Identification and three-dimensional structure of carnobacteriocin XY, a class IIb bacteriocin produced by Carnobacteria

Antimicrobial Peptide Synergies for Fighting Infectious Diseases

Antimicrobial peptides (AMPs) are essential elements of thehost defense system. Characterized by heterogenous structures and broad-spectrumaction, they are promising candidates for combating multidrug resistance. Thecombined use of AMPs with other antimicrobial agents provides a new arsenal ofdrugs with synergistic action, thereby overcoming the drawback of monotherapiesduring infections. AMPs kill microbes via pore formation, thus inhibitingintracellular functions. This mechanism of action by AMPs is an advantage overantibiotics as it hinders the development of drug resistance. The synergisticeffect of AMPs will allow the repurposing of conventional antimicrobials andenhance their clinical outcomes, reduce toxicity, and, most significantly,prevent the development of resistance. In this review, various synergies ofAMPs with antimicrobials and miscellaneous agents are discussed. The effect ofstructural diversity and chemical modification on AMP properties is firstaddressed and then different combinations that can lead to synergistic action,whether this combination is between AMPs and antimicrobials, or AMPs andmiscellaneous compounds, are attended. This review can serve as guidance whenredesigning and repurposing the use of AMPs in combination with other antimicrobialagents for enhanced clinical outcomes.

Gallocin A, an Atypical Two-Peptide Bacteriocin with Intramolecular Disulfide Bonds Required for Activity

Streptococcus gallolyticus subsp. gallolyticus (SGG) is an opportunistic gut pathogen associated with colorectal cancer. We previously showed that colonization of the murine colon by SGG in tumoral conditions was strongly enhanced by the production of gallocin A, a two-peptide bacteriocin. Here, we aimed to characterize the mechanisms of its action and resistance. Using a genetic approach, we demonstrated that gallocin A is composed of two peptides, GllA1 and GllA2, which are inactive alone and act together to kill "target" bacteria. We showed that gallocin A can kill phylogenetically close relatives of the pathogen. Importantly, we demonstrated that gallocin A peptides can insert themselves into membranes and permeabilize lipid bilayer vesicles. Next, we showed that the third gene of the gallocin A operon, gip, is necessary and sufficient to confer immunity to gallocin A. Structural modeling of GllA1 and GllA2 mature peptides suggested that both peptides form alpha-helical hairpins stabilized by intramolecular disulfide bridges. The presence of a disulfide bond in GllA1 and GllA2 was confirmed experimentally. Addition of disulfide-reducing agents abrogated gallocin A activity. Likewise, deletion of a gene encoding a surface protein with a thioredoxin-like domain impaired the ability of gallocin A to kill Enterococcus faecalis. Structural modeling of GIP revealed a hairpin-like structure strongly resembling those of the GllA1 and GllA2 mature peptides, suggesting a mechanism of immunity by competition with GllA1/2. Finally, identification of other class IIb bacteriocins exhibiting a similar alpha-helical hairpin fold stabilized with an intramolecular disulfide bridge suggests the existence of a new subclass of class IIb bacteriocins. IMPORTANCE Streptococcus gallolyticus subsp. gallolyticus (SGG), previously named Streptococcus bovis biotype I, is an opportunistic pathogen responsible for invasive infections (septicemia, endocarditis) in elderly people and is often associated with colon tumors. SGG is one of the first bacteria to be associated with the occurrence of colorectal cancer in humans. Previously, we showed that tumor-associated conditions in the colon provide SGG with an ideal environment to proliferate at the expense of phylogenetically and metabolically closely related commensal bacteria such as enterococci (1). SGG takes advantage of CRC-associated conditions to outcompete and substitute commensal members of the gut microbiota using a specific bacteriocin named gallocin, recently renamed gallocin A following the discovery of gallocin D in a peculiar SGG isolate. Here, we showed that gallocin A is a two-peptide bacteriocin and that both GllA1 and GllA2 peptides are required for antimicrobial activity. Gallocin A was shown to permeabilize bacterial membranes and kill phylogenetically closely related bacteria such as most streptococci, lactococci, and enterococci, probably through membrane pore formation. GllA1 and GllA2 secreted peptides are unusually long (42 and 60 amino acids long) and have very few charged amino acids compared to well-known class IIb bacteriocins. In silico modeling revealed that both GllA1 and GllA2 exhibit a similar hairpin-like conformation stabilized by an intramolecular disulfide bond. We also showed that the GIP immunity peptide forms a hairpin-like structure similar to GllA1/GllA2. Thus, we hypothesize that GIP blocks the formation of the GllA1/GllA2 complex by interacting with GllA1 or GllA2. Gallocin A may constitute the first class IIb bacteriocin which displays disulfide bridges important for its structure and activity and might be the founding member of a subtype of class IIb bacteriocins.

