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Iddo Friedberg - One of the best experts on this subject based on the ideXlab platform.
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a large scale prediction of bacteriocin gene blocks suggests a wide functional spectrum for Bacteriocins
BMC Bioinformatics, 2015Co-Authors: Stefan D Freed, James T Morton, Iddo FriedbergAbstract:Background Bacteriocins are peptide-derived molecules produced by bacteria, whose recently-discovered functions include virulence factors and signaling molecules as well as their better known roles as antibiotics. To date, close to five hundred Bacteriocins have been identified and classified. Recent discoveries have shown that Bacteriocins are highly diverse and widely distributed among bacterial species. Given the heterogeneity of bacteriocin compounds, many tools struggle with identifying novel Bacteriocins due to their vast sequence and structural diversity. Many Bacteriocins undergo post-translational processing or modifications necessary for the biosynthesis of the final mature form. Enzymatic modification of Bacteriocins as well as their export is achieved by proteins whose genes are often located in a discrete gene cluster proximal to the bacteriocin precursor gene, referred to as context genes in this study. Although Bacteriocins themselves are structurally diverse, context genes have been shown to be largely conserved across unrelated species.
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a large scale prediction of bacteriocin gene blocks suggests a wide functional spectrum for Bacteriocins
arXiv: Genomics, 2015Co-Authors: Stefan D Freed, James T Morton, Iddo FriedbergAbstract:Bacteriocins are peptide-derived molecules produced by bacteria, whose recently-discovered functions include virulence factors and signalling molecules as well as their better known roles as antibiotics. To date, close to five hundred Bacteriocins have been identified and classified. Recent discoveries have shown that Bacteriocins are highly diverse and widely distributed among bacterial species. Given the heterogeneity of bacteriocin compounds, many tools struggle with identifying novel Bacteriocins due to their vast sequence and structural diversity. Many Bacteriocins undergo post-translational processing or modifications necessary for the biosynthesis of the final mature form. Enzymatic modification of Bacteriocins as well as their export is achieved by proteins whose genes are often located in a discrete gene cluster proximal to the bacteriocin precursor gene, referred to as \textit{context genes} in this study. Although Bacteriocins themselves are structurally diverse, context genes have been shown to be largely conserved across unrelated species. Using this knowledge, we set out to identify new candidates for context genes which may clarify how Bacteriocins are synthesized, and identify new candidates for Bacteriocins that bear no sequence similarity to known toxins. To achieve these goals, we have developed a software tool, Bacteriocin Operon and gene block Associator (BOA) that can identify homologous bacteriocin associated gene clusters and predict novel ones. We discover that several phyla have a strong preference for bactericon genes, suggesting distinct functions for this group of molecules. Availability: this https URL
Jon Nissenmeyer - One of the best experts on this subject based on the ideXlab platform.
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the c terminal domain of pediocin like antimicrobial peptides class iia Bacteriocins is involved in specific recognition of the c terminal part of cognate immunity proteins and in determining the antimicrobial spectrum
Journal of Biological Chemistry, 2005Co-Authors: Line Johnsen, Gunnar Fimland, Jon NissenmeyerAbstract:Abstract The pediocin-like Bacteriocins contain two domains: a cationic N-terminal β-sheet domain that mediates binding of the bacteriocin to the target cell surface and a more hydrophobic C-terminal hairpin-like domain that penetrates into the hydrophobic part of the target cell membrane. The two domains are joined by a hinge, which enables movement of the domains relative to each other. In this study, 12 different hybrid Bacteriocins were constructed by exchanging domains between 5 different Bacteriocins. The hybrid Bacteriocins were by and large highly potent (i.e. similar potencies as the parental Bacteriocins) when constructed such that the recombination point was in the hinge region, indicating that the two domains function independently. The use of optimal recombination points was, however, crucial. Shifting the recombination point just one residue from the hinge could reduce the activity of the hybrid by 3–4 orders of magnitude. Most interestingly, the active hybrids displayed target cell specificities similar to those of the parental bacteriocin from which their membrane-penetrating C-terminal hairpin domain was derived. The results also indicate that the negatively charged aspartate reside in the hinge of most pediocin-like Bacteriocins interacts with the C-terminal hairpin domain, perhaps by interacting with the positively charged residue that is present at one of the last three positions in the C-terminal end of most pediocin-like Bacteriocins. Bacteria that produce pediocin-like Bacteriocins also produce a cognate immunity protein that protects the producer from being killed by its own bacteriocin. Four different active hybrid immunity proteins constructed by exchanging regions between three different immunity proteins were tested for their ability to confer immunity to the hybrid Bacteriocins. The results showed that the C-terminal half of the immunity proteins contains a region that directly or indirectly specifically recognizes the membrane-penetrating C-terminal hairpin domain of pediocin-like Bacteriocins. The implications these results have on how pediocin-like Bacteriocins and their immunity proteins interact with cellular specificity determinants (for instance a putative bacteriocin receptor) are discussed.
