuramic acid-pentapeptide (UDP-MurNAc-pentapeptide) in the cytoplasm. Using membrane preparations and a complete cascade of purified, recombinant late stage peptidoglycan biosynthetic enzymes (MraY, MurG, FemX, PBP2) and their respective purified substrates, we showed that NAI-107 forms complexes with bactoprenol-pyrophosphate-coupled precursors of the bacterial cell wall. Titration experiments indicate that first a 1:1 stoichiometric complex occurs, which then transforms into a 2:1 (peptide: lipid II) complex, when excess peptide is added. Furthermore, lipid II and related molecules obviously could not serve as anchor molecules for the formation of defined and stable nisin-like pores, however, slow membrane depolarization was observed after NAI-107 treatment, which could contribute to killing of the bacterial cell.

Actinoplanes lutulentus sp. nov., isolated from mucky soil in China

A novel actinomycete, designated strain NEAU-GRX6T, was isolated from mucky soil collected from a stream of Jinlong Mountain in Harbin, Heilongjiang Province, north China, and characterized using a polyphasic approach. The isolate formed irregular sporangia containing motile sporangiospores on the substrate mycelium. The whole-cell sugars were xylose, glucose and galactose. The predominant menaquinones were MK-9(H6), MK-10(H4) and MK-9(H4). The major fatty acids were C16:0, C15:0, C18:1ω9c, C17:1ω7c and C18:0. The phospholipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol. The DNA G+C content was 67 mol%. 16S rRNA gene sequence similarity studies showed that strain NEAU-GRX6T belonged to the genus Actinoplanes, being most closely related to Actinoplanes palleronii IFO 14916T (97.80% similarity) and Actinoplanes missouriensis NBRC 102363T (97.76%). However, the low observed levels of DNA-DNA relatedness allowed the isolate to be differentiated from the above-mentioned species of the genus Actinoplanes. Moreover, strain NEAU-GRX6T could also be distinguished from A. palleronii IFO 14916T and A. missouriensis NBRC 102363T by phenotypic characteristics. Therefore, it is proposed that strain NEAU-GRX6T represents a novel species of the genus Actinoplanes, for which the name Actinoplanes lutulentus sp. nov. is proposed. The type strain is strain NEAU-GRX6T (=CGMCC 4.7090T=DSM 45883T).

Improved lanthipeptide detection and prediction for antiSMASH

Lanthipeptides are a class of ribosomally synthesised and post-translationally modified peptide (RiPP) natural products from the bacterial secondary metabolism. Their name is derived from the characteristic lanthionine or methyl-lanthionine residues contained in the processed peptide. Lanthipeptides that possess an antibacterial activity are called lantibiotics. Whereas multiple tools exist to identify lanthipeptide gene clusters from genomic data, no programs are available to predict the post-translational modifications of lanthipeptides, such as the proteolytic cleavage of the leader peptide part or tailoring modifications based on the analysis of the gene cluster sequence. antiSMASH is a software pipeline for the identification of secondary metabolite biosynthetic clusters from genomic input and the prediction of products produced by the identified clusters. Here we present a novel antiSMASH module using a rule-based approach to combine signature motifs for biosynthetic enzymes and lanthipeptide-specific cleavage site motifs to identify lanthipeptide clusters in genomic data, assign the specific lanthipeptide class, predict prepeptide cleavage, tailoring reactions, and the processed molecular weight of the mature peptide products.

Characterization of the congeners in the lantibiotic NAI-107 complex

NAI-107, a lantibiotic produced by Microbispora sp. 107891, shows potent activity against multi-drug-resistant bacterial pathogens. It is produced as a complex of related molecules, which is unusual for ribosomally synthesized peptides. Here we describe the identification, characterization, and antibacterial activity of the congeners produced by Microbispora sp. 107891 and by the related Microbispora corallina NRRL 30420. These molecules differ by the presence of two, one, or zero hydroxyl groups at Pro-14, by the presence of a chlorine at Trp-4, and/or by the presence of a sulfoxide on the thioether of the first lanthionine.

Advances in the arsenal of tools available enabling the discovery of novel lantibiotics with therapeutic potential

INTRODUCTION

Lantibiotics are ribosomally synthesised peptides, which undergo extensive post-translational modification. Their mode of action and effectiveness against multi-drug-resistant pathogens, and relatively low toxicity, makes them attractive therapeutic options.

AREAS COVERED

This article provides background information on the four classes of lanthipeptides that have been described to date. Due to the clinical potential of these agents, specifically those from Class I and II, it is essential to identify organisms that harbour potentially interesting clusters encoding novel lantibiotics. Multiple emerging technologies have been applied to address this issue, including genome mining and specific bioinformatics programs designed to identify lantibiotic clusters present within the genome sequences. These clusters can then be effectively expressed using optimised heterologous expression systems, which are ideally amenable to large-scale production.