Structural Features, Mechanisms of Action, and Prospects for Practical Application of Class II Bacteriocins

Bacteriocins are antimicrobial peptides ribosomally synthesized by both Gram-negative and Gram-positive bacteria, as well as by archaea. Bacteriocins are usually active against phylogenetically related bacteria, providing competitive advantage to their producers in the natural bacterial environment. However, some bacteriocins are known to have a broader spectrum of antibacterial activity, including activity against multidrug-resistant bacterial strains. Multitude of bacteriocins studied to date are characterized by a wide variety of chemical structures and mechanisms of action. Existing classification systems for bacteriocins take into account structural features and biosynthetic pathways of bacteriocins, as well as the phylogenetic affiliation of their producing organisms. Heat-stable bacteriocins with molecular weight of less than 10 kDa from Gram-positive and Gram-negative producers are divided into post-translationally modified (class I) and unmodified peptides (class II). In recent years there has been an increasing interest in the class II bacteriocins as potential therapeutic agents that can help to combat antibiotic-resistant infections. Advantages of unmodified peptides are relative simplicity of their biotechnological production in heterologous systems and chemical synthesis. Potential for the combined use of bacteriocins with other antimicrobial agents allowing to enhance their efficacy, low probability of cross-resistance development, and ability of probiotic strains to produce bacteriocins in situ make them promising candidate compounds for creation of new drugs. The review focuses on structural diversity of the class II bacteriocins and their practical relevance.

Pan-genomic and comparative analysis of Pediococcus pentosaceus focused on the in silico assessment of pediocin-like bacteriocins

Bacteriocins are antimicrobial peptides produced by different species of bacteria, especially the Gram-positive lactic acid bacteria (LAB). Pediococcus pentosaceus is widely applied in the industry and stands out as Bacteriocin-Like Inhibitory Substances (BLIS) producer known to inhibit pathogens commonly considered a concern in the food industries. This study aimed to perform in silico comparisons of P. pentosaceus genomes available in the public GenBank database focusing on their pediocin-like bacteriocins repertoire. The pan-genome analysis evidenced a temporal signal in the pattern of gene gain and loss, supporting the hypothesis that the complete genetic repertoire of this group of bacteria is still uncovered. Thirteen bacteriocin genes from Class II and III were predicted in the accessory genome. Four pediocin-like bacteriocins (54% of the detected bacteriocin repertoire) and their accompanying immunity genes are highlighted; penocin A, coagulin A, pediocin PA-1, and plantaricin 423. Additionally, in silico, modeling of the pediocin-like bacteriocins revealed different configurations of the helix motif compared to other physically determined pediocin-like structures. Comparative and phylogenomic analyses support the hypothesis that a dynamic mechanism of bacteriocin acquisition and purging is not dependent on the bacterial isolation source origin. Synteny analysis revealed that while coagulin A, pediocin PA-1, and Plantaricin 423 loci are associated with insertion sequences mainly from the IS30 family and are likely of plasmid origin, penocin A lies in a conserved chromosomal locus. The results presented here provide insights into the unique pediocin-like bacteriocin peptide fold, genomic diversity, and the evolution of the bacteriocin genetic repertoire of P. pentosaceus, shedding new insights into the role of these biomolecules for application in inhibiting bacterial pathogens, and suggesting that prospecting and sequencing new strains is still an alternative to mining for new probiotic compounds.