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rapid two step procedure for large scale purification of pediocin like Bacteriocins and other cationic antimicrobial peptides from complex culture medium
Applied and Environmental Microbiology, 2002Co-Authors: Marianne Uteng, Jon Nissenmeyer, Ha â â Vard Hildeng Hauge, Ilia Brondz, Gunnar FimlandAbstract:A rapid and simple two-step procedure suitable for both small- and large-scale purification of pediocin-like Bacteriocins and other cationic peptides has been developed. In the first step, the bacterial culture was applied directly on a cation-exchange column (1-ml cation exchanger per 100-ml cell culture). Bacteria and anionic compounds passed through the column, and cationic Bacteriocins were subsequently eluted with 1 M NaCl. In the second step, the bacteriocin fraction was applied on a low-pressure, reverse-phase column and the Bacteriocins were detected as major optical density peaks upon elution with propanol. More than 80% of the activity that was initially in the culture supernatant was recovered in both purification steps, and the final bacteriocin preparation was more than 90% pure as judged by analytical reverse-phase chromatography and capillary electrophoresis.
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antagonistic activity of lactobacillus plantarum c11 two new two peptide Bacteriocins plantaricins ef and jk and the induction factor plantaricin a
Applied and Environmental Microbiology, 1998Co-Authors: Erlend L Anderssen, Dzung B. Diep, Ingolf F Nes, Vincent G H Eijsink, Jon NissenmeyerAbstract:were combined and when PlnJ and PlnK were combined. Complementary peptides were at least 10 3 times more active when they were combined than when they were present individually, and optimal activity was obtained when the complementary peptides were present in approximately equal amounts. The interaction between complementary peptides was specific, since neither PlnE nor PlnF could complement PlnJ or PlnK, and none of these peptides could complement the peptides constituting the two-peptide bacteriocin lactococcin G. Interestingly, PlnA, which acts as an extracellular signal (pheromone) that triggers bacteriocin production, also possessed a strain-specific antagonistic activity. No bacteriocin activity could be detected for PlnN. Ribosomally synthesized antimicrobial polypeptides, termed Bacteriocins, are produced by various lactic acid bacteria (LAB). LAB Bacteriocins are usually membrane-permeabilizing cationic peptides which seldom contain more than 60 amino acid residues (1, 14, 19, 21, 32). These peptide Bacteriocins may be classified into two main groups; group I consists of posttranslationally modified Bacteriocins, and group II consists of unmodified Bacteriocins. The modified group I Bacteriocins are called lantibiotics because they contain the thioether amino acid lanthionine, and often they contain other modified residues, such as methyllanthionine, dehydroalanine, dehydrobutyrine, and D-alanine (27, 29). The unmodified group II Bacteriocins include the pediocinlike Bacteriocins (all of which exhibit more than 25% sequence identity to pediocin PA-1), as well as several non-pediocin-like Bacteriocins, such as lactococcin A and the two-peptide bacteriocin lactococcin G (13, 19, 21, 22). Lactococcin G is classified as a two-peptide bacteriocin since it consists of two different peptides and antibacterial activity requires the complementary action of both peptides in approximately equal amounts (18, 22). The genes encoding the two peptides are next to each other in the same operon, together with the genes encoding the immunity protein (which protects the producer against lactococcin G) and the membrane-associated ABC transporter (which transfers lactococcin G across the membrane) (11a). Lactococcin G kills cells by permeabilizing the target cell membrane (18). When the two lactococcin G peptides interact with each other in the presence of membrane structures, they form amphiphilic a-helices that apparently are inserted into target cell membranes, which creates potassium-selective channels (11, 18). Since the isolation and characterization of lactococcin G, other two-peptide LAB Bacteriocins that have been described include lactacin F (2), lactobin A (which exhibits sequence similarity to lactacin F) (5), and thermophilin 13 (17). The two genes encoding the lactacin
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characterization of the Bacteriocins curvacin a from lactobacillus curvatus lth1174 and sakacin p from l sake lth673