EXPERT OPINION

The continuing expansion of publicly available genomes, particularly genomes from microorganisms isolated from under-explored environments, combined with powerful bioinformatics tools able to accurately identify clusters of interest are of paramount importance in the discovery of novel lantibiotics. Detailed analysis of clusters drastically reduces dereplication time, which was often problematic when using the traditional method of isolation, purification and then identification. Allowing a more focused direction of 'wet lab' work, targeting the most promising agents, greatly increases the chance of novel lantibiotic discovery and development. High-throughput screening strategies are also required to enable the efficient analysis of these potentially clinically relevant agents.

Understanding and manipulating antibiotic production in actinomycetes

Actinomycetes are prolific producers of natural products with a wide range of biological activities. Many of the compounds that they make (and derivatives thereof) are used extensively in medicine, most notably as clinically important antibiotics, and in agriculture. Moreover, these organisms remain a source of novel and potentially useful molecules, but maximizing their biosynthetic potential requires a better understanding of natural product biosynthesis. Recent developments in genome sequencing have greatly facilitated the identification of natural product biosynthetic gene clusters. In the present article, I summarize the recent contributions of our laboratory in applying genomic technologies to better understand and manipulate natural product biosynthesis in a range of different actinomycetes.

Insights into the evolution of lanthipeptide biosynthesis

Lanthipeptides are a group of posttranslationally modified peptide natural products that contain multiple thioether crosslinks. These crosslinks are formed by dehydration of Ser/Thr residues followed by addition of the thiols of Cys residues to the resulting dehydroamino acids. At least four different pathways to these polycyclic natural products have evolved, reflecting the high efficiency and evolvability of a posttranslational modification route to generate conformationally constrained peptides. The wealth of genomic information that has been made available in recent years has started to provide insights into how these remarkable pathways and their posttranslational modification machineries may have evolved. In this review, we discuss a model for the evolution of the lanthipeptide biosynthetic enzymes that has recently been developed based on the currently available data.

Anti-infective properties of bacteriocins: an update

Bacteriocin production is a widespread phenomenon among bacteria. Bacteriocins hold great promise for the treatment of diseases caused by pathogenic bacteria and could be used in the future as alternatives to existing antibiotics. The anti-infective potential of bacteriocins for inhibiting pathogens has been shown in various food matrices including cheese, meat, and vegetables. However, their inhibition of pathogens in vivo remains unclear and needs more investigation, due mainly to difficulties associated with demonstrating their health benefits. Many bacteriocins produced by established or potential probiotic organisms have been evaluated as potential therapeutic agents and interesting findings have been documented in vitro as well as in a few in vivo studies. Some recent in vivo studies point to the efficacy of bacteriocin-based treatments of human and animal infections. While further investigation remains necessary before the possibilities for bacteriocins in clinical practice can be described more fully, this review provides an overview of their potential applications to human and veterinary health.

Antimicrobial peptides: versatile biological properties

Antimicrobial peptides are diverse group of biologically active molecules with multidimensional properties. In recent past, a wide variety of AMPs with diverse structures have been reported from different sources such as plants, animals, mammals, and microorganisms. The presence of unusual amino acids and structural motifs in AMPs confers unique structural properties to the peptide that attribute for their specific mode of action. The ability of these active AMPs to act as multifunctional effector molecules such as signalling molecule, immune modulators, mitogen, antitumor, and contraceptive agent makes it an interesting candidate to study every aspect of their structural and biological properties for prophylactic and therapeutic applications. In addition, easy cloning and recombinant expression of AMPs in heterologous plant host systems provided a pipeline for production of disease resistant transgenic plants. Besides these properties, AMPs were also used as drug delivery vectors to deliver cell impermeable drugs to cell interior. The present review focuses on the diversity and broad spectrum antimicrobial activity of AMPs along with its multidimensional properties that could be exploited for the application of these bioactive peptides as a potential and promising drug candidate in pharmaceutical industries.

The antibiotic planosporicin coordinates its own production in the actinomycete Planomonospora alba

Planosporicin is a ribosomally synthesized, posttranslationally modified peptide lantibiotic produced by the actinomycete Planomonospora alba. It contains one methyl-lanthionine and four lanthionine bridges and inhibits cell wall biosynthesis in other Gram-positive bacteria probably by binding to lipid II, the immediate precursor for cell wall biosynthesis. Planosporicin production, which is encoded by a cluster of 15 genes, is confined to stationary phase in liquid culture and to the onset of morphological differentiation when P. alba is grown on agar. This growth phase-dependent gene expression is controlled transcriptionally by three pathway-specific regulatory proteins: an extracytoplasmic function σ factor (PspX), its cognate anti-σ factor (PspW), and a transcriptional activator (PspR) with a C-terminal helix-turn-helix DNA-binding domain. Using mutational analysis, S1 nuclease mapping, quantitative RT-PCR, and transcriptional fusions, we have determined the direct regulatory dependencies within the planosporicin gene cluster and present a model in which subinhibitory concentrations of the lantibiotic function in a feed-forward mechanism to elicit high levels of planosporicin production. We show that in addition to acting as an antibiotic, planosporicin can function as an extracellular signaling molecule to elicit precocious production of the lantibiotic, presumably ensuring synchronous and concerted lantibiotic biosynthesis in the wider population and, thus, the production of ecologically effective concentrations of the antibiotic.