Biosynthesis and Production of Class II Bacteriocins of Food-Associated Lactic Acid Bacteria

Bacteriocins are ribosomally synthesized peptides made by bacteria that inhibit the growth of similar or closely related bacterial strains. Class II bacteriocins are a class of bacteriocins that are heat-resistant and do not undergo extensive posttranslational modification. In lactic acid bacteria (LAB), class II bacteriocins are widely distributed, and some of them have been successfully applied as food preservatives or antibiotic alternatives. Class II bacteriocins can be further divided into four subcategories. In the same subcategory, variations were observed in terms of amino acid identity, peptide length, pI, etc. The production of class II bacteriocin is controlled by a dedicated gene cluster located in the plasmid or chromosome. Besides the pre-bacteriocin encoding gene, the gene cluster generally includes various combinations of immunity, transportation, and regulatory genes. Among class II bacteriocin-producing LAB, some strains/species showed low yield. A multitude of fermentation factors including medium composition, temperature, and pH have a strong influence on bacteriocin production which is usually strain-specific. Consequently, scientists are motivated to develop high-yielding strains through the genetic engineering approach. Thus, this review aims to present and discuss the distribution, sequence characteristics, as well as biosynthesis of class II bacteriocins of LAB. Moreover, the integration of modern biotechnology and genetics with conventional fermentation technology to improve bacteriocin production will also be discussed in this review.

SPI "sandwich": Combined SUMO-Peptide-Intein expression system and isolation procedure for improved stability and yield of peptides

Recombinant peptide production in Escherichia coli is often accomplished through cloning and expression of a fusion protein. The fusion protein partner generally has two requirements: (a) it contains an affinity tag to assist with purification and (b) it can be cleaved off to leave only the desired peptide sequence behind. Common soluble fusion partners include small ubiquitin-like modifier protein (SUMO), maltose-binding protein (MBP), glutathione S-transferase (GST), or intein proteins. However, heterologously expressed peptides can suffer from proteolytic degradation or instability. This degradation can pose a major issue for applications requiring a large amount of purified peptide, such as NMR structural assignments or biochemical assays. Improving peptide yield by testing various expression and isolation conditions requires a significant amount of effort and may not lead to improved results. Here, we cloned and expressed four different peptides as SUMO fusion proteins. These peptides (lactococcin A, leucocin A, faerocin MK, neopetrosiamide A) were truncated during expression and isolation as SUMO fusions, resulting in low yields of purified peptide. To prevent this degradation and improve yield, we designed a new expression system to create a "sandwiched" fusion protein of the form: His₆ -SUMO-peptide-intein (SPI). These sandwiched peptides were more stable and protected against degradation, resulting in improved yields (up to 17-fold) under a set of standard expression and isolation procedures. This SPI expression system uses only two commercially available vectors and standard protein purification techniques, and therefore may offer an economical and facile route to improve yields for peptides that undergo degradation.

Heterologous overexpression and preliminary antimicrobial activity test of salmocin M, a novel colicin M-like bacteriocin against Salmonella sp

Currently, it is extremely important to identify and describe new alternative compounds with potential antimicrobial properties. Since various natural biological systems are capable of producing active compounds with such properties, many of them have been the subject of intensive study. The aim of this work was to heterologously overexpress, purify and preliminarily investigate the antimicrobial activity of a novel bacteriocin found in Salmonella species. Overexpressed protein shows an amino acid structure homologous to the well-known colicin M and was never expressed previously in the E. coli platform. Purified salmocin M showed an inhibition spectrum against Salmonella and E. coli strains. To determine its potential as an antimicrobial agent for use in medicine or the food industry, preliminary antimicrobial tests against pathogenic bacteria were carried out. Our research demonstrates that bacteriocin can be produced efficiently in bacterial expression systems, which are one of the cheapest and the most popular platforms for recombinant protein production. Moreover, preliminary results of microbiological tests showed its activity against most of the bacterial strains in a dose-dependent manner.