Systematic and Applied Microbiology, 1992Co-Authors: Petra S Tichaczek, Ingolf F Nes, Jon Nissenmeyer, Rudi F Vogel, Walter P HammesAbstract:Summary Two bacteriocin producing strains, one of Lactobacillus curvatus and one of L. sake have been isolated employing a catalase-containing bacteriocin-screening-medium for lactobacilli. Both Bacteriocins were produced in the late exponential growth phase, and were not only active against closely related lactobacilli but also against the opportunistic food pathogens Listeria monocytogenes and Enterococcus faecalis . The inhibitory compounds were only slightly affected by heat treatment but distroyed by proteinase K and trypsin. Both Bacteriocins were purified to homogeneity by ammonium sulfate precipitation, cation exchange, hydrophobic interaction and reversed phase chromatography. The Bacteriocins from L. curvatus LTH1174 and L. sake LTH673 were termed curvacin A and sakacin P, respectively. Amino acid composition analysis and automated protein sequencing revealed that curvacin A and sakacin P are small peptides of 38–41 and 41 amino acid residues, respectively. No unusual amino acids were detected. In the N-terminal region curvacin A and sakacin P share the similar segment — Tyr-Gly-Asn-Gly-Val —. No sequence similarity was detected to previously characterized Bacteriocins indicating that these Bacteriocins are novel.
James T Morton - One of the best experts on this subject based on the ideXlab platform.
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a large scale prediction of bacteriocin gene blocks suggests a wide functional spectrum for Bacteriocins
BMC Bioinformatics, 2015Co-Authors: Stefan D Freed, James T Morton, Iddo FriedbergAbstract:Background Bacteriocins are peptide-derived molecules produced by bacteria, whose recently-discovered functions include virulence factors and signaling molecules as well as their better known roles as antibiotics. To date, close to five hundred Bacteriocins have been identified and classified. Recent discoveries have shown that Bacteriocins are highly diverse and widely distributed among bacterial species. Given the heterogeneity of bacteriocin compounds, many tools struggle with identifying novel Bacteriocins due to their vast sequence and structural diversity. Many Bacteriocins undergo post-translational processing or modifications necessary for the biosynthesis of the final mature form. Enzymatic modification of Bacteriocins as well as their export is achieved by proteins whose genes are often located in a discrete gene cluster proximal to the bacteriocin precursor gene, referred to as context genes in this study. Although Bacteriocins themselves are structurally diverse, context genes have been shown to be largely conserved across unrelated species.
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a large scale prediction of bacteriocin gene blocks suggests a wide functional spectrum for Bacteriocins
arXiv: Genomics, 2015Co-Authors: Stefan D Freed, James T Morton, Iddo FriedbergAbstract:Bacteriocins are peptide-derived molecules produced by bacteria, whose recently-discovered functions include virulence factors and signalling molecules as well as their better known roles as antibiotics. To date, close to five hundred Bacteriocins have been identified and classified. Recent discoveries have shown that Bacteriocins are highly diverse and widely distributed among bacterial species. Given the heterogeneity of bacteriocin compounds, many tools struggle with identifying novel Bacteriocins due to their vast sequence and structural diversity. Many Bacteriocins undergo post-translational processing or modifications necessary for the biosynthesis of the final mature form. Enzymatic modification of Bacteriocins as well as their export is achieved by proteins whose genes are often located in a discrete gene cluster proximal to the bacteriocin precursor gene, referred to as \textit{context genes} in this study. Although Bacteriocins themselves are structurally diverse, context genes have been shown to be largely conserved across unrelated species. Using this knowledge, we set out to identify new candidates for context genes which may clarify how Bacteriocins are synthesized, and identify new candidates for Bacteriocins that bear no sequence similarity to known toxins. To achieve these goals, we have developed a software tool, Bacteriocin Operon and gene block Associator (BOA) that can identify homologous bacteriocin associated gene clusters and predict novel ones. We discover that several phyla have a strong preference for bactericon genes, suggesting distinct functions for this group of molecules. Availability: this https URL
Kenji Sonomoto - One of the best experts on this subject based on the ideXlab platform.