Cloning and analysis of the planosporicin lantibiotic biosynthetic gene cluster of Planomonospora alba

The increasing prevalence of antibiotic resistance in bacterial pathogens has renewed focus on natural products with antimicrobial properties. Lantibiotics are ribosomally synthesized peptide antibiotics that are posttranslationally modified to introduce (methyl)lanthionine bridges. Actinomycetes are renowned for their ability to produce a large variety of antibiotics, many with clinical applications, but are known to make only a few lantibiotics. One such compound is planosporicin produced by Planomonospora alba, which inhibits cell wall biosynthesis in Gram-positive pathogens. Planosporicin is a type AI lantibiotic structurally similar to those which bind lipid II, the immediate precursor for cell wall biosynthesis. The gene cluster responsible for planosporicin biosynthesis was identified by genome mining and subsequently isolated from a P. alba cosmid library. A minimal cluster of 15 genes sufficient for planosporicin production was defined by heterologous expression in Nonomuraea sp. strain ATCC 39727, while deletion of the gene encoding the precursor peptide from P. alba, which abolished planosporicin production, was also used to confirm the identity of the gene cluster. Deletion of genes encoding likely biosynthetic enzymes identified through bioinformatic analysis revealed that they, too, are essential for planosporicin production in the native host. Reverse transcription-PCR (RT-PCR) analysis indicated that the planosporicin gene cluster is transcribed in three operons. Expression of one of these, pspEF, which encodes an ABC transporter, in Streptomyces coelicolor A3(2) conferred some degree of planosporicin resistance on the heterologous host. The inability to delete these genes from P. alba suggests that they play an essential role in immunity in the natural producer.

Saturation mutagenesis of lysine 12 leads to the identification of derivatives of nisin A with enhanced antimicrobial activity

It is becoming increasingly apparent that innovations from the "golden age" of antibiotics are becoming ineffective, resulting in a pressing need for novel therapeutics. The bacteriocin family of antimicrobial peptides has attracted much attention in recent years as a source of potential alternatives. The most intensively studied bacteriocin is nisin, a broad spectrum lantibiotic that inhibits gram-positive bacteria including important food pathogens and clinically relevant antibiotic resistant bacteria. Nisin is gene-encoded and, as such, is amenable to peptide bioengineering, facilitating the generation of novel derivatives that can be screened for desirable properties. It was to this end that we used a site-saturation mutagenesis approach to create a bank of producers of nisin A derivatives that differ with respect to the identity of residue 12 (normally lysine; K12). A number of these producers exhibited enhanced bioactivity and the nisin A K12A producer was deemed of greatest interest. Subsequent investigations with the purified antimicrobial highlighted the enhanced specific activity of this modified nisin against representative target strains from the genera Streptococcus, Bacillus, Lactococcus, Enterococcus and Staphylococcus.

Viable screening targets related to the bacterial cell wall

The synthesis of the bacterial peptidoglycan has been recognized for over 50 years as fertile ground for antibacterial discovery. Initially, empirical screening of natural products for inhibition of bacterial growth detected many chemical classes of antibiotics whose specific mechanisms of action were eventually dissected and defined. Of the nontoxic antibiotics discovered, most were found to be inhibitors of either protein synthesis or cell wall synthesis, which led to more directed screening for inhibitors of these pathways. Directed screening and design programs for cell wall inhibitors have been undertaken since the 1960s. In that time it has become clear that, while certain steps and intermediates have yielded selective inhibitors and are established targets, other potential targets have not yielded inhibitors whose antibacterial activity is proven to be solely due to that inhibition. Why has this search been so problematic? Are the established targets still worth pursuing? This review will attempt to answer these and other questions and evaluate the viability of targets related to peptidoglycan synthesis.

Micromonospora wenchangensis sp. nov., isolated from mangrove soil

An actinomycete, strain 2602GPT1-05(T), was isolated from a composite mangrove soil sample collected from Wenchang, Hainan province, China. Strain 2602GPT1-05(T) showed closest 16S rRNA gene sequence similarity to Micromonospora haikouensis 232617(T) (99.05 %), and phylogenetically clustered with Micromonospora haikouensis 232617(T), Micromonospora matsumotoense IMSNU 22003(T) (98.7 %) and Micromonospora rifamycinica AM105(T) (98.6 %) based on the 16S rRNA and gyrB gene sequence phylogenetic analysis. The strain harboured meso-DAP and glycine as major cell-wall amino acids, and MK-10(H6) and MK-9(H6) as predominant menaquinones. The characteristic whole-cell sugars were xylose, arabinose, glucose and galactose. The polar lipid profile comprised phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, phosphatidylglycerol, phosphatidylinositol mannosides, unknown phospholipid and an unknown phosphoglycolipid. The major cellular fatty acids were C18 : 1ω9c, iso-C15 : 0, 10-methyl C18 : 0 (tuberculostearic acid), C16 : 0, C18 : 0 and iso-C16 : 0. The DNA G+C content was 71.7 mol%. Furthermore, some physiological and biochemical properties and low DNA-DNA relatedness values enabled the strain to be differentiated from members of closely related species. On the basis of these phenotypic, genotypic and chemotaxonomic data, strain 2602GPT1-05(T) represents a novel species of the genus Micromonospora, for which the name Micromonospora wenchangensis sp. nov. is proposed. The type strain is 2602GPT1-05(T) ( = CCTCC AA 2012002(T) = DSM 45709(T)).