Transporter Protein-Guided Genome Mining for Head-to-Tail Cyclized Bacteriocins

Head-to-tail cyclized bacteriocins are ribosomally synthesized antimicrobial peptides that are defined by peptide backbone cyclization involving the N- and C- terminal amino acids. Their cyclic nature and overall three-dimensional fold confer superior stability against extreme pH and temperature conditions, and protease degradation. Most of the characterized head-to-tail cyclized bacteriocins were discovered through a traditional approach that involved the screening of bacterial isolates for antimicrobial activity and subsequent isolation and characterization of the active molecule. In this study, we performed genome mining using transporter protein sequences associated with experimentally validated head-to-tail cyclized bacteriocins as driver sequences to search for novel bacteriocins. Biosynthetic gene cluster analysis was then performed to select the high probability functional gene clusters. A total of 387 producer strains that encode putative head-to-tail cyclized bacteriocins were identified. Sequence and phylogenetic analyses revealed that this class of bacteriocins is more diverse than previously thought. Furthermore, our genome mining strategy captured hits that were not identified in precursor-based bioprospecting, showcasing the utility of this approach to expanding the repertoire of head-to-tail cyclized bacteriocins. This work sets the stage for future isolation of novel head-to-tail cyclized bacteriocins to serve as possible alternatives to traditional antibiotics and potentially help address the increasing threat posed by resistant pathogens.

Natural bacterial isolates as an inexhaustible source of new bacteriocins

Microorganisms isolated from various traditionally fermented food products prepared in households without commercial starter cultures are designated as natural isolates. In addition, this term is also used for microorganisms collected from various natural habitats or products (silage, soil, manure, plant and animal material, etc.) that do not contain any commercial starters or bacterial formulations. They are characterized by unique traits that are the result of the selective pressure of environmental conditions, as well as interactions with other organisms. The synthesis of antimicrobial molecules, including bacteriocins, is an evolutionary advantage and an adaptive feature that sets them apart from other microorganisms from a common environment. This review aims to underline the knowledge of bacteriocins produced by natural isolates, with a particular emphasis on the most common location of their genes and operons, plasmids, and the importance of the relationship between the plasmidome and the adaptive potential of the isolate. Applications of bacteriocins, ranging from natural food preservatives to supplements and drugs in pharmacology and medicine, will also be addressed. The latest challenges faced by researchers in isolating new natural isolates with desired characteristics will be discussed, as well as the production of new antimicrobials, nearly one century since the first discovery of colicins in 1925. KEY POINTS: • Natural bacterial isolates harbor unique properties shaped by diverse interactions. • Horizontal gene transfer enables constant engineering of new antimicrobials. • Fermented food products are important source of bacteriocin-producing natural isolates.

New Insight into Antimicrobial Compounds from Food and Marine-Sourced Carnobacterium Species through Phenotype and Genome Analyses

Carnobacteriummaltaromaticum and Carnobacteriumdivergens, isolated from food products, are lactic acid bacteria known to produce active and efficient bacteriocins. Other species, particularly those originating from marine sources, are less studied. The aim of the study is to select promising strains with antimicrobial potential by combining genomic and phenotypic approaches on large datasets comprising 12 Carnobacterium species. The biosynthetic gene cluster (BGCs) diversity of 39 publicly available Carnobacterium spp. genomes revealed 67 BGCs, distributed according to the species and ecological niches. From zero to six BGCs were predicted per strain and classified into four classes: terpene, NRPS (non-ribosomal peptide synthetase), NRPS-PKS (hybrid non-ribosomal peptide synthetase-polyketide synthase), RiPP (ribosomally synthesized and post-translationally modified peptide). In parallel, the antimicrobial activity of 260 strains from seafood products was evaluated. Among the 60% of active strains, three genomes were sequenced and submitted to a dereplication process. C. inhibens MIP2551 produced a high amountof H₂O₂, probably thanks to the presence of four oxidase-encoding genes. C. maltaromaticum EBP3019 and SF668 strains were highly efficient against Listeria monocytogenes. A new extracellular 16 kDa unmodified bacteriocin in the EBP3019 strain and five different bacteriocins in SF668 were highlighted. In this study, the overview of antimicrobial BGC and inhibitory activities of Carnobacterium spp. allowed the prediction of potential innovative natural products that could be relevant for biotechnological applications.