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Diversified transporters and pathways for bacteriocin secretion in gram-positive bacteria
Applied Microbiology and Biotechnology, 2018Co-Authors: Sen Zheng, Kenji SonomotoAbstract:Bacteriocins are ribosomally synthesised small antimicrobial peptides produced from a wide range of bacteria, and also rich sources for potential alternatives to traditional antibiotics. Many Bacteriocins have highly specific antibacterial activity against target pathogens, even including drug-resistant bacteria such as methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus . As the final and essential step during biosynthesis, the leader sequence removal and exportation of matured bacteriocin are lacking of research and therefore the last to be understood. In respect of production, bacteriocin precursor peptides are processed and exported by a group of membrane proteins from the ATP-binding cassette transporter family. The main aims of this article are to summarise knowledge till now on the leader signal and correlated transporters for bacteriocin secretion in gram-positive bacteria in a review for the first time, to introduce different strategies for higher production, and to offer new insights into many essential but still unanswered questions above for the purpose of more efficient bacteriocin utilisation.
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Diversified transporters and pathways for bacteriocin secretion in gram-positive bacteria
Applied Microbiology and Biotechnology, 2018Co-Authors: Sen Zheng, Kenji SonomotoAbstract:Bacteriocins are ribosomally synthesised small antimicrobial peptides produced from a wide range of bacteria, and also rich sources for potential alternatives to traditional antibiotics. Many Bacteriocins have highly specific antibacterial activity against target pathogens, even including drug-resistant bacteria such as methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus . As the final and essential step during biosynthesis, the leader sequence removal and exportation of matured bacteriocin are lacking of research and therefore the last to be understood. In respect of production, bacteriocin precursor peptides are processed and exported by a group of membrane proteins from the ATP-binding cassette transporter family. The main aims of this article are to summarise knowledge till now on the leader signal and correlated transporters for bacteriocin secretion in gram-positive bacteria in a review for the first time, to introduce different strategies for higher production, and to offer new insights into many essential but still unanswered questions above for the purpose of more efficient bacteriocin utilisation.
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New type non-lantibiotic Bacteriocins: circular and leaderless Bacteriocins
Beneficial Microbes, 2012Co-Authors: Yoshimitsu Masuda, Takeshi Zendo, Kenji SonomotoAbstract:Bacteriocins are antimicrobial peptides that are ribosomally synthesised by bacteria. Bacteriocins produced by Gram-positive bacteria, including lactic acid bacteria, are under focus as the next generation of safe natural biopreservatives and as therapeutic alternatives to antibiotics. Recently, two novel types of non-lantibiotic class II Bacteriocins have been reported with unique characteristics in their structure and biosynthesis mechanism. One is a circular bacteriocin that contains a head-to-tail structure in the mature form, and the other is a leaderless bacteriocin without an N-terminal extension in the precursor peptide. A circular structure can provide the peptide with remarkable stability against various stresses; indeed, circular Bacteriocins are known to possess higher stability than general linear Bacteriocins. Leaderless Bacteriocins are distinct from general Bacteriocins, because they do not contain N-terminal leader sequences, which are responsible for the recognition process during secret...
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Lactococcal membrane-permeabilizing antimicrobial peptides
Applied Microbiology and Biotechnology, 2010Co-Authors: Takeshi Zendo, Fuminori Yoneyama, Kenji SonomotoAbstract:A number of lactococcal antimicrobial peptides, Bacteriocins have been discovered and characterized. Since Lactococcus spp. are generally regarded as safe bacteria, their Bacteriocins are expected for various application uses. Most of lactococcal Bacteriocins exert antimicrobial activity via membrane permeabilization. The most studied and prominent bacteriocin, nisin A is characterized in the high activity and has been utilized as food preservatives for more than half a century. Recently, other lactococcal Bacteriocins such as lacticin Q were found to have distinguished features for further applications as the next generation to nisin.
Colin Hill - One of the best experts on this subject based on the ideXlab platform.
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Microbial production of Bacteriocins for use in foods
Microbial Production of Food Ingredients Enzymes and Nutraceuticals, 2013Co-Authors: D.g. Burke, R.p. Ross, Paul D Cotter, Colin HillAbstract:Abstract: Bacteriocins are ribosomally synthesised, antimicrobial peptides produced by bacteria. Many Bacteriocins produced by food grade lactic acid bacteria exhibit the potential to control spoilage and pathogenic bacteria in food. Here we review the means by which these Bacteriocins are employed by the food industry, that is through the production of Bacteriocins by bacteriocinogenic bacteria from within the food or by the addition of a bacteriocin to the food in the form of an ingredient or preservative.