Micromonospora sonneratiae sp. nov., isolated from a root of Sonneratia apetala

A novel endophytic actinomycete, strain 274745(T), was isolated from a root of Sonneratia apetala collected in a mangrove forest in Sanya, Hainan province, China. The 16S rRNA gene sequence of strain 274745(T) showed the greatest similarity to Micromonospora pattaloongensis TJ2-2(T) (98.3 %). Phylogenetic analysis based on the gyrB gene also supported the close relationship of these two strains. The predominant menaquinone was MK-10(H8) and the major fatty acids were iso-C15 : 0, C17 : 0 and anteiso-C15 : 0. The characteristic whole-cell sugars were xylose and mannose. The cell wall contained meso-diaminopimelic acid and glycine. The polar lipid profile mainly comprised phosphatidylethanolamine, phosphatidylinositol and diphosphatidylglycerol. The DNA G+C content was 71.6 mol%. Furthermore, a combination of DNA-DNA relatedness and some physiological and biochemical properties indicated that the novel strain could be readily distinguished from the closest phylogenetic relatives. On the basis of these phenotypic and genotypic data, strain 274745(T) represents a novel species of the genus Micromonospora, for which the name Micromonospora sonneratiae sp. nov. is proposed. The type strain is 274745(T) ( = CCTCC AA 2012003(T) = DSM 45704(T)).

Isolation and characterization of NAI-802, a new lantibiotic produced by two different Actinoplanes strains

Lantibiotics are biologically active peptides produced by Gram-positive bacteria. Starting from fermentation broth extracts preselected from a high-throughput screening program for discovering cell-wall inhibitors, we successfully isolated a new lantibiotic produced by Actinoplanes sp., designated as NAI-802. MS and NMR analysis together with explorative chemistry established that NAI-802 consists of 21 amino acids, 19 of which are identical to those present in the class II lantibiotic actagardine. Interestingly, NAI-802 carries one extra alanine and one extra arginine at the N- and C-termini, respectively. As expected from the overall higher positive charge, NAI-802 was slightly more active than actagardine against staphylococci and streptococci. Further improvement of its antibacterial activity was achieved by adding one additional positive charge through conversion of the C-terminal carboxylate into the corresponding basic amide. NAI-802 thus represents a novel promising candidate for treating Gram-positive infections caused by multidrug-resistant pathogens.

Xiangella phaseoli gen. nov., sp. nov., a member of the family Micromonosporaceae

A novel endophytic actinomycete, designated strain NEAU-J5(T) was isolated from roots of snap bean (Phaseolus vulgaris L.). Comparative analysis of the 16S rRNA gene sequence indicated that NEAU-J5(T) is phylogenetically related to members of the family Micromonosporaceae. The whole-cell sugars were galactose, mannose and glucose. The predominant menaquinones were MK-9(H4) and MK-9(H6). The major fatty acids were C16:0, C18:0, C17:1ω7c, iso-C15:0 and C17:0. The phospholipids were phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol and phosphatidylinositol mannoside. The DNA G+C content was 72.2 mol%. On the basis of the morphological and chemotaxonomic characteristics, phylogenetic analysis and characteristic patterns of 16S rRNA gene signature nucleotides, strain NEAU-J5(T) represents a novel species of a new genus within the family Micromonosporaceae, for which the name Xiangella phaseoli gen. nov., sp. nov. is proposed. The type strain of Xiangella phaseoli is strain NEAU-J5(T) (=CGMCC 4.7038(T)=DSM 45730(T)).

Evolution of lanthipeptide synthetases

Lanthionine-containing peptides (lanthipeptides) are a family of ribosomally synthesized and posttranslationally modified peptides containing (methyl)lanthionine residues. Here we present a phylogenomic study of the four currently known classes of lanthipeptide synthetases (LanB and LanC for class I, LanM for class II, LanKC for class III, and LanL for class IV). Although they possess very similar cyclase domains, class II-IV synthetases have evolved independently, and LanB and LanC enzymes appear to not always have coevolved. LanM enzymes from various phyla that have three cysteines ligated to a zinc ion (as opposed to the more common Cys-Cys-His ligand set) cluster together. Most importantly, the phylogenomic data suggest that for some scaffolds, the ring topology of the final lanthipeptides may be determined in part by the sequence of the precursor peptides and not just by the biosynthetic enzymes. This notion was supported by studies with two chimeric peptides, suggesting that the nisin and prochlorosin biosynthetic enzymes can produce the correct ring topologies of epilancin 15X and lacticin 481, respectively. These results highlight the potential of lanthipeptide synthetases for bioengineering and combinatorial biosynthesis. Our study also demonstrates unexplored areas of sequence space that may be fruitful for genome mining.