The membrane topology of immunity proteins for the two-peptide bacteriocins carnobacteriocin XY, lactococcin G, and lactococcin MN shows structural diversity

The two‐peptide bacteriocins produced by Gram‐positive bacteria require two different peptides, present in equimolar amounts, to elicit optimal antimicrobial activity. Producer organisms are protected from their bacteriocin by a dedicated immunity protein. The immunity proteins for two‐peptide bacteriocins contain putative transmembrane domains (TMDs) and might therefore be associated with the membrane. The immunity protein CbnZ for the two‐peptide bacteriocin carnobacteriocin XY (CbnXY) was identified by heterologously expressing the cbnZ gene in sensitive host strains. Using protein topology prediction methods and the dual pho‐lac reporter system, we mapped out the membrane topology of CbnZ, along with those of the immunity proteins LagC and LciM for the two‐peptide bacteriocins lactococcin G and lactococcin MN, respectively. Our results reveal wide structural variety between these immunity proteins that can contain as little as one TMD or as many as four TMDs.

Homologous Expression and Characterization of Gassericin T and Gassericin S, a Novel Class IIb Bacteriocin Produced by Lactobacillus gasseri LA327

Lactobacillus gasseri LA327, isolated from the large intestine tissue in humans, is a bacteriocinogenic strain with two kinds of class IIb bacteriocin structural genes, i.e., those for gassericin T (GT) and acidocin LF221A (Acd LF221A). In this study, DNA sequencing of the genes for GT and Acd LF221A from L. gasseri LA327 revealed that the amino acid sequences for GT corresponded with those for GT genes, except for GatK (histidine kinase). However, Acd LF221A genes had analogues which differed in at least one amino acid residue, to encode a class IIb bacteriocin designated gassericin S (GS). The LA327 strain retained antimicrobial activity after the deletion of the GT structural genes (gatAX); however, both GS and GT activities were lost by deletion of the putative ABC transporter gene (gatT). This indicates that the LA327 strain produces GS and GT and that GS secretion is performed via GT genes with the inclusion of gatT Homologous expression using deletion mutants of GS and GT, each containing a single peptide, elucidated that GS (GasAX) and GT (GatAX) showed synergistic activity as class IIb bacteriocins and that no synergistic activity was observed between GS and GT peptides. The molecular mass of GS was estimated to be theoretical ca. 5,400 Da by in situ activity assay after SDS-PAGE, clarifying that GS was actually expressed as an active class IIb bacteriocin. Furthermore, the stability of expressed GS to pH, heat, and protease was determined.IMPORTANCE Bacteriocins are regarded as potential alternatives for antibiotics in the absence of highly resistant bacteria. In particular, two-peptide (class IIb) bacteriocins exhibit the maximum activity through the synergy of two components, and their antimicrobial spectra are known to be relatively wide. However, there are few reports of synergistic activity of class IIb bacteriocins determined by isolation and purification of individual peptides. Our results clarified the interaction of each class IIb component peptide for GT and GS via the construction of homologous mutants, which were not dependent on the purification. These data may contribute to understanding the mechanisms of action by which class IIb bacteriocins exhibit wide antibacterial spectra.