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bacteriocin production a probiotic trait
Applied and Environmental Microbiology, 2012Co-Authors: Alleson Dobson, Paul R Ross, Paul D Cotter, Colin HillAbstract:Bacteriocins are an abundant and diverse group of ribosomally synthesized antimicrobial peptides produced by bacteria and archaea. Traditionally, bacteriocin production has been considered an important trait in the selection of probiotic strains, but until recently, few studies have definitively demonstrated the impact of bacteriocin production on the ability of a strain to compete within complex microbial communities and/or positively influence the health of the host. Although research in this area is still in its infancy, there is intriguing evidence to suggest that Bacteriocins may function in a number of ways within the gastrointestinal tract. Bacteriocins may facilitate the introduction of a producer into an established niche, directly inhibit the invasion of competing strains or pathogens, or modulate the composition of the microbiota and influence the host immune system. Here we review the role of bacteriocin production in complex microbial communities and their potential to enhance human health.
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Production of Multiple Bacteriocins from a Single Locus by Gastrointestinal Strains of Lactobacillus salivarius
Journal of Bacteriology, 2011Co-Authors: Eileen F. O'shea, Paul D Cotter, Paula M. O'connor, Emma J. Raftis, Paul W. O'toole, Catherine Stanton, R. Paul Ross, Colin HillAbstract:Bacteriocins produced by Lactobacillus salivarius isolates derived from a gastrointestinal origin have previously demonstrated efficacy for in vivo protection against Listeria monocytogenes infection. In this study, comparative genomic analysis was employed to investigate the intraspecies diversity of seven L. salivarius isolates of human and porcine intestinal origin, based on the genome of the well-characterized bacteriocin-producing strain L. salivarius UCC118. This revealed a highly conserved megaplasmid-borne gene cluster in these strains involved in the regulation and secretion of two-component class IIb Bacteriocins. However, considerable intraspecific variation was observed in the structural genes encoding the bacteriocin peptides. They ranged from close relatives of abp118, such as salivaricin P, which differs by 2 amino acids, to completely novel Bacteriocins, such as salivaricin T, which is characterized in this study. Salivaricin T inhibits closely related lactobacilli and bears little homology to previously characterized salivaricins. Interestingly, the two peptides responsible for salivaricin T activity, SalTα and SalTβ, share considerable identity with the component peptides of thermophilin 13, a bacteriocin produced by Streptococcus thermophilus. Furthermore, the salivaricin locus of strain DPC6488 also encodes an additional novel one-component class IId anti-listerial bacteriocin, salivaricin L. These findings suggest a high level of redundancy in the Bacteriocins that can be produced by intestinal L. salivarius isolates using the same enzymatic production and export machinery. Such diversity may contribute to their ability to dominate and compete within the complex microbiota of the mammalian gut.
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potential of bacteriocin producing lactic acid bacteria for improvements in food safety and quality
Biochimie, 2002Co-Authors: Lisa Osullivan, R.p. Ross, Colin HillAbstract:Abstract Lactic acid bacteria (LAB) have been used for centuries in the fermentation of a variety of dairy products. The preservative ability of LAB in foods is attributed to the production of anti-microbial metabolites including organic acids and Bacteriocins. Bacteriocins generally exert their anti-microbial action by interfering with the cell wall or the membrane of target organisms, either by inhibiting cell wall biosynthesis or causing pore formation, subsequently resulting in death. The incorporation of Bacteriocins as a biopreservative ingredient into model food systems has been studied extensively and has been shown to be effective in the control of pathogenic and spoilage microorganisms. However, a more practical and economic option of incorporating Bacteriocins into foods can be the direct addition of bacteriocin-producing cultures into food. This paper presents an overview of the potential for using bacteriocin-producing LAB in foods for the improvement of the safety and quality of the final product. It describes the different genera of LAB with potential as biopreservatives, and presents an up-to-date classification system for the Bacteriocins they produce. While the problems associated with the use of some bacteriocin-producing cultures in certain foods are elucidated, so also are the situations in which incorporation of the bacteriocin-producer into model food systems have been shown to be very effective.