Contribution of the Actinobacteria to the growing diversity of lantibiotics

Currently, 76 lantibiotics have been described; the vast majority being produced by members of the Firmicute phylum of bacteria. There is a growing number being identified from the Actinobacteria phylum and some of these exhibit novel modifications leading to an increased functional diversity among lantibiotics. In this review, we discuss the currently characterized lantibiotics highlighting the expanding diversity provided by those from the Actinobacteria. This increased diversity has the potential to expand lantibiotic applications as antimicrobials in foods and pharmaceuticals. In addition, a phylogenetic classification system based on the full prepropeptide sequences showed remarkable consistency with current classification systems and may provide a more rapid and convenient means for classifying lantibiotics.

Increasing the success rate of lantibiotic drug discovery by Synthetic Biology

INTRODUCTION

Lantibiotics are post-translationally modified antimicrobial peptides produced by bacteria from diverse environments that exhibit an activity against pathogenic bacteria comparable to that of medically used antibiotics. The actual need for new antimicrobials in therapeutics has placed them in the pipeline of antibiotic research, due not only to their high antimicrobial activity but also to the fact that they are directed to novel targets.

AREAS COVERED

This review covers the different approaches traditionally used in bacteriocin discovery, based on the isolation of bacteria from different habitats and determining their inhibitory spectrum against a set of relevant strains. It also elaborates on more recent approaches covering organic synthesis and semi-synthesis of lantibiotics, genomic and proteomic approaches and the application of Synthetic Biology to the field of antimicrobial drug discovery.

EXPERT OPINION

Lantibiotics show a great potential in fulfilling the requirements for new antimicrobials. Culture-dependent techniques are still applied to lantibiotic discovery producing successful results that can be furthered by employing high-throughput screening techniques and peptidogenomics. The necessity of culturing bacteria and growing them in specific conditions for lantibiotic expression, can hamper the discovery rate, especially in exotic or unculturable bacteria. Thus, a combination of genome mining procedures, to detect novel lantibiotic-related sequences, with heterologous production systems and high-throughput screening, offers a promising strategy. Furthermore, the characterization of the mechanism of action of many lantibiotics, and the development of "plug and play" peptide biosynthesis systems, offers the possibility of initiating the rational design of non-natural lantibiotics based on structure-activity relationships.

Chemical synthesis and biological activity of analogues of the lantibiotic epilancin 15X

Lantibiotics are a large family of antibacterial peptide natural products containing multiple post-translational modifications, including the thioether structures lanthionine and methyllanthionine. Efforts to probe structure-activity relationships and engineer improved pharmacological properties have driven the development of new methods to produce non-natural analogues of these compounds. In this study, solid-supported chemical synthesis was used to produce analogues of the potent lantibiotic epilancin 15X, in order to assess the importance of several N-terminal post-translational modifications for biological activity. Surprisingly, substitution of these moieties, including the unusual N-terminal D-lactyl moiety, resulted in relatively small changes in the antimicrobial activity and pore-forming ability of the peptides.

Discovery, biosynthesis, and engineering of lantipeptides

Aided by genome-mining strategies, knowledge of the prevalence and diversity of ribosomally synthesized natural products (RNPs) is rapidly increasing. Among these are the lantipeptides, posttranslationally modified peptides containing characteristic thioether cross-links imperative for bioactivity and stability. Though this family was once thought to be a limited class of antimicrobial compounds produced by gram-positive bacteria, new insights have revealed a much larger diversity of activity, structure, biosynthetic machinery, and producing organisms than previously appreciated. Detailed investigation of the enzymes responsible for installing the posttranslational modifications has resulted in improved in vivo and in vitro engineering systems focusing on enhancement of the therapeutic potential of these compounds. Although dozens of new lantipeptides have been isolated in recent years, bioinformatic analyses indicate that many hundreds more await discovery owing to the widespread frequency of lantipeptide biosynthetic machinery in bacterial genomes.

Decarbonylative approach to the synthesis of enamides from amino acids: stereoselective synthesis of the (Z)-aminovinyl-D-cysteine unit of mersacidin

The Pd- and Ni-promoted decarbonylation of amino acid thioesters proceeds smoothly to yield enamides. The synthesis of the (S)-(Z)-AviMeCys subunit of mersacidin, an MRSA-active lantibiotic, via this approach, is described.