NMR structures and mutational analysis of the two peptides constituting the bacteriocin plantaricin S

The structure of the individual peptides of the two-peptide bacteriocin plantaricin S, an antimicrobial peptide produced by a Lactobacillus plantarum strain, has been determined in DPC micelles. The two peptides of plantaricin S, Pls-α and Pls-β, form an α-helix from and including residue 8 to 24 with a less structured region around residue 16-19 and an amphiphilic α-helix from and including residue 7 to 23, respectively. Activity assays on single amino acid-substituted GxxxG and GxxxG-like motifs show that substituting the Ser and Gly residues in the G₉xxxG₁₃ motif in Pls-α and the S₁₇xxxG₂₁ motif in Pls-β reduced or drastically reduced the antimicrobial activity. The two-peptide bacteriocin muricidin contains GxxxG-like motifs at similar positions and displays 40-50% amino acid identity with plantaricin S. Activity assays of combinations of the peptides that constitute the bacteriocins plantaricin S and muricidin show that some combinations are highly active. Furthermore, sequence alignments show that the motifs important for plantaricin S activity align with identical motifs in muricidin. Based on sequence comparison and activity assays, a membrane-inserted model of plantaricin S in which the two peptides are oriented antiparallel relative to each other and where the GxxxG and GxxxG-like motifs important for activity come close in space, is proposed.

The expanding structural variety among bacteriocins from Gram-positive bacteria

Bacteria use various strategies to compete in an ecological niche, including the production of bacteriocins. Bacteriocins are ribosomally synthesized antibacterial peptides, and it has been postulated that the majority of Gram-positive bacteria produce one or more of these natural products. Bacteriocins can be used in food preservation and are also considered as potential alternatives to antibiotics. The majority of bacteriocins from Gram-positive bacteria had been traditionally divided into two major classes, namely lantibiotics, which are post-translationally modified bacteriocins, and unmodified bacteriocins. The last decade has seen an expanding number of ribosomally synthesized and post-translationally modified peptides (RiPPs) in Gram-positive bacteria that have antibacterial activity. These include linear azol(in)e-containing peptides, thiopeptides, bottromycins, glycocins, lasso peptides and lipolanthines. In addition, the three-dimensional (3D) structures of a number of modified and unmodified bacteriocins have been elucidated in recent years. This review gives an overview on the structural variety of bacteriocins from Gram-positive bacteria. It will focus on the chemical and 3D structures of these peptides, and their interactions with receptors and membranes, structure-function relationships and possible modes of action.

Protecting bactofencin A to enable its antimicrobial activity using mesoporous matrices

There is huge global concern surrounding the emergence of antimicrobial resistant bacteria and this is resulting in an inability to treat infectious diseases. This is due to a lack of new antimicrobials coming to the market and irresponsible use of traditional antibiotics. Bactofencin A, a novel antimicrobial peptide which shows potential as an antibiotic, is susceptible to enzyme degradation. To improve its solution stability and inherent activity, bactofencin A was loaded onto a traditional silica mesoporous matrix, SBA-15, and a periodic mesoporous organosilane, MSE. The loading of bactofencin A was considerably higher onto SBA-15 than MSE due to the hydrophilic nature of SBA-15. While there was no detectable peptide released from SBA-15 into phosphate buffered saline and only 20% of the peptide loaded onto MSE was released, the loaded matrices showed enhanced activity compared to the free peptide during in vitro antimicrobial assays. In addition, the mesoporous matrices were found to protect bactofencin A against enzymatic degradation where results showed that the SBA-15 and MSE with loaded bactofencin A exposed to trypsin inhibited the growth of S. aureus while a large decrease in activity was observed for free bactofencin upon exposure to trypsin. Thus, the activity and stability of bactofencin A can be enhanced using mesoporous matrices and these matrices may enable its potential development as a novel antibiotic. This work also shows that in silico studies looking at surface functional group and size complementarity between the peptide and the protective matrix could enable the systemic selection of a mesoporous matrix for individual bacteriocins with potential antimicrobial therapeutic properties.