Post-translational Modifications of Natural Antimicrobial Peptides and Strategies for Peptide Engineering

Natural antimicrobial peptides (AMPs) are gene-coded defense molecules discovered in all the three life domains: Eubacteria, Archaea, and Eukarya. The latter covers protists, fungi, plants, and animals. It is now recognized that amino acid composition, peptide sequence, and post-translational modifications determine to a large extent the structure and function of AMPs. This article systematically describes post-translational modifications of natural AMPs annotated in the antimicrobial peptide database (http://aps.unmc.edu/AP). Currently, 1147 out of 1755 AMPs in the database are modified and classified into more than 17 types. Through chemical modifications, the peptides fold into a variety of structural scaffolds that target bacterial surfaces or molecules within cells. Chemical modifications also confer desired functions to a particular peptide. Meanwhile, these modifications modulate other peptide properties such as stability. Elucidation of the relationship between AMP property and chemical modification inspires peptide engineering. Depending on the objective of our design, peptides may be modified in various ways so that the desired features can be enhanced whereas unwanted properties can be minimized. Therefore, peptide design plays an essential role in developing natural AMPs into a new generation of therapeutic molecules.

The Lantibiotic Lacticin 3147 Prevents Systemic Spread of Staphylococcus aureus in a Murine Infection Model

The objective of this study was to investigate the in vivo activity of the lantibiotic lacticin 3147 against the luminescent Staphylococcus aureus strain Xen 29 using a murine model. Female BALB/c mice (7 weeks old, 17 g) were divided into groups (n = 5) and infected with the Xen 29 strain via the intraperitoneal route at a dose of 1 × 10(6) cfu/animal. After 1.5 hr, the animals were treated subcutaneously with doses of phosphate-buffered saline (PBS; negative control) or lacticin 3147. Luminescent imaging was carried 3 and 5 hours postinfection. Mice were then sacrificed, and the levels of S. aureus Xen 29 in the liver, spleen, and kidneys were quantified. Notably, photoluminescence and culture-based analysis both revealed that lacticin 3147 successfully controlled the systemic spread of S. aureus in mice thus indicating that lacticin 3147 has potential as a chemotherapeutic agent for in vivo applications.

Biosynthesis of the antimicrobial peptide epilancin 15X and its N-terminal lactate

Lantibiotics are ribosomally synthesized and posttranslationally modified antimicrobial peptides. The recently discovered lantibiotic epilancin 15X produced by Staphylococcus epidermidis 15X154 contains an unusual N-terminal lactate group. To understand its biosynthesis, the epilancin 15X biosynthetic gene cluster was identified. The N-terminal lactate is produced by dehydration of a serine residue in the first position of the core peptide by ElxB, followed by proteolytic removal of the leader peptide by ElxP and hydrolysis of the resulting new N-terminal dehydroalanine. The pyruvate group thus formed is reduced to lactate by an NADPH-dependent oxidoreductase designated ElxO. The enzymatic activity of ElxB, ElxP, and ElxO were investigated in vitro or in vivo and the importance of the N-terminal modification for peptide stability against bacterial aminopeptidases was assessed.

Solution structure by nuclear magnetic resonance of the two lantibiotics 97518 and NAI-107

Lantibiotics 97518 and NAI-107, produced by the related genera Planomonospora and Microbispora respectively, are members of a family of nisin-related compounds. They represent promising compounds to treat infections caused by multiresistant Gram-positive pathogens. Despite their similar structure and a similar antibacterial spectrum, the two lantibiotics exhibit significant differences in their potency. To gain an insight into the structure-activity relationships, their conformational properties in solution are determined by NMR. After carrying out an NOE analysis of 2D (1)H NMR spectra, high-resolution 3D structures are determined using molecular dynamics simulations.

Asanoa hainanensis sp. nov., isolated from rhizosphere soil of Acrostichum speciosum in a mangrove, and emended description of the genus Asanoa

A Gram-reaction-positive, non-motile actinobacterium, designated strain 210121T, was isolated from rhizosphere soil of the mangrove fern Acrostichum speciosum. 16S rRNA gene sequence analysis showed that the isolate belonged to the genus Asanoa. DNA–DNA relatedness values between strain 210121T and the type strains of the three recognized species of the genus Asanoa were below the 70 % threshold recommended for distinguishing bacterial genomic species. The novel isolate contained glutamic acid, glycine, alanine and meso-A2pm as cell-wall amino acids, indicating peptidoglycan type A1γ. The characteristic whole-cell sugars were xylose, ribose, glucose and mannose. The predominant menaquinones were MK-9(H4), MK-9(H6) and MK-9(H8). The major fatty acids were iso-C16 : 0 (30.9 %), C17 : 0 (23.0 %), anteiso-C15 : 0 (14.9 %) and iso-C15 : 0 (12.3 %). The phospholipid profile comprised phosphatidylethanolamine, phosphatidylinositol mannosides and phospholipids of unknown structure containing glucosamine. The G+C content of the DNA was 70.3 mol%. On the basis of the phenotypic and genotypic data, strain 210121T ( = CGMCC 4.5593T  = DSM 45427T) represents a novel species of the genus Asanoa, for which the name Asanoa hainanensis sp. nov., is proposed. An emended description of the genus Asanoa is also proposed.

Transcription analysis of a lantibiotic gene cluster from Bifidobacterium longum DJO10A

Bifidobacterium longum DJO10A was previously demonstrated to produce a lantibiotic, but only during growth on agar media. To evaluate the feasibility of production of this lantibiotic in broth media, a transcription analysis of the lanA gene was undertaken. Comparative microarray analysis of broth and agar cultures of B. longum DJO10A revealed that the lantibiotic production, modification, transport/peptidase, and immunity genes were significantly upregulated in agar cultures, while the two-component regulatory genes were expressed equally under both conditions. This suggested that the signal transduction regulatory system should function in broth cultures. Real-time PCR and Northern hybridization confirmed that lanA gene expression was significantly repressed in broth cultures. A crude lantibiotic preparation from an agar-grown culture was obtained, and its antimicrobial spectrum analysis revealed a broad inhibition range. Addition of this extract to broth cultures of B. longum DJO10A induced lanA gene expression in a dose-dependent fashion. Subinoculation using >10% of an induced broth culture maintained lanA expression. The expression of lanA was log-phase specific, being significantly downregulated in stationary phase. Transcription start analysis of lanA revealed a 284-bp 5' untranslated region, which was proposed to be involved in repression of transcription, while an inverted repeat structure located at bp -75 relative to the transcription start was strategically located to likely function as a binding site for the two-component response regulator. Understanding the transcription regulation of this lanA gene is the first step toward enabling production of this novel and potentially interesting lantibiotic in broth cultures.

Evaluating the feasibility of lantibiotics as an alternative therapy against bacterial infections in humans

Since the commercialization and ubiquitous use of antibiotics in the 20th century, there has been a steady increase in the number of reports on resistant bacteria. In recent years, this situation has become even more dramatic. The relatively slow development of new drugs, especially those with novel modes of action on target bacteria, is not paired with the rapid rate of resistance appearance. Lantibiotics form a group of antimicrobial peptides of bacterial origin with a dual mechanism of action not shared by other therapeutic compounds in use. They have a high potency to inhibit diverse (multidrug resistant) bacteria, combined with a low tendency to generate resistance. These properties make lantibiotics attractive candidates for clinical applications. This paper discusses some of the most recent results obtained in lantibiotic clinical application, paying special attention to the pharmacokinetic and pharmacodynamic properties they display. The objective of this paper is to give insight into the actual clinical applicability of lantibiotics and to point to the unexplored aspects that should be addressed in future research. The authors feel that lantibiotics could increase the number of second line antibiotics for systemic use in the future; however, further research is still needed before this is possible.

Feed-forward regulation of microbisporicin biosynthesis in Microbispora corallina

Lantibiotics are ribosomally synthesized, posttranslationally modified peptide antibiotics. Microbisporicin is a potent lantibiotic produced by the actinomycete Microbispora corallina and contains unique chlorinated tryptophan and dihydroxyproline residues. The biosynthetic gene cluster for microbisporicin encodes several putative regulatory proteins, including, uniquely, an extracytoplasmic function (ECF) σ factor, σ(MibX), a likely cognate anti-σ factor, MibW, and a potential helix-turn-helix DNA binding protein, MibR. Here we examine the roles of these proteins in regulating microbisporicin biosynthesis. S1 nuclease protection assays were used to determine transcriptional start sites in the microbisporicin gene cluster and confirmed the presence of the likely ECF sigma factor -10 and -35 sequences in five out of six promoters. In contrast, the promoter of mibA, encoding the microbisporicin prepropeptide, has a typical Streptomyces vegetative sigma factor consensus sequence. The ECF sigma factor σ(MibX) was shown to interact with the putative anti-sigma factor MibW in Escherichia coli using bacterial two-hybrid analysis. σ(MibX) autoregulates its own expression but does not directly regulate expression of mibA. On the basis of quantitative reverse transcriptase PCR (qRT-PCR) data, we propose a model for the biosynthesis of microbisporicin in which MibR functions as an essential master regulator and the ECF sigma factor/anti-sigma factor pair, σ(MibX)/MibW, induces feed-forward biosynthesis of microbisporicin and producer immunity.

Efficacy of the new lantibiotic NAI-107 in experimental infections induced by multidrug-resistant Gram-positive pathogens

NAI-107 is a novel lantibiotic active against Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus (MRSA), glycopeptide-intermediate S. aureus (GISA), and vancomycin-resistant enterococci (VRE). The aim of this study was to evaluate the in vivo efficacy of NAI-107 in animal models of severe infection. In acute lethal infections induced with a penicillin-intermediate Streptococcus pneumoniae strain in immunocompetent mice, or with MRSA, GISA, and VRE strains in neutropenic mice, the 50% effective dose (ED(50)) values of NAI-107 were comparable or lower than those of reference compounds, irrespective of the strain and immune status (0.51 to 14.2 mg/kg of body weight for intravenous [i.v.] NAI-107, 5.1 to 22.4 for oral linezolid, and 22.4 for subcutaneous [s.c.] vancomycin). In the granuloma pouch model induced in rats with a MRSA strain, intravenous NAI-107 showed a dose-proportional bactericidal activity that, at a single 40-mg/kg dose, compared with 2 20-mg/kg doses at a 12-h or 24-h interval, caused a 3-log(10)-CFU/ml reduction of viable MRSA in exudates that persisted for more than 72 h. Rat endocarditis was induced with a MRSA strain and treated for five consecutive days. In a first experiment, using 5, 10, or 20 mg/kg/day, and in a second experiment, when 10 mg/kg at 12-h intervals was compared to 20 mg/kg/day, intravenous NAI-107 was effective in reducing the bacterial load in heart vegetations in a dose-proportional manner. Trough plasma levels, as determined on days 2 and 5, were several times higher than the NAI-107 minimal bactericidal concentration (MBC). NAI-107 binding to rat and human serum ranges between 93% and 98.6%. The rapid bactericidal activity of NAI-107 observed in vitro was thus confirmed by the efficacy in several models of experimental infection induced by Gram-positive pathogens, supporting further investigation of the compound.

Micromonospora rhizosphaerae sp. nov., isolated from mangrove rhizosphere soil

Strain 211018T was isolated from mangrove Excocaria agallocha rhizosphere soil. 16S rRNA gene sequence analysis showed the highest similarity to the type strains of Micromonospora olivasterospora DSM 43868T (98.6 %) and Micromonospora pattaloongensis TJ2-2T (98.4 %). gyrB gene sequence analysis also indicated that strain 211018T should be assigned to the genus Micromonospora. The characteristic whole-cell sugars are xylose, mannose and arabinose. The predominant menaquinone is MK-9(H4) and the major fatty acids are iso-C15 : 0 (27.5 %), 10-methyl C17 : 0 (14.2 %), C17 : 1 ω8c (12.8 %), iso-C16 : 0 (12.6 %), anteiso-C15 : 0 (6.1 %), iso-C17 : 0 (4.1 %) and anteiso-C17 : 0 (4.0 %). The phospholipid profile comprises phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. The DNA G+C content is 70.8 mol%. The chemotaxonomic data of the strain coincided with those of the genus Micromonospora. Furthermore, a combination of DNA–DNA hybridization results and some physiological and biochemical properties indicated that the novel strain could be readily distinguished from the closest phylogenetic relatives. On the basis of these phenotypic and genotypic data, strain 211018T represents a novel species of the genus Micromonospora, for which the name Micromonospora rhizosphaerae sp. nov. is proposed. The type strain is 211018T (=CGMCC 4.5599T =DSM 45431T).

β-Lactam and glycopeptide antibiotics: first and last line of defense?

Most infections are caused by bacteria, many of which are ever-evolving and resistant to nearly all available antibiotics. β-Lactams and glycopeptides are used to combat these infections by inhibiting bacterial cell-wall synthesis. This mechanism remains an interesting target in the search for new antibiotics in light of failed genomic approaches and the limited input of major pharmaceutical companies. Several strategies have enriched the pipeline of bacterial cell-wall inhibitors; examples include combining screening strategies with lesser-explored microbial diversity, or reinventing known scaffolds based on structure-function relationships. Drugs developed using novel strategies will contribute to the arsenal in fight against the continued emergence of bacterial resistance.

Microbisporicin gene cluster reveals unusual features of lantibiotic biosynthesis in actinomycetes

Lantibiotics are ribosomally synthesized, posttranslationally modified peptide antibiotics. The biosynthetic gene cluster for microbisporicin, a potent lantibiotic produced by the actinomycete Microbispora corallina containing chlorinated tryptophan and dihydroxyproline residues, was identified by genome scanning and isolated from an M. corallina cosmid library. Heterologous expression in Nonomuraea sp. ATCC 39727 confirmed that all of the genes required for microbisporicin biosynthesis were present in the cluster. Deletion, in M. corallina, of the gene (mibA) predicted to encode the prepropeptide abolished microbisporicin production. Further deletion analysis revealed insights into the biosynthesis of this unusual and potentially clinically useful lantibiotic, shedding light on mechanisms of regulation and self-resistance. In particular, we report an example of the involvement of a tryptophan halogenase in the modification of a ribosomally synthesized peptide and the pathway-specific regulation of an antibiotic biosynthetic gene cluster by an extracytoplasmic function sigma factor-anti-sigma factor complex.

Antibiotic discovery in the twenty-first century: current trends and future perspectives

New antibiotics are necessary to treat microbial pathogens that are becoming increasingly resistant to available treatment. Despite the medical need, the number of newly approved drugs continues to decline. We offer an overview of the pipeline for new antibiotics at different stages, from compounds in clinical development to newly discovered chemical classes. Consistent with historical data, the majority of antibiotics under clinical development are natural products or derivatives thereof. However, many of them also represent improved variants of marketed compounds, with the consequent risk of being only partially effective against the prevailing resistance mechanisms. In the discovery arena, instead, compounds with promising activities have been obtained from microbial sources and from chemical modification of antibiotic classes other than those in clinical use. Furthermore, new natural product scaffolds have also been discovered by ingenious screening programs. After providing selected examples, we offer our view on the future of antibiotic discovery.